Annotation of imach/src/imach.c, revision 1.208
1.208 ! brouard 1: /* $Id: imach.c,v 1.207 2015/10/27 17:36:57 brouard Exp $
1.126 brouard 2: $State: Exp $
1.163 brouard 3: $Log: imach.c,v $
1.208 ! brouard 4: Revision 1.207 2015/10/27 17:36:57 brouard
! 5: *** empty log message ***
! 6:
1.207 brouard 7: Revision 1.206 2015/10/24 07:14:11 brouard
8: *** empty log message ***
9:
1.206 brouard 10: Revision 1.205 2015/10/23 15:50:53 brouard
11: Summary: 0.98r3 some clarification for graphs on likelihood contributions
12:
1.205 brouard 13: Revision 1.204 2015/10/01 16:20:26 brouard
14: Summary: Some new graphs of contribution to likelihood
15:
1.204 brouard 16: Revision 1.203 2015/09/30 17:45:14 brouard
17: Summary: looking at better estimation of the hessian
18:
19: Also a better criteria for convergence to the period prevalence And
20: therefore adding the number of years needed to converge. (The
21: prevalence in any alive state shold sum to one
22:
1.203 brouard 23: Revision 1.202 2015/09/22 19:45:16 brouard
24: Summary: Adding some overall graph on contribution to likelihood. Might change
25:
1.202 brouard 26: Revision 1.201 2015/09/15 17:34:58 brouard
27: Summary: 0.98r0
28:
29: - Some new graphs like suvival functions
30: - Some bugs fixed like model=1+age+V2.
31:
1.201 brouard 32: Revision 1.200 2015/09/09 16:53:55 brouard
33: Summary: Big bug thanks to Flavia
34:
35: Even model=1+age+V2. did not work anymore
36:
1.200 brouard 37: Revision 1.199 2015/09/07 14:09:23 brouard
38: Summary: 0.98q6 changing default small png format for graph to vectorized svg.
39:
1.199 brouard 40: Revision 1.198 2015/09/03 07:14:39 brouard
41: Summary: 0.98q5 Flavia
42:
1.198 brouard 43: Revision 1.197 2015/09/01 18:24:39 brouard
44: *** empty log message ***
45:
1.197 brouard 46: Revision 1.196 2015/08/18 23:17:52 brouard
47: Summary: 0.98q5
48:
1.196 brouard 49: Revision 1.195 2015/08/18 16:28:39 brouard
50: Summary: Adding a hack for testing purpose
51:
52: After reading the title, ftol and model lines, if the comment line has
53: a q, starting with #q, the answer at the end of the run is quit. It
54: permits to run test files in batch with ctest. The former workaround was
55: $ echo q | imach foo.imach
56:
1.195 brouard 57: Revision 1.194 2015/08/18 13:32:00 brouard
58: Summary: Adding error when the covariance matrix doesn't contain the exact number of lines required by the model line.
59:
1.194 brouard 60: Revision 1.193 2015/08/04 07:17:42 brouard
61: Summary: 0.98q4
62:
1.193 brouard 63: Revision 1.192 2015/07/16 16:49:02 brouard
64: Summary: Fixing some outputs
65:
1.192 brouard 66: Revision 1.191 2015/07/14 10:00:33 brouard
67: Summary: Some fixes
68:
1.191 brouard 69: Revision 1.190 2015/05/05 08:51:13 brouard
70: Summary: Adding digits in output parameters (7 digits instead of 6)
71:
72: Fix 1+age+.
73:
1.190 brouard 74: Revision 1.189 2015/04/30 14:45:16 brouard
75: Summary: 0.98q2
76:
1.189 brouard 77: Revision 1.188 2015/04/30 08:27:53 brouard
78: *** empty log message ***
79:
1.188 brouard 80: Revision 1.187 2015/04/29 09:11:15 brouard
81: *** empty log message ***
82:
1.187 brouard 83: Revision 1.186 2015/04/23 12:01:52 brouard
84: Summary: V1*age is working now, version 0.98q1
85:
86: Some codes had been disabled in order to simplify and Vn*age was
87: working in the optimization phase, ie, giving correct MLE parameters,
88: but, as usual, outputs were not correct and program core dumped.
89:
1.186 brouard 90: Revision 1.185 2015/03/11 13:26:42 brouard
91: Summary: Inclusion of compile and links command line for Intel Compiler
92:
1.185 brouard 93: Revision 1.184 2015/03/11 11:52:39 brouard
94: Summary: Back from Windows 8. Intel Compiler
95:
1.184 brouard 96: Revision 1.183 2015/03/10 20:34:32 brouard
97: Summary: 0.98q0, trying with directest, mnbrak fixed
98:
99: We use directest instead of original Powell test; probably no
100: incidence on the results, but better justifications;
101: We fixed Numerical Recipes mnbrak routine which was wrong and gave
102: wrong results.
103:
1.183 brouard 104: Revision 1.182 2015/02/12 08:19:57 brouard
105: Summary: Trying to keep directest which seems simpler and more general
106: Author: Nicolas Brouard
107:
1.182 brouard 108: Revision 1.181 2015/02/11 23:22:24 brouard
109: Summary: Comments on Powell added
110:
111: Author:
112:
1.181 brouard 113: Revision 1.180 2015/02/11 17:33:45 brouard
114: Summary: Finishing move from main to function (hpijx and prevalence_limit)
115:
1.180 brouard 116: Revision 1.179 2015/01/04 09:57:06 brouard
117: Summary: back to OS/X
118:
1.179 brouard 119: Revision 1.178 2015/01/04 09:35:48 brouard
120: *** empty log message ***
121:
1.178 brouard 122: Revision 1.177 2015/01/03 18:40:56 brouard
123: Summary: Still testing ilc32 on OSX
124:
1.177 brouard 125: Revision 1.176 2015/01/03 16:45:04 brouard
126: *** empty log message ***
127:
1.176 brouard 128: Revision 1.175 2015/01/03 16:33:42 brouard
129: *** empty log message ***
130:
1.175 brouard 131: Revision 1.174 2015/01/03 16:15:49 brouard
132: Summary: Still in cross-compilation
133:
1.174 brouard 134: Revision 1.173 2015/01/03 12:06:26 brouard
135: Summary: trying to detect cross-compilation
136:
1.173 brouard 137: Revision 1.172 2014/12/27 12:07:47 brouard
138: Summary: Back from Visual Studio and Intel, options for compiling for Windows XP
139:
1.172 brouard 140: Revision 1.171 2014/12/23 13:26:59 brouard
141: Summary: Back from Visual C
142:
143: Still problem with utsname.h on Windows
144:
1.171 brouard 145: Revision 1.170 2014/12/23 11:17:12 brouard
146: Summary: Cleaning some \%% back to %%
147:
148: The escape was mandatory for a specific compiler (which one?), but too many warnings.
149:
1.170 brouard 150: Revision 1.169 2014/12/22 23:08:31 brouard
151: Summary: 0.98p
152:
153: Outputs some informations on compiler used, OS etc. Testing on different platforms.
154:
1.169 brouard 155: Revision 1.168 2014/12/22 15:17:42 brouard
1.170 brouard 156: Summary: update
1.169 brouard 157:
1.168 brouard 158: Revision 1.167 2014/12/22 13:50:56 brouard
159: Summary: Testing uname and compiler version and if compiled 32 or 64
160:
161: Testing on Linux 64
162:
1.167 brouard 163: Revision 1.166 2014/12/22 11:40:47 brouard
164: *** empty log message ***
165:
1.166 brouard 166: Revision 1.165 2014/12/16 11:20:36 brouard
167: Summary: After compiling on Visual C
168:
169: * imach.c (Module): Merging 1.61 to 1.162
170:
1.165 brouard 171: Revision 1.164 2014/12/16 10:52:11 brouard
172: Summary: Merging with Visual C after suppressing some warnings for unused variables. Also fixing Saito's bug 0.98Xn
173:
174: * imach.c (Module): Merging 1.61 to 1.162
175:
1.164 brouard 176: Revision 1.163 2014/12/16 10:30:11 brouard
177: * imach.c (Module): Merging 1.61 to 1.162
178:
1.163 brouard 179: Revision 1.162 2014/09/25 11:43:39 brouard
180: Summary: temporary backup 0.99!
181:
1.162 brouard 182: Revision 1.1 2014/09/16 11:06:58 brouard
183: Summary: With some code (wrong) for nlopt
184:
185: Author:
186:
187: Revision 1.161 2014/09/15 20:41:41 brouard
188: Summary: Problem with macro SQR on Intel compiler
189:
1.161 brouard 190: Revision 1.160 2014/09/02 09:24:05 brouard
191: *** empty log message ***
192:
1.160 brouard 193: Revision 1.159 2014/09/01 10:34:10 brouard
194: Summary: WIN32
195: Author: Brouard
196:
1.159 brouard 197: Revision 1.158 2014/08/27 17:11:51 brouard
198: *** empty log message ***
199:
1.158 brouard 200: Revision 1.157 2014/08/27 16:26:55 brouard
201: Summary: Preparing windows Visual studio version
202: Author: Brouard
203:
204: In order to compile on Visual studio, time.h is now correct and time_t
205: and tm struct should be used. difftime should be used but sometimes I
206: just make the differences in raw time format (time(&now).
207: Trying to suppress #ifdef LINUX
208: Add xdg-open for __linux in order to open default browser.
209:
1.157 brouard 210: Revision 1.156 2014/08/25 20:10:10 brouard
211: *** empty log message ***
212:
1.156 brouard 213: Revision 1.155 2014/08/25 18:32:34 brouard
214: Summary: New compile, minor changes
215: Author: Brouard
216:
1.155 brouard 217: Revision 1.154 2014/06/20 17:32:08 brouard
218: Summary: Outputs now all graphs of convergence to period prevalence
219:
1.154 brouard 220: Revision 1.153 2014/06/20 16:45:46 brouard
221: Summary: If 3 live state, convergence to period prevalence on same graph
222: Author: Brouard
223:
1.153 brouard 224: Revision 1.152 2014/06/18 17:54:09 brouard
225: Summary: open browser, use gnuplot on same dir than imach if not found in the path
226:
1.152 brouard 227: Revision 1.151 2014/06/18 16:43:30 brouard
228: *** empty log message ***
229:
1.151 brouard 230: Revision 1.150 2014/06/18 16:42:35 brouard
231: Summary: If gnuplot is not in the path try on same directory than imach binary (OSX)
232: Author: brouard
233:
1.150 brouard 234: Revision 1.149 2014/06/18 15:51:14 brouard
235: Summary: Some fixes in parameter files errors
236: Author: Nicolas Brouard
237:
1.149 brouard 238: Revision 1.148 2014/06/17 17:38:48 brouard
239: Summary: Nothing new
240: Author: Brouard
241:
242: Just a new packaging for OS/X version 0.98nS
243:
1.148 brouard 244: Revision 1.147 2014/06/16 10:33:11 brouard
245: *** empty log message ***
246:
1.147 brouard 247: Revision 1.146 2014/06/16 10:20:28 brouard
248: Summary: Merge
249: Author: Brouard
250:
251: Merge, before building revised version.
252:
1.146 brouard 253: Revision 1.145 2014/06/10 21:23:15 brouard
254: Summary: Debugging with valgrind
255: Author: Nicolas Brouard
256:
257: Lot of changes in order to output the results with some covariates
258: After the Edimburgh REVES conference 2014, it seems mandatory to
259: improve the code.
260: No more memory valgrind error but a lot has to be done in order to
261: continue the work of splitting the code into subroutines.
262: Also, decodemodel has been improved. Tricode is still not
263: optimal. nbcode should be improved. Documentation has been added in
264: the source code.
265:
1.144 brouard 266: Revision 1.143 2014/01/26 09:45:38 brouard
267: Summary: Version 0.98nR (to be improved, but gives same optimization results as 0.98k. Nice, promising
268:
269: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
270: (Module): Version 0.98nR Running ok, but output format still only works for three covariates.
271:
1.143 brouard 272: Revision 1.142 2014/01/26 03:57:36 brouard
273: Summary: gnuplot changed plot w l 1 has to be changed to plot w l lt 2
274:
275: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
276:
1.142 brouard 277: Revision 1.141 2014/01/26 02:42:01 brouard
278: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
279:
1.141 brouard 280: Revision 1.140 2011/09/02 10:37:54 brouard
281: Summary: times.h is ok with mingw32 now.
282:
1.140 brouard 283: Revision 1.139 2010/06/14 07:50:17 brouard
284: After the theft of my laptop, I probably lost some lines of codes which were not uploaded to the CVS tree.
285: I remember having already fixed agemin agemax which are pointers now but not cvs saved.
286:
1.139 brouard 287: Revision 1.138 2010/04/30 18:19:40 brouard
288: *** empty log message ***
289:
1.138 brouard 290: Revision 1.137 2010/04/29 18:11:38 brouard
291: (Module): Checking covariates for more complex models
292: than V1+V2. A lot of change to be done. Unstable.
293:
1.137 brouard 294: Revision 1.136 2010/04/26 20:30:53 brouard
295: (Module): merging some libgsl code. Fixing computation
296: of likelione (using inter/intrapolation if mle = 0) in order to
297: get same likelihood as if mle=1.
298: Some cleaning of code and comments added.
299:
1.136 brouard 300: Revision 1.135 2009/10/29 15:33:14 brouard
301: (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
302:
1.135 brouard 303: Revision 1.134 2009/10/29 13:18:53 brouard
304: (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
305:
1.134 brouard 306: Revision 1.133 2009/07/06 10:21:25 brouard
307: just nforces
308:
1.133 brouard 309: Revision 1.132 2009/07/06 08:22:05 brouard
310: Many tings
311:
1.132 brouard 312: Revision 1.131 2009/06/20 16:22:47 brouard
313: Some dimensions resccaled
314:
1.131 brouard 315: Revision 1.130 2009/05/26 06:44:34 brouard
316: (Module): Max Covariate is now set to 20 instead of 8. A
317: lot of cleaning with variables initialized to 0. Trying to make
318: V2+V3*age+V1+V4 strb=V3*age+V1+V4 working better.
319:
1.130 brouard 320: Revision 1.129 2007/08/31 13:49:27 lievre
321: Modification of the way of exiting when the covariate is not binary in order to see on the window the error message before exiting
322:
1.129 lievre 323: Revision 1.128 2006/06/30 13:02:05 brouard
324: (Module): Clarifications on computing e.j
325:
1.128 brouard 326: Revision 1.127 2006/04/28 18:11:50 brouard
327: (Module): Yes the sum of survivors was wrong since
328: imach-114 because nhstepm was no more computed in the age
329: loop. Now we define nhstepma in the age loop.
330: (Module): In order to speed up (in case of numerous covariates) we
331: compute health expectancies (without variances) in a first step
332: and then all the health expectancies with variances or standard
333: deviation (needs data from the Hessian matrices) which slows the
334: computation.
335: In the future we should be able to stop the program is only health
336: expectancies and graph are needed without standard deviations.
337:
1.127 brouard 338: Revision 1.126 2006/04/28 17:23:28 brouard
339: (Module): Yes the sum of survivors was wrong since
340: imach-114 because nhstepm was no more computed in the age
341: loop. Now we define nhstepma in the age loop.
342: Version 0.98h
343:
1.126 brouard 344: Revision 1.125 2006/04/04 15:20:31 lievre
345: Errors in calculation of health expectancies. Age was not initialized.
346: Forecasting file added.
347:
348: Revision 1.124 2006/03/22 17:13:53 lievre
349: Parameters are printed with %lf instead of %f (more numbers after the comma).
350: The log-likelihood is printed in the log file
351:
352: Revision 1.123 2006/03/20 10:52:43 brouard
353: * imach.c (Module): <title> changed, corresponds to .htm file
354: name. <head> headers where missing.
355:
356: * imach.c (Module): Weights can have a decimal point as for
357: English (a comma might work with a correct LC_NUMERIC environment,
358: otherwise the weight is truncated).
359: Modification of warning when the covariates values are not 0 or
360: 1.
361: Version 0.98g
362:
363: Revision 1.122 2006/03/20 09:45:41 brouard
364: (Module): Weights can have a decimal point as for
365: English (a comma might work with a correct LC_NUMERIC environment,
366: otherwise the weight is truncated).
367: Modification of warning when the covariates values are not 0 or
368: 1.
369: Version 0.98g
370:
371: Revision 1.121 2006/03/16 17:45:01 lievre
372: * imach.c (Module): Comments concerning covariates added
373:
374: * imach.c (Module): refinements in the computation of lli if
375: status=-2 in order to have more reliable computation if stepm is
376: not 1 month. Version 0.98f
377:
378: Revision 1.120 2006/03/16 15:10:38 lievre
379: (Module): refinements in the computation of lli if
380: status=-2 in order to have more reliable computation if stepm is
381: not 1 month. Version 0.98f
382:
383: Revision 1.119 2006/03/15 17:42:26 brouard
384: (Module): Bug if status = -2, the loglikelihood was
385: computed as likelihood omitting the logarithm. Version O.98e
386:
387: Revision 1.118 2006/03/14 18:20:07 brouard
388: (Module): varevsij Comments added explaining the second
389: table of variances if popbased=1 .
390: (Module): Covariances of eij, ekl added, graphs fixed, new html link.
391: (Module): Function pstamp added
392: (Module): Version 0.98d
393:
394: Revision 1.117 2006/03/14 17:16:22 brouard
395: (Module): varevsij Comments added explaining the second
396: table of variances if popbased=1 .
397: (Module): Covariances of eij, ekl added, graphs fixed, new html link.
398: (Module): Function pstamp added
399: (Module): Version 0.98d
400:
401: Revision 1.116 2006/03/06 10:29:27 brouard
402: (Module): Variance-covariance wrong links and
403: varian-covariance of ej. is needed (Saito).
404:
405: Revision 1.115 2006/02/27 12:17:45 brouard
406: (Module): One freematrix added in mlikeli! 0.98c
407:
408: Revision 1.114 2006/02/26 12:57:58 brouard
409: (Module): Some improvements in processing parameter
410: filename with strsep.
411:
412: Revision 1.113 2006/02/24 14:20:24 brouard
413: (Module): Memory leaks checks with valgrind and:
414: datafile was not closed, some imatrix were not freed and on matrix
415: allocation too.
416:
417: Revision 1.112 2006/01/30 09:55:26 brouard
418: (Module): Back to gnuplot.exe instead of wgnuplot.exe
419:
420: Revision 1.111 2006/01/25 20:38:18 brouard
421: (Module): Lots of cleaning and bugs added (Gompertz)
422: (Module): Comments can be added in data file. Missing date values
423: can be a simple dot '.'.
424:
425: Revision 1.110 2006/01/25 00:51:50 brouard
426: (Module): Lots of cleaning and bugs added (Gompertz)
427:
428: Revision 1.109 2006/01/24 19:37:15 brouard
429: (Module): Comments (lines starting with a #) are allowed in data.
430:
431: Revision 1.108 2006/01/19 18:05:42 lievre
432: Gnuplot problem appeared...
433: To be fixed
434:
435: Revision 1.107 2006/01/19 16:20:37 brouard
436: Test existence of gnuplot in imach path
437:
438: Revision 1.106 2006/01/19 13:24:36 brouard
439: Some cleaning and links added in html output
440:
441: Revision 1.105 2006/01/05 20:23:19 lievre
442: *** empty log message ***
443:
444: Revision 1.104 2005/09/30 16:11:43 lievre
445: (Module): sump fixed, loop imx fixed, and simplifications.
446: (Module): If the status is missing at the last wave but we know
447: that the person is alive, then we can code his/her status as -2
448: (instead of missing=-1 in earlier versions) and his/her
449: contributions to the likelihood is 1 - Prob of dying from last
450: health status (= 1-p13= p11+p12 in the easiest case of somebody in
451: the healthy state at last known wave). Version is 0.98
452:
453: Revision 1.103 2005/09/30 15:54:49 lievre
454: (Module): sump fixed, loop imx fixed, and simplifications.
455:
456: Revision 1.102 2004/09/15 17:31:30 brouard
457: Add the possibility to read data file including tab characters.
458:
459: Revision 1.101 2004/09/15 10:38:38 brouard
460: Fix on curr_time
461:
462: Revision 1.100 2004/07/12 18:29:06 brouard
463: Add version for Mac OS X. Just define UNIX in Makefile
464:
465: Revision 1.99 2004/06/05 08:57:40 brouard
466: *** empty log message ***
467:
468: Revision 1.98 2004/05/16 15:05:56 brouard
469: New version 0.97 . First attempt to estimate force of mortality
470: directly from the data i.e. without the need of knowing the health
471: state at each age, but using a Gompertz model: log u =a + b*age .
472: This is the basic analysis of mortality and should be done before any
473: other analysis, in order to test if the mortality estimated from the
474: cross-longitudinal survey is different from the mortality estimated
475: from other sources like vital statistic data.
476:
477: The same imach parameter file can be used but the option for mle should be -3.
478:
1.133 brouard 479: Agnès, who wrote this part of the code, tried to keep most of the
1.126 brouard 480: former routines in order to include the new code within the former code.
481:
482: The output is very simple: only an estimate of the intercept and of
483: the slope with 95% confident intervals.
484:
485: Current limitations:
486: A) Even if you enter covariates, i.e. with the
487: model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
488: B) There is no computation of Life Expectancy nor Life Table.
489:
490: Revision 1.97 2004/02/20 13:25:42 lievre
491: Version 0.96d. Population forecasting command line is (temporarily)
492: suppressed.
493:
494: Revision 1.96 2003/07/15 15:38:55 brouard
495: * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
496: rewritten within the same printf. Workaround: many printfs.
497:
498: Revision 1.95 2003/07/08 07:54:34 brouard
499: * imach.c (Repository):
500: (Repository): Using imachwizard code to output a more meaningful covariance
501: matrix (cov(a12,c31) instead of numbers.
502:
503: Revision 1.94 2003/06/27 13:00:02 brouard
504: Just cleaning
505:
506: Revision 1.93 2003/06/25 16:33:55 brouard
507: (Module): On windows (cygwin) function asctime_r doesn't
508: exist so I changed back to asctime which exists.
509: (Module): Version 0.96b
510:
511: Revision 1.92 2003/06/25 16:30:45 brouard
512: (Module): On windows (cygwin) function asctime_r doesn't
513: exist so I changed back to asctime which exists.
514:
515: Revision 1.91 2003/06/25 15:30:29 brouard
516: * imach.c (Repository): Duplicated warning errors corrected.
517: (Repository): Elapsed time after each iteration is now output. It
518: helps to forecast when convergence will be reached. Elapsed time
519: is stamped in powell. We created a new html file for the graphs
520: concerning matrix of covariance. It has extension -cov.htm.
521:
522: Revision 1.90 2003/06/24 12:34:15 brouard
523: (Module): Some bugs corrected for windows. Also, when
524: mle=-1 a template is output in file "or"mypar.txt with the design
525: of the covariance matrix to be input.
526:
527: Revision 1.89 2003/06/24 12:30:52 brouard
528: (Module): Some bugs corrected for windows. Also, when
529: mle=-1 a template is output in file "or"mypar.txt with the design
530: of the covariance matrix to be input.
531:
532: Revision 1.88 2003/06/23 17:54:56 brouard
533: * 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.
534:
535: Revision 1.87 2003/06/18 12:26:01 brouard
536: Version 0.96
537:
538: Revision 1.86 2003/06/17 20:04:08 brouard
539: (Module): Change position of html and gnuplot routines and added
540: routine fileappend.
541:
542: Revision 1.85 2003/06/17 13:12:43 brouard
543: * imach.c (Repository): Check when date of death was earlier that
544: current date of interview. It may happen when the death was just
545: prior to the death. In this case, dh was negative and likelihood
546: was wrong (infinity). We still send an "Error" but patch by
547: assuming that the date of death was just one stepm after the
548: interview.
549: (Repository): Because some people have very long ID (first column)
550: we changed int to long in num[] and we added a new lvector for
551: memory allocation. But we also truncated to 8 characters (left
552: truncation)
553: (Repository): No more line truncation errors.
554:
555: Revision 1.84 2003/06/13 21:44:43 brouard
556: * imach.c (Repository): Replace "freqsummary" at a correct
557: place. It differs from routine "prevalence" which may be called
558: many times. Probs is memory consuming and must be used with
559: parcimony.
560: Version 0.95a3 (should output exactly the same maximization than 0.8a2)
561:
562: Revision 1.83 2003/06/10 13:39:11 lievre
563: *** empty log message ***
564:
565: Revision 1.82 2003/06/05 15:57:20 brouard
566: Add log in imach.c and fullversion number is now printed.
567:
568: */
569: /*
570: Interpolated Markov Chain
571:
572: Short summary of the programme:
573:
574: This program computes Healthy Life Expectancies from
575: cross-longitudinal data. Cross-longitudinal data consist in: -1- a
576: first survey ("cross") where individuals from different ages are
577: interviewed on their health status or degree of disability (in the
578: case of a health survey which is our main interest) -2- at least a
579: second wave of interviews ("longitudinal") which measure each change
580: (if any) in individual health status. Health expectancies are
581: computed from the time spent in each health state according to a
582: model. More health states you consider, more time is necessary to reach the
583: Maximum Likelihood of the parameters involved in the model. The
584: simplest model is the multinomial logistic model where pij is the
585: probability to be observed in state j at the second wave
586: conditional to be observed in state i at the first wave. Therefore
587: the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
588: 'age' is age and 'sex' is a covariate. If you want to have a more
589: complex model than "constant and age", you should modify the program
590: where the markup *Covariates have to be included here again* invites
591: you to do it. More covariates you add, slower the
592: convergence.
593:
594: The advantage of this computer programme, compared to a simple
595: multinomial logistic model, is clear when the delay between waves is not
596: identical for each individual. Also, if a individual missed an
597: intermediate interview, the information is lost, but taken into
598: account using an interpolation or extrapolation.
599:
600: hPijx is the probability to be observed in state i at age x+h
601: conditional to the observed state i at age x. The delay 'h' can be
602: split into an exact number (nh*stepm) of unobserved intermediate
603: states. This elementary transition (by month, quarter,
604: semester or year) is modelled as a multinomial logistic. The hPx
605: matrix is simply the matrix product of nh*stepm elementary matrices
606: and the contribution of each individual to the likelihood is simply
607: hPijx.
608:
609: Also this programme outputs the covariance matrix of the parameters but also
610: of the life expectancies. It also computes the period (stable) prevalence.
611:
1.133 brouard 612: Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
613: Institut national d'études démographiques, Paris.
1.126 brouard 614: This software have been partly granted by Euro-REVES, a concerted action
615: from the European Union.
616: It is copyrighted identically to a GNU software product, ie programme and
617: software can be distributed freely for non commercial use. Latest version
618: can be accessed at http://euroreves.ined.fr/imach .
619:
620: Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
621: or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
622:
623: **********************************************************************/
624: /*
625: main
626: read parameterfile
627: read datafile
628: concatwav
629: freqsummary
630: if (mle >= 1)
631: mlikeli
632: print results files
633: if mle==1
634: computes hessian
635: read end of parameter file: agemin, agemax, bage, fage, estepm
636: begin-prev-date,...
637: open gnuplot file
638: open html file
1.145 brouard 639: period (stable) prevalence | pl_nom 1-1 2-2 etc by covariate
640: for age prevalim() | #****** V1=0 V2=1 V3=1 V4=0 ******
641: | 65 1 0 2 1 3 1 4 0 0.96326 0.03674
642: freexexit2 possible for memory heap.
643:
644: h Pij x | pij_nom ficrestpij
645: # Cov Agex agex+h hpijx with i,j= 1-1 1-2 1-3 2-1 2-2 2-3
646: 1 85 85 1.00000 0.00000 0.00000 0.00000 1.00000 0.00000
647: 1 85 86 0.68299 0.22291 0.09410 0.71093 0.00000 0.28907
648:
649: 1 65 99 0.00364 0.00322 0.99314 0.00350 0.00310 0.99340
650: 1 65 100 0.00214 0.00204 0.99581 0.00206 0.00196 0.99597
651: variance of p one-step probabilities varprob | prob_nom ficresprob #One-step probabilities and stand. devi in ()
652: Standard deviation of one-step probabilities | probcor_nom ficresprobcor #One-step probabilities and correlation matrix
653: Matrix of variance covariance of one-step probabilities | probcov_nom ficresprobcov #One-step probabilities and covariance matrix
654:
1.126 brouard 655: forecasting if prevfcast==1 prevforecast call prevalence()
656: health expectancies
657: Variance-covariance of DFLE
658: prevalence()
659: movingaverage()
660: varevsij()
661: if popbased==1 varevsij(,popbased)
662: total life expectancies
663: Variance of period (stable) prevalence
664: end
665: */
666:
1.187 brouard 667: /* #define DEBUG */
668: /* #define DEBUGBRENT */
1.203 brouard 669: /* #define DEBUGLINMIN */
670: /* #define DEBUGHESS */
671: #define DEBUGHESSIJ
672: /* #define LINMINORIGINAL /\* Don't use loop on scale in linmin (accepting nan)*\/ */
1.165 brouard 673: #define POWELL /* Instead of NLOPT */
1.192 brouard 674: #define POWELLF1F3 /* Skip test */
1.186 brouard 675: /* #define POWELLORIGINAL /\* Don't use Directest to decide new direction but original Powell test *\/ */
676: /* #define MNBRAKORIGINAL /\* Don't use mnbrak fix *\/ */
1.126 brouard 677:
678: #include <math.h>
679: #include <stdio.h>
680: #include <stdlib.h>
681: #include <string.h>
1.159 brouard 682:
683: #ifdef _WIN32
684: #include <io.h>
1.172 brouard 685: #include <windows.h>
686: #include <tchar.h>
1.159 brouard 687: #else
1.126 brouard 688: #include <unistd.h>
1.159 brouard 689: #endif
1.126 brouard 690:
691: #include <limits.h>
692: #include <sys/types.h>
1.171 brouard 693:
694: #if defined(__GNUC__)
695: #include <sys/utsname.h> /* Doesn't work on Windows */
696: #endif
697:
1.126 brouard 698: #include <sys/stat.h>
699: #include <errno.h>
1.159 brouard 700: /* extern int errno; */
1.126 brouard 701:
1.157 brouard 702: /* #ifdef LINUX */
703: /* #include <time.h> */
704: /* #include "timeval.h" */
705: /* #else */
706: /* #include <sys/time.h> */
707: /* #endif */
708:
1.126 brouard 709: #include <time.h>
710:
1.136 brouard 711: #ifdef GSL
712: #include <gsl/gsl_errno.h>
713: #include <gsl/gsl_multimin.h>
714: #endif
715:
1.167 brouard 716:
1.162 brouard 717: #ifdef NLOPT
718: #include <nlopt.h>
719: typedef struct {
720: double (* function)(double [] );
721: } myfunc_data ;
722: #endif
723:
1.126 brouard 724: /* #include <libintl.h> */
725: /* #define _(String) gettext (String) */
726:
1.141 brouard 727: #define MAXLINE 1024 /* Was 256. Overflow with 312 with 2 states and 4 covariates. Should be ok */
1.126 brouard 728:
729: #define GNUPLOTPROGRAM "gnuplot"
730: /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
731: #define FILENAMELENGTH 132
732:
733: #define GLOCK_ERROR_NOPATH -1 /* empty path */
734: #define GLOCK_ERROR_GETCWD -2 /* cannot get cwd */
735:
1.144 brouard 736: #define MAXPARM 128 /**< Maximum number of parameters for the optimization */
737: #define NPARMAX 64 /**< (nlstate+ndeath-1)*nlstate*ncovmodel */
1.126 brouard 738:
739: #define NINTERVMAX 8
1.144 brouard 740: #define NLSTATEMAX 8 /**< Maximum number of live states (for func) */
741: #define NDEATHMAX 8 /**< Maximum number of dead states (for func) */
742: #define NCOVMAX 20 /**< Maximum number of covariates, including generated covariates V1*V2 */
1.197 brouard 743: #define codtabm(h,k) (1 & (h-1) >> (k-1))+1
1.126 brouard 744: #define MAXN 20000
1.144 brouard 745: #define YEARM 12. /**< Number of months per year */
1.126 brouard 746: #define AGESUP 130
747: #define AGEBASE 40
1.194 brouard 748: #define AGEOVERFLOW 1.e20
1.164 brouard 749: #define AGEGOMP 10 /**< Minimal age for Gompertz adjustment */
1.157 brouard 750: #ifdef _WIN32
751: #define DIRSEPARATOR '\\'
752: #define CHARSEPARATOR "\\"
753: #define ODIRSEPARATOR '/'
754: #else
1.126 brouard 755: #define DIRSEPARATOR '/'
756: #define CHARSEPARATOR "/"
757: #define ODIRSEPARATOR '\\'
758: #endif
759:
1.208 ! brouard 760: /* $Id: imach.c,v 1.207 2015/10/27 17:36:57 brouard Exp $ */
1.126 brouard 761: /* $State: Exp $ */
1.196 brouard 762: #include "version.h"
763: char version[]=__IMACH_VERSION__;
1.204 brouard 764: 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";
1.208 ! brouard 765: char fullversion[]="$Revision: 1.207 $ $Date: 2015/10/27 17:36:57 $";
1.126 brouard 766: char strstart[80];
767: char optionfilext[10], optionfilefiname[FILENAMELENGTH];
1.130 brouard 768: int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings */
1.187 brouard 769: int nagesqr=0, nforce=0; /* nagesqr=1 if model is including age*age, number of forces */
1.145 brouard 770: /* Number of covariates model=V2+V1+ V3*age+V2*V4 */
771: int cptcovn=0; /**< cptcovn number of covariates added in the model (excepting constant and age and age*product) */
772: int cptcovt=0; /**< cptcovt number of covariates added in the model (excepting constant and age) */
773: int cptcovs=0; /**< cptcovs number of simple covariates V2+V1 =2 */
774: int cptcovage=0; /**< Number of covariates with age: V3*age only =1 */
775: int cptcovprodnoage=0; /**< Number of covariate products without age */
776: int cptcoveff=0; /* Total number of covariates to vary for printing results */
777: int cptcov=0; /* Working variable */
1.126 brouard 778: int npar=NPARMAX;
779: int nlstate=2; /* Number of live states */
780: int ndeath=1; /* Number of dead states */
1.130 brouard 781: int ncovmodel=0, ncovcol=0; /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
1.126 brouard 782: int popbased=0;
783:
784: int *wav; /* Number of waves for this individuual 0 is possible */
1.130 brouard 785: int maxwav=0; /* Maxim number of waves */
786: int jmin=0, jmax=0; /* min, max spacing between 2 waves */
787: int ijmin=0, ijmax=0; /* Individuals having jmin and jmax */
788: int gipmx=0, gsw=0; /* Global variables on the number of contributions
1.126 brouard 789: to the likelihood and the sum of weights (done by funcone)*/
1.130 brouard 790: int mle=1, weightopt=0;
1.126 brouard 791: int **mw; /* mw[mi][i] is number of the mi wave for this individual */
792: int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
793: int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
794: * wave mi and wave mi+1 is not an exact multiple of stepm. */
1.162 brouard 795: int countcallfunc=0; /* Count the number of calls to func */
1.130 brouard 796: double jmean=1; /* Mean space between 2 waves */
1.145 brouard 797: double **matprod2(); /* test */
1.126 brouard 798: double **oldm, **newm, **savm; /* Working pointers to matrices */
799: double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
1.136 brouard 800: /*FILE *fic ; */ /* Used in readdata only */
801: FILE *ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
1.126 brouard 802: FILE *ficlog, *ficrespow;
1.130 brouard 803: int globpr=0; /* Global variable for printing or not */
1.126 brouard 804: double fretone; /* Only one call to likelihood */
1.130 brouard 805: long ipmx=0; /* Number of contributions */
1.126 brouard 806: double sw; /* Sum of weights */
807: char filerespow[FILENAMELENGTH];
808: char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
809: FILE *ficresilk;
810: FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
811: FILE *ficresprobmorprev;
812: FILE *fichtm, *fichtmcov; /* Html File */
813: FILE *ficreseij;
814: char filerese[FILENAMELENGTH];
815: FILE *ficresstdeij;
816: char fileresstde[FILENAMELENGTH];
817: FILE *ficrescveij;
818: char filerescve[FILENAMELENGTH];
819: FILE *ficresvij;
820: char fileresv[FILENAMELENGTH];
821: FILE *ficresvpl;
822: char fileresvpl[FILENAMELENGTH];
823: char title[MAXLINE];
824: char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH], filerespl[FILENAMELENGTH];
825: char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
826: char tmpout[FILENAMELENGTH], tmpout2[FILENAMELENGTH];
827: char command[FILENAMELENGTH];
828: int outcmd=0;
829:
830: char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
1.202 brouard 831: char fileresu[FILENAMELENGTH]; /* fileres without r in front */
1.126 brouard 832: char filelog[FILENAMELENGTH]; /* Log file */
833: char filerest[FILENAMELENGTH];
834: char fileregp[FILENAMELENGTH];
835: char popfile[FILENAMELENGTH];
836:
837: char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
838:
1.157 brouard 839: /* struct timeval start_time, end_time, curr_time, last_time, forecast_time; */
840: /* struct timezone tzp; */
841: /* extern int gettimeofday(); */
842: struct tm tml, *gmtime(), *localtime();
843:
844: extern time_t time();
845:
846: struct tm start_time, end_time, curr_time, last_time, forecast_time;
847: time_t rstart_time, rend_time, rcurr_time, rlast_time, rforecast_time; /* raw time */
848: struct tm tm;
849:
1.126 brouard 850: char strcurr[80], strfor[80];
851:
852: char *endptr;
853: long lval;
854: double dval;
855:
856: #define NR_END 1
857: #define FREE_ARG char*
858: #define FTOL 1.0e-10
859:
860: #define NRANSI
861: #define ITMAX 200
862:
863: #define TOL 2.0e-4
864:
865: #define CGOLD 0.3819660
866: #define ZEPS 1.0e-10
867: #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);
868:
869: #define GOLD 1.618034
870: #define GLIMIT 100.0
871: #define TINY 1.0e-20
872:
873: static double maxarg1,maxarg2;
874: #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
875: #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
876:
877: #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
878: #define rint(a) floor(a+0.5)
1.166 brouard 879: /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/myutils_8h-source.html */
1.183 brouard 880: #define mytinydouble 1.0e-16
1.166 brouard 881: /* #define DEQUAL(a,b) (fabs((a)-(b))<mytinydouble) */
882: /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/mynrutils_8h-source.html */
883: /* static double dsqrarg; */
884: /* #define DSQR(a) (DEQUAL((dsqrarg=(a)),0.0) ? 0.0 : dsqrarg*dsqrarg) */
1.126 brouard 885: static double sqrarg;
886: #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
887: #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}
888: int agegomp= AGEGOMP;
889:
890: int imx;
891: int stepm=1;
892: /* Stepm, step in month: minimum step interpolation*/
893:
894: int estepm;
895: /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
896:
897: int m,nb;
898: long *num;
1.197 brouard 899: int firstpass=0, lastpass=4,*cod, *cens;
1.192 brouard 900: int *ncodemax; /* ncodemax[j]= Number of modalities of the j th
901: covariate for which somebody answered excluding
902: undefined. Usually 2: 0 and 1. */
903: int *ncodemaxwundef; /* ncodemax[j]= Number of modalities of the j th
904: covariate for which somebody answered including
905: undefined. Usually 3: -1, 0 and 1. */
1.126 brouard 906: double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
907: double **pmmij, ***probs;
908: double *ageexmed,*agecens;
909: double dateintmean=0;
910:
911: double *weight;
912: int **s; /* Status */
1.141 brouard 913: double *agedc;
1.145 brouard 914: double **covar; /**< covar[j,i], value of jth covariate for individual i,
1.141 brouard 915: * covar=matrix(0,NCOVMAX,1,n);
1.187 brouard 916: * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*age; */
1.141 brouard 917: double idx;
918: int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */
1.197 brouard 919: int *Tage;
1.145 brouard 920: int *Ndum; /** Freq of modality (tricode */
1.200 brouard 921: /* int **codtab;*/ /**< codtab=imatrix(1,100,1,10); */
1.141 brouard 922: int **Tvard, *Tprod, cptcovprod, *Tvaraff;
1.126 brouard 923: double *lsurv, *lpop, *tpop;
924:
1.143 brouard 925: double ftol=FTOL; /**< Tolerance for computing Max Likelihood */
926: double ftolhess; /**< Tolerance for computing hessian */
1.126 brouard 927:
928: /**************** split *************************/
929: static int split( char *path, char *dirc, char *name, char *ext, char *finame )
930: {
931: /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
932: the name of the file (name), its extension only (ext) and its first part of the name (finame)
933: */
934: char *ss; /* pointer */
1.186 brouard 935: int l1=0, l2=0; /* length counters */
1.126 brouard 936:
937: l1 = strlen(path ); /* length of path */
938: if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
939: ss= strrchr( path, DIRSEPARATOR ); /* find last / */
940: if ( ss == NULL ) { /* no directory, so determine current directory */
941: strcpy( name, path ); /* we got the fullname name because no directory */
942: /*if(strrchr(path, ODIRSEPARATOR )==NULL)
943: printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
944: /* get current working directory */
945: /* extern char* getcwd ( char *buf , int len);*/
1.184 brouard 946: #ifdef WIN32
947: if (_getcwd( dirc, FILENAME_MAX ) == NULL ) {
948: #else
949: if (getcwd(dirc, FILENAME_MAX) == NULL) {
950: #endif
1.126 brouard 951: return( GLOCK_ERROR_GETCWD );
952: }
953: /* got dirc from getcwd*/
954: printf(" DIRC = %s \n",dirc);
1.205 brouard 955: } else { /* strip directory from path */
1.126 brouard 956: ss++; /* after this, the filename */
957: l2 = strlen( ss ); /* length of filename */
958: if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
959: strcpy( name, ss ); /* save file name */
960: strncpy( dirc, path, l1 - l2 ); /* now the directory */
1.186 brouard 961: dirc[l1-l2] = '\0'; /* add zero */
1.126 brouard 962: printf(" DIRC2 = %s \n",dirc);
963: }
964: /* We add a separator at the end of dirc if not exists */
965: l1 = strlen( dirc ); /* length of directory */
966: if( dirc[l1-1] != DIRSEPARATOR ){
967: dirc[l1] = DIRSEPARATOR;
968: dirc[l1+1] = 0;
969: printf(" DIRC3 = %s \n",dirc);
970: }
971: ss = strrchr( name, '.' ); /* find last / */
972: if (ss >0){
973: ss++;
974: strcpy(ext,ss); /* save extension */
975: l1= strlen( name);
976: l2= strlen(ss)+1;
977: strncpy( finame, name, l1-l2);
978: finame[l1-l2]= 0;
979: }
980:
981: return( 0 ); /* we're done */
982: }
983:
984:
985: /******************************************/
986:
987: void replace_back_to_slash(char *s, char*t)
988: {
989: int i;
990: int lg=0;
991: i=0;
992: lg=strlen(t);
993: for(i=0; i<= lg; i++) {
994: (s[i] = t[i]);
995: if (t[i]== '\\') s[i]='/';
996: }
997: }
998:
1.132 brouard 999: char *trimbb(char *out, char *in)
1.137 brouard 1000: { /* Trim multiple blanks in line but keeps first blanks if line starts with blanks */
1.132 brouard 1001: char *s;
1002: s=out;
1003: while (*in != '\0'){
1.137 brouard 1004: while( *in == ' ' && *(in+1) == ' '){ /* && *(in+1) != '\0'){*/
1.132 brouard 1005: in++;
1006: }
1007: *out++ = *in++;
1008: }
1009: *out='\0';
1010: return s;
1011: }
1012:
1.187 brouard 1013: /* char *substrchaine(char *out, char *in, char *chain) */
1014: /* { */
1015: /* /\* Substract chain 'chain' from 'in', return and output 'out' *\/ */
1016: /* char *s, *t; */
1017: /* t=in;s=out; */
1018: /* while ((*in != *chain) && (*in != '\0')){ */
1019: /* *out++ = *in++; */
1020: /* } */
1021:
1022: /* /\* *in matches *chain *\/ */
1023: /* while ((*in++ == *chain++) && (*in != '\0')){ */
1024: /* printf("*in = %c, *out= %c *chain= %c \n", *in, *out, *chain); */
1025: /* } */
1026: /* in--; chain--; */
1027: /* while ( (*in != '\0')){ */
1028: /* printf("Bef *in = %c, *out= %c *chain= %c \n", *in, *out, *chain); */
1029: /* *out++ = *in++; */
1030: /* printf("Aft *in = %c, *out= %c *chain= %c \n", *in, *out, *chain); */
1031: /* } */
1032: /* *out='\0'; */
1033: /* out=s; */
1034: /* return out; */
1035: /* } */
1036: char *substrchaine(char *out, char *in, char *chain)
1037: {
1038: /* Substract chain 'chain' from 'in', return and output 'out' */
1039: /* in="V1+V1*age+age*age+V2", chain="age*age" */
1040:
1041: char *strloc;
1042:
1043: strcpy (out, in);
1044: strloc = strstr(out, chain); /* strloc points to out at age*age+V2 */
1045: printf("Bef strloc=%s chain=%s out=%s \n", strloc, chain, out);
1046: if(strloc != NULL){
1047: /* will affect out */ /* strloc+strlenc(chain)=+V2 */ /* Will also work in Unicode */
1048: memmove(strloc,strloc+strlen(chain), strlen(strloc+strlen(chain))+1);
1049: /* strcpy (strloc, strloc +strlen(chain));*/
1050: }
1051: printf("Aft strloc=%s chain=%s in=%s out=%s \n", strloc, chain, in, out);
1052: return out;
1053: }
1054:
1055:
1.145 brouard 1056: char *cutl(char *blocc, char *alocc, char *in, char occ)
1057: {
1.187 brouard 1058: /* cuts string in into blocc and alocc where blocc ends before FIRST occurence of char 'occ'
1.145 brouard 1059: and alocc starts after first occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
1.187 brouard 1060: gives blocc="abcdef" and alocc="ghi2j".
1.145 brouard 1061: If occ is not found blocc is null and alocc is equal to in. Returns blocc
1062: */
1.160 brouard 1063: char *s, *t;
1.145 brouard 1064: t=in;s=in;
1065: while ((*in != occ) && (*in != '\0')){
1066: *alocc++ = *in++;
1067: }
1068: if( *in == occ){
1069: *(alocc)='\0';
1070: s=++in;
1071: }
1072:
1073: if (s == t) {/* occ not found */
1074: *(alocc-(in-s))='\0';
1075: in=s;
1076: }
1077: while ( *in != '\0'){
1078: *blocc++ = *in++;
1079: }
1080:
1081: *blocc='\0';
1082: return t;
1083: }
1.137 brouard 1084: char *cutv(char *blocc, char *alocc, char *in, char occ)
1085: {
1.187 brouard 1086: /* cuts string in into blocc and alocc where blocc ends before LAST occurence of char 'occ'
1.137 brouard 1087: and alocc starts after last occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
1088: gives blocc="abcdef2ghi" and alocc="j".
1089: If occ is not found blocc is null and alocc is equal to in. Returns alocc
1090: */
1091: char *s, *t;
1092: t=in;s=in;
1093: while (*in != '\0'){
1094: while( *in == occ){
1095: *blocc++ = *in++;
1096: s=in;
1097: }
1098: *blocc++ = *in++;
1099: }
1100: if (s == t) /* occ not found */
1101: *(blocc-(in-s))='\0';
1102: else
1103: *(blocc-(in-s)-1)='\0';
1104: in=s;
1105: while ( *in != '\0'){
1106: *alocc++ = *in++;
1107: }
1108:
1109: *alocc='\0';
1110: return s;
1111: }
1112:
1.126 brouard 1113: int nbocc(char *s, char occ)
1114: {
1115: int i,j=0;
1116: int lg=20;
1117: i=0;
1118: lg=strlen(s);
1119: for(i=0; i<= lg; i++) {
1120: if (s[i] == occ ) j++;
1121: }
1122: return j;
1123: }
1124:
1.137 brouard 1125: /* void cutv(char *u,char *v, char*t, char occ) */
1126: /* { */
1127: /* /\* cuts string t into u and v where u ends before last occurence of char 'occ' */
1128: /* and v starts after last occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2') */
1129: /* gives u="abcdef2ghi" and v="j" *\/ */
1130: /* int i,lg,j,p=0; */
1131: /* i=0; */
1132: /* lg=strlen(t); */
1133: /* for(j=0; j<=lg-1; j++) { */
1134: /* if((t[j]!= occ) && (t[j+1]== occ)) p=j+1; */
1135: /* } */
1.126 brouard 1136:
1.137 brouard 1137: /* for(j=0; j<p; j++) { */
1138: /* (u[j] = t[j]); */
1139: /* } */
1140: /* u[p]='\0'; */
1.126 brouard 1141:
1.137 brouard 1142: /* for(j=0; j<= lg; j++) { */
1143: /* if (j>=(p+1))(v[j-p-1] = t[j]); */
1144: /* } */
1145: /* } */
1.126 brouard 1146:
1.160 brouard 1147: #ifdef _WIN32
1148: char * strsep(char **pp, const char *delim)
1149: {
1150: char *p, *q;
1151:
1152: if ((p = *pp) == NULL)
1153: return 0;
1154: if ((q = strpbrk (p, delim)) != NULL)
1155: {
1156: *pp = q + 1;
1157: *q = '\0';
1158: }
1159: else
1160: *pp = 0;
1161: return p;
1162: }
1163: #endif
1164:
1.126 brouard 1165: /********************** nrerror ********************/
1166:
1167: void nrerror(char error_text[])
1168: {
1169: fprintf(stderr,"ERREUR ...\n");
1170: fprintf(stderr,"%s\n",error_text);
1171: exit(EXIT_FAILURE);
1172: }
1173: /*********************** vector *******************/
1174: double *vector(int nl, int nh)
1175: {
1176: double *v;
1177: v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
1178: if (!v) nrerror("allocation failure in vector");
1179: return v-nl+NR_END;
1180: }
1181:
1182: /************************ free vector ******************/
1183: void free_vector(double*v, int nl, int nh)
1184: {
1185: free((FREE_ARG)(v+nl-NR_END));
1186: }
1187:
1188: /************************ivector *******************************/
1189: int *ivector(long nl,long nh)
1190: {
1191: int *v;
1192: v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
1193: if (!v) nrerror("allocation failure in ivector");
1194: return v-nl+NR_END;
1195: }
1196:
1197: /******************free ivector **************************/
1198: void free_ivector(int *v, long nl, long nh)
1199: {
1200: free((FREE_ARG)(v+nl-NR_END));
1201: }
1202:
1203: /************************lvector *******************************/
1204: long *lvector(long nl,long nh)
1205: {
1206: long *v;
1207: v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
1208: if (!v) nrerror("allocation failure in ivector");
1209: return v-nl+NR_END;
1210: }
1211:
1212: /******************free lvector **************************/
1213: void free_lvector(long *v, long nl, long nh)
1214: {
1215: free((FREE_ARG)(v+nl-NR_END));
1216: }
1217:
1218: /******************* imatrix *******************************/
1219: int **imatrix(long nrl, long nrh, long ncl, long nch)
1220: /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */
1221: {
1222: long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;
1223: int **m;
1224:
1225: /* allocate pointers to rows */
1226: m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));
1227: if (!m) nrerror("allocation failure 1 in matrix()");
1228: m += NR_END;
1229: m -= nrl;
1230:
1231:
1232: /* allocate rows and set pointers to them */
1233: m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));
1234: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
1235: m[nrl] += NR_END;
1236: m[nrl] -= ncl;
1237:
1238: for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;
1239:
1240: /* return pointer to array of pointers to rows */
1241: return m;
1242: }
1243:
1244: /****************** free_imatrix *************************/
1245: void free_imatrix(m,nrl,nrh,ncl,nch)
1246: int **m;
1247: long nch,ncl,nrh,nrl;
1248: /* free an int matrix allocated by imatrix() */
1249: {
1250: free((FREE_ARG) (m[nrl]+ncl-NR_END));
1251: free((FREE_ARG) (m+nrl-NR_END));
1252: }
1253:
1254: /******************* matrix *******************************/
1255: double **matrix(long nrl, long nrh, long ncl, long nch)
1256: {
1257: long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
1258: double **m;
1259:
1260: m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
1261: if (!m) nrerror("allocation failure 1 in matrix()");
1262: m += NR_END;
1263: m -= nrl;
1264:
1265: m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
1266: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
1267: m[nrl] += NR_END;
1268: m[nrl] -= ncl;
1269:
1270: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
1271: return m;
1.145 brouard 1272: /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) or &(m[1][0])
1273: m[i] = address of ith row of the table. &(m[i]) is its value which is another adress
1274: that of m[i][0]. In order to get the value p m[i][0] but it is unitialized.
1.126 brouard 1275: */
1276: }
1277:
1278: /*************************free matrix ************************/
1279: void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
1280: {
1281: free((FREE_ARG)(m[nrl]+ncl-NR_END));
1282: free((FREE_ARG)(m+nrl-NR_END));
1283: }
1284:
1285: /******************* ma3x *******************************/
1286: double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
1287: {
1288: long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
1289: double ***m;
1290:
1291: m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
1292: if (!m) nrerror("allocation failure 1 in matrix()");
1293: m += NR_END;
1294: m -= nrl;
1295:
1296: m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
1297: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
1298: m[nrl] += NR_END;
1299: m[nrl] -= ncl;
1300:
1301: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
1302:
1303: m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
1304: if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
1305: m[nrl][ncl] += NR_END;
1306: m[nrl][ncl] -= nll;
1307: for (j=ncl+1; j<=nch; j++)
1308: m[nrl][j]=m[nrl][j-1]+nlay;
1309:
1310: for (i=nrl+1; i<=nrh; i++) {
1311: m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
1312: for (j=ncl+1; j<=nch; j++)
1313: m[i][j]=m[i][j-1]+nlay;
1314: }
1315: return m;
1316: /* gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
1317: &(m[i][j][k]) <=> *((*(m+i) + j)+k)
1318: */
1319: }
1320:
1321: /*************************free ma3x ************************/
1322: void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
1323: {
1324: free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
1325: free((FREE_ARG)(m[nrl]+ncl-NR_END));
1326: free((FREE_ARG)(m+nrl-NR_END));
1327: }
1328:
1329: /*************** function subdirf ***********/
1330: char *subdirf(char fileres[])
1331: {
1332: /* Caution optionfilefiname is hidden */
1333: strcpy(tmpout,optionfilefiname);
1334: strcat(tmpout,"/"); /* Add to the right */
1335: strcat(tmpout,fileres);
1336: return tmpout;
1337: }
1338:
1339: /*************** function subdirf2 ***********/
1340: char *subdirf2(char fileres[], char *preop)
1341: {
1342:
1343: /* Caution optionfilefiname is hidden */
1344: strcpy(tmpout,optionfilefiname);
1345: strcat(tmpout,"/");
1346: strcat(tmpout,preop);
1347: strcat(tmpout,fileres);
1348: return tmpout;
1349: }
1350:
1351: /*************** function subdirf3 ***********/
1352: char *subdirf3(char fileres[], char *preop, char *preop2)
1353: {
1354:
1355: /* Caution optionfilefiname is hidden */
1356: strcpy(tmpout,optionfilefiname);
1357: strcat(tmpout,"/");
1358: strcat(tmpout,preop);
1359: strcat(tmpout,preop2);
1360: strcat(tmpout,fileres);
1361: return tmpout;
1362: }
1363:
1.162 brouard 1364: char *asc_diff_time(long time_sec, char ascdiff[])
1365: {
1366: long sec_left, days, hours, minutes;
1367: days = (time_sec) / (60*60*24);
1368: sec_left = (time_sec) % (60*60*24);
1369: hours = (sec_left) / (60*60) ;
1370: sec_left = (sec_left) %(60*60);
1371: minutes = (sec_left) /60;
1372: sec_left = (sec_left) % (60);
1373: sprintf(ascdiff,"%ld day(s) %ld hour(s) %ld minute(s) %ld second(s)",days, hours, minutes, sec_left);
1374: return ascdiff;
1375: }
1376:
1.126 brouard 1377: /***************** f1dim *************************/
1378: extern int ncom;
1379: extern double *pcom,*xicom;
1380: extern double (*nrfunc)(double []);
1381:
1382: double f1dim(double x)
1383: {
1384: int j;
1385: double f;
1386: double *xt;
1387:
1388: xt=vector(1,ncom);
1389: for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];
1390: f=(*nrfunc)(xt);
1391: free_vector(xt,1,ncom);
1392: return f;
1393: }
1394:
1395: /*****************brent *************************/
1396: double brent(double ax, double bx, double cx, double (*f)(double), double tol, double *xmin)
1.187 brouard 1397: {
1398: /* Given a function f, and given a bracketing triplet of abscissas ax, bx, cx (such that bx is
1399: * between ax and cx, and f(bx) is less than both f(ax) and f(cx) ), this routine isolates
1400: * the minimum to a fractional precision of about tol using Brent’s method. The abscissa of
1401: * the minimum is returned as xmin, and the minimum function value is returned as brent , the
1402: * returned function value.
1403: */
1.126 brouard 1404: int iter;
1405: double a,b,d,etemp;
1.159 brouard 1406: double fu=0,fv,fw,fx;
1.164 brouard 1407: double ftemp=0.;
1.126 brouard 1408: double p,q,r,tol1,tol2,u,v,w,x,xm;
1409: double e=0.0;
1410:
1411: a=(ax < cx ? ax : cx);
1412: b=(ax > cx ? ax : cx);
1413: x=w=v=bx;
1414: fw=fv=fx=(*f)(x);
1415: for (iter=1;iter<=ITMAX;iter++) {
1416: xm=0.5*(a+b);
1417: tol2=2.0*(tol1=tol*fabs(x)+ZEPS);
1418: /* if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
1419: printf(".");fflush(stdout);
1420: fprintf(ficlog,".");fflush(ficlog);
1.162 brouard 1421: #ifdef DEBUGBRENT
1.126 brouard 1422: 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);
1423: 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);
1424: /* if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
1425: #endif
1426: if (fabs(x-xm) <= (tol2-0.5*(b-a))){
1427: *xmin=x;
1428: return fx;
1429: }
1430: ftemp=fu;
1431: if (fabs(e) > tol1) {
1432: r=(x-w)*(fx-fv);
1433: q=(x-v)*(fx-fw);
1434: p=(x-v)*q-(x-w)*r;
1435: q=2.0*(q-r);
1436: if (q > 0.0) p = -p;
1437: q=fabs(q);
1438: etemp=e;
1439: e=d;
1440: if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))
1441: d=CGOLD*(e=(x >= xm ? a-x : b-x));
1442: else {
1443: d=p/q;
1444: u=x+d;
1445: if (u-a < tol2 || b-u < tol2)
1446: d=SIGN(tol1,xm-x);
1447: }
1448: } else {
1449: d=CGOLD*(e=(x >= xm ? a-x : b-x));
1450: }
1451: u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));
1452: fu=(*f)(u);
1453: if (fu <= fx) {
1454: if (u >= x) a=x; else b=x;
1455: SHFT(v,w,x,u)
1.183 brouard 1456: SHFT(fv,fw,fx,fu)
1457: } else {
1458: if (u < x) a=u; else b=u;
1459: if (fu <= fw || w == x) {
1460: v=w;
1461: w=u;
1462: fv=fw;
1463: fw=fu;
1464: } else if (fu <= fv || v == x || v == w) {
1465: v=u;
1466: fv=fu;
1467: }
1468: }
1.126 brouard 1469: }
1470: nrerror("Too many iterations in brent");
1471: *xmin=x;
1472: return fx;
1473: }
1474:
1475: /****************** mnbrak ***********************/
1476:
1477: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,
1478: double (*func)(double))
1.183 brouard 1479: { /* Given a function func , and given distinct initial points ax and bx , this routine searches in
1480: the downhill direction (defined by the function as evaluated at the initial points) and returns
1481: new points ax , bx , cx that bracket a minimum of the function. Also returned are the function
1482: values at the three points, fa, fb , and fc such that fa > fb and fb < fc.
1483: */
1.126 brouard 1484: double ulim,u,r,q, dum;
1485: double fu;
1.187 brouard 1486:
1487: double scale=10.;
1488: int iterscale=0;
1489:
1490: *fa=(*func)(*ax); /* xta[j]=pcom[j]+(*ax)*xicom[j]; fa=f(xta[j])*/
1491: *fb=(*func)(*bx); /* xtb[j]=pcom[j]+(*bx)*xicom[j]; fb=f(xtb[j]) */
1492:
1493:
1494: /* while(*fb != *fb){ /\* *ax should be ok, reducing distance to *ax *\/ */
1495: /* printf("Warning mnbrak *fb = %lf, *bx=%lf *ax=%lf *fa==%lf iter=%d\n",*fb, *bx, *ax, *fa, iterscale++); */
1496: /* *bx = *ax - (*ax - *bx)/scale; */
1497: /* *fb=(*func)(*bx); /\* xtb[j]=pcom[j]+(*bx)*xicom[j]; fb=f(xtb[j]) *\/ */
1498: /* } */
1499:
1.126 brouard 1500: if (*fb > *fa) {
1501: SHFT(dum,*ax,*bx,dum)
1.183 brouard 1502: SHFT(dum,*fb,*fa,dum)
1503: }
1.126 brouard 1504: *cx=(*bx)+GOLD*(*bx-*ax);
1505: *fc=(*func)(*cx);
1.183 brouard 1506: #ifdef DEBUG
1507: printf("mnbrak0 *fb=%.12e *fc=%.12e\n",*fb,*fc);
1508: fprintf(ficlog,"mnbrak0 *fb=%.12e *fc=%.12e\n",*fb,*fc);
1509: #endif
1510: while (*fb > *fc) { /* Declining a,b,c with fa> fb > fc */
1.126 brouard 1511: r=(*bx-*ax)*(*fb-*fc);
1512: q=(*bx-*cx)*(*fb-*fa);
1513: u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/
1.183 brouard 1514: (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); /* Minimum abscissa of a parabolic estimated from (a,fa), (b,fb) and (c,fc). */
1515: ulim=(*bx)+GLIMIT*(*cx-*bx); /* Maximum abscissa where function should be evaluated */
1516: if ((*bx-u)*(u-*cx) > 0.0) { /* if u_p is between b and c */
1.126 brouard 1517: fu=(*func)(u);
1.163 brouard 1518: #ifdef DEBUG
1519: /* f(x)=A(x-u)**2+f(u) */
1520: double A, fparabu;
1521: A= (*fb - *fa)/(*bx-*ax)/(*bx+*ax-2*u);
1522: fparabu= *fa - A*(*ax-u)*(*ax-u);
1523: 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);
1524: 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 1525: /* And thus,it can be that fu > *fc even if fparabu < *fc */
1526: /* mnbrak (*ax=7.666299858533, *fa=299039.693133272231), (*bx=8.595447774979, *fb=298976.598289369489),
1527: (*cx=10.098840694817, *fc=298946.631474258087), (*u=9.852501168332, fu=298948.773013752128, fparabu=298945.434711494134) */
1528: /* In that case, there is no bracket in the output! Routine is wrong with many consequences.*/
1.163 brouard 1529: #endif
1.184 brouard 1530: #ifdef MNBRAKORIGINAL
1.183 brouard 1531: #else
1.191 brouard 1532: /* if (fu > *fc) { */
1533: /* #ifdef DEBUG */
1534: /* printf("mnbrak4 fu > fc \n"); */
1535: /* fprintf(ficlog, "mnbrak4 fu > fc\n"); */
1536: /* #endif */
1537: /* /\* 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 *\\/ *\/ */
1538: /* /\* SHFT(*fa,*fc,fu,*fc) /\\* (b, u, c) is a bracket while test fb > fc will be fu > fc will exit *\\/ *\/ */
1539: /* dum=u; /\* Shifting c and u *\/ */
1540: /* u = *cx; */
1541: /* *cx = dum; */
1542: /* dum = fu; */
1543: /* fu = *fc; */
1544: /* *fc =dum; */
1545: /* } else { /\* end *\/ */
1546: /* #ifdef DEBUG */
1547: /* printf("mnbrak3 fu < fc \n"); */
1548: /* fprintf(ficlog, "mnbrak3 fu < fc\n"); */
1549: /* #endif */
1550: /* dum=u; /\* Shifting c and u *\/ */
1551: /* u = *cx; */
1552: /* *cx = dum; */
1553: /* dum = fu; */
1554: /* fu = *fc; */
1555: /* *fc =dum; */
1556: /* } */
1.183 brouard 1557: #ifdef DEBUG
1.191 brouard 1558: printf("mnbrak34 fu < or >= fc \n");
1559: fprintf(ficlog, "mnbrak34 fu < fc\n");
1.183 brouard 1560: #endif
1.191 brouard 1561: dum=u; /* Shifting c and u */
1562: u = *cx;
1563: *cx = dum;
1564: dum = fu;
1565: fu = *fc;
1566: *fc =dum;
1.183 brouard 1567: #endif
1.162 brouard 1568: } else if ((*cx-u)*(u-ulim) > 0.0) { /* u is after c but before ulim */
1.183 brouard 1569: #ifdef DEBUG
1570: printf("mnbrak2 u after c but before ulim\n");
1571: fprintf(ficlog, "mnbrak2 u after c but before ulim\n");
1572: #endif
1.126 brouard 1573: fu=(*func)(u);
1574: if (fu < *fc) {
1.183 brouard 1575: #ifdef DEBUG
1576: printf("mnbrak2 u after c but before ulim AND fu < fc\n");
1577: fprintf(ficlog, "mnbrak2 u after c but before ulim AND fu <fc \n");
1578: #endif
1.126 brouard 1579: SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))
1.183 brouard 1580: SHFT(*fb,*fc,fu,(*func)(u))
1581: }
1.162 brouard 1582: } else if ((u-ulim)*(ulim-*cx) >= 0.0) { /* u outside ulim (verifying that ulim is beyond c) */
1.183 brouard 1583: #ifdef DEBUG
1584: printf("mnbrak2 u outside ulim (verifying that ulim is beyond c)\n");
1585: fprintf(ficlog, "mnbrak2 u outside ulim (verifying that ulim is beyond c)\n");
1586: #endif
1.126 brouard 1587: u=ulim;
1588: fu=(*func)(u);
1.183 brouard 1589: } else { /* u could be left to b (if r > q parabola has a maximum) */
1590: #ifdef DEBUG
1591: printf("mnbrak2 u could be left to b (if r > q parabola has a maximum)\n");
1592: fprintf(ficlog, "mnbrak2 u could be left to b (if r > q parabola has a maximum)\n");
1593: #endif
1.126 brouard 1594: u=(*cx)+GOLD*(*cx-*bx);
1595: fu=(*func)(u);
1.183 brouard 1596: } /* end tests */
1.126 brouard 1597: SHFT(*ax,*bx,*cx,u)
1.183 brouard 1598: SHFT(*fa,*fb,*fc,fu)
1599: #ifdef DEBUG
1600: 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);
1601: 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);
1602: #endif
1603: } /* 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 1604: }
1605:
1606: /*************** linmin ************************/
1.162 brouard 1607: /* Given an n -dimensional point p[1..n] and an n -dimensional direction xi[1..n] , moves and
1608: resets p to where the function func(p) takes on a minimum along the direction xi from p ,
1609: and replaces xi by the actual vector displacement that p was moved. Also returns as fret
1610: the value of func at the returned location p . This is actually all accomplished by calling the
1611: routines mnbrak and brent .*/
1.126 brouard 1612: int ncom;
1613: double *pcom,*xicom;
1614: double (*nrfunc)(double []);
1615:
1616: void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))
1617: {
1618: double brent(double ax, double bx, double cx,
1619: double (*f)(double), double tol, double *xmin);
1620: double f1dim(double x);
1621: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,
1622: double *fc, double (*func)(double));
1623: int j;
1624: double xx,xmin,bx,ax;
1625: double fx,fb,fa;
1.187 brouard 1626:
1.203 brouard 1627: #ifdef LINMINORIGINAL
1628: #else
1629: double scale=10., axs, xxs; /* Scale added for infinity */
1630: #endif
1631:
1.126 brouard 1632: ncom=n;
1633: pcom=vector(1,n);
1634: xicom=vector(1,n);
1635: nrfunc=func;
1636: for (j=1;j<=n;j++) {
1637: pcom[j]=p[j];
1.202 brouard 1638: xicom[j]=xi[j]; /* Former scale xi[j] of currrent direction i */
1.126 brouard 1639: }
1.187 brouard 1640:
1.203 brouard 1641: #ifdef LINMINORIGINAL
1642: xx=1.;
1643: #else
1644: axs=0.0;
1645: xxs=1.;
1646: do{
1647: xx= xxs;
1648: #endif
1.187 brouard 1649: ax=0.;
1650: mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); /* Outputs: xtx[j]=pcom[j]+(*xx)*xicom[j]; fx=f(xtx[j]) */
1651: /* brackets with inputs ax=0 and xx=1, but points, pcom=p, and directions values, xicom=xi, are sent via f1dim(x) */
1652: /* 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)) */
1653: /* Outputs: fa=f(p(j)) and fx=f(p(j) + xxs * xi(j) ) and f(bx)= f(p(j)+ bx* xi(j)) */
1654: /* Given input ax=axs and xx=xxs, xx might be too far from ax to get a finite f(xx) */
1655: /* Searches on line, outputs (ax, xx, bx) such that fx < min(fa and fb) */
1656: /* 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 1657: #ifdef LINMINORIGINAL
1658: #else
1659: if (fx != fx){
1660: xxs=xxs/scale; /* Trying a smaller xx, closer to initial ax=0 */
1661: printf("|");
1662: fprintf(ficlog,"|");
1663: #ifdef DEBUGLINMIN
1664: 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);
1665: #endif
1666: }
1667: }while(fx != fx);
1668: #endif
1669:
1.191 brouard 1670: #ifdef DEBUGLINMIN
1671: 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 1672: 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 1673: #endif
1.187 brouard 1674: *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); /* Giving a bracketting triplet (ax, xx, bx), find a minimum, xmin, according to f1dim, *fret(xmin),*/
1675: /* fa = f(p[j] + ax * xi[j]), fx = f(p[j] + xx * xi[j]), fb = f(p[j] + bx * xi[j]) */
1676: /* fmin = f(p[j] + xmin * xi[j]) */
1677: /* P+lambda n in that direction (lambdamin), with TOL between abscisses */
1678: /* f1dim(xmin): for (j=1;j<=ncom;j++) xt[j]=pcom[j]+xmin*xicom[j]; */
1.126 brouard 1679: #ifdef DEBUG
1680: printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
1681: fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
1682: #endif
1.191 brouard 1683: #ifdef DEBUGLINMIN
1684: printf("linmin end ");
1.202 brouard 1685: fprintf(ficlog,"linmin end ");
1.191 brouard 1686: #endif
1.126 brouard 1687: for (j=1;j<=n;j++) {
1.203 brouard 1688: #ifdef LINMINORIGINAL
1689: xi[j] *= xmin;
1690: #else
1691: #ifdef DEBUGLINMIN
1692: if(xxs <1.0)
1693: printf(" before xi[%d]=%12.8f", j,xi[j]);
1694: #endif
1695: 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) */
1696: #ifdef DEBUGLINMIN
1697: if(xxs <1.0)
1698: 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 );
1699: #endif
1700: #endif
1.187 brouard 1701: p[j] += xi[j]; /* Parameters values are updated accordingly */
1.126 brouard 1702: }
1.191 brouard 1703: #ifdef DEBUGLINMIN
1.203 brouard 1704: printf("\n");
1.191 brouard 1705: printf("Comparing last *frec(xmin=%12.8f)=%12.8f from Brent and frec(0.)=%12.8f \n", xmin, *fret, (*func)(p));
1.202 brouard 1706: 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 1707: for (j=1;j<=n;j++) {
1.202 brouard 1708: printf(" xi[%d]= %14.10f p[%d]= %12.7f",j,xi[j],j,p[j]);
1709: fprintf(ficlog," xi[%d]= %14.10f p[%d]= %12.7f",j,xi[j],j,p[j]);
1710: if(j % ncovmodel == 0){
1.191 brouard 1711: printf("\n");
1.202 brouard 1712: fprintf(ficlog,"\n");
1713: }
1.191 brouard 1714: }
1.203 brouard 1715: #else
1.191 brouard 1716: #endif
1.126 brouard 1717: free_vector(xicom,1,n);
1718: free_vector(pcom,1,n);
1719: }
1720:
1721:
1722: /*************** powell ************************/
1.162 brouard 1723: /*
1724: Minimization of a function func of n variables. Input consists of an initial starting point
1725: p[1..n] ; an initial matrix xi[1..n][1..n] , whose columns contain the initial set of di-
1726: rections (usually the n unit vectors); and ftol , the fractional tolerance in the function value
1727: such that failure to decrease by more than this amount on one iteration signals doneness. On
1728: output, p is set to the best point found, xi is the then-current direction set, fret is the returned
1729: function value at p , and iter is the number of iterations taken. The routine linmin is used.
1730: */
1.126 brouard 1731: void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,
1732: double (*func)(double []))
1733: {
1734: void linmin(double p[], double xi[], int n, double *fret,
1735: double (*func)(double []));
1736: int i,ibig,j;
1737: double del,t,*pt,*ptt,*xit;
1.181 brouard 1738: double directest;
1.126 brouard 1739: double fp,fptt;
1740: double *xits;
1741: int niterf, itmp;
1742:
1743: pt=vector(1,n);
1744: ptt=vector(1,n);
1745: xit=vector(1,n);
1746: xits=vector(1,n);
1747: *fret=(*func)(p);
1748: for (j=1;j<=n;j++) pt[j]=p[j];
1.202 brouard 1749: rcurr_time = time(NULL);
1.126 brouard 1750: for (*iter=1;;++(*iter)) {
1.187 brouard 1751: fp=(*fret); /* From former iteration or initial value */
1.126 brouard 1752: ibig=0;
1753: del=0.0;
1.157 brouard 1754: rlast_time=rcurr_time;
1755: /* (void) gettimeofday(&curr_time,&tzp); */
1756: rcurr_time = time(NULL);
1757: curr_time = *localtime(&rcurr_time);
1758: printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, rcurr_time-rlast_time, rcurr_time-rstart_time);fflush(stdout);
1759: fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret,rcurr_time-rlast_time, rcurr_time-rstart_time); fflush(ficlog);
1760: /* fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tm_sec-start_time.tm_sec); */
1.192 brouard 1761: for (i=1;i<=n;i++) {
1.126 brouard 1762: printf(" %d %.12f",i, p[i]);
1763: fprintf(ficlog," %d %.12lf",i, p[i]);
1764: fprintf(ficrespow," %.12lf", p[i]);
1765: }
1766: printf("\n");
1767: fprintf(ficlog,"\n");
1768: fprintf(ficrespow,"\n");fflush(ficrespow);
1769: if(*iter <=3){
1.157 brouard 1770: tml = *localtime(&rcurr_time);
1771: strcpy(strcurr,asctime(&tml));
1772: rforecast_time=rcurr_time;
1.126 brouard 1773: itmp = strlen(strcurr);
1774: if(strcurr[itmp-1]=='\n') /* Windows outputs with a new line */
1775: strcurr[itmp-1]='\0';
1.162 brouard 1776: printf("\nConsidering the time needed for the last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
1.157 brouard 1777: fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
1.126 brouard 1778: for(niterf=10;niterf<=30;niterf+=10){
1.157 brouard 1779: rforecast_time=rcurr_time+(niterf-*iter)*(rcurr_time-rlast_time);
1780: forecast_time = *localtime(&rforecast_time);
1781: strcpy(strfor,asctime(&forecast_time));
1.126 brouard 1782: itmp = strlen(strfor);
1783: if(strfor[itmp-1]=='\n')
1784: strfor[itmp-1]='\0';
1.157 brouard 1785: 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);
1786: 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 1787: }
1788: }
1.187 brouard 1789: for (i=1;i<=n;i++) { /* For each direction i */
1790: for (j=1;j<=n;j++) xit[j]=xi[j][i]; /* Directions stored from previous iteration with previous scales */
1.126 brouard 1791: fptt=(*fret);
1792: #ifdef DEBUG
1.203 brouard 1793: printf("fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
1794: fprintf(ficlog, "fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
1.126 brouard 1795: #endif
1.203 brouard 1796: printf("%d",i);fflush(stdout); /* print direction (parameter) i */
1.126 brouard 1797: fprintf(ficlog,"%d",i);fflush(ficlog);
1.188 brouard 1798: linmin(p,xit,n,fret,func); /* Point p[n]. xit[n] has been loaded for direction i as input.*/
1799: /* Outputs are fret(new point p) p is updated and xit rescaled */
1800: if (fabs(fptt-(*fret)) > del) { /* We are keeping the max gain on each of the n directions */
1801: /* because that direction will be replaced unless the gain del is small */
1802: /* in comparison with the 'probable' gain, mu^2, with the last average direction. */
1803: /* Unless the n directions are conjugate some gain in the determinant may be obtained */
1804: /* with the new direction. */
1.126 brouard 1805: del=fabs(fptt-(*fret));
1806: ibig=i;
1807: }
1808: #ifdef DEBUG
1809: printf("%d %.12e",i,(*fret));
1810: fprintf(ficlog,"%d %.12e",i,(*fret));
1811: for (j=1;j<=n;j++) {
1812: xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
1813: printf(" x(%d)=%.12e",j,xit[j]);
1814: fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
1815: }
1816: for(j=1;j<=n;j++) {
1.162 brouard 1817: printf(" p(%d)=%.12e",j,p[j]);
1818: fprintf(ficlog," p(%d)=%.12e",j,p[j]);
1.126 brouard 1819: }
1820: printf("\n");
1821: fprintf(ficlog,"\n");
1822: #endif
1.187 brouard 1823: } /* end loop on each direction i */
1824: /* Convergence test will use last linmin estimation (fret) and compare former iteration (fp) */
1.188 brouard 1825: /* But p and xit have been updated at the end of linmin, *fret corresponds to new p, xit */
1.187 brouard 1826: /* New value of last point Pn is not computed, P(n-1) */
1.182 brouard 1827: if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) { /* Did we reach enough precision? */
1.188 brouard 1828: /* We could compare with a chi^2. chisquare(0.95,ddl=1)=3.84 */
1829: /* By adding age*age in a model, the new -2LL should be lower and the difference follows a */
1830: /* a chisquare statistics with 1 degree. To be significant at the 95% level, it should have */
1831: /* decreased of more than 3.84 */
1832: /* By adding age*age and V1*age the gain (-2LL) should be more than 5.99 (ddl=2) */
1833: /* By using V1+V2+V3, the gain should be 7.82, compared with basic 1+age. */
1834: /* By adding 10 parameters more the gain should be 18.31 */
1835:
1836: /* Starting the program with initial values given by a former maximization will simply change */
1837: /* the scales of the directions and the directions, because the are reset to canonical directions */
1838: /* Thus the first calls to linmin will give new points and better maximizations until fp-(*fret) is */
1839: /* under the tolerance value. If the tolerance is very small 1.e-9, it could last long. */
1.126 brouard 1840: #ifdef DEBUG
1841: int k[2],l;
1842: k[0]=1;
1843: k[1]=-1;
1844: printf("Max: %.12e",(*func)(p));
1845: fprintf(ficlog,"Max: %.12e",(*func)(p));
1846: for (j=1;j<=n;j++) {
1847: printf(" %.12e",p[j]);
1848: fprintf(ficlog," %.12e",p[j]);
1849: }
1850: printf("\n");
1851: fprintf(ficlog,"\n");
1852: for(l=0;l<=1;l++) {
1853: for (j=1;j<=n;j++) {
1854: ptt[j]=p[j]+(p[j]-pt[j])*k[l];
1855: printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
1856: fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
1857: }
1858: printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
1859: fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
1860: }
1861: #endif
1862:
1863:
1864: free_vector(xit,1,n);
1865: free_vector(xits,1,n);
1866: free_vector(ptt,1,n);
1867: free_vector(pt,1,n);
1868: return;
1.192 brouard 1869: } /* enough precision */
1.126 brouard 1870: if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");
1.181 brouard 1871: for (j=1;j<=n;j++) { /* Computes the extrapolated point P_0 + 2 (P_n-P_0) */
1.126 brouard 1872: ptt[j]=2.0*p[j]-pt[j];
1873: xit[j]=p[j]-pt[j];
1874: pt[j]=p[j];
1875: }
1.181 brouard 1876: fptt=(*func)(ptt); /* f_3 */
1.192 brouard 1877: #ifdef POWELLF1F3
1878: #else
1.161 brouard 1879: if (fptt < fp) { /* If extrapolated point is better, decide if we keep that new direction or not */
1.192 brouard 1880: #endif
1.162 brouard 1881: /* (x1 f1=fp), (x2 f2=*fret), (x3 f3=fptt), (xm fm) */
1.161 brouard 1882: /* From x1 (P0) distance of x2 is at h and x3 is 2h */
1.162 brouard 1883: /* Let f"(x2) be the 2nd derivative equal everywhere. */
1884: /* Then the parabolic through (x1,f1), (x2,f2) and (x3,f3) */
1885: /* will reach at f3 = fm + h^2/2 f"m ; f" = (f1 -2f2 +f3 ) / h**2 */
1.181 brouard 1886: /* Conditional for using this new direction is that mu^2 = (f1-2f2+f3)^2 /2 < del */
1.161 brouard 1887: /* t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); */
1.183 brouard 1888: #ifdef NRCORIGINAL
1889: t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)- del*SQR(fp-fptt); /* Original Numerical Recipes in C*/
1890: #else
1891: 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 1892: t= t- del*SQR(fp-fptt);
1.183 brouard 1893: #endif
1.202 brouard 1894: directest = fp-2.0*(*fret)+fptt - 2.0 * del; /* If delta was big enough we change it for a new direction */
1.161 brouard 1895: #ifdef DEBUG
1.181 brouard 1896: 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);
1897: 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 1898: printf("t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
1899: (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
1900: fprintf(ficlog,"t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
1901: (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
1902: 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);
1903: 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);
1904: #endif
1.183 brouard 1905: #ifdef POWELLORIGINAL
1906: if (t < 0.0) { /* Then we use it for new direction */
1907: #else
1.182 brouard 1908: if (directest*t < 0.0) { /* Contradiction between both tests */
1.202 brouard 1909: 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 1910: 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 1911: 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 1912: fprintf(ficlog,"f1-2f2+f3= %.12lf, f1-f2-del= %.12lf, f1-f3= %.12lf\n",fp-2.0*(*fret)+fptt, fp -(*fret) -del, fp-fptt);
1913: }
1.181 brouard 1914: if (directest < 0.0) { /* Then we use it for new direction */
1915: #endif
1.191 brouard 1916: #ifdef DEBUGLINMIN
1917: printf("Before linmin in direction P%d-P0\n",n);
1918: for (j=1;j<=n;j++) {
1.202 brouard 1919: printf(" Before xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
1920: fprintf(ficlog," Before xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
1921: if(j % ncovmodel == 0){
1.191 brouard 1922: printf("\n");
1.202 brouard 1923: fprintf(ficlog,"\n");
1924: }
1.191 brouard 1925: }
1926: #endif
1.187 brouard 1927: linmin(p,xit,n,fret,func); /* computes minimum on the extrapolated direction: changes p and rescales xit.*/
1.191 brouard 1928: #ifdef DEBUGLINMIN
1929: for (j=1;j<=n;j++) {
1930: printf("After xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
1.202 brouard 1931: fprintf(ficlog,"After xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
1932: if(j % ncovmodel == 0){
1.191 brouard 1933: printf("\n");
1.202 brouard 1934: fprintf(ficlog,"\n");
1935: }
1.191 brouard 1936: }
1937: #endif
1.126 brouard 1938: for (j=1;j<=n;j++) {
1.181 brouard 1939: xi[j][ibig]=xi[j][n]; /* Replace direction with biggest decrease by last direction n */
1940: xi[j][n]=xit[j]; /* and this nth direction by the by the average p_0 p_n */
1.126 brouard 1941: }
1.181 brouard 1942: printf("Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
1943: fprintf(ficlog,"Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
1.161 brouard 1944:
1.126 brouard 1945: #ifdef DEBUG
1.164 brouard 1946: printf("Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
1947: fprintf(ficlog,"Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
1.126 brouard 1948: for(j=1;j<=n;j++){
1949: printf(" %.12e",xit[j]);
1950: fprintf(ficlog," %.12e",xit[j]);
1951: }
1952: printf("\n");
1953: fprintf(ficlog,"\n");
1954: #endif
1.192 brouard 1955: } /* end of t or directest negative */
1956: #ifdef POWELLF1F3
1957: #else
1.162 brouard 1958: } /* end if (fptt < fp) */
1.192 brouard 1959: #endif
1960: } /* loop iteration */
1.126 brouard 1961: }
1962:
1963: /**** Prevalence limit (stable or period prevalence) ****************/
1964:
1.203 brouard 1965: double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int *ncvyear, int ij)
1.126 brouard 1966: {
1967: /* Computes the prevalence limit in each live state at age x by left multiplying the unit
1.203 brouard 1968: matrix by transitions matrix until convergence is reached with precision ftolpl */
1.206 brouard 1969: /* Wx= Wx-1 Px-1= Wx-2 Px-2 Px-1 = Wx-n Px-n ... Px-2 Px-1 I */
1970: /* Wx is row vector: population in state 1, population in state 2, population dead */
1971: /* or prevalence in state 1, prevalence in state 2, 0 */
1972: /* newm is the matrix after multiplications, its rows are identical at a factor */
1973: /* Initial matrix pimij */
1974: /* {0.85204250825084937, 0.13044499163996345, 0.017512500109187184, */
1975: /* 0.090851990222114765, 0.88271245433047185, 0.026435555447413338, */
1976: /* 0, 0 , 1} */
1977: /*
1978: * and after some iteration: */
1979: /* {0.45504275246439968, 0.42731458730878791, 0.11764266022681241, */
1980: /* 0.45201005341706885, 0.42865420071559901, 0.11933574586733192, */
1981: /* 0, 0 , 1} */
1982: /* And prevalence by suppressing the deaths are close to identical rows in prlim: */
1983: /* {0.51571254859325999, 0.4842874514067399, */
1984: /* 0.51326036147820708, 0.48673963852179264} */
1985: /* If we start from prlim again, prlim tends to a constant matrix */
1986:
1.126 brouard 1987: int i, ii,j,k;
1988: double min, max, maxmin, maxmax,sumnew=0.;
1.145 brouard 1989: /* double **matprod2(); */ /* test */
1.131 brouard 1990: double **out, cov[NCOVMAX+1], **pmij();
1.126 brouard 1991: double **newm;
1.208 ! brouard 1992: double agefin, delaymax=100. ; /* 100 Max number of years to converge */
1.203 brouard 1993: int ncvloop=0;
1.169 brouard 1994:
1.126 brouard 1995: for (ii=1;ii<=nlstate+ndeath;ii++)
1996: for (j=1;j<=nlstate+ndeath;j++){
1997: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1998: }
1.169 brouard 1999:
2000: cov[1]=1.;
2001:
2002: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
1.202 brouard 2003: /* Start at agefin= age, computes the matrix of passage and loops decreasing agefin until convergence is reached */
1.126 brouard 2004: for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
1.202 brouard 2005: ncvloop++;
1.126 brouard 2006: newm=savm;
2007: /* Covariates have to be included here again */
1.138 brouard 2008: cov[2]=agefin;
1.187 brouard 2009: if(nagesqr==1)
2010: cov[3]= agefin*agefin;;
1.138 brouard 2011: for (k=1; k<=cptcovn;k++) {
1.200 brouard 2012: /* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; */
2013: cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)];
1.198 brouard 2014: /* 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 2015: }
1.186 brouard 2016: /*wrong? for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
1.200 brouard 2017: /* for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]*cov[2]; */
2018: for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtabm(ij,k)]*cov[2];
1.186 brouard 2019: for (k=1; k<=cptcovprod;k++) /* Useless */
1.200 brouard 2020: /* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])] * nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])]; */
2021: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)];
1.138 brouard 2022:
2023: /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
2024: /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
2025: /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
1.145 brouard 2026: /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
2027: /* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind *\/ */
1.142 brouard 2028: out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /* Bug Valgrind */
1.138 brouard 2029:
1.126 brouard 2030: savm=oldm;
2031: oldm=newm;
2032: maxmax=0.;
2033: for(j=1;j<=nlstate;j++){
2034: min=1.;
2035: max=0.;
2036: for(i=1; i<=nlstate; i++) {
2037: sumnew=0;
2038: for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
2039: prlim[i][j]= newm[i][j]/(1-sumnew);
2040: max=FMAX(max,prlim[i][j]);
2041: min=FMIN(min,prlim[i][j]);
1.208 ! brouard 2042: /* 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 2043: }
1.203 brouard 2044: maxmin=(max-min)/(max+min)*2;
1.126 brouard 2045: maxmax=FMAX(maxmax,maxmin);
1.208 ! brouard 2046: /* for(i=1; i<=nlstate; i++) { */
! 2047: /* sumnew=0.; */
! 2048: /* sumnew+=prlim[i][j]; */
! 2049: /* } */
! 2050: /* prmimj = sumnew/(float)nlstate; /\* Means of various prevalence limits. */
1.169 brouard 2051: } /* j loop */
1.203 brouard 2052: *ncvyear= (int)age- (int)agefin;
1.208 ! brouard 2053: /* 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 2054: if(maxmax < ftolpl){
1.203 brouard 2055: /* 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 2056: return prlim;
2057: }
1.169 brouard 2058: } /* age loop */
1.208 ! brouard 2059: /* After some age loop it doesn't converge */
! 2060: printf("Warning: the stable prevalence at age %d did not converge with the required precision %g > ftolpl=%g within %.0f years. \n\
! 2061: Earliest age to start was %d-%d=%d, ncvloop=%d, ncvyear=%d\n", (int)age, maxmax, ftolpl, delaymax, (int)age, (int)delaymax, (int)agefin, ncvloop, *ncvyear);
! 2062: /* printf(" age= %d newm\n",(int)age); */
! 2063: /* for(i=1; i<=nlstate+ndeath; i++) { */
! 2064: /* for(j=1;j<=nlstate+ndeath;j++){ */
! 2065: /* printf(" %lf", newm[i][j]); */
! 2066: /* } */
! 2067: /* printf("\n"); */
! 2068: /* } */
! 2069: /* printf("\n"); */
! 2070: /* printf("prlim\n"); */
! 2071: /* for(i=1; i<=nlstate; i++) { */
! 2072: /* sumnew=0; */
! 2073: /* for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k]; */
! 2074: /* for(j=1;j<=nlstate;j++){ */
! 2075: /* prlim[i][j]= newm[i][j]/(1-sumnew); */
! 2076: /* printf(" %lf", prlim[i][j]); */
! 2077: /* } */
! 2078: /* printf("\n"); */
! 2079: /* } */
! 2080: /* printf("\n"); */
! 2081:
! 2082: /* 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 2083: return prlim; /* should not reach here */
1.126 brouard 2084: }
2085:
2086: /*************** transition probabilities ***************/
2087:
2088: double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
2089: {
1.138 brouard 2090: /* According to parameters values stored in x and the covariate's values stored in cov,
2091: computes the probability to be observed in state j being in state i by appying the
2092: model to the ncovmodel covariates (including constant and age).
2093: lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc]
2094: and, according on how parameters are entered, the position of the coefficient xij(nc) of the
2095: ncth covariate in the global vector x is given by the formula:
2096: j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
2097: j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
2098: Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
2099: sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.
2100: Outputs ps[i][j] the probability to be observed in j being in j according to
2101: the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
2102: */
2103: double s1, lnpijopii;
1.126 brouard 2104: /*double t34;*/
1.164 brouard 2105: int i,j, nc, ii, jj;
1.126 brouard 2106:
2107: for(i=1; i<= nlstate; i++){
2108: for(j=1; j<i;j++){
1.138 brouard 2109: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
2110: /*lnpijopii += param[i][j][nc]*cov[nc];*/
2111: lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
2112: /* printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
1.126 brouard 2113: }
1.138 brouard 2114: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
2115: /* printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
1.126 brouard 2116: }
2117: for(j=i+1; j<=nlstate+ndeath;j++){
1.138 brouard 2118: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
2119: /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
2120: lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
2121: /* printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
1.126 brouard 2122: }
1.138 brouard 2123: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
1.126 brouard 2124: }
2125: }
2126:
2127: for(i=1; i<= nlstate; i++){
2128: s1=0;
1.131 brouard 2129: for(j=1; j<i; j++){
1.138 brouard 2130: s1+=exp(ps[i][j]); /* In fact sums pij/pii */
1.131 brouard 2131: /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
2132: }
2133: for(j=i+1; j<=nlstate+ndeath; j++){
1.138 brouard 2134: s1+=exp(ps[i][j]); /* In fact sums pij/pii */
1.131 brouard 2135: /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
2136: }
1.138 brouard 2137: /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
1.126 brouard 2138: ps[i][i]=1./(s1+1.);
1.138 brouard 2139: /* Computing other pijs */
1.126 brouard 2140: for(j=1; j<i; j++)
2141: ps[i][j]= exp(ps[i][j])*ps[i][i];
2142: for(j=i+1; j<=nlstate+ndeath; j++)
2143: ps[i][j]= exp(ps[i][j])*ps[i][i];
2144: /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
2145: } /* end i */
2146:
2147: for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
2148: for(jj=1; jj<= nlstate+ndeath; jj++){
2149: ps[ii][jj]=0;
2150: ps[ii][ii]=1;
2151: }
2152: }
2153:
1.145 brouard 2154:
2155: /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
2156: /* for(jj=1; jj<= nlstate+ndeath; jj++){ */
2157: /* printf(" pmij ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
2158: /* } */
2159: /* printf("\n "); */
2160: /* } */
2161: /* printf("\n ");printf("%lf ",cov[2]);*/
2162: /*
1.126 brouard 2163: for(i=1; i<= npar; i++) printf("%f ",x[i]);
2164: goto end;*/
2165: return ps;
2166: }
2167:
2168: /**************** Product of 2 matrices ******************/
2169:
1.145 brouard 2170: double **matprod2(double **out, double **in,int nrl, int nrh, int ncl, int nch, int ncolol, int ncoloh, double **b)
1.126 brouard 2171: {
2172: /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
2173: b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
2174: /* in, b, out are matrice of pointers which should have been initialized
2175: before: only the contents of out is modified. The function returns
2176: a pointer to pointers identical to out */
1.145 brouard 2177: int i, j, k;
1.126 brouard 2178: for(i=nrl; i<= nrh; i++)
1.145 brouard 2179: for(k=ncolol; k<=ncoloh; k++){
2180: out[i][k]=0.;
2181: for(j=ncl; j<=nch; j++)
2182: out[i][k] +=in[i][j]*b[j][k];
2183: }
1.126 brouard 2184: return out;
2185: }
2186:
2187:
2188: /************* Higher Matrix Product ***************/
2189:
2190: double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
2191: {
2192: /* Computes the transition matrix starting at age 'age' over
2193: 'nhstepm*hstepm*stepm' months (i.e. until
2194: age (in years) age+nhstepm*hstepm*stepm/12) by multiplying
2195: nhstepm*hstepm matrices.
2196: Output is stored in matrix po[i][j][h] for h every 'hstepm' step
2197: (typically every 2 years instead of every month which is too big
2198: for the memory).
2199: Model is determined by parameters x and covariates have to be
2200: included manually here.
2201:
2202: */
2203:
2204: int i, j, d, h, k;
1.131 brouard 2205: double **out, cov[NCOVMAX+1];
1.126 brouard 2206: double **newm;
1.187 brouard 2207: double agexact;
1.126 brouard 2208:
2209: /* Hstepm could be zero and should return the unit matrix */
2210: for (i=1;i<=nlstate+ndeath;i++)
2211: for (j=1;j<=nlstate+ndeath;j++){
2212: oldm[i][j]=(i==j ? 1.0 : 0.0);
2213: po[i][j][0]=(i==j ? 1.0 : 0.0);
2214: }
2215: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
2216: for(h=1; h <=nhstepm; h++){
2217: for(d=1; d <=hstepm; d++){
2218: newm=savm;
2219: /* Covariates have to be included here again */
2220: cov[1]=1.;
1.187 brouard 2221: agexact=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
2222: cov[2]=agexact;
2223: if(nagesqr==1)
2224: cov[3]= agexact*agexact;
1.131 brouard 2225: for (k=1; k<=cptcovn;k++)
1.200 brouard 2226: cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)];
2227: /* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; */
1.186 brouard 2228: for (k=1; k<=cptcovage;k++) /* Should start at cptcovn+1 */
2229: /* cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
1.200 brouard 2230: cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
2231: /* cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,Tvar[Tage[k]])]*cov[2]; */
1.145 brouard 2232: for (k=1; k<=cptcovprod;k++) /* Useless because included in cptcovn */
1.200 brouard 2233: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)];
2234: /* 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 2235:
2236:
2237: /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
2238: /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
2239: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
2240: pmij(pmmij,cov,ncovmodel,x,nlstate));
2241: savm=oldm;
2242: oldm=newm;
2243: }
2244: for(i=1; i<=nlstate+ndeath; i++)
2245: for(j=1;j<=nlstate+ndeath;j++) {
2246: po[i][j][h]=newm[i][j];
1.128 brouard 2247: /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
1.126 brouard 2248: }
1.128 brouard 2249: /*printf("h=%d ",h);*/
1.126 brouard 2250: } /* end h */
1.128 brouard 2251: /* printf("\n H=%d \n",h); */
1.126 brouard 2252: return po;
2253: }
2254:
1.162 brouard 2255: #ifdef NLOPT
2256: double myfunc(unsigned n, const double *p1, double *grad, void *pd){
2257: double fret;
2258: double *xt;
2259: int j;
2260: myfunc_data *d2 = (myfunc_data *) pd;
2261: /* xt = (p1-1); */
2262: xt=vector(1,n);
2263: for (j=1;j<=n;j++) xt[j]=p1[j-1]; /* xt[1]=p1[0] */
2264:
2265: fret=(d2->function)(xt); /* p xt[1]@8 is fine */
2266: /* fret=(*func)(xt); /\* p xt[1]@8 is fine *\/ */
2267: printf("Function = %.12lf ",fret);
2268: for (j=1;j<=n;j++) printf(" %d %.8lf", j, xt[j]);
2269: printf("\n");
2270: free_vector(xt,1,n);
2271: return fret;
2272: }
2273: #endif
1.126 brouard 2274:
2275: /*************** log-likelihood *************/
2276: double func( double *x)
2277: {
2278: int i, ii, j, k, mi, d, kk;
1.131 brouard 2279: double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
1.126 brouard 2280: double **out;
2281: double sw; /* Sum of weights */
2282: double lli; /* Individual log likelihood */
2283: int s1, s2;
2284: double bbh, survp;
2285: long ipmx;
1.187 brouard 2286: double agexact;
1.126 brouard 2287: /*extern weight */
2288: /* We are differentiating ll according to initial status */
2289: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
2290: /*for(i=1;i<imx;i++)
2291: printf(" %d\n",s[4][i]);
2292: */
1.162 brouard 2293:
2294: ++countcallfunc;
2295:
1.126 brouard 2296: cov[1]=1.;
2297:
2298: for(k=1; k<=nlstate; k++) ll[k]=0.;
2299:
2300: if(mle==1){
2301: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1.138 brouard 2302: /* Computes the values of the ncovmodel covariates of the model
2303: depending if the covariates are fixed or variying (age dependent) and stores them in cov[]
2304: Then computes with function pmij which return a matrix p[i][j] giving the elementary probability
2305: to be observed in j being in i according to the model.
2306: */
1.145 brouard 2307: for (k=1; k<=cptcovn;k++){ /* Simple and product covariates without age* products */
1.187 brouard 2308: cov[2+nagesqr+k]=covar[Tvar[k]][i];
1.145 brouard 2309: }
1.137 brouard 2310: /* In model V2+V1*V4+age*V3+V3*V2 Tvar[1] is V2, Tvar[2=V1*V4]
1.138 brouard 2311: is 6, Tvar[3=age*V3] should not be computed because of age Tvar[4=V3*V2]
1.137 brouard 2312: has been calculated etc */
1.126 brouard 2313: for(mi=1; mi<= wav[i]-1; mi++){
2314: for (ii=1;ii<=nlstate+ndeath;ii++)
2315: for (j=1;j<=nlstate+ndeath;j++){
2316: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2317: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2318: }
2319: for(d=0; d<dh[mi][i]; d++){
2320: newm=savm;
1.187 brouard 2321: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
2322: cov[2]=agexact;
2323: if(nagesqr==1)
2324: cov[3]= agexact*agexact;
1.126 brouard 2325: for (kk=1; kk<=cptcovage;kk++) {
1.187 brouard 2326: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact; /* Tage[kk] gives the data-covariate associated with age */
1.126 brouard 2327: }
2328: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2329: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
2330: savm=oldm;
2331: oldm=newm;
2332: } /* end mult */
2333:
2334: /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
2335: /* But now since version 0.9 we anticipate for bias at large stepm.
2336: * If stepm is larger than one month (smallest stepm) and if the exact delay
2337: * (in months) between two waves is not a multiple of stepm, we rounded to
2338: * the nearest (and in case of equal distance, to the lowest) interval but now
2339: * we keep into memory the bias bh[mi][i] and also the previous matrix product
2340: * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
2341: * probability in order to take into account the bias as a fraction of the way
2342: * from savm to out if bh is negative or even beyond if bh is positive. bh varies
2343: * -stepm/2 to stepm/2 .
2344: * For stepm=1 the results are the same as for previous versions of Imach.
2345: * For stepm > 1 the results are less biased than in previous versions.
2346: */
2347: s1=s[mw[mi][i]][i];
2348: s2=s[mw[mi+1][i]][i];
2349: bbh=(double)bh[mi][i]/(double)stepm;
2350: /* bias bh is positive if real duration
2351: * is higher than the multiple of stepm and negative otherwise.
2352: */
2353: /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
2354: if( s2 > nlstate){
2355: /* i.e. if s2 is a death state and if the date of death is known
2356: then the contribution to the likelihood is the probability to
2357: die between last step unit time and current step unit time,
2358: which is also equal to probability to die before dh
2359: minus probability to die before dh-stepm .
2360: In version up to 0.92 likelihood was computed
2361: as if date of death was unknown. Death was treated as any other
2362: health state: the date of the interview describes the actual state
2363: and not the date of a change in health state. The former idea was
2364: to consider that at each interview the state was recorded
2365: (healthy, disable or death) and IMaCh was corrected; but when we
2366: introduced the exact date of death then we should have modified
2367: the contribution of an exact death to the likelihood. This new
2368: contribution is smaller and very dependent of the step unit
2369: stepm. It is no more the probability to die between last interview
2370: and month of death but the probability to survive from last
2371: interview up to one month before death multiplied by the
2372: probability to die within a month. Thanks to Chris
2373: Jackson for correcting this bug. Former versions increased
2374: mortality artificially. The bad side is that we add another loop
2375: which slows down the processing. The difference can be up to 10%
2376: lower mortality.
2377: */
1.183 brouard 2378: /* If, at the beginning of the maximization mostly, the
2379: cumulative probability or probability to be dead is
2380: constant (ie = 1) over time d, the difference is equal to
2381: 0. out[s1][3] = savm[s1][3]: probability, being at state
2382: s1 at precedent wave, to be dead a month before current
2383: wave is equal to probability, being at state s1 at
2384: precedent wave, to be dead at mont of the current
2385: wave. Then the observed probability (that this person died)
2386: is null according to current estimated parameter. In fact,
2387: it should be very low but not zero otherwise the log go to
2388: infinity.
2389: */
2390: /* #ifdef INFINITYORIGINAL */
2391: /* lli=log(out[s1][s2] - savm[s1][s2]); */
2392: /* #else */
2393: /* if ((out[s1][s2] - savm[s1][s2]) < mytinydouble) */
2394: /* lli=log(mytinydouble); */
2395: /* else */
2396: /* lli=log(out[s1][s2] - savm[s1][s2]); */
2397: /* #endif */
2398: lli=log(out[s1][s2] - savm[s1][s2]);
1.126 brouard 2399:
2400: } else if (s2==-2) {
2401: for (j=1,survp=0. ; j<=nlstate; j++)
2402: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
2403: /*survp += out[s1][j]; */
2404: lli= log(survp);
2405: }
2406:
2407: else if (s2==-4) {
2408: for (j=3,survp=0. ; j<=nlstate; j++)
2409: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
2410: lli= log(survp);
2411: }
2412:
2413: else if (s2==-5) {
2414: for (j=1,survp=0. ; j<=2; j++)
2415: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
2416: lli= log(survp);
2417: }
2418:
2419: else{
2420: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
2421: /* 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 */
2422: }
2423: /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
2424: /*if(lli ==000.0)*/
2425: /*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); */
2426: ipmx +=1;
2427: sw += weight[i];
2428: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1.183 brouard 2429: /* if (lli < log(mytinydouble)){ */
2430: /* 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); */
2431: /* 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]); */
2432: /* } */
1.126 brouard 2433: } /* end of wave */
2434: } /* end of individual */
2435: } else if(mle==2){
2436: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1.187 brouard 2437: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
1.126 brouard 2438: for(mi=1; mi<= wav[i]-1; mi++){
2439: for (ii=1;ii<=nlstate+ndeath;ii++)
2440: for (j=1;j<=nlstate+ndeath;j++){
2441: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2442: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2443: }
2444: for(d=0; d<=dh[mi][i]; d++){
2445: newm=savm;
1.187 brouard 2446: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
2447: cov[2]=agexact;
2448: if(nagesqr==1)
2449: cov[3]= agexact*agexact;
1.126 brouard 2450: for (kk=1; kk<=cptcovage;kk++) {
1.187 brouard 2451: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
1.126 brouard 2452: }
2453: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2454: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
2455: savm=oldm;
2456: oldm=newm;
2457: } /* end mult */
2458:
2459: s1=s[mw[mi][i]][i];
2460: s2=s[mw[mi+1][i]][i];
2461: bbh=(double)bh[mi][i]/(double)stepm;
2462: 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 */
2463: ipmx +=1;
2464: sw += weight[i];
2465: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
2466: } /* end of wave */
2467: } /* end of individual */
2468: } else if(mle==3){ /* exponential inter-extrapolation */
2469: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1.187 brouard 2470: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
1.126 brouard 2471: for(mi=1; mi<= wav[i]-1; mi++){
2472: for (ii=1;ii<=nlstate+ndeath;ii++)
2473: for (j=1;j<=nlstate+ndeath;j++){
2474: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2475: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2476: }
2477: for(d=0; d<dh[mi][i]; d++){
2478: newm=savm;
1.187 brouard 2479: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
2480: cov[2]=agexact;
2481: if(nagesqr==1)
2482: cov[3]= agexact*agexact;
1.126 brouard 2483: for (kk=1; kk<=cptcovage;kk++) {
1.187 brouard 2484: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
1.126 brouard 2485: }
2486: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2487: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
2488: savm=oldm;
2489: oldm=newm;
2490: } /* end mult */
2491:
2492: s1=s[mw[mi][i]][i];
2493: s2=s[mw[mi+1][i]][i];
2494: bbh=(double)bh[mi][i]/(double)stepm;
2495: 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 */
2496: ipmx +=1;
2497: sw += weight[i];
2498: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
2499: } /* end of wave */
2500: } /* end of individual */
2501: }else if (mle==4){ /* ml=4 no inter-extrapolation */
2502: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1.187 brouard 2503: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
1.126 brouard 2504: for(mi=1; mi<= wav[i]-1; mi++){
2505: for (ii=1;ii<=nlstate+ndeath;ii++)
2506: for (j=1;j<=nlstate+ndeath;j++){
2507: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2508: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2509: }
2510: for(d=0; d<dh[mi][i]; d++){
2511: newm=savm;
1.187 brouard 2512: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
2513: cov[2]=agexact;
2514: if(nagesqr==1)
2515: cov[3]= agexact*agexact;
1.126 brouard 2516: for (kk=1; kk<=cptcovage;kk++) {
1.187 brouard 2517: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
1.126 brouard 2518: }
2519:
2520: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2521: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
2522: savm=oldm;
2523: oldm=newm;
2524: } /* end mult */
2525:
2526: s1=s[mw[mi][i]][i];
2527: s2=s[mw[mi+1][i]][i];
2528: if( s2 > nlstate){
2529: lli=log(out[s1][s2] - savm[s1][s2]);
2530: }else{
2531: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
2532: }
2533: ipmx +=1;
2534: sw += weight[i];
2535: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
2536: /* 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]); */
2537: } /* end of wave */
2538: } /* end of individual */
2539: }else{ /* ml=5 no inter-extrapolation no jackson =0.8a */
2540: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1.187 brouard 2541: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
1.126 brouard 2542: for(mi=1; mi<= wav[i]-1; mi++){
2543: for (ii=1;ii<=nlstate+ndeath;ii++)
2544: for (j=1;j<=nlstate+ndeath;j++){
2545: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2546: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2547: }
2548: for(d=0; d<dh[mi][i]; d++){
2549: newm=savm;
1.187 brouard 2550: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
2551: cov[2]=agexact;
2552: if(nagesqr==1)
2553: cov[3]= agexact*agexact;
1.126 brouard 2554: for (kk=1; kk<=cptcovage;kk++) {
1.187 brouard 2555: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
1.126 brouard 2556: }
2557:
2558: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2559: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
2560: savm=oldm;
2561: oldm=newm;
2562: } /* end mult */
2563:
2564: s1=s[mw[mi][i]][i];
2565: s2=s[mw[mi+1][i]][i];
2566: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
2567: ipmx +=1;
2568: sw += weight[i];
2569: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
2570: /*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]);*/
2571: } /* end of wave */
2572: } /* end of individual */
2573: } /* End of if */
2574: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
2575: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
2576: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
2577: return -l;
2578: }
2579:
2580: /*************** log-likelihood *************/
2581: double funcone( double *x)
2582: {
2583: /* Same as likeli but slower because of a lot of printf and if */
2584: int i, ii, j, k, mi, d, kk;
1.131 brouard 2585: double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
1.126 brouard 2586: double **out;
2587: double lli; /* Individual log likelihood */
2588: double llt;
2589: int s1, s2;
2590: double bbh, survp;
1.187 brouard 2591: double agexact;
1.126 brouard 2592: /*extern weight */
2593: /* We are differentiating ll according to initial status */
2594: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
2595: /*for(i=1;i<imx;i++)
2596: printf(" %d\n",s[4][i]);
2597: */
2598: cov[1]=1.;
2599:
2600: for(k=1; k<=nlstate; k++) ll[k]=0.;
2601:
2602: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1.187 brouard 2603: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
1.126 brouard 2604: for(mi=1; mi<= wav[i]-1; mi++){
2605: for (ii=1;ii<=nlstate+ndeath;ii++)
2606: for (j=1;j<=nlstate+ndeath;j++){
2607: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2608: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2609: }
2610: for(d=0; d<dh[mi][i]; d++){
2611: newm=savm;
1.187 brouard 2612: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
2613: cov[2]=agexact;
2614: if(nagesqr==1)
2615: cov[3]= agexact*agexact;
1.126 brouard 2616: for (kk=1; kk<=cptcovage;kk++) {
1.187 brouard 2617: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
1.126 brouard 2618: }
1.187 brouard 2619:
1.145 brouard 2620: /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
1.126 brouard 2621: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2622: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1.145 brouard 2623: /* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, */
2624: /* 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); */
1.126 brouard 2625: savm=oldm;
2626: oldm=newm;
2627: } /* end mult */
2628:
2629: s1=s[mw[mi][i]][i];
2630: s2=s[mw[mi+1][i]][i];
2631: bbh=(double)bh[mi][i]/(double)stepm;
2632: /* bias is positive if real duration
2633: * is higher than the multiple of stepm and negative otherwise.
2634: */
2635: if( s2 > nlstate && (mle <5) ){ /* Jackson */
2636: lli=log(out[s1][s2] - savm[s1][s2]);
2637: } else if (s2==-2) {
2638: for (j=1,survp=0. ; j<=nlstate; j++)
2639: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
2640: lli= log(survp);
2641: }else if (mle==1){
2642: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
2643: } else if(mle==2){
2644: 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 */
2645: } else if(mle==3){ /* exponential inter-extrapolation */
2646: 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 */
2647: } else if (mle==4){ /* mle=4 no inter-extrapolation */
2648: lli=log(out[s1][s2]); /* Original formula */
1.136 brouard 2649: } else{ /* mle=0 back to 1 */
2650: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
2651: /*lli=log(out[s1][s2]); */ /* Original formula */
1.126 brouard 2652: } /* End of if */
2653: ipmx +=1;
2654: sw += weight[i];
2655: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1.132 brouard 2656: /*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 2657: if(globpr){
1.205 brouard 2658: fprintf(ficresilk,"%9ld %6.1f %6d %2d %2d %2d %2d %3d %11.6f %8.4f %8.3f\
1.126 brouard 2659: %11.6f %11.6f %11.6f ", \
1.205 brouard 2660: num[i], agexact, i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],weight[i]*gipmx/gsw,
1.126 brouard 2661: 2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
2662: for(k=1,llt=0.,l=0.; k<=nlstate; k++){
2663: llt +=ll[k]*gipmx/gsw;
2664: fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
2665: }
2666: fprintf(ficresilk," %10.6f\n", -llt);
2667: }
2668: } /* end of wave */
2669: } /* end of individual */
2670: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
2671: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
2672: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
2673: if(globpr==0){ /* First time we count the contributions and weights */
2674: gipmx=ipmx;
2675: gsw=sw;
2676: }
2677: return -l;
2678: }
2679:
2680:
2681: /*************** function likelione ***********/
2682: void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
2683: {
2684: /* This routine should help understanding what is done with
2685: the selection of individuals/waves and
2686: to check the exact contribution to the likelihood.
2687: Plotting could be done.
2688: */
2689: int k;
2690:
2691: if(*globpri !=0){ /* Just counts and sums, no printings */
1.201 brouard 2692: strcpy(fileresilk,"ILK_");
1.202 brouard 2693: strcat(fileresilk,fileresu);
1.126 brouard 2694: if((ficresilk=fopen(fileresilk,"w"))==NULL) {
2695: printf("Problem with resultfile: %s\n", fileresilk);
2696: fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
2697: }
1.205 brouard 2698: 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 2699: fprintf(ficresilk, "#num_i age i s1 s2 mi mw dh likeli weight %%weight 2wlli out sav ");
1.126 brouard 2700: /* i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
2701: for(k=1; k<=nlstate; k++)
2702: fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
2703: fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
2704: }
2705:
2706: *fretone=(*funcone)(p);
2707: if(*globpri !=0){
2708: fclose(ficresilk);
1.205 brouard 2709: if (mle ==0)
2710: fprintf(fichtm,"\n<br>File of contributions to the likelihood computed with initial parameters and mle = %d.",mle);
2711: else if(mle >=1)
2712: fprintf(fichtm,"\n<br>File of contributions to the likelihood computed with optimized parameters mle = %d.",mle);
2713: 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 2714:
1.208 ! brouard 2715:
! 2716: for (k=1; k<= nlstate ; k++) {
! 2717: fprintf(fichtm,"<br>- Probability p%dj by origin %d and destination j <a href=\"%s-p%dj.png\">%s-p%dj.png</a><br> \
! 2718: <img src=\"%s-p%dj.png\">",k,k,subdirf2(optionfilefiname,"ILK_"),k,subdirf2(optionfilefiname,"ILK_"),k,subdirf2(optionfilefiname,"ILK_"),k);
! 2719: }
1.207 brouard 2720: 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 2721: <img src=\"%s-ori.png\">",subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"));
1.207 brouard 2722: fprintf(fichtm,"<br>- and by state of destination <a href=\"%s-dest.png\">%s-dest.png</a><br> \
1.204 brouard 2723: <img src=\"%s-dest.png\">",subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"));
1.207 brouard 2724: fflush(fichtm);
1.205 brouard 2725: }
1.126 brouard 2726: return;
2727: }
2728:
2729:
2730: /*********** Maximum Likelihood Estimation ***************/
2731:
2732: void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
2733: {
1.165 brouard 2734: int i,j, iter=0;
1.126 brouard 2735: double **xi;
2736: double fret;
2737: double fretone; /* Only one call to likelihood */
2738: /* char filerespow[FILENAMELENGTH];*/
1.162 brouard 2739:
2740: #ifdef NLOPT
2741: int creturn;
2742: nlopt_opt opt;
2743: /* double lb[9] = { -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL }; /\* lower bounds *\/ */
2744: double *lb;
2745: double minf; /* the minimum objective value, upon return */
2746: double * p1; /* Shifted parameters from 0 instead of 1 */
2747: myfunc_data dinst, *d = &dinst;
2748: #endif
2749:
2750:
1.126 brouard 2751: xi=matrix(1,npar,1,npar);
2752: for (i=1;i<=npar;i++)
2753: for (j=1;j<=npar;j++)
2754: xi[i][j]=(i==j ? 1.0 : 0.0);
2755: printf("Powell\n"); fprintf(ficlog,"Powell\n");
1.201 brouard 2756: strcpy(filerespow,"POW_");
1.126 brouard 2757: strcat(filerespow,fileres);
2758: if((ficrespow=fopen(filerespow,"w"))==NULL) {
2759: printf("Problem with resultfile: %s\n", filerespow);
2760: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
2761: }
2762: fprintf(ficrespow,"# Powell\n# iter -2*LL");
2763: for (i=1;i<=nlstate;i++)
2764: for(j=1;j<=nlstate+ndeath;j++)
2765: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
2766: fprintf(ficrespow,"\n");
1.162 brouard 2767: #ifdef POWELL
1.126 brouard 2768: powell(p,xi,npar,ftol,&iter,&fret,func);
1.162 brouard 2769: #endif
1.126 brouard 2770:
1.162 brouard 2771: #ifdef NLOPT
2772: #ifdef NEWUOA
2773: opt = nlopt_create(NLOPT_LN_NEWUOA,npar);
2774: #else
2775: opt = nlopt_create(NLOPT_LN_BOBYQA,npar);
2776: #endif
2777: lb=vector(0,npar-1);
2778: for (i=0;i<npar;i++) lb[i]= -HUGE_VAL;
2779: nlopt_set_lower_bounds(opt, lb);
2780: nlopt_set_initial_step1(opt, 0.1);
2781:
2782: p1= (p+1); /* p *(p+1)@8 and p *(p1)@8 are equal p1[0]=p[1] */
2783: d->function = func;
2784: printf(" Func %.12lf \n",myfunc(npar,p1,NULL,d));
2785: nlopt_set_min_objective(opt, myfunc, d);
2786: nlopt_set_xtol_rel(opt, ftol);
2787: if ((creturn=nlopt_optimize(opt, p1, &minf)) < 0) {
2788: printf("nlopt failed! %d\n",creturn);
2789: }
2790: else {
2791: printf("found minimum after %d evaluations (NLOPT=%d)\n", countcallfunc ,NLOPT);
2792: printf("found minimum at f(%g,%g) = %0.10g\n", p[0], p[1], minf);
2793: iter=1; /* not equal */
2794: }
2795: nlopt_destroy(opt);
2796: #endif
1.126 brouard 2797: free_matrix(xi,1,npar,1,npar);
2798: fclose(ficrespow);
1.203 brouard 2799: printf("\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
2800: fprintf(ficlog,"\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
1.180 brouard 2801: fprintf(ficres,"#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
1.126 brouard 2802:
2803: }
2804:
2805: /**** Computes Hessian and covariance matrix ***/
1.203 brouard 2806: void hesscov(double **matcov, double **hess, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
1.126 brouard 2807: {
2808: double **a,**y,*x,pd;
1.203 brouard 2809: /* double **hess; */
1.164 brouard 2810: int i, j;
1.126 brouard 2811: int *indx;
2812:
2813: double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
1.203 brouard 2814: double hessij(double p[], double **hess, double delti[], int i, int j,double (*func)(double []),int npar);
1.126 brouard 2815: void lubksb(double **a, int npar, int *indx, double b[]) ;
2816: void ludcmp(double **a, int npar, int *indx, double *d) ;
2817: double gompertz(double p[]);
1.203 brouard 2818: /* hess=matrix(1,npar,1,npar); */
1.126 brouard 2819:
2820: printf("\nCalculation of the hessian matrix. Wait...\n");
2821: fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
2822: for (i=1;i<=npar;i++){
1.203 brouard 2823: printf("%d-",i);fflush(stdout);
2824: fprintf(ficlog,"%d-",i);fflush(ficlog);
1.126 brouard 2825:
2826: hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
2827:
2828: /* printf(" %f ",p[i]);
2829: printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
2830: }
2831:
2832: for (i=1;i<=npar;i++) {
2833: for (j=1;j<=npar;j++) {
2834: if (j>i) {
1.203 brouard 2835: printf(".%d-%d",i,j);fflush(stdout);
2836: fprintf(ficlog,".%d-%d",i,j);fflush(ficlog);
2837: hess[i][j]=hessij(p,hess, delti,i,j,func,npar);
1.126 brouard 2838:
2839: hess[j][i]=hess[i][j];
2840: /*printf(" %lf ",hess[i][j]);*/
2841: }
2842: }
2843: }
2844: printf("\n");
2845: fprintf(ficlog,"\n");
2846:
2847: printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
2848: fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
2849:
2850: a=matrix(1,npar,1,npar);
2851: y=matrix(1,npar,1,npar);
2852: x=vector(1,npar);
2853: indx=ivector(1,npar);
2854: for (i=1;i<=npar;i++)
2855: for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
2856: ludcmp(a,npar,indx,&pd);
2857:
2858: for (j=1;j<=npar;j++) {
2859: for (i=1;i<=npar;i++) x[i]=0;
2860: x[j]=1;
2861: lubksb(a,npar,indx,x);
2862: for (i=1;i<=npar;i++){
2863: matcov[i][j]=x[i];
2864: }
2865: }
2866:
2867: printf("\n#Hessian matrix#\n");
2868: fprintf(ficlog,"\n#Hessian matrix#\n");
2869: for (i=1;i<=npar;i++) {
2870: for (j=1;j<=npar;j++) {
1.203 brouard 2871: printf("%.6e ",hess[i][j]);
2872: fprintf(ficlog,"%.6e ",hess[i][j]);
1.126 brouard 2873: }
2874: printf("\n");
2875: fprintf(ficlog,"\n");
2876: }
2877:
1.203 brouard 2878: /* printf("\n#Covariance matrix#\n"); */
2879: /* fprintf(ficlog,"\n#Covariance matrix#\n"); */
2880: /* for (i=1;i<=npar;i++) { */
2881: /* for (j=1;j<=npar;j++) { */
2882: /* printf("%.6e ",matcov[i][j]); */
2883: /* fprintf(ficlog,"%.6e ",matcov[i][j]); */
2884: /* } */
2885: /* printf("\n"); */
2886: /* fprintf(ficlog,"\n"); */
2887: /* } */
2888:
1.126 brouard 2889: /* Recompute Inverse */
1.203 brouard 2890: /* for (i=1;i<=npar;i++) */
2891: /* for (j=1;j<=npar;j++) a[i][j]=matcov[i][j]; */
2892: /* ludcmp(a,npar,indx,&pd); */
2893:
2894: /* printf("\n#Hessian matrix recomputed#\n"); */
2895:
2896: /* for (j=1;j<=npar;j++) { */
2897: /* for (i=1;i<=npar;i++) x[i]=0; */
2898: /* x[j]=1; */
2899: /* lubksb(a,npar,indx,x); */
2900: /* for (i=1;i<=npar;i++){ */
2901: /* y[i][j]=x[i]; */
2902: /* printf("%.3e ",y[i][j]); */
2903: /* fprintf(ficlog,"%.3e ",y[i][j]); */
2904: /* } */
2905: /* printf("\n"); */
2906: /* fprintf(ficlog,"\n"); */
2907: /* } */
2908:
2909: /* Verifying the inverse matrix */
2910: #ifdef DEBUGHESS
2911: y=matprod2(y,hess,1,npar,1,npar,1,npar,matcov);
1.126 brouard 2912:
1.203 brouard 2913: printf("\n#Verification: multiplying the matrix of covariance by the Hessian matrix, should be unity:#\n");
2914: fprintf(ficlog,"\n#Verification: multiplying the matrix of covariance by the Hessian matrix. Should be unity:#\n");
1.126 brouard 2915:
2916: for (j=1;j<=npar;j++) {
2917: for (i=1;i<=npar;i++){
1.203 brouard 2918: printf("%.2f ",y[i][j]);
2919: fprintf(ficlog,"%.2f ",y[i][j]);
1.126 brouard 2920: }
2921: printf("\n");
2922: fprintf(ficlog,"\n");
2923: }
1.203 brouard 2924: #endif
1.126 brouard 2925:
2926: free_matrix(a,1,npar,1,npar);
2927: free_matrix(y,1,npar,1,npar);
2928: free_vector(x,1,npar);
2929: free_ivector(indx,1,npar);
1.203 brouard 2930: /* free_matrix(hess,1,npar,1,npar); */
1.126 brouard 2931:
2932:
2933: }
2934:
2935: /*************** hessian matrix ****************/
2936: double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
1.203 brouard 2937: { /* Around values of x, computes the function func and returns the scales delti and hessian */
1.126 brouard 2938: int i;
2939: int l=1, lmax=20;
1.203 brouard 2940: double k1,k2, res, fx;
1.132 brouard 2941: double p2[MAXPARM+1]; /* identical to x */
1.126 brouard 2942: double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
2943: int k=0,kmax=10;
2944: double l1;
2945:
2946: fx=func(x);
2947: for (i=1;i<=npar;i++) p2[i]=x[i];
1.145 brouard 2948: for(l=0 ; l <=lmax; l++){ /* Enlarging the zone around the Maximum */
1.126 brouard 2949: l1=pow(10,l);
2950: delts=delt;
2951: for(k=1 ; k <kmax; k=k+1){
2952: delt = delta*(l1*k);
2953: p2[theta]=x[theta] +delt;
1.145 brouard 2954: k1=func(p2)-fx; /* Might be negative if too close to the theoretical maximum */
1.126 brouard 2955: p2[theta]=x[theta]-delt;
2956: k2=func(p2)-fx;
2957: /*res= (k1-2.0*fx+k2)/delt/delt; */
1.203 brouard 2958: res= (k1+k2)/delt/delt/2.; /* Divided by 2 because L and not 2*L */
1.126 brouard 2959:
1.203 brouard 2960: #ifdef DEBUGHESSII
1.126 brouard 2961: 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);
2962: 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);
2963: #endif
2964: /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
2965: if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
2966: k=kmax;
2967: }
2968: else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
1.164 brouard 2969: k=kmax; l=lmax*10;
1.126 brouard 2970: }
2971: else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){
2972: delts=delt;
2973: }
1.203 brouard 2974: } /* End loop k */
1.126 brouard 2975: }
2976: delti[theta]=delts;
2977: return res;
2978:
2979: }
2980:
1.203 brouard 2981: double hessij( double x[], double **hess, double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
1.126 brouard 2982: {
2983: int i;
1.164 brouard 2984: int l=1, lmax=20;
1.126 brouard 2985: double k1,k2,k3,k4,res,fx;
1.132 brouard 2986: double p2[MAXPARM+1];
1.203 brouard 2987: int k, kmax=1;
2988: double v1, v2, cv12, lc1, lc2;
1.208 ! brouard 2989:
! 2990: int firstime=0;
1.203 brouard 2991:
1.126 brouard 2992: fx=func(x);
1.203 brouard 2993: for (k=1; k<=kmax; k=k+10) {
1.126 brouard 2994: for (i=1;i<=npar;i++) p2[i]=x[i];
1.203 brouard 2995: p2[thetai]=x[thetai]+delti[thetai]*k;
2996: p2[thetaj]=x[thetaj]+delti[thetaj]*k;
1.126 brouard 2997: k1=func(p2)-fx;
2998:
1.203 brouard 2999: p2[thetai]=x[thetai]+delti[thetai]*k;
3000: p2[thetaj]=x[thetaj]-delti[thetaj]*k;
1.126 brouard 3001: k2=func(p2)-fx;
3002:
1.203 brouard 3003: p2[thetai]=x[thetai]-delti[thetai]*k;
3004: p2[thetaj]=x[thetaj]+delti[thetaj]*k;
1.126 brouard 3005: k3=func(p2)-fx;
3006:
1.203 brouard 3007: p2[thetai]=x[thetai]-delti[thetai]*k;
3008: p2[thetaj]=x[thetaj]-delti[thetaj]*k;
1.126 brouard 3009: k4=func(p2)-fx;
1.203 brouard 3010: res=(k1-k2-k3+k4)/4.0/delti[thetai]/k/delti[thetaj]/k/2.; /* Because of L not 2*L */
3011: if(k1*k2*k3*k4 <0.){
1.208 ! brouard 3012: firstime=1;
1.203 brouard 3013: kmax=kmax+10;
1.208 ! brouard 3014: }
! 3015: if(kmax >=10 || firstime ==1){
1.203 brouard 3016: printf("Warning: directions %d-%d, you are not estimating the Hessian at the exact maximum likelihood; increase ftol=%.2e\n",thetai,thetaj, ftol);
3017: fprintf(ficlog,"Warning: directions %d-%d, you are not estimating the Hessian at the exact maximum likelihood; increase ftol=%.2e\n",thetai,thetaj, ftol);
3018: 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);
3019: 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);
3020: }
3021: #ifdef DEBUGHESSIJ
3022: v1=hess[thetai][thetai];
3023: v2=hess[thetaj][thetaj];
3024: cv12=res;
3025: /* Computing eigen value of Hessian matrix */
3026: lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
3027: lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
3028: if ((lc2 <0) || (lc1 <0) ){
3029: printf("Warning: sub Hessian matrix '%d%d' does not have positive eigen values \n",thetai,thetaj);
3030: fprintf(ficlog, "Warning: sub Hessian matrix '%d%d' does not have positive eigen values \n",thetai,thetaj);
3031: 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);
3032: 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);
3033: }
1.126 brouard 3034: #endif
3035: }
3036: return res;
3037: }
3038:
1.203 brouard 3039: /* Not done yet: Was supposed to fix if not exactly at the maximum */
3040: /* double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar) */
3041: /* { */
3042: /* int i; */
3043: /* int l=1, lmax=20; */
3044: /* double k1,k2,k3,k4,res,fx; */
3045: /* double p2[MAXPARM+1]; */
3046: /* double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4; */
3047: /* int k=0,kmax=10; */
3048: /* double l1; */
3049:
3050: /* fx=func(x); */
3051: /* for(l=0 ; l <=lmax; l++){ /\* Enlarging the zone around the Maximum *\/ */
3052: /* l1=pow(10,l); */
3053: /* delts=delt; */
3054: /* for(k=1 ; k <kmax; k=k+1){ */
3055: /* delt = delti*(l1*k); */
3056: /* for (i=1;i<=npar;i++) p2[i]=x[i]; */
3057: /* p2[thetai]=x[thetai]+delti[thetai]/k; */
3058: /* p2[thetaj]=x[thetaj]+delti[thetaj]/k; */
3059: /* k1=func(p2)-fx; */
3060:
3061: /* p2[thetai]=x[thetai]+delti[thetai]/k; */
3062: /* p2[thetaj]=x[thetaj]-delti[thetaj]/k; */
3063: /* k2=func(p2)-fx; */
3064:
3065: /* p2[thetai]=x[thetai]-delti[thetai]/k; */
3066: /* p2[thetaj]=x[thetaj]+delti[thetaj]/k; */
3067: /* k3=func(p2)-fx; */
3068:
3069: /* p2[thetai]=x[thetai]-delti[thetai]/k; */
3070: /* p2[thetaj]=x[thetaj]-delti[thetaj]/k; */
3071: /* k4=func(p2)-fx; */
3072: /* res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /\* Because of L not 2*L *\/ */
3073: /* #ifdef DEBUGHESSIJ */
3074: /* 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); */
3075: /* 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); */
3076: /* #endif */
3077: /* if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)|| (k4 <khi/nkhi/2.)|| (k4 <khi/nkhi/2.)){ */
3078: /* k=kmax; */
3079: /* } */
3080: /* else if((k1 >khi/nkhif) || (k2 >khi/nkhif) || (k4 >khi/nkhif) || (k4 >khi/nkhif)){ /\* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. *\/ */
3081: /* k=kmax; l=lmax*10; */
3082: /* } */
3083: /* else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ */
3084: /* delts=delt; */
3085: /* } */
3086: /* } /\* End loop k *\/ */
3087: /* } */
3088: /* delti[theta]=delts; */
3089: /* return res; */
3090: /* } */
3091:
3092:
1.126 brouard 3093: /************** Inverse of matrix **************/
3094: void ludcmp(double **a, int n, int *indx, double *d)
3095: {
3096: int i,imax,j,k;
3097: double big,dum,sum,temp;
3098: double *vv;
3099:
3100: vv=vector(1,n);
3101: *d=1.0;
3102: for (i=1;i<=n;i++) {
3103: big=0.0;
3104: for (j=1;j<=n;j++)
3105: if ((temp=fabs(a[i][j])) > big) big=temp;
3106: if (big == 0.0) nrerror("Singular matrix in routine ludcmp");
3107: vv[i]=1.0/big;
3108: }
3109: for (j=1;j<=n;j++) {
3110: for (i=1;i<j;i++) {
3111: sum=a[i][j];
3112: for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];
3113: a[i][j]=sum;
3114: }
3115: big=0.0;
3116: for (i=j;i<=n;i++) {
3117: sum=a[i][j];
3118: for (k=1;k<j;k++)
3119: sum -= a[i][k]*a[k][j];
3120: a[i][j]=sum;
3121: if ( (dum=vv[i]*fabs(sum)) >= big) {
3122: big=dum;
3123: imax=i;
3124: }
3125: }
3126: if (j != imax) {
3127: for (k=1;k<=n;k++) {
3128: dum=a[imax][k];
3129: a[imax][k]=a[j][k];
3130: a[j][k]=dum;
3131: }
3132: *d = -(*d);
3133: vv[imax]=vv[j];
3134: }
3135: indx[j]=imax;
3136: if (a[j][j] == 0.0) a[j][j]=TINY;
3137: if (j != n) {
3138: dum=1.0/(a[j][j]);
3139: for (i=j+1;i<=n;i++) a[i][j] *= dum;
3140: }
3141: }
3142: free_vector(vv,1,n); /* Doesn't work */
3143: ;
3144: }
3145:
3146: void lubksb(double **a, int n, int *indx, double b[])
3147: {
3148: int i,ii=0,ip,j;
3149: double sum;
3150:
3151: for (i=1;i<=n;i++) {
3152: ip=indx[i];
3153: sum=b[ip];
3154: b[ip]=b[i];
3155: if (ii)
3156: for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];
3157: else if (sum) ii=i;
3158: b[i]=sum;
3159: }
3160: for (i=n;i>=1;i--) {
3161: sum=b[i];
3162: for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];
3163: b[i]=sum/a[i][i];
3164: }
3165: }
3166:
3167: void pstamp(FILE *fichier)
3168: {
1.196 brouard 3169: fprintf(fichier,"# %s.%s\n#IMaCh version %s, %s\n#%s\n# %s", optionfilefiname,optionfilext,version,copyright, fullversion, strstart);
1.126 brouard 3170: }
3171:
3172: /************ Frequencies ********************/
3173: 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[])
3174: { /* Some frequencies */
3175:
1.164 brouard 3176: int i, m, jk, j1, bool, z1,j;
1.126 brouard 3177: int first;
3178: double ***freq; /* Frequencies */
3179: double *pp, **prop;
3180: double pos,posprop, k2, dateintsum=0,k2cpt=0;
3181: char fileresp[FILENAMELENGTH];
3182:
3183: pp=vector(1,nlstate);
3184: prop=matrix(1,nlstate,iagemin,iagemax+3);
1.201 brouard 3185: strcpy(fileresp,"P_");
3186: strcat(fileresp,fileresu);
1.126 brouard 3187: if((ficresp=fopen(fileresp,"w"))==NULL) {
3188: printf("Problem with prevalence resultfile: %s\n", fileresp);
3189: fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
3190: exit(0);
3191: }
3192: freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
3193: j1=0;
3194:
3195: j=cptcoveff;
3196: if (cptcovn<1) {j=1;ncodemax[1]=1;}
3197:
3198: first=1;
3199:
1.169 brouard 3200: /* for(k1=1; k1<=j ; k1++){ */ /* Loop on covariates */
3201: /* for(i1=1; i1<=ncodemax[k1];i1++){ */ /* Now it is 2 */
3202: /* j1++; */
1.145 brouard 3203: for (j1 = 1; j1 <= (int) pow(2,cptcoveff); j1++){
1.126 brouard 3204: /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
3205: scanf("%d", i);*/
3206: for (i=-5; i<=nlstate+ndeath; i++)
3207: for (jk=-5; jk<=nlstate+ndeath; jk++)
3208: for(m=iagemin; m <= iagemax+3; m++)
3209: freq[i][jk][m]=0;
1.143 brouard 3210:
3211: for (i=1; i<=nlstate; i++)
3212: for(m=iagemin; m <= iagemax+3; m++)
3213: prop[i][m]=0;
1.126 brouard 3214:
3215: dateintsum=0;
3216: k2cpt=0;
3217: for (i=1; i<=imx; i++) {
3218: bool=1;
1.144 brouard 3219: if (cptcovn>0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
3220: for (z1=1; z1<=cptcoveff; z1++)
1.198 brouard 3221: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]){
1.145 brouard 3222: /* Tests if the value of each of the covariates of i is equal to filter j1 */
1.144 brouard 3223: bool=0;
1.198 brouard 3224: /* 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",
3225: bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtabm(j1,z1),
3226: j1,z1,nbcode[Tvaraff[z1]][codtabm(j1,z1)],j1);*/
3227: /* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtabm(7,3)=1 and nbcde[3][?]=1*/
1.144 brouard 3228: }
1.126 brouard 3229: }
1.144 brouard 3230:
1.126 brouard 3231: if (bool==1){
3232: for(m=firstpass; m<=lastpass; m++){
3233: k2=anint[m][i]+(mint[m][i]/12.);
3234: /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
3235: if(agev[m][i]==0) agev[m][i]=iagemax+1;
3236: if(agev[m][i]==1) agev[m][i]=iagemax+2;
3237: if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
3238: if (m<lastpass) {
3239: freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
3240: freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
3241: }
3242:
3243: if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
3244: dateintsum=dateintsum+k2;
3245: k2cpt++;
3246: }
3247: /*}*/
3248: }
3249: }
1.145 brouard 3250: } /* end i */
1.126 brouard 3251:
3252: /* fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
3253: pstamp(ficresp);
3254: if (cptcovn>0) {
3255: fprintf(ficresp, "\n#********** Variable ");
1.198 brouard 3256: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.126 brouard 3257: fprintf(ficresp, "**********\n#");
1.143 brouard 3258: fprintf(ficlog, "\n#********** Variable ");
1.198 brouard 3259: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficlog, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.143 brouard 3260: fprintf(ficlog, "**********\n#");
1.126 brouard 3261: }
3262: for(i=1; i<=nlstate;i++)
3263: fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
3264: fprintf(ficresp, "\n");
3265:
3266: for(i=iagemin; i <= iagemax+3; i++){
3267: if(i==iagemax+3){
3268: fprintf(ficlog,"Total");
3269: }else{
3270: if(first==1){
3271: first=0;
3272: printf("See log file for details...\n");
3273: }
3274: fprintf(ficlog,"Age %d", i);
3275: }
3276: for(jk=1; jk <=nlstate ; jk++){
3277: for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
3278: pp[jk] += freq[jk][m][i];
3279: }
3280: for(jk=1; jk <=nlstate ; jk++){
3281: for(m=-1, pos=0; m <=0 ; m++)
3282: pos += freq[jk][m][i];
3283: if(pp[jk]>=1.e-10){
3284: if(first==1){
1.132 brouard 3285: printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
1.126 brouard 3286: }
3287: fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
3288: }else{
3289: if(first==1)
3290: printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
3291: fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
3292: }
3293: }
3294:
3295: for(jk=1; jk <=nlstate ; jk++){
3296: for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
3297: pp[jk] += freq[jk][m][i];
3298: }
3299: for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
3300: pos += pp[jk];
3301: posprop += prop[jk][i];
3302: }
3303: for(jk=1; jk <=nlstate ; jk++){
3304: if(pos>=1.e-5){
3305: if(first==1)
3306: printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
3307: fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
3308: }else{
3309: if(first==1)
3310: printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
3311: fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
3312: }
3313: if( i <= iagemax){
3314: if(pos>=1.e-5){
3315: fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
3316: /*probs[i][jk][j1]= pp[jk]/pos;*/
3317: /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
3318: }
3319: else
3320: fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
3321: }
3322: }
3323:
3324: for(jk=-1; jk <=nlstate+ndeath; jk++)
3325: for(m=-1; m <=nlstate+ndeath; m++)
3326: if(freq[jk][m][i] !=0 ) {
3327: if(first==1)
3328: printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
3329: fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
3330: }
3331: if(i <= iagemax)
3332: fprintf(ficresp,"\n");
3333: if(first==1)
3334: printf("Others in log...\n");
3335: fprintf(ficlog,"\n");
3336: }
1.145 brouard 3337: /*}*/
1.126 brouard 3338: }
3339: dateintmean=dateintsum/k2cpt;
3340:
3341: fclose(ficresp);
3342: free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
3343: free_vector(pp,1,nlstate);
3344: free_matrix(prop,1,nlstate,iagemin, iagemax+3);
3345: /* End of Freq */
3346: }
3347:
3348: /************ Prevalence ********************/
3349: 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)
3350: {
3351: /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
3352: in each health status at the date of interview (if between dateprev1 and dateprev2).
3353: We still use firstpass and lastpass as another selection.
3354: */
3355:
1.164 brouard 3356: int i, m, jk, j1, bool, z1,j;
3357:
3358: double **prop;
3359: double posprop;
1.126 brouard 3360: double y2; /* in fractional years */
3361: int iagemin, iagemax;
1.145 brouard 3362: int first; /** to stop verbosity which is redirected to log file */
1.126 brouard 3363:
3364: iagemin= (int) agemin;
3365: iagemax= (int) agemax;
3366: /*pp=vector(1,nlstate);*/
3367: prop=matrix(1,nlstate,iagemin,iagemax+3);
3368: /* freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
3369: j1=0;
3370:
1.145 brouard 3371: /*j=cptcoveff;*/
1.126 brouard 3372: if (cptcovn<1) {j=1;ncodemax[1]=1;}
3373:
1.145 brouard 3374: first=1;
3375: for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){
3376: /*for(i1=1; i1<=ncodemax[k1];i1++){
3377: j1++;*/
1.126 brouard 3378:
3379: for (i=1; i<=nlstate; i++)
3380: for(m=iagemin; m <= iagemax+3; m++)
3381: prop[i][m]=0.0;
3382:
3383: for (i=1; i<=imx; i++) { /* Each individual */
3384: bool=1;
3385: if (cptcovn>0) {
3386: for (z1=1; z1<=cptcoveff; z1++)
1.198 brouard 3387: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)])
1.126 brouard 3388: bool=0;
3389: }
3390: if (bool==1) {
3391: for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
3392: y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
3393: if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
3394: if(agev[m][i]==0) agev[m][i]=iagemax+1;
3395: if(agev[m][i]==1) agev[m][i]=iagemax+2;
3396: 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);
3397: if (s[m][i]>0 && s[m][i]<=nlstate) {
3398: /*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]]);*/
3399: prop[s[m][i]][(int)agev[m][i]] += weight[i];
3400: prop[s[m][i]][iagemax+3] += weight[i];
3401: }
3402: }
3403: } /* end selection of waves */
3404: }
3405: }
3406: for(i=iagemin; i <= iagemax+3; i++){
3407: for(jk=1,posprop=0; jk <=nlstate ; jk++) {
3408: posprop += prop[jk][i];
3409: }
1.145 brouard 3410:
1.126 brouard 3411: for(jk=1; jk <=nlstate ; jk++){
3412: if( i <= iagemax){
3413: if(posprop>=1.e-5){
3414: probs[i][jk][j1]= prop[jk][i]/posprop;
1.145 brouard 3415: } else{
3416: if(first==1){
3417: first=0;
3418: 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]);
3419: }
3420: }
1.126 brouard 3421: }
3422: }/* end jk */
3423: }/* end i */
1.145 brouard 3424: /*} *//* end i1 */
3425: } /* end j1 */
1.126 brouard 3426:
3427: /* free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
3428: /*free_vector(pp,1,nlstate);*/
3429: free_matrix(prop,1,nlstate, iagemin,iagemax+3);
3430: } /* End of prevalence */
3431:
3432: /************* Waves Concatenation ***************/
3433:
3434: 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)
3435: {
3436: /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
3437: Death is a valid wave (if date is known).
3438: mw[mi][i] is the mi (mi=1 to wav[i]) effective wave of individual i
3439: dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
3440: and mw[mi+1][i]. dh depends on stepm.
3441: */
3442:
3443: int i, mi, m;
3444: /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
3445: double sum=0., jmean=0.;*/
3446: int first;
3447: int j, k=0,jk, ju, jl;
3448: double sum=0.;
3449: first=0;
1.164 brouard 3450: jmin=100000;
1.126 brouard 3451: jmax=-1;
3452: jmean=0.;
3453: for(i=1; i<=imx; i++){
3454: mi=0;
3455: m=firstpass;
3456: while(s[m][i] <= nlstate){
3457: if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
3458: mw[++mi][i]=m;
3459: if(m >=lastpass)
3460: break;
3461: else
3462: m++;
3463: }/* end while */
3464: if (s[m][i] > nlstate){
3465: mi++; /* Death is another wave */
3466: /* if(mi==0) never been interviewed correctly before death */
3467: /* Only death is a correct wave */
3468: mw[mi][i]=m;
3469: }
3470:
3471: wav[i]=mi;
3472: if(mi==0){
3473: nbwarn++;
3474: if(first==0){
3475: printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
3476: first=1;
3477: }
3478: if(first==1){
3479: fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
3480: }
3481: } /* end mi==0 */
3482: } /* End individuals */
3483:
3484: for(i=1; i<=imx; i++){
3485: for(mi=1; mi<wav[i];mi++){
3486: if (stepm <=0)
3487: dh[mi][i]=1;
3488: else{
3489: if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
3490: if (agedc[i] < 2*AGESUP) {
3491: j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);
3492: if(j==0) j=1; /* Survives at least one month after exam */
3493: else if(j<0){
3494: nberr++;
3495: 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]);
3496: j=1; /* Temporary Dangerous patch */
3497: 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);
3498: 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]);
3499: 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);
3500: }
3501: k=k+1;
3502: if (j >= jmax){
3503: jmax=j;
3504: ijmax=i;
3505: }
3506: if (j <= jmin){
3507: jmin=j;
3508: ijmin=i;
3509: }
3510: sum=sum+j;
3511: /*if (j<0) printf("j=%d num=%d \n",j,i);*/
3512: /* printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
3513: }
3514: }
3515: else{
3516: j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
3517: /* 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]); */
3518:
3519: k=k+1;
3520: if (j >= jmax) {
3521: jmax=j;
3522: ijmax=i;
3523: }
3524: else if (j <= jmin){
3525: jmin=j;
3526: ijmin=i;
3527: }
3528: /* if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
3529: /*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]);*/
3530: if(j<0){
3531: nberr++;
3532: 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]);
3533: 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]);
3534: }
3535: sum=sum+j;
3536: }
3537: jk= j/stepm;
3538: jl= j -jk*stepm;
3539: ju= j -(jk+1)*stepm;
3540: if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
3541: if(jl==0){
3542: dh[mi][i]=jk;
3543: bh[mi][i]=0;
3544: }else{ /* We want a negative bias in order to only have interpolation ie
1.136 brouard 3545: * to avoid the price of an extra matrix product in likelihood */
1.126 brouard 3546: dh[mi][i]=jk+1;
3547: bh[mi][i]=ju;
3548: }
3549: }else{
3550: if(jl <= -ju){
3551: dh[mi][i]=jk;
3552: bh[mi][i]=jl; /* bias is positive if real duration
3553: * is higher than the multiple of stepm and negative otherwise.
3554: */
3555: }
3556: else{
3557: dh[mi][i]=jk+1;
3558: bh[mi][i]=ju;
3559: }
3560: if(dh[mi][i]==0){
3561: dh[mi][i]=1; /* At least one step */
3562: bh[mi][i]=ju; /* At least one step */
3563: /* 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);*/
3564: }
3565: } /* end if mle */
3566: }
3567: } /* end wave */
3568: }
3569: jmean=sum/k;
3570: 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 3571: 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 3572: }
3573:
3574: /*********** Tricode ****************************/
1.145 brouard 3575: void tricode(int *Tvar, int **nbcode, int imx, int *Ndum)
1.126 brouard 3576: {
1.144 brouard 3577: /**< Uses cptcovn+2*cptcovprod as the number of covariates */
3578: /* 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 3579: * Boring subroutine which should only output nbcode[Tvar[j]][k]
1.145 brouard 3580: * Tvar[5] in V2+V1+V3*age+V2*V4 is 2 (V2)
1.169 brouard 3581: * nbcode[Tvar[j]][1]=
1.144 brouard 3582: */
1.130 brouard 3583:
1.145 brouard 3584: int ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
1.136 brouard 3585: int modmaxcovj=0; /* Modality max of covariates j */
1.145 brouard 3586: int cptcode=0; /* Modality max of covariates j */
3587: int modmincovj=0; /* Modality min of covariates j */
3588:
3589:
1.126 brouard 3590: cptcoveff=0;
3591:
1.144 brouard 3592: for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */
1.126 brouard 3593:
1.145 brouard 3594: /* Loop on covariates without age and products */
1.186 brouard 3595: for (j=1; j<=(cptcovs); j++) { /* From model V1 + V2*age+ V3 + V3*V4 keeps V1 + V3 = 2 only */
1.192 brouard 3596: for (k=-1; k < maxncov; k++) Ndum[k]=0;
1.186 brouard 3597: for (i=1; i<=imx; i++) { /* Loop on individuals: reads the data file to get the maximum value of the
1.136 brouard 3598: modality of this covariate Vj*/
1.145 brouard 3599: ij=(int)(covar[Tvar[j]][i]); /* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i
3600: * If product of Vn*Vm, still boolean *:
3601: * If it was coded 1, 2, 3, 4 should be splitted into 3 boolean variables
3602: * 1 => 0 0 0, 2 => 0 0 1, 3 => 0 1 1, 4=1 0 0 */
3603: /* Finds for covariate j, n=Tvar[j] of Vn . ij is the
1.136 brouard 3604: modality of the nth covariate of individual i. */
1.145 brouard 3605: if (ij > modmaxcovj)
3606: modmaxcovj=ij;
3607: else if (ij < modmincovj)
3608: modmincovj=ij;
3609: if ((ij < -1) && (ij > NCOVMAX)){
3610: printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX );
3611: exit(1);
3612: }else
1.136 brouard 3613: Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/
1.145 brouard 3614: /* If coded 1, 2, 3 , counts the number of 1 Ndum[1], number of 2, Ndum[2], etc */
1.126 brouard 3615: /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
1.136 brouard 3616: /* getting the maximum value of the modality of the covariate
3617: (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and
3618: female is 1, then modmaxcovj=1.*/
1.192 brouard 3619: } /* end for loop on individuals i */
1.145 brouard 3620: printf(" Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", j, Tvar[j], modmincovj, modmaxcovj);
1.192 brouard 3621: 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 3622: cptcode=modmaxcovj;
1.137 brouard 3623: /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */
1.145 brouard 3624: /*for (i=0; i<=cptcode; i++) {*/
1.192 brouard 3625: for (k=modmincovj; k<=modmaxcovj; k++) { /* k=-1 ? 0 and 1*//* For each value k of the modality of model-cov j */
3626: printf("Frequencies of covariates %d ie V%d with value %d: %d\n", j, Tvar[j], k, Ndum[k]);
3627: fprintf(ficlog, "Frequencies of covariates %d ie V%d with value %d: %d\n", j, Tvar[j], k, Ndum[k]);
3628: if( Ndum[k] != 0 ){ /* Counts if nobody answered modality k ie empty modality, we skip it and reorder */
3629: if( k != -1){
3630: ncodemax[j]++; /* ncodemax[j]= Number of modalities of the j th
3631: covariate for which somebody answered excluding
3632: undefined. Usually 2: 0 and 1. */
3633: }
3634: ncodemaxwundef[j]++; /* ncodemax[j]= Number of modalities of the j th
3635: covariate for which somebody answered including
3636: undefined. Usually 3: -1, 0 and 1. */
1.145 brouard 3637: }
3638: /* In fact ncodemax[j]=2 (dichotom. variables only) but it could be more for
3639: historical reasons: 3 if coded 1, 2, 3 and 4 and Ndum[2]=0 */
1.131 brouard 3640: } /* Ndum[-1] number of undefined modalities */
1.126 brouard 3641:
1.136 brouard 3642: /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */
1.186 brouard 3643: /* For covariate j, modalities could be 1, 2, 3, 4, 5, 6, 7.
3644: 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 3645: modmincovj=3; modmaxcovj = 7;
1.186 brouard 3646: There are only 3 modalities non empty 3, 6, 7 (or 2 if 27 is too few) : ncodemax[j]=3;
3647: which will be coded 0, 1, 2 which in binary on 2=3-1 digits are 0=00 1=01, 2=10;
3648: defining two dummy variables: variables V1_1 and V1_2.
1.145 brouard 3649: nbcode[Tvar[j]][ij]=k;
3650: nbcode[Tvar[j]][1]=0;
3651: nbcode[Tvar[j]][2]=1;
3652: nbcode[Tvar[j]][3]=2;
1.197 brouard 3653: To be continued (not working yet).
1.145 brouard 3654: */
1.197 brouard 3655: ij=0; /* ij is similar to i but can jump over null modalities */
3656: 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*/
3657: if (Ndum[i] == 0) { /* If nobody responded to this modality k */
1.192 brouard 3658: break;
3659: }
3660: ij++;
1.197 brouard 3661: 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 3662: cptcode = ij; /* New max modality for covar j */
3663: } /* end of loop on modality i=-1 to 1 or more */
3664:
3665: /* for (k=0; k<= cptcode; k++) { /\* k=-1 ? k=0 to 1 *\//\* Could be 1 to 4 *\//\* cptcode=modmaxcovj *\/ */
3666: /* /\*recode from 0 *\/ */
3667: /* k is a modality. If we have model=V1+V1*sex */
3668: /* then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
3669: /* But if some modality were not used, it is recoded from 0 to a newer modmaxcovj=cptcode *\/ */
3670: /* } */
3671: /* /\* cptcode = ij; *\/ /\* New max modality for covar j *\/ */
3672: /* if (ij > ncodemax[j]) { */
3673: /* printf( " Error ij=%d > ncodemax[%d]=%d\n", ij, j, ncodemax[j]); */
3674: /* fprintf(ficlog, " Error ij=%d > ncodemax[%d]=%d\n", ij, j, ncodemax[j]); */
3675: /* break; */
3676: /* } */
3677: /* } /\* end of loop on modality k *\/ */
1.137 brouard 3678: } /* end of loop on model-covariate j. nbcode[Tvarj][1]=0 and nbcode[Tvarj][2]=1 sets the value of covariate j*/
3679:
1.145 brouard 3680: for (k=-1; k< maxncov; k++) Ndum[k]=0;
1.137 brouard 3681:
1.187 brouard 3682: for (i=1; i<=ncovmodel-2-nagesqr; i++) { /* -2, cste and age and eventually age*age */
1.145 brouard 3683: /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
3684: ij=Tvar[i]; /* Tvar might be -1 if status was unknown */
1.187 brouard 3685: Ndum[ij]++; /* Might be supersed V1 + V1*age */
1.145 brouard 3686: }
1.126 brouard 3687:
1.192 brouard 3688: ij=0;
1.145 brouard 3689: for (i=0; i<= maxncov-1; i++) { /* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) */
3690: /*printf("Ndum[%d]=%d\n",i, Ndum[i]);*/
1.126 brouard 3691: if((Ndum[i]!=0) && (i<=ncovcol)){
1.192 brouard 3692: ij++;
1.145 brouard 3693: /*printf("diff Ndum[%d]=%d\n",i, Ndum[i]);*/
3694: Tvaraff[ij]=i; /*For printing (unclear) */
1.192 brouard 3695: }else{
3696: /* Tvaraff[ij]=0; */
3697: }
1.126 brouard 3698: }
1.192 brouard 3699: /* ij--; */
1.144 brouard 3700: cptcoveff=ij; /*Number of total covariates*/
1.145 brouard 3701:
1.126 brouard 3702: }
3703:
1.145 brouard 3704:
1.126 brouard 3705: /*********** Health Expectancies ****************/
3706:
1.127 brouard 3707: 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 3708:
3709: {
3710: /* Health expectancies, no variances */
1.164 brouard 3711: int i, j, nhstepm, hstepm, h, nstepm;
1.126 brouard 3712: int nhstepma, nstepma; /* Decreasing with age */
3713: double age, agelim, hf;
3714: double ***p3mat;
3715: double eip;
3716:
3717: pstamp(ficreseij);
3718: fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
3719: fprintf(ficreseij,"# Age");
3720: for(i=1; i<=nlstate;i++){
3721: for(j=1; j<=nlstate;j++){
3722: fprintf(ficreseij," e%1d%1d ",i,j);
3723: }
3724: fprintf(ficreseij," e%1d. ",i);
3725: }
3726: fprintf(ficreseij,"\n");
3727:
3728:
3729: if(estepm < stepm){
3730: printf ("Problem %d lower than %d\n",estepm, stepm);
3731: }
3732: else hstepm=estepm;
3733: /* We compute the life expectancy from trapezoids spaced every estepm months
3734: * This is mainly to measure the difference between two models: for example
3735: * if stepm=24 months pijx are given only every 2 years and by summing them
3736: * we are calculating an estimate of the Life Expectancy assuming a linear
3737: * progression in between and thus overestimating or underestimating according
3738: * to the curvature of the survival function. If, for the same date, we
3739: * estimate the model with stepm=1 month, we can keep estepm to 24 months
3740: * to compare the new estimate of Life expectancy with the same linear
3741: * hypothesis. A more precise result, taking into account a more precise
3742: * curvature will be obtained if estepm is as small as stepm. */
3743:
3744: /* For example we decided to compute the life expectancy with the smallest unit */
3745: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
3746: nhstepm is the number of hstepm from age to agelim
3747: nstepm is the number of stepm from age to agelin.
3748: Look at hpijx to understand the reason of that which relies in memory size
3749: and note for a fixed period like estepm months */
3750: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
3751: survival function given by stepm (the optimization length). Unfortunately it
3752: means that if the survival funtion is printed only each two years of age and if
3753: you sum them up and add 1 year (area under the trapezoids) you won't get the same
3754: results. So we changed our mind and took the option of the best precision.
3755: */
3756: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
3757:
3758: agelim=AGESUP;
3759: /* If stepm=6 months */
3760: /* Computed by stepm unit matrices, product of hstepm matrices, stored
3761: in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
3762:
3763: /* nhstepm age range expressed in number of stepm */
3764: nstepm=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
3765: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
3766: /* if (stepm >= YEARM) hstepm=1;*/
3767: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
3768: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3769:
3770: for (age=bage; age<=fage; age ++){
3771: nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
3772: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
3773: /* if (stepm >= YEARM) hstepm=1;*/
3774: nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
3775:
3776: /* If stepm=6 months */
3777: /* Computed by stepm unit matrices, product of hstepma matrices, stored
3778: in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
3779:
3780: hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
3781:
3782: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
3783:
3784: printf("%d|",(int)age);fflush(stdout);
3785: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
3786:
3787: /* Computing expectancies */
3788: for(i=1; i<=nlstate;i++)
3789: for(j=1; j<=nlstate;j++)
3790: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
3791: eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
3792:
3793: /* 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]);*/
3794:
3795: }
3796:
3797: fprintf(ficreseij,"%3.0f",age );
3798: for(i=1; i<=nlstate;i++){
3799: eip=0;
3800: for(j=1; j<=nlstate;j++){
3801: eip +=eij[i][j][(int)age];
3802: fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
3803: }
3804: fprintf(ficreseij,"%9.4f", eip );
3805: }
3806: fprintf(ficreseij,"\n");
3807:
3808: }
3809: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3810: printf("\n");
3811: fprintf(ficlog,"\n");
3812:
3813: }
3814:
1.127 brouard 3815: 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 3816:
3817: {
3818: /* Covariances of health expectancies eij and of total life expectancies according
3819: to initial status i, ei. .
3820: */
3821: int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
3822: int nhstepma, nstepma; /* Decreasing with age */
3823: double age, agelim, hf;
3824: double ***p3matp, ***p3matm, ***varhe;
3825: double **dnewm,**doldm;
3826: double *xp, *xm;
3827: double **gp, **gm;
3828: double ***gradg, ***trgradg;
3829: int theta;
3830:
3831: double eip, vip;
3832:
3833: varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
3834: xp=vector(1,npar);
3835: xm=vector(1,npar);
3836: dnewm=matrix(1,nlstate*nlstate,1,npar);
3837: doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
3838:
3839: pstamp(ficresstdeij);
3840: fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
3841: fprintf(ficresstdeij,"# Age");
3842: for(i=1; i<=nlstate;i++){
3843: for(j=1; j<=nlstate;j++)
3844: fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
3845: fprintf(ficresstdeij," e%1d. ",i);
3846: }
3847: fprintf(ficresstdeij,"\n");
3848:
3849: pstamp(ficrescveij);
3850: fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
3851: fprintf(ficrescveij,"# Age");
3852: for(i=1; i<=nlstate;i++)
3853: for(j=1; j<=nlstate;j++){
3854: cptj= (j-1)*nlstate+i;
3855: for(i2=1; i2<=nlstate;i2++)
3856: for(j2=1; j2<=nlstate;j2++){
3857: cptj2= (j2-1)*nlstate+i2;
3858: if(cptj2 <= cptj)
3859: fprintf(ficrescveij," %1d%1d,%1d%1d",i,j,i2,j2);
3860: }
3861: }
3862: fprintf(ficrescveij,"\n");
3863:
3864: if(estepm < stepm){
3865: printf ("Problem %d lower than %d\n",estepm, stepm);
3866: }
3867: else hstepm=estepm;
3868: /* We compute the life expectancy from trapezoids spaced every estepm months
3869: * This is mainly to measure the difference between two models: for example
3870: * if stepm=24 months pijx are given only every 2 years and by summing them
3871: * we are calculating an estimate of the Life Expectancy assuming a linear
3872: * progression in between and thus overestimating or underestimating according
3873: * to the curvature of the survival function. If, for the same date, we
3874: * estimate the model with stepm=1 month, we can keep estepm to 24 months
3875: * to compare the new estimate of Life expectancy with the same linear
3876: * hypothesis. A more precise result, taking into account a more precise
3877: * curvature will be obtained if estepm is as small as stepm. */
3878:
3879: /* For example we decided to compute the life expectancy with the smallest unit */
3880: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
3881: nhstepm is the number of hstepm from age to agelim
3882: nstepm is the number of stepm from age to agelin.
3883: Look at hpijx to understand the reason of that which relies in memory size
3884: and note for a fixed period like estepm months */
3885: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
3886: survival function given by stepm (the optimization length). Unfortunately it
3887: means that if the survival funtion is printed only each two years of age and if
3888: you sum them up and add 1 year (area under the trapezoids) you won't get the same
3889: results. So we changed our mind and took the option of the best precision.
3890: */
3891: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
3892:
3893: /* If stepm=6 months */
3894: /* nhstepm age range expressed in number of stepm */
3895: agelim=AGESUP;
3896: nstepm=(int) rint((agelim-bage)*YEARM/stepm);
3897: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
3898: /* if (stepm >= YEARM) hstepm=1;*/
3899: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
3900:
3901: p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3902: p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3903: gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
3904: trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
3905: gp=matrix(0,nhstepm,1,nlstate*nlstate);
3906: gm=matrix(0,nhstepm,1,nlstate*nlstate);
3907:
3908: for (age=bage; age<=fage; age ++){
3909: nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
3910: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
3911: /* if (stepm >= YEARM) hstepm=1;*/
3912: nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
3913:
3914: /* If stepm=6 months */
3915: /* Computed by stepm unit matrices, product of hstepma matrices, stored
3916: in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
3917:
3918: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
3919:
3920: /* Computing Variances of health expectancies */
3921: /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
3922: decrease memory allocation */
3923: for(theta=1; theta <=npar; theta++){
3924: for(i=1; i<=npar; i++){
3925: xp[i] = x[i] + (i==theta ?delti[theta]:0);
3926: xm[i] = x[i] - (i==theta ?delti[theta]:0);
3927: }
3928: hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);
3929: hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);
3930:
3931: for(j=1; j<= nlstate; j++){
3932: for(i=1; i<=nlstate; i++){
3933: for(h=0; h<=nhstepm-1; h++){
3934: gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
3935: gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
3936: }
3937: }
3938: }
3939:
3940: for(ij=1; ij<= nlstate*nlstate; ij++)
3941: for(h=0; h<=nhstepm-1; h++){
3942: gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
3943: }
3944: }/* End theta */
3945:
3946:
3947: for(h=0; h<=nhstepm-1; h++)
3948: for(j=1; j<=nlstate*nlstate;j++)
3949: for(theta=1; theta <=npar; theta++)
3950: trgradg[h][j][theta]=gradg[h][theta][j];
3951:
3952:
3953: for(ij=1;ij<=nlstate*nlstate;ij++)
3954: for(ji=1;ji<=nlstate*nlstate;ji++)
3955: varhe[ij][ji][(int)age] =0.;
3956:
3957: printf("%d|",(int)age);fflush(stdout);
3958: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
3959: for(h=0;h<=nhstepm-1;h++){
3960: for(k=0;k<=nhstepm-1;k++){
3961: matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
3962: matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
3963: for(ij=1;ij<=nlstate*nlstate;ij++)
3964: for(ji=1;ji<=nlstate*nlstate;ji++)
3965: varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
3966: }
3967: }
3968:
3969: /* Computing expectancies */
3970: hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
3971: for(i=1; i<=nlstate;i++)
3972: for(j=1; j<=nlstate;j++)
3973: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
3974: eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
3975:
3976: /* 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]);*/
3977:
3978: }
3979:
3980: fprintf(ficresstdeij,"%3.0f",age );
3981: for(i=1; i<=nlstate;i++){
3982: eip=0.;
3983: vip=0.;
3984: for(j=1; j<=nlstate;j++){
3985: eip += eij[i][j][(int)age];
3986: for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
3987: vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
3988: fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
3989: }
3990: fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
3991: }
3992: fprintf(ficresstdeij,"\n");
3993:
3994: fprintf(ficrescveij,"%3.0f",age );
3995: for(i=1; i<=nlstate;i++)
3996: for(j=1; j<=nlstate;j++){
3997: cptj= (j-1)*nlstate+i;
3998: for(i2=1; i2<=nlstate;i2++)
3999: for(j2=1; j2<=nlstate;j2++){
4000: cptj2= (j2-1)*nlstate+i2;
4001: if(cptj2 <= cptj)
4002: fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
4003: }
4004: }
4005: fprintf(ficrescveij,"\n");
4006:
4007: }
4008: free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
4009: free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
4010: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
4011: free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
4012: free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4013: free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4014: printf("\n");
4015: fprintf(ficlog,"\n");
4016:
4017: free_vector(xm,1,npar);
4018: free_vector(xp,1,npar);
4019: free_matrix(dnewm,1,nlstate*nlstate,1,npar);
4020: free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
4021: free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
4022: }
4023:
4024: /************ Variance ******************/
1.203 brouard 4025: 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 4026: {
4027: /* Variance of health expectancies */
4028: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
4029: /* double **newm;*/
1.169 brouard 4030: /* int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav)*/
4031:
4032: int movingaverage();
1.126 brouard 4033: double **dnewm,**doldm;
4034: double **dnewmp,**doldmp;
4035: int i, j, nhstepm, hstepm, h, nstepm ;
1.164 brouard 4036: int k;
1.126 brouard 4037: double *xp;
4038: double **gp, **gm; /* for var eij */
4039: double ***gradg, ***trgradg; /*for var eij */
4040: double **gradgp, **trgradgp; /* for var p point j */
4041: double *gpp, *gmp; /* for var p point j */
4042: double **varppt; /* for var p point j nlstate to nlstate+ndeath */
4043: double ***p3mat;
4044: double age,agelim, hf;
4045: double ***mobaverage;
4046: int theta;
4047: char digit[4];
4048: char digitp[25];
4049:
4050: char fileresprobmorprev[FILENAMELENGTH];
4051:
4052: if(popbased==1){
4053: if(mobilav!=0)
1.201 brouard 4054: strcpy(digitp,"-POPULBASED-MOBILAV_");
4055: else strcpy(digitp,"-POPULBASED-NOMOBIL_");
1.126 brouard 4056: }
4057: else
1.201 brouard 4058: strcpy(digitp,"-STABLBASED_");
1.126 brouard 4059:
4060: if (mobilav!=0) {
4061: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4062: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
4063: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
4064: printf(" Error in movingaverage mobilav=%d\n",mobilav);
4065: }
4066: }
4067:
1.201 brouard 4068: strcpy(fileresprobmorprev,"PRMORPREV-");
1.126 brouard 4069: sprintf(digit,"%-d",ij);
4070: /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
4071: strcat(fileresprobmorprev,digit); /* Tvar to be done */
4072: strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
1.202 brouard 4073: strcat(fileresprobmorprev,fileresu);
1.126 brouard 4074: if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
4075: printf("Problem with resultfile: %s\n", fileresprobmorprev);
4076: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
4077: }
4078: printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
4079: fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
4080: pstamp(ficresprobmorprev);
4081: 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);
4082: fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
4083: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
4084: fprintf(ficresprobmorprev," p.%-d SE",j);
4085: for(i=1; i<=nlstate;i++)
4086: fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
4087: }
4088: fprintf(ficresprobmorprev,"\n");
1.208 ! brouard 4089:
1.126 brouard 4090: fprintf(ficgp,"\n# Routine varevsij");
1.200 brouard 4091: fprintf(ficgp,"\nunset title \n");
4092: /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
1.126 brouard 4093: 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");
4094: fprintf(fichtm,"\n<br>%s <br>\n",digitp);
4095: /* } */
4096: varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
4097: pstamp(ficresvij);
4098: fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n# (weighted average of eij where weights are ");
4099: if(popbased==1)
1.128 brouard 4100: 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 4101: else
4102: fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
4103: fprintf(ficresvij,"# Age");
4104: for(i=1; i<=nlstate;i++)
4105: for(j=1; j<=nlstate;j++)
4106: fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
4107: fprintf(ficresvij,"\n");
4108:
4109: xp=vector(1,npar);
4110: dnewm=matrix(1,nlstate,1,npar);
4111: doldm=matrix(1,nlstate,1,nlstate);
4112: dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
4113: doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
4114:
4115: gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
4116: gpp=vector(nlstate+1,nlstate+ndeath);
4117: gmp=vector(nlstate+1,nlstate+ndeath);
4118: trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
4119:
4120: if(estepm < stepm){
4121: printf ("Problem %d lower than %d\n",estepm, stepm);
4122: }
4123: else hstepm=estepm;
4124: /* For example we decided to compute the life expectancy with the smallest unit */
4125: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
4126: nhstepm is the number of hstepm from age to agelim
1.208 ! brouard 4127: nstepm is the number of stepm from age to agelim.
! 4128: Look at function hpijx to understand why (it is linked to memory size questions)
! 4129: we decided (b) to get a life expectancy respecting the most precise curvature of the
1.126 brouard 4130: survival function given by stepm (the optimization length). Unfortunately it
4131: means that if the survival funtion is printed every two years of age and if
4132: you sum them up and add 1 year (area under the trapezoids) you won't get the same
4133: results. So we changed our mind and took the option of the best precision.
4134: */
4135: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
4136: agelim = AGESUP;
4137: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
4138: nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
4139: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
4140: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4141: gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
4142: gp=matrix(0,nhstepm,1,nlstate);
4143: gm=matrix(0,nhstepm,1,nlstate);
4144:
4145:
4146: for(theta=1; theta <=npar; theta++){
4147: for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
4148: xp[i] = x[i] + (i==theta ?delti[theta]:0);
4149: }
4150: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
1.203 brouard 4151: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyear,ij);
1.126 brouard 4152:
4153: if (popbased==1) {
4154: if(mobilav ==0){
4155: for(i=1; i<=nlstate;i++)
4156: prlim[i][i]=probs[(int)age][i][ij];
4157: }else{ /* mobilav */
4158: for(i=1; i<=nlstate;i++)
4159: prlim[i][i]=mobaverage[(int)age][i][ij];
4160: }
4161: }
4162:
4163: for(j=1; j<= nlstate; j++){
4164: for(h=0; h<=nhstepm; h++){
4165: for(i=1, gp[h][j]=0.;i<=nlstate;i++)
4166: gp[h][j] += prlim[i][i]*p3mat[i][j][h];
4167: }
4168: }
4169: /* This for computing probability of death (h=1 means
4170: computed over hstepm matrices product = hstepm*stepm months)
4171: as a weighted average of prlim.
4172: */
4173: for(j=nlstate+1;j<=nlstate+ndeath;j++){
4174: for(i=1,gpp[j]=0.; i<= nlstate; i++)
4175: gpp[j] += prlim[i][i]*p3mat[i][j][1];
4176: }
4177: /* end probability of death */
4178:
4179: for(i=1; i<=npar; i++) /* Computes gradient x - delta */
4180: xp[i] = x[i] - (i==theta ?delti[theta]:0);
4181: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
1.203 brouard 4182: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyear, ij);
1.126 brouard 4183:
4184: if (popbased==1) {
4185: if(mobilav ==0){
4186: for(i=1; i<=nlstate;i++)
4187: prlim[i][i]=probs[(int)age][i][ij];
4188: }else{ /* mobilav */
4189: for(i=1; i<=nlstate;i++)
4190: prlim[i][i]=mobaverage[(int)age][i][ij];
4191: }
4192: }
4193:
1.128 brouard 4194: for(j=1; j<= nlstate; j++){ /* Sum of wi * eij = e.j */
1.126 brouard 4195: for(h=0; h<=nhstepm; h++){
4196: for(i=1, gm[h][j]=0.;i<=nlstate;i++)
4197: gm[h][j] += prlim[i][i]*p3mat[i][j][h];
4198: }
4199: }
4200: /* This for computing probability of death (h=1 means
4201: computed over hstepm matrices product = hstepm*stepm months)
4202: as a weighted average of prlim.
4203: */
4204: for(j=nlstate+1;j<=nlstate+ndeath;j++){
4205: for(i=1,gmp[j]=0.; i<= nlstate; i++)
4206: gmp[j] += prlim[i][i]*p3mat[i][j][1];
4207: }
4208: /* end probability of death */
4209:
4210: for(j=1; j<= nlstate; j++) /* vareij */
4211: for(h=0; h<=nhstepm; h++){
4212: gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
4213: }
4214:
4215: for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
4216: gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
4217: }
4218:
4219: } /* End theta */
4220:
4221: trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
4222:
4223: for(h=0; h<=nhstepm; h++) /* veij */
4224: for(j=1; j<=nlstate;j++)
4225: for(theta=1; theta <=npar; theta++)
4226: trgradg[h][j][theta]=gradg[h][theta][j];
4227:
4228: for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
4229: for(theta=1; theta <=npar; theta++)
4230: trgradgp[j][theta]=gradgp[theta][j];
4231:
4232:
4233: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
4234: for(i=1;i<=nlstate;i++)
4235: for(j=1;j<=nlstate;j++)
4236: vareij[i][j][(int)age] =0.;
4237:
4238: for(h=0;h<=nhstepm;h++){
4239: for(k=0;k<=nhstepm;k++){
4240: matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
4241: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
4242: for(i=1;i<=nlstate;i++)
4243: for(j=1;j<=nlstate;j++)
4244: vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
4245: }
4246: }
4247:
4248: /* pptj */
4249: matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
4250: matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
4251: for(j=nlstate+1;j<=nlstate+ndeath;j++)
4252: for(i=nlstate+1;i<=nlstate+ndeath;i++)
4253: varppt[j][i]=doldmp[j][i];
4254: /* end ppptj */
4255: /* x centered again */
4256: hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);
1.203 brouard 4257: prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ncvyear,ij);
1.126 brouard 4258:
4259: if (popbased==1) {
4260: if(mobilav ==0){
4261: for(i=1; i<=nlstate;i++)
4262: prlim[i][i]=probs[(int)age][i][ij];
4263: }else{ /* mobilav */
4264: for(i=1; i<=nlstate;i++)
4265: prlim[i][i]=mobaverage[(int)age][i][ij];
4266: }
4267: }
4268:
4269: /* This for computing probability of death (h=1 means
4270: computed over hstepm (estepm) matrices product = hstepm*stepm months)
4271: as a weighted average of prlim.
4272: */
4273: for(j=nlstate+1;j<=nlstate+ndeath;j++){
4274: for(i=1,gmp[j]=0.;i<= nlstate; i++)
4275: gmp[j] += prlim[i][i]*p3mat[i][j][1];
4276: }
4277: /* end probability of death */
4278:
4279: fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
4280: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
4281: fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
4282: for(i=1; i<=nlstate;i++){
4283: fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
4284: }
4285: }
4286: fprintf(ficresprobmorprev,"\n");
4287:
4288: fprintf(ficresvij,"%.0f ",age );
4289: for(i=1; i<=nlstate;i++)
4290: for(j=1; j<=nlstate;j++){
4291: fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
4292: }
4293: fprintf(ficresvij,"\n");
4294: free_matrix(gp,0,nhstepm,1,nlstate);
4295: free_matrix(gm,0,nhstepm,1,nlstate);
4296: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
4297: free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
4298: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4299: } /* End age */
4300: free_vector(gpp,nlstate+1,nlstate+ndeath);
4301: free_vector(gmp,nlstate+1,nlstate+ndeath);
4302: free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
4303: free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
1.199 brouard 4304: /* fprintf(ficgp,"\nunset parametric;unset label; set ter png small size 320, 240"); */
4305: fprintf(ficgp,"\nunset parametric;unset label; set ter svg size 640, 480");
1.126 brouard 4306: /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
1.131 brouard 4307: fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
1.201 brouard 4308: fprintf(ficgp,"\nset out \"%s%s.svg\";",subdirf3(optionfilefiname,"VARMUPTJGR-",digitp),digit);
1.126 brouard 4309: /* fprintf(ficgp,"\n plot \"%s\" u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
4310: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
4311: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
1.145 brouard 4312: fprintf(ficgp,"\n plot \"%s\" u 1:($3) not w l lt 1 ",subdirf(fileresprobmorprev));
1.170 brouard 4313: fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)) t \"95%% interval\" w l lt 2 ",subdirf(fileresprobmorprev));
1.145 brouard 4314: fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)) not w l lt 2 ",subdirf(fileresprobmorprev));
1.126 brouard 4315: 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 4316: 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 4317: /* 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 4318: */
1.199 brouard 4319: /* fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.svg\";replot;",digitp,optionfilefiname,digit); */
1.201 brouard 4320: fprintf(ficgp,"\nset out;\nset out \"%s%s.svg\";replot;set out;\n",subdirf3(optionfilefiname,"VARMUPTJGR-",digitp),digit);
1.126 brouard 4321:
4322: free_vector(xp,1,npar);
4323: free_matrix(doldm,1,nlstate,1,nlstate);
4324: free_matrix(dnewm,1,nlstate,1,npar);
4325: free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
4326: free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
4327: free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
4328: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4329: fclose(ficresprobmorprev);
4330: fflush(ficgp);
4331: fflush(fichtm);
4332: } /* end varevsij */
4333:
4334: /************ Variance of prevlim ******************/
1.203 brouard 4335: 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 4336: {
1.205 brouard 4337: /* Variance of prevalence limit for each state ij using current parameters x[] and estimates of neighbourhood give by delti*/
1.126 brouard 4338: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
1.164 brouard 4339:
1.126 brouard 4340: double **dnewm,**doldm;
4341: int i, j, nhstepm, hstepm;
4342: double *xp;
4343: double *gp, *gm;
4344: double **gradg, **trgradg;
1.208 ! brouard 4345: double **mgm, **mgp;
1.126 brouard 4346: double age,agelim;
4347: int theta;
4348:
4349: pstamp(ficresvpl);
4350: fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
4351: fprintf(ficresvpl,"# Age");
4352: for(i=1; i<=nlstate;i++)
4353: fprintf(ficresvpl," %1d-%1d",i,i);
4354: fprintf(ficresvpl,"\n");
4355:
4356: xp=vector(1,npar);
4357: dnewm=matrix(1,nlstate,1,npar);
4358: doldm=matrix(1,nlstate,1,nlstate);
4359:
4360: hstepm=1*YEARM; /* Every year of age */
4361: hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
4362: agelim = AGESUP;
4363: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
4364: nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
4365: if (stepm >= YEARM) hstepm=1;
4366: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
1.208 ! brouard 4367: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
1.126 brouard 4368: gradg=matrix(1,npar,1,nlstate);
1.208 ! brouard 4369: mgp=matrix(1,npar,1,nlstate);
! 4370: mgm=matrix(1,npar,1,nlstate);
1.126 brouard 4371: gp=vector(1,nlstate);
4372: gm=vector(1,nlstate);
4373:
4374: for(theta=1; theta <=npar; theta++){
4375: for(i=1; i<=npar; i++){ /* Computes gradient */
4376: xp[i] = x[i] + (i==theta ?delti[theta]:0);
4377: }
1.208 ! brouard 4378: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij); /* Missing or not useful because 1 year */
1.203 brouard 4379: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyear,ij);
1.208 ! brouard 4380: for(i=1;i<=nlstate;i++){
1.126 brouard 4381: gp[i] = prlim[i][i];
1.208 ! brouard 4382: mgp[theta][i] = prlim[i][i];
! 4383: }
1.126 brouard 4384: for(i=1; i<=npar; i++) /* Computes gradient */
4385: xp[i] = x[i] - (i==theta ?delti[theta]:0);
1.203 brouard 4386: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyear,ij);
1.208 ! brouard 4387: for(i=1;i<=nlstate;i++){
1.126 brouard 4388: gm[i] = prlim[i][i];
1.208 ! brouard 4389: mgm[theta][i] = prlim[i][i];
! 4390: }
1.126 brouard 4391: for(i=1;i<=nlstate;i++)
4392: gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
4393: } /* End theta */
4394:
4395: trgradg =matrix(1,nlstate,1,npar);
4396:
4397: for(j=1; j<=nlstate;j++)
4398: for(theta=1; theta <=npar; theta++)
4399: trgradg[j][theta]=gradg[theta][j];
1.208 ! brouard 4400: if((int)age==68 ||(int)age== 69 ){
! 4401: printf("\nmgm mgp %d ",(int)age);
! 4402: for(j=1; j<=nlstate;j++){
! 4403: printf("%d ",j);
! 4404: for(theta=1; theta <=npar; theta++)
! 4405: printf("%d %lf %lf",theta,mgm[theta][j],mgp[theta][j]);
! 4406: printf("\n ");
! 4407: }
! 4408: }
! 4409: if((int)age==68 ||(int)age== 69 ){
! 4410: printf("\n gradg %d ",(int)age);
! 4411: for(j=1; j<=nlstate;j++){
! 4412: printf("%d ",j);
! 4413: for(theta=1; theta <=npar; theta++)
! 4414: printf("%d %lf ",theta,gradg[theta][j]);
! 4415: printf("\n ");
! 4416: }
! 4417: }
1.126 brouard 4418:
4419: for(i=1;i<=nlstate;i++)
4420: varpl[i][(int)age] =0.;
1.208 ! brouard 4421: if((int)age==68 ||(int)age== 69 ){
1.205 brouard 4422: matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
4423: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
4424: }else{
1.126 brouard 4425: matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
4426: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
1.205 brouard 4427: }
1.126 brouard 4428: for(i=1;i<=nlstate;i++)
4429: varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
4430:
4431: fprintf(ficresvpl,"%.0f ",age );
4432: for(i=1; i<=nlstate;i++)
4433: fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
4434: fprintf(ficresvpl,"\n");
4435: free_vector(gp,1,nlstate);
4436: free_vector(gm,1,nlstate);
1.208 ! brouard 4437: free_matrix(mgm,1,npar,1,nlstate);
! 4438: free_matrix(mgp,1,npar,1,nlstate);
1.126 brouard 4439: free_matrix(gradg,1,npar,1,nlstate);
4440: free_matrix(trgradg,1,nlstate,1,npar);
4441: } /* End age */
4442:
4443: free_vector(xp,1,npar);
4444: free_matrix(doldm,1,nlstate,1,npar);
4445: free_matrix(dnewm,1,nlstate,1,nlstate);
4446:
4447: }
4448:
4449: /************ Variance of one-step probabilities ******************/
4450: 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[])
4451: {
1.164 brouard 4452: int i, j=0, k1, l1, tj;
1.126 brouard 4453: int k2, l2, j1, z1;
1.164 brouard 4454: int k=0, l;
1.145 brouard 4455: int first=1, first1, first2;
1.126 brouard 4456: double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
4457: double **dnewm,**doldm;
4458: double *xp;
4459: double *gp, *gm;
4460: double **gradg, **trgradg;
4461: double **mu;
1.164 brouard 4462: double age, cov[NCOVMAX+1];
1.126 brouard 4463: double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
4464: int theta;
4465: char fileresprob[FILENAMELENGTH];
4466: char fileresprobcov[FILENAMELENGTH];
4467: char fileresprobcor[FILENAMELENGTH];
4468: double ***varpij;
4469:
1.201 brouard 4470: strcpy(fileresprob,"PROB_");
1.126 brouard 4471: strcat(fileresprob,fileres);
4472: if((ficresprob=fopen(fileresprob,"w"))==NULL) {
4473: printf("Problem with resultfile: %s\n", fileresprob);
4474: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
4475: }
1.201 brouard 4476: strcpy(fileresprobcov,"PROBCOV_");
1.202 brouard 4477: strcat(fileresprobcov,fileresu);
1.126 brouard 4478: if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
4479: printf("Problem with resultfile: %s\n", fileresprobcov);
4480: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
4481: }
1.201 brouard 4482: strcpy(fileresprobcor,"PROBCOR_");
1.202 brouard 4483: strcat(fileresprobcor,fileresu);
1.126 brouard 4484: if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
4485: printf("Problem with resultfile: %s\n", fileresprobcor);
4486: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
4487: }
4488: printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
4489: fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
4490: printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
4491: fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
4492: printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
4493: fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
4494: pstamp(ficresprob);
4495: fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
4496: fprintf(ficresprob,"# Age");
4497: pstamp(ficresprobcov);
4498: fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
4499: fprintf(ficresprobcov,"# Age");
4500: pstamp(ficresprobcor);
4501: fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
4502: fprintf(ficresprobcor,"# Age");
4503:
4504:
4505: for(i=1; i<=nlstate;i++)
4506: for(j=1; j<=(nlstate+ndeath);j++){
4507: fprintf(ficresprob," p%1d-%1d (SE)",i,j);
4508: fprintf(ficresprobcov," p%1d-%1d ",i,j);
4509: fprintf(ficresprobcor," p%1d-%1d ",i,j);
4510: }
4511: /* fprintf(ficresprob,"\n");
4512: fprintf(ficresprobcov,"\n");
4513: fprintf(ficresprobcor,"\n");
4514: */
1.131 brouard 4515: xp=vector(1,npar);
1.126 brouard 4516: dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
4517: doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
4518: mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
4519: varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
4520: first=1;
4521: fprintf(ficgp,"\n# Routine varprob");
4522: fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
4523: fprintf(fichtm,"\n");
4524:
1.200 brouard 4525: 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 4526: 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);
4527: fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated \
1.126 brouard 4528: and drawn. It helps understanding how is the covariance between two incidences.\
4529: They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
4530: 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. \
4531: It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
4532: would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
4533: standard deviations wide on each axis. <br>\
4534: Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
4535: and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
4536: To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
4537:
4538: cov[1]=1;
1.145 brouard 4539: /* tj=cptcoveff; */
4540: tj = (int) pow(2,cptcoveff);
1.126 brouard 4541: if (cptcovn<1) {tj=1;ncodemax[1]=1;}
4542: j1=0;
1.145 brouard 4543: for(j1=1; j1<=tj;j1++){
4544: /*for(i1=1; i1<=ncodemax[t];i1++){ */
4545: /*j1++;*/
1.126 brouard 4546: if (cptcovn>0) {
4547: fprintf(ficresprob, "\n#********** Variable ");
1.198 brouard 4548: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.126 brouard 4549: fprintf(ficresprob, "**********\n#\n");
4550: fprintf(ficresprobcov, "\n#********** Variable ");
1.198 brouard 4551: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.126 brouard 4552: fprintf(ficresprobcov, "**********\n#\n");
4553:
4554: fprintf(ficgp, "\n#********** Variable ");
1.198 brouard 4555: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.126 brouard 4556: fprintf(ficgp, "**********\n#\n");
4557:
4558:
4559: fprintf(fichtmcov, "\n<hr size=\"2\" color=\"#EC5E5E\">********** Variable ");
1.198 brouard 4560: for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.126 brouard 4561: fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
4562:
4563: fprintf(ficresprobcor, "\n#********** Variable ");
1.198 brouard 4564: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.126 brouard 4565: fprintf(ficresprobcor, "**********\n#");
4566: }
4567:
1.145 brouard 4568: gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
4569: trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
4570: gp=vector(1,(nlstate)*(nlstate+ndeath));
4571: gm=vector(1,(nlstate)*(nlstate+ndeath));
1.126 brouard 4572: for (age=bage; age<=fage; age ++){
4573: cov[2]=age;
1.187 brouard 4574: if(nagesqr==1)
4575: cov[3]= age*age;
1.126 brouard 4576: for (k=1; k<=cptcovn;k++) {
1.200 brouard 4577: cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(j1,k)];
4578: /*cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(j1,Tvar[k])];*//* j1 1 2 3 4
1.145 brouard 4579: * 1 1 1 1 1
4580: * 2 2 1 1 1
4581: * 3 1 2 1 1
4582: */
4583: /* nbcode[1][1]=0 nbcode[1][2]=1;*/
1.126 brouard 4584: }
1.186 brouard 4585: /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
1.200 brouard 4586: for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
1.126 brouard 4587: for (k=1; k<=cptcovprod;k++)
1.200 brouard 4588: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)];
1.126 brouard 4589:
4590:
4591: for(theta=1; theta <=npar; theta++){
4592: for(i=1; i<=npar; i++)
4593: xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
4594:
4595: pmij(pmmij,cov,ncovmodel,xp,nlstate);
4596:
4597: k=0;
4598: for(i=1; i<= (nlstate); i++){
4599: for(j=1; j<=(nlstate+ndeath);j++){
4600: k=k+1;
4601: gp[k]=pmmij[i][j];
4602: }
4603: }
4604:
4605: for(i=1; i<=npar; i++)
4606: xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
4607:
4608: pmij(pmmij,cov,ncovmodel,xp,nlstate);
4609: k=0;
4610: for(i=1; i<=(nlstate); i++){
4611: for(j=1; j<=(nlstate+ndeath);j++){
4612: k=k+1;
4613: gm[k]=pmmij[i][j];
4614: }
4615: }
4616:
4617: for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)
4618: gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];
4619: }
4620:
4621: for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
4622: for(theta=1; theta <=npar; theta++)
4623: trgradg[j][theta]=gradg[theta][j];
4624:
4625: matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);
4626: matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
4627:
4628: pmij(pmmij,cov,ncovmodel,x,nlstate);
4629:
4630: k=0;
4631: for(i=1; i<=(nlstate); i++){
4632: for(j=1; j<=(nlstate+ndeath);j++){
4633: k=k+1;
4634: mu[k][(int) age]=pmmij[i][j];
4635: }
4636: }
4637: for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
4638: for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
4639: varpij[i][j][(int)age] = doldm[i][j];
4640:
4641: /*printf("\n%d ",(int)age);
4642: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
4643: printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
4644: fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
4645: }*/
4646:
4647: fprintf(ficresprob,"\n%d ",(int)age);
4648: fprintf(ficresprobcov,"\n%d ",(int)age);
4649: fprintf(ficresprobcor,"\n%d ",(int)age);
4650:
4651: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
4652: fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
4653: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
4654: fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
4655: fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
4656: }
4657: i=0;
4658: for (k=1; k<=(nlstate);k++){
4659: for (l=1; l<=(nlstate+ndeath);l++){
1.145 brouard 4660: i++;
1.126 brouard 4661: fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
4662: fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
4663: for (j=1; j<=i;j++){
1.145 brouard 4664: /* printf(" k=%d l=%d i=%d j=%d\n",k,l,i,j);fflush(stdout); */
1.126 brouard 4665: fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
4666: fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
4667: }
4668: }
4669: }/* end of loop for state */
4670: } /* end of loop for age */
1.145 brouard 4671: free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
4672: free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
4673: free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
4674: free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
4675:
1.126 brouard 4676: /* Confidence intervalle of pij */
4677: /*
1.131 brouard 4678: fprintf(ficgp,"\nunset parametric;unset label");
1.126 brouard 4679: fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
4680: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
4681: 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);
4682: fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
4683: fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
4684: fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
4685: */
4686:
4687: /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
1.145 brouard 4688: first1=1;first2=2;
1.126 brouard 4689: for (k2=1; k2<=(nlstate);k2++){
4690: for (l2=1; l2<=(nlstate+ndeath);l2++){
4691: if(l2==k2) continue;
4692: j=(k2-1)*(nlstate+ndeath)+l2;
4693: for (k1=1; k1<=(nlstate);k1++){
4694: for (l1=1; l1<=(nlstate+ndeath);l1++){
4695: if(l1==k1) continue;
4696: i=(k1-1)*(nlstate+ndeath)+l1;
4697: if(i<=j) continue;
4698: for (age=bage; age<=fage; age ++){
4699: if ((int)age %5==0){
4700: v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
4701: v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
4702: cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
4703: mu1=mu[i][(int) age]/stepm*YEARM ;
4704: mu2=mu[j][(int) age]/stepm*YEARM;
4705: c12=cv12/sqrt(v1*v2);
4706: /* Computing eigen value of matrix of covariance */
4707: lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
4708: lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
1.135 brouard 4709: if ((lc2 <0) || (lc1 <0) ){
1.145 brouard 4710: if(first2==1){
4711: first1=0;
4712: 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);
4713: }
4714: 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);
4715: /* lc1=fabs(lc1); */ /* If we want to have them positive */
4716: /* lc2=fabs(lc2); */
1.135 brouard 4717: }
4718:
1.126 brouard 4719: /* Eigen vectors */
4720: v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
4721: /*v21=sqrt(1.-v11*v11); *//* error */
4722: v21=(lc1-v1)/cv12*v11;
4723: v12=-v21;
4724: v22=v11;
4725: tnalp=v21/v11;
4726: if(first1==1){
4727: first1=0;
4728: 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);
4729: }
4730: 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);
4731: /*printf(fignu*/
4732: /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
4733: /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
4734: if(first==1){
4735: first=0;
1.200 brouard 4736: fprintf(ficgp,"\n# Ellipsoids of confidence\n#\n");
1.126 brouard 4737: fprintf(ficgp,"\nset parametric;unset label");
4738: 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 4739: fprintf(ficgp,"\nset ter svg size 640, 480");
1.126 brouard 4740: fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
1.201 brouard 4741: :<a href=\"%s_%d%1d%1d-%1d%1d.svg\">\
4742: %s_%d%1d%1d-%1d%1d.svg</A>, ",k1,l1,k2,l2,\
4743: subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2,\
4744: subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
4745: fprintf(fichtmcov,"\n<br><img src=\"%s_%d%1d%1d-%1d%1d.svg\"> ",subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
1.126 brouard 4746: fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
1.201 brouard 4747: fprintf(ficgp,"\nset out \"%s_%d%1d%1d-%1d%1d.svg\"",subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
1.126 brouard 4748: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
4749: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
4750: 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",\
4751: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
4752: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
4753: }else{
4754: first=0;
4755: fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
4756: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
4757: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
4758: 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",\
4759: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
4760: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
4761: }/* if first */
4762: } /* age mod 5 */
4763: } /* end loop age */
1.201 brouard 4764: 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 4765: first=1;
4766: } /*l12 */
4767: } /* k12 */
4768: } /*l1 */
4769: }/* k1 */
1.169 brouard 4770: /* } */ /* loop covariates */
1.126 brouard 4771: }
4772: free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
4773: free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
4774: free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
4775: free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
4776: free_vector(xp,1,npar);
4777: fclose(ficresprob);
4778: fclose(ficresprobcov);
4779: fclose(ficresprobcor);
4780: fflush(ficgp);
4781: fflush(fichtmcov);
4782: }
4783:
4784:
4785: /******************* Printing html file ***********/
1.201 brouard 4786: void printinghtml(char fileresu[], char title[], char datafile[], int firstpass, \
1.126 brouard 4787: int lastpass, int stepm, int weightopt, char model[],\
4788: int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
4789: int popforecast, int estepm ,\
4790: double jprev1, double mprev1,double anprev1, \
4791: double jprev2, double mprev2,double anprev2){
4792: int jj1, k1, i1, cpt;
4793:
4794: fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
4795: <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
4796: </ul>");
4797: fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \
4798: - 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 4799: jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileresu,"P_"),subdirf2(fileresu,"P_"));
1.126 brouard 4800: fprintf(fichtm,"\
4801: - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
1.201 brouard 4802: stepm,subdirf2(fileresu,"PIJ_"),subdirf2(fileresu,"PIJ_"));
1.126 brouard 4803: fprintf(fichtm,"\
4804: - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
1.201 brouard 4805: subdirf2(fileresu,"PL_"),subdirf2(fileresu,"PL_"));
1.126 brouard 4806: fprintf(fichtm,"\
1.128 brouard 4807: - (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 4808: <a href=\"%s\">%s</a> <br>\n",
1.201 brouard 4809: estepm,subdirf2(fileresu,"E_"),subdirf2(fileresu,"E_"));
1.126 brouard 4810: fprintf(fichtm,"\
4811: - Population projections by age and states: \
1.201 brouard 4812: <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileresu,"F_"),subdirf2(fileresu,"F_"));
1.126 brouard 4813:
4814: fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
4815:
1.145 brouard 4816: m=pow(2,cptcoveff);
1.126 brouard 4817: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
4818:
4819: jj1=0;
4820: for(k1=1; k1<=m;k1++){
1.192 brouard 4821: /* for(i1=1; i1<=ncodemax[k1];i1++){ */
1.126 brouard 4822: jj1++;
4823: if (cptcovn > 0) {
4824: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
1.192 brouard 4825: for (cpt=1; cpt<=cptcoveff;cpt++){
1.198 brouard 4826: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]);
4827: printf(" V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]);fflush(stdout);
1.192 brouard 4828: }
1.126 brouard 4829: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
4830: }
1.201 brouard 4831: /* aij, bij */
4832: 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> \
4833: <img src=\"%s_%d-1.svg\">",subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1);
1.126 brouard 4834: /* Pij */
1.202 brouard 4835: 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 4836: <img src=\"%s_%d-2.svg\">",stepm,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1);
1.126 brouard 4837: /* Quasi-incidences */
1.201 brouard 4838: fprintf(fichtm,"<br>\n- Iij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
4839: before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too,\
4840: incidence (rates) are the limit when h tends to zero of the ratio of the probability hPij \
4841: divided by h: hPij/h : <a href=\"%s_%d-3.svg\">%s_%d-3.svg</a><br> \
4842: <img src=\"%s_%d-3.svg\">",stepm,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1);
4843: /* Survival functions (period) in state j */
4844: for(cpt=1; cpt<=nlstate;cpt++){
4845: 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> \
4846: <img src=\"%s_%d-%d.svg\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"LIJ_"),cpt,jj1,subdirf2(optionfilefiname,"LIJ_"),cpt,jj1,subdirf2(optionfilefiname,"LIJ_"),cpt,jj1);
4847: }
4848: /* State specific survival functions (period) */
4849: for(cpt=1; cpt<=nlstate;cpt++){
1.208 ! brouard 4850: fprintf(fichtm,"<br>\n- Survival functions from state %d in each live state and total.\
1.201 brouard 4851: Or probability to survive in various states (1 to %d) being in state %d at different ages.\
4852: <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);
4853: }
4854: /* Period (stable) prevalence in each health state */
4855: for(cpt=1; cpt<=nlstate;cpt++){
4856: 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> \
4857: <img src=\"%s_%d-%d.svg\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"P_"),cpt,jj1,subdirf2(optionfilefiname,"P_"),cpt,jj1,subdirf2(optionfilefiname,"P_"),cpt,jj1);
4858: }
1.126 brouard 4859: for(cpt=1; cpt<=nlstate;cpt++) {
1.205 brouard 4860: 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 4861: <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 4862: }
1.192 brouard 4863: /* } /\* end i1 *\/ */
1.126 brouard 4864: }/* End k1 */
4865: fprintf(fichtm,"</ul>");
4866:
4867: fprintf(fichtm,"\
4868: \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
1.193 brouard 4869: - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br> \
1.203 brouard 4870: - 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 4871: But because parameters are usually highly correlated (a higher incidence of disability \
4872: and a higher incidence of recovery can give very close observed transition) it might \
4873: be very useful to look not only at linear confidence intervals estimated from the \
4874: variances but at the covariance matrix. And instead of looking at the estimated coefficients \
4875: (parameters) of the logistic regression, it might be more meaningful to visualize the \
4876: covariance matrix of the one-step probabilities. \
4877: See page 'Matrix of variance-covariance of one-step probabilities' below. \n", rfileres,rfileres);
1.126 brouard 4878:
1.193 brouard 4879: fprintf(fichtm," - Standard deviation of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
1.201 brouard 4880: subdirf2(fileresu,"PROB_"),subdirf2(fileresu,"PROB_"));
1.126 brouard 4881: fprintf(fichtm,"\
4882: - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
1.201 brouard 4883: subdirf2(fileresu,"PROBCOV_"),subdirf2(fileresu,"PROBCOV_"));
1.126 brouard 4884:
4885: fprintf(fichtm,"\
4886: - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
1.201 brouard 4887: subdirf2(fileresu,"PROBCOR_"),subdirf2(fileresu,"PROBCOR_"));
1.126 brouard 4888: fprintf(fichtm,"\
4889: - 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): \
4890: <a href=\"%s\">%s</a> <br>\n</li>",
1.201 brouard 4891: estepm,subdirf2(fileresu,"CVE_"),subdirf2(fileresu,"CVE_"));
1.126 brouard 4892: fprintf(fichtm,"\
4893: - (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): \
4894: <a href=\"%s\">%s</a> <br>\n</li>",
1.201 brouard 4895: estepm,subdirf2(fileresu,"STDE_"),subdirf2(fileresu,"STDE_"));
1.126 brouard 4896: fprintf(fichtm,"\
1.128 brouard 4897: - 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 4898: estepm, subdirf2(fileresu,"V_"),subdirf2(fileresu,"V_"));
1.126 brouard 4899: fprintf(fichtm,"\
1.128 brouard 4900: - 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 4901: estepm, subdirf2(fileresu,"T_"),subdirf2(fileresu,"T_"));
1.126 brouard 4902: fprintf(fichtm,"\
4903: - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
1.201 brouard 4904: subdirf2(fileresu,"VPL_"),subdirf2(fileresu,"VPL_"));
1.126 brouard 4905:
4906: /* if(popforecast==1) fprintf(fichtm,"\n */
4907: /* - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
4908: /* - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
4909: /* <br>",fileres,fileres,fileres,fileres); */
4910: /* else */
4911: /* 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); */
4912: fflush(fichtm);
4913: fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
4914:
1.145 brouard 4915: m=pow(2,cptcoveff);
1.126 brouard 4916: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
4917:
4918: jj1=0;
4919: for(k1=1; k1<=m;k1++){
1.192 brouard 4920: /* for(i1=1; i1<=ncodemax[k1];i1++){ */
1.126 brouard 4921: jj1++;
4922: if (cptcovn > 0) {
4923: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
4924: for (cpt=1; cpt<=cptcoveff;cpt++)
1.198 brouard 4925: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]);
1.126 brouard 4926: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
4927: }
4928: for(cpt=1; cpt<=nlstate;cpt++) {
4929: fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
1.205 brouard 4930: prevalence (with 95%% confidence interval) in state (%d): <a href=\"%s_%d%d.svg\"> %s_%d-%d.svg <br>\
4931: <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 4932: }
4933: fprintf(fichtm,"\n<br>- Total life expectancy by age and \
1.128 brouard 4934: health expectancies in states (1) and (2). If popbased=1 the smooth (due to the model) \
4935: true period expectancies (those weighted with period prevalences are also\
4936: drawn in addition to the population based expectancies computed using\
1.205 brouard 4937: observed and cahotic prevalences: <a href=\"%s_%d.svg\">%s_%d.svg<br>\
4938: <img src=\"%s_%d.svg\">",subdirf2(optionfilefiname,"E_"),jj1,subdirf2(optionfilefiname,"E_"),jj1,subdirf2(optionfilefiname,"E_"),jj1);
1.192 brouard 4939: /* } /\* end i1 *\/ */
1.126 brouard 4940: }/* End k1 */
4941: fprintf(fichtm,"</ul>");
4942: fflush(fichtm);
4943: }
4944:
4945: /******************* Gnuplot file **************/
1.201 brouard 4946: void printinggnuplot(char fileresu[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
1.126 brouard 4947:
4948: char dirfileres[132],optfileres[132];
1.164 brouard 4949: int cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,ij=0,l=0;
1.130 brouard 4950: int ng=0;
1.201 brouard 4951: int vpopbased;
1.126 brouard 4952: /* if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
4953: /* printf("Problem with file %s",optionfilegnuplot); */
4954: /* fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
4955: /* } */
4956:
4957: /*#ifdef windows */
4958: fprintf(ficgp,"cd \"%s\" \n",pathc);
4959: /*#endif */
4960: m=pow(2,cptcoveff);
4961:
1.202 brouard 4962: /* Contribution to likelihood */
4963: /* Plot the probability implied in the likelihood */
4964: fprintf(ficgp,"\n# Contributions to the Likelihood, mle >=1. For mle=4 no interpolation, pure matrix products.\n#\n");
4965: fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Likelihood (-2Log(L))\";");
4966: /* fprintf(ficgp,"\nset ter svg size 640, 480"); */ /* Too big for svg */
1.205 brouard 4967: fprintf(ficgp,"\nset ter pngcairo size 640, 480");
1.204 brouard 4968: /* nice for mle=4 plot by number of matrix products.
1.202 brouard 4969: replot "rrtest1/toto.txt" u 2:($4 == 1 && $5==2 ? $9 : 1/0):5 t "p12" with point lc 1 */
4970: /* replot exp(p1+p2*x)/(1+exp(p1+p2*x)+exp(p3+p4*x)+exp(p5+p6*x)) t "p12(x)" */
4971: /* fprintf(ficgp,"\nset out \"%s.svg\";",subdirf2(optionfilefiname,"ILK_")); */
1.204 brouard 4972: fprintf(ficgp,"\nset out \"%s-dest.png\";",subdirf2(optionfilefiname,"ILK_"));
1.205 brouard 4973: 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 4974: fprintf(ficgp,"\nset out \"%s-ori.png\";",subdirf2(optionfilefiname,"ILK_"));
1.205 brouard 4975: 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 4976: for (i=1; i<= nlstate ; i ++) {
4977: fprintf(ficgp,"\nset out \"%s-p%dj.png\";set ylabel \"Probability for each individual/wave\";",subdirf2(optionfilefiname,"ILK_"),i);
1.205 brouard 4978: fprintf(ficgp,"unset log;\n# plot weighted, mean weight should have point size of 0.5\n plot \"%s\"",subdirf(fileresilk));
4979: 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 4980: for (j=2; j<= nlstate+ndeath ; j ++) {
1.205 brouard 4981: 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 4982: }
4983: fprintf(ficgp,";\nset out; unset ylabel;\n");
4984: }
4985: /* 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 */
4986: /* fprintf(ficgp,"\nset log y;plot \"%s\" u 2:(-$11):3 t \"All sample, all transitions\" with dots lc variable",subdirf(fileresilk)); */
4987: /* 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 4988: fprintf(ficgp,"\nset out;unset log\n");
1.202 brouard 4989: /* fprintf(ficgp,"\nset out \"%s.svg\"; replot; set out; # bug gnuplot",subdirf2(optionfilefiname,"ILK_")); */
4990:
1.126 brouard 4991: strcpy(dirfileres,optionfilefiname);
4992: strcpy(optfileres,"vpl");
4993: /* 1eme*/
1.201 brouard 4994: fprintf(ficgp,"\n# 1st: Period (stable) prevalence with CI: 'VPL_' files\n");
1.126 brouard 4995: for (cpt=1; cpt<= nlstate ; cpt ++) {
1.145 brouard 4996: for (k1=1; k1<= m ; k1 ++) { /* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */
1.201 brouard 4997: fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"V_"),cpt,k1);
4998: fprintf(ficgp,"\n#set out \"V_%s_%d-%d.svg\" \n",optionfilefiname,cpt,k1);
1.126 brouard 4999: fprintf(ficgp,"set xlabel \"Age\" \n\
5000: set ylabel \"Probability\" \n\
1.199 brouard 5001: set ter svg size 640, 480\n\
1.201 brouard 5002: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"%%lf",ageminpar,fage,subdirf2(fileresu,"VPL_"),k1-1,k1-1);
1.126 brouard 5003:
5004: for (i=1; i<= nlstate ; i ++) {
1.170 brouard 5005: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
5006: else fprintf(ficgp," %%*lf (%%*lf)");
1.126 brouard 5007: }
1.201 brouard 5008: 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 5009: for (i=1; i<= nlstate ; i ++) {
1.170 brouard 5010: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
5011: else fprintf(ficgp," %%*lf (%%*lf)");
1.126 brouard 5012: }
1.201 brouard 5013: fprintf(ficgp,"\" t\"95%% CI\" w l lt 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"%%lf",subdirf2(fileresu,"VPL_"),k1-1,k1-1);
1.126 brouard 5014: for (i=1; i<= nlstate ; i ++) {
1.170 brouard 5015: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
5016: else fprintf(ficgp," %%*lf (%%*lf)");
1.126 brouard 5017: }
1.201 brouard 5018: fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l lt 2",subdirf2(fileresu,"P_"),k1-1,k1-1,2+4*(cpt-1));
5019: fprintf(ficgp,"\nset out \n");
5020: } /* k1 */
5021: } /* cpt */
1.126 brouard 5022: /*2 eme*/
1.153 brouard 5023: fprintf(ficgp,"\n# 2nd: Total life expectancy with CI: 't' files\n");
1.126 brouard 5024: for (k1=1; k1<= m ; k1 ++) {
1.201 brouard 5025: fprintf(ficgp,"\nset out \"%s_%d.svg\" \n",subdirf2(optionfilefiname,"E_"),k1);
5026: for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
5027: if(vpopbased==0)
5028: fprintf(ficgp,"set ylabel \"Years\" \nset ter svg size 640, 480\nplot [%.f:%.f] ",ageminpar,fage);
5029: else
5030: fprintf(ficgp,"\nreplot ");
5031: for (i=1; i<= nlstate+1 ; i ++) {
5032: k=2*i;
5033: 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);
5034: for (j=1; j<= nlstate+1 ; j ++) {
5035: if (j==i) fprintf(ficgp," %%lf (%%lf)");
5036: else fprintf(ficgp," %%*lf (%%*lf)");
5037: }
5038: if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l lt %d, \\\n",i);
5039: else fprintf(ficgp,"\" t\"LE in state (%d)\" w l lt %d, \\\n",i-1,i+1);
5040: 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);
5041: for (j=1; j<= nlstate+1 ; j ++) {
5042: if (j==i) fprintf(ficgp," %%lf (%%lf)");
5043: else fprintf(ficgp," %%*lf (%%*lf)");
5044: }
5045: fprintf(ficgp,"\" t\"\" w l lt 0,");
5046: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2==%d && $4!=0 ? $4+$5*2 : 1/0) \"%%lf %%lf %%lf",subdirf2(fileresu,"T_"),k1-1,k1-1,vpopbased);
5047: for (j=1; j<= nlstate+1 ; j ++) {
5048: if (j==i) fprintf(ficgp," %%lf (%%lf)");
5049: else fprintf(ficgp," %%*lf (%%*lf)");
5050: }
5051: if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l lt 0");
5052: else fprintf(ficgp,"\" t\"\" w l lt 0,\\\n");
5053: } /* state */
5054: } /* vpopbased */
5055: fprintf(ficgp,"\nset out;set out \"%s_%d.svg\"; replot; set out; \n",subdirf2(optionfilefiname,"E_"),k1); /* Buggy gnuplot */
5056: } /* k1 */
1.126 brouard 5057: /*3eme*/
5058:
5059: for (k1=1; k1<= m ; k1 ++) {
5060: for (cpt=1; cpt<= nlstate ; cpt ++) {
5061: /* k=2+nlstate*(2*cpt-2); */
5062: k=2+(nlstate+1)*(cpt-1);
1.201 brouard 5063: fprintf(ficgp,"\nset out \"%s_%d%d.svg\" \n",subdirf2(optionfilefiname,"EXP_"),cpt,k1);
1.199 brouard 5064: fprintf(ficgp,"set ter svg size 640, 480\n\
1.201 brouard 5065: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileresu,"E_"),k1-1,k1-1,k,cpt);
1.126 brouard 5066: /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
5067: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
5068: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
5069: fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
5070: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
5071: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
5072:
5073: */
5074: for (i=1; i< nlstate ; i ++) {
1.201 brouard 5075: 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 5076: /* 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);*/
5077:
5078: }
1.201 brouard 5079: 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 5080: }
5081: }
5082:
1.201 brouard 5083: /* Survival functions (period) from state i in state j by initial state i */
5084: for (k1=1; k1<= m ; k1 ++) { /* For each multivariate if any */
5085: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
5086: k=3;
5087: fprintf(ficgp,"\n#\n#\n# Survival functions in state j : 'lij' files, cov=%d state=%d",k1, cpt);
5088: fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"LIJ_"),cpt,k1);
5089: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability to be alive\" \n\
5090: set ter svg size 640, 480\n\
5091: unset log y\n\
5092: plot [%.f:%.f] ", ageminpar, agemaxpar);
5093: for (i=1; i<= nlstate ; i ++){
5094: if(i==1)
5095: fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
5096: else
5097: fprintf(ficgp,", '' ");
5098: l=(nlstate+ndeath)*(i-1)+1;
5099: fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
5100: for (j=2; j<= nlstate+ndeath ; j ++)
5101: fprintf(ficgp,"+$%d",k+l+j-1);
5102: fprintf(ficgp,")) t \"l(%d,%d)\" w l",i,cpt);
5103: } /* nlstate */
5104: fprintf(ficgp,"\nset out\n");
5105: } /* end cpt state*/
5106: } /* end covariate */
5107:
5108: /* Survival functions (period) from state i in state j by final state j */
1.202 brouard 5109: for (k1=1; k1<= m ; k1 ++) { /* For each covariate if any */
1.201 brouard 5110: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each inital state */
5111: k=3;
5112: 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);
5113: fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"LIJT_"),cpt,k1);
5114: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability to be alive\" \n\
5115: set ter svg size 640, 480\n\
5116: unset log y\n\
5117: plot [%.f:%.f] ", ageminpar, agemaxpar);
5118: for (j=1; j<= nlstate ; j ++){ /* Lived in state j */
5119: if(j==1)
5120: fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
5121: else
5122: fprintf(ficgp,", '' ");
5123: l=(nlstate+ndeath)*(cpt-1) +j;
5124: fprintf(ficgp," u (($1==%d && (floor($2)%%5 == 0)) ? ($3):1/0):($%d",k1,k+l);
5125: /* for (i=2; i<= nlstate+ndeath ; i ++) */
5126: /* fprintf(ficgp,"+$%d",k+l+i-1); */
5127: fprintf(ficgp,") t \"l(%d,%d)\" w l",cpt,j);
5128: } /* nlstate */
5129: fprintf(ficgp,", '' ");
5130: fprintf(ficgp," u (($1==%d && (floor($2)%%5 == 0)) ? ($3):1/0):(",k1);
5131: for (j=1; j<= nlstate ; j ++){ /* Lived in state j */
5132: l=(nlstate+ndeath)*(cpt-1) +j;
5133: if(j < nlstate)
5134: fprintf(ficgp,"$%d +",k+l);
5135: else
5136: fprintf(ficgp,"$%d) t\"l(%d,.)\" w l",k+l,cpt);
5137: }
5138: fprintf(ficgp,"\nset out\n");
5139: } /* end cpt state*/
5140: } /* end covariate */
5141:
1.202 brouard 5142: /* CV preval stable (period) for each covariate */
5143: for (k1=1; k1<= m ; k1 ++) { /* For each covariate if any */
1.153 brouard 5144: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
1.126 brouard 5145: k=3;
1.153 brouard 5146: fprintf(ficgp,"\n#\n#\n#CV preval stable (period): 'pij' files, cov=%d state=%d",k1, cpt);
1.201 brouard 5147: fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"P_"),cpt,k1);
1.126 brouard 5148: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
1.199 brouard 5149: set ter svg size 640, 480\n\
1.126 brouard 5150: unset log y\n\
1.153 brouard 5151: plot [%.f:%.f] ", ageminpar, agemaxpar);
5152: for (i=1; i<= nlstate ; i ++){
5153: if(i==1)
1.201 brouard 5154: fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
1.153 brouard 5155: else
5156: fprintf(ficgp,", '' ");
1.154 brouard 5157: l=(nlstate+ndeath)*(i-1)+1;
5158: fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
1.201 brouard 5159: for (j=2; j<= nlstate ; j ++)
5160: fprintf(ficgp,"+$%d",k+l+j-1);
1.153 brouard 5161: fprintf(ficgp,")) t \"prev(%d,%d)\" w l",i,cpt);
5162: } /* nlstate */
1.201 brouard 5163: fprintf(ficgp,"\nset out\n");
1.153 brouard 5164: } /* end cpt state*/
5165: } /* end covariate */
1.201 brouard 5166:
1.126 brouard 5167: /* proba elementaires */
1.187 brouard 5168: fprintf(ficgp,"\n##############\n#MLE estimated parameters\n#############\n");
1.126 brouard 5169: for(i=1,jk=1; i <=nlstate; i++){
1.187 brouard 5170: fprintf(ficgp,"# initial state %d\n",i);
1.126 brouard 5171: for(k=1; k <=(nlstate+ndeath); k++){
5172: if (k != i) {
1.187 brouard 5173: fprintf(ficgp,"# current state %d\n",k);
1.126 brouard 5174: for(j=1; j <=ncovmodel; j++){
1.187 brouard 5175: fprintf(ficgp,"p%d=%f; ",jk,p[jk]);
1.126 brouard 5176: jk++;
5177: }
1.187 brouard 5178: fprintf(ficgp,"\n");
1.126 brouard 5179: }
5180: }
5181: }
1.187 brouard 5182: fprintf(ficgp,"##############\n#\n");
5183:
1.145 brouard 5184: /*goto avoid;*/
1.200 brouard 5185: fprintf(ficgp,"\n##############\n#Graphics of probabilities or incidences\n#############\n");
1.187 brouard 5186: fprintf(ficgp,"# logi(p12/p11)=a12+b12*age+c12age*age+d12*V1+e12*V1*age\n");
5187: fprintf(ficgp,"# logi(p12/p11)=p1 +p2*age +p3*age*age+ p4*V1+ p5*V1*age\n");
5188: fprintf(ficgp,"# logi(p13/p11)=a13+b13*age+c13age*age+d13*V1+e13*V1*age\n");
5189: fprintf(ficgp,"# logi(p13/p11)=p6 +p7*age +p8*age*age+ p9*V1+ p10*V1*age\n");
5190: fprintf(ficgp,"# p12+p13+p14+p11=1=p11(1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n");
5191: fprintf(ficgp,"# +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age)+...)\n");
5192: fprintf(ficgp,"# p11=1/(1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n");
5193: fprintf(ficgp,"# +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age)+...)\n");
5194: fprintf(ficgp,"# p12=exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)/\n");
5195: fprintf(ficgp,"# (1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n");
5196: fprintf(ficgp,"# +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age))\n");
5197: fprintf(ficgp,"# +exp(a14+b14*age+c14age*age+d14*V1+e14*V1*age)+...)\n");
5198: fprintf(ficgp,"#\n");
1.201 brouard 5199: for(ng=1; ng<=3;ng++){ /* Number of graphics: first is logit, 2nd is probabilities, third is incidences per year*/
1.187 brouard 5200: fprintf(ficgp,"# ng=%d\n",ng);
5201: fprintf(ficgp,"# jk=1 to 2^%d=%d\n",cptcoveff,m);
1.126 brouard 5202: for(jk=1; jk <=m; jk++) {
1.187 brouard 5203: fprintf(ficgp,"# jk=%d\n",jk);
1.201 brouard 5204: fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" ",subdirf2(optionfilefiname,"PE_"),jk,ng);
5205: fprintf(ficgp,"\nset ter svg size 640, 480 ");
5206: if (ng==1){
5207: fprintf(ficgp,"\nset ylabel \"Value of the logit of the model\"\n"); /* exp(a12+b12*x) could be nice */
5208: fprintf(ficgp,"\nunset log y");
5209: }else if (ng==2){
5210: fprintf(ficgp,"\nset ylabel \"Probability\"\n");
5211: fprintf(ficgp,"\nset log y");
5212: }else if (ng==3){
1.126 brouard 5213: fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
1.201 brouard 5214: fprintf(ficgp,"\nset log y");
5215: }else
5216: fprintf(ficgp,"\nunset title ");
5217: fprintf(ficgp,"\nplot [%.f:%.f] ",ageminpar,agemaxpar);
1.126 brouard 5218: i=1;
5219: for(k2=1; k2<=nlstate; k2++) {
5220: k3=i;
5221: for(k=1; k<=(nlstate+ndeath); k++) {
5222: if (k != k2){
1.201 brouard 5223: switch( ng) {
5224: case 1:
1.187 brouard 5225: if(nagesqr==0)
1.201 brouard 5226: fprintf(ficgp," p%d+p%d*x",i,i+1);
1.187 brouard 5227: else /* nagesqr =1 */
1.201 brouard 5228: fprintf(ficgp," p%d+p%d*x+p%d*x*x",i,i+1,i+1+nagesqr);
5229: break;
5230: case 2: /* ng=2 */
1.187 brouard 5231: if(nagesqr==0)
5232: fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
5233: else /* nagesqr =1 */
1.201 brouard 5234: fprintf(ficgp," exp(p%d+p%d*x+p%d*x*x",i,i+1,i+1+nagesqr);
5235: break;
5236: case 3:
5237: if(nagesqr==0)
5238: fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
5239: else /* nagesqr =1 */
5240: fprintf(ficgp," %f*exp(p%d+p%d*x+p%d*x*x",YEARM/stepm,i,i+1,i+1+nagesqr);
5241: break;
5242: }
1.141 brouard 5243: ij=1;/* To be checked else nbcode[0][0] wrong */
1.187 brouard 5244: for(j=3; j <=ncovmodel-nagesqr; j++) {
1.197 brouard 5245: /* printf("Tage[%d]=%d, j=%d\n", ij, Tage[ij], j); */
5246: if(ij <=cptcovage) { /* Bug valgrind */
5247: if((j-2)==Tage[ij]) { /* Bug valgrind */
1.200 brouard 5248: fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);
5249: /* fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(jk,Tvar[j-2])]); */
1.197 brouard 5250: ij++;
5251: }
1.186 brouard 5252: }
5253: else
1.198 brouard 5254: fprintf(ficgp,"+p%d*%d",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);
1.126 brouard 5255: }
1.201 brouard 5256: if(ng != 1){
5257: fprintf(ficgp,")/(1");
1.126 brouard 5258:
1.201 brouard 5259: for(k1=1; k1 <=nlstate; k1++){
5260: if(nagesqr==0)
5261: fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
5262: else /* nagesqr =1 */
5263: 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);
5264:
5265: ij=1;
5266: for(j=3; j <=ncovmodel-nagesqr; j++){
5267: if(ij <=cptcovage) { /* Bug valgrind */
5268: if((j-2)==Tage[ij]) { /* Bug valgrind */
5269: fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);
5270: /* fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(jk,Tvar[j-2])]); */
5271: ij++;
5272: }
1.197 brouard 5273: }
1.201 brouard 5274: else
5275: fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);
1.186 brouard 5276: }
1.201 brouard 5277: fprintf(ficgp,")");
1.126 brouard 5278: }
5279: fprintf(ficgp,")");
1.201 brouard 5280: if(ng ==2)
5281: fprintf(ficgp," t \"p%d%d\" ", k2,k);
5282: else /* ng= 3 */
5283: fprintf(ficgp," t \"i%d%d\" ", k2,k);
5284: }else{ /* end ng <> 1 */
5285: fprintf(ficgp," t \"logit(p%d%d)\" ", k2,k);
1.126 brouard 5286: }
5287: if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
5288: i=i+ncovmodel;
5289: }
5290: } /* end k */
5291: } /* end k2 */
1.201 brouard 5292: fprintf(ficgp,"\n set out\n");
1.126 brouard 5293: } /* end jk */
5294: } /* end ng */
1.164 brouard 5295: /* avoid: */
1.126 brouard 5296: fflush(ficgp);
5297: } /* end gnuplot */
5298:
5299:
5300: /*************** Moving average **************/
5301: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
5302:
5303: int i, cpt, cptcod;
5304: int modcovmax =1;
5305: int mobilavrange, mob;
5306: double age;
5307:
5308: modcovmax=2*cptcoveff;/* Max number of modalities. We suppose
5309: a covariate has 2 modalities */
5310: if (cptcovn<1) modcovmax=1; /* At least 1 pass */
5311:
5312: if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
5313: if(mobilav==1) mobilavrange=5; /* default */
5314: else mobilavrange=mobilav;
5315: for (age=bage; age<=fage; age++)
5316: for (i=1; i<=nlstate;i++)
5317: for (cptcod=1;cptcod<=modcovmax;cptcod++)
5318: mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
5319: /* We keep the original values on the extreme ages bage, fage and for
5320: fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
5321: we use a 5 terms etc. until the borders are no more concerned.
5322: */
5323: for (mob=3;mob <=mobilavrange;mob=mob+2){
5324: for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
5325: for (i=1; i<=nlstate;i++){
5326: for (cptcod=1;cptcod<=modcovmax;cptcod++){
5327: mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
5328: for (cpt=1;cpt<=(mob-1)/2;cpt++){
5329: mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
5330: mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
5331: }
5332: mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
5333: }
5334: }
5335: }/* end age */
5336: }/* end mob */
5337: }else return -1;
5338: return 0;
5339: }/* End movingaverage */
5340:
5341:
5342: /************** Forecasting ******************/
1.169 brouard 5343: 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 5344: /* proj1, year, month, day of starting projection
5345: agemin, agemax range of age
5346: dateprev1 dateprev2 range of dates during which prevalence is computed
5347: anproj2 year of en of projection (same day and month as proj1).
5348: */
1.164 brouard 5349: int yearp, stepsize, hstepm, nhstepm, j, k, cptcod, i, h, i1;
1.126 brouard 5350: double agec; /* generic age */
5351: double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
5352: double *popeffectif,*popcount;
5353: double ***p3mat;
5354: double ***mobaverage;
5355: char fileresf[FILENAMELENGTH];
5356:
5357: agelim=AGESUP;
5358: prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
5359:
1.201 brouard 5360: strcpy(fileresf,"F_");
5361: strcat(fileresf,fileresu);
1.126 brouard 5362: if((ficresf=fopen(fileresf,"w"))==NULL) {
5363: printf("Problem with forecast resultfile: %s\n", fileresf);
5364: fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
5365: }
5366: printf("Computing forecasting: result on file '%s' \n", fileresf);
5367: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
5368:
5369: if (cptcoveff==0) ncodemax[cptcoveff]=1;
5370:
5371: if (mobilav!=0) {
5372: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
5373: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
5374: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
5375: printf(" Error in movingaverage mobilav=%d\n",mobilav);
5376: }
5377: }
5378:
5379: stepsize=(int) (stepm+YEARM-1)/YEARM;
5380: if (stepm<=12) stepsize=1;
5381: if(estepm < stepm){
5382: printf ("Problem %d lower than %d\n",estepm, stepm);
5383: }
5384: else hstepm=estepm;
5385:
5386: hstepm=hstepm/stepm;
5387: yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp and
5388: fractional in yp1 */
5389: anprojmean=yp;
5390: yp2=modf((yp1*12),&yp);
5391: mprojmean=yp;
5392: yp1=modf((yp2*30.5),&yp);
5393: jprojmean=yp;
5394: if(jprojmean==0) jprojmean=1;
5395: if(mprojmean==0) jprojmean=1;
5396:
5397: i1=cptcoveff;
5398: if (cptcovn < 1){i1=1;}
5399:
5400: fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);
5401:
5402: fprintf(ficresf,"#****** Routine prevforecast **\n");
5403:
5404: /* if (h==(int)(YEARM*yearp)){ */
5405: for(cptcov=1, k=0;cptcov<=i1;cptcov++){
5406: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
5407: k=k+1;
5408: fprintf(ficresf,"\n#******");
5409: for(j=1;j<=cptcoveff;j++) {
1.198 brouard 5410: 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 5411: }
5412: fprintf(ficresf,"******\n");
5413: fprintf(ficresf,"# Covariate valuofcovar yearproj age");
5414: for(j=1; j<=nlstate+ndeath;j++){
5415: for(i=1; i<=nlstate;i++)
5416: fprintf(ficresf," p%d%d",i,j);
5417: fprintf(ficresf," p.%d",j);
5418: }
5419: for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {
5420: fprintf(ficresf,"\n");
5421: fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);
5422:
5423: for (agec=fage; agec>=(ageminpar-1); agec--){
5424: nhstepm=(int) rint((agelim-agec)*YEARM/stepm);
5425: nhstepm = nhstepm/hstepm;
5426: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5427: oldm=oldms;savm=savms;
5428: hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);
5429:
5430: for (h=0; h<=nhstepm; h++){
5431: if (h*hstepm/YEARM*stepm ==yearp) {
5432: fprintf(ficresf,"\n");
5433: for(j=1;j<=cptcoveff;j++)
1.198 brouard 5434: fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.126 brouard 5435: fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
5436: }
5437: for(j=1; j<=nlstate+ndeath;j++) {
5438: ppij=0.;
5439: for(i=1; i<=nlstate;i++) {
5440: if (mobilav==1)
5441: ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
5442: else {
5443: ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
5444: }
5445: if (h*hstepm/YEARM*stepm== yearp) {
5446: fprintf(ficresf," %.3f", p3mat[i][j][h]);
5447: }
5448: } /* end i */
5449: if (h*hstepm/YEARM*stepm==yearp) {
5450: fprintf(ficresf," %.3f", ppij);
5451: }
5452: }/* end j */
5453: } /* end h */
5454: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5455: } /* end agec */
5456: } /* end yearp */
5457: } /* end cptcod */
5458: } /* end cptcov */
5459:
5460: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
5461:
5462: fclose(ficresf);
5463: }
5464:
5465: /************** Forecasting *****not tested NB*************/
1.169 brouard 5466: 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 5467:
5468: int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
5469: int *popage;
5470: double calagedatem, agelim, kk1, kk2;
5471: double *popeffectif,*popcount;
5472: double ***p3mat,***tabpop,***tabpopprev;
5473: double ***mobaverage;
5474: char filerespop[FILENAMELENGTH];
5475:
5476: tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
5477: tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
5478: agelim=AGESUP;
5479: calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
5480:
5481: prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
5482:
5483:
1.201 brouard 5484: strcpy(filerespop,"POP_");
5485: strcat(filerespop,fileresu);
1.126 brouard 5486: if((ficrespop=fopen(filerespop,"w"))==NULL) {
5487: printf("Problem with forecast resultfile: %s\n", filerespop);
5488: fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
5489: }
5490: printf("Computing forecasting: result on file '%s' \n", filerespop);
5491: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
5492:
5493: if (cptcoveff==0) ncodemax[cptcoveff]=1;
5494:
5495: if (mobilav!=0) {
5496: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
5497: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
5498: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
5499: printf(" Error in movingaverage mobilav=%d\n",mobilav);
5500: }
5501: }
5502:
5503: stepsize=(int) (stepm+YEARM-1)/YEARM;
5504: if (stepm<=12) stepsize=1;
5505:
5506: agelim=AGESUP;
5507:
5508: hstepm=1;
5509: hstepm=hstepm/stepm;
5510:
5511: if (popforecast==1) {
5512: if((ficpop=fopen(popfile,"r"))==NULL) {
5513: printf("Problem with population file : %s\n",popfile);exit(0);
5514: fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
5515: }
5516: popage=ivector(0,AGESUP);
5517: popeffectif=vector(0,AGESUP);
5518: popcount=vector(0,AGESUP);
5519:
5520: i=1;
5521: while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
5522:
5523: imx=i;
5524: for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
5525: }
5526:
5527: for(cptcov=1,k=0;cptcov<=i2;cptcov++){
5528: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
5529: k=k+1;
5530: fprintf(ficrespop,"\n#******");
5531: for(j=1;j<=cptcoveff;j++) {
1.198 brouard 5532: fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.126 brouard 5533: }
5534: fprintf(ficrespop,"******\n");
5535: fprintf(ficrespop,"# Age");
5536: for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
5537: if (popforecast==1) fprintf(ficrespop," [Population]");
5538:
5539: for (cpt=0; cpt<=0;cpt++) {
5540: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
5541:
5542: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
5543: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
5544: nhstepm = nhstepm/hstepm;
5545:
5546: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5547: oldm=oldms;savm=savms;
5548: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
5549:
5550: for (h=0; h<=nhstepm; h++){
5551: if (h==(int) (calagedatem+YEARM*cpt)) {
5552: fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
5553: }
5554: for(j=1; j<=nlstate+ndeath;j++) {
5555: kk1=0.;kk2=0;
5556: for(i=1; i<=nlstate;i++) {
5557: if (mobilav==1)
5558: kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
5559: else {
5560: kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
5561: }
5562: }
5563: if (h==(int)(calagedatem+12*cpt)){
5564: tabpop[(int)(agedeb)][j][cptcod]=kk1;
5565: /*fprintf(ficrespop," %.3f", kk1);
5566: if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
5567: }
5568: }
5569: for(i=1; i<=nlstate;i++){
5570: kk1=0.;
5571: for(j=1; j<=nlstate;j++){
5572: kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];
5573: }
5574: tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
5575: }
5576:
5577: if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++)
5578: fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
5579: }
5580: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5581: }
5582: }
5583:
5584: /******/
5585:
5586: for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {
5587: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
5588: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
5589: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
5590: nhstepm = nhstepm/hstepm;
5591:
5592: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5593: oldm=oldms;savm=savms;
5594: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
5595: for (h=0; h<=nhstepm; h++){
5596: if (h==(int) (calagedatem+YEARM*cpt)) {
5597: fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
5598: }
5599: for(j=1; j<=nlstate+ndeath;j++) {
5600: kk1=0.;kk2=0;
5601: for(i=1; i<=nlstate;i++) {
5602: kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];
5603: }
5604: if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);
5605: }
5606: }
5607: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5608: }
5609: }
5610: }
5611: }
5612:
5613: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
5614:
5615: if (popforecast==1) {
5616: free_ivector(popage,0,AGESUP);
5617: free_vector(popeffectif,0,AGESUP);
5618: free_vector(popcount,0,AGESUP);
5619: }
5620: free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
5621: free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
5622: fclose(ficrespop);
5623: } /* End of popforecast */
5624:
5625: int fileappend(FILE *fichier, char *optionfich)
5626: {
5627: if((fichier=fopen(optionfich,"a"))==NULL) {
5628: printf("Problem with file: %s\n", optionfich);
5629: fprintf(ficlog,"Problem with file: %s\n", optionfich);
5630: return (0);
5631: }
5632: fflush(fichier);
5633: return (1);
5634: }
5635:
5636:
5637: /**************** function prwizard **********************/
5638: void prwizard(int ncovmodel, int nlstate, int ndeath, char model[], FILE *ficparo)
5639: {
5640:
5641: /* Wizard to print covariance matrix template */
5642:
1.164 brouard 5643: char ca[32], cb[32];
5644: int i,j, k, li, lj, lk, ll, jj, npar, itimes;
1.126 brouard 5645: int numlinepar;
5646:
5647: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
5648: fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
5649: for(i=1; i <=nlstate; i++){
5650: jj=0;
5651: for(j=1; j <=nlstate+ndeath; j++){
5652: if(j==i) continue;
5653: jj++;
5654: /*ca[0]= k+'a'-1;ca[1]='\0';*/
5655: printf("%1d%1d",i,j);
5656: fprintf(ficparo,"%1d%1d",i,j);
5657: for(k=1; k<=ncovmodel;k++){
5658: /* printf(" %lf",param[i][j][k]); */
5659: /* fprintf(ficparo," %lf",param[i][j][k]); */
5660: printf(" 0.");
5661: fprintf(ficparo," 0.");
5662: }
5663: printf("\n");
5664: fprintf(ficparo,"\n");
5665: }
5666: }
5667: printf("# Scales (for hessian or gradient estimation)\n");
5668: fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
5669: npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
5670: for(i=1; i <=nlstate; i++){
5671: jj=0;
5672: for(j=1; j <=nlstate+ndeath; j++){
5673: if(j==i) continue;
5674: jj++;
5675: fprintf(ficparo,"%1d%1d",i,j);
5676: printf("%1d%1d",i,j);
5677: fflush(stdout);
5678: for(k=1; k<=ncovmodel;k++){
5679: /* printf(" %le",delti3[i][j][k]); */
5680: /* fprintf(ficparo," %le",delti3[i][j][k]); */
5681: printf(" 0.");
5682: fprintf(ficparo," 0.");
5683: }
5684: numlinepar++;
5685: printf("\n");
5686: fprintf(ficparo,"\n");
5687: }
5688: }
5689: printf("# Covariance matrix\n");
5690: /* # 121 Var(a12)\n\ */
5691: /* # 122 Cov(b12,a12) Var(b12)\n\ */
5692: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
5693: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
5694: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
5695: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
5696: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
5697: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
5698: fflush(stdout);
5699: fprintf(ficparo,"# Covariance matrix\n");
5700: /* # 121 Var(a12)\n\ */
5701: /* # 122 Cov(b12,a12) Var(b12)\n\ */
5702: /* # ...\n\ */
5703: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
5704:
5705: for(itimes=1;itimes<=2;itimes++){
5706: jj=0;
5707: for(i=1; i <=nlstate; i++){
5708: for(j=1; j <=nlstate+ndeath; j++){
5709: if(j==i) continue;
5710: for(k=1; k<=ncovmodel;k++){
5711: jj++;
5712: ca[0]= k+'a'-1;ca[1]='\0';
5713: if(itimes==1){
5714: printf("#%1d%1d%d",i,j,k);
5715: fprintf(ficparo,"#%1d%1d%d",i,j,k);
5716: }else{
5717: printf("%1d%1d%d",i,j,k);
5718: fprintf(ficparo,"%1d%1d%d",i,j,k);
5719: /* printf(" %.5le",matcov[i][j]); */
5720: }
5721: ll=0;
5722: for(li=1;li <=nlstate; li++){
5723: for(lj=1;lj <=nlstate+ndeath; lj++){
5724: if(lj==li) continue;
5725: for(lk=1;lk<=ncovmodel;lk++){
5726: ll++;
5727: if(ll<=jj){
5728: cb[0]= lk +'a'-1;cb[1]='\0';
5729: if(ll<jj){
5730: if(itimes==1){
5731: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
5732: fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
5733: }else{
5734: printf(" 0.");
5735: fprintf(ficparo," 0.");
5736: }
5737: }else{
5738: if(itimes==1){
5739: printf(" Var(%s%1d%1d)",ca,i,j);
5740: fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
5741: }else{
5742: printf(" 0.");
5743: fprintf(ficparo," 0.");
5744: }
5745: }
5746: }
5747: } /* end lk */
5748: } /* end lj */
5749: } /* end li */
5750: printf("\n");
5751: fprintf(ficparo,"\n");
5752: numlinepar++;
5753: } /* end k*/
5754: } /*end j */
5755: } /* end i */
5756: } /* end itimes */
5757:
5758: } /* end of prwizard */
5759: /******************* Gompertz Likelihood ******************************/
5760: double gompertz(double x[])
5761: {
5762: double A,B,L=0.0,sump=0.,num=0.;
5763: int i,n=0; /* n is the size of the sample */
5764:
5765: for (i=0;i<=imx-1 ; i++) {
5766: sump=sump+weight[i];
5767: /* sump=sump+1;*/
5768: num=num+1;
5769: }
5770:
5771:
5772: /* for (i=0; i<=imx; i++)
5773: 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]);*/
5774:
5775: for (i=1;i<=imx ; i++)
5776: {
5777: if (cens[i] == 1 && wav[i]>1)
5778: A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
5779:
5780: if (cens[i] == 0 && wav[i]>1)
5781: A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
5782: +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);
5783:
5784: /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
5785: if (wav[i] > 1 ) { /* ??? */
5786: L=L+A*weight[i];
5787: /* 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]);*/
5788: }
5789: }
5790:
5791: /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
5792:
5793: return -2*L*num/sump;
5794: }
5795:
1.136 brouard 5796: #ifdef GSL
5797: /******************* Gompertz_f Likelihood ******************************/
5798: double gompertz_f(const gsl_vector *v, void *params)
5799: {
5800: double A,B,LL=0.0,sump=0.,num=0.;
5801: double *x= (double *) v->data;
5802: int i,n=0; /* n is the size of the sample */
5803:
5804: for (i=0;i<=imx-1 ; i++) {
5805: sump=sump+weight[i];
5806: /* sump=sump+1;*/
5807: num=num+1;
5808: }
5809:
5810:
5811: /* for (i=0; i<=imx; i++)
5812: 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]);*/
5813: printf("x[0]=%lf x[1]=%lf\n",x[0],x[1]);
5814: for (i=1;i<=imx ; i++)
5815: {
5816: if (cens[i] == 1 && wav[i]>1)
5817: A=-x[0]/(x[1])*(exp(x[1]*(agecens[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)));
5818:
5819: if (cens[i] == 0 && wav[i]>1)
5820: A=-x[0]/(x[1])*(exp(x[1]*(agedc[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)))
5821: +log(x[0]/YEARM)+x[1]*(agedc[i]-agegomp)+log(YEARM);
5822:
5823: /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
5824: if (wav[i] > 1 ) { /* ??? */
5825: LL=LL+A*weight[i];
5826: /* 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]);*/
5827: }
5828: }
5829:
5830: /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
5831: printf("x[0]=%lf x[1]=%lf -2*LL*num/sump=%lf\n",x[0],x[1],-2*LL*num/sump);
5832:
5833: return -2*LL*num/sump;
5834: }
5835: #endif
5836:
1.126 brouard 5837: /******************* Printing html file ***********/
1.201 brouard 5838: void printinghtmlmort(char fileresu[], char title[], char datafile[], int firstpass, \
1.126 brouard 5839: int lastpass, int stepm, int weightopt, char model[],\
5840: int imx, double p[],double **matcov,double agemortsup){
5841: int i,k;
5842:
5843: fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
5844: fprintf(fichtm," mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
5845: for (i=1;i<=2;i++)
5846: 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 5847: fprintf(fichtm,"<br><br><img src=\"graphmort.svg\">");
1.126 brouard 5848: fprintf(fichtm,"</ul>");
5849:
5850: fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
5851:
5852: 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>");
5853:
5854: for (k=agegomp;k<(agemortsup-2);k++)
5855: 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]);
5856:
5857:
5858: fflush(fichtm);
5859: }
5860:
5861: /******************* Gnuplot file **************/
1.201 brouard 5862: void printinggnuplotmort(char fileresu[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
1.126 brouard 5863:
5864: char dirfileres[132],optfileres[132];
1.164 brouard 5865:
1.126 brouard 5866: int ng;
5867:
5868:
5869: /*#ifdef windows */
5870: fprintf(ficgp,"cd \"%s\" \n",pathc);
5871: /*#endif */
5872:
5873:
5874: strcpy(dirfileres,optionfilefiname);
5875: strcpy(optfileres,"vpl");
1.199 brouard 5876: fprintf(ficgp,"set out \"graphmort.svg\"\n ");
1.126 brouard 5877: fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n ");
1.199 brouard 5878: fprintf(ficgp, "set ter svg size 640, 480\n set log y\n");
1.145 brouard 5879: /* fprintf(ficgp, "set size 0.65,0.65\n"); */
1.126 brouard 5880: fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
5881:
5882: }
5883:
1.136 brouard 5884: int readdata(char datafile[], int firstobs, int lastobs, int *imax)
5885: {
1.126 brouard 5886:
1.136 brouard 5887: /*-------- data file ----------*/
5888: FILE *fic;
5889: char dummy[]=" ";
1.164 brouard 5890: int i=0, j=0, n=0;
1.136 brouard 5891: int linei, month, year,iout;
5892: char line[MAXLINE], linetmp[MAXLINE];
1.164 brouard 5893: char stra[MAXLINE], strb[MAXLINE];
1.136 brouard 5894: char *stratrunc;
5895: int lstra;
1.126 brouard 5896:
5897:
1.136 brouard 5898: if((fic=fopen(datafile,"r"))==NULL) {
1.195 brouard 5899: printf("Problem while opening datafile: %s\n", datafile);fflush(stdout);
5900: fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);fflush(ficlog);return 1;
1.136 brouard 5901: }
1.126 brouard 5902:
1.136 brouard 5903: i=1;
5904: linei=0;
5905: while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
5906: linei=linei+1;
5907: for(j=strlen(line); j>=0;j--){ /* Untabifies line */
5908: if(line[j] == '\t')
5909: line[j] = ' ';
5910: }
5911: for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){
5912: ;
5913: };
5914: line[j+1]=0; /* Trims blanks at end of line */
5915: if(line[0]=='#'){
5916: fprintf(ficlog,"Comment line\n%s\n",line);
5917: printf("Comment line\n%s\n",line);
5918: continue;
5919: }
5920: trimbb(linetmp,line); /* Trims multiple blanks in line */
1.164 brouard 5921: strcpy(line, linetmp);
1.136 brouard 5922:
1.126 brouard 5923:
1.136 brouard 5924: for (j=maxwav;j>=1;j--){
1.137 brouard 5925: cutv(stra, strb, line, ' ');
1.136 brouard 5926: if(strb[0]=='.') { /* Missing status */
5927: lval=-1;
5928: }else{
5929: errno=0;
5930: lval=strtol(strb,&endptr,10);
5931: /* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
5932: if( strb[0]=='\0' || (*endptr != '\0')){
1.141 brouard 5933: 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);
5934: 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 5935: return 1;
5936: }
5937: }
5938: s[j][i]=lval;
5939:
5940: strcpy(line,stra);
5941: cutv(stra, strb,line,' ');
1.169 brouard 5942: if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
1.136 brouard 5943: }
1.169 brouard 5944: else if( (iout=sscanf(strb,"%s.",dummy)) != 0){
1.136 brouard 5945: month=99;
5946: year=9999;
5947: }else{
1.141 brouard 5948: 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);
5949: 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 5950: return 1;
5951: }
5952: anint[j][i]= (double) year;
5953: mint[j][i]= (double)month;
5954: strcpy(line,stra);
5955: } /* ENd Waves */
5956:
5957: cutv(stra, strb,line,' ');
1.169 brouard 5958: if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
1.136 brouard 5959: }
1.169 brouard 5960: else if( (iout=sscanf(strb,"%s.",dummy)) != 0){
1.136 brouard 5961: month=99;
5962: year=9999;
5963: }else{
1.141 brouard 5964: 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);
5965: 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 5966: return 1;
5967: }
5968: andc[i]=(double) year;
5969: moisdc[i]=(double) month;
5970: strcpy(line,stra);
5971:
5972: cutv(stra, strb,line,' ');
1.169 brouard 5973: if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
1.136 brouard 5974: }
1.169 brouard 5975: else if( (iout=sscanf(strb,"%s.", dummy)) != 0){
1.136 brouard 5976: month=99;
5977: year=9999;
5978: }else{
1.141 brouard 5979: 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);
5980: 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 5981: return 1;
5982: }
5983: if (year==9999) {
1.141 brouard 5984: 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);
5985: 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 5986: return 1;
1.126 brouard 5987:
1.136 brouard 5988: }
5989: annais[i]=(double)(year);
5990: moisnais[i]=(double)(month);
5991: strcpy(line,stra);
5992:
5993: cutv(stra, strb,line,' ');
5994: errno=0;
5995: dval=strtod(strb,&endptr);
5996: if( strb[0]=='\0' || (*endptr != '\0')){
1.141 brouard 5997: printf("Error reading data around '%f' at line number %d, \"%s\" for individual %d\nShould be a weight. Exiting.\n",dval, i,line,linei);
5998: 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 5999: fflush(ficlog);
6000: return 1;
6001: }
6002: weight[i]=dval;
6003: strcpy(line,stra);
6004:
6005: for (j=ncovcol;j>=1;j--){
6006: cutv(stra, strb,line,' ');
6007: if(strb[0]=='.') { /* Missing status */
6008: lval=-1;
6009: }else{
6010: errno=0;
6011: lval=strtol(strb,&endptr,10);
6012: if( strb[0]=='\0' || (*endptr != '\0')){
1.141 brouard 6013: 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);
6014: 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 6015: return 1;
6016: }
6017: }
6018: if(lval <-1 || lval >1){
1.141 brouard 6019: printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
1.136 brouard 6020: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
6021: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
6022: For example, for multinomial values like 1, 2 and 3,\n \
6023: build V1=0 V2=0 for the reference value (1),\n \
6024: V1=1 V2=0 for (2) \n \
6025: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
6026: output of IMaCh is often meaningless.\n \
6027: Exiting.\n",lval,linei, i,line,j);
1.141 brouard 6028: fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
1.136 brouard 6029: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
6030: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
6031: For example, for multinomial values like 1, 2 and 3,\n \
6032: build V1=0 V2=0 for the reference value (1),\n \
6033: V1=1 V2=0 for (2) \n \
6034: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
6035: output of IMaCh is often meaningless.\n \
6036: Exiting.\n",lval,linei, i,line,j);fflush(ficlog);
6037: return 1;
6038: }
6039: covar[j][i]=(double)(lval);
6040: strcpy(line,stra);
6041: }
6042: lstra=strlen(stra);
6043:
6044: if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
6045: stratrunc = &(stra[lstra-9]);
6046: num[i]=atol(stratrunc);
6047: }
6048: else
6049: num[i]=atol(stra);
6050: /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
6051: 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;}*/
6052:
6053: i=i+1;
6054: } /* End loop reading data */
1.126 brouard 6055:
1.136 brouard 6056: *imax=i-1; /* Number of individuals */
6057: fclose(fic);
6058:
6059: return (0);
1.164 brouard 6060: /* endread: */
1.136 brouard 6061: printf("Exiting readdata: ");
6062: fclose(fic);
6063: return (1);
1.126 brouard 6064:
6065:
6066:
1.136 brouard 6067: }
1.145 brouard 6068: void removespace(char *str) {
6069: char *p1 = str, *p2 = str;
6070: do
6071: while (*p2 == ' ')
6072: p2++;
1.169 brouard 6073: while (*p1++ == *p2++);
1.145 brouard 6074: }
6075:
6076: int decodemodel ( char model[], int lastobs) /**< This routine decode the model and returns:
1.187 brouard 6077: * Model V1+V2+V3+V8+V7*V8+V5*V6+V8*age+V3*age+age*age
6078: * - nagesqr = 1 if age*age in the model, otherwise 0.
6079: * - cptcovt total number of covariates of the model nbocc(+)+1 = 8 excepting constant and age and age*age
6080: * - cptcovn or number of covariates k of the models excluding age*products =6 and age*age
1.145 brouard 6081: * - cptcovage number of covariates with age*products =2
6082: * - cptcovs number of simple covariates
6083: * - 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
6084: * which is a new column after the 9 (ncovcol) variables.
6085: * - if k is a product Vn*Vm covar[k][i] is filled with correct values for each individual
6086: * - Tprod[l] gives the kth covariates of the product Vn*Vm l=1 to cptcovprod-cptcovage
6087: * Tprod[1]@2 {5, 6}: position of first product V7*V8 is 5, and second V5*V6 is 6.
6088: * - Tvard[k] p Tvard[1][1]@4 {7, 8, 5, 6} for V7*V8 and V5*V6 .
6089: */
1.136 brouard 6090: {
1.145 brouard 6091: int i, j, k, ks;
1.164 brouard 6092: int j1, k1, k2;
1.136 brouard 6093: char modelsav[80];
1.145 brouard 6094: char stra[80], strb[80], strc[80], strd[80],stre[80];
1.187 brouard 6095: char *strpt;
1.136 brouard 6096:
1.145 brouard 6097: /*removespace(model);*/
1.136 brouard 6098: if (strlen(model) >1){ /* If there is at least 1 covariate */
1.145 brouard 6099: j=0, j1=0, k1=0, k2=-1, ks=0, cptcovn=0;
1.137 brouard 6100: if (strstr(model,"AGE") !=0){
1.192 brouard 6101: printf("Error. AGE must be in lower case 'age' model=1+age+%s. ",model);
6102: fprintf(ficlog,"Error. AGE must be in lower case model=1+age+%s. ",model);fflush(ficlog);
1.136 brouard 6103: return 1;
6104: }
1.141 brouard 6105: if (strstr(model,"v") !=0){
6106: printf("Error. 'v' must be in upper case 'V' model=%s ",model);
6107: fprintf(ficlog,"Error. 'v' must be in upper case model=%s ",model);fflush(ficlog);
6108: return 1;
6109: }
1.187 brouard 6110: strcpy(modelsav,model);
6111: if ((strpt=strstr(model,"age*age")) !=0){
6112: printf(" strpt=%s, model=%s\n",strpt, model);
6113: if(strpt != model){
6114: printf("Error in model: 'model=%s'; 'age*age' should in first place before other covariates\n \
1.192 brouard 6115: 'model=1+age+age*age+V1.' or 'model=1+age+age*age+V1+V1*age.', please swap as well as \n \
1.187 brouard 6116: corresponding column of parameters.\n",model);
6117: fprintf(ficlog,"Error in model: 'model=%s'; 'age*age' should in first place before other covariates\n \
1.192 brouard 6118: 'model=1+age+age*age+V1.' or 'model=1+age+age*age+V1+V1*age.', please swap as well as \n \
1.187 brouard 6119: corresponding column of parameters.\n",model); fflush(ficlog);
6120: return 1;
6121: }
6122:
6123: nagesqr=1;
6124: if (strstr(model,"+age*age") !=0)
6125: substrchaine(modelsav, model, "+age*age");
6126: else if (strstr(model,"age*age+") !=0)
6127: substrchaine(modelsav, model, "age*age+");
6128: else
6129: substrchaine(modelsav, model, "age*age");
6130: }else
6131: nagesqr=0;
6132: if (strlen(modelsav) >1){
6133: j=nbocc(modelsav,'+'); /**< j=Number of '+' */
6134: j1=nbocc(modelsav,'*'); /**< j1=Number of '*' */
6135: cptcovs=j+1-j1; /**< Number of simple covariates V1+V1*age+V3 +V3*V4+age*age=> V1 + V3 =2 */
6136: cptcovt= j+1; /* Number of total covariates in the model, not including
6137: * cst, age and age*age
6138: * V1+V1*age+ V3 + V3*V4+age*age=> 4*/
6139: /* including age products which are counted in cptcovage.
6140: * but the covariates which are products must be treated
6141: * separately: ncovn=4- 2=2 (V1+V3). */
6142: cptcovprod=j1; /**< Number of products V1*V2 +v3*age = 2 */
6143: cptcovprodnoage=0; /**< Number of covariate products without age: V3*V4 =1 */
6144:
6145:
6146: /* Design
6147: * V1 V2 V3 V4 V5 V6 V7 V8 V9 Weight
6148: * < ncovcol=8 >
6149: * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8
6150: * k= 1 2 3 4 5 6 7 8
6151: * cptcovn number of covariates (not including constant and age ) = # of + plus 1 = 7+1=8
6152: * covar[k,i], value of kth covariate if not including age for individual i:
6153: * covar[1][i]= (V2), covar[4][i]=(V3), covar[8][i]=(V8)
6154: * Tvar[k] # of the kth covariate: Tvar[1]=2 Tvar[4]=3 Tvar[8]=8
6155: * if multiplied by age: V3*age Tvar[3=V3*age]=3 (V3) Tvar[7]=8 and
6156: * Tage[++cptcovage]=k
6157: * if products, new covar are created after ncovcol with k1
6158: * Tvar[k]=ncovcol+k1; # of the kth covariate product: Tvar[5]=ncovcol+1=10 Tvar[6]=ncovcol+1=11
6159: * Tprod[k1]=k; Tprod[1]=5 Tprod[2]= 6; gives the position of the k1th product
6160: * 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
6161: * Tvar[cptcovn+k2]=Tvard[k1][1];Tvar[cptcovn+k2+1]=Tvard[k1][2];
6162: * Tvar[8+1]=5;Tvar[8+2]=6;Tvar[8+3]=7;Tvar[8+4]=8 inverted
6163: * V1 V2 V3 V4 V5 V6 V7 V8 V9 V10 V11
6164: * < ncovcol=8 >
6165: * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8 d1 d1 d2 d2
6166: * k= 1 2 3 4 5 6 7 8 9 10 11 12
6167: * Tvar[k]= 2 1 3 3 10 11 8 8 5 6 7 8
6168: * p Tvar[1]@12={2, 1, 3, 3, 11, 10, 8, 8, 7, 8, 5, 6}
6169: * p Tprod[1]@2={ 6, 5}
6170: *p Tvard[1][1]@4= {7, 8, 5, 6}
6171: * covar[k][i]= V2 V1 ? V3 V5*V6? V7*V8? ? V8
6172: * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
6173: *How to reorganize?
6174: * Model V1 + V2 + V3 + V8 + V5*V6 + V7*V8 + V3*age + V8*age
6175: * Tvars {2, 1, 3, 3, 11, 10, 8, 8, 7, 8, 5, 6}
6176: * {2, 1, 4, 8, 5, 6, 3, 7}
6177: * Struct []
6178: */
1.145 brouard 6179:
1.187 brouard 6180: /* This loop fills the array Tvar from the string 'model'.*/
6181: /* j is the number of + signs in the model V1+V2+V3 j=2 i=3 to 1 */
6182: /* modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4 */
6183: /* k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tage[cptcovage=1]=4 */
6184: /* k=3 V4 Tvar[k=3]= 4 (from V4) */
6185: /* k=2 V1 Tvar[k=2]= 1 (from V1) */
6186: /* k=1 Tvar[1]=2 (from V2) */
6187: /* k=5 Tvar[5] */
6188: /* for (k=1; k<=cptcovn;k++) { */
1.198 brouard 6189: /* cov[2+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; */
1.187 brouard 6190: /* } */
1.198 brouard 6191: /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,Tvar[Tage[k])]]*cov[2]; */
1.187 brouard 6192: /*
6193: * Treating invertedly V2+V1+V3*age+V2*V4 is as if written V2*V4 +V3*age + V1 + V2 */
6194: for(k=cptcovt; k>=1;k--) /**< Number of covariates */
1.145 brouard 6195: Tvar[k]=0;
1.187 brouard 6196: cptcovage=0;
6197: for(k=1; k<=cptcovt;k++){ /* Loop on total covariates of the model */
6198: cutl(stra,strb,modelsav,'+'); /* keeps in strb after the first '+'
6199: modelsav==V2+V1+V4+V3*age strb=V3*age stra=V2+V1+V4 */
6200: if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
6201: /* printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
6202: /*scanf("%d",i);*/
6203: if (strchr(strb,'*')) { /**< Model includes a product V2+V1+V4+V3*age strb=V3*age */
6204: cutl(strc,strd,strb,'*'); /**< strd*strc Vm*Vn: strb=V3*age(input) strc=age strd=V3 ; V3*V2 strc=V2, strd=V3 */
6205: if (strcmp(strc,"age")==0) { /**< Model includes age: Vn*age */
6206: /* covar is not filled and then is empty */
6207: cptcovprod--;
6208: cutl(stre,strb,strd,'V'); /* strd=V3(input): stre="3" */
6209: Tvar[k]=atoi(stre); /* V2+V1+V4+V3*age Tvar[4]=3 ; V1+V2*age Tvar[2]=2; V1+V1*age Tvar[2]=1 */
6210: cptcovage++; /* Sums the number of covariates which include age as a product */
6211: Tage[cptcovage]=k; /* Tvar[4]=3, Tage[1] = 4 or V1+V1*age Tvar[2]=1, Tage[1]=2 */
6212: /*printf("stre=%s ", stre);*/
6213: } else if (strcmp(strd,"age")==0) { /* or age*Vn */
6214: cptcovprod--;
6215: cutl(stre,strb,strc,'V');
6216: Tvar[k]=atoi(stre);
6217: cptcovage++;
6218: Tage[cptcovage]=k;
6219: } else { /* Age is not in the model product V2+V1+V1*V4+V3*age+V3*V2 strb=V3*V2*/
6220: /* loops on k1=1 (V3*V2) and k1=2 V4*V3 */
6221: cptcovn++;
6222: cptcovprodnoage++;k1++;
6223: cutl(stre,strb,strc,'V'); /* strc= Vn, stre is n; strb=V3*V2 stre=3 strc=*/
6224: Tvar[k]=ncovcol+k1; /* For model-covariate k tells which data-covariate to use but
6225: because this model-covariate is a construction we invent a new column
6226: ncovcol + k1
6227: If already ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2
6228: Tvar[3=V1*V4]=4+1 Tvar[5=V3*V2]=4 + 2= 6, etc */
6229: cutl(strc,strb,strd,'V'); /* strd was Vm, strc is m */
6230: Tprod[k1]=k; /* Tprod[1]=3(=V1*V4) for V2+V1+V1*V4+age*V3+V3*V2 */
6231: Tvard[k1][1] =atoi(strc); /* m 1 for V1*/
6232: Tvard[k1][2] =atoi(stre); /* n 4 for V4*/
6233: k2=k2+2;
6234: Tvar[cptcovt+k2]=Tvard[k1][1]; /* Tvar[(cptcovt=4+k2=1)=5]= 1 (V1) */
6235: Tvar[cptcovt+k2+1]=Tvard[k1][2]; /* Tvar[(cptcovt=4+(k2=1)+1)=6]= 4 (V4) */
6236: for (i=1; i<=lastobs;i++){
6237: /* Computes the new covariate which is a product of
6238: covar[n][i]* covar[m][i] and stores it at ncovol+k1 May not be defined */
6239: covar[ncovcol+k1][i]=covar[atoi(stre)][i]*covar[atoi(strc)][i];
6240: }
6241: } /* End age is not in the model */
6242: } /* End if model includes a product */
6243: else { /* no more sum */
6244: /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
6245: /* scanf("%d",i);*/
6246: cutl(strd,strc,strb,'V');
6247: ks++; /**< Number of simple covariates */
1.145 brouard 6248: cptcovn++;
1.187 brouard 6249: Tvar[k]=atoi(strd);
6250: }
6251: strcpy(modelsav,stra); /* modelsav=V2+V1+V4 stra=V2+V1+V4 */
6252: /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
6253: scanf("%d",i);*/
6254: } /* end of loop + on total covariates */
6255: } /* end if strlen(modelsave == 0) age*age might exist */
6256: } /* end if strlen(model == 0) */
1.136 brouard 6257:
6258: /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
6259: If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
6260:
6261: /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
6262: printf("cptcovprod=%d ", cptcovprod);
6263: fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
6264:
6265: scanf("%d ",i);*/
6266:
6267:
1.137 brouard 6268: return (0); /* with covar[new additional covariate if product] and Tage if age */
1.164 brouard 6269: /*endread:*/
1.136 brouard 6270: printf("Exiting decodemodel: ");
6271: return (1);
6272: }
6273:
1.169 brouard 6274: int calandcheckages(int imx, int maxwav, double *agemin, double *agemax, int *nberr, int *nbwarn )
1.136 brouard 6275: {
6276: int i, m;
6277:
6278: for (i=1; i<=imx; i++) {
6279: for(m=2; (m<= maxwav); m++) {
6280: if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
6281: anint[m][i]=9999;
6282: s[m][i]=-1;
6283: }
6284: if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
1.169 brouard 6285: *nberr = *nberr + 1;
6286: 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);
6287: 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 6288: s[m][i]=-1;
6289: }
6290: if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
1.169 brouard 6291: (*nberr)++;
1.136 brouard 6292: 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]);
6293: 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]);
6294: s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
6295: }
6296: }
6297: }
6298:
6299: for (i=1; i<=imx; i++) {
6300: agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
6301: for(m=firstpass; (m<= lastpass); m++){
6302: if(s[m][i] >0 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){
6303: if (s[m][i] >= nlstate+1) {
1.169 brouard 6304: if(agedc[i]>0){
6305: if((int)moisdc[i]!=99 && (int)andc[i]!=9999){
1.136 brouard 6306: agev[m][i]=agedc[i];
6307: /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
1.169 brouard 6308: }else {
1.136 brouard 6309: if ((int)andc[i]!=9999){
6310: nbwarn++;
6311: printf("Warning negative age at death: %ld line:%d\n",num[i],i);
6312: fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
6313: agev[m][i]=-1;
6314: }
6315: }
1.169 brouard 6316: } /* agedc > 0 */
1.136 brouard 6317: }
6318: else if(s[m][i] !=9){ /* Standard case, age in fractional
6319: years but with the precision of a month */
6320: agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
6321: if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
6322: agev[m][i]=1;
6323: else if(agev[m][i] < *agemin){
6324: *agemin=agev[m][i];
6325: printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], *agemin);
6326: }
6327: else if(agev[m][i] >*agemax){
6328: *agemax=agev[m][i];
1.156 brouard 6329: /* printf(" Max anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.2f\n",m,i,anint[m][i], i,annais[i], *agemax);*/
1.136 brouard 6330: }
6331: /*agev[m][i]=anint[m][i]-annais[i];*/
6332: /* agev[m][i] = age[i]+2*m;*/
6333: }
6334: else { /* =9 */
6335: agev[m][i]=1;
6336: s[m][i]=-1;
6337: }
6338: }
6339: else /*= 0 Unknown */
6340: agev[m][i]=1;
6341: }
6342:
6343: }
6344: for (i=1; i<=imx; i++) {
6345: for(m=firstpass; (m<=lastpass); m++){
6346: if (s[m][i] > (nlstate+ndeath)) {
1.169 brouard 6347: (*nberr)++;
1.136 brouard 6348: 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);
6349: 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);
6350: return 1;
6351: }
6352: }
6353: }
6354:
6355: /*for (i=1; i<=imx; i++){
6356: for (m=firstpass; (m<lastpass); m++){
6357: printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
6358: }
6359:
6360: }*/
6361:
6362:
1.139 brouard 6363: printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
6364: fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
1.136 brouard 6365:
6366: return (0);
1.164 brouard 6367: /* endread:*/
1.136 brouard 6368: printf("Exiting calandcheckages: ");
6369: return (1);
6370: }
6371:
1.172 brouard 6372: #if defined(_MSC_VER)
6373: /*printf("Visual C++ compiler: %s \n;", _MSC_FULL_VER);*/
6374: /*fprintf(ficlog, "Visual C++ compiler: %s \n;", _MSC_FULL_VER);*/
6375: //#include "stdafx.h"
6376: //#include <stdio.h>
6377: //#include <tchar.h>
6378: //#include <windows.h>
6379: //#include <iostream>
6380: typedef BOOL(WINAPI *LPFN_ISWOW64PROCESS) (HANDLE, PBOOL);
6381:
6382: LPFN_ISWOW64PROCESS fnIsWow64Process;
6383:
6384: BOOL IsWow64()
6385: {
6386: BOOL bIsWow64 = FALSE;
6387:
6388: //typedef BOOL (APIENTRY *LPFN_ISWOW64PROCESS)
6389: // (HANDLE, PBOOL);
6390:
6391: //LPFN_ISWOW64PROCESS fnIsWow64Process;
6392:
6393: HMODULE module = GetModuleHandle(_T("kernel32"));
6394: const char funcName[] = "IsWow64Process";
6395: fnIsWow64Process = (LPFN_ISWOW64PROCESS)
6396: GetProcAddress(module, funcName);
6397:
6398: if (NULL != fnIsWow64Process)
6399: {
6400: if (!fnIsWow64Process(GetCurrentProcess(),
6401: &bIsWow64))
6402: //throw std::exception("Unknown error");
6403: printf("Unknown error\n");
6404: }
6405: return bIsWow64 != FALSE;
6406: }
6407: #endif
1.177 brouard 6408:
1.191 brouard 6409: void syscompilerinfo(int logged)
1.167 brouard 6410: {
6411: /* #include "syscompilerinfo.h"*/
1.185 brouard 6412: /* command line Intel compiler 32bit windows, XP compatible:*/
6413: /* /GS /W3 /Gy
6414: /Zc:wchar_t /Zi /O2 /Fd"Release\vc120.pdb" /D "WIN32" /D "NDEBUG" /D
6415: "_CONSOLE" /D "_LIB" /D "_USING_V110_SDK71_" /D "_UNICODE" /D
6416: "UNICODE" /Qipo /Zc:forScope /Gd /Oi /MT /Fa"Release\" /EHsc /nologo
1.186 brouard 6417: /Fo"Release\" /Qprof-dir "Release\" /Fp"Release\IMaCh.pch"
6418: */
6419: /* 64 bits */
1.185 brouard 6420: /*
6421: /GS /W3 /Gy
6422: /Zc:wchar_t /Zi /O2 /Fd"x64\Release\vc120.pdb" /D "WIN32" /D "NDEBUG"
6423: /D "_CONSOLE" /D "_LIB" /D "_UNICODE" /D "UNICODE" /Qipo /Zc:forScope
6424: /Oi /MD /Fa"x64\Release\" /EHsc /nologo /Fo"x64\Release\" /Qprof-dir
6425: "x64\Release\" /Fp"x64\Release\IMaCh.pch" */
6426: /* Optimization are useless and O3 is slower than O2 */
6427: /*
6428: /GS /W3 /Gy /Zc:wchar_t /Zi /O3 /Fd"x64\Release\vc120.pdb" /D "WIN32"
6429: /D "NDEBUG" /D "_CONSOLE" /D "_LIB" /D "_UNICODE" /D "UNICODE" /Qipo
6430: /Zc:forScope /Oi /MD /Fa"x64\Release\" /EHsc /nologo /Qparallel
6431: /Fo"x64\Release\" /Qprof-dir "x64\Release\" /Fp"x64\Release\IMaCh.pch"
6432: */
1.186 brouard 6433: /* Link is */ /* /OUT:"visual studio
1.185 brouard 6434: 2013\Projects\IMaCh\Release\IMaCh.exe" /MANIFEST /NXCOMPAT
6435: /PDB:"visual studio
6436: 2013\Projects\IMaCh\Release\IMaCh.pdb" /DYNAMICBASE
6437: "kernel32.lib" "user32.lib" "gdi32.lib" "winspool.lib"
6438: "comdlg32.lib" "advapi32.lib" "shell32.lib" "ole32.lib"
6439: "oleaut32.lib" "uuid.lib" "odbc32.lib" "odbccp32.lib"
6440: /MACHINE:X86 /OPT:REF /SAFESEH /INCREMENTAL:NO
6441: /SUBSYSTEM:CONSOLE",5.01" /MANIFESTUAC:"level='asInvoker'
6442: uiAccess='false'"
6443: /ManifestFile:"Release\IMaCh.exe.intermediate.manifest" /OPT:ICF
6444: /NOLOGO /TLBID:1
6445: */
1.177 brouard 6446: #if defined __INTEL_COMPILER
1.178 brouard 6447: #if defined(__GNUC__)
6448: struct utsname sysInfo; /* For Intel on Linux and OS/X */
6449: #endif
1.177 brouard 6450: #elif defined(__GNUC__)
1.179 brouard 6451: #ifndef __APPLE__
1.174 brouard 6452: #include <gnu/libc-version.h> /* Only on gnu */
1.179 brouard 6453: #endif
1.177 brouard 6454: struct utsname sysInfo;
1.178 brouard 6455: int cross = CROSS;
6456: if (cross){
6457: printf("Cross-");
1.191 brouard 6458: if(logged) fprintf(ficlog, "Cross-");
1.178 brouard 6459: }
1.174 brouard 6460: #endif
6461:
1.171 brouard 6462: #include <stdint.h>
1.178 brouard 6463:
1.191 brouard 6464: printf("Compiled with:");if(logged)fprintf(ficlog,"Compiled with:");
1.169 brouard 6465: #if defined(__clang__)
1.191 brouard 6466: printf(" Clang/LLVM");if(logged)fprintf(ficlog," Clang/LLVM"); /* Clang/LLVM. ---------------------------------------------- */
1.169 brouard 6467: #endif
6468: #if defined(__ICC) || defined(__INTEL_COMPILER)
1.191 brouard 6469: printf(" Intel ICC/ICPC");if(logged)fprintf(ficlog," Intel ICC/ICPC");/* Intel ICC/ICPC. ------------------------------------------ */
1.169 brouard 6470: #endif
6471: #if defined(__GNUC__) || defined(__GNUG__)
1.191 brouard 6472: printf(" GNU GCC/G++");if(logged)fprintf(ficlog," GNU GCC/G++");/* GNU GCC/G++. --------------------------------------------- */
1.169 brouard 6473: #endif
6474: #if defined(__HP_cc) || defined(__HP_aCC)
1.191 brouard 6475: printf(" Hewlett-Packard C/aC++");if(logged)fprintf(fcilog," Hewlett-Packard C/aC++"); /* Hewlett-Packard C/aC++. ---------------------------------- */
1.169 brouard 6476: #endif
6477: #if defined(__IBMC__) || defined(__IBMCPP__)
1.191 brouard 6478: printf(" IBM XL C/C++"); if(logged) fprintf(ficlog," IBM XL C/C++");/* IBM XL C/C++. -------------------------------------------- */
1.169 brouard 6479: #endif
6480: #if defined(_MSC_VER)
1.191 brouard 6481: printf(" Microsoft Visual Studio");if(logged)fprintf(ficlog," Microsoft Visual Studio");/* Microsoft Visual Studio. --------------------------------- */
1.169 brouard 6482: #endif
6483: #if defined(__PGI)
1.191 brouard 6484: printf(" Portland Group PGCC/PGCPP");if(logged) fprintf(ficlog," Portland Group PGCC/PGCPP");/* Portland Group PGCC/PGCPP. ------------------------------- */
1.169 brouard 6485: #endif
6486: #if defined(__SUNPRO_C) || defined(__SUNPRO_CC)
1.191 brouard 6487: printf(" Oracle Solaris Studio");if(logged)fprintf(ficlog," Oracle Solaris Studio\n");/* Oracle Solaris Studio. ----------------------------------- */
1.167 brouard 6488: #endif
1.191 brouard 6489: printf(" for "); if (logged) fprintf(ficlog, " for ");
1.169 brouard 6490:
1.167 brouard 6491: // http://stackoverflow.com/questions/4605842/how-to-identify-platform-compiler-from-preprocessor-macros
6492: #ifdef _WIN32 // note the underscore: without it, it's not msdn official!
6493: // Windows (x64 and x86)
1.191 brouard 6494: printf("Windows (x64 and x86) ");if(logged) fprintf(ficlog,"Windows (x64 and x86) ");
1.167 brouard 6495: #elif __unix__ // all unices, not all compilers
6496: // Unix
1.191 brouard 6497: printf("Unix ");if(logged) fprintf(ficlog,"Unix ");
1.167 brouard 6498: #elif __linux__
6499: // linux
1.191 brouard 6500: printf("linux ");if(logged) fprintf(ficlog,"linux ");
1.167 brouard 6501: #elif __APPLE__
1.174 brouard 6502: // Mac OS, not sure if this is covered by __posix__ and/or __unix__ though..
1.191 brouard 6503: printf("Mac OS ");if(logged) fprintf(ficlog,"Mac OS ");
1.167 brouard 6504: #endif
6505:
6506: /* __MINGW32__ */
6507: /* __CYGWIN__ */
6508: /* __MINGW64__ */
6509: // http://msdn.microsoft.com/en-us/library/b0084kay.aspx
6510: /* _MSC_VER //the Visual C++ compiler is 17.00.51106.1, the _MSC_VER macro evaluates to 1700. Type cl /? */
6511: /* _MSC_FULL_VER //the Visual C++ compiler is 15.00.20706.01, the _MSC_FULL_VER macro evaluates to 150020706 */
6512: /* _WIN64 // Defined for applications for Win64. */
6513: /* _M_X64 // Defined for compilations that target x64 processors. */
6514: /* _DEBUG // Defined when you compile with /LDd, /MDd, and /MTd. */
1.171 brouard 6515:
1.167 brouard 6516: #if UINTPTR_MAX == 0xffffffff
1.191 brouard 6517: printf(" 32-bit"); if(logged) fprintf(ficlog," 32-bit");/* 32-bit */
1.167 brouard 6518: #elif UINTPTR_MAX == 0xffffffffffffffff
1.191 brouard 6519: printf(" 64-bit"); if(logged) fprintf(ficlog," 64-bit");/* 64-bit */
1.167 brouard 6520: #else
1.191 brouard 6521: printf(" wtf-bit"); if(logged) fprintf(ficlog," wtf-bit");/* wtf */
1.167 brouard 6522: #endif
6523:
1.169 brouard 6524: #if defined(__GNUC__)
6525: # if defined(__GNUC_PATCHLEVEL__)
6526: # define __GNUC_VERSION__ (__GNUC__ * 10000 \
6527: + __GNUC_MINOR__ * 100 \
6528: + __GNUC_PATCHLEVEL__)
6529: # else
6530: # define __GNUC_VERSION__ (__GNUC__ * 10000 \
6531: + __GNUC_MINOR__ * 100)
6532: # endif
1.174 brouard 6533: printf(" using GNU C version %d.\n", __GNUC_VERSION__);
1.191 brouard 6534: if(logged) fprintf(ficlog, " using GNU C version %d.\n", __GNUC_VERSION__);
1.176 brouard 6535:
6536: if (uname(&sysInfo) != -1) {
6537: printf("Running on: %s %s %s %s %s\n",sysInfo.sysname, sysInfo.nodename, sysInfo.release, sysInfo.version, sysInfo.machine);
1.191 brouard 6538: 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 6539: }
6540: else
6541: perror("uname() error");
1.179 brouard 6542: //#ifndef __INTEL_COMPILER
6543: #if !defined (__INTEL_COMPILER) && !defined(__APPLE__)
1.174 brouard 6544: printf("GNU libc version: %s\n", gnu_get_libc_version());
1.191 brouard 6545: if(logged) fprintf(ficlog,"GNU libc version: %s\n", gnu_get_libc_version());
1.177 brouard 6546: #endif
1.169 brouard 6547: #endif
1.172 brouard 6548:
6549: // void main()
6550: // {
1.169 brouard 6551: #if defined(_MSC_VER)
1.174 brouard 6552: if (IsWow64()){
1.191 brouard 6553: printf("\nThe program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n");
6554: if (logged) fprintf(ficlog, "\nThe program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n");
1.174 brouard 6555: }
6556: else{
1.191 brouard 6557: printf("\nThe program is not running under WOW64 (i.e probably on a 64bit Windows).\n");
6558: if (logged) fprintf(ficlog, "\nThe programm is not running under WOW64 (i.e probably on a 64bit Windows).\n");
1.174 brouard 6559: }
1.172 brouard 6560: // printf("\nPress Enter to continue...");
6561: // getchar();
6562: // }
6563:
1.169 brouard 6564: #endif
6565:
1.167 brouard 6566:
6567: }
1.136 brouard 6568:
1.203 brouard 6569: int prevalence_limit(double *p, double **prlim, double ageminpar, double agemaxpar, double ftolpl, int *ncvyear){
1.180 brouard 6570: /*--------------- Prevalence limit (period or stable prevalence) --------------*/
6571: int i, j, k, i1 ;
1.202 brouard 6572: /* double ftolpl = 1.e-10; */
1.180 brouard 6573: double age, agebase, agelim;
1.203 brouard 6574: double tot;
1.180 brouard 6575:
1.202 brouard 6576: strcpy(filerespl,"PL_");
6577: strcat(filerespl,fileresu);
6578: if((ficrespl=fopen(filerespl,"w"))==NULL) {
6579: printf("Problem with period (stable) prevalence resultfile: %s\n", filerespl);return 1;
6580: fprintf(ficlog,"Problem with period (stable) prevalence resultfile: %s\n", filerespl);return 1;
6581: }
6582: printf("Computing period (stable) prevalence: result on file '%s' \n", filerespl);
6583: fprintf(ficlog,"Computing period (stable) prevalence: result on file '%s' \n", filerespl);
6584: pstamp(ficrespl);
1.203 brouard 6585: fprintf(ficrespl,"# Period (stable) prevalence. Precision given by ftolpl=%g \n", ftolpl);
1.202 brouard 6586: fprintf(ficrespl,"#Age ");
6587: for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
6588: fprintf(ficrespl,"\n");
1.180 brouard 6589:
6590: /* prlim=matrix(1,nlstate,1,nlstate);*/ /* back in main */
6591:
6592: agebase=ageminpar;
6593: agelim=agemaxpar;
6594:
6595: i1=pow(2,cptcoveff);
6596: if (cptcovn < 1){i1=1;}
6597:
6598: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
6599: /* for(cptcov=1,k=0;cptcov<=1;cptcov++){ */
6600: //for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
6601: k=k+1;
6602: /* to clean */
1.198 brouard 6603: //printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtabm(cptcod,cptcov));
1.200 brouard 6604: fprintf(ficrespl,"#******");
6605: printf("#******");
6606: fprintf(ficlog,"#******");
1.180 brouard 6607: for(j=1;j<=cptcoveff;j++) {
1.198 brouard 6608: fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
6609: printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
6610: fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.180 brouard 6611: }
6612: fprintf(ficrespl,"******\n");
6613: printf("******\n");
6614: fprintf(ficlog,"******\n");
6615:
6616: fprintf(ficrespl,"#Age ");
6617: for(j=1;j<=cptcoveff;j++) {
1.200 brouard 6618: fprintf(ficrespl,"V%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.180 brouard 6619: }
1.203 brouard 6620: for(i=1; i<=nlstate;i++) fprintf(ficrespl," %d-%d ",i,i);
6621: fprintf(ficrespl,"Total Years_to_converge\n");
1.180 brouard 6622:
6623: for (age=agebase; age<=agelim; age++){
6624: /* for (age=agebase; age<=agebase; age++){ */
1.203 brouard 6625: prevalim(prlim, nlstate, p, age, oldm, savm, ftolpl, ncvyear, k);
1.180 brouard 6626: fprintf(ficrespl,"%.0f ",age );
6627: for(j=1;j<=cptcoveff;j++)
1.198 brouard 6628: fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.203 brouard 6629: tot=0.;
6630: for(i=1; i<=nlstate;i++){
6631: tot += prlim[i][i];
1.180 brouard 6632: fprintf(ficrespl," %.5f", prlim[i][i]);
1.203 brouard 6633: }
6634: fprintf(ficrespl," %.3f %d\n", tot, *ncvyear);
1.180 brouard 6635: } /* Age */
6636: /* was end of cptcod */
6637: } /* cptcov */
1.184 brouard 6638: return 0;
1.180 brouard 6639: }
6640:
6641: int hPijx(double *p, int bage, int fage){
6642: /*------------- h Pij x at various ages ------------*/
6643:
6644: int stepsize;
6645: int agelim;
6646: int hstepm;
6647: int nhstepm;
6648: int h, i, i1, j, k;
6649:
6650: double agedeb;
6651: double ***p3mat;
6652:
1.201 brouard 6653: strcpy(filerespij,"PIJ_"); strcat(filerespij,fileresu);
1.180 brouard 6654: if((ficrespij=fopen(filerespij,"w"))==NULL) {
6655: printf("Problem with Pij resultfile: %s\n", filerespij); return 1;
6656: fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij); return 1;
6657: }
6658: printf("Computing pij: result on file '%s' \n", filerespij);
6659: fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
6660:
6661: stepsize=(int) (stepm+YEARM-1)/YEARM;
6662: /*if (stepm<=24) stepsize=2;*/
6663:
6664: agelim=AGESUP;
6665: hstepm=stepsize*YEARM; /* Every year of age */
6666: hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
6667:
6668: /* hstepm=1; aff par mois*/
6669: pstamp(ficrespij);
6670: fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
6671: i1= pow(2,cptcoveff);
1.183 brouard 6672: /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */
6673: /* /\*for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*\/ */
6674: /* k=k+1; */
6675: for (k=1; k <= (int) pow(2,cptcoveff); k++){
6676: fprintf(ficrespij,"\n#****** ");
6677: for(j=1;j<=cptcoveff;j++)
1.198 brouard 6678: fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.183 brouard 6679: fprintf(ficrespij,"******\n");
6680:
6681: for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
6682: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
6683: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
6684:
6685: /* nhstepm=nhstepm*YEARM; aff par mois*/
1.180 brouard 6686:
1.183 brouard 6687: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
6688: oldm=oldms;savm=savms;
6689: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
6690: fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
6691: for(i=1; i<=nlstate;i++)
6692: for(j=1; j<=nlstate+ndeath;j++)
6693: fprintf(ficrespij," %1d-%1d",i,j);
6694: fprintf(ficrespij,"\n");
6695: for (h=0; h<=nhstepm; h++){
6696: /*agedebphstep = agedeb + h*hstepm/YEARM*stepm;*/
6697: fprintf(ficrespij,"%d %3.f %3.f",k, agedeb, agedeb + h*hstepm/YEARM*stepm );
1.180 brouard 6698: for(i=1; i<=nlstate;i++)
6699: for(j=1; j<=nlstate+ndeath;j++)
1.183 brouard 6700: fprintf(ficrespij," %.5f", p3mat[i][j][h]);
1.180 brouard 6701: fprintf(ficrespij,"\n");
6702: }
1.183 brouard 6703: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
6704: fprintf(ficrespij,"\n");
6705: }
1.180 brouard 6706: /*}*/
6707: }
1.184 brouard 6708: return 0;
1.180 brouard 6709: }
6710:
6711:
1.136 brouard 6712: /***********************************************/
6713: /**************** Main Program *****************/
6714: /***********************************************/
6715:
6716: int main(int argc, char *argv[])
6717: {
6718: #ifdef GSL
6719: const gsl_multimin_fminimizer_type *T;
6720: size_t iteri = 0, it;
6721: int rval = GSL_CONTINUE;
6722: int status = GSL_SUCCESS;
6723: double ssval;
6724: #endif
6725: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
1.164 brouard 6726: int i,j, k, n=MAXN,iter=0,m,size=100, cptcod;
1.203 brouard 6727: int ncvyearnp=0;
6728: int *ncvyear=&ncvyearnp; /* Number of years needed for the period prevalence to converge */
1.164 brouard 6729: int jj, ll, li, lj, lk;
1.136 brouard 6730: int numlinepar=0; /* Current linenumber of parameter file */
1.197 brouard 6731: int num_filled;
1.136 brouard 6732: int itimes;
6733: int NDIM=2;
6734: int vpopbased=0;
6735:
1.164 brouard 6736: char ca[32], cb[32];
1.136 brouard 6737: /* FILE *fichtm; *//* Html File */
6738: /* FILE *ficgp;*/ /*Gnuplot File */
6739: struct stat info;
1.191 brouard 6740: double agedeb=0.;
1.194 brouard 6741:
6742: double ageminpar=AGEOVERFLOW,agemin=AGEOVERFLOW, agemaxpar=-AGEOVERFLOW, agemax=-AGEOVERFLOW;
1.136 brouard 6743:
1.165 brouard 6744: double fret;
1.191 brouard 6745: double dum=0.; /* Dummy variable */
1.136 brouard 6746: double ***p3mat;
6747: double ***mobaverage;
1.164 brouard 6748:
6749: char line[MAXLINE];
1.197 brouard 6750: char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE];
6751:
6752: char model[MAXLINE], modeltemp[MAXLINE];
1.136 brouard 6753: char pathr[MAXLINE], pathimach[MAXLINE];
1.164 brouard 6754: char *tok, *val; /* pathtot */
1.136 brouard 6755: int firstobs=1, lastobs=10;
1.195 brouard 6756: int c, h , cpt, c2;
1.191 brouard 6757: int jl=0;
6758: int i1, j1, jk, stepsize=0;
1.194 brouard 6759: int count=0;
6760:
1.164 brouard 6761: int *tab;
1.136 brouard 6762: int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
6763: int mobilav=0,popforecast=0;
1.191 brouard 6764: int hstepm=0, nhstepm=0;
1.136 brouard 6765: int agemortsup;
6766: float sumlpop=0.;
6767: double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
6768: double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
6769:
1.191 brouard 6770: double bage=0, fage=110., age, agelim=0., agebase=0.;
1.136 brouard 6771: double ftolpl=FTOL;
6772: double **prlim;
6773: double ***param; /* Matrix of parameters */
6774: double *p;
6775: double **matcov; /* Matrix of covariance */
1.203 brouard 6776: double **hess; /* Hessian matrix */
1.136 brouard 6777: double ***delti3; /* Scale */
6778: double *delti; /* Scale */
6779: double ***eij, ***vareij;
6780: double **varpl; /* Variances of prevalence limits by age */
6781: double *epj, vepp;
1.164 brouard 6782:
1.136 brouard 6783: double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
6784: double **ximort;
1.145 brouard 6785: char *alph[]={"a","a","b","c","d","e"}, str[4]="1234";
1.136 brouard 6786: int *dcwave;
6787:
1.164 brouard 6788: char z[1]="c";
1.136 brouard 6789:
6790: /*char *strt;*/
6791: char strtend[80];
1.126 brouard 6792:
1.164 brouard 6793:
1.126 brouard 6794: /* setlocale (LC_ALL, ""); */
6795: /* bindtextdomain (PACKAGE, LOCALEDIR); */
6796: /* textdomain (PACKAGE); */
6797: /* setlocale (LC_CTYPE, ""); */
6798: /* setlocale (LC_MESSAGES, ""); */
6799:
6800: /* gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
1.157 brouard 6801: rstart_time = time(NULL);
6802: /* (void) gettimeofday(&start_time,&tzp);*/
6803: start_time = *localtime(&rstart_time);
1.126 brouard 6804: curr_time=start_time;
1.157 brouard 6805: /*tml = *localtime(&start_time.tm_sec);*/
6806: /* strcpy(strstart,asctime(&tml)); */
6807: strcpy(strstart,asctime(&start_time));
1.126 brouard 6808:
6809: /* printf("Localtime (at start)=%s",strstart); */
1.157 brouard 6810: /* tp.tm_sec = tp.tm_sec +86400; */
6811: /* tm = *localtime(&start_time.tm_sec); */
1.126 brouard 6812: /* tmg.tm_year=tmg.tm_year +dsign*dyear; */
6813: /* tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
6814: /* tmg.tm_hour=tmg.tm_hour + 1; */
1.157 brouard 6815: /* tp.tm_sec = mktime(&tmg); */
1.126 brouard 6816: /* strt=asctime(&tmg); */
6817: /* printf("Time(after) =%s",strstart); */
6818: /* (void) time (&time_value);
6819: * printf("time=%d,t-=%d\n",time_value,time_value-86400);
6820: * tm = *localtime(&time_value);
6821: * strstart=asctime(&tm);
6822: * printf("tim_value=%d,asctime=%s\n",time_value,strstart);
6823: */
6824:
6825: nberr=0; /* Number of errors and warnings */
6826: nbwarn=0;
1.184 brouard 6827: #ifdef WIN32
6828: _getcwd(pathcd, size);
6829: #else
1.126 brouard 6830: getcwd(pathcd, size);
1.184 brouard 6831: #endif
1.191 brouard 6832: syscompilerinfo(0);
1.196 brouard 6833: printf("\nIMaCh version %s, %s\n%s",version, copyright, fullversion);
1.126 brouard 6834: if(argc <=1){
6835: printf("\nEnter the parameter file name: ");
1.205 brouard 6836: if(!fgets(pathr,FILENAMELENGTH,stdin)){
6837: printf("ERROR Empty parameter file name\n");
6838: goto end;
6839: }
1.126 brouard 6840: i=strlen(pathr);
6841: if(pathr[i-1]=='\n')
6842: pathr[i-1]='\0';
1.156 brouard 6843: i=strlen(pathr);
1.205 brouard 6844: if(i >= 1 && pathr[i-1]==' ') {/* This may happen when dragging on oS/X! */
1.156 brouard 6845: pathr[i-1]='\0';
1.205 brouard 6846: }
6847: i=strlen(pathr);
6848: if( i==0 ){
6849: printf("ERROR Empty parameter file name\n");
6850: goto end;
6851: }
6852: for (tok = pathr; tok != NULL; ){
1.126 brouard 6853: printf("Pathr |%s|\n",pathr);
6854: while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
6855: printf("val= |%s| pathr=%s\n",val,pathr);
6856: strcpy (pathtot, val);
6857: if(pathr[0] == '\0') break; /* Dirty */
6858: }
6859: }
6860: else{
6861: strcpy(pathtot,argv[1]);
6862: }
6863: /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
6864: /*cygwin_split_path(pathtot,path,optionfile);
6865: printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
6866: /* cutv(path,optionfile,pathtot,'\\');*/
6867:
6868: /* Split argv[0], imach program to get pathimach */
6869: printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
6870: split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
6871: printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
6872: /* strcpy(pathimach,argv[0]); */
6873: /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
6874: split(pathtot,path,optionfile,optionfilext,optionfilefiname);
6875: printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
1.184 brouard 6876: #ifdef WIN32
6877: _chdir(path); /* Can be a relative path */
6878: if(_getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */
6879: #else
1.126 brouard 6880: chdir(path); /* Can be a relative path */
1.184 brouard 6881: if (getcwd(pathcd, MAXLINE) > 0) /* So pathcd is the full path */
6882: #endif
6883: printf("Current directory %s!\n",pathcd);
1.126 brouard 6884: strcpy(command,"mkdir ");
6885: strcat(command,optionfilefiname);
6886: if((outcmd=system(command)) != 0){
1.169 brouard 6887: printf("Directory already exists (or can't create it) %s%s, err=%d\n",path,optionfilefiname,outcmd);
1.126 brouard 6888: /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
6889: /* fclose(ficlog); */
6890: /* exit(1); */
6891: }
6892: /* if((imk=mkdir(optionfilefiname))<0){ */
6893: /* perror("mkdir"); */
6894: /* } */
6895:
6896: /*-------- arguments in the command line --------*/
6897:
1.186 brouard 6898: /* Main Log file */
1.126 brouard 6899: strcat(filelog, optionfilefiname);
6900: strcat(filelog,".log"); /* */
6901: if((ficlog=fopen(filelog,"w"))==NULL) {
6902: printf("Problem with logfile %s\n",filelog);
6903: goto end;
6904: }
6905: fprintf(ficlog,"Log filename:%s\n",filelog);
1.197 brouard 6906: fprintf(ficlog,"Version %s %s",version,fullversion);
1.126 brouard 6907: fprintf(ficlog,"\nEnter the parameter file name: \n");
6908: fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
6909: path=%s \n\
6910: optionfile=%s\n\
6911: optionfilext=%s\n\
1.156 brouard 6912: optionfilefiname='%s'\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
1.126 brouard 6913:
1.197 brouard 6914: syscompilerinfo(1);
1.167 brouard 6915:
1.126 brouard 6916: printf("Local time (at start):%s",strstart);
6917: fprintf(ficlog,"Local time (at start): %s",strstart);
6918: fflush(ficlog);
6919: /* (void) gettimeofday(&curr_time,&tzp); */
1.157 brouard 6920: /* printf("Elapsed time %d\n", asc_diff_time(curr_time.tm_sec-start_time.tm_sec,tmpout)); */
1.126 brouard 6921:
6922: /* */
6923: strcpy(fileres,"r");
6924: strcat(fileres, optionfilefiname);
1.201 brouard 6925: strcat(fileresu, optionfilefiname); /* Without r in front */
1.126 brouard 6926: strcat(fileres,".txt"); /* Other files have txt extension */
1.201 brouard 6927: strcat(fileresu,".txt"); /* Other files have txt extension */
1.126 brouard 6928:
1.186 brouard 6929: /* Main ---------arguments file --------*/
1.126 brouard 6930:
6931: if((ficpar=fopen(optionfile,"r"))==NULL) {
1.155 brouard 6932: printf("Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
6933: fprintf(ficlog,"Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
1.126 brouard 6934: fflush(ficlog);
1.149 brouard 6935: /* goto end; */
6936: exit(70);
1.126 brouard 6937: }
6938:
6939:
6940:
6941: strcpy(filereso,"o");
1.201 brouard 6942: strcat(filereso,fileresu);
1.126 brouard 6943: if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
6944: printf("Problem with Output resultfile: %s\n", filereso);
6945: fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
6946: fflush(ficlog);
6947: goto end;
6948: }
6949:
6950: /* Reads comments: lines beginning with '#' */
6951: numlinepar=0;
1.197 brouard 6952:
6953: /* First parameter line */
6954: while(fgets(line, MAXLINE, ficpar)) {
6955: /* If line starts with a # it is a comment */
6956: if (line[0] == '#') {
6957: numlinepar++;
6958: fputs(line,stdout);
6959: fputs(line,ficparo);
6960: fputs(line,ficlog);
6961: continue;
6962: }else
6963: break;
6964: }
6965: if((num_filled=sscanf(line,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", \
6966: title, datafile, &lastobs, &firstpass,&lastpass)) !=EOF){
6967: if (num_filled != 5) {
6968: printf("Should be 5 parameters\n");
6969: }
1.126 brouard 6970: numlinepar++;
1.197 brouard 6971: printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", title, datafile, lastobs, firstpass,lastpass);
6972: }
6973: /* Second parameter line */
6974: while(fgets(line, MAXLINE, ficpar)) {
6975: /* If line starts with a # it is a comment */
6976: if (line[0] == '#') {
6977: numlinepar++;
6978: fputs(line,stdout);
6979: fputs(line,ficparo);
6980: fputs(line,ficlog);
6981: continue;
6982: }else
6983: break;
6984: }
6985: if((num_filled=sscanf(line,"ftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\n", \
6986: &ftol, &stepm, &ncovcol, &nlstate, &ndeath, &maxwav, &mle, &weightopt)) !=EOF){
6987: if (num_filled != 8) {
6988: printf("Not 8\n");
6989: }
6990: 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 6991: }
1.203 brouard 6992: /* ftolpl=6*ftol*1.e5; /\* 6.e-3 make convergences in less than 80 loops for the prevalence limit *\/ */
6993: ftolpl=6.e-3; /* 6.e-3 make convergences in less than 80 loops for the prevalence limit */
1.197 brouard 6994: /* Third parameter line */
6995: while(fgets(line, MAXLINE, ficpar)) {
6996: /* If line starts with a # it is a comment */
6997: if (line[0] == '#') {
6998: numlinepar++;
6999: fputs(line,stdout);
7000: fputs(line,ficparo);
7001: fputs(line,ficlog);
7002: continue;
7003: }else
7004: break;
7005: }
1.201 brouard 7006: if((num_filled=sscanf(line,"model=1+age%[^.\n]", model)) !=EOF){
7007: if (num_filled == 0)
7008: model[0]='\0';
7009: else if (num_filled != 1){
1.197 brouard 7010: printf("ERROR %d: Model should be at minimum 'model=1+age.' %s\n",num_filled, line);
7011: fprintf(ficlog,"ERROR %d: Model should be at minimum 'model=1+age.' %s\n",num_filled, line);
7012: model[0]='\0';
7013: goto end;
7014: }
7015: else{
7016: if (model[0]=='+'){
7017: for(i=1; i<=strlen(model);i++)
7018: modeltemp[i-1]=model[i];
1.201 brouard 7019: strcpy(model,modeltemp);
1.197 brouard 7020: }
7021: }
1.199 brouard 7022: /* printf(" model=1+age%s modeltemp= %s, model=%s\n",model, modeltemp, model);fflush(stdout); */
1.203 brouard 7023: printf("model=1+age+%s\n",model);fflush(stdout);
1.197 brouard 7024: }
7025: /* 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); */
7026: /* numlinepar=numlinepar+3; /\* In general *\/ */
7027: /* 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 7028: 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);
7029: 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 7030: fflush(ficlog);
1.190 brouard 7031: /* if(model[0]=='#'|| model[0]== '\0'){ */
7032: if(model[0]=='#'){
1.187 brouard 7033: printf("Error in 'model' line: model should start with 'model=1+age+' and end with '.' \n \
7034: 'model=1+age+.' or 'model=1+age+V1.' or 'model=1+age+age*age+V1+V1*age.' or \n \
7035: 'model=1+age+V1+V2.' or 'model=1+age+V1+V2+V1*V2.' etc. \n"); \
7036: if(mle != -1){
7037: printf("Fix the model line and run imach with mle=-1 to get a correct template of the parameter file.\n");
7038: exit(1);
7039: }
7040: }
1.126 brouard 7041: while((c=getc(ficpar))=='#' && c!= EOF){
7042: ungetc(c,ficpar);
7043: fgets(line, MAXLINE, ficpar);
7044: numlinepar++;
1.195 brouard 7045: if(line[1]=='q'){ /* This #q will quit imach (the answer is q) */
7046: z[0]=line[1];
7047: }
7048: /* printf("****line [1] = %c \n",line[1]); */
1.141 brouard 7049: fputs(line, stdout);
7050: //puts(line);
1.126 brouard 7051: fputs(line,ficparo);
7052: fputs(line,ficlog);
7053: }
7054: ungetc(c,ficpar);
7055:
7056:
1.145 brouard 7057: covar=matrix(0,NCOVMAX,1,n); /**< used in readdata */
1.136 brouard 7058: cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement plus one, indepently of n in Vn*/
7059: /* v1+v2+v3+v2*v4+v5*age makes cptcovn = 5
7060: v1+v2*age+v2*v3 makes cptcovn = 3
7061: */
7062: if (strlen(model)>1)
1.187 brouard 7063: 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 7064: else
1.187 brouard 7065: ncovmodel=2; /* Constant and age */
1.133 brouard 7066: nforce= (nlstate+ndeath-1)*nlstate; /* Number of forces ij from state i to j */
7067: npar= nforce*ncovmodel; /* Number of parameters like aij*/
1.131 brouard 7068: if(npar >MAXPARM || nlstate >NLSTATEMAX || ndeath >NDEATHMAX || ncovmodel>NCOVMAX){
7069: 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);
7070: 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);
7071: fflush(stdout);
7072: fclose (ficlog);
7073: goto end;
7074: }
1.126 brouard 7075: delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
7076: delti=delti3[1][1];
7077: /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
7078: if(mle==-1){ /* Print a wizard for help writing covariance matrix */
7079: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
1.191 brouard 7080: printf(" You chose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
7081: fprintf(ficlog," You chose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
1.126 brouard 7082: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
7083: fclose (ficparo);
7084: fclose (ficlog);
7085: goto end;
7086: exit(0);
7087: }
1.186 brouard 7088: else if(mle==-3) { /* Main Wizard */
1.126 brouard 7089: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
1.192 brouard 7090: printf(" You chose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
7091: fprintf(ficlog," You chose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
1.126 brouard 7092: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
7093: matcov=matrix(1,npar,1,npar);
1.203 brouard 7094: hess=matrix(1,npar,1,npar);
1.126 brouard 7095: }
7096: else{
1.145 brouard 7097: /* Read guessed parameters */
1.126 brouard 7098: /* Reads comments: lines beginning with '#' */
7099: while((c=getc(ficpar))=='#' && c!= EOF){
7100: ungetc(c,ficpar);
7101: fgets(line, MAXLINE, ficpar);
7102: numlinepar++;
1.141 brouard 7103: fputs(line,stdout);
1.126 brouard 7104: fputs(line,ficparo);
7105: fputs(line,ficlog);
7106: }
7107: ungetc(c,ficpar);
7108:
7109: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
7110: for(i=1; i <=nlstate; i++){
7111: j=0;
7112: for(jj=1; jj <=nlstate+ndeath; jj++){
7113: if(jj==i) continue;
7114: j++;
7115: fscanf(ficpar,"%1d%1d",&i1,&j1);
1.193 brouard 7116: if ((i1 != i) || (j1 != jj)){
1.126 brouard 7117: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \
7118: It might be a problem of design; if ncovcol and the model are correct\n \
7119: run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1);
7120: exit(1);
7121: }
7122: fprintf(ficparo,"%1d%1d",i1,j1);
7123: if(mle==1)
1.193 brouard 7124: printf("%1d%1d",i,jj);
7125: fprintf(ficlog,"%1d%1d",i,jj);
1.126 brouard 7126: for(k=1; k<=ncovmodel;k++){
7127: fscanf(ficpar," %lf",¶m[i][j][k]);
7128: if(mle==1){
7129: printf(" %lf",param[i][j][k]);
7130: fprintf(ficlog," %lf",param[i][j][k]);
7131: }
7132: else
7133: fprintf(ficlog," %lf",param[i][j][k]);
7134: fprintf(ficparo," %lf",param[i][j][k]);
7135: }
7136: fscanf(ficpar,"\n");
7137: numlinepar++;
7138: if(mle==1)
7139: printf("\n");
7140: fprintf(ficlog,"\n");
7141: fprintf(ficparo,"\n");
7142: }
7143: }
7144: fflush(ficlog);
7145:
1.145 brouard 7146: /* Reads scales values */
1.126 brouard 7147: p=param[1][1];
7148:
7149: /* Reads comments: lines beginning with '#' */
7150: while((c=getc(ficpar))=='#' && c!= EOF){
7151: ungetc(c,ficpar);
7152: fgets(line, MAXLINE, ficpar);
7153: numlinepar++;
1.141 brouard 7154: fputs(line,stdout);
1.126 brouard 7155: fputs(line,ficparo);
7156: fputs(line,ficlog);
7157: }
7158: ungetc(c,ficpar);
7159:
7160: for(i=1; i <=nlstate; i++){
7161: for(j=1; j <=nlstate+ndeath-1; j++){
7162: fscanf(ficpar,"%1d%1d",&i1,&j1);
1.164 brouard 7163: if ( (i1-i) * (j1-j) != 0){
1.126 brouard 7164: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
7165: exit(1);
7166: }
7167: printf("%1d%1d",i,j);
7168: fprintf(ficparo,"%1d%1d",i1,j1);
7169: fprintf(ficlog,"%1d%1d",i1,j1);
7170: for(k=1; k<=ncovmodel;k++){
7171: fscanf(ficpar,"%le",&delti3[i][j][k]);
7172: printf(" %le",delti3[i][j][k]);
7173: fprintf(ficparo," %le",delti3[i][j][k]);
7174: fprintf(ficlog," %le",delti3[i][j][k]);
7175: }
7176: fscanf(ficpar,"\n");
7177: numlinepar++;
7178: printf("\n");
7179: fprintf(ficparo,"\n");
7180: fprintf(ficlog,"\n");
7181: }
7182: }
7183: fflush(ficlog);
7184:
1.145 brouard 7185: /* Reads covariance matrix */
1.126 brouard 7186: delti=delti3[1][1];
7187:
7188:
7189: /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
7190:
7191: /* Reads comments: lines beginning with '#' */
7192: while((c=getc(ficpar))=='#' && c!= EOF){
7193: ungetc(c,ficpar);
7194: fgets(line, MAXLINE, ficpar);
7195: numlinepar++;
1.141 brouard 7196: fputs(line,stdout);
1.126 brouard 7197: fputs(line,ficparo);
7198: fputs(line,ficlog);
7199: }
7200: ungetc(c,ficpar);
7201:
7202: matcov=matrix(1,npar,1,npar);
1.203 brouard 7203: hess=matrix(1,npar,1,npar);
1.131 brouard 7204: for(i=1; i <=npar; i++)
7205: for(j=1; j <=npar; j++) matcov[i][j]=0.;
7206:
1.194 brouard 7207: /* Scans npar lines */
1.126 brouard 7208: for(i=1; i <=npar; i++){
1.194 brouard 7209: count=fscanf(ficpar,"%1d%1d%1d",&i1,&j1,&jk);
7210: if(count != 3){
7211: printf("Error! Error in parameter file %s at line %d after line starting with %1d%1d%1d\n\
7212: This is probably because your covariance matrix doesn't \n contain exactly %d lines corresponding to your model line '1+age+%s'.\n\
7213: Please run with mle=-1 to get a correct covariance matrix.\n",optionfile,numlinepar, i1,j1,jk, npar, model);
7214: fprintf(ficlog,"Error! Error in parameter file %s at line %d after line starting with %1d%1d%1d\n\
7215: This is probably because your covariance matrix doesn't \n contain exactly %d lines corresponding to your model line '1+age+%s'.\n\
7216: Please run with mle=-1 to get a correct covariance matrix.\n",optionfile,numlinepar, i1,j1,jk, npar, model);
7217: exit(1);
7218: }else
1.126 brouard 7219: if(mle==1)
1.194 brouard 7220: printf("%1d%1d%1d",i1,j1,jk);
7221: fprintf(ficlog,"%1d%1d%1d",i1,j1,jk);
7222: fprintf(ficparo,"%1d%1d%1d",i1,j1,jk);
1.126 brouard 7223: for(j=1; j <=i; j++){
7224: fscanf(ficpar," %le",&matcov[i][j]);
7225: if(mle==1){
7226: printf(" %.5le",matcov[i][j]);
7227: }
7228: fprintf(ficlog," %.5le",matcov[i][j]);
7229: fprintf(ficparo," %.5le",matcov[i][j]);
7230: }
7231: fscanf(ficpar,"\n");
7232: numlinepar++;
7233: if(mle==1)
7234: printf("\n");
7235: fprintf(ficlog,"\n");
7236: fprintf(ficparo,"\n");
7237: }
1.194 brouard 7238: /* End of read covariance matrix npar lines */
1.126 brouard 7239: for(i=1; i <=npar; i++)
7240: for(j=i+1;j<=npar;j++)
7241: matcov[i][j]=matcov[j][i];
7242:
7243: if(mle==1)
7244: printf("\n");
7245: fprintf(ficlog,"\n");
7246:
7247: fflush(ficlog);
7248:
7249: /*-------- Rewriting parameter file ----------*/
7250: strcpy(rfileres,"r"); /* "Rparameterfile */
7251: strcat(rfileres,optionfilefiname); /* Parameter file first name*/
7252: strcat(rfileres,"."); /* */
7253: strcat(rfileres,optionfilext); /* Other files have txt extension */
7254: if((ficres =fopen(rfileres,"w"))==NULL) {
1.201 brouard 7255: printf("Problem writing new parameter file: %s\n", rfileres);goto end;
7256: fprintf(ficlog,"Problem writing new parameter file: %s\n", rfileres);goto end;
1.126 brouard 7257: }
7258: fprintf(ficres,"#%s\n",version);
7259: } /* End of mle != -3 */
7260:
1.186 brouard 7261: /* Main data
7262: */
1.126 brouard 7263: n= lastobs;
7264: num=lvector(1,n);
7265: moisnais=vector(1,n);
7266: annais=vector(1,n);
7267: moisdc=vector(1,n);
7268: andc=vector(1,n);
7269: agedc=vector(1,n);
7270: cod=ivector(1,n);
7271: weight=vector(1,n);
7272: for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
7273: mint=matrix(1,maxwav,1,n);
7274: anint=matrix(1,maxwav,1,n);
1.131 brouard 7275: s=imatrix(1,maxwav+1,1,n); /* s[i][j] health state for wave i and individual j */
1.126 brouard 7276: tab=ivector(1,NCOVMAX);
1.144 brouard 7277: ncodemax=ivector(1,NCOVMAX); /* Number of code per covariate; if O and 1 only, 2**ncov; V1+V2+V3+V4=>16 */
1.192 brouard 7278: 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 7279:
1.136 brouard 7280: /* Reads data from file datafile */
7281: if (readdata(datafile, firstobs, lastobs, &imx)==1)
7282: goto end;
7283:
7284: /* Calculation of the number of parameters from char model */
1.137 brouard 7285: /* modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4
7286: k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tag[cptcovage=1]=4
7287: k=3 V4 Tvar[k=3]= 4 (from V4)
7288: k=2 V1 Tvar[k=2]= 1 (from V1)
7289: k=1 Tvar[1]=2 (from V2)
7290: */
7291: Tvar=ivector(1,NCOVMAX); /* Was 15 changed to NCOVMAX. */
7292: /* V2+V1+V4+age*V3 is a model with 4 covariates (3 plus signs).
7293: For each model-covariate stores the data-covariate id. Tvar[1]=2, Tvar[2]=1, Tvar[3]=4,
7294: Tvar[4=age*V3] is 3 and 'age' is recorded in Tage.
7295: */
7296: /* For model-covariate k tells which data-covariate to use but
7297: because this model-covariate is a construction we invent a new column
7298: ncovcol + k1
7299: If already ncovcol=4 and model=V2+V1+V1*V4+age*V3
7300: Tvar[3=V1*V4]=4+1 etc */
1.145 brouard 7301: Tprod=ivector(1,NCOVMAX); /* Gives the position of a product */
1.137 brouard 7302: /* Tprod[k1=1]=3(=V1*V4) for V2+V1+V1*V4+age*V3
7303: if V2+V1+V1*V4+age*V3+V3*V2 TProd[k1=2]=5 (V3*V2)
7304: */
1.145 brouard 7305: Tvaraff=ivector(1,NCOVMAX); /* Unclear */
7306: 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 7307: * For V3*V2 (in V2+V1+V1*V4+age*V3+V3*V2), V3*V2 position is 2nd.
7308: * Tvard[k1=2][1]=3 (V3) Tvard[k1=2][2]=2(V2) */
1.145 brouard 7309: Tage=ivector(1,NCOVMAX); /* Gives the covariate id of covariates associated with age: V2 + V1 + age*V4 + V3*age
1.137 brouard 7310: 4 covariates (3 plus signs)
7311: Tage[1=V3*age]= 4; Tage[2=age*V4] = 3
7312: */
1.136 brouard 7313:
1.186 brouard 7314: /* Main decodemodel */
7315:
1.187 brouard 7316:
1.136 brouard 7317: if(decodemodel(model, lastobs) == 1)
7318: goto end;
7319:
1.137 brouard 7320: if((double)(lastobs-imx)/(double)imx > 1.10){
7321: nbwarn++;
7322: 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);
7323: 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);
7324: }
1.136 brouard 7325: /* if(mle==1){*/
1.137 brouard 7326: if (weightopt != 1) { /* Maximisation without weights. We can have weights different from 1 but want no weight*/
7327: for(i=1;i<=imx;i++) weight[i]=1.0; /* changed to imx */
1.136 brouard 7328: }
7329:
7330: /*-calculation of age at interview from date of interview and age at death -*/
7331: agev=matrix(1,maxwav,1,imx);
7332:
7333: if(calandcheckages(imx, maxwav, &agemin, &agemax, &nberr, &nbwarn) == 1)
7334: goto end;
7335:
1.126 brouard 7336:
1.136 brouard 7337: agegomp=(int)agemin;
7338: free_vector(moisnais,1,n);
7339: free_vector(annais,1,n);
1.126 brouard 7340: /* free_matrix(mint,1,maxwav,1,n);
7341: free_matrix(anint,1,maxwav,1,n);*/
7342: free_vector(moisdc,1,n);
7343: free_vector(andc,1,n);
1.145 brouard 7344: /* */
7345:
1.126 brouard 7346: wav=ivector(1,imx);
7347: dh=imatrix(1,lastpass-firstpass+1,1,imx);
7348: bh=imatrix(1,lastpass-firstpass+1,1,imx);
7349: mw=imatrix(1,lastpass-firstpass+1,1,imx);
7350:
7351: /* Concatenates waves */
7352: concatwav(wav, dh, bh, mw, s, agedc, agev, firstpass, lastpass, imx, nlstate, stepm);
1.145 brouard 7353: /* */
7354:
1.126 brouard 7355: /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
7356:
7357: nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
7358: ncodemax[1]=1;
1.145 brouard 7359: Ndum =ivector(-1,NCOVMAX);
1.187 brouard 7360: if (ncovmodel-nagesqr > 2 ) /* That is if covariate other than cst, age and age*age */
1.145 brouard 7361: tricode(Tvar,nbcode,imx, Ndum); /**< Fills nbcode[Tvar[j]][l]; */
1.186 brouard 7362: /* Nbcode gives the value of the lth modality of jth covariate, in
7363: V2+V1*age, there are 3 covariates Tvar[2]=1 (V1).*/
7364: /* 1 to ncodemax[j] is the maximum value of this jth covariate */
1.145 brouard 7365:
1.200 brouard 7366: /* codtab=imatrix(1,100,1,10);*/ /* codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) */
1.198 brouard 7367: /*printf(" codtab[1,1],codtab[100,10]=%d,%d\n", codtab[1][1],codtabm(100,10));*/
1.186 brouard 7368: /* codtab gives the value 1 or 2 of the hth combination of k covariates (1 or 2).*/
1.145 brouard 7369: h=0;
7370:
7371:
7372: /*if (cptcovn > 0) */
1.126 brouard 7373:
1.145 brouard 7374:
1.126 brouard 7375: m=pow(2,cptcoveff);
7376:
1.144 brouard 7377: /**< codtab(h,k) k = codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) + 1
1.186 brouard 7378: * For k=4 covariates, h goes from 1 to 2**k
7379: * codtabm(h,k)= 1 & (h-1) >> (k-1) ;
7380: * h\k 1 2 3 4
1.143 brouard 7381: *______________________________
7382: * 1 i=1 1 i=1 1 i=1 1 i=1 1
7383: * 2 2 1 1 1
7384: * 3 i=2 1 2 1 1
7385: * 4 2 2 1 1
7386: * 5 i=3 1 i=2 1 2 1
7387: * 6 2 1 2 1
7388: * 7 i=4 1 2 2 1
7389: * 8 2 2 2 1
1.197 brouard 7390: * 9 i=5 1 i=3 1 i=2 1 2
7391: * 10 2 1 1 2
7392: * 11 i=6 1 2 1 2
7393: * 12 2 2 1 2
7394: * 13 i=7 1 i=4 1 2 2
7395: * 14 2 1 2 2
7396: * 15 i=8 1 2 2 2
7397: * 16 2 2 2 2
1.143 brouard 7398: */
1.202 brouard 7399: /* /\* for(h=1; h <=100 ;h++){ *\/ */
7400: /* /\* printf("h=%2d ", h); *\/ */
7401: /* /\* for(k=1; k <=10; k++){ *\/ */
7402: /* /\* printf("k=%d %d ",k,codtabm(h,k)); *\/ */
7403: /* /\* codtab[h][k]=codtabm(h,k); *\/ */
7404: /* /\* } *\/ */
7405: /* /\* printf("\n"); *\/ */
7406: /* } */
1.197 brouard 7407: /* for(k=1;k<=cptcoveff; k++){ /\* scans any effective covariate *\/ */
7408: /* 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 *\/ */
7409: /* for(j=1; j <= ncodemax[k]; j++){ /\* For each modality of this covariate ncodemax=2*\/ */
7410: /* for(cpt=1; cpt <=pow(2,k-1); cpt++){ /\* cpt=1 to 8/2**(3+1-1 or 3+1-3) =1 or 4 *\/ */
7411: /* h++; */
7412: /* if (h>m) */
7413: /* h=1; */
7414: /* codtab[h][k]=j; */
7415: /* /\* codtab[12][3]=1; *\/ */
7416: /* /\*codtab[h][Tvar[k]]=j;*\/ */
7417: /* /\* 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]]); *\/ */
7418: /* } */
7419: /* } */
7420: /* } */
7421: /* } */
1.126 brouard 7422: /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);
7423: codtab[1][2]=1;codtab[2][2]=2; */
1.197 brouard 7424: /* for(i=1; i <=m ;i++){ */
7425: /* for(k=1; k <=cptcovn; k++){ */
7426: /* printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff); */
7427: /* } */
7428: /* printf("\n"); */
7429: /* } */
7430: /* scanf("%d",i);*/
1.145 brouard 7431:
7432: free_ivector(Ndum,-1,NCOVMAX);
7433:
7434:
1.126 brouard 7435:
1.186 brouard 7436: /* Initialisation of ----------- gnuplot -------------*/
1.126 brouard 7437: strcpy(optionfilegnuplot,optionfilefiname);
7438: if(mle==-3)
1.201 brouard 7439: strcat(optionfilegnuplot,"-MORT_");
1.126 brouard 7440: strcat(optionfilegnuplot,".gp");
7441:
7442: if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
7443: printf("Problem with file %s",optionfilegnuplot);
7444: }
7445: else{
1.204 brouard 7446: fprintf(ficgp,"\n# IMaCh-%s\n", version);
1.126 brouard 7447: fprintf(ficgp,"# %s\n", optionfilegnuplot);
1.141 brouard 7448: //fprintf(ficgp,"set missing 'NaNq'\n");
7449: fprintf(ficgp,"set datafile missing 'NaNq'\n");
1.126 brouard 7450: }
7451: /* fclose(ficgp);*/
1.186 brouard 7452:
7453:
7454: /* Initialisation of --------- index.htm --------*/
1.126 brouard 7455:
7456: strcpy(optionfilehtm,optionfilefiname); /* Main html file */
7457: if(mle==-3)
1.201 brouard 7458: strcat(optionfilehtm,"-MORT_");
1.126 brouard 7459: strcat(optionfilehtm,".htm");
7460: if((fichtm=fopen(optionfilehtm,"w"))==NULL) {
1.131 brouard 7461: printf("Problem with %s \n",optionfilehtm);
7462: exit(0);
1.126 brouard 7463: }
7464:
7465: strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
7466: strcat(optionfilehtmcov,"-cov.htm");
7467: if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL) {
7468: printf("Problem with %s \n",optionfilehtmcov), exit(0);
7469: }
7470: else{
7471: fprintf(fichtmcov,"<html><head>\n<title>IMaCh Cov %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
7472: <hr size=\"2\" color=\"#EC5E5E\"> \n\
1.204 brouard 7473: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n",\
1.126 brouard 7474: optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
7475: }
7476:
1.204 brouard 7477: 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> \
7478: <hr size=\"2\" color=\"#EC5E5E\"> \n\
7479: <font size=\"2\">IMaCh-%s <br> %s</font> \
1.126 brouard 7480: <hr size=\"2\" color=\"#EC5E5E\"> \n\
1.204 brouard 7481: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n\
1.126 brouard 7482: \n\
7483: <hr size=\"2\" color=\"#EC5E5E\">\
7484: <ul><li><h4>Parameter files</h4>\n\
7485: - Parameter file: <a href=\"%s.%s\">%s.%s</a><br>\n\
7486: - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
7487: - Log file of the run: <a href=\"%s\">%s</a><br>\n\
7488: - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
7489: - Date and time at start: %s</ul>\n",\
7490: optionfilehtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
7491: optionfilefiname,optionfilext,optionfilefiname,optionfilext,\
7492: fileres,fileres,\
7493: filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
7494: fflush(fichtm);
7495:
7496: strcpy(pathr,path);
7497: strcat(pathr,optionfilefiname);
1.184 brouard 7498: #ifdef WIN32
7499: _chdir(optionfilefiname); /* Move to directory named optionfile */
7500: #else
1.126 brouard 7501: chdir(optionfilefiname); /* Move to directory named optionfile */
1.184 brouard 7502: #endif
7503:
1.126 brouard 7504:
7505: /* Calculates basic frequencies. Computes observed prevalence at single age
7506: and prints on file fileres'p'. */
7507: freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart);
7508:
7509: fprintf(fichtm,"\n");
7510: fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
7511: Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
7512: Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
7513: imx,agemin,agemax,jmin,jmax,jmean);
7514: pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
7515: oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
7516: newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
7517: savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
7518: oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
7519:
7520:
7521: /* For Powell, parameters are in a vector p[] starting at p[1]
7522: so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
7523: p=param[1][1]; /* *(*(*(param +1)+1)+0) */
7524:
7525: globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
1.186 brouard 7526: /* For mortality only */
1.126 brouard 7527: if (mle==-3){
1.136 brouard 7528: ximort=matrix(1,NDIM,1,NDIM);
1.186 brouard 7529: /* ximort=gsl_matrix_alloc(1,NDIM,1,NDIM); */
1.126 brouard 7530: cens=ivector(1,n);
7531: ageexmed=vector(1,n);
7532: agecens=vector(1,n);
7533: dcwave=ivector(1,n);
7534:
7535: for (i=1; i<=imx; i++){
7536: dcwave[i]=-1;
7537: for (m=firstpass; m<=lastpass; m++)
7538: if (s[m][i]>nlstate) {
7539: dcwave[i]=m;
7540: /* printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
7541: break;
7542: }
7543: }
7544:
7545: for (i=1; i<=imx; i++) {
7546: if (wav[i]>0){
7547: ageexmed[i]=agev[mw[1][i]][i];
7548: j=wav[i];
7549: agecens[i]=1.;
7550:
7551: if (ageexmed[i]> 1 && wav[i] > 0){
7552: agecens[i]=agev[mw[j][i]][i];
7553: cens[i]= 1;
7554: }else if (ageexmed[i]< 1)
7555: cens[i]= -1;
7556: if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
7557: cens[i]=0 ;
7558: }
7559: else cens[i]=-1;
7560: }
7561:
7562: for (i=1;i<=NDIM;i++) {
7563: for (j=1;j<=NDIM;j++)
7564: ximort[i][j]=(i == j ? 1.0 : 0.0);
7565: }
7566:
1.145 brouard 7567: /*p[1]=0.0268; p[NDIM]=0.083;*/
1.126 brouard 7568: /*printf("%lf %lf", p[1], p[2]);*/
7569:
7570:
1.136 brouard 7571: #ifdef GSL
7572: printf("GSL optimization\n"); fprintf(ficlog,"Powell\n");
1.162 brouard 7573: #else
1.126 brouard 7574: printf("Powell\n"); fprintf(ficlog,"Powell\n");
1.136 brouard 7575: #endif
1.201 brouard 7576: strcpy(filerespow,"POW-MORT_");
7577: strcat(filerespow,fileresu);
1.126 brouard 7578: if((ficrespow=fopen(filerespow,"w"))==NULL) {
7579: printf("Problem with resultfile: %s\n", filerespow);
7580: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
7581: }
1.136 brouard 7582: #ifdef GSL
7583: fprintf(ficrespow,"# GSL optimization\n# iter -2*LL");
1.162 brouard 7584: #else
1.126 brouard 7585: fprintf(ficrespow,"# Powell\n# iter -2*LL");
1.136 brouard 7586: #endif
1.126 brouard 7587: /* for (i=1;i<=nlstate;i++)
7588: for(j=1;j<=nlstate+ndeath;j++)
7589: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
7590: */
7591: fprintf(ficrespow,"\n");
1.136 brouard 7592: #ifdef GSL
7593: /* gsl starts here */
7594: T = gsl_multimin_fminimizer_nmsimplex;
7595: gsl_multimin_fminimizer *sfm = NULL;
7596: gsl_vector *ss, *x;
7597: gsl_multimin_function minex_func;
7598:
7599: /* Initial vertex size vector */
7600: ss = gsl_vector_alloc (NDIM);
7601:
7602: if (ss == NULL){
7603: GSL_ERROR_VAL ("failed to allocate space for ss", GSL_ENOMEM, 0);
7604: }
7605: /* Set all step sizes to 1 */
7606: gsl_vector_set_all (ss, 0.001);
7607:
7608: /* Starting point */
1.126 brouard 7609:
1.136 brouard 7610: x = gsl_vector_alloc (NDIM);
7611:
7612: if (x == NULL){
7613: gsl_vector_free(ss);
7614: GSL_ERROR_VAL ("failed to allocate space for x", GSL_ENOMEM, 0);
7615: }
7616:
7617: /* Initialize method and iterate */
7618: /* p[1]=0.0268; p[NDIM]=0.083; */
1.186 brouard 7619: /* gsl_vector_set(x, 0, 0.0268); */
7620: /* gsl_vector_set(x, 1, 0.083); */
1.136 brouard 7621: gsl_vector_set(x, 0, p[1]);
7622: gsl_vector_set(x, 1, p[2]);
7623:
7624: minex_func.f = &gompertz_f;
7625: minex_func.n = NDIM;
7626: minex_func.params = (void *)&p; /* ??? */
7627:
7628: sfm = gsl_multimin_fminimizer_alloc (T, NDIM);
7629: gsl_multimin_fminimizer_set (sfm, &minex_func, x, ss);
7630:
7631: printf("Iterations beginning .....\n\n");
7632: printf("Iter. # Intercept Slope -Log Likelihood Simplex size\n");
7633:
7634: iteri=0;
7635: while (rval == GSL_CONTINUE){
7636: iteri++;
7637: status = gsl_multimin_fminimizer_iterate(sfm);
7638:
7639: if (status) printf("error: %s\n", gsl_strerror (status));
7640: fflush(0);
7641:
7642: if (status)
7643: break;
7644:
7645: rval = gsl_multimin_test_size (gsl_multimin_fminimizer_size (sfm), 1e-6);
7646: ssval = gsl_multimin_fminimizer_size (sfm);
7647:
7648: if (rval == GSL_SUCCESS)
7649: printf ("converged to a local maximum at\n");
7650:
7651: printf("%5d ", iteri);
7652: for (it = 0; it < NDIM; it++){
7653: printf ("%10.5f ", gsl_vector_get (sfm->x, it));
7654: }
7655: printf("f() = %-10.5f ssize = %.7f\n", sfm->fval, ssval);
7656: }
7657:
7658: printf("\n\n Please note: Program should be run many times with varying starting points to detemine global maximum\n\n");
7659:
7660: gsl_vector_free(x); /* initial values */
7661: gsl_vector_free(ss); /* inital step size */
7662: for (it=0; it<NDIM; it++){
7663: p[it+1]=gsl_vector_get(sfm->x,it);
7664: fprintf(ficrespow," %.12lf", p[it]);
7665: }
7666: gsl_multimin_fminimizer_free (sfm); /* p *(sfm.x.data) et p *(sfm.x.data+1) */
7667: #endif
7668: #ifdef POWELL
7669: powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
7670: #endif
1.126 brouard 7671: fclose(ficrespow);
7672:
1.203 brouard 7673: hesscov(matcov, hess, p, NDIM, delti, 1e-4, gompertz);
1.126 brouard 7674:
7675: for(i=1; i <=NDIM; i++)
7676: for(j=i+1;j<=NDIM;j++)
7677: matcov[i][j]=matcov[j][i];
7678:
7679: printf("\nCovariance matrix\n ");
1.203 brouard 7680: fprintf(ficlog,"\nCovariance matrix\n ");
1.126 brouard 7681: for(i=1; i <=NDIM; i++) {
7682: for(j=1;j<=NDIM;j++){
7683: printf("%f ",matcov[i][j]);
1.203 brouard 7684: fprintf(ficlog,"%f ",matcov[i][j]);
1.126 brouard 7685: }
1.203 brouard 7686: printf("\n "); fprintf(ficlog,"\n ");
1.126 brouard 7687: }
7688:
7689: printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
1.193 brouard 7690: for (i=1;i<=NDIM;i++) {
1.126 brouard 7691: printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
1.193 brouard 7692: fprintf(ficlog,"%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
7693: }
1.126 brouard 7694: lsurv=vector(1,AGESUP);
7695: lpop=vector(1,AGESUP);
7696: tpop=vector(1,AGESUP);
7697: lsurv[agegomp]=100000;
7698:
7699: for (k=agegomp;k<=AGESUP;k++) {
7700: agemortsup=k;
7701: if (p[1]*exp(p[2]*(k-agegomp))>1) break;
7702: }
7703:
7704: for (k=agegomp;k<agemortsup;k++)
7705: lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
7706:
7707: for (k=agegomp;k<agemortsup;k++){
7708: lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
7709: sumlpop=sumlpop+lpop[k];
7710: }
7711:
7712: tpop[agegomp]=sumlpop;
7713: for (k=agegomp;k<(agemortsup-3);k++){
7714: /* tpop[k+1]=2;*/
7715: tpop[k+1]=tpop[k]-lpop[k];
7716: }
7717:
7718:
7719: printf("\nAge lx qx dx Lx Tx e(x)\n");
7720: for (k=agegomp;k<(agemortsup-2);k++)
7721: 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]);
7722:
7723:
7724: replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
1.194 brouard 7725: if(ageminpar == AGEOVERFLOW ||agemaxpar == AGEOVERFLOW){
7726: printf("Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
7727: This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\
7728: Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
7729: fprintf(ficlog,"Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
7730: This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\
7731: Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
7732: }else
1.201 brouard 7733: printinggnuplotmort(fileresu, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
7734: printinghtmlmort(fileresu,title,datafile, firstpass, lastpass, \
1.126 brouard 7735: stepm, weightopt,\
7736: model,imx,p,matcov,agemortsup);
7737:
7738: free_vector(lsurv,1,AGESUP);
7739: free_vector(lpop,1,AGESUP);
7740: free_vector(tpop,1,AGESUP);
1.136 brouard 7741: #ifdef GSL
7742: free_ivector(cens,1,n);
7743: free_vector(agecens,1,n);
7744: free_ivector(dcwave,1,n);
7745: free_matrix(ximort,1,NDIM,1,NDIM);
7746: #endif
1.186 brouard 7747: } /* Endof if mle==-3 mortality only */
1.205 brouard 7748: /* Standard */
7749: else{ /* For mle !=- 3, could be 0 or 1 or 4 etc. */
7750: globpr=0;/* Computes sum of likelihood for globpr=1 and funcone */
7751: /* Computes likelihood for initial parameters, uses funcone to compute gpimx and gsw */
1.132 brouard 7752: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
1.126 brouard 7753: printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
7754: for (k=1; k<=npar;k++)
7755: printf(" %d %8.5f",k,p[k]);
7756: printf("\n");
1.205 brouard 7757: if(mle>=1){ /* Could be 1 or 2, Real Maximization */
7758: /* mlikeli uses func not funcone */
7759: mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
7760: }
7761: if(mle==0) {/* No optimization, will print the likelihoods for the datafile */
7762: globpr=0;/* Computes sum of likelihood for globpr=1 and funcone */
7763: /* Computes likelihood for initial parameters, uses funcone to compute gpimx and gsw */
7764: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
7765: }
7766: globpr=1; /* again, to print the individual contributions using computed gpimx and gsw */
1.126 brouard 7767: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
7768: printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
7769: for (k=1; k<=npar;k++)
7770: printf(" %d %8.5f",k,p[k]);
7771: printf("\n");
7772:
7773: /*--------- results files --------------*/
1.192 brouard 7774: 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 7775:
7776:
7777: fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
7778: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
7779: fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
7780: for(i=1,jk=1; i <=nlstate; i++){
7781: for(k=1; k <=(nlstate+ndeath); k++){
7782: if (k != i) {
7783: printf("%d%d ",i,k);
7784: fprintf(ficlog,"%d%d ",i,k);
7785: fprintf(ficres,"%1d%1d ",i,k);
7786: for(j=1; j <=ncovmodel; j++){
1.190 brouard 7787: printf("%12.7f ",p[jk]);
7788: fprintf(ficlog,"%12.7f ",p[jk]);
7789: fprintf(ficres,"%12.7f ",p[jk]);
1.126 brouard 7790: jk++;
7791: }
7792: printf("\n");
7793: fprintf(ficlog,"\n");
7794: fprintf(ficres,"\n");
7795: }
7796: }
7797: }
1.203 brouard 7798: if(mle != 0){
7799: /* Computing hessian and covariance matrix only at a peak of the Likelihood, that is after optimization */
1.126 brouard 7800: ftolhess=ftol; /* Usually correct */
1.203 brouard 7801: hesscov(matcov, hess, p, npar, delti, ftolhess, func);
7802: 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");
7803: 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");
7804: for(i=1,jk=1; i <=nlstate; i++){
7805: for(k=1; k <=(nlstate+ndeath); k++){
7806: if (k != i) {
7807: printf("%d%d ",i,k);
7808: fprintf(ficlog,"%d%d ",i,k);
7809: for(j=1; j <=ncovmodel; j++){
7810: 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]));
7811: 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]));
7812: jk++;
7813: }
7814: printf("\n");
7815: fprintf(ficlog,"\n");
1.193 brouard 7816: }
7817: }
7818: }
1.203 brouard 7819: } /* end of hesscov and Wald tests */
1.193 brouard 7820:
1.203 brouard 7821: /* */
1.126 brouard 7822: fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
7823: printf("# Scales (for hessian or gradient estimation)\n");
7824: fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
7825: for(i=1,jk=1; i <=nlstate; i++){
7826: for(j=1; j <=nlstate+ndeath; j++){
7827: if (j!=i) {
7828: fprintf(ficres,"%1d%1d",i,j);
7829: printf("%1d%1d",i,j);
7830: fprintf(ficlog,"%1d%1d",i,j);
7831: for(k=1; k<=ncovmodel;k++){
7832: printf(" %.5e",delti[jk]);
7833: fprintf(ficlog," %.5e",delti[jk]);
7834: fprintf(ficres," %.5e",delti[jk]);
7835: jk++;
7836: }
7837: printf("\n");
7838: fprintf(ficlog,"\n");
7839: fprintf(ficres,"\n");
7840: }
7841: }
7842: }
7843:
7844: 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 7845: if(mle >= 1) /* To big for the screen */
1.126 brouard 7846: 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");
7847: 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");
7848: /* # 121 Var(a12)\n\ */
7849: /* # 122 Cov(b12,a12) Var(b12)\n\ */
7850: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
7851: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
7852: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
7853: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
7854: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
7855: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
7856:
7857:
7858: /* Just to have a covariance matrix which will be more understandable
7859: even is we still don't want to manage dictionary of variables
7860: */
7861: for(itimes=1;itimes<=2;itimes++){
7862: jj=0;
7863: for(i=1; i <=nlstate; i++){
7864: for(j=1; j <=nlstate+ndeath; j++){
7865: if(j==i) continue;
7866: for(k=1; k<=ncovmodel;k++){
7867: jj++;
7868: ca[0]= k+'a'-1;ca[1]='\0';
7869: if(itimes==1){
7870: if(mle>=1)
7871: printf("#%1d%1d%d",i,j,k);
7872: fprintf(ficlog,"#%1d%1d%d",i,j,k);
7873: fprintf(ficres,"#%1d%1d%d",i,j,k);
7874: }else{
7875: if(mle>=1)
7876: printf("%1d%1d%d",i,j,k);
7877: fprintf(ficlog,"%1d%1d%d",i,j,k);
7878: fprintf(ficres,"%1d%1d%d",i,j,k);
7879: }
7880: ll=0;
7881: for(li=1;li <=nlstate; li++){
7882: for(lj=1;lj <=nlstate+ndeath; lj++){
7883: if(lj==li) continue;
7884: for(lk=1;lk<=ncovmodel;lk++){
7885: ll++;
7886: if(ll<=jj){
7887: cb[0]= lk +'a'-1;cb[1]='\0';
7888: if(ll<jj){
7889: if(itimes==1){
7890: if(mle>=1)
7891: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
7892: fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
7893: fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
7894: }else{
7895: if(mle>=1)
7896: printf(" %.5e",matcov[jj][ll]);
7897: fprintf(ficlog," %.5e",matcov[jj][ll]);
7898: fprintf(ficres," %.5e",matcov[jj][ll]);
7899: }
7900: }else{
7901: if(itimes==1){
7902: if(mle>=1)
7903: printf(" Var(%s%1d%1d)",ca,i,j);
7904: fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
7905: fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
7906: }else{
7907: if(mle>=1)
1.203 brouard 7908: printf(" %.7e",matcov[jj][ll]);
7909: fprintf(ficlog," %.7e",matcov[jj][ll]);
7910: fprintf(ficres," %.7e",matcov[jj][ll]);
1.126 brouard 7911: }
7912: }
7913: }
7914: } /* end lk */
7915: } /* end lj */
7916: } /* end li */
7917: if(mle>=1)
7918: printf("\n");
7919: fprintf(ficlog,"\n");
7920: fprintf(ficres,"\n");
7921: numlinepar++;
7922: } /* end k*/
7923: } /*end j */
7924: } /* end i */
7925: } /* end itimes */
7926:
7927: fflush(ficlog);
7928: fflush(ficres);
7929:
7930: while((c=getc(ficpar))=='#' && c!= EOF){
7931: ungetc(c,ficpar);
7932: fgets(line, MAXLINE, ficpar);
1.141 brouard 7933: fputs(line,stdout);
1.126 brouard 7934: fputs(line,ficparo);
7935: }
7936: ungetc(c,ficpar);
7937:
7938: estepm=0;
7939: fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
7940: if (estepm==0 || estepm < stepm) estepm=stepm;
7941: if (fage <= 2) {
7942: bage = ageminpar;
7943: fage = agemaxpar;
7944: }
7945:
7946: fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
7947: fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
7948: fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
1.186 brouard 7949:
7950: /* Other stuffs, more or less useful */
1.126 brouard 7951: while((c=getc(ficpar))=='#' && c!= EOF){
7952: ungetc(c,ficpar);
7953: fgets(line, MAXLINE, ficpar);
1.141 brouard 7954: fputs(line,stdout);
1.126 brouard 7955: fputs(line,ficparo);
7956: }
7957: ungetc(c,ficpar);
7958:
7959: 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);
7960: 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);
7961: 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);
7962: printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
7963: 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);
7964:
7965: while((c=getc(ficpar))=='#' && c!= EOF){
7966: ungetc(c,ficpar);
7967: fgets(line, MAXLINE, ficpar);
1.141 brouard 7968: fputs(line,stdout);
1.126 brouard 7969: fputs(line,ficparo);
7970: }
7971: ungetc(c,ficpar);
7972:
7973:
7974: dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
7975: dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
7976:
7977: fscanf(ficpar,"pop_based=%d\n",&popbased);
1.193 brouard 7978: fprintf(ficlog,"pop_based=%d\n",popbased);
1.126 brouard 7979: fprintf(ficparo,"pop_based=%d\n",popbased);
7980: fprintf(ficres,"pop_based=%d\n",popbased);
7981:
7982: while((c=getc(ficpar))=='#' && c!= EOF){
7983: ungetc(c,ficpar);
7984: fgets(line, MAXLINE, ficpar);
1.141 brouard 7985: fputs(line,stdout);
1.126 brouard 7986: fputs(line,ficparo);
7987: }
7988: ungetc(c,ficpar);
7989:
7990: 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);
7991: 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);
7992: 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);
7993: 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);
7994: 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);
7995: /* day and month of proj2 are not used but only year anproj2.*/
7996:
7997:
7998:
1.145 brouard 7999: /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint); */
8000: /* ,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2); */
1.126 brouard 8001:
8002: replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
1.194 brouard 8003: if(ageminpar == AGEOVERFLOW ||agemaxpar == -AGEOVERFLOW){
8004: printf("Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
8005: This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\
8006: Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
8007: fprintf(ficlog,"Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
8008: This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\
8009: Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
8010: }else
1.201 brouard 8011: printinggnuplot(fileresu, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
1.126 brouard 8012:
1.201 brouard 8013: printinghtml(fileresu,title,datafile, firstpass, lastpass, stepm, weightopt,\
1.126 brouard 8014: model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
8015: jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
8016:
8017: /*------------ free_vector -------------*/
8018: /* chdir(path); */
8019:
8020: free_ivector(wav,1,imx);
8021: free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
8022: free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
8023: free_imatrix(mw,1,lastpass-firstpass+1,1,imx);
8024: free_lvector(num,1,n);
8025: free_vector(agedc,1,n);
8026: /*free_matrix(covar,0,NCOVMAX,1,n);*/
8027: /*free_matrix(covar,1,NCOVMAX,1,n);*/
8028: fclose(ficparo);
8029: fclose(ficres);
8030:
8031:
1.186 brouard 8032: /* Other results (useful)*/
8033:
8034:
1.126 brouard 8035: /*--------------- Prevalence limit (period or stable prevalence) --------------*/
1.180 brouard 8036: /*#include "prevlim.h"*/ /* Use ficrespl, ficlog */
8037: prlim=matrix(1,nlstate,1,nlstate);
1.203 brouard 8038: prevalence_limit(p, prlim, ageminpar, agemaxpar, ftolpl, ncvyear);
1.126 brouard 8039: fclose(ficrespl);
8040:
1.145 brouard 8041: #ifdef FREEEXIT2
8042: #include "freeexit2.h"
8043: #endif
8044:
1.126 brouard 8045: /*------------- h Pij x at various ages ------------*/
1.180 brouard 8046: /*#include "hpijx.h"*/
8047: hPijx(p, bage, fage);
1.145 brouard 8048: fclose(ficrespij);
1.126 brouard 8049:
1.145 brouard 8050: /*-------------- Variance of one-step probabilities---*/
8051: k=1;
1.126 brouard 8052: varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
8053:
8054:
8055: probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
8056: for(i=1;i<=AGESUP;i++)
8057: for(j=1;j<=NCOVMAX;j++)
8058: for(k=1;k<=NCOVMAX;k++)
8059: probs[i][j][k]=0.;
8060:
8061: /*---------- Forecasting ------------------*/
8062: /*if((stepm == 1) && (strcmp(model,".")==0)){*/
8063: if(prevfcast==1){
8064: /* if(stepm ==1){*/
1.201 brouard 8065: prevforecast(fileresu, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
1.126 brouard 8066: /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
8067: /* } */
8068: /* else{ */
8069: /* erreur=108; */
8070: /* 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); */
8071: /* 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); */
8072: /* } */
8073: }
1.186 brouard 8074:
8075: /* ------ Other prevalence ratios------------ */
1.126 brouard 8076:
1.127 brouard 8077: /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
8078:
8079: prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
8080: /* 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",\
8081: ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
8082: */
1.126 brouard 8083:
1.127 brouard 8084: if (mobilav!=0) {
8085: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
8086: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
8087: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
8088: printf(" Error in movingaverage mobilav=%d\n",mobilav);
8089: }
1.126 brouard 8090: }
8091:
8092:
1.127 brouard 8093: /*---------- Health expectancies, no variances ------------*/
8094:
1.201 brouard 8095: strcpy(filerese,"E_");
8096: strcat(filerese,fileresu);
1.126 brouard 8097: if((ficreseij=fopen(filerese,"w"))==NULL) {
8098: printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
8099: fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
8100: }
1.208 ! brouard 8101: printf("Computing Health Expectancies: result on file '%s' ...", filerese);fflush(stdout);
! 8102: fprintf(ficlog,"Computing Health Expectancies: result on file '%s' ...", filerese);fflush(ficlog);
1.145 brouard 8103: /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
8104: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
8105:
8106: for (k=1; k <= (int) pow(2,cptcoveff); k++){
1.127 brouard 8107: fprintf(ficreseij,"\n#****** ");
8108: for(j=1;j<=cptcoveff;j++) {
1.200 brouard 8109: fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.127 brouard 8110: }
8111: fprintf(ficreseij,"******\n");
8112:
8113: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
8114: oldm=oldms;savm=savms;
8115: evsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart);
8116:
8117: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
1.145 brouard 8118: /*}*/
1.127 brouard 8119: }
8120: fclose(ficreseij);
1.208 ! brouard 8121: printf("done evsij\n");fflush(stdout);
! 8122: fprintf(ficlog,"done evsij\n");fflush(ficlog);
1.127 brouard 8123:
8124: /*---------- Health expectancies and variances ------------*/
8125:
8126:
1.201 brouard 8127: strcpy(filerest,"T_");
8128: strcat(filerest,fileresu);
1.127 brouard 8129: if((ficrest=fopen(filerest,"w"))==NULL) {
8130: printf("Problem with total LE resultfile: %s\n", filerest);goto end;
8131: fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
8132: }
1.208 ! brouard 8133: printf("Computing Total Life expectancies with their standard errors: file '%s' ...\n", filerest); fflush(stdout);
! 8134: fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' ...\n", filerest); fflush(ficlog);
1.127 brouard 8135:
1.126 brouard 8136:
1.201 brouard 8137: strcpy(fileresstde,"STDE_");
8138: strcat(fileresstde,fileresu);
1.126 brouard 8139: if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {
8140: printf("Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
8141: fprintf(ficlog,"Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
8142: }
1.208 ! brouard 8143: printf(" Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
! 8144: fprintf(ficlog," Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
1.126 brouard 8145:
1.201 brouard 8146: strcpy(filerescve,"CVE_");
8147: strcat(filerescve,fileresu);
1.126 brouard 8148: if((ficrescveij=fopen(filerescve,"w"))==NULL) {
8149: printf("Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
8150: fprintf(ficlog,"Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
8151: }
1.208 ! brouard 8152: printf(" Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
! 8153: fprintf(ficlog," Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
1.126 brouard 8154:
1.201 brouard 8155: strcpy(fileresv,"V_");
8156: strcat(fileresv,fileresu);
1.126 brouard 8157: if((ficresvij=fopen(fileresv,"w"))==NULL) {
8158: printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
8159: fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
8160: }
1.208 ! brouard 8161: printf(" Computing Variance-covariance of DFLEs: file '%s' ... ", fileresv);fflush(stdout);
! 8162: fprintf(ficlog," Computing Variance-covariance of DFLEs: file '%s' ... ", fileresv);fflush(ficlog);
1.126 brouard 8163:
1.145 brouard 8164: /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
8165: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
8166:
8167: for (k=1; k <= (int) pow(2,cptcoveff); k++){
1.208 ! brouard 8168: fprintf(ficrest,"\n#****** ");
! 8169: for(j=1;j<=cptcoveff;j++)
! 8170: fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
! 8171: fprintf(ficrest,"******\n");
! 8172:
! 8173: fprintf(ficresstdeij,"\n#****** ");
! 8174: fprintf(ficrescveij,"\n#****** ");
! 8175: for(j=1;j<=cptcoveff;j++) {
! 8176: fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
! 8177: fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
! 8178: }
! 8179: fprintf(ficresstdeij,"******\n");
! 8180: fprintf(ficrescveij,"******\n");
! 8181:
! 8182: fprintf(ficresvij,"\n#****** ");
! 8183: for(j=1;j<=cptcoveff;j++)
! 8184: fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
! 8185: fprintf(ficresvij,"******\n");
! 8186:
! 8187: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
! 8188: oldm=oldms;savm=savms;
! 8189: printf(" cvevsij %d, ",k);
! 8190: fprintf(ficlog, " cvevsij %d, ",k);
! 8191: cvevsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);
! 8192: printf(" end cvevsij \n ");
! 8193: fprintf(ficlog, " end cvevsij \n ");
! 8194:
! 8195: /*
! 8196: */
! 8197: /* goto endfree; */
! 8198:
! 8199: vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
! 8200: pstamp(ficrest);
! 8201:
! 8202:
! 8203: for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
! 8204: oldm=oldms;savm=savms; /* ZZ Segmentation fault */
! 8205: cptcod= 0; /* To be deleted */
! 8206: printf("varevsij %d \n",vpopbased);
! 8207: fprintf(ficlog, "varevsij %d \n",vpopbased);
! 8208: 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 */
! 8209: 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 ");
! 8210: if(vpopbased==1)
! 8211: 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);
! 8212: else
! 8213: fprintf(ficrest,"the age specific period (stable) prevalences in each health state \n");
! 8214: fprintf(ficrest,"# Age popbased mobilav e.. (std) ");
! 8215: for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
! 8216: fprintf(ficrest,"\n");
! 8217: /* printf("Which p?\n"); for(i=1;i<=npar;i++)printf("p[i=%d]=%lf,",i,p[i]);printf("\n"); */
! 8218: epj=vector(1,nlstate+1);
! 8219: printf("Computing age specific period (stable) prevalences in each health state \n");
! 8220: fprintf(ficlog,"Computing age specific period (stable) prevalences in each health state \n");
! 8221: for(age=bage; age <=fage ;age++){
! 8222: prevalim(prlim, nlstate, p, age, oldm, savm, ftolpl, ncvyear, k); /*ZZ Is it the correct prevalim */
! 8223: if (vpopbased==1) {
! 8224: if(mobilav ==0){
! 8225: for(i=1; i<=nlstate;i++)
! 8226: prlim[i][i]=probs[(int)age][i][k];
! 8227: }else{ /* mobilav */
! 8228: for(i=1; i<=nlstate;i++)
! 8229: prlim[i][i]=mobaverage[(int)age][i][k];
1.126 brouard 8230: }
1.208 ! brouard 8231: }
! 8232:
! 8233: fprintf(ficrest," %4.0f %d %d",age, vpopbased, mobilav);
! 8234: /* fprintf(ficrest," %4.0f %d %d %d %d",age, vpopbased, mobilav,Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); */ /* to be done */
! 8235: /* printf(" age %4.0f ",age); */
! 8236: for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
! 8237: for(i=1, epj[j]=0.;i <=nlstate;i++) {
! 8238: epj[j] += prlim[i][i]*eij[i][j][(int)age];
! 8239: /*ZZZ printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
! 8240: /* printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]); */
1.126 brouard 8241: }
1.208 ! brouard 8242: epj[nlstate+1] +=epj[j];
! 8243: }
! 8244: /* printf(" age %4.0f \n",age); */
! 8245:
! 8246: for(i=1, vepp=0.;i <=nlstate;i++)
! 8247: for(j=1;j <=nlstate;j++)
! 8248: vepp += vareij[i][j][(int)age];
! 8249: fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
! 8250: for(j=1;j <=nlstate;j++){
! 8251: fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
1.126 brouard 8252: }
1.208 ! brouard 8253: fprintf(ficrest,"\n");
1.126 brouard 8254: }
1.208 ! brouard 8255: } /* End vpopbased */
! 8256: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
! 8257: free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
! 8258: free_vector(epj,1,nlstate+1);
! 8259: printf("done \n");fflush(stdout);
! 8260: fprintf(ficlog,"done\n");fflush(ficlog);
! 8261:
1.145 brouard 8262: /*}*/
1.208 ! brouard 8263: } /* End k */
1.126 brouard 8264: free_vector(weight,1,n);
1.145 brouard 8265: free_imatrix(Tvard,1,NCOVMAX,1,2);
1.126 brouard 8266: free_imatrix(s,1,maxwav+1,1,n);
8267: free_matrix(anint,1,maxwav,1,n);
8268: free_matrix(mint,1,maxwav,1,n);
8269: free_ivector(cod,1,n);
8270: free_ivector(tab,1,NCOVMAX);
8271: fclose(ficresstdeij);
8272: fclose(ficrescveij);
8273: fclose(ficresvij);
8274: fclose(ficrest);
1.208 ! brouard 8275: printf("done Health expectancies\n");fflush(stdout);
! 8276: fprintf(ficlog,"done Health expectancies\n");fflush(ficlog);
1.126 brouard 8277: fclose(ficpar);
8278:
8279: /*------- Variance of period (stable) prevalence------*/
8280:
1.201 brouard 8281: strcpy(fileresvpl,"VPL_");
8282: strcat(fileresvpl,fileresu);
1.126 brouard 8283: if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
8284: printf("Problem with variance of period (stable) prevalence resultfile: %s\n", fileresvpl);
8285: exit(0);
8286: }
1.208 ! brouard 8287: printf("Computing Variance-covariance of period (stable) prevalence: file '%s' ...", fileresvpl);fflush(stdout);
! 8288: fprintf(ficlog, "Computing Variance-covariance of period (stable) prevalence: file '%s' ...", fileresvpl);fflush(ficlog);
1.126 brouard 8289:
1.145 brouard 8290: /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
8291: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
8292:
8293: for (k=1; k <= (int) pow(2,cptcoveff); k++){
8294: fprintf(ficresvpl,"\n#****** ");
1.126 brouard 8295: for(j=1;j<=cptcoveff;j++)
1.200 brouard 8296: fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.126 brouard 8297: fprintf(ficresvpl,"******\n");
8298:
8299: varpl=matrix(1,nlstate,(int) bage, (int) fage);
8300: oldm=oldms;savm=savms;
1.203 brouard 8301: varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl, ncvyear, k, strstart);
1.126 brouard 8302: free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
1.145 brouard 8303: /*}*/
1.126 brouard 8304: }
8305:
8306: fclose(ficresvpl);
1.208 ! brouard 8307: printf("done variance-covariance of period prevalence\n");fflush(stdout);
! 8308: fprintf(ficlog,"done variance-covariance of period prevalence\n");fflush(ficlog);
1.126 brouard 8309:
8310: /*---------- End : free ----------------*/
8311: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
8312: free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
8313: } /* mle==-3 arrives here for freeing */
1.164 brouard 8314: /* endfree:*/
1.141 brouard 8315: free_matrix(prlim,1,nlstate,1,nlstate); /*here or after loop ? */
1.126 brouard 8316: free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
8317: free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
8318: free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
8319: free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
8320: free_matrix(covar,0,NCOVMAX,1,n);
8321: free_matrix(matcov,1,npar,1,npar);
1.203 brouard 8322: free_matrix(hess,1,npar,1,npar);
1.126 brouard 8323: /*free_vector(delti,1,npar);*/
8324: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
8325: free_matrix(agev,1,maxwav,1,imx);
8326: free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
8327:
1.145 brouard 8328: free_ivector(ncodemax,1,NCOVMAX);
1.192 brouard 8329: free_ivector(ncodemaxwundef,1,NCOVMAX);
1.145 brouard 8330: free_ivector(Tvar,1,NCOVMAX);
8331: free_ivector(Tprod,1,NCOVMAX);
8332: free_ivector(Tvaraff,1,NCOVMAX);
8333: free_ivector(Tage,1,NCOVMAX);
1.126 brouard 8334:
8335: free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
1.200 brouard 8336: /* free_imatrix(codtab,1,100,1,10); */
1.126 brouard 8337: fflush(fichtm);
8338: fflush(ficgp);
8339:
8340:
8341: if((nberr >0) || (nbwarn>0)){
8342: printf("End of Imach with %d errors and/or %d warnings\n",nberr,nbwarn);
8343: fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
8344: }else{
8345: printf("End of Imach\n");
8346: fprintf(ficlog,"End of Imach\n");
8347: }
8348: printf("See log file on %s\n",filelog);
8349: /* gettimeofday(&end_time, (struct timezone*)0);*/ /* after time */
1.157 brouard 8350: /*(void) gettimeofday(&end_time,&tzp);*/
8351: rend_time = time(NULL);
8352: end_time = *localtime(&rend_time);
8353: /* tml = *localtime(&end_time.tm_sec); */
8354: strcpy(strtend,asctime(&end_time));
1.126 brouard 8355: printf("Local time at start %s\nLocal time at end %s",strstart, strtend);
8356: fprintf(ficlog,"Local time at start %s\nLocal time at end %s\n",strstart, strtend);
1.157 brouard 8357: printf("Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
1.126 brouard 8358:
1.157 brouard 8359: printf("Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
8360: fprintf(ficlog,"Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
8361: fprintf(ficlog,"Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
1.126 brouard 8362: /* printf("Total time was %d uSec.\n", total_usecs);*/
8363: /* if(fileappend(fichtm,optionfilehtm)){ */
8364: fprintf(fichtm,"<br>Local time at start %s<br>Local time at end %s<br>\n</body></html>",strstart, strtend);
8365: fclose(fichtm);
8366: fprintf(fichtmcov,"<br>Local time at start %s<br>Local time at end %s<br>\n</body></html>",strstart, strtend);
8367: fclose(fichtmcov);
8368: fclose(ficgp);
8369: fclose(ficlog);
8370: /*------ End -----------*/
8371:
8372:
8373: printf("Before Current directory %s!\n",pathcd);
1.184 brouard 8374: #ifdef WIN32
8375: if (_chdir(pathcd) != 0)
8376: printf("Can't move to directory %s!\n",path);
8377: if(_getcwd(pathcd,MAXLINE) > 0)
8378: #else
1.126 brouard 8379: if(chdir(pathcd) != 0)
1.184 brouard 8380: printf("Can't move to directory %s!\n", path);
8381: if (getcwd(pathcd, MAXLINE) > 0)
8382: #endif
1.126 brouard 8383: printf("Current directory %s!\n",pathcd);
8384: /*strcat(plotcmd,CHARSEPARATOR);*/
8385: sprintf(plotcmd,"gnuplot");
1.157 brouard 8386: #ifdef _WIN32
1.126 brouard 8387: sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
8388: #endif
8389: if(!stat(plotcmd,&info)){
1.158 brouard 8390: printf("Error or gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
1.126 brouard 8391: if(!stat(getenv("GNUPLOTBIN"),&info)){
1.158 brouard 8392: printf("Error or gnuplot program not found: '%s' Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);
1.126 brouard 8393: }else
8394: strcpy(pplotcmd,plotcmd);
1.157 brouard 8395: #ifdef __unix
1.126 brouard 8396: strcpy(plotcmd,GNUPLOTPROGRAM);
8397: if(!stat(plotcmd,&info)){
1.158 brouard 8398: printf("Error gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
1.126 brouard 8399: }else
8400: strcpy(pplotcmd,plotcmd);
8401: #endif
8402: }else
8403: strcpy(pplotcmd,plotcmd);
8404:
8405: sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
1.158 brouard 8406: printf("Starting graphs with: '%s'\n",plotcmd);fflush(stdout);
1.126 brouard 8407:
8408: if((outcmd=system(plotcmd)) != 0){
1.158 brouard 8409: printf("gnuplot command might not be in your path: '%s', err=%d\n", plotcmd, outcmd);
1.154 brouard 8410: printf("\n Trying if gnuplot resides on the same directory that IMaCh\n");
1.152 brouard 8411: sprintf(plotcmd,"%sgnuplot %s", pathimach, optionfilegnuplot);
1.150 brouard 8412: if((outcmd=system(plotcmd)) != 0)
1.153 brouard 8413: printf("\n Still a problem with gnuplot command %s, err=%d\n", plotcmd, outcmd);
1.126 brouard 8414: }
1.158 brouard 8415: printf(" Successful, please wait...");
1.126 brouard 8416: while (z[0] != 'q') {
8417: /* chdir(path); */
1.154 brouard 8418: printf("\nType e to edit results with your browser, g to graph again and q for exit: ");
1.126 brouard 8419: scanf("%s",z);
8420: /* if (z[0] == 'c') system("./imach"); */
8421: if (z[0] == 'e') {
1.158 brouard 8422: #ifdef __APPLE__
1.152 brouard 8423: sprintf(pplotcmd, "open %s", optionfilehtm);
1.157 brouard 8424: #elif __linux
8425: sprintf(pplotcmd, "xdg-open %s", optionfilehtm);
1.153 brouard 8426: #else
1.152 brouard 8427: sprintf(pplotcmd, "%s", optionfilehtm);
1.153 brouard 8428: #endif
8429: printf("Starting browser with: %s",pplotcmd);fflush(stdout);
8430: system(pplotcmd);
1.126 brouard 8431: }
8432: else if (z[0] == 'g') system(plotcmd);
8433: else if (z[0] == 'q') exit(0);
8434: }
8435: end:
8436: while (z[0] != 'q') {
1.195 brouard 8437: printf("\nType q for exiting: "); fflush(stdout);
1.126 brouard 8438: scanf("%s",z);
8439: }
8440: }
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