Annotation of imach/src/imach.c, revision 1.209
1.209 ! brouard 1: /* $Id: imach.c,v 1.208 2015/11/17 14:31:57 brouard Exp $
1.126 brouard 2: $State: Exp $
1.163 brouard 3: $Log: imach.c,v $
1.209 ! brouard 4: Revision 1.208 2015/11/17 14:31:57 brouard
! 5: Summary: temporary
! 6:
1.208 brouard 7: Revision 1.207 2015/10/27 17:36:57 brouard
8: *** empty log message ***
9:
1.207 brouard 10: Revision 1.206 2015/10/24 07:14:11 brouard
11: *** empty log message ***
12:
1.206 brouard 13: Revision 1.205 2015/10/23 15:50:53 brouard
14: Summary: 0.98r3 some clarification for graphs on likelihood contributions
15:
1.205 brouard 16: Revision 1.204 2015/10/01 16:20:26 brouard
17: Summary: Some new graphs of contribution to likelihood
18:
1.204 brouard 19: Revision 1.203 2015/09/30 17:45:14 brouard
20: Summary: looking at better estimation of the hessian
21:
22: Also a better criteria for convergence to the period prevalence And
23: therefore adding the number of years needed to converge. (The
24: prevalence in any alive state shold sum to one
25:
1.203 brouard 26: Revision 1.202 2015/09/22 19:45:16 brouard
27: Summary: Adding some overall graph on contribution to likelihood. Might change
28:
1.202 brouard 29: Revision 1.201 2015/09/15 17:34:58 brouard
30: Summary: 0.98r0
31:
32: - Some new graphs like suvival functions
33: - Some bugs fixed like model=1+age+V2.
34:
1.201 brouard 35: Revision 1.200 2015/09/09 16:53:55 brouard
36: Summary: Big bug thanks to Flavia
37:
38: Even model=1+age+V2. did not work anymore
39:
1.200 brouard 40: Revision 1.199 2015/09/07 14:09:23 brouard
41: Summary: 0.98q6 changing default small png format for graph to vectorized svg.
42:
1.199 brouard 43: Revision 1.198 2015/09/03 07:14:39 brouard
44: Summary: 0.98q5 Flavia
45:
1.198 brouard 46: Revision 1.197 2015/09/01 18:24:39 brouard
47: *** empty log message ***
48:
1.197 brouard 49: Revision 1.196 2015/08/18 23:17:52 brouard
50: Summary: 0.98q5
51:
1.196 brouard 52: Revision 1.195 2015/08/18 16:28:39 brouard
53: Summary: Adding a hack for testing purpose
54:
55: After reading the title, ftol and model lines, if the comment line has
56: a q, starting with #q, the answer at the end of the run is quit. It
57: permits to run test files in batch with ctest. The former workaround was
58: $ echo q | imach foo.imach
59:
1.195 brouard 60: Revision 1.194 2015/08/18 13:32:00 brouard
61: Summary: Adding error when the covariance matrix doesn't contain the exact number of lines required by the model line.
62:
1.194 brouard 63: Revision 1.193 2015/08/04 07:17:42 brouard
64: Summary: 0.98q4
65:
1.193 brouard 66: Revision 1.192 2015/07/16 16:49:02 brouard
67: Summary: Fixing some outputs
68:
1.192 brouard 69: Revision 1.191 2015/07/14 10:00:33 brouard
70: Summary: Some fixes
71:
1.191 brouard 72: Revision 1.190 2015/05/05 08:51:13 brouard
73: Summary: Adding digits in output parameters (7 digits instead of 6)
74:
75: Fix 1+age+.
76:
1.190 brouard 77: Revision 1.189 2015/04/30 14:45:16 brouard
78: Summary: 0.98q2
79:
1.189 brouard 80: Revision 1.188 2015/04/30 08:27:53 brouard
81: *** empty log message ***
82:
1.188 brouard 83: Revision 1.187 2015/04/29 09:11:15 brouard
84: *** empty log message ***
85:
1.187 brouard 86: Revision 1.186 2015/04/23 12:01:52 brouard
87: Summary: V1*age is working now, version 0.98q1
88:
89: Some codes had been disabled in order to simplify and Vn*age was
90: working in the optimization phase, ie, giving correct MLE parameters,
91: but, as usual, outputs were not correct and program core dumped.
92:
1.186 brouard 93: Revision 1.185 2015/03/11 13:26:42 brouard
94: Summary: Inclusion of compile and links command line for Intel Compiler
95:
1.185 brouard 96: Revision 1.184 2015/03/11 11:52:39 brouard
97: Summary: Back from Windows 8. Intel Compiler
98:
1.184 brouard 99: Revision 1.183 2015/03/10 20:34:32 brouard
100: Summary: 0.98q0, trying with directest, mnbrak fixed
101:
102: We use directest instead of original Powell test; probably no
103: incidence on the results, but better justifications;
104: We fixed Numerical Recipes mnbrak routine which was wrong and gave
105: wrong results.
106:
1.183 brouard 107: Revision 1.182 2015/02/12 08:19:57 brouard
108: Summary: Trying to keep directest which seems simpler and more general
109: Author: Nicolas Brouard
110:
1.182 brouard 111: Revision 1.181 2015/02/11 23:22:24 brouard
112: Summary: Comments on Powell added
113:
114: Author:
115:
1.181 brouard 116: Revision 1.180 2015/02/11 17:33:45 brouard
117: Summary: Finishing move from main to function (hpijx and prevalence_limit)
118:
1.180 brouard 119: Revision 1.179 2015/01/04 09:57:06 brouard
120: Summary: back to OS/X
121:
1.179 brouard 122: Revision 1.178 2015/01/04 09:35:48 brouard
123: *** empty log message ***
124:
1.178 brouard 125: Revision 1.177 2015/01/03 18:40:56 brouard
126: Summary: Still testing ilc32 on OSX
127:
1.177 brouard 128: Revision 1.176 2015/01/03 16:45:04 brouard
129: *** empty log message ***
130:
1.176 brouard 131: Revision 1.175 2015/01/03 16:33:42 brouard
132: *** empty log message ***
133:
1.175 brouard 134: Revision 1.174 2015/01/03 16:15:49 brouard
135: Summary: Still in cross-compilation
136:
1.174 brouard 137: Revision 1.173 2015/01/03 12:06:26 brouard
138: Summary: trying to detect cross-compilation
139:
1.173 brouard 140: Revision 1.172 2014/12/27 12:07:47 brouard
141: Summary: Back from Visual Studio and Intel, options for compiling for Windows XP
142:
1.172 brouard 143: Revision 1.171 2014/12/23 13:26:59 brouard
144: Summary: Back from Visual C
145:
146: Still problem with utsname.h on Windows
147:
1.171 brouard 148: Revision 1.170 2014/12/23 11:17:12 brouard
149: Summary: Cleaning some \%% back to %%
150:
151: The escape was mandatory for a specific compiler (which one?), but too many warnings.
152:
1.170 brouard 153: Revision 1.169 2014/12/22 23:08:31 brouard
154: Summary: 0.98p
155:
156: Outputs some informations on compiler used, OS etc. Testing on different platforms.
157:
1.169 brouard 158: Revision 1.168 2014/12/22 15:17:42 brouard
1.170 brouard 159: Summary: update
1.169 brouard 160:
1.168 brouard 161: Revision 1.167 2014/12/22 13:50:56 brouard
162: Summary: Testing uname and compiler version and if compiled 32 or 64
163:
164: Testing on Linux 64
165:
1.167 brouard 166: Revision 1.166 2014/12/22 11:40:47 brouard
167: *** empty log message ***
168:
1.166 brouard 169: Revision 1.165 2014/12/16 11:20:36 brouard
170: Summary: After compiling on Visual C
171:
172: * imach.c (Module): Merging 1.61 to 1.162
173:
1.165 brouard 174: Revision 1.164 2014/12/16 10:52:11 brouard
175: Summary: Merging with Visual C after suppressing some warnings for unused variables. Also fixing Saito's bug 0.98Xn
176:
177: * imach.c (Module): Merging 1.61 to 1.162
178:
1.164 brouard 179: Revision 1.163 2014/12/16 10:30:11 brouard
180: * imach.c (Module): Merging 1.61 to 1.162
181:
1.163 brouard 182: Revision 1.162 2014/09/25 11:43:39 brouard
183: Summary: temporary backup 0.99!
184:
1.162 brouard 185: Revision 1.1 2014/09/16 11:06:58 brouard
186: Summary: With some code (wrong) for nlopt
187:
188: Author:
189:
190: Revision 1.161 2014/09/15 20:41:41 brouard
191: Summary: Problem with macro SQR on Intel compiler
192:
1.161 brouard 193: Revision 1.160 2014/09/02 09:24:05 brouard
194: *** empty log message ***
195:
1.160 brouard 196: Revision 1.159 2014/09/01 10:34:10 brouard
197: Summary: WIN32
198: Author: Brouard
199:
1.159 brouard 200: Revision 1.158 2014/08/27 17:11:51 brouard
201: *** empty log message ***
202:
1.158 brouard 203: Revision 1.157 2014/08/27 16:26:55 brouard
204: Summary: Preparing windows Visual studio version
205: Author: Brouard
206:
207: In order to compile on Visual studio, time.h is now correct and time_t
208: and tm struct should be used. difftime should be used but sometimes I
209: just make the differences in raw time format (time(&now).
210: Trying to suppress #ifdef LINUX
211: Add xdg-open for __linux in order to open default browser.
212:
1.157 brouard 213: Revision 1.156 2014/08/25 20:10:10 brouard
214: *** empty log message ***
215:
1.156 brouard 216: Revision 1.155 2014/08/25 18:32:34 brouard
217: Summary: New compile, minor changes
218: Author: Brouard
219:
1.155 brouard 220: Revision 1.154 2014/06/20 17:32:08 brouard
221: Summary: Outputs now all graphs of convergence to period prevalence
222:
1.154 brouard 223: Revision 1.153 2014/06/20 16:45:46 brouard
224: Summary: If 3 live state, convergence to period prevalence on same graph
225: Author: Brouard
226:
1.153 brouard 227: Revision 1.152 2014/06/18 17:54:09 brouard
228: Summary: open browser, use gnuplot on same dir than imach if not found in the path
229:
1.152 brouard 230: Revision 1.151 2014/06/18 16:43:30 brouard
231: *** empty log message ***
232:
1.151 brouard 233: Revision 1.150 2014/06/18 16:42:35 brouard
234: Summary: If gnuplot is not in the path try on same directory than imach binary (OSX)
235: Author: brouard
236:
1.150 brouard 237: Revision 1.149 2014/06/18 15:51:14 brouard
238: Summary: Some fixes in parameter files errors
239: Author: Nicolas Brouard
240:
1.149 brouard 241: Revision 1.148 2014/06/17 17:38:48 brouard
242: Summary: Nothing new
243: Author: Brouard
244:
245: Just a new packaging for OS/X version 0.98nS
246:
1.148 brouard 247: Revision 1.147 2014/06/16 10:33:11 brouard
248: *** empty log message ***
249:
1.147 brouard 250: Revision 1.146 2014/06/16 10:20:28 brouard
251: Summary: Merge
252: Author: Brouard
253:
254: Merge, before building revised version.
255:
1.146 brouard 256: Revision 1.145 2014/06/10 21:23:15 brouard
257: Summary: Debugging with valgrind
258: Author: Nicolas Brouard
259:
260: Lot of changes in order to output the results with some covariates
261: After the Edimburgh REVES conference 2014, it seems mandatory to
262: improve the code.
263: No more memory valgrind error but a lot has to be done in order to
264: continue the work of splitting the code into subroutines.
265: Also, decodemodel has been improved. Tricode is still not
266: optimal. nbcode should be improved. Documentation has been added in
267: the source code.
268:
1.144 brouard 269: Revision 1.143 2014/01/26 09:45:38 brouard
270: Summary: Version 0.98nR (to be improved, but gives same optimization results as 0.98k. Nice, promising
271:
272: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
273: (Module): Version 0.98nR Running ok, but output format still only works for three covariates.
274:
1.143 brouard 275: Revision 1.142 2014/01/26 03:57:36 brouard
276: Summary: gnuplot changed plot w l 1 has to be changed to plot w l lt 2
277:
278: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
279:
1.142 brouard 280: Revision 1.141 2014/01/26 02:42:01 brouard
281: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
282:
1.141 brouard 283: Revision 1.140 2011/09/02 10:37:54 brouard
284: Summary: times.h is ok with mingw32 now.
285:
1.140 brouard 286: Revision 1.139 2010/06/14 07:50:17 brouard
287: After the theft of my laptop, I probably lost some lines of codes which were not uploaded to the CVS tree.
288: I remember having already fixed agemin agemax which are pointers now but not cvs saved.
289:
1.139 brouard 290: Revision 1.138 2010/04/30 18:19:40 brouard
291: *** empty log message ***
292:
1.138 brouard 293: Revision 1.137 2010/04/29 18:11:38 brouard
294: (Module): Checking covariates for more complex models
295: than V1+V2. A lot of change to be done. Unstable.
296:
1.137 brouard 297: Revision 1.136 2010/04/26 20:30:53 brouard
298: (Module): merging some libgsl code. Fixing computation
299: of likelione (using inter/intrapolation if mle = 0) in order to
300: get same likelihood as if mle=1.
301: Some cleaning of code and comments added.
302:
1.136 brouard 303: Revision 1.135 2009/10/29 15:33:14 brouard
304: (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
305:
1.135 brouard 306: Revision 1.134 2009/10/29 13:18:53 brouard
307: (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
308:
1.134 brouard 309: Revision 1.133 2009/07/06 10:21:25 brouard
310: just nforces
311:
1.133 brouard 312: Revision 1.132 2009/07/06 08:22:05 brouard
313: Many tings
314:
1.132 brouard 315: Revision 1.131 2009/06/20 16:22:47 brouard
316: Some dimensions resccaled
317:
1.131 brouard 318: Revision 1.130 2009/05/26 06:44:34 brouard
319: (Module): Max Covariate is now set to 20 instead of 8. A
320: lot of cleaning with variables initialized to 0. Trying to make
321: V2+V3*age+V1+V4 strb=V3*age+V1+V4 working better.
322:
1.130 brouard 323: Revision 1.129 2007/08/31 13:49:27 lievre
324: Modification of the way of exiting when the covariate is not binary in order to see on the window the error message before exiting
325:
1.129 lievre 326: Revision 1.128 2006/06/30 13:02:05 brouard
327: (Module): Clarifications on computing e.j
328:
1.128 brouard 329: Revision 1.127 2006/04/28 18:11:50 brouard
330: (Module): Yes the sum of survivors was wrong since
331: imach-114 because nhstepm was no more computed in the age
332: loop. Now we define nhstepma in the age loop.
333: (Module): In order to speed up (in case of numerous covariates) we
334: compute health expectancies (without variances) in a first step
335: and then all the health expectancies with variances or standard
336: deviation (needs data from the Hessian matrices) which slows the
337: computation.
338: In the future we should be able to stop the program is only health
339: expectancies and graph are needed without standard deviations.
340:
1.127 brouard 341: Revision 1.126 2006/04/28 17:23:28 brouard
342: (Module): Yes the sum of survivors was wrong since
343: imach-114 because nhstepm was no more computed in the age
344: loop. Now we define nhstepma in the age loop.
345: Version 0.98h
346:
1.126 brouard 347: Revision 1.125 2006/04/04 15:20:31 lievre
348: Errors in calculation of health expectancies. Age was not initialized.
349: Forecasting file added.
350:
351: Revision 1.124 2006/03/22 17:13:53 lievre
352: Parameters are printed with %lf instead of %f (more numbers after the comma).
353: The log-likelihood is printed in the log file
354:
355: Revision 1.123 2006/03/20 10:52:43 brouard
356: * imach.c (Module): <title> changed, corresponds to .htm file
357: name. <head> headers where missing.
358:
359: * imach.c (Module): Weights can have a decimal point as for
360: English (a comma might work with a correct LC_NUMERIC environment,
361: otherwise the weight is truncated).
362: Modification of warning when the covariates values are not 0 or
363: 1.
364: Version 0.98g
365:
366: Revision 1.122 2006/03/20 09:45:41 brouard
367: (Module): Weights can have a decimal point as for
368: English (a comma might work with a correct LC_NUMERIC environment,
369: otherwise the weight is truncated).
370: Modification of warning when the covariates values are not 0 or
371: 1.
372: Version 0.98g
373:
374: Revision 1.121 2006/03/16 17:45:01 lievre
375: * imach.c (Module): Comments concerning covariates added
376:
377: * imach.c (Module): refinements in the computation of lli if
378: status=-2 in order to have more reliable computation if stepm is
379: not 1 month. Version 0.98f
380:
381: Revision 1.120 2006/03/16 15:10:38 lievre
382: (Module): refinements in the computation of lli if
383: status=-2 in order to have more reliable computation if stepm is
384: not 1 month. Version 0.98f
385:
386: Revision 1.119 2006/03/15 17:42:26 brouard
387: (Module): Bug if status = -2, the loglikelihood was
388: computed as likelihood omitting the logarithm. Version O.98e
389:
390: Revision 1.118 2006/03/14 18:20:07 brouard
391: (Module): varevsij Comments added explaining the second
392: table of variances if popbased=1 .
393: (Module): Covariances of eij, ekl added, graphs fixed, new html link.
394: (Module): Function pstamp added
395: (Module): Version 0.98d
396:
397: Revision 1.117 2006/03/14 17:16:22 brouard
398: (Module): varevsij Comments added explaining the second
399: table of variances if popbased=1 .
400: (Module): Covariances of eij, ekl added, graphs fixed, new html link.
401: (Module): Function pstamp added
402: (Module): Version 0.98d
403:
404: Revision 1.116 2006/03/06 10:29:27 brouard
405: (Module): Variance-covariance wrong links and
406: varian-covariance of ej. is needed (Saito).
407:
408: Revision 1.115 2006/02/27 12:17:45 brouard
409: (Module): One freematrix added in mlikeli! 0.98c
410:
411: Revision 1.114 2006/02/26 12:57:58 brouard
412: (Module): Some improvements in processing parameter
413: filename with strsep.
414:
415: Revision 1.113 2006/02/24 14:20:24 brouard
416: (Module): Memory leaks checks with valgrind and:
417: datafile was not closed, some imatrix were not freed and on matrix
418: allocation too.
419:
420: Revision 1.112 2006/01/30 09:55:26 brouard
421: (Module): Back to gnuplot.exe instead of wgnuplot.exe
422:
423: Revision 1.111 2006/01/25 20:38:18 brouard
424: (Module): Lots of cleaning and bugs added (Gompertz)
425: (Module): Comments can be added in data file. Missing date values
426: can be a simple dot '.'.
427:
428: Revision 1.110 2006/01/25 00:51:50 brouard
429: (Module): Lots of cleaning and bugs added (Gompertz)
430:
431: Revision 1.109 2006/01/24 19:37:15 brouard
432: (Module): Comments (lines starting with a #) are allowed in data.
433:
434: Revision 1.108 2006/01/19 18:05:42 lievre
435: Gnuplot problem appeared...
436: To be fixed
437:
438: Revision 1.107 2006/01/19 16:20:37 brouard
439: Test existence of gnuplot in imach path
440:
441: Revision 1.106 2006/01/19 13:24:36 brouard
442: Some cleaning and links added in html output
443:
444: Revision 1.105 2006/01/05 20:23:19 lievre
445: *** empty log message ***
446:
447: Revision 1.104 2005/09/30 16:11:43 lievre
448: (Module): sump fixed, loop imx fixed, and simplifications.
449: (Module): If the status is missing at the last wave but we know
450: that the person is alive, then we can code his/her status as -2
451: (instead of missing=-1 in earlier versions) and his/her
452: contributions to the likelihood is 1 - Prob of dying from last
453: health status (= 1-p13= p11+p12 in the easiest case of somebody in
454: the healthy state at last known wave). Version is 0.98
455:
456: Revision 1.103 2005/09/30 15:54:49 lievre
457: (Module): sump fixed, loop imx fixed, and simplifications.
458:
459: Revision 1.102 2004/09/15 17:31:30 brouard
460: Add the possibility to read data file including tab characters.
461:
462: Revision 1.101 2004/09/15 10:38:38 brouard
463: Fix on curr_time
464:
465: Revision 1.100 2004/07/12 18:29:06 brouard
466: Add version for Mac OS X. Just define UNIX in Makefile
467:
468: Revision 1.99 2004/06/05 08:57:40 brouard
469: *** empty log message ***
470:
471: Revision 1.98 2004/05/16 15:05:56 brouard
472: New version 0.97 . First attempt to estimate force of mortality
473: directly from the data i.e. without the need of knowing the health
474: state at each age, but using a Gompertz model: log u =a + b*age .
475: This is the basic analysis of mortality and should be done before any
476: other analysis, in order to test if the mortality estimated from the
477: cross-longitudinal survey is different from the mortality estimated
478: from other sources like vital statistic data.
479:
480: The same imach parameter file can be used but the option for mle should be -3.
481:
1.133 brouard 482: Agnès, who wrote this part of the code, tried to keep most of the
1.126 brouard 483: former routines in order to include the new code within the former code.
484:
485: The output is very simple: only an estimate of the intercept and of
486: the slope with 95% confident intervals.
487:
488: Current limitations:
489: A) Even if you enter covariates, i.e. with the
490: model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
491: B) There is no computation of Life Expectancy nor Life Table.
492:
493: Revision 1.97 2004/02/20 13:25:42 lievre
494: Version 0.96d. Population forecasting command line is (temporarily)
495: suppressed.
496:
497: Revision 1.96 2003/07/15 15:38:55 brouard
498: * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
499: rewritten within the same printf. Workaround: many printfs.
500:
501: Revision 1.95 2003/07/08 07:54:34 brouard
502: * imach.c (Repository):
503: (Repository): Using imachwizard code to output a more meaningful covariance
504: matrix (cov(a12,c31) instead of numbers.
505:
506: Revision 1.94 2003/06/27 13:00:02 brouard
507: Just cleaning
508:
509: Revision 1.93 2003/06/25 16:33:55 brouard
510: (Module): On windows (cygwin) function asctime_r doesn't
511: exist so I changed back to asctime which exists.
512: (Module): Version 0.96b
513:
514: Revision 1.92 2003/06/25 16:30:45 brouard
515: (Module): On windows (cygwin) function asctime_r doesn't
516: exist so I changed back to asctime which exists.
517:
518: Revision 1.91 2003/06/25 15:30:29 brouard
519: * imach.c (Repository): Duplicated warning errors corrected.
520: (Repository): Elapsed time after each iteration is now output. It
521: helps to forecast when convergence will be reached. Elapsed time
522: is stamped in powell. We created a new html file for the graphs
523: concerning matrix of covariance. It has extension -cov.htm.
524:
525: Revision 1.90 2003/06/24 12:34:15 brouard
526: (Module): Some bugs corrected for windows. Also, when
527: mle=-1 a template is output in file "or"mypar.txt with the design
528: of the covariance matrix to be input.
529:
530: Revision 1.89 2003/06/24 12:30:52 brouard
531: (Module): Some bugs corrected for windows. Also, when
532: mle=-1 a template is output in file "or"mypar.txt with the design
533: of the covariance matrix to be input.
534:
535: Revision 1.88 2003/06/23 17:54:56 brouard
536: * 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.
537:
538: Revision 1.87 2003/06/18 12:26:01 brouard
539: Version 0.96
540:
541: Revision 1.86 2003/06/17 20:04:08 brouard
542: (Module): Change position of html and gnuplot routines and added
543: routine fileappend.
544:
545: Revision 1.85 2003/06/17 13:12:43 brouard
546: * imach.c (Repository): Check when date of death was earlier that
547: current date of interview. It may happen when the death was just
548: prior to the death. In this case, dh was negative and likelihood
549: was wrong (infinity). We still send an "Error" but patch by
550: assuming that the date of death was just one stepm after the
551: interview.
552: (Repository): Because some people have very long ID (first column)
553: we changed int to long in num[] and we added a new lvector for
554: memory allocation. But we also truncated to 8 characters (left
555: truncation)
556: (Repository): No more line truncation errors.
557:
558: Revision 1.84 2003/06/13 21:44:43 brouard
559: * imach.c (Repository): Replace "freqsummary" at a correct
560: place. It differs from routine "prevalence" which may be called
561: many times. Probs is memory consuming and must be used with
562: parcimony.
563: Version 0.95a3 (should output exactly the same maximization than 0.8a2)
564:
565: Revision 1.83 2003/06/10 13:39:11 lievre
566: *** empty log message ***
567:
568: Revision 1.82 2003/06/05 15:57:20 brouard
569: Add log in imach.c and fullversion number is now printed.
570:
571: */
572: /*
573: Interpolated Markov Chain
574:
575: Short summary of the programme:
576:
577: This program computes Healthy Life Expectancies from
578: cross-longitudinal data. Cross-longitudinal data consist in: -1- a
579: first survey ("cross") where individuals from different ages are
580: interviewed on their health status or degree of disability (in the
581: case of a health survey which is our main interest) -2- at least a
582: second wave of interviews ("longitudinal") which measure each change
583: (if any) in individual health status. Health expectancies are
584: computed from the time spent in each health state according to a
585: model. More health states you consider, more time is necessary to reach the
586: Maximum Likelihood of the parameters involved in the model. The
587: simplest model is the multinomial logistic model where pij is the
588: probability to be observed in state j at the second wave
589: conditional to be observed in state i at the first wave. Therefore
590: the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
591: 'age' is age and 'sex' is a covariate. If you want to have a more
592: complex model than "constant and age", you should modify the program
593: where the markup *Covariates have to be included here again* invites
594: you to do it. More covariates you add, slower the
595: convergence.
596:
597: The advantage of this computer programme, compared to a simple
598: multinomial logistic model, is clear when the delay between waves is not
599: identical for each individual. Also, if a individual missed an
600: intermediate interview, the information is lost, but taken into
601: account using an interpolation or extrapolation.
602:
603: hPijx is the probability to be observed in state i at age x+h
604: conditional to the observed state i at age x. The delay 'h' can be
605: split into an exact number (nh*stepm) of unobserved intermediate
606: states. This elementary transition (by month, quarter,
607: semester or year) is modelled as a multinomial logistic. The hPx
608: matrix is simply the matrix product of nh*stepm elementary matrices
609: and the contribution of each individual to the likelihood is simply
610: hPijx.
611:
612: Also this programme outputs the covariance matrix of the parameters but also
613: of the life expectancies. It also computes the period (stable) prevalence.
614:
1.133 brouard 615: Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
616: Institut national d'études démographiques, Paris.
1.126 brouard 617: This software have been partly granted by Euro-REVES, a concerted action
618: from the European Union.
619: It is copyrighted identically to a GNU software product, ie programme and
620: software can be distributed freely for non commercial use. Latest version
621: can be accessed at http://euroreves.ined.fr/imach .
622:
623: Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
624: or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
625:
626: **********************************************************************/
627: /*
628: main
629: read parameterfile
630: read datafile
631: concatwav
632: freqsummary
633: if (mle >= 1)
634: mlikeli
635: print results files
636: if mle==1
637: computes hessian
638: read end of parameter file: agemin, agemax, bage, fage, estepm
639: begin-prev-date,...
640: open gnuplot file
641: open html file
1.145 brouard 642: period (stable) prevalence | pl_nom 1-1 2-2 etc by covariate
643: for age prevalim() | #****** V1=0 V2=1 V3=1 V4=0 ******
644: | 65 1 0 2 1 3 1 4 0 0.96326 0.03674
645: freexexit2 possible for memory heap.
646:
647: h Pij x | pij_nom ficrestpij
648: # Cov Agex agex+h hpijx with i,j= 1-1 1-2 1-3 2-1 2-2 2-3
649: 1 85 85 1.00000 0.00000 0.00000 0.00000 1.00000 0.00000
650: 1 85 86 0.68299 0.22291 0.09410 0.71093 0.00000 0.28907
651:
652: 1 65 99 0.00364 0.00322 0.99314 0.00350 0.00310 0.99340
653: 1 65 100 0.00214 0.00204 0.99581 0.00206 0.00196 0.99597
654: variance of p one-step probabilities varprob | prob_nom ficresprob #One-step probabilities and stand. devi in ()
655: Standard deviation of one-step probabilities | probcor_nom ficresprobcor #One-step probabilities and correlation matrix
656: Matrix of variance covariance of one-step probabilities | probcov_nom ficresprobcov #One-step probabilities and covariance matrix
657:
1.126 brouard 658: forecasting if prevfcast==1 prevforecast call prevalence()
659: health expectancies
660: Variance-covariance of DFLE
661: prevalence()
662: movingaverage()
663: varevsij()
664: if popbased==1 varevsij(,popbased)
665: total life expectancies
666: Variance of period (stable) prevalence
667: end
668: */
669:
1.187 brouard 670: /* #define DEBUG */
671: /* #define DEBUGBRENT */
1.203 brouard 672: /* #define DEBUGLINMIN */
673: /* #define DEBUGHESS */
674: #define DEBUGHESSIJ
675: /* #define LINMINORIGINAL /\* Don't use loop on scale in linmin (accepting nan)*\/ */
1.165 brouard 676: #define POWELL /* Instead of NLOPT */
1.192 brouard 677: #define POWELLF1F3 /* Skip test */
1.186 brouard 678: /* #define POWELLORIGINAL /\* Don't use Directest to decide new direction but original Powell test *\/ */
679: /* #define MNBRAKORIGINAL /\* Don't use mnbrak fix *\/ */
1.126 brouard 680:
681: #include <math.h>
682: #include <stdio.h>
683: #include <stdlib.h>
684: #include <string.h>
1.159 brouard 685:
686: #ifdef _WIN32
687: #include <io.h>
1.172 brouard 688: #include <windows.h>
689: #include <tchar.h>
1.159 brouard 690: #else
1.126 brouard 691: #include <unistd.h>
1.159 brouard 692: #endif
1.126 brouard 693:
694: #include <limits.h>
695: #include <sys/types.h>
1.171 brouard 696:
697: #if defined(__GNUC__)
698: #include <sys/utsname.h> /* Doesn't work on Windows */
699: #endif
700:
1.126 brouard 701: #include <sys/stat.h>
702: #include <errno.h>
1.159 brouard 703: /* extern int errno; */
1.126 brouard 704:
1.157 brouard 705: /* #ifdef LINUX */
706: /* #include <time.h> */
707: /* #include "timeval.h" */
708: /* #else */
709: /* #include <sys/time.h> */
710: /* #endif */
711:
1.126 brouard 712: #include <time.h>
713:
1.136 brouard 714: #ifdef GSL
715: #include <gsl/gsl_errno.h>
716: #include <gsl/gsl_multimin.h>
717: #endif
718:
1.167 brouard 719:
1.162 brouard 720: #ifdef NLOPT
721: #include <nlopt.h>
722: typedef struct {
723: double (* function)(double [] );
724: } myfunc_data ;
725: #endif
726:
1.126 brouard 727: /* #include <libintl.h> */
728: /* #define _(String) gettext (String) */
729:
1.141 brouard 730: #define MAXLINE 1024 /* Was 256. Overflow with 312 with 2 states and 4 covariates. Should be ok */
1.126 brouard 731:
732: #define GNUPLOTPROGRAM "gnuplot"
733: /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
734: #define FILENAMELENGTH 132
735:
736: #define GLOCK_ERROR_NOPATH -1 /* empty path */
737: #define GLOCK_ERROR_GETCWD -2 /* cannot get cwd */
738:
1.144 brouard 739: #define MAXPARM 128 /**< Maximum number of parameters for the optimization */
740: #define NPARMAX 64 /**< (nlstate+ndeath-1)*nlstate*ncovmodel */
1.126 brouard 741:
742: #define NINTERVMAX 8
1.144 brouard 743: #define NLSTATEMAX 8 /**< Maximum number of live states (for func) */
744: #define NDEATHMAX 8 /**< Maximum number of dead states (for func) */
745: #define NCOVMAX 20 /**< Maximum number of covariates, including generated covariates V1*V2 */
1.197 brouard 746: #define codtabm(h,k) (1 & (h-1) >> (k-1))+1
1.126 brouard 747: #define MAXN 20000
1.144 brouard 748: #define YEARM 12. /**< Number of months per year */
1.126 brouard 749: #define AGESUP 130
750: #define AGEBASE 40
1.194 brouard 751: #define AGEOVERFLOW 1.e20
1.164 brouard 752: #define AGEGOMP 10 /**< Minimal age for Gompertz adjustment */
1.157 brouard 753: #ifdef _WIN32
754: #define DIRSEPARATOR '\\'
755: #define CHARSEPARATOR "\\"
756: #define ODIRSEPARATOR '/'
757: #else
1.126 brouard 758: #define DIRSEPARATOR '/'
759: #define CHARSEPARATOR "/"
760: #define ODIRSEPARATOR '\\'
761: #endif
762:
1.209 ! brouard 763: /* $Id: imach.c,v 1.208 2015/11/17 14:31:57 brouard Exp $ */
1.126 brouard 764: /* $State: Exp $ */
1.196 brouard 765: #include "version.h"
766: char version[]=__IMACH_VERSION__;
1.204 brouard 767: 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";
1.209 ! brouard 768: char fullversion[]="$Revision: 1.208 $ $Date: 2015/11/17 14:31:57 $";
1.126 brouard 769: char strstart[80];
770: char optionfilext[10], optionfilefiname[FILENAMELENGTH];
1.130 brouard 771: int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings */
1.187 brouard 772: int nagesqr=0, nforce=0; /* nagesqr=1 if model is including age*age, number of forces */
1.145 brouard 773: /* Number of covariates model=V2+V1+ V3*age+V2*V4 */
774: int cptcovn=0; /**< cptcovn number of covariates added in the model (excepting constant and age and age*product) */
775: int cptcovt=0; /**< cptcovt number of covariates added in the model (excepting constant and age) */
776: int cptcovs=0; /**< cptcovs number of simple covariates V2+V1 =2 */
777: int cptcovage=0; /**< Number of covariates with age: V3*age only =1 */
778: int cptcovprodnoage=0; /**< Number of covariate products without age */
779: int cptcoveff=0; /* Total number of covariates to vary for printing results */
780: int cptcov=0; /* Working variable */
1.126 brouard 781: int npar=NPARMAX;
782: int nlstate=2; /* Number of live states */
783: int ndeath=1; /* Number of dead states */
1.130 brouard 784: int ncovmodel=0, ncovcol=0; /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
1.126 brouard 785: int popbased=0;
786:
787: int *wav; /* Number of waves for this individuual 0 is possible */
1.130 brouard 788: int maxwav=0; /* Maxim number of waves */
789: int jmin=0, jmax=0; /* min, max spacing between 2 waves */
790: int ijmin=0, ijmax=0; /* Individuals having jmin and jmax */
791: int gipmx=0, gsw=0; /* Global variables on the number of contributions
1.126 brouard 792: to the likelihood and the sum of weights (done by funcone)*/
1.130 brouard 793: int mle=1, weightopt=0;
1.126 brouard 794: int **mw; /* mw[mi][i] is number of the mi wave for this individual */
795: int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
796: int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
797: * wave mi and wave mi+1 is not an exact multiple of stepm. */
1.162 brouard 798: int countcallfunc=0; /* Count the number of calls to func */
1.130 brouard 799: double jmean=1; /* Mean space between 2 waves */
1.145 brouard 800: double **matprod2(); /* test */
1.126 brouard 801: double **oldm, **newm, **savm; /* Working pointers to matrices */
802: double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
1.136 brouard 803: /*FILE *fic ; */ /* Used in readdata only */
804: FILE *ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
1.126 brouard 805: FILE *ficlog, *ficrespow;
1.130 brouard 806: int globpr=0; /* Global variable for printing or not */
1.126 brouard 807: double fretone; /* Only one call to likelihood */
1.130 brouard 808: long ipmx=0; /* Number of contributions */
1.126 brouard 809: double sw; /* Sum of weights */
810: char filerespow[FILENAMELENGTH];
811: char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
812: FILE *ficresilk;
813: FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
814: FILE *ficresprobmorprev;
815: FILE *fichtm, *fichtmcov; /* Html File */
816: FILE *ficreseij;
817: char filerese[FILENAMELENGTH];
818: FILE *ficresstdeij;
819: char fileresstde[FILENAMELENGTH];
820: FILE *ficrescveij;
821: char filerescve[FILENAMELENGTH];
822: FILE *ficresvij;
823: char fileresv[FILENAMELENGTH];
824: FILE *ficresvpl;
825: char fileresvpl[FILENAMELENGTH];
826: char title[MAXLINE];
827: char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH], filerespl[FILENAMELENGTH];
828: char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
829: char tmpout[FILENAMELENGTH], tmpout2[FILENAMELENGTH];
830: char command[FILENAMELENGTH];
831: int outcmd=0;
832:
833: char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
1.202 brouard 834: char fileresu[FILENAMELENGTH]; /* fileres without r in front */
1.126 brouard 835: char filelog[FILENAMELENGTH]; /* Log file */
836: char filerest[FILENAMELENGTH];
837: char fileregp[FILENAMELENGTH];
838: char popfile[FILENAMELENGTH];
839:
840: char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
841:
1.157 brouard 842: /* struct timeval start_time, end_time, curr_time, last_time, forecast_time; */
843: /* struct timezone tzp; */
844: /* extern int gettimeofday(); */
845: struct tm tml, *gmtime(), *localtime();
846:
847: extern time_t time();
848:
849: struct tm start_time, end_time, curr_time, last_time, forecast_time;
850: time_t rstart_time, rend_time, rcurr_time, rlast_time, rforecast_time; /* raw time */
851: struct tm tm;
852:
1.126 brouard 853: char strcurr[80], strfor[80];
854:
855: char *endptr;
856: long lval;
857: double dval;
858:
859: #define NR_END 1
860: #define FREE_ARG char*
861: #define FTOL 1.0e-10
862:
863: #define NRANSI
864: #define ITMAX 200
865:
866: #define TOL 2.0e-4
867:
868: #define CGOLD 0.3819660
869: #define ZEPS 1.0e-10
870: #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);
871:
872: #define GOLD 1.618034
873: #define GLIMIT 100.0
874: #define TINY 1.0e-20
875:
876: static double maxarg1,maxarg2;
877: #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
878: #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
879:
880: #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
881: #define rint(a) floor(a+0.5)
1.166 brouard 882: /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/myutils_8h-source.html */
1.183 brouard 883: #define mytinydouble 1.0e-16
1.166 brouard 884: /* #define DEQUAL(a,b) (fabs((a)-(b))<mytinydouble) */
885: /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/mynrutils_8h-source.html */
886: /* static double dsqrarg; */
887: /* #define DSQR(a) (DEQUAL((dsqrarg=(a)),0.0) ? 0.0 : dsqrarg*dsqrarg) */
1.126 brouard 888: static double sqrarg;
889: #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
890: #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}
891: int agegomp= AGEGOMP;
892:
893: int imx;
894: int stepm=1;
895: /* Stepm, step in month: minimum step interpolation*/
896:
897: int estepm;
898: /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
899:
900: int m,nb;
901: long *num;
1.197 brouard 902: int firstpass=0, lastpass=4,*cod, *cens;
1.192 brouard 903: int *ncodemax; /* ncodemax[j]= Number of modalities of the j th
904: covariate for which somebody answered excluding
905: undefined. Usually 2: 0 and 1. */
906: int *ncodemaxwundef; /* ncodemax[j]= Number of modalities of the j th
907: covariate for which somebody answered including
908: undefined. Usually 3: -1, 0 and 1. */
1.126 brouard 909: double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
910: double **pmmij, ***probs;
911: double *ageexmed,*agecens;
912: double dateintmean=0;
913:
914: double *weight;
915: int **s; /* Status */
1.141 brouard 916: double *agedc;
1.145 brouard 917: double **covar; /**< covar[j,i], value of jth covariate for individual i,
1.141 brouard 918: * covar=matrix(0,NCOVMAX,1,n);
1.187 brouard 919: * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*age; */
1.141 brouard 920: double idx;
921: int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */
1.197 brouard 922: int *Tage;
1.145 brouard 923: int *Ndum; /** Freq of modality (tricode */
1.200 brouard 924: /* int **codtab;*/ /**< codtab=imatrix(1,100,1,10); */
1.141 brouard 925: int **Tvard, *Tprod, cptcovprod, *Tvaraff;
1.126 brouard 926: double *lsurv, *lpop, *tpop;
927:
1.143 brouard 928: double ftol=FTOL; /**< Tolerance for computing Max Likelihood */
929: double ftolhess; /**< Tolerance for computing hessian */
1.126 brouard 930:
931: /**************** split *************************/
932: static int split( char *path, char *dirc, char *name, char *ext, char *finame )
933: {
934: /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
935: the name of the file (name), its extension only (ext) and its first part of the name (finame)
936: */
937: char *ss; /* pointer */
1.186 brouard 938: int l1=0, l2=0; /* length counters */
1.126 brouard 939:
940: l1 = strlen(path ); /* length of path */
941: if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
942: ss= strrchr( path, DIRSEPARATOR ); /* find last / */
943: if ( ss == NULL ) { /* no directory, so determine current directory */
944: strcpy( name, path ); /* we got the fullname name because no directory */
945: /*if(strrchr(path, ODIRSEPARATOR )==NULL)
946: printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
947: /* get current working directory */
948: /* extern char* getcwd ( char *buf , int len);*/
1.184 brouard 949: #ifdef WIN32
950: if (_getcwd( dirc, FILENAME_MAX ) == NULL ) {
951: #else
952: if (getcwd(dirc, FILENAME_MAX) == NULL) {
953: #endif
1.126 brouard 954: return( GLOCK_ERROR_GETCWD );
955: }
956: /* got dirc from getcwd*/
957: printf(" DIRC = %s \n",dirc);
1.205 brouard 958: } else { /* strip directory from path */
1.126 brouard 959: ss++; /* after this, the filename */
960: l2 = strlen( ss ); /* length of filename */
961: if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
962: strcpy( name, ss ); /* save file name */
963: strncpy( dirc, path, l1 - l2 ); /* now the directory */
1.186 brouard 964: dirc[l1-l2] = '\0'; /* add zero */
1.126 brouard 965: printf(" DIRC2 = %s \n",dirc);
966: }
967: /* We add a separator at the end of dirc if not exists */
968: l1 = strlen( dirc ); /* length of directory */
969: if( dirc[l1-1] != DIRSEPARATOR ){
970: dirc[l1] = DIRSEPARATOR;
971: dirc[l1+1] = 0;
972: printf(" DIRC3 = %s \n",dirc);
973: }
974: ss = strrchr( name, '.' ); /* find last / */
975: if (ss >0){
976: ss++;
977: strcpy(ext,ss); /* save extension */
978: l1= strlen( name);
979: l2= strlen(ss)+1;
980: strncpy( finame, name, l1-l2);
981: finame[l1-l2]= 0;
982: }
983:
984: return( 0 ); /* we're done */
985: }
986:
987:
988: /******************************************/
989:
990: void replace_back_to_slash(char *s, char*t)
991: {
992: int i;
993: int lg=0;
994: i=0;
995: lg=strlen(t);
996: for(i=0; i<= lg; i++) {
997: (s[i] = t[i]);
998: if (t[i]== '\\') s[i]='/';
999: }
1000: }
1001:
1.132 brouard 1002: char *trimbb(char *out, char *in)
1.137 brouard 1003: { /* Trim multiple blanks in line but keeps first blanks if line starts with blanks */
1.132 brouard 1004: char *s;
1005: s=out;
1006: while (*in != '\0'){
1.137 brouard 1007: while( *in == ' ' && *(in+1) == ' '){ /* && *(in+1) != '\0'){*/
1.132 brouard 1008: in++;
1009: }
1010: *out++ = *in++;
1011: }
1012: *out='\0';
1013: return s;
1014: }
1015:
1.187 brouard 1016: /* char *substrchaine(char *out, char *in, char *chain) */
1017: /* { */
1018: /* /\* Substract chain 'chain' from 'in', return and output 'out' *\/ */
1019: /* char *s, *t; */
1020: /* t=in;s=out; */
1021: /* while ((*in != *chain) && (*in != '\0')){ */
1022: /* *out++ = *in++; */
1023: /* } */
1024:
1025: /* /\* *in matches *chain *\/ */
1026: /* while ((*in++ == *chain++) && (*in != '\0')){ */
1027: /* printf("*in = %c, *out= %c *chain= %c \n", *in, *out, *chain); */
1028: /* } */
1029: /* in--; chain--; */
1030: /* while ( (*in != '\0')){ */
1031: /* printf("Bef *in = %c, *out= %c *chain= %c \n", *in, *out, *chain); */
1032: /* *out++ = *in++; */
1033: /* printf("Aft *in = %c, *out= %c *chain= %c \n", *in, *out, *chain); */
1034: /* } */
1035: /* *out='\0'; */
1036: /* out=s; */
1037: /* return out; */
1038: /* } */
1039: char *substrchaine(char *out, char *in, char *chain)
1040: {
1041: /* Substract chain 'chain' from 'in', return and output 'out' */
1042: /* in="V1+V1*age+age*age+V2", chain="age*age" */
1043:
1044: char *strloc;
1045:
1046: strcpy (out, in);
1047: strloc = strstr(out, chain); /* strloc points to out at age*age+V2 */
1048: printf("Bef strloc=%s chain=%s out=%s \n", strloc, chain, out);
1049: if(strloc != NULL){
1050: /* will affect out */ /* strloc+strlenc(chain)=+V2 */ /* Will also work in Unicode */
1051: memmove(strloc,strloc+strlen(chain), strlen(strloc+strlen(chain))+1);
1052: /* strcpy (strloc, strloc +strlen(chain));*/
1053: }
1054: printf("Aft strloc=%s chain=%s in=%s out=%s \n", strloc, chain, in, out);
1055: return out;
1056: }
1057:
1058:
1.145 brouard 1059: char *cutl(char *blocc, char *alocc, char *in, char occ)
1060: {
1.187 brouard 1061: /* cuts string in into blocc and alocc where blocc ends before FIRST occurence of char 'occ'
1.145 brouard 1062: and alocc starts after first occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
1.187 brouard 1063: gives blocc="abcdef" and alocc="ghi2j".
1.145 brouard 1064: If occ is not found blocc is null and alocc is equal to in. Returns blocc
1065: */
1.160 brouard 1066: char *s, *t;
1.145 brouard 1067: t=in;s=in;
1068: while ((*in != occ) && (*in != '\0')){
1069: *alocc++ = *in++;
1070: }
1071: if( *in == occ){
1072: *(alocc)='\0';
1073: s=++in;
1074: }
1075:
1076: if (s == t) {/* occ not found */
1077: *(alocc-(in-s))='\0';
1078: in=s;
1079: }
1080: while ( *in != '\0'){
1081: *blocc++ = *in++;
1082: }
1083:
1084: *blocc='\0';
1085: return t;
1086: }
1.137 brouard 1087: char *cutv(char *blocc, char *alocc, char *in, char occ)
1088: {
1.187 brouard 1089: /* cuts string in into blocc and alocc where blocc ends before LAST occurence of char 'occ'
1.137 brouard 1090: and alocc starts after last occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
1091: gives blocc="abcdef2ghi" and alocc="j".
1092: If occ is not found blocc is null and alocc is equal to in. Returns alocc
1093: */
1094: char *s, *t;
1095: t=in;s=in;
1096: while (*in != '\0'){
1097: while( *in == occ){
1098: *blocc++ = *in++;
1099: s=in;
1100: }
1101: *blocc++ = *in++;
1102: }
1103: if (s == t) /* occ not found */
1104: *(blocc-(in-s))='\0';
1105: else
1106: *(blocc-(in-s)-1)='\0';
1107: in=s;
1108: while ( *in != '\0'){
1109: *alocc++ = *in++;
1110: }
1111:
1112: *alocc='\0';
1113: return s;
1114: }
1115:
1.126 brouard 1116: int nbocc(char *s, char occ)
1117: {
1118: int i,j=0;
1119: int lg=20;
1120: i=0;
1121: lg=strlen(s);
1122: for(i=0; i<= lg; i++) {
1123: if (s[i] == occ ) j++;
1124: }
1125: return j;
1126: }
1127:
1.137 brouard 1128: /* void cutv(char *u,char *v, char*t, char occ) */
1129: /* { */
1130: /* /\* cuts string t into u and v where u ends before last occurence of char 'occ' */
1131: /* and v starts after last occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2') */
1132: /* gives u="abcdef2ghi" and v="j" *\/ */
1133: /* int i,lg,j,p=0; */
1134: /* i=0; */
1135: /* lg=strlen(t); */
1136: /* for(j=0; j<=lg-1; j++) { */
1137: /* if((t[j]!= occ) && (t[j+1]== occ)) p=j+1; */
1138: /* } */
1.126 brouard 1139:
1.137 brouard 1140: /* for(j=0; j<p; j++) { */
1141: /* (u[j] = t[j]); */
1142: /* } */
1143: /* u[p]='\0'; */
1.126 brouard 1144:
1.137 brouard 1145: /* for(j=0; j<= lg; j++) { */
1146: /* if (j>=(p+1))(v[j-p-1] = t[j]); */
1147: /* } */
1148: /* } */
1.126 brouard 1149:
1.160 brouard 1150: #ifdef _WIN32
1151: char * strsep(char **pp, const char *delim)
1152: {
1153: char *p, *q;
1154:
1155: if ((p = *pp) == NULL)
1156: return 0;
1157: if ((q = strpbrk (p, delim)) != NULL)
1158: {
1159: *pp = q + 1;
1160: *q = '\0';
1161: }
1162: else
1163: *pp = 0;
1164: return p;
1165: }
1166: #endif
1167:
1.126 brouard 1168: /********************** nrerror ********************/
1169:
1170: void nrerror(char error_text[])
1171: {
1172: fprintf(stderr,"ERREUR ...\n");
1173: fprintf(stderr,"%s\n",error_text);
1174: exit(EXIT_FAILURE);
1175: }
1176: /*********************** vector *******************/
1177: double *vector(int nl, int nh)
1178: {
1179: double *v;
1180: v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
1181: if (!v) nrerror("allocation failure in vector");
1182: return v-nl+NR_END;
1183: }
1184:
1185: /************************ free vector ******************/
1186: void free_vector(double*v, int nl, int nh)
1187: {
1188: free((FREE_ARG)(v+nl-NR_END));
1189: }
1190:
1191: /************************ivector *******************************/
1192: int *ivector(long nl,long nh)
1193: {
1194: int *v;
1195: v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
1196: if (!v) nrerror("allocation failure in ivector");
1197: return v-nl+NR_END;
1198: }
1199:
1200: /******************free ivector **************************/
1201: void free_ivector(int *v, long nl, long nh)
1202: {
1203: free((FREE_ARG)(v+nl-NR_END));
1204: }
1205:
1206: /************************lvector *******************************/
1207: long *lvector(long nl,long nh)
1208: {
1209: long *v;
1210: v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
1211: if (!v) nrerror("allocation failure in ivector");
1212: return v-nl+NR_END;
1213: }
1214:
1215: /******************free lvector **************************/
1216: void free_lvector(long *v, long nl, long nh)
1217: {
1218: free((FREE_ARG)(v+nl-NR_END));
1219: }
1220:
1221: /******************* imatrix *******************************/
1222: int **imatrix(long nrl, long nrh, long ncl, long nch)
1223: /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */
1224: {
1225: long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;
1226: int **m;
1227:
1228: /* allocate pointers to rows */
1229: m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));
1230: if (!m) nrerror("allocation failure 1 in matrix()");
1231: m += NR_END;
1232: m -= nrl;
1233:
1234:
1235: /* allocate rows and set pointers to them */
1236: m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));
1237: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
1238: m[nrl] += NR_END;
1239: m[nrl] -= ncl;
1240:
1241: for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;
1242:
1243: /* return pointer to array of pointers to rows */
1244: return m;
1245: }
1246:
1247: /****************** free_imatrix *************************/
1248: void free_imatrix(m,nrl,nrh,ncl,nch)
1249: int **m;
1250: long nch,ncl,nrh,nrl;
1251: /* free an int matrix allocated by imatrix() */
1252: {
1253: free((FREE_ARG) (m[nrl]+ncl-NR_END));
1254: free((FREE_ARG) (m+nrl-NR_END));
1255: }
1256:
1257: /******************* matrix *******************************/
1258: double **matrix(long nrl, long nrh, long ncl, long nch)
1259: {
1260: long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
1261: double **m;
1262:
1263: m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
1264: if (!m) nrerror("allocation failure 1 in matrix()");
1265: m += NR_END;
1266: m -= nrl;
1267:
1268: m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
1269: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
1270: m[nrl] += NR_END;
1271: m[nrl] -= ncl;
1272:
1273: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
1274: return m;
1.145 brouard 1275: /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) or &(m[1][0])
1276: m[i] = address of ith row of the table. &(m[i]) is its value which is another adress
1277: that of m[i][0]. In order to get the value p m[i][0] but it is unitialized.
1.126 brouard 1278: */
1279: }
1280:
1281: /*************************free matrix ************************/
1282: void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
1283: {
1284: free((FREE_ARG)(m[nrl]+ncl-NR_END));
1285: free((FREE_ARG)(m+nrl-NR_END));
1286: }
1287:
1288: /******************* ma3x *******************************/
1289: double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
1290: {
1291: long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
1292: double ***m;
1293:
1294: m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
1295: if (!m) nrerror("allocation failure 1 in matrix()");
1296: m += NR_END;
1297: m -= nrl;
1298:
1299: m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
1300: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
1301: m[nrl] += NR_END;
1302: m[nrl] -= ncl;
1303:
1304: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
1305:
1306: m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
1307: if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
1308: m[nrl][ncl] += NR_END;
1309: m[nrl][ncl] -= nll;
1310: for (j=ncl+1; j<=nch; j++)
1311: m[nrl][j]=m[nrl][j-1]+nlay;
1312:
1313: for (i=nrl+1; i<=nrh; i++) {
1314: m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
1315: for (j=ncl+1; j<=nch; j++)
1316: m[i][j]=m[i][j-1]+nlay;
1317: }
1318: return m;
1319: /* gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
1320: &(m[i][j][k]) <=> *((*(m+i) + j)+k)
1321: */
1322: }
1323:
1324: /*************************free ma3x ************************/
1325: void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
1326: {
1327: free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
1328: free((FREE_ARG)(m[nrl]+ncl-NR_END));
1329: free((FREE_ARG)(m+nrl-NR_END));
1330: }
1331:
1332: /*************** function subdirf ***********/
1333: char *subdirf(char fileres[])
1334: {
1335: /* Caution optionfilefiname is hidden */
1336: strcpy(tmpout,optionfilefiname);
1337: strcat(tmpout,"/"); /* Add to the right */
1338: strcat(tmpout,fileres);
1339: return tmpout;
1340: }
1341:
1342: /*************** function subdirf2 ***********/
1343: char *subdirf2(char fileres[], char *preop)
1344: {
1345:
1346: /* Caution optionfilefiname is hidden */
1347: strcpy(tmpout,optionfilefiname);
1348: strcat(tmpout,"/");
1349: strcat(tmpout,preop);
1350: strcat(tmpout,fileres);
1351: return tmpout;
1352: }
1353:
1354: /*************** function subdirf3 ***********/
1355: char *subdirf3(char fileres[], char *preop, char *preop2)
1356: {
1357:
1358: /* Caution optionfilefiname is hidden */
1359: strcpy(tmpout,optionfilefiname);
1360: strcat(tmpout,"/");
1361: strcat(tmpout,preop);
1362: strcat(tmpout,preop2);
1363: strcat(tmpout,fileres);
1364: return tmpout;
1365: }
1366:
1.162 brouard 1367: char *asc_diff_time(long time_sec, char ascdiff[])
1368: {
1369: long sec_left, days, hours, minutes;
1370: days = (time_sec) / (60*60*24);
1371: sec_left = (time_sec) % (60*60*24);
1372: hours = (sec_left) / (60*60) ;
1373: sec_left = (sec_left) %(60*60);
1374: minutes = (sec_left) /60;
1375: sec_left = (sec_left) % (60);
1376: sprintf(ascdiff,"%ld day(s) %ld hour(s) %ld minute(s) %ld second(s)",days, hours, minutes, sec_left);
1377: return ascdiff;
1378: }
1379:
1.126 brouard 1380: /***************** f1dim *************************/
1381: extern int ncom;
1382: extern double *pcom,*xicom;
1383: extern double (*nrfunc)(double []);
1384:
1385: double f1dim(double x)
1386: {
1387: int j;
1388: double f;
1389: double *xt;
1390:
1391: xt=vector(1,ncom);
1392: for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];
1393: f=(*nrfunc)(xt);
1394: free_vector(xt,1,ncom);
1395: return f;
1396: }
1397:
1398: /*****************brent *************************/
1399: double brent(double ax, double bx, double cx, double (*f)(double), double tol, double *xmin)
1.187 brouard 1400: {
1401: /* Given a function f, and given a bracketing triplet of abscissas ax, bx, cx (such that bx is
1402: * between ax and cx, and f(bx) is less than both f(ax) and f(cx) ), this routine isolates
1403: * the minimum to a fractional precision of about tol using Brent’s method. The abscissa of
1404: * the minimum is returned as xmin, and the minimum function value is returned as brent , the
1405: * returned function value.
1406: */
1.126 brouard 1407: int iter;
1408: double a,b,d,etemp;
1.159 brouard 1409: double fu=0,fv,fw,fx;
1.164 brouard 1410: double ftemp=0.;
1.126 brouard 1411: double p,q,r,tol1,tol2,u,v,w,x,xm;
1412: double e=0.0;
1413:
1414: a=(ax < cx ? ax : cx);
1415: b=(ax > cx ? ax : cx);
1416: x=w=v=bx;
1417: fw=fv=fx=(*f)(x);
1418: for (iter=1;iter<=ITMAX;iter++) {
1419: xm=0.5*(a+b);
1420: tol2=2.0*(tol1=tol*fabs(x)+ZEPS);
1421: /* if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
1422: printf(".");fflush(stdout);
1423: fprintf(ficlog,".");fflush(ficlog);
1.162 brouard 1424: #ifdef DEBUGBRENT
1.126 brouard 1425: 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);
1426: 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);
1427: /* if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
1428: #endif
1429: if (fabs(x-xm) <= (tol2-0.5*(b-a))){
1430: *xmin=x;
1431: return fx;
1432: }
1433: ftemp=fu;
1434: if (fabs(e) > tol1) {
1435: r=(x-w)*(fx-fv);
1436: q=(x-v)*(fx-fw);
1437: p=(x-v)*q-(x-w)*r;
1438: q=2.0*(q-r);
1439: if (q > 0.0) p = -p;
1440: q=fabs(q);
1441: etemp=e;
1442: e=d;
1443: if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))
1444: d=CGOLD*(e=(x >= xm ? a-x : b-x));
1445: else {
1446: d=p/q;
1447: u=x+d;
1448: if (u-a < tol2 || b-u < tol2)
1449: d=SIGN(tol1,xm-x);
1450: }
1451: } else {
1452: d=CGOLD*(e=(x >= xm ? a-x : b-x));
1453: }
1454: u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));
1455: fu=(*f)(u);
1456: if (fu <= fx) {
1457: if (u >= x) a=x; else b=x;
1458: SHFT(v,w,x,u)
1.183 brouard 1459: SHFT(fv,fw,fx,fu)
1460: } else {
1461: if (u < x) a=u; else b=u;
1462: if (fu <= fw || w == x) {
1463: v=w;
1464: w=u;
1465: fv=fw;
1466: fw=fu;
1467: } else if (fu <= fv || v == x || v == w) {
1468: v=u;
1469: fv=fu;
1470: }
1471: }
1.126 brouard 1472: }
1473: nrerror("Too many iterations in brent");
1474: *xmin=x;
1475: return fx;
1476: }
1477:
1478: /****************** mnbrak ***********************/
1479:
1480: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,
1481: double (*func)(double))
1.183 brouard 1482: { /* Given a function func , and given distinct initial points ax and bx , this routine searches in
1483: the downhill direction (defined by the function as evaluated at the initial points) and returns
1484: new points ax , bx , cx that bracket a minimum of the function. Also returned are the function
1485: values at the three points, fa, fb , and fc such that fa > fb and fb < fc.
1486: */
1.126 brouard 1487: double ulim,u,r,q, dum;
1488: double fu;
1.187 brouard 1489:
1490: double scale=10.;
1491: int iterscale=0;
1492:
1493: *fa=(*func)(*ax); /* xta[j]=pcom[j]+(*ax)*xicom[j]; fa=f(xta[j])*/
1494: *fb=(*func)(*bx); /* xtb[j]=pcom[j]+(*bx)*xicom[j]; fb=f(xtb[j]) */
1495:
1496:
1497: /* while(*fb != *fb){ /\* *ax should be ok, reducing distance to *ax *\/ */
1498: /* printf("Warning mnbrak *fb = %lf, *bx=%lf *ax=%lf *fa==%lf iter=%d\n",*fb, *bx, *ax, *fa, iterscale++); */
1499: /* *bx = *ax - (*ax - *bx)/scale; */
1500: /* *fb=(*func)(*bx); /\* xtb[j]=pcom[j]+(*bx)*xicom[j]; fb=f(xtb[j]) *\/ */
1501: /* } */
1502:
1.126 brouard 1503: if (*fb > *fa) {
1504: SHFT(dum,*ax,*bx,dum)
1.183 brouard 1505: SHFT(dum,*fb,*fa,dum)
1506: }
1.126 brouard 1507: *cx=(*bx)+GOLD*(*bx-*ax);
1508: *fc=(*func)(*cx);
1.183 brouard 1509: #ifdef DEBUG
1510: printf("mnbrak0 *fb=%.12e *fc=%.12e\n",*fb,*fc);
1511: fprintf(ficlog,"mnbrak0 *fb=%.12e *fc=%.12e\n",*fb,*fc);
1512: #endif
1513: while (*fb > *fc) { /* Declining a,b,c with fa> fb > fc */
1.126 brouard 1514: r=(*bx-*ax)*(*fb-*fc);
1515: q=(*bx-*cx)*(*fb-*fa);
1516: u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/
1.183 brouard 1517: (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); /* Minimum abscissa of a parabolic estimated from (a,fa), (b,fb) and (c,fc). */
1518: ulim=(*bx)+GLIMIT*(*cx-*bx); /* Maximum abscissa where function should be evaluated */
1519: if ((*bx-u)*(u-*cx) > 0.0) { /* if u_p is between b and c */
1.126 brouard 1520: fu=(*func)(u);
1.163 brouard 1521: #ifdef DEBUG
1522: /* f(x)=A(x-u)**2+f(u) */
1523: double A, fparabu;
1524: A= (*fb - *fa)/(*bx-*ax)/(*bx+*ax-2*u);
1525: fparabu= *fa - A*(*ax-u)*(*ax-u);
1526: 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);
1527: 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 1528: /* And thus,it can be that fu > *fc even if fparabu < *fc */
1529: /* mnbrak (*ax=7.666299858533, *fa=299039.693133272231), (*bx=8.595447774979, *fb=298976.598289369489),
1530: (*cx=10.098840694817, *fc=298946.631474258087), (*u=9.852501168332, fu=298948.773013752128, fparabu=298945.434711494134) */
1531: /* In that case, there is no bracket in the output! Routine is wrong with many consequences.*/
1.163 brouard 1532: #endif
1.184 brouard 1533: #ifdef MNBRAKORIGINAL
1.183 brouard 1534: #else
1.191 brouard 1535: /* if (fu > *fc) { */
1536: /* #ifdef DEBUG */
1537: /* printf("mnbrak4 fu > fc \n"); */
1538: /* fprintf(ficlog, "mnbrak4 fu > fc\n"); */
1539: /* #endif */
1540: /* /\* 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 *\\/ *\/ */
1541: /* /\* SHFT(*fa,*fc,fu,*fc) /\\* (b, u, c) is a bracket while test fb > fc will be fu > fc will exit *\\/ *\/ */
1542: /* dum=u; /\* Shifting c and u *\/ */
1543: /* u = *cx; */
1544: /* *cx = dum; */
1545: /* dum = fu; */
1546: /* fu = *fc; */
1547: /* *fc =dum; */
1548: /* } else { /\* end *\/ */
1549: /* #ifdef DEBUG */
1550: /* printf("mnbrak3 fu < fc \n"); */
1551: /* fprintf(ficlog, "mnbrak3 fu < fc\n"); */
1552: /* #endif */
1553: /* dum=u; /\* Shifting c and u *\/ */
1554: /* u = *cx; */
1555: /* *cx = dum; */
1556: /* dum = fu; */
1557: /* fu = *fc; */
1558: /* *fc =dum; */
1559: /* } */
1.183 brouard 1560: #ifdef DEBUG
1.191 brouard 1561: printf("mnbrak34 fu < or >= fc \n");
1562: fprintf(ficlog, "mnbrak34 fu < fc\n");
1.183 brouard 1563: #endif
1.191 brouard 1564: dum=u; /* Shifting c and u */
1565: u = *cx;
1566: *cx = dum;
1567: dum = fu;
1568: fu = *fc;
1569: *fc =dum;
1.183 brouard 1570: #endif
1.162 brouard 1571: } else if ((*cx-u)*(u-ulim) > 0.0) { /* u is after c but before ulim */
1.183 brouard 1572: #ifdef DEBUG
1573: printf("mnbrak2 u after c but before ulim\n");
1574: fprintf(ficlog, "mnbrak2 u after c but before ulim\n");
1575: #endif
1.126 brouard 1576: fu=(*func)(u);
1577: if (fu < *fc) {
1.183 brouard 1578: #ifdef DEBUG
1579: printf("mnbrak2 u after c but before ulim AND fu < fc\n");
1580: fprintf(ficlog, "mnbrak2 u after c but before ulim AND fu <fc \n");
1581: #endif
1.126 brouard 1582: SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))
1.183 brouard 1583: SHFT(*fb,*fc,fu,(*func)(u))
1584: }
1.162 brouard 1585: } else if ((u-ulim)*(ulim-*cx) >= 0.0) { /* u outside ulim (verifying that ulim is beyond c) */
1.183 brouard 1586: #ifdef DEBUG
1587: printf("mnbrak2 u outside ulim (verifying that ulim is beyond c)\n");
1588: fprintf(ficlog, "mnbrak2 u outside ulim (verifying that ulim is beyond c)\n");
1589: #endif
1.126 brouard 1590: u=ulim;
1591: fu=(*func)(u);
1.183 brouard 1592: } else { /* u could be left to b (if r > q parabola has a maximum) */
1593: #ifdef DEBUG
1594: printf("mnbrak2 u could be left to b (if r > q parabola has a maximum)\n");
1595: fprintf(ficlog, "mnbrak2 u could be left to b (if r > q parabola has a maximum)\n");
1596: #endif
1.126 brouard 1597: u=(*cx)+GOLD*(*cx-*bx);
1598: fu=(*func)(u);
1.183 brouard 1599: } /* end tests */
1.126 brouard 1600: SHFT(*ax,*bx,*cx,u)
1.183 brouard 1601: SHFT(*fa,*fb,*fc,fu)
1602: #ifdef DEBUG
1603: 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);
1604: 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);
1605: #endif
1606: } /* 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 1607: }
1608:
1609: /*************** linmin ************************/
1.162 brouard 1610: /* Given an n -dimensional point p[1..n] and an n -dimensional direction xi[1..n] , moves and
1611: resets p to where the function func(p) takes on a minimum along the direction xi from p ,
1612: and replaces xi by the actual vector displacement that p was moved. Also returns as fret
1613: the value of func at the returned location p . This is actually all accomplished by calling the
1614: routines mnbrak and brent .*/
1.126 brouard 1615: int ncom;
1616: double *pcom,*xicom;
1617: double (*nrfunc)(double []);
1618:
1619: void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))
1620: {
1621: double brent(double ax, double bx, double cx,
1622: double (*f)(double), double tol, double *xmin);
1623: double f1dim(double x);
1624: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,
1625: double *fc, double (*func)(double));
1626: int j;
1627: double xx,xmin,bx,ax;
1628: double fx,fb,fa;
1.187 brouard 1629:
1.203 brouard 1630: #ifdef LINMINORIGINAL
1631: #else
1632: double scale=10., axs, xxs; /* Scale added for infinity */
1633: #endif
1634:
1.126 brouard 1635: ncom=n;
1636: pcom=vector(1,n);
1637: xicom=vector(1,n);
1638: nrfunc=func;
1639: for (j=1;j<=n;j++) {
1640: pcom[j]=p[j];
1.202 brouard 1641: xicom[j]=xi[j]; /* Former scale xi[j] of currrent direction i */
1.126 brouard 1642: }
1.187 brouard 1643:
1.203 brouard 1644: #ifdef LINMINORIGINAL
1645: xx=1.;
1646: #else
1647: axs=0.0;
1648: xxs=1.;
1649: do{
1650: xx= xxs;
1651: #endif
1.187 brouard 1652: ax=0.;
1653: mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); /* Outputs: xtx[j]=pcom[j]+(*xx)*xicom[j]; fx=f(xtx[j]) */
1654: /* brackets with inputs ax=0 and xx=1, but points, pcom=p, and directions values, xicom=xi, are sent via f1dim(x) */
1655: /* 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)) */
1656: /* Outputs: fa=f(p(j)) and fx=f(p(j) + xxs * xi(j) ) and f(bx)= f(p(j)+ bx* xi(j)) */
1657: /* Given input ax=axs and xx=xxs, xx might be too far from ax to get a finite f(xx) */
1658: /* Searches on line, outputs (ax, xx, bx) such that fx < min(fa and fb) */
1659: /* 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 1660: #ifdef LINMINORIGINAL
1661: #else
1662: if (fx != fx){
1663: xxs=xxs/scale; /* Trying a smaller xx, closer to initial ax=0 */
1664: printf("|");
1665: fprintf(ficlog,"|");
1666: #ifdef DEBUGLINMIN
1667: 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);
1668: #endif
1669: }
1670: }while(fx != fx);
1671: #endif
1672:
1.191 brouard 1673: #ifdef DEBUGLINMIN
1674: 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 1675: 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 1676: #endif
1.187 brouard 1677: *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); /* Giving a bracketting triplet (ax, xx, bx), find a minimum, xmin, according to f1dim, *fret(xmin),*/
1678: /* fa = f(p[j] + ax * xi[j]), fx = f(p[j] + xx * xi[j]), fb = f(p[j] + bx * xi[j]) */
1679: /* fmin = f(p[j] + xmin * xi[j]) */
1680: /* P+lambda n in that direction (lambdamin), with TOL between abscisses */
1681: /* f1dim(xmin): for (j=1;j<=ncom;j++) xt[j]=pcom[j]+xmin*xicom[j]; */
1.126 brouard 1682: #ifdef DEBUG
1683: printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
1684: fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
1685: #endif
1.191 brouard 1686: #ifdef DEBUGLINMIN
1687: printf("linmin end ");
1.202 brouard 1688: fprintf(ficlog,"linmin end ");
1.191 brouard 1689: #endif
1.126 brouard 1690: for (j=1;j<=n;j++) {
1.203 brouard 1691: #ifdef LINMINORIGINAL
1692: xi[j] *= xmin;
1693: #else
1694: #ifdef DEBUGLINMIN
1695: if(xxs <1.0)
1696: printf(" before xi[%d]=%12.8f", j,xi[j]);
1697: #endif
1698: 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) */
1699: #ifdef DEBUGLINMIN
1700: if(xxs <1.0)
1701: 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 );
1702: #endif
1703: #endif
1.187 brouard 1704: p[j] += xi[j]; /* Parameters values are updated accordingly */
1.126 brouard 1705: }
1.191 brouard 1706: #ifdef DEBUGLINMIN
1.203 brouard 1707: printf("\n");
1.191 brouard 1708: printf("Comparing last *frec(xmin=%12.8f)=%12.8f from Brent and frec(0.)=%12.8f \n", xmin, *fret, (*func)(p));
1.202 brouard 1709: 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 1710: for (j=1;j<=n;j++) {
1.202 brouard 1711: printf(" xi[%d]= %14.10f p[%d]= %12.7f",j,xi[j],j,p[j]);
1712: fprintf(ficlog," xi[%d]= %14.10f p[%d]= %12.7f",j,xi[j],j,p[j]);
1713: if(j % ncovmodel == 0){
1.191 brouard 1714: printf("\n");
1.202 brouard 1715: fprintf(ficlog,"\n");
1716: }
1.191 brouard 1717: }
1.203 brouard 1718: #else
1.191 brouard 1719: #endif
1.126 brouard 1720: free_vector(xicom,1,n);
1721: free_vector(pcom,1,n);
1722: }
1723:
1724:
1725: /*************** powell ************************/
1.162 brouard 1726: /*
1727: Minimization of a function func of n variables. Input consists of an initial starting point
1728: p[1..n] ; an initial matrix xi[1..n][1..n] , whose columns contain the initial set of di-
1729: rections (usually the n unit vectors); and ftol , the fractional tolerance in the function value
1730: such that failure to decrease by more than this amount on one iteration signals doneness. On
1731: output, p is set to the best point found, xi is the then-current direction set, fret is the returned
1732: function value at p , and iter is the number of iterations taken. The routine linmin is used.
1733: */
1.126 brouard 1734: void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,
1735: double (*func)(double []))
1736: {
1737: void linmin(double p[], double xi[], int n, double *fret,
1738: double (*func)(double []));
1739: int i,ibig,j;
1740: double del,t,*pt,*ptt,*xit;
1.181 brouard 1741: double directest;
1.126 brouard 1742: double fp,fptt;
1743: double *xits;
1744: int niterf, itmp;
1745:
1746: pt=vector(1,n);
1747: ptt=vector(1,n);
1748: xit=vector(1,n);
1749: xits=vector(1,n);
1750: *fret=(*func)(p);
1751: for (j=1;j<=n;j++) pt[j]=p[j];
1.202 brouard 1752: rcurr_time = time(NULL);
1.126 brouard 1753: for (*iter=1;;++(*iter)) {
1.187 brouard 1754: fp=(*fret); /* From former iteration or initial value */
1.126 brouard 1755: ibig=0;
1756: del=0.0;
1.157 brouard 1757: rlast_time=rcurr_time;
1758: /* (void) gettimeofday(&curr_time,&tzp); */
1759: rcurr_time = time(NULL);
1760: curr_time = *localtime(&rcurr_time);
1761: printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, rcurr_time-rlast_time, rcurr_time-rstart_time);fflush(stdout);
1762: fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret,rcurr_time-rlast_time, rcurr_time-rstart_time); fflush(ficlog);
1763: /* fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tm_sec-start_time.tm_sec); */
1.192 brouard 1764: for (i=1;i<=n;i++) {
1.126 brouard 1765: printf(" %d %.12f",i, p[i]);
1766: fprintf(ficlog," %d %.12lf",i, p[i]);
1767: fprintf(ficrespow," %.12lf", p[i]);
1768: }
1769: printf("\n");
1770: fprintf(ficlog,"\n");
1771: fprintf(ficrespow,"\n");fflush(ficrespow);
1772: if(*iter <=3){
1.157 brouard 1773: tml = *localtime(&rcurr_time);
1774: strcpy(strcurr,asctime(&tml));
1775: rforecast_time=rcurr_time;
1.126 brouard 1776: itmp = strlen(strcurr);
1777: if(strcurr[itmp-1]=='\n') /* Windows outputs with a new line */
1778: strcurr[itmp-1]='\0';
1.162 brouard 1779: printf("\nConsidering the time needed for the last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
1.157 brouard 1780: fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
1.126 brouard 1781: for(niterf=10;niterf<=30;niterf+=10){
1.157 brouard 1782: rforecast_time=rcurr_time+(niterf-*iter)*(rcurr_time-rlast_time);
1783: forecast_time = *localtime(&rforecast_time);
1784: strcpy(strfor,asctime(&forecast_time));
1.126 brouard 1785: itmp = strlen(strfor);
1786: if(strfor[itmp-1]=='\n')
1787: strfor[itmp-1]='\0';
1.157 brouard 1788: 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);
1789: 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 1790: }
1791: }
1.187 brouard 1792: for (i=1;i<=n;i++) { /* For each direction i */
1793: for (j=1;j<=n;j++) xit[j]=xi[j][i]; /* Directions stored from previous iteration with previous scales */
1.126 brouard 1794: fptt=(*fret);
1795: #ifdef DEBUG
1.203 brouard 1796: printf("fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
1797: fprintf(ficlog, "fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
1.126 brouard 1798: #endif
1.203 brouard 1799: printf("%d",i);fflush(stdout); /* print direction (parameter) i */
1.126 brouard 1800: fprintf(ficlog,"%d",i);fflush(ficlog);
1.188 brouard 1801: linmin(p,xit,n,fret,func); /* Point p[n]. xit[n] has been loaded for direction i as input.*/
1802: /* Outputs are fret(new point p) p is updated and xit rescaled */
1803: if (fabs(fptt-(*fret)) > del) { /* We are keeping the max gain on each of the n directions */
1804: /* because that direction will be replaced unless the gain del is small */
1805: /* in comparison with the 'probable' gain, mu^2, with the last average direction. */
1806: /* Unless the n directions are conjugate some gain in the determinant may be obtained */
1807: /* with the new direction. */
1.126 brouard 1808: del=fabs(fptt-(*fret));
1809: ibig=i;
1810: }
1811: #ifdef DEBUG
1812: printf("%d %.12e",i,(*fret));
1813: fprintf(ficlog,"%d %.12e",i,(*fret));
1814: for (j=1;j<=n;j++) {
1815: xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
1816: printf(" x(%d)=%.12e",j,xit[j]);
1817: fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
1818: }
1819: for(j=1;j<=n;j++) {
1.162 brouard 1820: printf(" p(%d)=%.12e",j,p[j]);
1821: fprintf(ficlog," p(%d)=%.12e",j,p[j]);
1.126 brouard 1822: }
1823: printf("\n");
1824: fprintf(ficlog,"\n");
1825: #endif
1.187 brouard 1826: } /* end loop on each direction i */
1827: /* Convergence test will use last linmin estimation (fret) and compare former iteration (fp) */
1.188 brouard 1828: /* But p and xit have been updated at the end of linmin, *fret corresponds to new p, xit */
1.187 brouard 1829: /* New value of last point Pn is not computed, P(n-1) */
1.182 brouard 1830: if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) { /* Did we reach enough precision? */
1.188 brouard 1831: /* We could compare with a chi^2. chisquare(0.95,ddl=1)=3.84 */
1832: /* By adding age*age in a model, the new -2LL should be lower and the difference follows a */
1833: /* a chisquare statistics with 1 degree. To be significant at the 95% level, it should have */
1834: /* decreased of more than 3.84 */
1835: /* By adding age*age and V1*age the gain (-2LL) should be more than 5.99 (ddl=2) */
1836: /* By using V1+V2+V3, the gain should be 7.82, compared with basic 1+age. */
1837: /* By adding 10 parameters more the gain should be 18.31 */
1838:
1839: /* Starting the program with initial values given by a former maximization will simply change */
1840: /* the scales of the directions and the directions, because the are reset to canonical directions */
1841: /* Thus the first calls to linmin will give new points and better maximizations until fp-(*fret) is */
1842: /* under the tolerance value. If the tolerance is very small 1.e-9, it could last long. */
1.126 brouard 1843: #ifdef DEBUG
1844: int k[2],l;
1845: k[0]=1;
1846: k[1]=-1;
1847: printf("Max: %.12e",(*func)(p));
1848: fprintf(ficlog,"Max: %.12e",(*func)(p));
1849: for (j=1;j<=n;j++) {
1850: printf(" %.12e",p[j]);
1851: fprintf(ficlog," %.12e",p[j]);
1852: }
1853: printf("\n");
1854: fprintf(ficlog,"\n");
1855: for(l=0;l<=1;l++) {
1856: for (j=1;j<=n;j++) {
1857: ptt[j]=p[j]+(p[j]-pt[j])*k[l];
1858: printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
1859: fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
1860: }
1861: printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
1862: fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
1863: }
1864: #endif
1865:
1866:
1867: free_vector(xit,1,n);
1868: free_vector(xits,1,n);
1869: free_vector(ptt,1,n);
1870: free_vector(pt,1,n);
1871: return;
1.192 brouard 1872: } /* enough precision */
1.126 brouard 1873: if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");
1.181 brouard 1874: for (j=1;j<=n;j++) { /* Computes the extrapolated point P_0 + 2 (P_n-P_0) */
1.126 brouard 1875: ptt[j]=2.0*p[j]-pt[j];
1876: xit[j]=p[j]-pt[j];
1877: pt[j]=p[j];
1878: }
1.181 brouard 1879: fptt=(*func)(ptt); /* f_3 */
1.192 brouard 1880: #ifdef POWELLF1F3
1881: #else
1.161 brouard 1882: if (fptt < fp) { /* If extrapolated point is better, decide if we keep that new direction or not */
1.192 brouard 1883: #endif
1.162 brouard 1884: /* (x1 f1=fp), (x2 f2=*fret), (x3 f3=fptt), (xm fm) */
1.161 brouard 1885: /* From x1 (P0) distance of x2 is at h and x3 is 2h */
1.162 brouard 1886: /* Let f"(x2) be the 2nd derivative equal everywhere. */
1887: /* Then the parabolic through (x1,f1), (x2,f2) and (x3,f3) */
1888: /* will reach at f3 = fm + h^2/2 f"m ; f" = (f1 -2f2 +f3 ) / h**2 */
1.181 brouard 1889: /* Conditional for using this new direction is that mu^2 = (f1-2f2+f3)^2 /2 < del */
1.161 brouard 1890: /* t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); */
1.183 brouard 1891: #ifdef NRCORIGINAL
1892: t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)- del*SQR(fp-fptt); /* Original Numerical Recipes in C*/
1893: #else
1894: 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 1895: t= t- del*SQR(fp-fptt);
1.183 brouard 1896: #endif
1.202 brouard 1897: directest = fp-2.0*(*fret)+fptt - 2.0 * del; /* If delta was big enough we change it for a new direction */
1.161 brouard 1898: #ifdef DEBUG
1.181 brouard 1899: 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);
1900: 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 1901: printf("t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
1902: (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
1903: fprintf(ficlog,"t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
1904: (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
1905: 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);
1906: 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);
1907: #endif
1.183 brouard 1908: #ifdef POWELLORIGINAL
1909: if (t < 0.0) { /* Then we use it for new direction */
1910: #else
1.182 brouard 1911: if (directest*t < 0.0) { /* Contradiction between both tests */
1.202 brouard 1912: 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 1913: 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 1914: 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 1915: fprintf(ficlog,"f1-2f2+f3= %.12lf, f1-f2-del= %.12lf, f1-f3= %.12lf\n",fp-2.0*(*fret)+fptt, fp -(*fret) -del, fp-fptt);
1916: }
1.181 brouard 1917: if (directest < 0.0) { /* Then we use it for new direction */
1918: #endif
1.191 brouard 1919: #ifdef DEBUGLINMIN
1920: printf("Before linmin in direction P%d-P0\n",n);
1921: for (j=1;j<=n;j++) {
1.202 brouard 1922: printf(" Before xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
1923: fprintf(ficlog," Before xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
1924: if(j % ncovmodel == 0){
1.191 brouard 1925: printf("\n");
1.202 brouard 1926: fprintf(ficlog,"\n");
1927: }
1.191 brouard 1928: }
1929: #endif
1.187 brouard 1930: linmin(p,xit,n,fret,func); /* computes minimum on the extrapolated direction: changes p and rescales xit.*/
1.191 brouard 1931: #ifdef DEBUGLINMIN
1932: for (j=1;j<=n;j++) {
1933: printf("After xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
1.202 brouard 1934: fprintf(ficlog,"After xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
1935: if(j % ncovmodel == 0){
1.191 brouard 1936: printf("\n");
1.202 brouard 1937: fprintf(ficlog,"\n");
1938: }
1.191 brouard 1939: }
1940: #endif
1.126 brouard 1941: for (j=1;j<=n;j++) {
1.181 brouard 1942: xi[j][ibig]=xi[j][n]; /* Replace direction with biggest decrease by last direction n */
1943: xi[j][n]=xit[j]; /* and this nth direction by the by the average p_0 p_n */
1.126 brouard 1944: }
1.181 brouard 1945: printf("Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
1946: fprintf(ficlog,"Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
1.161 brouard 1947:
1.126 brouard 1948: #ifdef DEBUG
1.164 brouard 1949: printf("Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
1950: fprintf(ficlog,"Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
1.126 brouard 1951: for(j=1;j<=n;j++){
1952: printf(" %.12e",xit[j]);
1953: fprintf(ficlog," %.12e",xit[j]);
1954: }
1955: printf("\n");
1956: fprintf(ficlog,"\n");
1957: #endif
1.192 brouard 1958: } /* end of t or directest negative */
1959: #ifdef POWELLF1F3
1960: #else
1.162 brouard 1961: } /* end if (fptt < fp) */
1.192 brouard 1962: #endif
1963: } /* loop iteration */
1.126 brouard 1964: }
1965:
1966: /**** Prevalence limit (stable or period prevalence) ****************/
1967:
1.203 brouard 1968: double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int *ncvyear, int ij)
1.126 brouard 1969: {
1970: /* Computes the prevalence limit in each live state at age x by left multiplying the unit
1.203 brouard 1971: matrix by transitions matrix until convergence is reached with precision ftolpl */
1.206 brouard 1972: /* Wx= Wx-1 Px-1= Wx-2 Px-2 Px-1 = Wx-n Px-n ... Px-2 Px-1 I */
1973: /* Wx is row vector: population in state 1, population in state 2, population dead */
1974: /* or prevalence in state 1, prevalence in state 2, 0 */
1975: /* newm is the matrix after multiplications, its rows are identical at a factor */
1976: /* Initial matrix pimij */
1977: /* {0.85204250825084937, 0.13044499163996345, 0.017512500109187184, */
1978: /* 0.090851990222114765, 0.88271245433047185, 0.026435555447413338, */
1979: /* 0, 0 , 1} */
1980: /*
1981: * and after some iteration: */
1982: /* {0.45504275246439968, 0.42731458730878791, 0.11764266022681241, */
1983: /* 0.45201005341706885, 0.42865420071559901, 0.11933574586733192, */
1984: /* 0, 0 , 1} */
1985: /* And prevalence by suppressing the deaths are close to identical rows in prlim: */
1986: /* {0.51571254859325999, 0.4842874514067399, */
1987: /* 0.51326036147820708, 0.48673963852179264} */
1988: /* If we start from prlim again, prlim tends to a constant matrix */
1989:
1.126 brouard 1990: int i, ii,j,k;
1.209 ! brouard 1991: double *min, *max, *meandiff, maxmax,sumnew=0.;
1.145 brouard 1992: /* double **matprod2(); */ /* test */
1.131 brouard 1993: double **out, cov[NCOVMAX+1], **pmij();
1.126 brouard 1994: double **newm;
1.209 ! brouard 1995: double agefin, delaymax=200. ; /* 100 Max number of years to converge */
1.203 brouard 1996: int ncvloop=0;
1.169 brouard 1997:
1.209 ! brouard 1998: min=vector(1,nlstate);
! 1999: max=vector(1,nlstate);
! 2000: meandiff=vector(1,nlstate);
! 2001:
1.126 brouard 2002: for (ii=1;ii<=nlstate+ndeath;ii++)
2003: for (j=1;j<=nlstate+ndeath;j++){
2004: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2005: }
1.169 brouard 2006:
2007: cov[1]=1.;
2008:
2009: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
1.202 brouard 2010: /* Start at agefin= age, computes the matrix of passage and loops decreasing agefin until convergence is reached */
1.126 brouard 2011: for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
1.202 brouard 2012: ncvloop++;
1.126 brouard 2013: newm=savm;
2014: /* Covariates have to be included here again */
1.138 brouard 2015: cov[2]=agefin;
1.187 brouard 2016: if(nagesqr==1)
2017: cov[3]= agefin*agefin;;
1.138 brouard 2018: for (k=1; k<=cptcovn;k++) {
1.200 brouard 2019: /* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; */
2020: cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)];
1.198 brouard 2021: /* 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 2022: }
1.186 brouard 2023: /*wrong? for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
1.200 brouard 2024: /* for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]*cov[2]; */
2025: for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtabm(ij,k)]*cov[2];
1.186 brouard 2026: for (k=1; k<=cptcovprod;k++) /* Useless */
1.200 brouard 2027: /* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])] * nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])]; */
2028: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)];
1.138 brouard 2029:
2030: /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
2031: /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
2032: /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
1.145 brouard 2033: /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
2034: /* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind *\/ */
1.142 brouard 2035: out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /* Bug Valgrind */
1.138 brouard 2036:
1.126 brouard 2037: savm=oldm;
2038: oldm=newm;
1.209 ! brouard 2039:
! 2040: for(j=1; j<=nlstate; j++){
! 2041: max[j]=0.;
! 2042: min[j]=1.;
! 2043: }
! 2044: for(i=1;i<=nlstate;i++){
! 2045: sumnew=0;
! 2046: for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
! 2047: for(j=1; j<=nlstate; j++){
! 2048: prlim[i][j]= newm[i][j]/(1-sumnew);
! 2049: max[j]=FMAX(max[j],prlim[i][j]);
! 2050: min[j]=FMIN(min[j],prlim[i][j]);
! 2051: }
! 2052: }
! 2053:
1.126 brouard 2054: maxmax=0.;
1.209 ! brouard 2055: for(j=1; j<=nlstate; j++){
! 2056: meandiff[j]=(max[j]-min[j])/(max[j]+min[j])*2.; /* mean difference for each column */
! 2057: maxmax=FMAX(maxmax,meandiff[j]);
! 2058: /* printf(" age= %d meandiff[%d]=%f, agefin=%d max[%d]=%f min[%d]=%f maxmax=%f\n", (int)age, j, meandiff[j],(int)agefin, j, max[j], j, min[j],maxmax); */
1.169 brouard 2059: } /* j loop */
1.203 brouard 2060: *ncvyear= (int)age- (int)agefin;
1.208 brouard 2061: /* 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 2062: if(maxmax < ftolpl){
1.209 ! brouard 2063: /* printf("maxmax=%lf ncvloop=%ld, age=%d, agefin=%d ncvyear=%d \n", maxmax, ncvloop, (int)age, (int)agefin, *ncvyear); */
! 2064: free_vector(min,1,nlstate);
! 2065: free_vector(max,1,nlstate);
! 2066: free_vector(meandiff,1,nlstate);
1.126 brouard 2067: return prlim;
2068: }
1.169 brouard 2069: } /* age loop */
1.208 brouard 2070: /* After some age loop it doesn't converge */
1.209 ! brouard 2071: printf("Warning: the stable prevalence at age %d did not converge with the required precision (%g > ftolpl=%g) within %.0f years. Try to lower 'ftolpl'. \n\
1.208 brouard 2072: Earliest age to start was %d-%d=%d, ncvloop=%d, ncvyear=%d\n", (int)age, maxmax, ftolpl, delaymax, (int)age, (int)delaymax, (int)agefin, ncvloop, *ncvyear);
1.209 ! brouard 2073: /* 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); */
! 2074: free_vector(min,1,nlstate);
! 2075: free_vector(max,1,nlstate);
! 2076: free_vector(meandiff,1,nlstate);
1.208 brouard 2077:
1.169 brouard 2078: return prlim; /* should not reach here */
1.126 brouard 2079: }
2080:
2081: /*************** transition probabilities ***************/
2082:
2083: double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
2084: {
1.138 brouard 2085: /* According to parameters values stored in x and the covariate's values stored in cov,
2086: computes the probability to be observed in state j being in state i by appying the
2087: model to the ncovmodel covariates (including constant and age).
2088: lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc]
2089: and, according on how parameters are entered, the position of the coefficient xij(nc) of the
2090: ncth covariate in the global vector x is given by the formula:
2091: j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
2092: j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
2093: Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
2094: sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.
2095: Outputs ps[i][j] the probability to be observed in j being in j according to
2096: the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
2097: */
2098: double s1, lnpijopii;
1.126 brouard 2099: /*double t34;*/
1.164 brouard 2100: int i,j, nc, ii, jj;
1.126 brouard 2101:
2102: for(i=1; i<= nlstate; i++){
2103: for(j=1; j<i;j++){
1.138 brouard 2104: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
2105: /*lnpijopii += param[i][j][nc]*cov[nc];*/
2106: lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
2107: /* printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
1.126 brouard 2108: }
1.138 brouard 2109: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
2110: /* printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
1.126 brouard 2111: }
2112: for(j=i+1; j<=nlstate+ndeath;j++){
1.138 brouard 2113: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
2114: /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
2115: lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
2116: /* printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
1.126 brouard 2117: }
1.138 brouard 2118: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
1.126 brouard 2119: }
2120: }
2121:
2122: for(i=1; i<= nlstate; i++){
2123: s1=0;
1.131 brouard 2124: for(j=1; j<i; j++){
1.138 brouard 2125: s1+=exp(ps[i][j]); /* In fact sums pij/pii */
1.131 brouard 2126: /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
2127: }
2128: for(j=i+1; j<=nlstate+ndeath; j++){
1.138 brouard 2129: s1+=exp(ps[i][j]); /* In fact sums pij/pii */
1.131 brouard 2130: /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
2131: }
1.138 brouard 2132: /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
1.126 brouard 2133: ps[i][i]=1./(s1+1.);
1.138 brouard 2134: /* Computing other pijs */
1.126 brouard 2135: for(j=1; j<i; j++)
2136: ps[i][j]= exp(ps[i][j])*ps[i][i];
2137: for(j=i+1; j<=nlstate+ndeath; j++)
2138: ps[i][j]= exp(ps[i][j])*ps[i][i];
2139: /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
2140: } /* end i */
2141:
2142: for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
2143: for(jj=1; jj<= nlstate+ndeath; jj++){
2144: ps[ii][jj]=0;
2145: ps[ii][ii]=1;
2146: }
2147: }
2148:
1.145 brouard 2149:
2150: /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
2151: /* for(jj=1; jj<= nlstate+ndeath; jj++){ */
2152: /* printf(" pmij ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
2153: /* } */
2154: /* printf("\n "); */
2155: /* } */
2156: /* printf("\n ");printf("%lf ",cov[2]);*/
2157: /*
1.126 brouard 2158: for(i=1; i<= npar; i++) printf("%f ",x[i]);
2159: goto end;*/
2160: return ps;
2161: }
2162:
2163: /**************** Product of 2 matrices ******************/
2164:
1.145 brouard 2165: double **matprod2(double **out, double **in,int nrl, int nrh, int ncl, int nch, int ncolol, int ncoloh, double **b)
1.126 brouard 2166: {
2167: /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
2168: b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
2169: /* in, b, out are matrice of pointers which should have been initialized
2170: before: only the contents of out is modified. The function returns
2171: a pointer to pointers identical to out */
1.145 brouard 2172: int i, j, k;
1.126 brouard 2173: for(i=nrl; i<= nrh; i++)
1.145 brouard 2174: for(k=ncolol; k<=ncoloh; k++){
2175: out[i][k]=0.;
2176: for(j=ncl; j<=nch; j++)
2177: out[i][k] +=in[i][j]*b[j][k];
2178: }
1.126 brouard 2179: return out;
2180: }
2181:
2182:
2183: /************* Higher Matrix Product ***************/
2184:
2185: double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
2186: {
2187: /* Computes the transition matrix starting at age 'age' over
2188: 'nhstepm*hstepm*stepm' months (i.e. until
2189: age (in years) age+nhstepm*hstepm*stepm/12) by multiplying
2190: nhstepm*hstepm matrices.
2191: Output is stored in matrix po[i][j][h] for h every 'hstepm' step
2192: (typically every 2 years instead of every month which is too big
2193: for the memory).
2194: Model is determined by parameters x and covariates have to be
2195: included manually here.
2196:
2197: */
2198:
2199: int i, j, d, h, k;
1.131 brouard 2200: double **out, cov[NCOVMAX+1];
1.126 brouard 2201: double **newm;
1.187 brouard 2202: double agexact;
1.126 brouard 2203:
2204: /* Hstepm could be zero and should return the unit matrix */
2205: for (i=1;i<=nlstate+ndeath;i++)
2206: for (j=1;j<=nlstate+ndeath;j++){
2207: oldm[i][j]=(i==j ? 1.0 : 0.0);
2208: po[i][j][0]=(i==j ? 1.0 : 0.0);
2209: }
2210: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
2211: for(h=1; h <=nhstepm; h++){
2212: for(d=1; d <=hstepm; d++){
2213: newm=savm;
2214: /* Covariates have to be included here again */
2215: cov[1]=1.;
1.187 brouard 2216: agexact=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
2217: cov[2]=agexact;
2218: if(nagesqr==1)
2219: cov[3]= agexact*agexact;
1.131 brouard 2220: for (k=1; k<=cptcovn;k++)
1.200 brouard 2221: cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)];
2222: /* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; */
1.186 brouard 2223: for (k=1; k<=cptcovage;k++) /* Should start at cptcovn+1 */
2224: /* cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
1.200 brouard 2225: cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
2226: /* cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,Tvar[Tage[k]])]*cov[2]; */
1.145 brouard 2227: for (k=1; k<=cptcovprod;k++) /* Useless because included in cptcovn */
1.200 brouard 2228: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)];
2229: /* 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 2230:
2231:
2232: /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
2233: /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
2234: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
2235: pmij(pmmij,cov,ncovmodel,x,nlstate));
2236: savm=oldm;
2237: oldm=newm;
2238: }
2239: for(i=1; i<=nlstate+ndeath; i++)
2240: for(j=1;j<=nlstate+ndeath;j++) {
2241: po[i][j][h]=newm[i][j];
1.128 brouard 2242: /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
1.126 brouard 2243: }
1.128 brouard 2244: /*printf("h=%d ",h);*/
1.126 brouard 2245: } /* end h */
1.128 brouard 2246: /* printf("\n H=%d \n",h); */
1.126 brouard 2247: return po;
2248: }
2249:
1.162 brouard 2250: #ifdef NLOPT
2251: double myfunc(unsigned n, const double *p1, double *grad, void *pd){
2252: double fret;
2253: double *xt;
2254: int j;
2255: myfunc_data *d2 = (myfunc_data *) pd;
2256: /* xt = (p1-1); */
2257: xt=vector(1,n);
2258: for (j=1;j<=n;j++) xt[j]=p1[j-1]; /* xt[1]=p1[0] */
2259:
2260: fret=(d2->function)(xt); /* p xt[1]@8 is fine */
2261: /* fret=(*func)(xt); /\* p xt[1]@8 is fine *\/ */
2262: printf("Function = %.12lf ",fret);
2263: for (j=1;j<=n;j++) printf(" %d %.8lf", j, xt[j]);
2264: printf("\n");
2265: free_vector(xt,1,n);
2266: return fret;
2267: }
2268: #endif
1.126 brouard 2269:
2270: /*************** log-likelihood *************/
2271: double func( double *x)
2272: {
2273: int i, ii, j, k, mi, d, kk;
1.131 brouard 2274: double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
1.126 brouard 2275: double **out;
2276: double sw; /* Sum of weights */
2277: double lli; /* Individual log likelihood */
2278: int s1, s2;
2279: double bbh, survp;
2280: long ipmx;
1.187 brouard 2281: double agexact;
1.126 brouard 2282: /*extern weight */
2283: /* We are differentiating ll according to initial status */
2284: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
2285: /*for(i=1;i<imx;i++)
2286: printf(" %d\n",s[4][i]);
2287: */
1.162 brouard 2288:
2289: ++countcallfunc;
2290:
1.126 brouard 2291: cov[1]=1.;
2292:
2293: for(k=1; k<=nlstate; k++) ll[k]=0.;
2294:
2295: if(mle==1){
2296: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1.138 brouard 2297: /* Computes the values of the ncovmodel covariates of the model
2298: depending if the covariates are fixed or variying (age dependent) and stores them in cov[]
2299: Then computes with function pmij which return a matrix p[i][j] giving the elementary probability
2300: to be observed in j being in i according to the model.
2301: */
1.145 brouard 2302: for (k=1; k<=cptcovn;k++){ /* Simple and product covariates without age* products */
1.187 brouard 2303: cov[2+nagesqr+k]=covar[Tvar[k]][i];
1.145 brouard 2304: }
1.137 brouard 2305: /* In model V2+V1*V4+age*V3+V3*V2 Tvar[1] is V2, Tvar[2=V1*V4]
1.138 brouard 2306: is 6, Tvar[3=age*V3] should not be computed because of age Tvar[4=V3*V2]
1.137 brouard 2307: has been calculated etc */
1.126 brouard 2308: for(mi=1; mi<= wav[i]-1; mi++){
2309: for (ii=1;ii<=nlstate+ndeath;ii++)
2310: for (j=1;j<=nlstate+ndeath;j++){
2311: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2312: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2313: }
2314: for(d=0; d<dh[mi][i]; d++){
2315: newm=savm;
1.187 brouard 2316: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
2317: cov[2]=agexact;
2318: if(nagesqr==1)
2319: cov[3]= agexact*agexact;
1.126 brouard 2320: for (kk=1; kk<=cptcovage;kk++) {
1.187 brouard 2321: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact; /* Tage[kk] gives the data-covariate associated with age */
1.126 brouard 2322: }
2323: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2324: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
2325: savm=oldm;
2326: oldm=newm;
2327: } /* end mult */
2328:
2329: /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
2330: /* But now since version 0.9 we anticipate for bias at large stepm.
2331: * If stepm is larger than one month (smallest stepm) and if the exact delay
2332: * (in months) between two waves is not a multiple of stepm, we rounded to
2333: * the nearest (and in case of equal distance, to the lowest) interval but now
2334: * we keep into memory the bias bh[mi][i] and also the previous matrix product
2335: * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
2336: * probability in order to take into account the bias as a fraction of the way
2337: * from savm to out if bh is negative or even beyond if bh is positive. bh varies
2338: * -stepm/2 to stepm/2 .
2339: * For stepm=1 the results are the same as for previous versions of Imach.
2340: * For stepm > 1 the results are less biased than in previous versions.
2341: */
2342: s1=s[mw[mi][i]][i];
2343: s2=s[mw[mi+1][i]][i];
2344: bbh=(double)bh[mi][i]/(double)stepm;
2345: /* bias bh is positive if real duration
2346: * is higher than the multiple of stepm and negative otherwise.
2347: */
2348: /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
2349: if( s2 > nlstate){
2350: /* i.e. if s2 is a death state and if the date of death is known
2351: then the contribution to the likelihood is the probability to
2352: die between last step unit time and current step unit time,
2353: which is also equal to probability to die before dh
2354: minus probability to die before dh-stepm .
2355: In version up to 0.92 likelihood was computed
2356: as if date of death was unknown. Death was treated as any other
2357: health state: the date of the interview describes the actual state
2358: and not the date of a change in health state. The former idea was
2359: to consider that at each interview the state was recorded
2360: (healthy, disable or death) and IMaCh was corrected; but when we
2361: introduced the exact date of death then we should have modified
2362: the contribution of an exact death to the likelihood. This new
2363: contribution is smaller and very dependent of the step unit
2364: stepm. It is no more the probability to die between last interview
2365: and month of death but the probability to survive from last
2366: interview up to one month before death multiplied by the
2367: probability to die within a month. Thanks to Chris
2368: Jackson for correcting this bug. Former versions increased
2369: mortality artificially. The bad side is that we add another loop
2370: which slows down the processing. The difference can be up to 10%
2371: lower mortality.
2372: */
1.183 brouard 2373: /* If, at the beginning of the maximization mostly, the
2374: cumulative probability or probability to be dead is
2375: constant (ie = 1) over time d, the difference is equal to
2376: 0. out[s1][3] = savm[s1][3]: probability, being at state
2377: s1 at precedent wave, to be dead a month before current
2378: wave is equal to probability, being at state s1 at
2379: precedent wave, to be dead at mont of the current
2380: wave. Then the observed probability (that this person died)
2381: is null according to current estimated parameter. In fact,
2382: it should be very low but not zero otherwise the log go to
2383: infinity.
2384: */
2385: /* #ifdef INFINITYORIGINAL */
2386: /* lli=log(out[s1][s2] - savm[s1][s2]); */
2387: /* #else */
2388: /* if ((out[s1][s2] - savm[s1][s2]) < mytinydouble) */
2389: /* lli=log(mytinydouble); */
2390: /* else */
2391: /* lli=log(out[s1][s2] - savm[s1][s2]); */
2392: /* #endif */
2393: lli=log(out[s1][s2] - savm[s1][s2]);
1.126 brouard 2394:
2395: } else if (s2==-2) {
2396: for (j=1,survp=0. ; j<=nlstate; j++)
2397: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
2398: /*survp += out[s1][j]; */
2399: lli= log(survp);
2400: }
2401:
2402: else if (s2==-4) {
2403: for (j=3,survp=0. ; j<=nlstate; j++)
2404: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
2405: lli= log(survp);
2406: }
2407:
2408: else if (s2==-5) {
2409: for (j=1,survp=0. ; j<=2; j++)
2410: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
2411: lli= log(survp);
2412: }
2413:
2414: else{
2415: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
2416: /* 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 */
2417: }
2418: /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
2419: /*if(lli ==000.0)*/
2420: /*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); */
2421: ipmx +=1;
2422: sw += weight[i];
2423: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1.183 brouard 2424: /* if (lli < log(mytinydouble)){ */
2425: /* 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); */
2426: /* 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]); */
2427: /* } */
1.126 brouard 2428: } /* end of wave */
2429: } /* end of individual */
2430: } else if(mle==2){
2431: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1.187 brouard 2432: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
1.126 brouard 2433: for(mi=1; mi<= wav[i]-1; mi++){
2434: for (ii=1;ii<=nlstate+ndeath;ii++)
2435: for (j=1;j<=nlstate+ndeath;j++){
2436: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2437: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2438: }
2439: for(d=0; d<=dh[mi][i]; d++){
2440: newm=savm;
1.187 brouard 2441: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
2442: cov[2]=agexact;
2443: if(nagesqr==1)
2444: cov[3]= agexact*agexact;
1.126 brouard 2445: for (kk=1; kk<=cptcovage;kk++) {
1.187 brouard 2446: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
1.126 brouard 2447: }
2448: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2449: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
2450: savm=oldm;
2451: oldm=newm;
2452: } /* end mult */
2453:
2454: s1=s[mw[mi][i]][i];
2455: s2=s[mw[mi+1][i]][i];
2456: bbh=(double)bh[mi][i]/(double)stepm;
2457: 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 */
2458: ipmx +=1;
2459: sw += weight[i];
2460: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
2461: } /* end of wave */
2462: } /* end of individual */
2463: } else if(mle==3){ /* exponential inter-extrapolation */
2464: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1.187 brouard 2465: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
1.126 brouard 2466: for(mi=1; mi<= wav[i]-1; mi++){
2467: for (ii=1;ii<=nlstate+ndeath;ii++)
2468: for (j=1;j<=nlstate+ndeath;j++){
2469: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2470: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2471: }
2472: for(d=0; d<dh[mi][i]; d++){
2473: newm=savm;
1.187 brouard 2474: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
2475: cov[2]=agexact;
2476: if(nagesqr==1)
2477: cov[3]= agexact*agexact;
1.126 brouard 2478: for (kk=1; kk<=cptcovage;kk++) {
1.187 brouard 2479: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
1.126 brouard 2480: }
2481: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2482: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
2483: savm=oldm;
2484: oldm=newm;
2485: } /* end mult */
2486:
2487: s1=s[mw[mi][i]][i];
2488: s2=s[mw[mi+1][i]][i];
2489: bbh=(double)bh[mi][i]/(double)stepm;
2490: 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 */
2491: ipmx +=1;
2492: sw += weight[i];
2493: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
2494: } /* end of wave */
2495: } /* end of individual */
2496: }else if (mle==4){ /* ml=4 no inter-extrapolation */
2497: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1.187 brouard 2498: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
1.126 brouard 2499: for(mi=1; mi<= wav[i]-1; mi++){
2500: for (ii=1;ii<=nlstate+ndeath;ii++)
2501: for (j=1;j<=nlstate+ndeath;j++){
2502: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2503: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2504: }
2505: for(d=0; d<dh[mi][i]; d++){
2506: newm=savm;
1.187 brouard 2507: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
2508: cov[2]=agexact;
2509: if(nagesqr==1)
2510: cov[3]= agexact*agexact;
1.126 brouard 2511: for (kk=1; kk<=cptcovage;kk++) {
1.187 brouard 2512: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
1.126 brouard 2513: }
2514:
2515: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2516: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
2517: savm=oldm;
2518: oldm=newm;
2519: } /* end mult */
2520:
2521: s1=s[mw[mi][i]][i];
2522: s2=s[mw[mi+1][i]][i];
2523: if( s2 > nlstate){
2524: lli=log(out[s1][s2] - savm[s1][s2]);
2525: }else{
2526: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
2527: }
2528: ipmx +=1;
2529: sw += weight[i];
2530: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
2531: /* 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]); */
2532: } /* end of wave */
2533: } /* end of individual */
2534: }else{ /* ml=5 no inter-extrapolation no jackson =0.8a */
2535: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1.187 brouard 2536: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
1.126 brouard 2537: for(mi=1; mi<= wav[i]-1; mi++){
2538: for (ii=1;ii<=nlstate+ndeath;ii++)
2539: for (j=1;j<=nlstate+ndeath;j++){
2540: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2541: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2542: }
2543: for(d=0; d<dh[mi][i]; d++){
2544: newm=savm;
1.187 brouard 2545: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
2546: cov[2]=agexact;
2547: if(nagesqr==1)
2548: cov[3]= agexact*agexact;
1.126 brouard 2549: for (kk=1; kk<=cptcovage;kk++) {
1.187 brouard 2550: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
1.126 brouard 2551: }
2552:
2553: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2554: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
2555: savm=oldm;
2556: oldm=newm;
2557: } /* end mult */
2558:
2559: s1=s[mw[mi][i]][i];
2560: s2=s[mw[mi+1][i]][i];
2561: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
2562: ipmx +=1;
2563: sw += weight[i];
2564: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
2565: /*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]);*/
2566: } /* end of wave */
2567: } /* end of individual */
2568: } /* End of if */
2569: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
2570: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
2571: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
2572: return -l;
2573: }
2574:
2575: /*************** log-likelihood *************/
2576: double funcone( double *x)
2577: {
2578: /* Same as likeli but slower because of a lot of printf and if */
2579: int i, ii, j, k, mi, d, kk;
1.131 brouard 2580: double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
1.126 brouard 2581: double **out;
2582: double lli; /* Individual log likelihood */
2583: double llt;
2584: int s1, s2;
2585: double bbh, survp;
1.187 brouard 2586: double agexact;
1.126 brouard 2587: /*extern weight */
2588: /* We are differentiating ll according to initial status */
2589: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
2590: /*for(i=1;i<imx;i++)
2591: printf(" %d\n",s[4][i]);
2592: */
2593: cov[1]=1.;
2594:
2595: for(k=1; k<=nlstate; k++) ll[k]=0.;
2596:
2597: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1.187 brouard 2598: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
1.126 brouard 2599: for(mi=1; mi<= wav[i]-1; mi++){
2600: for (ii=1;ii<=nlstate+ndeath;ii++)
2601: for (j=1;j<=nlstate+ndeath;j++){
2602: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2603: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2604: }
2605: for(d=0; d<dh[mi][i]; d++){
2606: newm=savm;
1.187 brouard 2607: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
2608: cov[2]=agexact;
2609: if(nagesqr==1)
2610: cov[3]= agexact*agexact;
1.126 brouard 2611: for (kk=1; kk<=cptcovage;kk++) {
1.187 brouard 2612: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
1.126 brouard 2613: }
1.187 brouard 2614:
1.145 brouard 2615: /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
1.126 brouard 2616: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2617: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1.145 brouard 2618: /* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, */
2619: /* 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); */
1.126 brouard 2620: savm=oldm;
2621: oldm=newm;
2622: } /* end mult */
2623:
2624: s1=s[mw[mi][i]][i];
2625: s2=s[mw[mi+1][i]][i];
2626: bbh=(double)bh[mi][i]/(double)stepm;
2627: /* bias is positive if real duration
2628: * is higher than the multiple of stepm and negative otherwise.
2629: */
2630: if( s2 > nlstate && (mle <5) ){ /* Jackson */
2631: lli=log(out[s1][s2] - savm[s1][s2]);
2632: } else if (s2==-2) {
2633: for (j=1,survp=0. ; j<=nlstate; j++)
2634: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
2635: lli= log(survp);
2636: }else if (mle==1){
2637: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
2638: } else if(mle==2){
2639: 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 */
2640: } else if(mle==3){ /* exponential inter-extrapolation */
2641: 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 */
2642: } else if (mle==4){ /* mle=4 no inter-extrapolation */
2643: lli=log(out[s1][s2]); /* Original formula */
1.136 brouard 2644: } else{ /* mle=0 back to 1 */
2645: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
2646: /*lli=log(out[s1][s2]); */ /* Original formula */
1.126 brouard 2647: } /* End of if */
2648: ipmx +=1;
2649: sw += weight[i];
2650: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1.132 brouard 2651: /*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 2652: if(globpr){
1.205 brouard 2653: fprintf(ficresilk,"%9ld %6.1f %6d %2d %2d %2d %2d %3d %11.6f %8.4f %8.3f\
1.126 brouard 2654: %11.6f %11.6f %11.6f ", \
1.205 brouard 2655: num[i], agexact, i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],weight[i]*gipmx/gsw,
1.126 brouard 2656: 2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
2657: for(k=1,llt=0.,l=0.; k<=nlstate; k++){
2658: llt +=ll[k]*gipmx/gsw;
2659: fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
2660: }
2661: fprintf(ficresilk," %10.6f\n", -llt);
2662: }
2663: } /* end of wave */
2664: } /* end of individual */
2665: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
2666: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
2667: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
2668: if(globpr==0){ /* First time we count the contributions and weights */
2669: gipmx=ipmx;
2670: gsw=sw;
2671: }
2672: return -l;
2673: }
2674:
2675:
2676: /*************** function likelione ***********/
2677: void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
2678: {
2679: /* This routine should help understanding what is done with
2680: the selection of individuals/waves and
2681: to check the exact contribution to the likelihood.
2682: Plotting could be done.
2683: */
2684: int k;
2685:
2686: if(*globpri !=0){ /* Just counts and sums, no printings */
1.201 brouard 2687: strcpy(fileresilk,"ILK_");
1.202 brouard 2688: strcat(fileresilk,fileresu);
1.126 brouard 2689: if((ficresilk=fopen(fileresilk,"w"))==NULL) {
2690: printf("Problem with resultfile: %s\n", fileresilk);
2691: fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
2692: }
1.205 brouard 2693: 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 2694: fprintf(ficresilk, "#num_i age i s1 s2 mi mw dh likeli weight %%weight 2wlli out sav ");
1.126 brouard 2695: /* i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
2696: for(k=1; k<=nlstate; k++)
2697: fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
2698: fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
2699: }
2700:
2701: *fretone=(*funcone)(p);
2702: if(*globpri !=0){
2703: fclose(ficresilk);
1.205 brouard 2704: if (mle ==0)
2705: fprintf(fichtm,"\n<br>File of contributions to the likelihood computed with initial parameters and mle = %d.",mle);
2706: else if(mle >=1)
2707: fprintf(fichtm,"\n<br>File of contributions to the likelihood computed with optimized parameters mle = %d.",mle);
2708: 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 2709:
1.208 brouard 2710:
2711: for (k=1; k<= nlstate ; k++) {
2712: fprintf(fichtm,"<br>- Probability p%dj by origin %d and destination j <a href=\"%s-p%dj.png\">%s-p%dj.png</a><br> \
2713: <img src=\"%s-p%dj.png\">",k,k,subdirf2(optionfilefiname,"ILK_"),k,subdirf2(optionfilefiname,"ILK_"),k,subdirf2(optionfilefiname,"ILK_"),k);
2714: }
1.207 brouard 2715: 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 2716: <img src=\"%s-ori.png\">",subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"));
1.207 brouard 2717: fprintf(fichtm,"<br>- and by state of destination <a href=\"%s-dest.png\">%s-dest.png</a><br> \
1.204 brouard 2718: <img src=\"%s-dest.png\">",subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"));
1.207 brouard 2719: fflush(fichtm);
1.205 brouard 2720: }
1.126 brouard 2721: return;
2722: }
2723:
2724:
2725: /*********** Maximum Likelihood Estimation ***************/
2726:
2727: void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
2728: {
1.165 brouard 2729: int i,j, iter=0;
1.126 brouard 2730: double **xi;
2731: double fret;
2732: double fretone; /* Only one call to likelihood */
2733: /* char filerespow[FILENAMELENGTH];*/
1.162 brouard 2734:
2735: #ifdef NLOPT
2736: int creturn;
2737: nlopt_opt opt;
2738: /* double lb[9] = { -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL }; /\* lower bounds *\/ */
2739: double *lb;
2740: double minf; /* the minimum objective value, upon return */
2741: double * p1; /* Shifted parameters from 0 instead of 1 */
2742: myfunc_data dinst, *d = &dinst;
2743: #endif
2744:
2745:
1.126 brouard 2746: xi=matrix(1,npar,1,npar);
2747: for (i=1;i<=npar;i++)
2748: for (j=1;j<=npar;j++)
2749: xi[i][j]=(i==j ? 1.0 : 0.0);
2750: printf("Powell\n"); fprintf(ficlog,"Powell\n");
1.201 brouard 2751: strcpy(filerespow,"POW_");
1.126 brouard 2752: strcat(filerespow,fileres);
2753: if((ficrespow=fopen(filerespow,"w"))==NULL) {
2754: printf("Problem with resultfile: %s\n", filerespow);
2755: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
2756: }
2757: fprintf(ficrespow,"# Powell\n# iter -2*LL");
2758: for (i=1;i<=nlstate;i++)
2759: for(j=1;j<=nlstate+ndeath;j++)
2760: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
2761: fprintf(ficrespow,"\n");
1.162 brouard 2762: #ifdef POWELL
1.126 brouard 2763: powell(p,xi,npar,ftol,&iter,&fret,func);
1.162 brouard 2764: #endif
1.126 brouard 2765:
1.162 brouard 2766: #ifdef NLOPT
2767: #ifdef NEWUOA
2768: opt = nlopt_create(NLOPT_LN_NEWUOA,npar);
2769: #else
2770: opt = nlopt_create(NLOPT_LN_BOBYQA,npar);
2771: #endif
2772: lb=vector(0,npar-1);
2773: for (i=0;i<npar;i++) lb[i]= -HUGE_VAL;
2774: nlopt_set_lower_bounds(opt, lb);
2775: nlopt_set_initial_step1(opt, 0.1);
2776:
2777: p1= (p+1); /* p *(p+1)@8 and p *(p1)@8 are equal p1[0]=p[1] */
2778: d->function = func;
2779: printf(" Func %.12lf \n",myfunc(npar,p1,NULL,d));
2780: nlopt_set_min_objective(opt, myfunc, d);
2781: nlopt_set_xtol_rel(opt, ftol);
2782: if ((creturn=nlopt_optimize(opt, p1, &minf)) < 0) {
2783: printf("nlopt failed! %d\n",creturn);
2784: }
2785: else {
2786: printf("found minimum after %d evaluations (NLOPT=%d)\n", countcallfunc ,NLOPT);
2787: printf("found minimum at f(%g,%g) = %0.10g\n", p[0], p[1], minf);
2788: iter=1; /* not equal */
2789: }
2790: nlopt_destroy(opt);
2791: #endif
1.126 brouard 2792: free_matrix(xi,1,npar,1,npar);
2793: fclose(ficrespow);
1.203 brouard 2794: printf("\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
2795: fprintf(ficlog,"\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
1.180 brouard 2796: fprintf(ficres,"#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
1.126 brouard 2797:
2798: }
2799:
2800: /**** Computes Hessian and covariance matrix ***/
1.203 brouard 2801: void hesscov(double **matcov, double **hess, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
1.126 brouard 2802: {
2803: double **a,**y,*x,pd;
1.203 brouard 2804: /* double **hess; */
1.164 brouard 2805: int i, j;
1.126 brouard 2806: int *indx;
2807:
2808: double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
1.203 brouard 2809: double hessij(double p[], double **hess, double delti[], int i, int j,double (*func)(double []),int npar);
1.126 brouard 2810: void lubksb(double **a, int npar, int *indx, double b[]) ;
2811: void ludcmp(double **a, int npar, int *indx, double *d) ;
2812: double gompertz(double p[]);
1.203 brouard 2813: /* hess=matrix(1,npar,1,npar); */
1.126 brouard 2814:
2815: printf("\nCalculation of the hessian matrix. Wait...\n");
2816: fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
2817: for (i=1;i<=npar;i++){
1.203 brouard 2818: printf("%d-",i);fflush(stdout);
2819: fprintf(ficlog,"%d-",i);fflush(ficlog);
1.126 brouard 2820:
2821: hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
2822:
2823: /* printf(" %f ",p[i]);
2824: printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
2825: }
2826:
2827: for (i=1;i<=npar;i++) {
2828: for (j=1;j<=npar;j++) {
2829: if (j>i) {
1.203 brouard 2830: printf(".%d-%d",i,j);fflush(stdout);
2831: fprintf(ficlog,".%d-%d",i,j);fflush(ficlog);
2832: hess[i][j]=hessij(p,hess, delti,i,j,func,npar);
1.126 brouard 2833:
2834: hess[j][i]=hess[i][j];
2835: /*printf(" %lf ",hess[i][j]);*/
2836: }
2837: }
2838: }
2839: printf("\n");
2840: fprintf(ficlog,"\n");
2841:
2842: printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
2843: fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
2844:
2845: a=matrix(1,npar,1,npar);
2846: y=matrix(1,npar,1,npar);
2847: x=vector(1,npar);
2848: indx=ivector(1,npar);
2849: for (i=1;i<=npar;i++)
2850: for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
2851: ludcmp(a,npar,indx,&pd);
2852:
2853: for (j=1;j<=npar;j++) {
2854: for (i=1;i<=npar;i++) x[i]=0;
2855: x[j]=1;
2856: lubksb(a,npar,indx,x);
2857: for (i=1;i<=npar;i++){
2858: matcov[i][j]=x[i];
2859: }
2860: }
2861:
2862: printf("\n#Hessian matrix#\n");
2863: fprintf(ficlog,"\n#Hessian matrix#\n");
2864: for (i=1;i<=npar;i++) {
2865: for (j=1;j<=npar;j++) {
1.203 brouard 2866: printf("%.6e ",hess[i][j]);
2867: fprintf(ficlog,"%.6e ",hess[i][j]);
1.126 brouard 2868: }
2869: printf("\n");
2870: fprintf(ficlog,"\n");
2871: }
2872:
1.203 brouard 2873: /* printf("\n#Covariance matrix#\n"); */
2874: /* fprintf(ficlog,"\n#Covariance matrix#\n"); */
2875: /* for (i=1;i<=npar;i++) { */
2876: /* for (j=1;j<=npar;j++) { */
2877: /* printf("%.6e ",matcov[i][j]); */
2878: /* fprintf(ficlog,"%.6e ",matcov[i][j]); */
2879: /* } */
2880: /* printf("\n"); */
2881: /* fprintf(ficlog,"\n"); */
2882: /* } */
2883:
1.126 brouard 2884: /* Recompute Inverse */
1.203 brouard 2885: /* for (i=1;i<=npar;i++) */
2886: /* for (j=1;j<=npar;j++) a[i][j]=matcov[i][j]; */
2887: /* ludcmp(a,npar,indx,&pd); */
2888:
2889: /* printf("\n#Hessian matrix recomputed#\n"); */
2890:
2891: /* for (j=1;j<=npar;j++) { */
2892: /* for (i=1;i<=npar;i++) x[i]=0; */
2893: /* x[j]=1; */
2894: /* lubksb(a,npar,indx,x); */
2895: /* for (i=1;i<=npar;i++){ */
2896: /* y[i][j]=x[i]; */
2897: /* printf("%.3e ",y[i][j]); */
2898: /* fprintf(ficlog,"%.3e ",y[i][j]); */
2899: /* } */
2900: /* printf("\n"); */
2901: /* fprintf(ficlog,"\n"); */
2902: /* } */
2903:
2904: /* Verifying the inverse matrix */
2905: #ifdef DEBUGHESS
2906: y=matprod2(y,hess,1,npar,1,npar,1,npar,matcov);
1.126 brouard 2907:
1.203 brouard 2908: printf("\n#Verification: multiplying the matrix of covariance by the Hessian matrix, should be unity:#\n");
2909: fprintf(ficlog,"\n#Verification: multiplying the matrix of covariance by the Hessian matrix. Should be unity:#\n");
1.126 brouard 2910:
2911: for (j=1;j<=npar;j++) {
2912: for (i=1;i<=npar;i++){
1.203 brouard 2913: printf("%.2f ",y[i][j]);
2914: fprintf(ficlog,"%.2f ",y[i][j]);
1.126 brouard 2915: }
2916: printf("\n");
2917: fprintf(ficlog,"\n");
2918: }
1.203 brouard 2919: #endif
1.126 brouard 2920:
2921: free_matrix(a,1,npar,1,npar);
2922: free_matrix(y,1,npar,1,npar);
2923: free_vector(x,1,npar);
2924: free_ivector(indx,1,npar);
1.203 brouard 2925: /* free_matrix(hess,1,npar,1,npar); */
1.126 brouard 2926:
2927:
2928: }
2929:
2930: /*************** hessian matrix ****************/
2931: double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
1.203 brouard 2932: { /* Around values of x, computes the function func and returns the scales delti and hessian */
1.126 brouard 2933: int i;
2934: int l=1, lmax=20;
1.203 brouard 2935: double k1,k2, res, fx;
1.132 brouard 2936: double p2[MAXPARM+1]; /* identical to x */
1.126 brouard 2937: double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
2938: int k=0,kmax=10;
2939: double l1;
2940:
2941: fx=func(x);
2942: for (i=1;i<=npar;i++) p2[i]=x[i];
1.145 brouard 2943: for(l=0 ; l <=lmax; l++){ /* Enlarging the zone around the Maximum */
1.126 brouard 2944: l1=pow(10,l);
2945: delts=delt;
2946: for(k=1 ; k <kmax; k=k+1){
2947: delt = delta*(l1*k);
2948: p2[theta]=x[theta] +delt;
1.145 brouard 2949: k1=func(p2)-fx; /* Might be negative if too close to the theoretical maximum */
1.126 brouard 2950: p2[theta]=x[theta]-delt;
2951: k2=func(p2)-fx;
2952: /*res= (k1-2.0*fx+k2)/delt/delt; */
1.203 brouard 2953: res= (k1+k2)/delt/delt/2.; /* Divided by 2 because L and not 2*L */
1.126 brouard 2954:
1.203 brouard 2955: #ifdef DEBUGHESSII
1.126 brouard 2956: 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);
2957: 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);
2958: #endif
2959: /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
2960: if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
2961: k=kmax;
2962: }
2963: else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
1.164 brouard 2964: k=kmax; l=lmax*10;
1.126 brouard 2965: }
2966: else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){
2967: delts=delt;
2968: }
1.203 brouard 2969: } /* End loop k */
1.126 brouard 2970: }
2971: delti[theta]=delts;
2972: return res;
2973:
2974: }
2975:
1.203 brouard 2976: double hessij( double x[], double **hess, double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
1.126 brouard 2977: {
2978: int i;
1.164 brouard 2979: int l=1, lmax=20;
1.126 brouard 2980: double k1,k2,k3,k4,res,fx;
1.132 brouard 2981: double p2[MAXPARM+1];
1.203 brouard 2982: int k, kmax=1;
2983: double v1, v2, cv12, lc1, lc2;
1.208 brouard 2984:
2985: int firstime=0;
1.203 brouard 2986:
1.126 brouard 2987: fx=func(x);
1.203 brouard 2988: for (k=1; k<=kmax; k=k+10) {
1.126 brouard 2989: for (i=1;i<=npar;i++) p2[i]=x[i];
1.203 brouard 2990: p2[thetai]=x[thetai]+delti[thetai]*k;
2991: p2[thetaj]=x[thetaj]+delti[thetaj]*k;
1.126 brouard 2992: k1=func(p2)-fx;
2993:
1.203 brouard 2994: p2[thetai]=x[thetai]+delti[thetai]*k;
2995: p2[thetaj]=x[thetaj]-delti[thetaj]*k;
1.126 brouard 2996: k2=func(p2)-fx;
2997:
1.203 brouard 2998: p2[thetai]=x[thetai]-delti[thetai]*k;
2999: p2[thetaj]=x[thetaj]+delti[thetaj]*k;
1.126 brouard 3000: k3=func(p2)-fx;
3001:
1.203 brouard 3002: p2[thetai]=x[thetai]-delti[thetai]*k;
3003: p2[thetaj]=x[thetaj]-delti[thetaj]*k;
1.126 brouard 3004: k4=func(p2)-fx;
1.203 brouard 3005: res=(k1-k2-k3+k4)/4.0/delti[thetai]/k/delti[thetaj]/k/2.; /* Because of L not 2*L */
3006: if(k1*k2*k3*k4 <0.){
1.208 brouard 3007: firstime=1;
1.203 brouard 3008: kmax=kmax+10;
1.208 brouard 3009: }
3010: if(kmax >=10 || firstime ==1){
1.203 brouard 3011: printf("Warning: directions %d-%d, you are not estimating the Hessian at the exact maximum likelihood; increase ftol=%.2e\n",thetai,thetaj, ftol);
3012: fprintf(ficlog,"Warning: directions %d-%d, you are not estimating the Hessian at the exact maximum likelihood; increase ftol=%.2e\n",thetai,thetaj, ftol);
3013: 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);
3014: 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);
3015: }
3016: #ifdef DEBUGHESSIJ
3017: v1=hess[thetai][thetai];
3018: v2=hess[thetaj][thetaj];
3019: cv12=res;
3020: /* Computing eigen value of Hessian matrix */
3021: lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
3022: lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
3023: if ((lc2 <0) || (lc1 <0) ){
3024: printf("Warning: sub Hessian matrix '%d%d' does not have positive eigen values \n",thetai,thetaj);
3025: fprintf(ficlog, "Warning: sub Hessian matrix '%d%d' does not have positive eigen values \n",thetai,thetaj);
3026: 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);
3027: 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);
3028: }
1.126 brouard 3029: #endif
3030: }
3031: return res;
3032: }
3033:
1.203 brouard 3034: /* Not done yet: Was supposed to fix if not exactly at the maximum */
3035: /* double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar) */
3036: /* { */
3037: /* int i; */
3038: /* int l=1, lmax=20; */
3039: /* double k1,k2,k3,k4,res,fx; */
3040: /* double p2[MAXPARM+1]; */
3041: /* double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4; */
3042: /* int k=0,kmax=10; */
3043: /* double l1; */
3044:
3045: /* fx=func(x); */
3046: /* for(l=0 ; l <=lmax; l++){ /\* Enlarging the zone around the Maximum *\/ */
3047: /* l1=pow(10,l); */
3048: /* delts=delt; */
3049: /* for(k=1 ; k <kmax; k=k+1){ */
3050: /* delt = delti*(l1*k); */
3051: /* for (i=1;i<=npar;i++) p2[i]=x[i]; */
3052: /* p2[thetai]=x[thetai]+delti[thetai]/k; */
3053: /* p2[thetaj]=x[thetaj]+delti[thetaj]/k; */
3054: /* k1=func(p2)-fx; */
3055:
3056: /* p2[thetai]=x[thetai]+delti[thetai]/k; */
3057: /* p2[thetaj]=x[thetaj]-delti[thetaj]/k; */
3058: /* k2=func(p2)-fx; */
3059:
3060: /* p2[thetai]=x[thetai]-delti[thetai]/k; */
3061: /* p2[thetaj]=x[thetaj]+delti[thetaj]/k; */
3062: /* k3=func(p2)-fx; */
3063:
3064: /* p2[thetai]=x[thetai]-delti[thetai]/k; */
3065: /* p2[thetaj]=x[thetaj]-delti[thetaj]/k; */
3066: /* k4=func(p2)-fx; */
3067: /* res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /\* Because of L not 2*L *\/ */
3068: /* #ifdef DEBUGHESSIJ */
3069: /* 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); */
3070: /* 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); */
3071: /* #endif */
3072: /* if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)|| (k4 <khi/nkhi/2.)|| (k4 <khi/nkhi/2.)){ */
3073: /* k=kmax; */
3074: /* } */
3075: /* else if((k1 >khi/nkhif) || (k2 >khi/nkhif) || (k4 >khi/nkhif) || (k4 >khi/nkhif)){ /\* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. *\/ */
3076: /* k=kmax; l=lmax*10; */
3077: /* } */
3078: /* else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ */
3079: /* delts=delt; */
3080: /* } */
3081: /* } /\* End loop k *\/ */
3082: /* } */
3083: /* delti[theta]=delts; */
3084: /* return res; */
3085: /* } */
3086:
3087:
1.126 brouard 3088: /************** Inverse of matrix **************/
3089: void ludcmp(double **a, int n, int *indx, double *d)
3090: {
3091: int i,imax,j,k;
3092: double big,dum,sum,temp;
3093: double *vv;
3094:
3095: vv=vector(1,n);
3096: *d=1.0;
3097: for (i=1;i<=n;i++) {
3098: big=0.0;
3099: for (j=1;j<=n;j++)
3100: if ((temp=fabs(a[i][j])) > big) big=temp;
3101: if (big == 0.0) nrerror("Singular matrix in routine ludcmp");
3102: vv[i]=1.0/big;
3103: }
3104: for (j=1;j<=n;j++) {
3105: for (i=1;i<j;i++) {
3106: sum=a[i][j];
3107: for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];
3108: a[i][j]=sum;
3109: }
3110: big=0.0;
3111: for (i=j;i<=n;i++) {
3112: sum=a[i][j];
3113: for (k=1;k<j;k++)
3114: sum -= a[i][k]*a[k][j];
3115: a[i][j]=sum;
3116: if ( (dum=vv[i]*fabs(sum)) >= big) {
3117: big=dum;
3118: imax=i;
3119: }
3120: }
3121: if (j != imax) {
3122: for (k=1;k<=n;k++) {
3123: dum=a[imax][k];
3124: a[imax][k]=a[j][k];
3125: a[j][k]=dum;
3126: }
3127: *d = -(*d);
3128: vv[imax]=vv[j];
3129: }
3130: indx[j]=imax;
3131: if (a[j][j] == 0.0) a[j][j]=TINY;
3132: if (j != n) {
3133: dum=1.0/(a[j][j]);
3134: for (i=j+1;i<=n;i++) a[i][j] *= dum;
3135: }
3136: }
3137: free_vector(vv,1,n); /* Doesn't work */
3138: ;
3139: }
3140:
3141: void lubksb(double **a, int n, int *indx, double b[])
3142: {
3143: int i,ii=0,ip,j;
3144: double sum;
3145:
3146: for (i=1;i<=n;i++) {
3147: ip=indx[i];
3148: sum=b[ip];
3149: b[ip]=b[i];
3150: if (ii)
3151: for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];
3152: else if (sum) ii=i;
3153: b[i]=sum;
3154: }
3155: for (i=n;i>=1;i--) {
3156: sum=b[i];
3157: for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];
3158: b[i]=sum/a[i][i];
3159: }
3160: }
3161:
3162: void pstamp(FILE *fichier)
3163: {
1.196 brouard 3164: fprintf(fichier,"# %s.%s\n#IMaCh version %s, %s\n#%s\n# %s", optionfilefiname,optionfilext,version,copyright, fullversion, strstart);
1.126 brouard 3165: }
3166:
3167: /************ Frequencies ********************/
3168: 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[])
3169: { /* Some frequencies */
3170:
1.164 brouard 3171: int i, m, jk, j1, bool, z1,j;
1.126 brouard 3172: int first;
3173: double ***freq; /* Frequencies */
3174: double *pp, **prop;
3175: double pos,posprop, k2, dateintsum=0,k2cpt=0;
3176: char fileresp[FILENAMELENGTH];
3177:
3178: pp=vector(1,nlstate);
3179: prop=matrix(1,nlstate,iagemin,iagemax+3);
1.201 brouard 3180: strcpy(fileresp,"P_");
3181: strcat(fileresp,fileresu);
1.126 brouard 3182: if((ficresp=fopen(fileresp,"w"))==NULL) {
3183: printf("Problem with prevalence resultfile: %s\n", fileresp);
3184: fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
3185: exit(0);
3186: }
3187: freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
3188: j1=0;
3189:
3190: j=cptcoveff;
3191: if (cptcovn<1) {j=1;ncodemax[1]=1;}
3192:
3193: first=1;
3194:
1.169 brouard 3195: /* for(k1=1; k1<=j ; k1++){ */ /* Loop on covariates */
3196: /* for(i1=1; i1<=ncodemax[k1];i1++){ */ /* Now it is 2 */
3197: /* j1++; */
1.145 brouard 3198: for (j1 = 1; j1 <= (int) pow(2,cptcoveff); j1++){
1.126 brouard 3199: /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
3200: scanf("%d", i);*/
3201: for (i=-5; i<=nlstate+ndeath; i++)
3202: for (jk=-5; jk<=nlstate+ndeath; jk++)
3203: for(m=iagemin; m <= iagemax+3; m++)
3204: freq[i][jk][m]=0;
1.143 brouard 3205:
3206: for (i=1; i<=nlstate; i++)
3207: for(m=iagemin; m <= iagemax+3; m++)
3208: prop[i][m]=0;
1.126 brouard 3209:
3210: dateintsum=0;
3211: k2cpt=0;
3212: for (i=1; i<=imx; i++) {
3213: bool=1;
1.144 brouard 3214: if (cptcovn>0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
3215: for (z1=1; z1<=cptcoveff; z1++)
1.198 brouard 3216: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]){
1.145 brouard 3217: /* Tests if the value of each of the covariates of i is equal to filter j1 */
1.144 brouard 3218: bool=0;
1.198 brouard 3219: /* 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",
3220: bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtabm(j1,z1),
3221: j1,z1,nbcode[Tvaraff[z1]][codtabm(j1,z1)],j1);*/
3222: /* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtabm(7,3)=1 and nbcde[3][?]=1*/
1.144 brouard 3223: }
1.126 brouard 3224: }
1.144 brouard 3225:
1.126 brouard 3226: if (bool==1){
3227: for(m=firstpass; m<=lastpass; m++){
3228: k2=anint[m][i]+(mint[m][i]/12.);
3229: /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
3230: if(agev[m][i]==0) agev[m][i]=iagemax+1;
3231: if(agev[m][i]==1) agev[m][i]=iagemax+2;
3232: if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
3233: if (m<lastpass) {
3234: freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
3235: freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
3236: }
3237:
3238: if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
3239: dateintsum=dateintsum+k2;
3240: k2cpt++;
3241: }
3242: /*}*/
3243: }
3244: }
1.145 brouard 3245: } /* end i */
1.126 brouard 3246:
3247: /* fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
3248: pstamp(ficresp);
3249: if (cptcovn>0) {
3250: fprintf(ficresp, "\n#********** Variable ");
1.198 brouard 3251: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.126 brouard 3252: fprintf(ficresp, "**********\n#");
1.143 brouard 3253: fprintf(ficlog, "\n#********** Variable ");
1.198 brouard 3254: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficlog, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.143 brouard 3255: fprintf(ficlog, "**********\n#");
1.126 brouard 3256: }
3257: for(i=1; i<=nlstate;i++)
3258: fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
3259: fprintf(ficresp, "\n");
3260:
3261: for(i=iagemin; i <= iagemax+3; i++){
3262: if(i==iagemax+3){
3263: fprintf(ficlog,"Total");
3264: }else{
3265: if(first==1){
3266: first=0;
3267: printf("See log file for details...\n");
3268: }
3269: fprintf(ficlog,"Age %d", i);
3270: }
3271: for(jk=1; jk <=nlstate ; jk++){
3272: for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
3273: pp[jk] += freq[jk][m][i];
3274: }
3275: for(jk=1; jk <=nlstate ; jk++){
3276: for(m=-1, pos=0; m <=0 ; m++)
3277: pos += freq[jk][m][i];
3278: if(pp[jk]>=1.e-10){
3279: if(first==1){
1.132 brouard 3280: printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
1.126 brouard 3281: }
3282: fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
3283: }else{
3284: if(first==1)
3285: printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
3286: fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
3287: }
3288: }
3289:
3290: for(jk=1; jk <=nlstate ; jk++){
3291: for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
3292: pp[jk] += freq[jk][m][i];
3293: }
3294: for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
3295: pos += pp[jk];
3296: posprop += prop[jk][i];
3297: }
3298: for(jk=1; jk <=nlstate ; jk++){
3299: if(pos>=1.e-5){
3300: if(first==1)
3301: printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
3302: fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
3303: }else{
3304: if(first==1)
3305: printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
3306: fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
3307: }
3308: if( i <= iagemax){
3309: if(pos>=1.e-5){
3310: fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
3311: /*probs[i][jk][j1]= pp[jk]/pos;*/
3312: /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
3313: }
3314: else
3315: fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
3316: }
3317: }
3318:
3319: for(jk=-1; jk <=nlstate+ndeath; jk++)
3320: for(m=-1; m <=nlstate+ndeath; m++)
3321: if(freq[jk][m][i] !=0 ) {
3322: if(first==1)
3323: printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
3324: fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
3325: }
3326: if(i <= iagemax)
3327: fprintf(ficresp,"\n");
3328: if(first==1)
3329: printf("Others in log...\n");
3330: fprintf(ficlog,"\n");
3331: }
1.145 brouard 3332: /*}*/
1.126 brouard 3333: }
3334: dateintmean=dateintsum/k2cpt;
3335:
3336: fclose(ficresp);
3337: free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
3338: free_vector(pp,1,nlstate);
3339: free_matrix(prop,1,nlstate,iagemin, iagemax+3);
3340: /* End of Freq */
3341: }
3342:
3343: /************ Prevalence ********************/
3344: 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)
3345: {
3346: /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
3347: in each health status at the date of interview (if between dateprev1 and dateprev2).
3348: We still use firstpass and lastpass as another selection.
3349: */
3350:
1.164 brouard 3351: int i, m, jk, j1, bool, z1,j;
3352:
3353: double **prop;
3354: double posprop;
1.126 brouard 3355: double y2; /* in fractional years */
3356: int iagemin, iagemax;
1.145 brouard 3357: int first; /** to stop verbosity which is redirected to log file */
1.126 brouard 3358:
3359: iagemin= (int) agemin;
3360: iagemax= (int) agemax;
3361: /*pp=vector(1,nlstate);*/
3362: prop=matrix(1,nlstate,iagemin,iagemax+3);
3363: /* freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
3364: j1=0;
3365:
1.145 brouard 3366: /*j=cptcoveff;*/
1.126 brouard 3367: if (cptcovn<1) {j=1;ncodemax[1]=1;}
3368:
1.145 brouard 3369: first=1;
3370: for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){
3371: /*for(i1=1; i1<=ncodemax[k1];i1++){
3372: j1++;*/
1.126 brouard 3373:
3374: for (i=1; i<=nlstate; i++)
3375: for(m=iagemin; m <= iagemax+3; m++)
3376: prop[i][m]=0.0;
3377:
3378: for (i=1; i<=imx; i++) { /* Each individual */
3379: bool=1;
3380: if (cptcovn>0) {
3381: for (z1=1; z1<=cptcoveff; z1++)
1.198 brouard 3382: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)])
1.126 brouard 3383: bool=0;
3384: }
3385: if (bool==1) {
3386: for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
3387: y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
3388: if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
3389: if(agev[m][i]==0) agev[m][i]=iagemax+1;
3390: if(agev[m][i]==1) agev[m][i]=iagemax+2;
3391: 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);
3392: if (s[m][i]>0 && s[m][i]<=nlstate) {
3393: /*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]]);*/
3394: prop[s[m][i]][(int)agev[m][i]] += weight[i];
3395: prop[s[m][i]][iagemax+3] += weight[i];
3396: }
3397: }
3398: } /* end selection of waves */
3399: }
3400: }
3401: for(i=iagemin; i <= iagemax+3; i++){
3402: for(jk=1,posprop=0; jk <=nlstate ; jk++) {
3403: posprop += prop[jk][i];
3404: }
1.145 brouard 3405:
1.126 brouard 3406: for(jk=1; jk <=nlstate ; jk++){
3407: if( i <= iagemax){
3408: if(posprop>=1.e-5){
3409: probs[i][jk][j1]= prop[jk][i]/posprop;
1.145 brouard 3410: } else{
3411: if(first==1){
3412: first=0;
3413: 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]);
3414: }
3415: }
1.126 brouard 3416: }
3417: }/* end jk */
3418: }/* end i */
1.145 brouard 3419: /*} *//* end i1 */
3420: } /* end j1 */
1.126 brouard 3421:
3422: /* free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
3423: /*free_vector(pp,1,nlstate);*/
3424: free_matrix(prop,1,nlstate, iagemin,iagemax+3);
3425: } /* End of prevalence */
3426:
3427: /************* Waves Concatenation ***************/
3428:
3429: 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)
3430: {
3431: /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
3432: Death is a valid wave (if date is known).
3433: mw[mi][i] is the mi (mi=1 to wav[i]) effective wave of individual i
3434: dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
3435: and mw[mi+1][i]. dh depends on stepm.
3436: */
3437:
3438: int i, mi, m;
3439: /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
3440: double sum=0., jmean=0.;*/
3441: int first;
3442: int j, k=0,jk, ju, jl;
3443: double sum=0.;
3444: first=0;
1.164 brouard 3445: jmin=100000;
1.126 brouard 3446: jmax=-1;
3447: jmean=0.;
3448: for(i=1; i<=imx; i++){
3449: mi=0;
3450: m=firstpass;
3451: while(s[m][i] <= nlstate){
3452: if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
3453: mw[++mi][i]=m;
3454: if(m >=lastpass)
3455: break;
3456: else
3457: m++;
3458: }/* end while */
3459: if (s[m][i] > nlstate){
3460: mi++; /* Death is another wave */
3461: /* if(mi==0) never been interviewed correctly before death */
3462: /* Only death is a correct wave */
3463: mw[mi][i]=m;
3464: }
3465:
3466: wav[i]=mi;
3467: if(mi==0){
3468: nbwarn++;
3469: if(first==0){
3470: printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
3471: first=1;
3472: }
3473: if(first==1){
3474: fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
3475: }
3476: } /* end mi==0 */
3477: } /* End individuals */
3478:
3479: for(i=1; i<=imx; i++){
3480: for(mi=1; mi<wav[i];mi++){
3481: if (stepm <=0)
3482: dh[mi][i]=1;
3483: else{
3484: if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
3485: if (agedc[i] < 2*AGESUP) {
3486: j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);
3487: if(j==0) j=1; /* Survives at least one month after exam */
3488: else if(j<0){
3489: nberr++;
3490: 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]);
3491: j=1; /* Temporary Dangerous patch */
3492: 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);
3493: 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]);
3494: 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);
3495: }
3496: k=k+1;
3497: if (j >= jmax){
3498: jmax=j;
3499: ijmax=i;
3500: }
3501: if (j <= jmin){
3502: jmin=j;
3503: ijmin=i;
3504: }
3505: sum=sum+j;
3506: /*if (j<0) printf("j=%d num=%d \n",j,i);*/
3507: /* printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
3508: }
3509: }
3510: else{
3511: j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
3512: /* 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]); */
3513:
3514: k=k+1;
3515: if (j >= jmax) {
3516: jmax=j;
3517: ijmax=i;
3518: }
3519: else if (j <= jmin){
3520: jmin=j;
3521: ijmin=i;
3522: }
3523: /* if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
3524: /*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]);*/
3525: if(j<0){
3526: nberr++;
3527: 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]);
3528: 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]);
3529: }
3530: sum=sum+j;
3531: }
3532: jk= j/stepm;
3533: jl= j -jk*stepm;
3534: ju= j -(jk+1)*stepm;
3535: if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
3536: if(jl==0){
3537: dh[mi][i]=jk;
3538: bh[mi][i]=0;
3539: }else{ /* We want a negative bias in order to only have interpolation ie
1.136 brouard 3540: * to avoid the price of an extra matrix product in likelihood */
1.126 brouard 3541: dh[mi][i]=jk+1;
3542: bh[mi][i]=ju;
3543: }
3544: }else{
3545: if(jl <= -ju){
3546: dh[mi][i]=jk;
3547: bh[mi][i]=jl; /* bias is positive if real duration
3548: * is higher than the multiple of stepm and negative otherwise.
3549: */
3550: }
3551: else{
3552: dh[mi][i]=jk+1;
3553: bh[mi][i]=ju;
3554: }
3555: if(dh[mi][i]==0){
3556: dh[mi][i]=1; /* At least one step */
3557: bh[mi][i]=ju; /* At least one step */
3558: /* 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);*/
3559: }
3560: } /* end if mle */
3561: }
3562: } /* end wave */
3563: }
3564: jmean=sum/k;
3565: 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 3566: 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 3567: }
3568:
3569: /*********** Tricode ****************************/
1.145 brouard 3570: void tricode(int *Tvar, int **nbcode, int imx, int *Ndum)
1.126 brouard 3571: {
1.144 brouard 3572: /**< Uses cptcovn+2*cptcovprod as the number of covariates */
3573: /* 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 3574: * Boring subroutine which should only output nbcode[Tvar[j]][k]
1.145 brouard 3575: * Tvar[5] in V2+V1+V3*age+V2*V4 is 2 (V2)
1.169 brouard 3576: * nbcode[Tvar[j]][1]=
1.144 brouard 3577: */
1.130 brouard 3578:
1.145 brouard 3579: int ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
1.136 brouard 3580: int modmaxcovj=0; /* Modality max of covariates j */
1.145 brouard 3581: int cptcode=0; /* Modality max of covariates j */
3582: int modmincovj=0; /* Modality min of covariates j */
3583:
3584:
1.126 brouard 3585: cptcoveff=0;
3586:
1.144 brouard 3587: for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */
1.126 brouard 3588:
1.145 brouard 3589: /* Loop on covariates without age and products */
1.186 brouard 3590: for (j=1; j<=(cptcovs); j++) { /* From model V1 + V2*age+ V3 + V3*V4 keeps V1 + V3 = 2 only */
1.192 brouard 3591: for (k=-1; k < maxncov; k++) Ndum[k]=0;
1.186 brouard 3592: for (i=1; i<=imx; i++) { /* Loop on individuals: reads the data file to get the maximum value of the
1.136 brouard 3593: modality of this covariate Vj*/
1.145 brouard 3594: ij=(int)(covar[Tvar[j]][i]); /* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i
3595: * If product of Vn*Vm, still boolean *:
3596: * If it was coded 1, 2, 3, 4 should be splitted into 3 boolean variables
3597: * 1 => 0 0 0, 2 => 0 0 1, 3 => 0 1 1, 4=1 0 0 */
3598: /* Finds for covariate j, n=Tvar[j] of Vn . ij is the
1.136 brouard 3599: modality of the nth covariate of individual i. */
1.145 brouard 3600: if (ij > modmaxcovj)
3601: modmaxcovj=ij;
3602: else if (ij < modmincovj)
3603: modmincovj=ij;
3604: if ((ij < -1) && (ij > NCOVMAX)){
3605: printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX );
3606: exit(1);
3607: }else
1.136 brouard 3608: Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/
1.145 brouard 3609: /* If coded 1, 2, 3 , counts the number of 1 Ndum[1], number of 2, Ndum[2], etc */
1.126 brouard 3610: /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
1.136 brouard 3611: /* getting the maximum value of the modality of the covariate
3612: (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and
3613: female is 1, then modmaxcovj=1.*/
1.192 brouard 3614: } /* end for loop on individuals i */
1.145 brouard 3615: printf(" Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", j, Tvar[j], modmincovj, modmaxcovj);
1.192 brouard 3616: 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 3617: cptcode=modmaxcovj;
1.137 brouard 3618: /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */
1.145 brouard 3619: /*for (i=0; i<=cptcode; i++) {*/
1.192 brouard 3620: for (k=modmincovj; k<=modmaxcovj; k++) { /* k=-1 ? 0 and 1*//* For each value k of the modality of model-cov j */
3621: printf("Frequencies of covariates %d ie V%d with value %d: %d\n", j, Tvar[j], k, Ndum[k]);
3622: fprintf(ficlog, "Frequencies of covariates %d ie V%d with value %d: %d\n", j, Tvar[j], k, Ndum[k]);
3623: if( Ndum[k] != 0 ){ /* Counts if nobody answered modality k ie empty modality, we skip it and reorder */
3624: if( k != -1){
3625: ncodemax[j]++; /* ncodemax[j]= Number of modalities of the j th
3626: covariate for which somebody answered excluding
3627: undefined. Usually 2: 0 and 1. */
3628: }
3629: ncodemaxwundef[j]++; /* ncodemax[j]= Number of modalities of the j th
3630: covariate for which somebody answered including
3631: undefined. Usually 3: -1, 0 and 1. */
1.145 brouard 3632: }
3633: /* In fact ncodemax[j]=2 (dichotom. variables only) but it could be more for
3634: historical reasons: 3 if coded 1, 2, 3 and 4 and Ndum[2]=0 */
1.131 brouard 3635: } /* Ndum[-1] number of undefined modalities */
1.126 brouard 3636:
1.136 brouard 3637: /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */
1.186 brouard 3638: /* For covariate j, modalities could be 1, 2, 3, 4, 5, 6, 7.
3639: 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 3640: modmincovj=3; modmaxcovj = 7;
1.186 brouard 3641: There are only 3 modalities non empty 3, 6, 7 (or 2 if 27 is too few) : ncodemax[j]=3;
3642: which will be coded 0, 1, 2 which in binary on 2=3-1 digits are 0=00 1=01, 2=10;
3643: defining two dummy variables: variables V1_1 and V1_2.
1.145 brouard 3644: nbcode[Tvar[j]][ij]=k;
3645: nbcode[Tvar[j]][1]=0;
3646: nbcode[Tvar[j]][2]=1;
3647: nbcode[Tvar[j]][3]=2;
1.197 brouard 3648: To be continued (not working yet).
1.145 brouard 3649: */
1.197 brouard 3650: ij=0; /* ij is similar to i but can jump over null modalities */
3651: 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*/
3652: if (Ndum[i] == 0) { /* If nobody responded to this modality k */
1.192 brouard 3653: break;
3654: }
3655: ij++;
1.197 brouard 3656: 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 3657: cptcode = ij; /* New max modality for covar j */
3658: } /* end of loop on modality i=-1 to 1 or more */
3659:
3660: /* for (k=0; k<= cptcode; k++) { /\* k=-1 ? k=0 to 1 *\//\* Could be 1 to 4 *\//\* cptcode=modmaxcovj *\/ */
3661: /* /\*recode from 0 *\/ */
3662: /* k is a modality. If we have model=V1+V1*sex */
3663: /* then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
3664: /* But if some modality were not used, it is recoded from 0 to a newer modmaxcovj=cptcode *\/ */
3665: /* } */
3666: /* /\* cptcode = ij; *\/ /\* New max modality for covar j *\/ */
3667: /* if (ij > ncodemax[j]) { */
3668: /* printf( " Error ij=%d > ncodemax[%d]=%d\n", ij, j, ncodemax[j]); */
3669: /* fprintf(ficlog, " Error ij=%d > ncodemax[%d]=%d\n", ij, j, ncodemax[j]); */
3670: /* break; */
3671: /* } */
3672: /* } /\* end of loop on modality k *\/ */
1.137 brouard 3673: } /* end of loop on model-covariate j. nbcode[Tvarj][1]=0 and nbcode[Tvarj][2]=1 sets the value of covariate j*/
3674:
1.145 brouard 3675: for (k=-1; k< maxncov; k++) Ndum[k]=0;
1.137 brouard 3676:
1.187 brouard 3677: for (i=1; i<=ncovmodel-2-nagesqr; i++) { /* -2, cste and age and eventually age*age */
1.145 brouard 3678: /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
3679: ij=Tvar[i]; /* Tvar might be -1 if status was unknown */
1.187 brouard 3680: Ndum[ij]++; /* Might be supersed V1 + V1*age */
1.145 brouard 3681: }
1.126 brouard 3682:
1.192 brouard 3683: ij=0;
1.145 brouard 3684: for (i=0; i<= maxncov-1; i++) { /* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) */
3685: /*printf("Ndum[%d]=%d\n",i, Ndum[i]);*/
1.126 brouard 3686: if((Ndum[i]!=0) && (i<=ncovcol)){
1.192 brouard 3687: ij++;
1.145 brouard 3688: /*printf("diff Ndum[%d]=%d\n",i, Ndum[i]);*/
3689: Tvaraff[ij]=i; /*For printing (unclear) */
1.192 brouard 3690: }else{
3691: /* Tvaraff[ij]=0; */
3692: }
1.126 brouard 3693: }
1.192 brouard 3694: /* ij--; */
1.144 brouard 3695: cptcoveff=ij; /*Number of total covariates*/
1.145 brouard 3696:
1.126 brouard 3697: }
3698:
1.145 brouard 3699:
1.126 brouard 3700: /*********** Health Expectancies ****************/
3701:
1.127 brouard 3702: 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 3703:
3704: {
3705: /* Health expectancies, no variances */
1.164 brouard 3706: int i, j, nhstepm, hstepm, h, nstepm;
1.126 brouard 3707: int nhstepma, nstepma; /* Decreasing with age */
3708: double age, agelim, hf;
3709: double ***p3mat;
3710: double eip;
3711:
3712: pstamp(ficreseij);
3713: fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
3714: fprintf(ficreseij,"# Age");
3715: for(i=1; i<=nlstate;i++){
3716: for(j=1; j<=nlstate;j++){
3717: fprintf(ficreseij," e%1d%1d ",i,j);
3718: }
3719: fprintf(ficreseij," e%1d. ",i);
3720: }
3721: fprintf(ficreseij,"\n");
3722:
3723:
3724: if(estepm < stepm){
3725: printf ("Problem %d lower than %d\n",estepm, stepm);
3726: }
3727: else hstepm=estepm;
3728: /* We compute the life expectancy from trapezoids spaced every estepm months
3729: * This is mainly to measure the difference between two models: for example
3730: * if stepm=24 months pijx are given only every 2 years and by summing them
3731: * we are calculating an estimate of the Life Expectancy assuming a linear
3732: * progression in between and thus overestimating or underestimating according
3733: * to the curvature of the survival function. If, for the same date, we
3734: * estimate the model with stepm=1 month, we can keep estepm to 24 months
3735: * to compare the new estimate of Life expectancy with the same linear
3736: * hypothesis. A more precise result, taking into account a more precise
3737: * curvature will be obtained if estepm is as small as stepm. */
3738:
3739: /* For example we decided to compute the life expectancy with the smallest unit */
3740: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
3741: nhstepm is the number of hstepm from age to agelim
3742: nstepm is the number of stepm from age to agelin.
3743: Look at hpijx to understand the reason of that which relies in memory size
3744: and note for a fixed period like estepm months */
3745: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
3746: survival function given by stepm (the optimization length). Unfortunately it
3747: means that if the survival funtion is printed only each two years of age and if
3748: you sum them up and add 1 year (area under the trapezoids) you won't get the same
3749: results. So we changed our mind and took the option of the best precision.
3750: */
3751: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
3752:
3753: agelim=AGESUP;
3754: /* If stepm=6 months */
3755: /* Computed by stepm unit matrices, product of hstepm matrices, stored
3756: in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
3757:
3758: /* nhstepm age range expressed in number of stepm */
3759: nstepm=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
3760: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
3761: /* if (stepm >= YEARM) hstepm=1;*/
3762: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
3763: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3764:
3765: for (age=bage; age<=fage; age ++){
3766: nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
3767: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
3768: /* if (stepm >= YEARM) hstepm=1;*/
3769: nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
3770:
3771: /* If stepm=6 months */
3772: /* Computed by stepm unit matrices, product of hstepma matrices, stored
3773: in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
3774:
3775: hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
3776:
3777: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
3778:
3779: printf("%d|",(int)age);fflush(stdout);
3780: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
3781:
3782: /* Computing expectancies */
3783: for(i=1; i<=nlstate;i++)
3784: for(j=1; j<=nlstate;j++)
3785: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
3786: eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
3787:
3788: /* 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]);*/
3789:
3790: }
3791:
3792: fprintf(ficreseij,"%3.0f",age );
3793: for(i=1; i<=nlstate;i++){
3794: eip=0;
3795: for(j=1; j<=nlstate;j++){
3796: eip +=eij[i][j][(int)age];
3797: fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
3798: }
3799: fprintf(ficreseij,"%9.4f", eip );
3800: }
3801: fprintf(ficreseij,"\n");
3802:
3803: }
3804: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3805: printf("\n");
3806: fprintf(ficlog,"\n");
3807:
3808: }
3809:
1.127 brouard 3810: 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 3811:
3812: {
3813: /* Covariances of health expectancies eij and of total life expectancies according
3814: to initial status i, ei. .
3815: */
3816: int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
3817: int nhstepma, nstepma; /* Decreasing with age */
3818: double age, agelim, hf;
3819: double ***p3matp, ***p3matm, ***varhe;
3820: double **dnewm,**doldm;
3821: double *xp, *xm;
3822: double **gp, **gm;
3823: double ***gradg, ***trgradg;
3824: int theta;
3825:
3826: double eip, vip;
3827:
3828: varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
3829: xp=vector(1,npar);
3830: xm=vector(1,npar);
3831: dnewm=matrix(1,nlstate*nlstate,1,npar);
3832: doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
3833:
3834: pstamp(ficresstdeij);
3835: fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
3836: fprintf(ficresstdeij,"# Age");
3837: for(i=1; i<=nlstate;i++){
3838: for(j=1; j<=nlstate;j++)
3839: fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
3840: fprintf(ficresstdeij," e%1d. ",i);
3841: }
3842: fprintf(ficresstdeij,"\n");
3843:
3844: pstamp(ficrescveij);
3845: fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
3846: fprintf(ficrescveij,"# Age");
3847: for(i=1; i<=nlstate;i++)
3848: for(j=1; j<=nlstate;j++){
3849: cptj= (j-1)*nlstate+i;
3850: for(i2=1; i2<=nlstate;i2++)
3851: for(j2=1; j2<=nlstate;j2++){
3852: cptj2= (j2-1)*nlstate+i2;
3853: if(cptj2 <= cptj)
3854: fprintf(ficrescveij," %1d%1d,%1d%1d",i,j,i2,j2);
3855: }
3856: }
3857: fprintf(ficrescveij,"\n");
3858:
3859: if(estepm < stepm){
3860: printf ("Problem %d lower than %d\n",estepm, stepm);
3861: }
3862: else hstepm=estepm;
3863: /* We compute the life expectancy from trapezoids spaced every estepm months
3864: * This is mainly to measure the difference between two models: for example
3865: * if stepm=24 months pijx are given only every 2 years and by summing them
3866: * we are calculating an estimate of the Life Expectancy assuming a linear
3867: * progression in between and thus overestimating or underestimating according
3868: * to the curvature of the survival function. If, for the same date, we
3869: * estimate the model with stepm=1 month, we can keep estepm to 24 months
3870: * to compare the new estimate of Life expectancy with the same linear
3871: * hypothesis. A more precise result, taking into account a more precise
3872: * curvature will be obtained if estepm is as small as stepm. */
3873:
3874: /* For example we decided to compute the life expectancy with the smallest unit */
3875: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
3876: nhstepm is the number of hstepm from age to agelim
3877: nstepm is the number of stepm from age to agelin.
3878: Look at hpijx to understand the reason of that which relies in memory size
3879: and note for a fixed period like estepm months */
3880: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
3881: survival function given by stepm (the optimization length). Unfortunately it
3882: means that if the survival funtion is printed only each two years of age and if
3883: you sum them up and add 1 year (area under the trapezoids) you won't get the same
3884: results. So we changed our mind and took the option of the best precision.
3885: */
3886: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
3887:
3888: /* If stepm=6 months */
3889: /* nhstepm age range expressed in number of stepm */
3890: agelim=AGESUP;
3891: nstepm=(int) rint((agelim-bage)*YEARM/stepm);
3892: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
3893: /* if (stepm >= YEARM) hstepm=1;*/
3894: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
3895:
3896: p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3897: p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3898: gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
3899: trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
3900: gp=matrix(0,nhstepm,1,nlstate*nlstate);
3901: gm=matrix(0,nhstepm,1,nlstate*nlstate);
3902:
3903: for (age=bage; age<=fage; age ++){
3904: nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
3905: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
3906: /* if (stepm >= YEARM) hstepm=1;*/
3907: nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
3908:
3909: /* If stepm=6 months */
3910: /* Computed by stepm unit matrices, product of hstepma matrices, stored
3911: in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
3912:
3913: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
3914:
3915: /* Computing Variances of health expectancies */
3916: /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
3917: decrease memory allocation */
3918: for(theta=1; theta <=npar; theta++){
3919: for(i=1; i<=npar; i++){
3920: xp[i] = x[i] + (i==theta ?delti[theta]:0);
3921: xm[i] = x[i] - (i==theta ?delti[theta]:0);
3922: }
3923: hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);
3924: hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);
3925:
3926: for(j=1; j<= nlstate; j++){
3927: for(i=1; i<=nlstate; i++){
3928: for(h=0; h<=nhstepm-1; h++){
3929: gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
3930: gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
3931: }
3932: }
3933: }
3934:
3935: for(ij=1; ij<= nlstate*nlstate; ij++)
3936: for(h=0; h<=nhstepm-1; h++){
3937: gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
3938: }
3939: }/* End theta */
3940:
3941:
3942: for(h=0; h<=nhstepm-1; h++)
3943: for(j=1; j<=nlstate*nlstate;j++)
3944: for(theta=1; theta <=npar; theta++)
3945: trgradg[h][j][theta]=gradg[h][theta][j];
3946:
3947:
3948: for(ij=1;ij<=nlstate*nlstate;ij++)
3949: for(ji=1;ji<=nlstate*nlstate;ji++)
3950: varhe[ij][ji][(int)age] =0.;
3951:
3952: printf("%d|",(int)age);fflush(stdout);
3953: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
3954: for(h=0;h<=nhstepm-1;h++){
3955: for(k=0;k<=nhstepm-1;k++){
3956: matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
3957: matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
3958: for(ij=1;ij<=nlstate*nlstate;ij++)
3959: for(ji=1;ji<=nlstate*nlstate;ji++)
3960: varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
3961: }
3962: }
3963:
3964: /* Computing expectancies */
3965: hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
3966: for(i=1; i<=nlstate;i++)
3967: for(j=1; j<=nlstate;j++)
3968: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
3969: eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
3970:
3971: /* 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]);*/
3972:
3973: }
3974:
3975: fprintf(ficresstdeij,"%3.0f",age );
3976: for(i=1; i<=nlstate;i++){
3977: eip=0.;
3978: vip=0.;
3979: for(j=1; j<=nlstate;j++){
3980: eip += eij[i][j][(int)age];
3981: for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
3982: vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
3983: fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
3984: }
3985: fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
3986: }
3987: fprintf(ficresstdeij,"\n");
3988:
3989: fprintf(ficrescveij,"%3.0f",age );
3990: for(i=1; i<=nlstate;i++)
3991: for(j=1; j<=nlstate;j++){
3992: cptj= (j-1)*nlstate+i;
3993: for(i2=1; i2<=nlstate;i2++)
3994: for(j2=1; j2<=nlstate;j2++){
3995: cptj2= (j2-1)*nlstate+i2;
3996: if(cptj2 <= cptj)
3997: fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
3998: }
3999: }
4000: fprintf(ficrescveij,"\n");
4001:
4002: }
4003: free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
4004: free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
4005: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
4006: free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
4007: free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4008: free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4009: printf("\n");
4010: fprintf(ficlog,"\n");
4011:
4012: free_vector(xm,1,npar);
4013: free_vector(xp,1,npar);
4014: free_matrix(dnewm,1,nlstate*nlstate,1,npar);
4015: free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
4016: free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
4017: }
4018:
4019: /************ Variance ******************/
1.209 ! brouard 4020: void varevsij(char optionfilefiname[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int *ncvyearp, int ij, int estepm, int cptcov, int cptcod, int popbased, int mobilav, char strstart[])
1.126 brouard 4021: {
4022: /* Variance of health expectancies */
4023: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
4024: /* double **newm;*/
1.169 brouard 4025: /* int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav)*/
4026:
4027: int movingaverage();
1.126 brouard 4028: double **dnewm,**doldm;
4029: double **dnewmp,**doldmp;
4030: int i, j, nhstepm, hstepm, h, nstepm ;
1.164 brouard 4031: int k;
1.126 brouard 4032: double *xp;
4033: double **gp, **gm; /* for var eij */
4034: double ***gradg, ***trgradg; /*for var eij */
4035: double **gradgp, **trgradgp; /* for var p point j */
4036: double *gpp, *gmp; /* for var p point j */
4037: double **varppt; /* for var p point j nlstate to nlstate+ndeath */
4038: double ***p3mat;
4039: double age,agelim, hf;
4040: double ***mobaverage;
4041: int theta;
4042: char digit[4];
4043: char digitp[25];
4044:
4045: char fileresprobmorprev[FILENAMELENGTH];
4046:
4047: if(popbased==1){
4048: if(mobilav!=0)
1.201 brouard 4049: strcpy(digitp,"-POPULBASED-MOBILAV_");
4050: else strcpy(digitp,"-POPULBASED-NOMOBIL_");
1.126 brouard 4051: }
4052: else
1.201 brouard 4053: strcpy(digitp,"-STABLBASED_");
1.126 brouard 4054:
4055: if (mobilav!=0) {
4056: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4057: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
4058: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
4059: printf(" Error in movingaverage mobilav=%d\n",mobilav);
4060: }
4061: }
4062:
1.201 brouard 4063: strcpy(fileresprobmorprev,"PRMORPREV-");
1.126 brouard 4064: sprintf(digit,"%-d",ij);
4065: /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
4066: strcat(fileresprobmorprev,digit); /* Tvar to be done */
4067: strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
1.202 brouard 4068: strcat(fileresprobmorprev,fileresu);
1.126 brouard 4069: if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
4070: printf("Problem with resultfile: %s\n", fileresprobmorprev);
4071: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
4072: }
4073: printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
4074: fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
4075: pstamp(ficresprobmorprev);
4076: 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);
4077: fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
4078: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
4079: fprintf(ficresprobmorprev," p.%-d SE",j);
4080: for(i=1; i<=nlstate;i++)
4081: fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
4082: }
4083: fprintf(ficresprobmorprev,"\n");
1.208 brouard 4084:
1.126 brouard 4085: fprintf(ficgp,"\n# Routine varevsij");
1.200 brouard 4086: fprintf(ficgp,"\nunset title \n");
4087: /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
1.126 brouard 4088: 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");
4089: fprintf(fichtm,"\n<br>%s <br>\n",digitp);
4090: /* } */
4091: varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
4092: pstamp(ficresvij);
4093: fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n# (weighted average of eij where weights are ");
4094: if(popbased==1)
1.128 brouard 4095: 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 4096: else
4097: fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
4098: fprintf(ficresvij,"# Age");
4099: for(i=1; i<=nlstate;i++)
4100: for(j=1; j<=nlstate;j++)
4101: fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
4102: fprintf(ficresvij,"\n");
4103:
4104: xp=vector(1,npar);
4105: dnewm=matrix(1,nlstate,1,npar);
4106: doldm=matrix(1,nlstate,1,nlstate);
4107: dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
4108: doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
4109:
4110: gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
4111: gpp=vector(nlstate+1,nlstate+ndeath);
4112: gmp=vector(nlstate+1,nlstate+ndeath);
4113: trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
4114:
4115: if(estepm < stepm){
4116: printf ("Problem %d lower than %d\n",estepm, stepm);
4117: }
4118: else hstepm=estepm;
4119: /* For example we decided to compute the life expectancy with the smallest unit */
4120: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
4121: nhstepm is the number of hstepm from age to agelim
1.208 brouard 4122: nstepm is the number of stepm from age to agelim.
1.209 ! brouard 4123: Look at function hpijx to understand why because of memory size limitations,
1.208 brouard 4124: we decided (b) to get a life expectancy respecting the most precise curvature of the
1.126 brouard 4125: survival function given by stepm (the optimization length). Unfortunately it
4126: means that if the survival funtion is printed every two years of age and if
4127: you sum them up and add 1 year (area under the trapezoids) you won't get the same
4128: results. So we changed our mind and took the option of the best precision.
4129: */
4130: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
4131: agelim = AGESUP;
4132: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
4133: nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
4134: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
4135: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4136: gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
4137: gp=matrix(0,nhstepm,1,nlstate);
4138: gm=matrix(0,nhstepm,1,nlstate);
4139:
4140:
4141: for(theta=1; theta <=npar; theta++){
4142: for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
4143: xp[i] = x[i] + (i==theta ?delti[theta]:0);
4144: }
1.209 ! brouard 4145:
! 4146: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij);
1.126 brouard 4147:
4148: if (popbased==1) {
4149: if(mobilav ==0){
4150: for(i=1; i<=nlstate;i++)
4151: prlim[i][i]=probs[(int)age][i][ij];
4152: }else{ /* mobilav */
4153: for(i=1; i<=nlstate;i++)
4154: prlim[i][i]=mobaverage[(int)age][i][ij];
4155: }
4156: }
4157:
1.209 ! brouard 4158: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij); /* Returns p3mat[i][j][h] for h=1 to nhstepm */
1.126 brouard 4159: for(j=1; j<= nlstate; j++){
4160: for(h=0; h<=nhstepm; h++){
4161: for(i=1, gp[h][j]=0.;i<=nlstate;i++)
4162: gp[h][j] += prlim[i][i]*p3mat[i][j][h];
4163: }
4164: }
1.209 ! brouard 4165: /* Next for computing probability of death (h=1 means
1.126 brouard 4166: computed over hstepm matrices product = hstepm*stepm months)
4167: as a weighted average of prlim.
4168: */
4169: for(j=nlstate+1;j<=nlstate+ndeath;j++){
4170: for(i=1,gpp[j]=0.; i<= nlstate; i++)
4171: gpp[j] += prlim[i][i]*p3mat[i][j][1];
4172: }
4173: /* end probability of death */
4174:
4175: for(i=1; i<=npar; i++) /* Computes gradient x - delta */
4176: xp[i] = x[i] - (i==theta ?delti[theta]:0);
1.209 ! brouard 4177:
! 4178: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp, ij);
1.126 brouard 4179:
4180: if (popbased==1) {
4181: if(mobilav ==0){
4182: for(i=1; i<=nlstate;i++)
4183: prlim[i][i]=probs[(int)age][i][ij];
4184: }else{ /* mobilav */
4185: for(i=1; i<=nlstate;i++)
4186: prlim[i][i]=mobaverage[(int)age][i][ij];
4187: }
4188: }
4189:
1.209 ! brouard 4190: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
! 4191:
1.128 brouard 4192: for(j=1; j<= nlstate; j++){ /* Sum of wi * eij = e.j */
1.126 brouard 4193: for(h=0; h<=nhstepm; h++){
4194: for(i=1, gm[h][j]=0.;i<=nlstate;i++)
4195: gm[h][j] += prlim[i][i]*p3mat[i][j][h];
4196: }
4197: }
4198: /* This for computing probability of death (h=1 means
4199: computed over hstepm matrices product = hstepm*stepm months)
4200: as a weighted average of prlim.
4201: */
4202: for(j=nlstate+1;j<=nlstate+ndeath;j++){
4203: for(i=1,gmp[j]=0.; i<= nlstate; i++)
4204: gmp[j] += prlim[i][i]*p3mat[i][j][1];
4205: }
4206: /* end probability of death */
4207:
4208: for(j=1; j<= nlstate; j++) /* vareij */
4209: for(h=0; h<=nhstepm; h++){
4210: gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
4211: }
4212:
4213: for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
4214: gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
4215: }
4216:
4217: } /* End theta */
4218:
4219: trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
4220:
4221: for(h=0; h<=nhstepm; h++) /* veij */
4222: for(j=1; j<=nlstate;j++)
4223: for(theta=1; theta <=npar; theta++)
4224: trgradg[h][j][theta]=gradg[h][theta][j];
4225:
4226: for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
4227: for(theta=1; theta <=npar; theta++)
4228: trgradgp[j][theta]=gradgp[theta][j];
4229:
4230:
4231: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
4232: for(i=1;i<=nlstate;i++)
4233: for(j=1;j<=nlstate;j++)
4234: vareij[i][j][(int)age] =0.;
4235:
4236: for(h=0;h<=nhstepm;h++){
4237: for(k=0;k<=nhstepm;k++){
4238: matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
4239: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
4240: for(i=1;i<=nlstate;i++)
4241: for(j=1;j<=nlstate;j++)
4242: vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
4243: }
4244: }
4245:
4246: /* pptj */
4247: matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
4248: matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
4249: for(j=nlstate+1;j<=nlstate+ndeath;j++)
4250: for(i=nlstate+1;i<=nlstate+ndeath;i++)
4251: varppt[j][i]=doldmp[j][i];
4252: /* end ppptj */
4253: /* x centered again */
1.209 ! brouard 4254:
! 4255: prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ncvyearp,ij);
1.126 brouard 4256:
4257: if (popbased==1) {
4258: if(mobilav ==0){
4259: for(i=1; i<=nlstate;i++)
4260: prlim[i][i]=probs[(int)age][i][ij];
4261: }else{ /* mobilav */
4262: for(i=1; i<=nlstate;i++)
4263: prlim[i][i]=mobaverage[(int)age][i][ij];
4264: }
4265: }
4266:
4267: /* This for computing probability of death (h=1 means
4268: computed over hstepm (estepm) matrices product = hstepm*stepm months)
4269: as a weighted average of prlim.
4270: */
1.209 ! brouard 4271: hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);
1.126 brouard 4272: for(j=nlstate+1;j<=nlstate+ndeath;j++){
4273: for(i=1,gmp[j]=0.;i<= nlstate; i++)
4274: gmp[j] += prlim[i][i]*p3mat[i][j][1];
4275: }
4276: /* end probability of death */
4277:
4278: fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
4279: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
4280: fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
4281: for(i=1; i<=nlstate;i++){
4282: fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
4283: }
4284: }
4285: fprintf(ficresprobmorprev,"\n");
4286:
4287: fprintf(ficresvij,"%.0f ",age );
4288: for(i=1; i<=nlstate;i++)
4289: for(j=1; j<=nlstate;j++){
4290: fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
4291: }
4292: fprintf(ficresvij,"\n");
4293: free_matrix(gp,0,nhstepm,1,nlstate);
4294: free_matrix(gm,0,nhstepm,1,nlstate);
4295: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
4296: free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
4297: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4298: } /* End age */
4299: free_vector(gpp,nlstate+1,nlstate+ndeath);
4300: free_vector(gmp,nlstate+1,nlstate+ndeath);
4301: free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
4302: free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
1.199 brouard 4303: /* fprintf(ficgp,"\nunset parametric;unset label; set ter png small size 320, 240"); */
4304: fprintf(ficgp,"\nunset parametric;unset label; set ter svg size 640, 480");
1.126 brouard 4305: /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
1.131 brouard 4306: fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
1.201 brouard 4307: fprintf(ficgp,"\nset out \"%s%s.svg\";",subdirf3(optionfilefiname,"VARMUPTJGR-",digitp),digit);
1.126 brouard 4308: /* fprintf(ficgp,"\n plot \"%s\" u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
4309: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
4310: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
1.145 brouard 4311: fprintf(ficgp,"\n plot \"%s\" u 1:($3) not w l lt 1 ",subdirf(fileresprobmorprev));
1.170 brouard 4312: fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)) t \"95%% interval\" w l lt 2 ",subdirf(fileresprobmorprev));
1.145 brouard 4313: fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)) not w l lt 2 ",subdirf(fileresprobmorprev));
1.126 brouard 4314: 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 4315: 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 4316: /* 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 4317: */
1.199 brouard 4318: /* fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.svg\";replot;",digitp,optionfilefiname,digit); */
1.201 brouard 4319: fprintf(ficgp,"\nset out;\nset out \"%s%s.svg\";replot;set out;\n",subdirf3(optionfilefiname,"VARMUPTJGR-",digitp),digit);
1.126 brouard 4320:
4321: free_vector(xp,1,npar);
4322: free_matrix(doldm,1,nlstate,1,nlstate);
4323: free_matrix(dnewm,1,nlstate,1,npar);
4324: free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
4325: free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
4326: free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
4327: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4328: fclose(ficresprobmorprev);
4329: fflush(ficgp);
4330: fflush(fichtm);
4331: } /* end varevsij */
4332:
4333: /************ Variance of prevlim ******************/
1.209 ! brouard 4334: void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int *ncvyearp, int ij, char strstart[])
1.126 brouard 4335: {
1.205 brouard 4336: /* Variance of prevalence limit for each state ij using current parameters x[] and estimates of neighbourhood give by delti*/
1.126 brouard 4337: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
1.164 brouard 4338:
1.126 brouard 4339: double **dnewm,**doldm;
4340: int i, j, nhstepm, hstepm;
4341: double *xp;
4342: double *gp, *gm;
4343: double **gradg, **trgradg;
1.208 brouard 4344: double **mgm, **mgp;
1.126 brouard 4345: double age,agelim;
4346: int theta;
4347:
4348: pstamp(ficresvpl);
4349: fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
4350: fprintf(ficresvpl,"# Age");
4351: for(i=1; i<=nlstate;i++)
4352: fprintf(ficresvpl," %1d-%1d",i,i);
4353: fprintf(ficresvpl,"\n");
4354:
4355: xp=vector(1,npar);
4356: dnewm=matrix(1,nlstate,1,npar);
4357: doldm=matrix(1,nlstate,1,nlstate);
4358:
4359: hstepm=1*YEARM; /* Every year of age */
4360: hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
4361: agelim = AGESUP;
4362: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
4363: nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
4364: if (stepm >= YEARM) hstepm=1;
4365: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
4366: gradg=matrix(1,npar,1,nlstate);
1.208 brouard 4367: mgp=matrix(1,npar,1,nlstate);
4368: mgm=matrix(1,npar,1,nlstate);
1.126 brouard 4369: gp=vector(1,nlstate);
4370: gm=vector(1,nlstate);
4371:
4372: for(theta=1; theta <=npar; theta++){
4373: for(i=1; i<=npar; i++){ /* Computes gradient */
4374: xp[i] = x[i] + (i==theta ?delti[theta]:0);
4375: }
1.209 ! brouard 4376: if((int)age==79 ||(int)age== 80 ||(int)age== 81 )
! 4377: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij);
! 4378: else
! 4379: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,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);
1.209 ! brouard 4386: if((int)age==79 ||(int)age== 80 ||(int)age== 81 )
! 4387: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij);
! 4388: else
! 4389: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij);
1.208 brouard 4390: for(i=1;i<=nlstate;i++){
1.126 brouard 4391: gm[i] = prlim[i][i];
1.208 brouard 4392: mgm[theta][i] = prlim[i][i];
4393: }
1.126 brouard 4394: for(i=1;i<=nlstate;i++)
4395: gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
1.209 ! brouard 4396: /* gradg[theta][2]= -gradg[theta][1]; */ /* For testing if nlstate=2 */
1.126 brouard 4397: } /* End theta */
4398:
4399: trgradg =matrix(1,nlstate,1,npar);
4400:
4401: for(j=1; j<=nlstate;j++)
4402: for(theta=1; theta <=npar; theta++)
4403: trgradg[j][theta]=gradg[theta][j];
1.209 ! brouard 4404: /* if((int)age==79 ||(int)age== 80 ||(int)age== 81 ){ */
! 4405: /* printf("\nmgm mgp %d ",(int)age); */
! 4406: /* for(j=1; j<=nlstate;j++){ */
! 4407: /* printf(" %d ",j); */
! 4408: /* for(theta=1; theta <=npar; theta++) */
! 4409: /* printf(" %d %lf %lf",theta,mgm[theta][j],mgp[theta][j]); */
! 4410: /* printf("\n "); */
! 4411: /* } */
! 4412: /* } */
! 4413: /* if((int)age==79 ||(int)age== 80 ||(int)age== 81 ){ */
! 4414: /* printf("\n gradg %d ",(int)age); */
! 4415: /* for(j=1; j<=nlstate;j++){ */
! 4416: /* printf("%d ",j); */
! 4417: /* for(theta=1; theta <=npar; theta++) */
! 4418: /* printf("%d %lf ",theta,gradg[theta][j]); */
! 4419: /* printf("\n "); */
! 4420: /* } */
! 4421: /* } */
1.126 brouard 4422:
4423: for(i=1;i<=nlstate;i++)
4424: varpl[i][(int)age] =0.;
1.209 ! brouard 4425: if((int)age==79 ||(int)age== 80 ||(int)age== 81){
1.205 brouard 4426: matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
4427: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
4428: }else{
1.126 brouard 4429: matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
4430: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
1.205 brouard 4431: }
1.126 brouard 4432: for(i=1;i<=nlstate;i++)
4433: varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
4434:
4435: fprintf(ficresvpl,"%.0f ",age );
4436: for(i=1; i<=nlstate;i++)
4437: fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
4438: fprintf(ficresvpl,"\n");
4439: free_vector(gp,1,nlstate);
4440: free_vector(gm,1,nlstate);
1.208 brouard 4441: free_matrix(mgm,1,npar,1,nlstate);
4442: free_matrix(mgp,1,npar,1,nlstate);
1.126 brouard 4443: free_matrix(gradg,1,npar,1,nlstate);
4444: free_matrix(trgradg,1,nlstate,1,npar);
4445: } /* End age */
4446:
4447: free_vector(xp,1,npar);
4448: free_matrix(doldm,1,nlstate,1,npar);
4449: free_matrix(dnewm,1,nlstate,1,nlstate);
4450:
4451: }
4452:
4453: /************ Variance of one-step probabilities ******************/
4454: 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[])
4455: {
1.164 brouard 4456: int i, j=0, k1, l1, tj;
1.126 brouard 4457: int k2, l2, j1, z1;
1.164 brouard 4458: int k=0, l;
1.145 brouard 4459: int first=1, first1, first2;
1.126 brouard 4460: double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
4461: double **dnewm,**doldm;
4462: double *xp;
4463: double *gp, *gm;
4464: double **gradg, **trgradg;
4465: double **mu;
1.164 brouard 4466: double age, cov[NCOVMAX+1];
1.126 brouard 4467: double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
4468: int theta;
4469: char fileresprob[FILENAMELENGTH];
4470: char fileresprobcov[FILENAMELENGTH];
4471: char fileresprobcor[FILENAMELENGTH];
4472: double ***varpij;
4473:
1.201 brouard 4474: strcpy(fileresprob,"PROB_");
1.126 brouard 4475: strcat(fileresprob,fileres);
4476: if((ficresprob=fopen(fileresprob,"w"))==NULL) {
4477: printf("Problem with resultfile: %s\n", fileresprob);
4478: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
4479: }
1.201 brouard 4480: strcpy(fileresprobcov,"PROBCOV_");
1.202 brouard 4481: strcat(fileresprobcov,fileresu);
1.126 brouard 4482: if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
4483: printf("Problem with resultfile: %s\n", fileresprobcov);
4484: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
4485: }
1.201 brouard 4486: strcpy(fileresprobcor,"PROBCOR_");
1.202 brouard 4487: strcat(fileresprobcor,fileresu);
1.126 brouard 4488: if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
4489: printf("Problem with resultfile: %s\n", fileresprobcor);
4490: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
4491: }
4492: printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
4493: fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
4494: printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
4495: fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
4496: printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
4497: fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
4498: pstamp(ficresprob);
4499: fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
4500: fprintf(ficresprob,"# Age");
4501: pstamp(ficresprobcov);
4502: fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
4503: fprintf(ficresprobcov,"# Age");
4504: pstamp(ficresprobcor);
4505: fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
4506: fprintf(ficresprobcor,"# Age");
4507:
4508:
4509: for(i=1; i<=nlstate;i++)
4510: for(j=1; j<=(nlstate+ndeath);j++){
4511: fprintf(ficresprob," p%1d-%1d (SE)",i,j);
4512: fprintf(ficresprobcov," p%1d-%1d ",i,j);
4513: fprintf(ficresprobcor," p%1d-%1d ",i,j);
4514: }
4515: /* fprintf(ficresprob,"\n");
4516: fprintf(ficresprobcov,"\n");
4517: fprintf(ficresprobcor,"\n");
4518: */
1.131 brouard 4519: xp=vector(1,npar);
1.126 brouard 4520: dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
4521: doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
4522: mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
4523: varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
4524: first=1;
4525: fprintf(ficgp,"\n# Routine varprob");
4526: fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
4527: fprintf(fichtm,"\n");
4528:
1.200 brouard 4529: 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 4530: 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);
4531: fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated \
1.126 brouard 4532: and drawn. It helps understanding how is the covariance between two incidences.\
4533: They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
4534: 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. \
4535: It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
4536: would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
4537: standard deviations wide on each axis. <br>\
4538: Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
4539: and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
4540: To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
4541:
4542: cov[1]=1;
1.145 brouard 4543: /* tj=cptcoveff; */
4544: tj = (int) pow(2,cptcoveff);
1.126 brouard 4545: if (cptcovn<1) {tj=1;ncodemax[1]=1;}
4546: j1=0;
1.145 brouard 4547: for(j1=1; j1<=tj;j1++){
4548: /*for(i1=1; i1<=ncodemax[t];i1++){ */
4549: /*j1++;*/
1.126 brouard 4550: if (cptcovn>0) {
4551: fprintf(ficresprob, "\n#********** Variable ");
1.198 brouard 4552: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.126 brouard 4553: fprintf(ficresprob, "**********\n#\n");
4554: fprintf(ficresprobcov, "\n#********** Variable ");
1.198 brouard 4555: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.126 brouard 4556: fprintf(ficresprobcov, "**********\n#\n");
4557:
4558: fprintf(ficgp, "\n#********** Variable ");
1.198 brouard 4559: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.126 brouard 4560: fprintf(ficgp, "**********\n#\n");
4561:
4562:
4563: fprintf(fichtmcov, "\n<hr size=\"2\" color=\"#EC5E5E\">********** Variable ");
1.198 brouard 4564: for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.126 brouard 4565: fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
4566:
4567: fprintf(ficresprobcor, "\n#********** Variable ");
1.198 brouard 4568: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.126 brouard 4569: fprintf(ficresprobcor, "**********\n#");
4570: }
4571:
1.145 brouard 4572: gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
4573: trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
4574: gp=vector(1,(nlstate)*(nlstate+ndeath));
4575: gm=vector(1,(nlstate)*(nlstate+ndeath));
1.126 brouard 4576: for (age=bage; age<=fage; age ++){
4577: cov[2]=age;
1.187 brouard 4578: if(nagesqr==1)
4579: cov[3]= age*age;
1.126 brouard 4580: for (k=1; k<=cptcovn;k++) {
1.200 brouard 4581: cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(j1,k)];
4582: /*cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(j1,Tvar[k])];*//* j1 1 2 3 4
1.145 brouard 4583: * 1 1 1 1 1
4584: * 2 2 1 1 1
4585: * 3 1 2 1 1
4586: */
4587: /* nbcode[1][1]=0 nbcode[1][2]=1;*/
1.126 brouard 4588: }
1.186 brouard 4589: /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
1.200 brouard 4590: for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
1.126 brouard 4591: for (k=1; k<=cptcovprod;k++)
1.200 brouard 4592: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)];
1.126 brouard 4593:
4594:
4595: for(theta=1; theta <=npar; theta++){
4596: for(i=1; i<=npar; i++)
4597: xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
4598:
4599: pmij(pmmij,cov,ncovmodel,xp,nlstate);
4600:
4601: k=0;
4602: for(i=1; i<= (nlstate); i++){
4603: for(j=1; j<=(nlstate+ndeath);j++){
4604: k=k+1;
4605: gp[k]=pmmij[i][j];
4606: }
4607: }
4608:
4609: for(i=1; i<=npar; i++)
4610: xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
4611:
4612: pmij(pmmij,cov,ncovmodel,xp,nlstate);
4613: k=0;
4614: for(i=1; i<=(nlstate); i++){
4615: for(j=1; j<=(nlstate+ndeath);j++){
4616: k=k+1;
4617: gm[k]=pmmij[i][j];
4618: }
4619: }
4620:
4621: for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)
4622: gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];
4623: }
4624:
4625: for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
4626: for(theta=1; theta <=npar; theta++)
4627: trgradg[j][theta]=gradg[theta][j];
4628:
4629: matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);
4630: matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
4631:
4632: pmij(pmmij,cov,ncovmodel,x,nlstate);
4633:
4634: k=0;
4635: for(i=1; i<=(nlstate); i++){
4636: for(j=1; j<=(nlstate+ndeath);j++){
4637: k=k+1;
4638: mu[k][(int) age]=pmmij[i][j];
4639: }
4640: }
4641: for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
4642: for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
4643: varpij[i][j][(int)age] = doldm[i][j];
4644:
4645: /*printf("\n%d ",(int)age);
4646: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
4647: printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
4648: fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
4649: }*/
4650:
4651: fprintf(ficresprob,"\n%d ",(int)age);
4652: fprintf(ficresprobcov,"\n%d ",(int)age);
4653: fprintf(ficresprobcor,"\n%d ",(int)age);
4654:
4655: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
4656: fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
4657: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
4658: fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
4659: fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
4660: }
4661: i=0;
4662: for (k=1; k<=(nlstate);k++){
4663: for (l=1; l<=(nlstate+ndeath);l++){
1.145 brouard 4664: i++;
1.126 brouard 4665: fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
4666: fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
4667: for (j=1; j<=i;j++){
1.145 brouard 4668: /* printf(" k=%d l=%d i=%d j=%d\n",k,l,i,j);fflush(stdout); */
1.126 brouard 4669: fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
4670: fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
4671: }
4672: }
4673: }/* end of loop for state */
4674: } /* end of loop for age */
1.145 brouard 4675: free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
4676: free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
4677: free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
4678: free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
4679:
1.126 brouard 4680: /* Confidence intervalle of pij */
4681: /*
1.131 brouard 4682: fprintf(ficgp,"\nunset parametric;unset label");
1.126 brouard 4683: fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
4684: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
4685: 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);
4686: fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
4687: fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
4688: fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
4689: */
4690:
4691: /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
1.145 brouard 4692: first1=1;first2=2;
1.126 brouard 4693: for (k2=1; k2<=(nlstate);k2++){
4694: for (l2=1; l2<=(nlstate+ndeath);l2++){
4695: if(l2==k2) continue;
4696: j=(k2-1)*(nlstate+ndeath)+l2;
4697: for (k1=1; k1<=(nlstate);k1++){
4698: for (l1=1; l1<=(nlstate+ndeath);l1++){
4699: if(l1==k1) continue;
4700: i=(k1-1)*(nlstate+ndeath)+l1;
4701: if(i<=j) continue;
4702: for (age=bage; age<=fage; age ++){
4703: if ((int)age %5==0){
4704: v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
4705: v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
4706: cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
4707: mu1=mu[i][(int) age]/stepm*YEARM ;
4708: mu2=mu[j][(int) age]/stepm*YEARM;
4709: c12=cv12/sqrt(v1*v2);
4710: /* Computing eigen value of matrix of covariance */
4711: lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
4712: lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
1.135 brouard 4713: if ((lc2 <0) || (lc1 <0) ){
1.145 brouard 4714: if(first2==1){
4715: first1=0;
4716: 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);
4717: }
4718: 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);
4719: /* lc1=fabs(lc1); */ /* If we want to have them positive */
4720: /* lc2=fabs(lc2); */
1.135 brouard 4721: }
4722:
1.126 brouard 4723: /* Eigen vectors */
4724: v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
4725: /*v21=sqrt(1.-v11*v11); *//* error */
4726: v21=(lc1-v1)/cv12*v11;
4727: v12=-v21;
4728: v22=v11;
4729: tnalp=v21/v11;
4730: if(first1==1){
4731: first1=0;
4732: 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);
4733: }
4734: 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);
4735: /*printf(fignu*/
4736: /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
4737: /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
4738: if(first==1){
4739: first=0;
1.200 brouard 4740: fprintf(ficgp,"\n# Ellipsoids of confidence\n#\n");
1.126 brouard 4741: fprintf(ficgp,"\nset parametric;unset label");
4742: 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 4743: fprintf(ficgp,"\nset ter svg size 640, 480");
1.126 brouard 4744: fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
1.201 brouard 4745: :<a href=\"%s_%d%1d%1d-%1d%1d.svg\">\
4746: %s_%d%1d%1d-%1d%1d.svg</A>, ",k1,l1,k2,l2,\
4747: subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2,\
4748: subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
4749: fprintf(fichtmcov,"\n<br><img src=\"%s_%d%1d%1d-%1d%1d.svg\"> ",subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
1.126 brouard 4750: fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
1.201 brouard 4751: fprintf(ficgp,"\nset out \"%s_%d%1d%1d-%1d%1d.svg\"",subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
1.126 brouard 4752: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
4753: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
4754: 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",\
4755: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
4756: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
4757: }else{
4758: first=0;
4759: fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
4760: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
4761: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
4762: 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",\
4763: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
4764: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
4765: }/* if first */
4766: } /* age mod 5 */
4767: } /* end loop age */
1.201 brouard 4768: 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 4769: first=1;
4770: } /*l12 */
4771: } /* k12 */
4772: } /*l1 */
4773: }/* k1 */
1.169 brouard 4774: /* } */ /* loop covariates */
1.126 brouard 4775: }
4776: free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
4777: free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
4778: free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
4779: free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
4780: free_vector(xp,1,npar);
4781: fclose(ficresprob);
4782: fclose(ficresprobcov);
4783: fclose(ficresprobcor);
4784: fflush(ficgp);
4785: fflush(fichtmcov);
4786: }
4787:
4788:
4789: /******************* Printing html file ***********/
1.201 brouard 4790: void printinghtml(char fileresu[], char title[], char datafile[], int firstpass, \
1.126 brouard 4791: int lastpass, int stepm, int weightopt, char model[],\
4792: int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
4793: int popforecast, int estepm ,\
4794: double jprev1, double mprev1,double anprev1, \
4795: double jprev2, double mprev2,double anprev2){
4796: int jj1, k1, i1, cpt;
4797:
4798: fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
4799: <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
4800: </ul>");
4801: fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \
4802: - 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 4803: jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileresu,"P_"),subdirf2(fileresu,"P_"));
1.126 brouard 4804: fprintf(fichtm,"\
4805: - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
1.201 brouard 4806: stepm,subdirf2(fileresu,"PIJ_"),subdirf2(fileresu,"PIJ_"));
1.126 brouard 4807: fprintf(fichtm,"\
4808: - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
1.201 brouard 4809: subdirf2(fileresu,"PL_"),subdirf2(fileresu,"PL_"));
1.126 brouard 4810: fprintf(fichtm,"\
1.128 brouard 4811: - (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 4812: <a href=\"%s\">%s</a> <br>\n",
1.201 brouard 4813: estepm,subdirf2(fileresu,"E_"),subdirf2(fileresu,"E_"));
1.126 brouard 4814: fprintf(fichtm,"\
4815: - Population projections by age and states: \
1.201 brouard 4816: <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileresu,"F_"),subdirf2(fileresu,"F_"));
1.126 brouard 4817:
4818: fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
4819:
1.145 brouard 4820: m=pow(2,cptcoveff);
1.126 brouard 4821: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
4822:
4823: jj1=0;
4824: for(k1=1; k1<=m;k1++){
1.192 brouard 4825: /* for(i1=1; i1<=ncodemax[k1];i1++){ */
1.126 brouard 4826: jj1++;
4827: if (cptcovn > 0) {
4828: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
1.192 brouard 4829: for (cpt=1; cpt<=cptcoveff;cpt++){
1.198 brouard 4830: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]);
4831: printf(" V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]);fflush(stdout);
1.192 brouard 4832: }
1.126 brouard 4833: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
4834: }
1.201 brouard 4835: /* aij, bij */
4836: 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> \
4837: <img src=\"%s_%d-1.svg\">",subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1);
1.126 brouard 4838: /* Pij */
1.202 brouard 4839: 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 4840: <img src=\"%s_%d-2.svg\">",stepm,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1);
1.126 brouard 4841: /* Quasi-incidences */
1.201 brouard 4842: fprintf(fichtm,"<br>\n- Iij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
4843: before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too,\
4844: incidence (rates) are the limit when h tends to zero of the ratio of the probability hPij \
4845: divided by h: hPij/h : <a href=\"%s_%d-3.svg\">%s_%d-3.svg</a><br> \
4846: <img src=\"%s_%d-3.svg\">",stepm,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1);
4847: /* Survival functions (period) in state j */
4848: for(cpt=1; cpt<=nlstate;cpt++){
4849: 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> \
4850: <img src=\"%s_%d-%d.svg\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"LIJ_"),cpt,jj1,subdirf2(optionfilefiname,"LIJ_"),cpt,jj1,subdirf2(optionfilefiname,"LIJ_"),cpt,jj1);
4851: }
4852: /* State specific survival functions (period) */
4853: for(cpt=1; cpt<=nlstate;cpt++){
1.208 brouard 4854: fprintf(fichtm,"<br>\n- Survival functions from state %d in each live state and total.\
1.201 brouard 4855: Or probability to survive in various states (1 to %d) being in state %d at different ages.\
4856: <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);
4857: }
4858: /* Period (stable) prevalence in each health state */
4859: for(cpt=1; cpt<=nlstate;cpt++){
4860: 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> \
4861: <img src=\"%s_%d-%d.svg\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"P_"),cpt,jj1,subdirf2(optionfilefiname,"P_"),cpt,jj1,subdirf2(optionfilefiname,"P_"),cpt,jj1);
4862: }
1.126 brouard 4863: for(cpt=1; cpt<=nlstate;cpt++) {
1.205 brouard 4864: 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 4865: <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 4866: }
1.192 brouard 4867: /* } /\* end i1 *\/ */
1.126 brouard 4868: }/* End k1 */
4869: fprintf(fichtm,"</ul>");
4870:
4871: fprintf(fichtm,"\
4872: \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
1.193 brouard 4873: - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br> \
1.203 brouard 4874: - 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 4875: But because parameters are usually highly correlated (a higher incidence of disability \
4876: and a higher incidence of recovery can give very close observed transition) it might \
4877: be very useful to look not only at linear confidence intervals estimated from the \
4878: variances but at the covariance matrix. And instead of looking at the estimated coefficients \
4879: (parameters) of the logistic regression, it might be more meaningful to visualize the \
4880: covariance matrix of the one-step probabilities. \
4881: See page 'Matrix of variance-covariance of one-step probabilities' below. \n", rfileres,rfileres);
1.126 brouard 4882:
1.193 brouard 4883: fprintf(fichtm," - Standard deviation of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
1.201 brouard 4884: subdirf2(fileresu,"PROB_"),subdirf2(fileresu,"PROB_"));
1.126 brouard 4885: fprintf(fichtm,"\
4886: - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
1.201 brouard 4887: subdirf2(fileresu,"PROBCOV_"),subdirf2(fileresu,"PROBCOV_"));
1.126 brouard 4888:
4889: fprintf(fichtm,"\
4890: - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
1.201 brouard 4891: subdirf2(fileresu,"PROBCOR_"),subdirf2(fileresu,"PROBCOR_"));
1.126 brouard 4892: fprintf(fichtm,"\
4893: - 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): \
4894: <a href=\"%s\">%s</a> <br>\n</li>",
1.201 brouard 4895: estepm,subdirf2(fileresu,"CVE_"),subdirf2(fileresu,"CVE_"));
1.126 brouard 4896: fprintf(fichtm,"\
4897: - (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): \
4898: <a href=\"%s\">%s</a> <br>\n</li>",
1.201 brouard 4899: estepm,subdirf2(fileresu,"STDE_"),subdirf2(fileresu,"STDE_"));
1.126 brouard 4900: fprintf(fichtm,"\
1.128 brouard 4901: - 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 4902: estepm, subdirf2(fileresu,"V_"),subdirf2(fileresu,"V_"));
1.126 brouard 4903: fprintf(fichtm,"\
1.128 brouard 4904: - 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 4905: estepm, subdirf2(fileresu,"T_"),subdirf2(fileresu,"T_"));
1.126 brouard 4906: fprintf(fichtm,"\
4907: - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
1.201 brouard 4908: subdirf2(fileresu,"VPL_"),subdirf2(fileresu,"VPL_"));
1.126 brouard 4909:
4910: /* if(popforecast==1) fprintf(fichtm,"\n */
4911: /* - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
4912: /* - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
4913: /* <br>",fileres,fileres,fileres,fileres); */
4914: /* else */
4915: /* 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); */
4916: fflush(fichtm);
4917: fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
4918:
1.145 brouard 4919: m=pow(2,cptcoveff);
1.126 brouard 4920: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
4921:
4922: jj1=0;
4923: for(k1=1; k1<=m;k1++){
1.192 brouard 4924: /* for(i1=1; i1<=ncodemax[k1];i1++){ */
1.126 brouard 4925: jj1++;
4926: if (cptcovn > 0) {
4927: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
4928: for (cpt=1; cpt<=cptcoveff;cpt++)
1.198 brouard 4929: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]);
1.126 brouard 4930: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
4931: }
4932: for(cpt=1; cpt<=nlstate;cpt++) {
4933: fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
1.205 brouard 4934: prevalence (with 95%% confidence interval) in state (%d): <a href=\"%s_%d%d.svg\"> %s_%d-%d.svg <br>\
4935: <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 4936: }
4937: fprintf(fichtm,"\n<br>- Total life expectancy by age and \
1.128 brouard 4938: health expectancies in states (1) and (2). If popbased=1 the smooth (due to the model) \
4939: true period expectancies (those weighted with period prevalences are also\
4940: drawn in addition to the population based expectancies computed using\
1.205 brouard 4941: observed and cahotic prevalences: <a href=\"%s_%d.svg\">%s_%d.svg<br>\
4942: <img src=\"%s_%d.svg\">",subdirf2(optionfilefiname,"E_"),jj1,subdirf2(optionfilefiname,"E_"),jj1,subdirf2(optionfilefiname,"E_"),jj1);
1.192 brouard 4943: /* } /\* end i1 *\/ */
1.126 brouard 4944: }/* End k1 */
4945: fprintf(fichtm,"</ul>");
4946: fflush(fichtm);
4947: }
4948:
4949: /******************* Gnuplot file **************/
1.201 brouard 4950: void printinggnuplot(char fileresu[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
1.126 brouard 4951:
4952: char dirfileres[132],optfileres[132];
1.164 brouard 4953: int cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,ij=0,l=0;
1.130 brouard 4954: int ng=0;
1.201 brouard 4955: int vpopbased;
1.126 brouard 4956: /* if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
4957: /* printf("Problem with file %s",optionfilegnuplot); */
4958: /* fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
4959: /* } */
4960:
4961: /*#ifdef windows */
4962: fprintf(ficgp,"cd \"%s\" \n",pathc);
4963: /*#endif */
4964: m=pow(2,cptcoveff);
4965:
1.202 brouard 4966: /* Contribution to likelihood */
4967: /* Plot the probability implied in the likelihood */
4968: fprintf(ficgp,"\n# Contributions to the Likelihood, mle >=1. For mle=4 no interpolation, pure matrix products.\n#\n");
4969: fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Likelihood (-2Log(L))\";");
4970: /* fprintf(ficgp,"\nset ter svg size 640, 480"); */ /* Too big for svg */
1.205 brouard 4971: fprintf(ficgp,"\nset ter pngcairo size 640, 480");
1.204 brouard 4972: /* nice for mle=4 plot by number of matrix products.
1.202 brouard 4973: replot "rrtest1/toto.txt" u 2:($4 == 1 && $5==2 ? $9 : 1/0):5 t "p12" with point lc 1 */
4974: /* replot exp(p1+p2*x)/(1+exp(p1+p2*x)+exp(p3+p4*x)+exp(p5+p6*x)) t "p12(x)" */
4975: /* fprintf(ficgp,"\nset out \"%s.svg\";",subdirf2(optionfilefiname,"ILK_")); */
1.204 brouard 4976: fprintf(ficgp,"\nset out \"%s-dest.png\";",subdirf2(optionfilefiname,"ILK_"));
1.205 brouard 4977: 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 4978: fprintf(ficgp,"\nset out \"%s-ori.png\";",subdirf2(optionfilefiname,"ILK_"));
1.205 brouard 4979: 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 4980: for (i=1; i<= nlstate ; i ++) {
4981: fprintf(ficgp,"\nset out \"%s-p%dj.png\";set ylabel \"Probability for each individual/wave\";",subdirf2(optionfilefiname,"ILK_"),i);
1.205 brouard 4982: fprintf(ficgp,"unset log;\n# plot weighted, mean weight should have point size of 0.5\n plot \"%s\"",subdirf(fileresilk));
4983: 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 4984: for (j=2; j<= nlstate+ndeath ; j ++) {
1.205 brouard 4985: 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 4986: }
4987: fprintf(ficgp,";\nset out; unset ylabel;\n");
4988: }
4989: /* 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 */
4990: /* fprintf(ficgp,"\nset log y;plot \"%s\" u 2:(-$11):3 t \"All sample, all transitions\" with dots lc variable",subdirf(fileresilk)); */
4991: /* 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 4992: fprintf(ficgp,"\nset out;unset log\n");
1.202 brouard 4993: /* fprintf(ficgp,"\nset out \"%s.svg\"; replot; set out; # bug gnuplot",subdirf2(optionfilefiname,"ILK_")); */
4994:
1.126 brouard 4995: strcpy(dirfileres,optionfilefiname);
4996: strcpy(optfileres,"vpl");
4997: /* 1eme*/
1.201 brouard 4998: fprintf(ficgp,"\n# 1st: Period (stable) prevalence with CI: 'VPL_' files\n");
1.126 brouard 4999: for (cpt=1; cpt<= nlstate ; cpt ++) {
1.145 brouard 5000: for (k1=1; k1<= m ; k1 ++) { /* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */
1.201 brouard 5001: fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"V_"),cpt,k1);
5002: fprintf(ficgp,"\n#set out \"V_%s_%d-%d.svg\" \n",optionfilefiname,cpt,k1);
1.126 brouard 5003: fprintf(ficgp,"set xlabel \"Age\" \n\
5004: set ylabel \"Probability\" \n\
1.199 brouard 5005: set ter svg size 640, 480\n\
1.201 brouard 5006: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"%%lf",ageminpar,fage,subdirf2(fileresu,"VPL_"),k1-1,k1-1);
1.126 brouard 5007:
5008: for (i=1; i<= nlstate ; i ++) {
1.170 brouard 5009: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
5010: else fprintf(ficgp," %%*lf (%%*lf)");
1.126 brouard 5011: }
1.201 brouard 5012: 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 5013: for (i=1; i<= nlstate ; i ++) {
1.170 brouard 5014: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
5015: else fprintf(ficgp," %%*lf (%%*lf)");
1.126 brouard 5016: }
1.201 brouard 5017: fprintf(ficgp,"\" t\"95%% CI\" w l lt 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"%%lf",subdirf2(fileresu,"VPL_"),k1-1,k1-1);
1.126 brouard 5018: for (i=1; i<= nlstate ; i ++) {
1.170 brouard 5019: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
5020: else fprintf(ficgp," %%*lf (%%*lf)");
1.126 brouard 5021: }
1.201 brouard 5022: fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l lt 2",subdirf2(fileresu,"P_"),k1-1,k1-1,2+4*(cpt-1));
5023: fprintf(ficgp,"\nset out \n");
5024: } /* k1 */
5025: } /* cpt */
1.126 brouard 5026: /*2 eme*/
1.153 brouard 5027: fprintf(ficgp,"\n# 2nd: Total life expectancy with CI: 't' files\n");
1.126 brouard 5028: for (k1=1; k1<= m ; k1 ++) {
1.201 brouard 5029: fprintf(ficgp,"\nset out \"%s_%d.svg\" \n",subdirf2(optionfilefiname,"E_"),k1);
5030: for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
5031: if(vpopbased==0)
5032: fprintf(ficgp,"set ylabel \"Years\" \nset ter svg size 640, 480\nplot [%.f:%.f] ",ageminpar,fage);
5033: else
5034: fprintf(ficgp,"\nreplot ");
5035: for (i=1; i<= nlstate+1 ; i ++) {
5036: k=2*i;
5037: 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);
5038: for (j=1; j<= nlstate+1 ; j ++) {
5039: if (j==i) fprintf(ficgp," %%lf (%%lf)");
5040: else fprintf(ficgp," %%*lf (%%*lf)");
5041: }
5042: if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l lt %d, \\\n",i);
5043: else fprintf(ficgp,"\" t\"LE in state (%d)\" w l lt %d, \\\n",i-1,i+1);
5044: 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);
5045: for (j=1; j<= nlstate+1 ; j ++) {
5046: if (j==i) fprintf(ficgp," %%lf (%%lf)");
5047: else fprintf(ficgp," %%*lf (%%*lf)");
5048: }
5049: fprintf(ficgp,"\" t\"\" w l lt 0,");
5050: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2==%d && $4!=0 ? $4+$5*2 : 1/0) \"%%lf %%lf %%lf",subdirf2(fileresu,"T_"),k1-1,k1-1,vpopbased);
5051: for (j=1; j<= nlstate+1 ; j ++) {
5052: if (j==i) fprintf(ficgp," %%lf (%%lf)");
5053: else fprintf(ficgp," %%*lf (%%*lf)");
5054: }
5055: if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l lt 0");
5056: else fprintf(ficgp,"\" t\"\" w l lt 0,\\\n");
5057: } /* state */
5058: } /* vpopbased */
5059: fprintf(ficgp,"\nset out;set out \"%s_%d.svg\"; replot; set out; \n",subdirf2(optionfilefiname,"E_"),k1); /* Buggy gnuplot */
5060: } /* k1 */
1.126 brouard 5061: /*3eme*/
5062:
5063: for (k1=1; k1<= m ; k1 ++) {
5064: for (cpt=1; cpt<= nlstate ; cpt ++) {
5065: /* k=2+nlstate*(2*cpt-2); */
5066: k=2+(nlstate+1)*(cpt-1);
1.201 brouard 5067: fprintf(ficgp,"\nset out \"%s_%d%d.svg\" \n",subdirf2(optionfilefiname,"EXP_"),cpt,k1);
1.199 brouard 5068: fprintf(ficgp,"set ter svg size 640, 480\n\
1.201 brouard 5069: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileresu,"E_"),k1-1,k1-1,k,cpt);
1.126 brouard 5070: /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
5071: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
5072: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
5073: fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
5074: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
5075: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
5076:
5077: */
5078: for (i=1; i< nlstate ; i ++) {
1.201 brouard 5079: 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 5080: /* 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);*/
5081:
5082: }
1.201 brouard 5083: 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 5084: }
5085: }
5086:
1.201 brouard 5087: /* Survival functions (period) from state i in state j by initial state i */
5088: for (k1=1; k1<= m ; k1 ++) { /* For each multivariate if any */
5089: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
5090: k=3;
5091: fprintf(ficgp,"\n#\n#\n# Survival functions in state j : 'lij' files, cov=%d state=%d",k1, cpt);
5092: fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"LIJ_"),cpt,k1);
5093: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability to be alive\" \n\
5094: set ter svg size 640, 480\n\
5095: unset log y\n\
5096: plot [%.f:%.f] ", ageminpar, agemaxpar);
5097: for (i=1; i<= nlstate ; i ++){
5098: if(i==1)
5099: fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
5100: else
5101: fprintf(ficgp,", '' ");
5102: l=(nlstate+ndeath)*(i-1)+1;
5103: fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
5104: for (j=2; j<= nlstate+ndeath ; j ++)
5105: fprintf(ficgp,"+$%d",k+l+j-1);
5106: fprintf(ficgp,")) t \"l(%d,%d)\" w l",i,cpt);
5107: } /* nlstate */
5108: fprintf(ficgp,"\nset out\n");
5109: } /* end cpt state*/
5110: } /* end covariate */
5111:
5112: /* Survival functions (period) from state i in state j by final state j */
1.202 brouard 5113: for (k1=1; k1<= m ; k1 ++) { /* For each covariate if any */
1.201 brouard 5114: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each inital state */
5115: k=3;
5116: 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);
5117: fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"LIJT_"),cpt,k1);
5118: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability to be alive\" \n\
5119: set ter svg size 640, 480\n\
5120: unset log y\n\
5121: plot [%.f:%.f] ", ageminpar, agemaxpar);
5122: for (j=1; j<= nlstate ; j ++){ /* Lived in state j */
5123: if(j==1)
5124: fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
5125: else
5126: fprintf(ficgp,", '' ");
5127: l=(nlstate+ndeath)*(cpt-1) +j;
5128: fprintf(ficgp," u (($1==%d && (floor($2)%%5 == 0)) ? ($3):1/0):($%d",k1,k+l);
5129: /* for (i=2; i<= nlstate+ndeath ; i ++) */
5130: /* fprintf(ficgp,"+$%d",k+l+i-1); */
5131: fprintf(ficgp,") t \"l(%d,%d)\" w l",cpt,j);
5132: } /* nlstate */
5133: fprintf(ficgp,", '' ");
5134: fprintf(ficgp," u (($1==%d && (floor($2)%%5 == 0)) ? ($3):1/0):(",k1);
5135: for (j=1; j<= nlstate ; j ++){ /* Lived in state j */
5136: l=(nlstate+ndeath)*(cpt-1) +j;
5137: if(j < nlstate)
5138: fprintf(ficgp,"$%d +",k+l);
5139: else
5140: fprintf(ficgp,"$%d) t\"l(%d,.)\" w l",k+l,cpt);
5141: }
5142: fprintf(ficgp,"\nset out\n");
5143: } /* end cpt state*/
5144: } /* end covariate */
5145:
1.202 brouard 5146: /* CV preval stable (period) for each covariate */
5147: for (k1=1; k1<= m ; k1 ++) { /* For each covariate if any */
1.153 brouard 5148: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
1.126 brouard 5149: k=3;
1.153 brouard 5150: fprintf(ficgp,"\n#\n#\n#CV preval stable (period): 'pij' files, cov=%d state=%d",k1, cpt);
1.201 brouard 5151: fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"P_"),cpt,k1);
1.126 brouard 5152: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
1.199 brouard 5153: set ter svg size 640, 480\n\
1.126 brouard 5154: unset log y\n\
1.153 brouard 5155: plot [%.f:%.f] ", ageminpar, agemaxpar);
5156: for (i=1; i<= nlstate ; i ++){
5157: if(i==1)
1.201 brouard 5158: fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
1.153 brouard 5159: else
5160: fprintf(ficgp,", '' ");
1.154 brouard 5161: l=(nlstate+ndeath)*(i-1)+1;
5162: fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
1.201 brouard 5163: for (j=2; j<= nlstate ; j ++)
5164: fprintf(ficgp,"+$%d",k+l+j-1);
1.153 brouard 5165: fprintf(ficgp,")) t \"prev(%d,%d)\" w l",i,cpt);
5166: } /* nlstate */
1.201 brouard 5167: fprintf(ficgp,"\nset out\n");
1.153 brouard 5168: } /* end cpt state*/
5169: } /* end covariate */
1.201 brouard 5170:
1.126 brouard 5171: /* proba elementaires */
1.187 brouard 5172: fprintf(ficgp,"\n##############\n#MLE estimated parameters\n#############\n");
1.126 brouard 5173: for(i=1,jk=1; i <=nlstate; i++){
1.187 brouard 5174: fprintf(ficgp,"# initial state %d\n",i);
1.126 brouard 5175: for(k=1; k <=(nlstate+ndeath); k++){
5176: if (k != i) {
1.187 brouard 5177: fprintf(ficgp,"# current state %d\n",k);
1.126 brouard 5178: for(j=1; j <=ncovmodel; j++){
1.187 brouard 5179: fprintf(ficgp,"p%d=%f; ",jk,p[jk]);
1.126 brouard 5180: jk++;
5181: }
1.187 brouard 5182: fprintf(ficgp,"\n");
1.126 brouard 5183: }
5184: }
5185: }
1.187 brouard 5186: fprintf(ficgp,"##############\n#\n");
5187:
1.145 brouard 5188: /*goto avoid;*/
1.200 brouard 5189: fprintf(ficgp,"\n##############\n#Graphics of probabilities or incidences\n#############\n");
1.187 brouard 5190: fprintf(ficgp,"# logi(p12/p11)=a12+b12*age+c12age*age+d12*V1+e12*V1*age\n");
5191: fprintf(ficgp,"# logi(p12/p11)=p1 +p2*age +p3*age*age+ p4*V1+ p5*V1*age\n");
5192: fprintf(ficgp,"# logi(p13/p11)=a13+b13*age+c13age*age+d13*V1+e13*V1*age\n");
5193: fprintf(ficgp,"# logi(p13/p11)=p6 +p7*age +p8*age*age+ p9*V1+ p10*V1*age\n");
5194: fprintf(ficgp,"# p12+p13+p14+p11=1=p11(1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n");
5195: fprintf(ficgp,"# +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age)+...)\n");
5196: fprintf(ficgp,"# p11=1/(1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n");
5197: fprintf(ficgp,"# +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age)+...)\n");
5198: fprintf(ficgp,"# p12=exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)/\n");
5199: fprintf(ficgp,"# (1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n");
5200: fprintf(ficgp,"# +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age))\n");
5201: fprintf(ficgp,"# +exp(a14+b14*age+c14age*age+d14*V1+e14*V1*age)+...)\n");
5202: fprintf(ficgp,"#\n");
1.201 brouard 5203: for(ng=1; ng<=3;ng++){ /* Number of graphics: first is logit, 2nd is probabilities, third is incidences per year*/
1.187 brouard 5204: fprintf(ficgp,"# ng=%d\n",ng);
5205: fprintf(ficgp,"# jk=1 to 2^%d=%d\n",cptcoveff,m);
1.126 brouard 5206: for(jk=1; jk <=m; jk++) {
1.187 brouard 5207: fprintf(ficgp,"# jk=%d\n",jk);
1.201 brouard 5208: fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" ",subdirf2(optionfilefiname,"PE_"),jk,ng);
5209: fprintf(ficgp,"\nset ter svg size 640, 480 ");
5210: if (ng==1){
5211: fprintf(ficgp,"\nset ylabel \"Value of the logit of the model\"\n"); /* exp(a12+b12*x) could be nice */
5212: fprintf(ficgp,"\nunset log y");
5213: }else if (ng==2){
5214: fprintf(ficgp,"\nset ylabel \"Probability\"\n");
5215: fprintf(ficgp,"\nset log y");
5216: }else if (ng==3){
1.126 brouard 5217: fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
1.201 brouard 5218: fprintf(ficgp,"\nset log y");
5219: }else
5220: fprintf(ficgp,"\nunset title ");
5221: fprintf(ficgp,"\nplot [%.f:%.f] ",ageminpar,agemaxpar);
1.126 brouard 5222: i=1;
5223: for(k2=1; k2<=nlstate; k2++) {
5224: k3=i;
5225: for(k=1; k<=(nlstate+ndeath); k++) {
5226: if (k != k2){
1.201 brouard 5227: switch( ng) {
5228: case 1:
1.187 brouard 5229: if(nagesqr==0)
1.201 brouard 5230: fprintf(ficgp," p%d+p%d*x",i,i+1);
1.187 brouard 5231: else /* nagesqr =1 */
1.201 brouard 5232: fprintf(ficgp," p%d+p%d*x+p%d*x*x",i,i+1,i+1+nagesqr);
5233: break;
5234: case 2: /* ng=2 */
1.187 brouard 5235: if(nagesqr==0)
5236: fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
5237: else /* nagesqr =1 */
1.201 brouard 5238: fprintf(ficgp," exp(p%d+p%d*x+p%d*x*x",i,i+1,i+1+nagesqr);
5239: break;
5240: case 3:
5241: if(nagesqr==0)
5242: fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
5243: else /* nagesqr =1 */
5244: fprintf(ficgp," %f*exp(p%d+p%d*x+p%d*x*x",YEARM/stepm,i,i+1,i+1+nagesqr);
5245: break;
5246: }
1.141 brouard 5247: ij=1;/* To be checked else nbcode[0][0] wrong */
1.187 brouard 5248: for(j=3; j <=ncovmodel-nagesqr; j++) {
1.197 brouard 5249: /* printf("Tage[%d]=%d, j=%d\n", ij, Tage[ij], j); */
5250: if(ij <=cptcovage) { /* Bug valgrind */
5251: if((j-2)==Tage[ij]) { /* Bug valgrind */
1.200 brouard 5252: fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);
5253: /* fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(jk,Tvar[j-2])]); */
1.197 brouard 5254: ij++;
5255: }
1.186 brouard 5256: }
5257: else
1.198 brouard 5258: fprintf(ficgp,"+p%d*%d",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);
1.126 brouard 5259: }
1.201 brouard 5260: if(ng != 1){
5261: fprintf(ficgp,")/(1");
1.126 brouard 5262:
1.201 brouard 5263: for(k1=1; k1 <=nlstate; k1++){
5264: if(nagesqr==0)
5265: fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
5266: else /* nagesqr =1 */
5267: 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);
5268:
5269: ij=1;
5270: for(j=3; j <=ncovmodel-nagesqr; j++){
5271: if(ij <=cptcovage) { /* Bug valgrind */
5272: if((j-2)==Tage[ij]) { /* Bug valgrind */
5273: fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);
5274: /* fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(jk,Tvar[j-2])]); */
5275: ij++;
5276: }
1.197 brouard 5277: }
1.201 brouard 5278: else
5279: fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);
1.186 brouard 5280: }
1.201 brouard 5281: fprintf(ficgp,")");
1.126 brouard 5282: }
5283: fprintf(ficgp,")");
1.201 brouard 5284: if(ng ==2)
5285: fprintf(ficgp," t \"p%d%d\" ", k2,k);
5286: else /* ng= 3 */
5287: fprintf(ficgp," t \"i%d%d\" ", k2,k);
5288: }else{ /* end ng <> 1 */
5289: fprintf(ficgp," t \"logit(p%d%d)\" ", k2,k);
1.126 brouard 5290: }
5291: if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
5292: i=i+ncovmodel;
5293: }
5294: } /* end k */
5295: } /* end k2 */
1.201 brouard 5296: fprintf(ficgp,"\n set out\n");
1.126 brouard 5297: } /* end jk */
5298: } /* end ng */
1.164 brouard 5299: /* avoid: */
1.126 brouard 5300: fflush(ficgp);
5301: } /* end gnuplot */
5302:
5303:
5304: /*************** Moving average **************/
5305: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
5306:
5307: int i, cpt, cptcod;
5308: int modcovmax =1;
5309: int mobilavrange, mob;
5310: double age;
5311:
5312: modcovmax=2*cptcoveff;/* Max number of modalities. We suppose
5313: a covariate has 2 modalities */
5314: if (cptcovn<1) modcovmax=1; /* At least 1 pass */
5315:
5316: if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
5317: if(mobilav==1) mobilavrange=5; /* default */
5318: else mobilavrange=mobilav;
5319: for (age=bage; age<=fage; age++)
5320: for (i=1; i<=nlstate;i++)
5321: for (cptcod=1;cptcod<=modcovmax;cptcod++)
5322: mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
5323: /* We keep the original values on the extreme ages bage, fage and for
5324: fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
5325: we use a 5 terms etc. until the borders are no more concerned.
5326: */
5327: for (mob=3;mob <=mobilavrange;mob=mob+2){
5328: for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
5329: for (i=1; i<=nlstate;i++){
5330: for (cptcod=1;cptcod<=modcovmax;cptcod++){
5331: mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
5332: for (cpt=1;cpt<=(mob-1)/2;cpt++){
5333: mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
5334: mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
5335: }
5336: mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
5337: }
5338: }
5339: }/* end age */
5340: }/* end mob */
5341: }else return -1;
5342: return 0;
5343: }/* End movingaverage */
5344:
5345:
5346: /************** Forecasting ******************/
1.169 brouard 5347: 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 5348: /* proj1, year, month, day of starting projection
5349: agemin, agemax range of age
5350: dateprev1 dateprev2 range of dates during which prevalence is computed
5351: anproj2 year of en of projection (same day and month as proj1).
5352: */
1.164 brouard 5353: int yearp, stepsize, hstepm, nhstepm, j, k, cptcod, i, h, i1;
1.126 brouard 5354: double agec; /* generic age */
5355: double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
5356: double *popeffectif,*popcount;
5357: double ***p3mat;
5358: double ***mobaverage;
5359: char fileresf[FILENAMELENGTH];
5360:
5361: agelim=AGESUP;
5362: prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
5363:
1.201 brouard 5364: strcpy(fileresf,"F_");
5365: strcat(fileresf,fileresu);
1.126 brouard 5366: if((ficresf=fopen(fileresf,"w"))==NULL) {
5367: printf("Problem with forecast resultfile: %s\n", fileresf);
5368: fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
5369: }
5370: printf("Computing forecasting: result on file '%s' \n", fileresf);
5371: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
5372:
5373: if (cptcoveff==0) ncodemax[cptcoveff]=1;
5374:
5375: if (mobilav!=0) {
5376: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
5377: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
5378: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
5379: printf(" Error in movingaverage mobilav=%d\n",mobilav);
5380: }
5381: }
5382:
5383: stepsize=(int) (stepm+YEARM-1)/YEARM;
5384: if (stepm<=12) stepsize=1;
5385: if(estepm < stepm){
5386: printf ("Problem %d lower than %d\n",estepm, stepm);
5387: }
5388: else hstepm=estepm;
5389:
5390: hstepm=hstepm/stepm;
5391: yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp and
5392: fractional in yp1 */
5393: anprojmean=yp;
5394: yp2=modf((yp1*12),&yp);
5395: mprojmean=yp;
5396: yp1=modf((yp2*30.5),&yp);
5397: jprojmean=yp;
5398: if(jprojmean==0) jprojmean=1;
5399: if(mprojmean==0) jprojmean=1;
5400:
5401: i1=cptcoveff;
5402: if (cptcovn < 1){i1=1;}
5403:
5404: fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);
5405:
5406: fprintf(ficresf,"#****** Routine prevforecast **\n");
5407:
5408: /* if (h==(int)(YEARM*yearp)){ */
5409: for(cptcov=1, k=0;cptcov<=i1;cptcov++){
5410: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
5411: k=k+1;
5412: fprintf(ficresf,"\n#******");
5413: for(j=1;j<=cptcoveff;j++) {
1.198 brouard 5414: 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 5415: }
5416: fprintf(ficresf,"******\n");
5417: fprintf(ficresf,"# Covariate valuofcovar yearproj age");
5418: for(j=1; j<=nlstate+ndeath;j++){
5419: for(i=1; i<=nlstate;i++)
5420: fprintf(ficresf," p%d%d",i,j);
5421: fprintf(ficresf," p.%d",j);
5422: }
5423: for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {
5424: fprintf(ficresf,"\n");
5425: fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);
5426:
5427: for (agec=fage; agec>=(ageminpar-1); agec--){
5428: nhstepm=(int) rint((agelim-agec)*YEARM/stepm);
5429: nhstepm = nhstepm/hstepm;
5430: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5431: oldm=oldms;savm=savms;
5432: hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);
5433:
5434: for (h=0; h<=nhstepm; h++){
5435: if (h*hstepm/YEARM*stepm ==yearp) {
5436: fprintf(ficresf,"\n");
5437: for(j=1;j<=cptcoveff;j++)
1.198 brouard 5438: fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.126 brouard 5439: fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
5440: }
5441: for(j=1; j<=nlstate+ndeath;j++) {
5442: ppij=0.;
5443: for(i=1; i<=nlstate;i++) {
5444: if (mobilav==1)
5445: ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
5446: else {
5447: ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
5448: }
5449: if (h*hstepm/YEARM*stepm== yearp) {
5450: fprintf(ficresf," %.3f", p3mat[i][j][h]);
5451: }
5452: } /* end i */
5453: if (h*hstepm/YEARM*stepm==yearp) {
5454: fprintf(ficresf," %.3f", ppij);
5455: }
5456: }/* end j */
5457: } /* end h */
5458: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5459: } /* end agec */
5460: } /* end yearp */
5461: } /* end cptcod */
5462: } /* end cptcov */
5463:
5464: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
5465:
5466: fclose(ficresf);
5467: }
5468:
5469: /************** Forecasting *****not tested NB*************/
1.169 brouard 5470: 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 5471:
5472: int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
5473: int *popage;
5474: double calagedatem, agelim, kk1, kk2;
5475: double *popeffectif,*popcount;
5476: double ***p3mat,***tabpop,***tabpopprev;
5477: double ***mobaverage;
5478: char filerespop[FILENAMELENGTH];
5479:
5480: tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
5481: tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
5482: agelim=AGESUP;
5483: calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
5484:
5485: prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
5486:
5487:
1.201 brouard 5488: strcpy(filerespop,"POP_");
5489: strcat(filerespop,fileresu);
1.126 brouard 5490: if((ficrespop=fopen(filerespop,"w"))==NULL) {
5491: printf("Problem with forecast resultfile: %s\n", filerespop);
5492: fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
5493: }
5494: printf("Computing forecasting: result on file '%s' \n", filerespop);
5495: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
5496:
5497: if (cptcoveff==0) ncodemax[cptcoveff]=1;
5498:
5499: if (mobilav!=0) {
5500: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
5501: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
5502: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
5503: printf(" Error in movingaverage mobilav=%d\n",mobilav);
5504: }
5505: }
5506:
5507: stepsize=(int) (stepm+YEARM-1)/YEARM;
5508: if (stepm<=12) stepsize=1;
5509:
5510: agelim=AGESUP;
5511:
5512: hstepm=1;
5513: hstepm=hstepm/stepm;
5514:
5515: if (popforecast==1) {
5516: if((ficpop=fopen(popfile,"r"))==NULL) {
5517: printf("Problem with population file : %s\n",popfile);exit(0);
5518: fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
5519: }
5520: popage=ivector(0,AGESUP);
5521: popeffectif=vector(0,AGESUP);
5522: popcount=vector(0,AGESUP);
5523:
5524: i=1;
5525: while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
5526:
5527: imx=i;
5528: for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
5529: }
5530:
5531: for(cptcov=1,k=0;cptcov<=i2;cptcov++){
5532: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
5533: k=k+1;
5534: fprintf(ficrespop,"\n#******");
5535: for(j=1;j<=cptcoveff;j++) {
1.198 brouard 5536: fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.126 brouard 5537: }
5538: fprintf(ficrespop,"******\n");
5539: fprintf(ficrespop,"# Age");
5540: for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
5541: if (popforecast==1) fprintf(ficrespop," [Population]");
5542:
5543: for (cpt=0; cpt<=0;cpt++) {
5544: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
5545:
5546: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
5547: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
5548: nhstepm = nhstepm/hstepm;
5549:
5550: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5551: oldm=oldms;savm=savms;
5552: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
5553:
5554: for (h=0; h<=nhstepm; h++){
5555: if (h==(int) (calagedatem+YEARM*cpt)) {
5556: fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
5557: }
5558: for(j=1; j<=nlstate+ndeath;j++) {
5559: kk1=0.;kk2=0;
5560: for(i=1; i<=nlstate;i++) {
5561: if (mobilav==1)
5562: kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
5563: else {
5564: kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
5565: }
5566: }
5567: if (h==(int)(calagedatem+12*cpt)){
5568: tabpop[(int)(agedeb)][j][cptcod]=kk1;
5569: /*fprintf(ficrespop," %.3f", kk1);
5570: if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
5571: }
5572: }
5573: for(i=1; i<=nlstate;i++){
5574: kk1=0.;
5575: for(j=1; j<=nlstate;j++){
5576: kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];
5577: }
5578: tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
5579: }
5580:
5581: if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++)
5582: fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
5583: }
5584: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5585: }
5586: }
5587:
5588: /******/
5589:
5590: for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {
5591: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
5592: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
5593: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
5594: nhstepm = nhstepm/hstepm;
5595:
5596: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5597: oldm=oldms;savm=savms;
5598: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
5599: for (h=0; h<=nhstepm; h++){
5600: if (h==(int) (calagedatem+YEARM*cpt)) {
5601: fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
5602: }
5603: for(j=1; j<=nlstate+ndeath;j++) {
5604: kk1=0.;kk2=0;
5605: for(i=1; i<=nlstate;i++) {
5606: kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];
5607: }
5608: if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);
5609: }
5610: }
5611: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5612: }
5613: }
5614: }
5615: }
5616:
5617: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
5618:
5619: if (popforecast==1) {
5620: free_ivector(popage,0,AGESUP);
5621: free_vector(popeffectif,0,AGESUP);
5622: free_vector(popcount,0,AGESUP);
5623: }
5624: free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
5625: free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
5626: fclose(ficrespop);
5627: } /* End of popforecast */
5628:
5629: int fileappend(FILE *fichier, char *optionfich)
5630: {
5631: if((fichier=fopen(optionfich,"a"))==NULL) {
5632: printf("Problem with file: %s\n", optionfich);
5633: fprintf(ficlog,"Problem with file: %s\n", optionfich);
5634: return (0);
5635: }
5636: fflush(fichier);
5637: return (1);
5638: }
5639:
5640:
5641: /**************** function prwizard **********************/
5642: void prwizard(int ncovmodel, int nlstate, int ndeath, char model[], FILE *ficparo)
5643: {
5644:
5645: /* Wizard to print covariance matrix template */
5646:
1.164 brouard 5647: char ca[32], cb[32];
5648: int i,j, k, li, lj, lk, ll, jj, npar, itimes;
1.126 brouard 5649: int numlinepar;
5650:
5651: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
5652: fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
5653: for(i=1; i <=nlstate; i++){
5654: jj=0;
5655: for(j=1; j <=nlstate+ndeath; j++){
5656: if(j==i) continue;
5657: jj++;
5658: /*ca[0]= k+'a'-1;ca[1]='\0';*/
5659: printf("%1d%1d",i,j);
5660: fprintf(ficparo,"%1d%1d",i,j);
5661: for(k=1; k<=ncovmodel;k++){
5662: /* printf(" %lf",param[i][j][k]); */
5663: /* fprintf(ficparo," %lf",param[i][j][k]); */
5664: printf(" 0.");
5665: fprintf(ficparo," 0.");
5666: }
5667: printf("\n");
5668: fprintf(ficparo,"\n");
5669: }
5670: }
5671: printf("# Scales (for hessian or gradient estimation)\n");
5672: fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
5673: npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
5674: for(i=1; i <=nlstate; i++){
5675: jj=0;
5676: for(j=1; j <=nlstate+ndeath; j++){
5677: if(j==i) continue;
5678: jj++;
5679: fprintf(ficparo,"%1d%1d",i,j);
5680: printf("%1d%1d",i,j);
5681: fflush(stdout);
5682: for(k=1; k<=ncovmodel;k++){
5683: /* printf(" %le",delti3[i][j][k]); */
5684: /* fprintf(ficparo," %le",delti3[i][j][k]); */
5685: printf(" 0.");
5686: fprintf(ficparo," 0.");
5687: }
5688: numlinepar++;
5689: printf("\n");
5690: fprintf(ficparo,"\n");
5691: }
5692: }
5693: printf("# Covariance matrix\n");
5694: /* # 121 Var(a12)\n\ */
5695: /* # 122 Cov(b12,a12) Var(b12)\n\ */
5696: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
5697: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
5698: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
5699: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
5700: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
5701: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
5702: fflush(stdout);
5703: fprintf(ficparo,"# Covariance matrix\n");
5704: /* # 121 Var(a12)\n\ */
5705: /* # 122 Cov(b12,a12) Var(b12)\n\ */
5706: /* # ...\n\ */
5707: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
5708:
5709: for(itimes=1;itimes<=2;itimes++){
5710: jj=0;
5711: for(i=1; i <=nlstate; i++){
5712: for(j=1; j <=nlstate+ndeath; j++){
5713: if(j==i) continue;
5714: for(k=1; k<=ncovmodel;k++){
5715: jj++;
5716: ca[0]= k+'a'-1;ca[1]='\0';
5717: if(itimes==1){
5718: printf("#%1d%1d%d",i,j,k);
5719: fprintf(ficparo,"#%1d%1d%d",i,j,k);
5720: }else{
5721: printf("%1d%1d%d",i,j,k);
5722: fprintf(ficparo,"%1d%1d%d",i,j,k);
5723: /* printf(" %.5le",matcov[i][j]); */
5724: }
5725: ll=0;
5726: for(li=1;li <=nlstate; li++){
5727: for(lj=1;lj <=nlstate+ndeath; lj++){
5728: if(lj==li) continue;
5729: for(lk=1;lk<=ncovmodel;lk++){
5730: ll++;
5731: if(ll<=jj){
5732: cb[0]= lk +'a'-1;cb[1]='\0';
5733: if(ll<jj){
5734: if(itimes==1){
5735: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
5736: fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
5737: }else{
5738: printf(" 0.");
5739: fprintf(ficparo," 0.");
5740: }
5741: }else{
5742: if(itimes==1){
5743: printf(" Var(%s%1d%1d)",ca,i,j);
5744: fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
5745: }else{
5746: printf(" 0.");
5747: fprintf(ficparo," 0.");
5748: }
5749: }
5750: }
5751: } /* end lk */
5752: } /* end lj */
5753: } /* end li */
5754: printf("\n");
5755: fprintf(ficparo,"\n");
5756: numlinepar++;
5757: } /* end k*/
5758: } /*end j */
5759: } /* end i */
5760: } /* end itimes */
5761:
5762: } /* end of prwizard */
5763: /******************* Gompertz Likelihood ******************************/
5764: double gompertz(double x[])
5765: {
5766: double A,B,L=0.0,sump=0.,num=0.;
5767: int i,n=0; /* n is the size of the sample */
5768:
5769: for (i=0;i<=imx-1 ; i++) {
5770: sump=sump+weight[i];
5771: /* sump=sump+1;*/
5772: num=num+1;
5773: }
5774:
5775:
5776: /* for (i=0; i<=imx; i++)
5777: 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]);*/
5778:
5779: for (i=1;i<=imx ; i++)
5780: {
5781: if (cens[i] == 1 && wav[i]>1)
5782: A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
5783:
5784: if (cens[i] == 0 && wav[i]>1)
5785: A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
5786: +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);
5787:
5788: /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
5789: if (wav[i] > 1 ) { /* ??? */
5790: L=L+A*weight[i];
5791: /* 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]);*/
5792: }
5793: }
5794:
5795: /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
5796:
5797: return -2*L*num/sump;
5798: }
5799:
1.136 brouard 5800: #ifdef GSL
5801: /******************* Gompertz_f Likelihood ******************************/
5802: double gompertz_f(const gsl_vector *v, void *params)
5803: {
5804: double A,B,LL=0.0,sump=0.,num=0.;
5805: double *x= (double *) v->data;
5806: int i,n=0; /* n is the size of the sample */
5807:
5808: for (i=0;i<=imx-1 ; i++) {
5809: sump=sump+weight[i];
5810: /* sump=sump+1;*/
5811: num=num+1;
5812: }
5813:
5814:
5815: /* for (i=0; i<=imx; i++)
5816: 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]);*/
5817: printf("x[0]=%lf x[1]=%lf\n",x[0],x[1]);
5818: for (i=1;i<=imx ; i++)
5819: {
5820: if (cens[i] == 1 && wav[i]>1)
5821: A=-x[0]/(x[1])*(exp(x[1]*(agecens[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)));
5822:
5823: if (cens[i] == 0 && wav[i]>1)
5824: A=-x[0]/(x[1])*(exp(x[1]*(agedc[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)))
5825: +log(x[0]/YEARM)+x[1]*(agedc[i]-agegomp)+log(YEARM);
5826:
5827: /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
5828: if (wav[i] > 1 ) { /* ??? */
5829: LL=LL+A*weight[i];
5830: /* 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]);*/
5831: }
5832: }
5833:
5834: /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
5835: printf("x[0]=%lf x[1]=%lf -2*LL*num/sump=%lf\n",x[0],x[1],-2*LL*num/sump);
5836:
5837: return -2*LL*num/sump;
5838: }
5839: #endif
5840:
1.126 brouard 5841: /******************* Printing html file ***********/
1.201 brouard 5842: void printinghtmlmort(char fileresu[], char title[], char datafile[], int firstpass, \
1.126 brouard 5843: int lastpass, int stepm, int weightopt, char model[],\
5844: int imx, double p[],double **matcov,double agemortsup){
5845: int i,k;
5846:
5847: fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
5848: fprintf(fichtm," mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
5849: for (i=1;i<=2;i++)
5850: 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 5851: fprintf(fichtm,"<br><br><img src=\"graphmort.svg\">");
1.126 brouard 5852: fprintf(fichtm,"</ul>");
5853:
5854: fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
5855:
5856: 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>");
5857:
5858: for (k=agegomp;k<(agemortsup-2);k++)
5859: 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]);
5860:
5861:
5862: fflush(fichtm);
5863: }
5864:
5865: /******************* Gnuplot file **************/
1.201 brouard 5866: void printinggnuplotmort(char fileresu[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
1.126 brouard 5867:
5868: char dirfileres[132],optfileres[132];
1.164 brouard 5869:
1.126 brouard 5870: int ng;
5871:
5872:
5873: /*#ifdef windows */
5874: fprintf(ficgp,"cd \"%s\" \n",pathc);
5875: /*#endif */
5876:
5877:
5878: strcpy(dirfileres,optionfilefiname);
5879: strcpy(optfileres,"vpl");
1.199 brouard 5880: fprintf(ficgp,"set out \"graphmort.svg\"\n ");
1.126 brouard 5881: fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n ");
1.199 brouard 5882: fprintf(ficgp, "set ter svg size 640, 480\n set log y\n");
1.145 brouard 5883: /* fprintf(ficgp, "set size 0.65,0.65\n"); */
1.126 brouard 5884: fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
5885:
5886: }
5887:
1.136 brouard 5888: int readdata(char datafile[], int firstobs, int lastobs, int *imax)
5889: {
1.126 brouard 5890:
1.136 brouard 5891: /*-------- data file ----------*/
5892: FILE *fic;
5893: char dummy[]=" ";
1.164 brouard 5894: int i=0, j=0, n=0;
1.136 brouard 5895: int linei, month, year,iout;
5896: char line[MAXLINE], linetmp[MAXLINE];
1.164 brouard 5897: char stra[MAXLINE], strb[MAXLINE];
1.136 brouard 5898: char *stratrunc;
5899: int lstra;
1.126 brouard 5900:
5901:
1.136 brouard 5902: if((fic=fopen(datafile,"r"))==NULL) {
1.195 brouard 5903: printf("Problem while opening datafile: %s\n", datafile);fflush(stdout);
5904: fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);fflush(ficlog);return 1;
1.136 brouard 5905: }
1.126 brouard 5906:
1.136 brouard 5907: i=1;
5908: linei=0;
5909: while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
5910: linei=linei+1;
5911: for(j=strlen(line); j>=0;j--){ /* Untabifies line */
5912: if(line[j] == '\t')
5913: line[j] = ' ';
5914: }
5915: for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){
5916: ;
5917: };
5918: line[j+1]=0; /* Trims blanks at end of line */
5919: if(line[0]=='#'){
5920: fprintf(ficlog,"Comment line\n%s\n",line);
5921: printf("Comment line\n%s\n",line);
5922: continue;
5923: }
5924: trimbb(linetmp,line); /* Trims multiple blanks in line */
1.164 brouard 5925: strcpy(line, linetmp);
1.136 brouard 5926:
1.126 brouard 5927:
1.136 brouard 5928: for (j=maxwav;j>=1;j--){
1.137 brouard 5929: cutv(stra, strb, line, ' ');
1.136 brouard 5930: if(strb[0]=='.') { /* Missing status */
5931: lval=-1;
5932: }else{
5933: errno=0;
5934: lval=strtol(strb,&endptr,10);
5935: /* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
5936: if( strb[0]=='\0' || (*endptr != '\0')){
1.141 brouard 5937: 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);
5938: 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 5939: return 1;
5940: }
5941: }
5942: s[j][i]=lval;
5943:
5944: strcpy(line,stra);
5945: cutv(stra, strb,line,' ');
1.169 brouard 5946: if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
1.136 brouard 5947: }
1.169 brouard 5948: else if( (iout=sscanf(strb,"%s.",dummy)) != 0){
1.136 brouard 5949: month=99;
5950: year=9999;
5951: }else{
1.141 brouard 5952: 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);
5953: 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 5954: return 1;
5955: }
5956: anint[j][i]= (double) year;
5957: mint[j][i]= (double)month;
5958: strcpy(line,stra);
5959: } /* ENd Waves */
5960:
5961: cutv(stra, strb,line,' ');
1.169 brouard 5962: if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
1.136 brouard 5963: }
1.169 brouard 5964: else if( (iout=sscanf(strb,"%s.",dummy)) != 0){
1.136 brouard 5965: month=99;
5966: year=9999;
5967: }else{
1.141 brouard 5968: 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);
5969: 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 5970: return 1;
5971: }
5972: andc[i]=(double) year;
5973: moisdc[i]=(double) month;
5974: strcpy(line,stra);
5975:
5976: cutv(stra, strb,line,' ');
1.169 brouard 5977: if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
1.136 brouard 5978: }
1.169 brouard 5979: else if( (iout=sscanf(strb,"%s.", dummy)) != 0){
1.136 brouard 5980: month=99;
5981: year=9999;
5982: }else{
1.141 brouard 5983: 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);
5984: 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 5985: return 1;
5986: }
5987: if (year==9999) {
1.141 brouard 5988: 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);
5989: 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 5990: return 1;
1.126 brouard 5991:
1.136 brouard 5992: }
5993: annais[i]=(double)(year);
5994: moisnais[i]=(double)(month);
5995: strcpy(line,stra);
5996:
5997: cutv(stra, strb,line,' ');
5998: errno=0;
5999: dval=strtod(strb,&endptr);
6000: if( strb[0]=='\0' || (*endptr != '\0')){
1.141 brouard 6001: printf("Error reading data around '%f' at line number %d, \"%s\" for individual %d\nShould be a weight. Exiting.\n",dval, i,line,linei);
6002: 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 6003: fflush(ficlog);
6004: return 1;
6005: }
6006: weight[i]=dval;
6007: strcpy(line,stra);
6008:
6009: for (j=ncovcol;j>=1;j--){
6010: cutv(stra, strb,line,' ');
6011: if(strb[0]=='.') { /* Missing status */
6012: lval=-1;
6013: }else{
6014: errno=0;
6015: lval=strtol(strb,&endptr,10);
6016: if( strb[0]=='\0' || (*endptr != '\0')){
1.141 brouard 6017: 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);
6018: 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 6019: return 1;
6020: }
6021: }
6022: if(lval <-1 || lval >1){
1.141 brouard 6023: printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
1.136 brouard 6024: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
6025: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
6026: For example, for multinomial values like 1, 2 and 3,\n \
6027: build V1=0 V2=0 for the reference value (1),\n \
6028: V1=1 V2=0 for (2) \n \
6029: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
6030: output of IMaCh is often meaningless.\n \
6031: Exiting.\n",lval,linei, i,line,j);
1.141 brouard 6032: fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
1.136 brouard 6033: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
6034: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
6035: For example, for multinomial values like 1, 2 and 3,\n \
6036: build V1=0 V2=0 for the reference value (1),\n \
6037: V1=1 V2=0 for (2) \n \
6038: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
6039: output of IMaCh is often meaningless.\n \
6040: Exiting.\n",lval,linei, i,line,j);fflush(ficlog);
6041: return 1;
6042: }
6043: covar[j][i]=(double)(lval);
6044: strcpy(line,stra);
6045: }
6046: lstra=strlen(stra);
6047:
6048: if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
6049: stratrunc = &(stra[lstra-9]);
6050: num[i]=atol(stratrunc);
6051: }
6052: else
6053: num[i]=atol(stra);
6054: /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
6055: 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;}*/
6056:
6057: i=i+1;
6058: } /* End loop reading data */
1.126 brouard 6059:
1.136 brouard 6060: *imax=i-1; /* Number of individuals */
6061: fclose(fic);
6062:
6063: return (0);
1.164 brouard 6064: /* endread: */
1.136 brouard 6065: printf("Exiting readdata: ");
6066: fclose(fic);
6067: return (1);
1.126 brouard 6068:
6069:
6070:
1.136 brouard 6071: }
1.145 brouard 6072: void removespace(char *str) {
6073: char *p1 = str, *p2 = str;
6074: do
6075: while (*p2 == ' ')
6076: p2++;
1.169 brouard 6077: while (*p1++ == *p2++);
1.145 brouard 6078: }
6079:
6080: int decodemodel ( char model[], int lastobs) /**< This routine decode the model and returns:
1.187 brouard 6081: * Model V1+V2+V3+V8+V7*V8+V5*V6+V8*age+V3*age+age*age
6082: * - nagesqr = 1 if age*age in the model, otherwise 0.
6083: * - cptcovt total number of covariates of the model nbocc(+)+1 = 8 excepting constant and age and age*age
6084: * - cptcovn or number of covariates k of the models excluding age*products =6 and age*age
1.145 brouard 6085: * - cptcovage number of covariates with age*products =2
6086: * - cptcovs number of simple covariates
6087: * - 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
6088: * which is a new column after the 9 (ncovcol) variables.
6089: * - if k is a product Vn*Vm covar[k][i] is filled with correct values for each individual
6090: * - Tprod[l] gives the kth covariates of the product Vn*Vm l=1 to cptcovprod-cptcovage
6091: * Tprod[1]@2 {5, 6}: position of first product V7*V8 is 5, and second V5*V6 is 6.
6092: * - Tvard[k] p Tvard[1][1]@4 {7, 8, 5, 6} for V7*V8 and V5*V6 .
6093: */
1.136 brouard 6094: {
1.145 brouard 6095: int i, j, k, ks;
1.164 brouard 6096: int j1, k1, k2;
1.136 brouard 6097: char modelsav[80];
1.145 brouard 6098: char stra[80], strb[80], strc[80], strd[80],stre[80];
1.187 brouard 6099: char *strpt;
1.136 brouard 6100:
1.145 brouard 6101: /*removespace(model);*/
1.136 brouard 6102: if (strlen(model) >1){ /* If there is at least 1 covariate */
1.145 brouard 6103: j=0, j1=0, k1=0, k2=-1, ks=0, cptcovn=0;
1.137 brouard 6104: if (strstr(model,"AGE") !=0){
1.192 brouard 6105: printf("Error. AGE must be in lower case 'age' model=1+age+%s. ",model);
6106: fprintf(ficlog,"Error. AGE must be in lower case model=1+age+%s. ",model);fflush(ficlog);
1.136 brouard 6107: return 1;
6108: }
1.141 brouard 6109: if (strstr(model,"v") !=0){
6110: printf("Error. 'v' must be in upper case 'V' model=%s ",model);
6111: fprintf(ficlog,"Error. 'v' must be in upper case model=%s ",model);fflush(ficlog);
6112: return 1;
6113: }
1.187 brouard 6114: strcpy(modelsav,model);
6115: if ((strpt=strstr(model,"age*age")) !=0){
6116: printf(" strpt=%s, model=%s\n",strpt, model);
6117: if(strpt != model){
6118: printf("Error in model: 'model=%s'; 'age*age' should in first place before other covariates\n \
1.192 brouard 6119: 'model=1+age+age*age+V1.' or 'model=1+age+age*age+V1+V1*age.', please swap as well as \n \
1.187 brouard 6120: corresponding column of parameters.\n",model);
6121: fprintf(ficlog,"Error in model: 'model=%s'; 'age*age' should in first place before other covariates\n \
1.192 brouard 6122: 'model=1+age+age*age+V1.' or 'model=1+age+age*age+V1+V1*age.', please swap as well as \n \
1.187 brouard 6123: corresponding column of parameters.\n",model); fflush(ficlog);
6124: return 1;
6125: }
6126:
6127: nagesqr=1;
6128: if (strstr(model,"+age*age") !=0)
6129: substrchaine(modelsav, model, "+age*age");
6130: else if (strstr(model,"age*age+") !=0)
6131: substrchaine(modelsav, model, "age*age+");
6132: else
6133: substrchaine(modelsav, model, "age*age");
6134: }else
6135: nagesqr=0;
6136: if (strlen(modelsav) >1){
6137: j=nbocc(modelsav,'+'); /**< j=Number of '+' */
6138: j1=nbocc(modelsav,'*'); /**< j1=Number of '*' */
6139: cptcovs=j+1-j1; /**< Number of simple covariates V1+V1*age+V3 +V3*V4+age*age=> V1 + V3 =2 */
6140: cptcovt= j+1; /* Number of total covariates in the model, not including
6141: * cst, age and age*age
6142: * V1+V1*age+ V3 + V3*V4+age*age=> 4*/
6143: /* including age products which are counted in cptcovage.
6144: * but the covariates which are products must be treated
6145: * separately: ncovn=4- 2=2 (V1+V3). */
6146: cptcovprod=j1; /**< Number of products V1*V2 +v3*age = 2 */
6147: cptcovprodnoage=0; /**< Number of covariate products without age: V3*V4 =1 */
6148:
6149:
6150: /* Design
6151: * V1 V2 V3 V4 V5 V6 V7 V8 V9 Weight
6152: * < ncovcol=8 >
6153: * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8
6154: * k= 1 2 3 4 5 6 7 8
6155: * cptcovn number of covariates (not including constant and age ) = # of + plus 1 = 7+1=8
6156: * covar[k,i], value of kth covariate if not including age for individual i:
6157: * covar[1][i]= (V2), covar[4][i]=(V3), covar[8][i]=(V8)
6158: * Tvar[k] # of the kth covariate: Tvar[1]=2 Tvar[4]=3 Tvar[8]=8
6159: * if multiplied by age: V3*age Tvar[3=V3*age]=3 (V3) Tvar[7]=8 and
6160: * Tage[++cptcovage]=k
6161: * if products, new covar are created after ncovcol with k1
6162: * Tvar[k]=ncovcol+k1; # of the kth covariate product: Tvar[5]=ncovcol+1=10 Tvar[6]=ncovcol+1=11
6163: * Tprod[k1]=k; Tprod[1]=5 Tprod[2]= 6; gives the position of the k1th product
6164: * 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
6165: * Tvar[cptcovn+k2]=Tvard[k1][1];Tvar[cptcovn+k2+1]=Tvard[k1][2];
6166: * Tvar[8+1]=5;Tvar[8+2]=6;Tvar[8+3]=7;Tvar[8+4]=8 inverted
6167: * V1 V2 V3 V4 V5 V6 V7 V8 V9 V10 V11
6168: * < ncovcol=8 >
6169: * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8 d1 d1 d2 d2
6170: * k= 1 2 3 4 5 6 7 8 9 10 11 12
6171: * Tvar[k]= 2 1 3 3 10 11 8 8 5 6 7 8
6172: * p Tvar[1]@12={2, 1, 3, 3, 11, 10, 8, 8, 7, 8, 5, 6}
6173: * p Tprod[1]@2={ 6, 5}
6174: *p Tvard[1][1]@4= {7, 8, 5, 6}
6175: * covar[k][i]= V2 V1 ? V3 V5*V6? V7*V8? ? V8
6176: * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
6177: *How to reorganize?
6178: * Model V1 + V2 + V3 + V8 + V5*V6 + V7*V8 + V3*age + V8*age
6179: * Tvars {2, 1, 3, 3, 11, 10, 8, 8, 7, 8, 5, 6}
6180: * {2, 1, 4, 8, 5, 6, 3, 7}
6181: * Struct []
6182: */
1.145 brouard 6183:
1.187 brouard 6184: /* This loop fills the array Tvar from the string 'model'.*/
6185: /* j is the number of + signs in the model V1+V2+V3 j=2 i=3 to 1 */
6186: /* modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4 */
6187: /* k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tage[cptcovage=1]=4 */
6188: /* k=3 V4 Tvar[k=3]= 4 (from V4) */
6189: /* k=2 V1 Tvar[k=2]= 1 (from V1) */
6190: /* k=1 Tvar[1]=2 (from V2) */
6191: /* k=5 Tvar[5] */
6192: /* for (k=1; k<=cptcovn;k++) { */
1.198 brouard 6193: /* cov[2+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; */
1.187 brouard 6194: /* } */
1.198 brouard 6195: /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,Tvar[Tage[k])]]*cov[2]; */
1.187 brouard 6196: /*
6197: * Treating invertedly V2+V1+V3*age+V2*V4 is as if written V2*V4 +V3*age + V1 + V2 */
6198: for(k=cptcovt; k>=1;k--) /**< Number of covariates */
1.145 brouard 6199: Tvar[k]=0;
1.187 brouard 6200: cptcovage=0;
6201: for(k=1; k<=cptcovt;k++){ /* Loop on total covariates of the model */
6202: cutl(stra,strb,modelsav,'+'); /* keeps in strb after the first '+'
6203: modelsav==V2+V1+V4+V3*age strb=V3*age stra=V2+V1+V4 */
6204: if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
6205: /* printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
6206: /*scanf("%d",i);*/
6207: if (strchr(strb,'*')) { /**< Model includes a product V2+V1+V4+V3*age strb=V3*age */
6208: cutl(strc,strd,strb,'*'); /**< strd*strc Vm*Vn: strb=V3*age(input) strc=age strd=V3 ; V3*V2 strc=V2, strd=V3 */
6209: if (strcmp(strc,"age")==0) { /**< Model includes age: Vn*age */
6210: /* covar is not filled and then is empty */
6211: cptcovprod--;
6212: cutl(stre,strb,strd,'V'); /* strd=V3(input): stre="3" */
6213: Tvar[k]=atoi(stre); /* V2+V1+V4+V3*age Tvar[4]=3 ; V1+V2*age Tvar[2]=2; V1+V1*age Tvar[2]=1 */
6214: cptcovage++; /* Sums the number of covariates which include age as a product */
6215: Tage[cptcovage]=k; /* Tvar[4]=3, Tage[1] = 4 or V1+V1*age Tvar[2]=1, Tage[1]=2 */
6216: /*printf("stre=%s ", stre);*/
6217: } else if (strcmp(strd,"age")==0) { /* or age*Vn */
6218: cptcovprod--;
6219: cutl(stre,strb,strc,'V');
6220: Tvar[k]=atoi(stre);
6221: cptcovage++;
6222: Tage[cptcovage]=k;
6223: } else { /* Age is not in the model product V2+V1+V1*V4+V3*age+V3*V2 strb=V3*V2*/
6224: /* loops on k1=1 (V3*V2) and k1=2 V4*V3 */
6225: cptcovn++;
6226: cptcovprodnoage++;k1++;
6227: cutl(stre,strb,strc,'V'); /* strc= Vn, stre is n; strb=V3*V2 stre=3 strc=*/
6228: Tvar[k]=ncovcol+k1; /* For model-covariate k tells which data-covariate to use but
6229: because this model-covariate is a construction we invent a new column
6230: ncovcol + k1
6231: If already ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2
6232: Tvar[3=V1*V4]=4+1 Tvar[5=V3*V2]=4 + 2= 6, etc */
6233: cutl(strc,strb,strd,'V'); /* strd was Vm, strc is m */
6234: Tprod[k1]=k; /* Tprod[1]=3(=V1*V4) for V2+V1+V1*V4+age*V3+V3*V2 */
6235: Tvard[k1][1] =atoi(strc); /* m 1 for V1*/
6236: Tvard[k1][2] =atoi(stre); /* n 4 for V4*/
6237: k2=k2+2;
6238: Tvar[cptcovt+k2]=Tvard[k1][1]; /* Tvar[(cptcovt=4+k2=1)=5]= 1 (V1) */
6239: Tvar[cptcovt+k2+1]=Tvard[k1][2]; /* Tvar[(cptcovt=4+(k2=1)+1)=6]= 4 (V4) */
6240: for (i=1; i<=lastobs;i++){
6241: /* Computes the new covariate which is a product of
6242: covar[n][i]* covar[m][i] and stores it at ncovol+k1 May not be defined */
6243: covar[ncovcol+k1][i]=covar[atoi(stre)][i]*covar[atoi(strc)][i];
6244: }
6245: } /* End age is not in the model */
6246: } /* End if model includes a product */
6247: else { /* no more sum */
6248: /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
6249: /* scanf("%d",i);*/
6250: cutl(strd,strc,strb,'V');
6251: ks++; /**< Number of simple covariates */
1.145 brouard 6252: cptcovn++;
1.187 brouard 6253: Tvar[k]=atoi(strd);
6254: }
6255: strcpy(modelsav,stra); /* modelsav=V2+V1+V4 stra=V2+V1+V4 */
6256: /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
6257: scanf("%d",i);*/
6258: } /* end of loop + on total covariates */
6259: } /* end if strlen(modelsave == 0) age*age might exist */
6260: } /* end if strlen(model == 0) */
1.136 brouard 6261:
6262: /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
6263: If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
6264:
6265: /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
6266: printf("cptcovprod=%d ", cptcovprod);
6267: fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
6268:
6269: scanf("%d ",i);*/
6270:
6271:
1.137 brouard 6272: return (0); /* with covar[new additional covariate if product] and Tage if age */
1.164 brouard 6273: /*endread:*/
1.136 brouard 6274: printf("Exiting decodemodel: ");
6275: return (1);
6276: }
6277:
1.169 brouard 6278: int calandcheckages(int imx, int maxwav, double *agemin, double *agemax, int *nberr, int *nbwarn )
1.136 brouard 6279: {
6280: int i, m;
6281:
6282: for (i=1; i<=imx; i++) {
6283: for(m=2; (m<= maxwav); m++) {
6284: if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
6285: anint[m][i]=9999;
6286: s[m][i]=-1;
6287: }
6288: if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
1.169 brouard 6289: *nberr = *nberr + 1;
6290: 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);
6291: 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 6292: s[m][i]=-1;
6293: }
6294: if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
1.169 brouard 6295: (*nberr)++;
1.136 brouard 6296: 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]);
6297: 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]);
6298: s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
6299: }
6300: }
6301: }
6302:
6303: for (i=1; i<=imx; i++) {
6304: agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
6305: for(m=firstpass; (m<= lastpass); m++){
6306: if(s[m][i] >0 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){
6307: if (s[m][i] >= nlstate+1) {
1.169 brouard 6308: if(agedc[i]>0){
6309: if((int)moisdc[i]!=99 && (int)andc[i]!=9999){
1.136 brouard 6310: agev[m][i]=agedc[i];
6311: /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
1.169 brouard 6312: }else {
1.136 brouard 6313: if ((int)andc[i]!=9999){
6314: nbwarn++;
6315: printf("Warning negative age at death: %ld line:%d\n",num[i],i);
6316: fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
6317: agev[m][i]=-1;
6318: }
6319: }
1.169 brouard 6320: } /* agedc > 0 */
1.136 brouard 6321: }
6322: else if(s[m][i] !=9){ /* Standard case, age in fractional
6323: years but with the precision of a month */
6324: agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
6325: if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
6326: agev[m][i]=1;
6327: else if(agev[m][i] < *agemin){
6328: *agemin=agev[m][i];
6329: printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], *agemin);
6330: }
6331: else if(agev[m][i] >*agemax){
6332: *agemax=agev[m][i];
1.156 brouard 6333: /* printf(" Max anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.2f\n",m,i,anint[m][i], i,annais[i], *agemax);*/
1.136 brouard 6334: }
6335: /*agev[m][i]=anint[m][i]-annais[i];*/
6336: /* agev[m][i] = age[i]+2*m;*/
6337: }
6338: else { /* =9 */
6339: agev[m][i]=1;
6340: s[m][i]=-1;
6341: }
6342: }
6343: else /*= 0 Unknown */
6344: agev[m][i]=1;
6345: }
6346:
6347: }
6348: for (i=1; i<=imx; i++) {
6349: for(m=firstpass; (m<=lastpass); m++){
6350: if (s[m][i] > (nlstate+ndeath)) {
1.169 brouard 6351: (*nberr)++;
1.136 brouard 6352: 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);
6353: 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);
6354: return 1;
6355: }
6356: }
6357: }
6358:
6359: /*for (i=1; i<=imx; i++){
6360: for (m=firstpass; (m<lastpass); m++){
6361: printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
6362: }
6363:
6364: }*/
6365:
6366:
1.139 brouard 6367: printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
6368: fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
1.136 brouard 6369:
6370: return (0);
1.164 brouard 6371: /* endread:*/
1.136 brouard 6372: printf("Exiting calandcheckages: ");
6373: return (1);
6374: }
6375:
1.172 brouard 6376: #if defined(_MSC_VER)
6377: /*printf("Visual C++ compiler: %s \n;", _MSC_FULL_VER);*/
6378: /*fprintf(ficlog, "Visual C++ compiler: %s \n;", _MSC_FULL_VER);*/
6379: //#include "stdafx.h"
6380: //#include <stdio.h>
6381: //#include <tchar.h>
6382: //#include <windows.h>
6383: //#include <iostream>
6384: typedef BOOL(WINAPI *LPFN_ISWOW64PROCESS) (HANDLE, PBOOL);
6385:
6386: LPFN_ISWOW64PROCESS fnIsWow64Process;
6387:
6388: BOOL IsWow64()
6389: {
6390: BOOL bIsWow64 = FALSE;
6391:
6392: //typedef BOOL (APIENTRY *LPFN_ISWOW64PROCESS)
6393: // (HANDLE, PBOOL);
6394:
6395: //LPFN_ISWOW64PROCESS fnIsWow64Process;
6396:
6397: HMODULE module = GetModuleHandle(_T("kernel32"));
6398: const char funcName[] = "IsWow64Process";
6399: fnIsWow64Process = (LPFN_ISWOW64PROCESS)
6400: GetProcAddress(module, funcName);
6401:
6402: if (NULL != fnIsWow64Process)
6403: {
6404: if (!fnIsWow64Process(GetCurrentProcess(),
6405: &bIsWow64))
6406: //throw std::exception("Unknown error");
6407: printf("Unknown error\n");
6408: }
6409: return bIsWow64 != FALSE;
6410: }
6411: #endif
1.177 brouard 6412:
1.191 brouard 6413: void syscompilerinfo(int logged)
1.167 brouard 6414: {
6415: /* #include "syscompilerinfo.h"*/
1.185 brouard 6416: /* command line Intel compiler 32bit windows, XP compatible:*/
6417: /* /GS /W3 /Gy
6418: /Zc:wchar_t /Zi /O2 /Fd"Release\vc120.pdb" /D "WIN32" /D "NDEBUG" /D
6419: "_CONSOLE" /D "_LIB" /D "_USING_V110_SDK71_" /D "_UNICODE" /D
6420: "UNICODE" /Qipo /Zc:forScope /Gd /Oi /MT /Fa"Release\" /EHsc /nologo
1.186 brouard 6421: /Fo"Release\" /Qprof-dir "Release\" /Fp"Release\IMaCh.pch"
6422: */
6423: /* 64 bits */
1.185 brouard 6424: /*
6425: /GS /W3 /Gy
6426: /Zc:wchar_t /Zi /O2 /Fd"x64\Release\vc120.pdb" /D "WIN32" /D "NDEBUG"
6427: /D "_CONSOLE" /D "_LIB" /D "_UNICODE" /D "UNICODE" /Qipo /Zc:forScope
6428: /Oi /MD /Fa"x64\Release\" /EHsc /nologo /Fo"x64\Release\" /Qprof-dir
6429: "x64\Release\" /Fp"x64\Release\IMaCh.pch" */
6430: /* Optimization are useless and O3 is slower than O2 */
6431: /*
6432: /GS /W3 /Gy /Zc:wchar_t /Zi /O3 /Fd"x64\Release\vc120.pdb" /D "WIN32"
6433: /D "NDEBUG" /D "_CONSOLE" /D "_LIB" /D "_UNICODE" /D "UNICODE" /Qipo
6434: /Zc:forScope /Oi /MD /Fa"x64\Release\" /EHsc /nologo /Qparallel
6435: /Fo"x64\Release\" /Qprof-dir "x64\Release\" /Fp"x64\Release\IMaCh.pch"
6436: */
1.186 brouard 6437: /* Link is */ /* /OUT:"visual studio
1.185 brouard 6438: 2013\Projects\IMaCh\Release\IMaCh.exe" /MANIFEST /NXCOMPAT
6439: /PDB:"visual studio
6440: 2013\Projects\IMaCh\Release\IMaCh.pdb" /DYNAMICBASE
6441: "kernel32.lib" "user32.lib" "gdi32.lib" "winspool.lib"
6442: "comdlg32.lib" "advapi32.lib" "shell32.lib" "ole32.lib"
6443: "oleaut32.lib" "uuid.lib" "odbc32.lib" "odbccp32.lib"
6444: /MACHINE:X86 /OPT:REF /SAFESEH /INCREMENTAL:NO
6445: /SUBSYSTEM:CONSOLE",5.01" /MANIFESTUAC:"level='asInvoker'
6446: uiAccess='false'"
6447: /ManifestFile:"Release\IMaCh.exe.intermediate.manifest" /OPT:ICF
6448: /NOLOGO /TLBID:1
6449: */
1.177 brouard 6450: #if defined __INTEL_COMPILER
1.178 brouard 6451: #if defined(__GNUC__)
6452: struct utsname sysInfo; /* For Intel on Linux and OS/X */
6453: #endif
1.177 brouard 6454: #elif defined(__GNUC__)
1.179 brouard 6455: #ifndef __APPLE__
1.174 brouard 6456: #include <gnu/libc-version.h> /* Only on gnu */
1.179 brouard 6457: #endif
1.177 brouard 6458: struct utsname sysInfo;
1.178 brouard 6459: int cross = CROSS;
6460: if (cross){
6461: printf("Cross-");
1.191 brouard 6462: if(logged) fprintf(ficlog, "Cross-");
1.178 brouard 6463: }
1.174 brouard 6464: #endif
6465:
1.171 brouard 6466: #include <stdint.h>
1.178 brouard 6467:
1.191 brouard 6468: printf("Compiled with:");if(logged)fprintf(ficlog,"Compiled with:");
1.169 brouard 6469: #if defined(__clang__)
1.191 brouard 6470: printf(" Clang/LLVM");if(logged)fprintf(ficlog," Clang/LLVM"); /* Clang/LLVM. ---------------------------------------------- */
1.169 brouard 6471: #endif
6472: #if defined(__ICC) || defined(__INTEL_COMPILER)
1.191 brouard 6473: printf(" Intel ICC/ICPC");if(logged)fprintf(ficlog," Intel ICC/ICPC");/* Intel ICC/ICPC. ------------------------------------------ */
1.169 brouard 6474: #endif
6475: #if defined(__GNUC__) || defined(__GNUG__)
1.191 brouard 6476: printf(" GNU GCC/G++");if(logged)fprintf(ficlog," GNU GCC/G++");/* GNU GCC/G++. --------------------------------------------- */
1.169 brouard 6477: #endif
6478: #if defined(__HP_cc) || defined(__HP_aCC)
1.191 brouard 6479: printf(" Hewlett-Packard C/aC++");if(logged)fprintf(fcilog," Hewlett-Packard C/aC++"); /* Hewlett-Packard C/aC++. ---------------------------------- */
1.169 brouard 6480: #endif
6481: #if defined(__IBMC__) || defined(__IBMCPP__)
1.191 brouard 6482: printf(" IBM XL C/C++"); if(logged) fprintf(ficlog," IBM XL C/C++");/* IBM XL C/C++. -------------------------------------------- */
1.169 brouard 6483: #endif
6484: #if defined(_MSC_VER)
1.191 brouard 6485: printf(" Microsoft Visual Studio");if(logged)fprintf(ficlog," Microsoft Visual Studio");/* Microsoft Visual Studio. --------------------------------- */
1.169 brouard 6486: #endif
6487: #if defined(__PGI)
1.191 brouard 6488: printf(" Portland Group PGCC/PGCPP");if(logged) fprintf(ficlog," Portland Group PGCC/PGCPP");/* Portland Group PGCC/PGCPP. ------------------------------- */
1.169 brouard 6489: #endif
6490: #if defined(__SUNPRO_C) || defined(__SUNPRO_CC)
1.191 brouard 6491: printf(" Oracle Solaris Studio");if(logged)fprintf(ficlog," Oracle Solaris Studio\n");/* Oracle Solaris Studio. ----------------------------------- */
1.167 brouard 6492: #endif
1.191 brouard 6493: printf(" for "); if (logged) fprintf(ficlog, " for ");
1.169 brouard 6494:
1.167 brouard 6495: // http://stackoverflow.com/questions/4605842/how-to-identify-platform-compiler-from-preprocessor-macros
6496: #ifdef _WIN32 // note the underscore: without it, it's not msdn official!
6497: // Windows (x64 and x86)
1.191 brouard 6498: printf("Windows (x64 and x86) ");if(logged) fprintf(ficlog,"Windows (x64 and x86) ");
1.167 brouard 6499: #elif __unix__ // all unices, not all compilers
6500: // Unix
1.191 brouard 6501: printf("Unix ");if(logged) fprintf(ficlog,"Unix ");
1.167 brouard 6502: #elif __linux__
6503: // linux
1.191 brouard 6504: printf("linux ");if(logged) fprintf(ficlog,"linux ");
1.167 brouard 6505: #elif __APPLE__
1.174 brouard 6506: // Mac OS, not sure if this is covered by __posix__ and/or __unix__ though..
1.191 brouard 6507: printf("Mac OS ");if(logged) fprintf(ficlog,"Mac OS ");
1.167 brouard 6508: #endif
6509:
6510: /* __MINGW32__ */
6511: /* __CYGWIN__ */
6512: /* __MINGW64__ */
6513: // http://msdn.microsoft.com/en-us/library/b0084kay.aspx
6514: /* _MSC_VER //the Visual C++ compiler is 17.00.51106.1, the _MSC_VER macro evaluates to 1700. Type cl /? */
6515: /* _MSC_FULL_VER //the Visual C++ compiler is 15.00.20706.01, the _MSC_FULL_VER macro evaluates to 150020706 */
6516: /* _WIN64 // Defined for applications for Win64. */
6517: /* _M_X64 // Defined for compilations that target x64 processors. */
6518: /* _DEBUG // Defined when you compile with /LDd, /MDd, and /MTd. */
1.171 brouard 6519:
1.167 brouard 6520: #if UINTPTR_MAX == 0xffffffff
1.191 brouard 6521: printf(" 32-bit"); if(logged) fprintf(ficlog," 32-bit");/* 32-bit */
1.167 brouard 6522: #elif UINTPTR_MAX == 0xffffffffffffffff
1.191 brouard 6523: printf(" 64-bit"); if(logged) fprintf(ficlog," 64-bit");/* 64-bit */
1.167 brouard 6524: #else
1.191 brouard 6525: printf(" wtf-bit"); if(logged) fprintf(ficlog," wtf-bit");/* wtf */
1.167 brouard 6526: #endif
6527:
1.169 brouard 6528: #if defined(__GNUC__)
6529: # if defined(__GNUC_PATCHLEVEL__)
6530: # define __GNUC_VERSION__ (__GNUC__ * 10000 \
6531: + __GNUC_MINOR__ * 100 \
6532: + __GNUC_PATCHLEVEL__)
6533: # else
6534: # define __GNUC_VERSION__ (__GNUC__ * 10000 \
6535: + __GNUC_MINOR__ * 100)
6536: # endif
1.174 brouard 6537: printf(" using GNU C version %d.\n", __GNUC_VERSION__);
1.191 brouard 6538: if(logged) fprintf(ficlog, " using GNU C version %d.\n", __GNUC_VERSION__);
1.176 brouard 6539:
6540: if (uname(&sysInfo) != -1) {
6541: printf("Running on: %s %s %s %s %s\n",sysInfo.sysname, sysInfo.nodename, sysInfo.release, sysInfo.version, sysInfo.machine);
1.191 brouard 6542: 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 6543: }
6544: else
6545: perror("uname() error");
1.179 brouard 6546: //#ifndef __INTEL_COMPILER
6547: #if !defined (__INTEL_COMPILER) && !defined(__APPLE__)
1.174 brouard 6548: printf("GNU libc version: %s\n", gnu_get_libc_version());
1.191 brouard 6549: if(logged) fprintf(ficlog,"GNU libc version: %s\n", gnu_get_libc_version());
1.177 brouard 6550: #endif
1.169 brouard 6551: #endif
1.172 brouard 6552:
6553: // void main()
6554: // {
1.169 brouard 6555: #if defined(_MSC_VER)
1.174 brouard 6556: if (IsWow64()){
1.191 brouard 6557: printf("\nThe program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n");
6558: if (logged) fprintf(ficlog, "\nThe program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n");
1.174 brouard 6559: }
6560: else{
1.191 brouard 6561: printf("\nThe program is not running under WOW64 (i.e probably on a 64bit Windows).\n");
6562: if (logged) fprintf(ficlog, "\nThe programm is not running under WOW64 (i.e probably on a 64bit Windows).\n");
1.174 brouard 6563: }
1.172 brouard 6564: // printf("\nPress Enter to continue...");
6565: // getchar();
6566: // }
6567:
1.169 brouard 6568: #endif
6569:
1.167 brouard 6570:
6571: }
1.136 brouard 6572:
1.209 ! brouard 6573: int prevalence_limit(double *p, double **prlim, double ageminpar, double agemaxpar, double ftolpl, int *ncvyearp){
1.180 brouard 6574: /*--------------- Prevalence limit (period or stable prevalence) --------------*/
6575: int i, j, k, i1 ;
1.202 brouard 6576: /* double ftolpl = 1.e-10; */
1.180 brouard 6577: double age, agebase, agelim;
1.203 brouard 6578: double tot;
1.180 brouard 6579:
1.202 brouard 6580: strcpy(filerespl,"PL_");
6581: strcat(filerespl,fileresu);
6582: if((ficrespl=fopen(filerespl,"w"))==NULL) {
6583: printf("Problem with period (stable) prevalence resultfile: %s\n", filerespl);return 1;
6584: fprintf(ficlog,"Problem with period (stable) prevalence resultfile: %s\n", filerespl);return 1;
6585: }
6586: printf("Computing period (stable) prevalence: result on file '%s' \n", filerespl);
6587: fprintf(ficlog,"Computing period (stable) prevalence: result on file '%s' \n", filerespl);
6588: pstamp(ficrespl);
1.203 brouard 6589: fprintf(ficrespl,"# Period (stable) prevalence. Precision given by ftolpl=%g \n", ftolpl);
1.202 brouard 6590: fprintf(ficrespl,"#Age ");
6591: for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
6592: fprintf(ficrespl,"\n");
1.180 brouard 6593:
6594: /* prlim=matrix(1,nlstate,1,nlstate);*/ /* back in main */
6595:
6596: agebase=ageminpar;
6597: agelim=agemaxpar;
6598:
6599: i1=pow(2,cptcoveff);
6600: if (cptcovn < 1){i1=1;}
6601:
6602: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
6603: /* for(cptcov=1,k=0;cptcov<=1;cptcov++){ */
6604: //for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
6605: k=k+1;
6606: /* to clean */
1.198 brouard 6607: //printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtabm(cptcod,cptcov));
1.200 brouard 6608: fprintf(ficrespl,"#******");
6609: printf("#******");
6610: fprintf(ficlog,"#******");
1.180 brouard 6611: for(j=1;j<=cptcoveff;j++) {
1.198 brouard 6612: fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
6613: printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
6614: fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.180 brouard 6615: }
6616: fprintf(ficrespl,"******\n");
6617: printf("******\n");
6618: fprintf(ficlog,"******\n");
6619:
6620: fprintf(ficrespl,"#Age ");
6621: for(j=1;j<=cptcoveff;j++) {
1.200 brouard 6622: fprintf(ficrespl,"V%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.180 brouard 6623: }
1.203 brouard 6624: for(i=1; i<=nlstate;i++) fprintf(ficrespl," %d-%d ",i,i);
6625: fprintf(ficrespl,"Total Years_to_converge\n");
1.180 brouard 6626:
6627: for (age=agebase; age<=agelim; age++){
6628: /* for (age=agebase; age<=agebase; age++){ */
1.209 ! brouard 6629: prevalim(prlim, nlstate, p, age, oldm, savm, ftolpl, ncvyearp, k);
1.180 brouard 6630: fprintf(ficrespl,"%.0f ",age );
6631: for(j=1;j<=cptcoveff;j++)
1.198 brouard 6632: fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.203 brouard 6633: tot=0.;
6634: for(i=1; i<=nlstate;i++){
6635: tot += prlim[i][i];
1.180 brouard 6636: fprintf(ficrespl," %.5f", prlim[i][i]);
1.203 brouard 6637: }
1.209 ! brouard 6638: fprintf(ficrespl," %.3f %d\n", tot, *ncvyearp);
1.180 brouard 6639: } /* Age */
6640: /* was end of cptcod */
6641: } /* cptcov */
1.184 brouard 6642: return 0;
1.180 brouard 6643: }
6644:
6645: int hPijx(double *p, int bage, int fage){
6646: /*------------- h Pij x at various ages ------------*/
6647:
6648: int stepsize;
6649: int agelim;
6650: int hstepm;
6651: int nhstepm;
6652: int h, i, i1, j, k;
6653:
6654: double agedeb;
6655: double ***p3mat;
6656:
1.201 brouard 6657: strcpy(filerespij,"PIJ_"); strcat(filerespij,fileresu);
1.180 brouard 6658: if((ficrespij=fopen(filerespij,"w"))==NULL) {
6659: printf("Problem with Pij resultfile: %s\n", filerespij); return 1;
6660: fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij); return 1;
6661: }
6662: printf("Computing pij: result on file '%s' \n", filerespij);
6663: fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
6664:
6665: stepsize=(int) (stepm+YEARM-1)/YEARM;
6666: /*if (stepm<=24) stepsize=2;*/
6667:
6668: agelim=AGESUP;
6669: hstepm=stepsize*YEARM; /* Every year of age */
6670: hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
6671:
6672: /* hstepm=1; aff par mois*/
6673: pstamp(ficrespij);
6674: fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
6675: i1= pow(2,cptcoveff);
1.183 brouard 6676: /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */
6677: /* /\*for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*\/ */
6678: /* k=k+1; */
6679: for (k=1; k <= (int) pow(2,cptcoveff); k++){
6680: fprintf(ficrespij,"\n#****** ");
6681: for(j=1;j<=cptcoveff;j++)
1.198 brouard 6682: fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.183 brouard 6683: fprintf(ficrespij,"******\n");
6684:
6685: for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
6686: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
6687: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
6688:
6689: /* nhstepm=nhstepm*YEARM; aff par mois*/
1.180 brouard 6690:
1.183 brouard 6691: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
6692: oldm=oldms;savm=savms;
6693: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
6694: fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
6695: for(i=1; i<=nlstate;i++)
6696: for(j=1; j<=nlstate+ndeath;j++)
6697: fprintf(ficrespij," %1d-%1d",i,j);
6698: fprintf(ficrespij,"\n");
6699: for (h=0; h<=nhstepm; h++){
6700: /*agedebphstep = agedeb + h*hstepm/YEARM*stepm;*/
6701: fprintf(ficrespij,"%d %3.f %3.f",k, agedeb, agedeb + h*hstepm/YEARM*stepm );
1.180 brouard 6702: for(i=1; i<=nlstate;i++)
6703: for(j=1; j<=nlstate+ndeath;j++)
1.183 brouard 6704: fprintf(ficrespij," %.5f", p3mat[i][j][h]);
1.180 brouard 6705: fprintf(ficrespij,"\n");
6706: }
1.183 brouard 6707: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
6708: fprintf(ficrespij,"\n");
6709: }
1.180 brouard 6710: /*}*/
6711: }
1.184 brouard 6712: return 0;
1.180 brouard 6713: }
6714:
6715:
1.136 brouard 6716: /***********************************************/
6717: /**************** Main Program *****************/
6718: /***********************************************/
6719:
6720: int main(int argc, char *argv[])
6721: {
6722: #ifdef GSL
6723: const gsl_multimin_fminimizer_type *T;
6724: size_t iteri = 0, it;
6725: int rval = GSL_CONTINUE;
6726: int status = GSL_SUCCESS;
6727: double ssval;
6728: #endif
6729: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
1.164 brouard 6730: int i,j, k, n=MAXN,iter=0,m,size=100, cptcod;
1.209 ! brouard 6731: int ncvyear=0; /* Number of years needed for the period prevalence to converge */
1.164 brouard 6732: int jj, ll, li, lj, lk;
1.136 brouard 6733: int numlinepar=0; /* Current linenumber of parameter file */
1.197 brouard 6734: int num_filled;
1.136 brouard 6735: int itimes;
6736: int NDIM=2;
6737: int vpopbased=0;
6738:
1.164 brouard 6739: char ca[32], cb[32];
1.136 brouard 6740: /* FILE *fichtm; *//* Html File */
6741: /* FILE *ficgp;*/ /*Gnuplot File */
6742: struct stat info;
1.191 brouard 6743: double agedeb=0.;
1.194 brouard 6744:
6745: double ageminpar=AGEOVERFLOW,agemin=AGEOVERFLOW, agemaxpar=-AGEOVERFLOW, agemax=-AGEOVERFLOW;
1.136 brouard 6746:
1.165 brouard 6747: double fret;
1.191 brouard 6748: double dum=0.; /* Dummy variable */
1.136 brouard 6749: double ***p3mat;
6750: double ***mobaverage;
1.164 brouard 6751:
6752: char line[MAXLINE];
1.197 brouard 6753: char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE];
6754:
6755: char model[MAXLINE], modeltemp[MAXLINE];
1.136 brouard 6756: char pathr[MAXLINE], pathimach[MAXLINE];
1.164 brouard 6757: char *tok, *val; /* pathtot */
1.136 brouard 6758: int firstobs=1, lastobs=10;
1.195 brouard 6759: int c, h , cpt, c2;
1.191 brouard 6760: int jl=0;
6761: int i1, j1, jk, stepsize=0;
1.194 brouard 6762: int count=0;
6763:
1.164 brouard 6764: int *tab;
1.136 brouard 6765: int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
6766: int mobilav=0,popforecast=0;
1.191 brouard 6767: int hstepm=0, nhstepm=0;
1.136 brouard 6768: int agemortsup;
6769: float sumlpop=0.;
6770: double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
6771: double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
6772:
1.191 brouard 6773: double bage=0, fage=110., age, agelim=0., agebase=0.;
1.136 brouard 6774: double ftolpl=FTOL;
6775: double **prlim;
6776: double ***param; /* Matrix of parameters */
6777: double *p;
6778: double **matcov; /* Matrix of covariance */
1.203 brouard 6779: double **hess; /* Hessian matrix */
1.136 brouard 6780: double ***delti3; /* Scale */
6781: double *delti; /* Scale */
6782: double ***eij, ***vareij;
6783: double **varpl; /* Variances of prevalence limits by age */
6784: double *epj, vepp;
1.164 brouard 6785:
1.136 brouard 6786: double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
6787: double **ximort;
1.145 brouard 6788: char *alph[]={"a","a","b","c","d","e"}, str[4]="1234";
1.136 brouard 6789: int *dcwave;
6790:
1.164 brouard 6791: char z[1]="c";
1.136 brouard 6792:
6793: /*char *strt;*/
6794: char strtend[80];
1.126 brouard 6795:
1.164 brouard 6796:
1.126 brouard 6797: /* setlocale (LC_ALL, ""); */
6798: /* bindtextdomain (PACKAGE, LOCALEDIR); */
6799: /* textdomain (PACKAGE); */
6800: /* setlocale (LC_CTYPE, ""); */
6801: /* setlocale (LC_MESSAGES, ""); */
6802:
6803: /* gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
1.157 brouard 6804: rstart_time = time(NULL);
6805: /* (void) gettimeofday(&start_time,&tzp);*/
6806: start_time = *localtime(&rstart_time);
1.126 brouard 6807: curr_time=start_time;
1.157 brouard 6808: /*tml = *localtime(&start_time.tm_sec);*/
6809: /* strcpy(strstart,asctime(&tml)); */
6810: strcpy(strstart,asctime(&start_time));
1.126 brouard 6811:
6812: /* printf("Localtime (at start)=%s",strstart); */
1.157 brouard 6813: /* tp.tm_sec = tp.tm_sec +86400; */
6814: /* tm = *localtime(&start_time.tm_sec); */
1.126 brouard 6815: /* tmg.tm_year=tmg.tm_year +dsign*dyear; */
6816: /* tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
6817: /* tmg.tm_hour=tmg.tm_hour + 1; */
1.157 brouard 6818: /* tp.tm_sec = mktime(&tmg); */
1.126 brouard 6819: /* strt=asctime(&tmg); */
6820: /* printf("Time(after) =%s",strstart); */
6821: /* (void) time (&time_value);
6822: * printf("time=%d,t-=%d\n",time_value,time_value-86400);
6823: * tm = *localtime(&time_value);
6824: * strstart=asctime(&tm);
6825: * printf("tim_value=%d,asctime=%s\n",time_value,strstart);
6826: */
6827:
6828: nberr=0; /* Number of errors and warnings */
6829: nbwarn=0;
1.184 brouard 6830: #ifdef WIN32
6831: _getcwd(pathcd, size);
6832: #else
1.126 brouard 6833: getcwd(pathcd, size);
1.184 brouard 6834: #endif
1.191 brouard 6835: syscompilerinfo(0);
1.196 brouard 6836: printf("\nIMaCh version %s, %s\n%s",version, copyright, fullversion);
1.126 brouard 6837: if(argc <=1){
6838: printf("\nEnter the parameter file name: ");
1.205 brouard 6839: if(!fgets(pathr,FILENAMELENGTH,stdin)){
6840: printf("ERROR Empty parameter file name\n");
6841: goto end;
6842: }
1.126 brouard 6843: i=strlen(pathr);
6844: if(pathr[i-1]=='\n')
6845: pathr[i-1]='\0';
1.156 brouard 6846: i=strlen(pathr);
1.205 brouard 6847: if(i >= 1 && pathr[i-1]==' ') {/* This may happen when dragging on oS/X! */
1.156 brouard 6848: pathr[i-1]='\0';
1.205 brouard 6849: }
6850: i=strlen(pathr);
6851: if( i==0 ){
6852: printf("ERROR Empty parameter file name\n");
6853: goto end;
6854: }
6855: for (tok = pathr; tok != NULL; ){
1.126 brouard 6856: printf("Pathr |%s|\n",pathr);
6857: while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
6858: printf("val= |%s| pathr=%s\n",val,pathr);
6859: strcpy (pathtot, val);
6860: if(pathr[0] == '\0') break; /* Dirty */
6861: }
6862: }
6863: else{
6864: strcpy(pathtot,argv[1]);
6865: }
6866: /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
6867: /*cygwin_split_path(pathtot,path,optionfile);
6868: printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
6869: /* cutv(path,optionfile,pathtot,'\\');*/
6870:
6871: /* Split argv[0], imach program to get pathimach */
6872: printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
6873: split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
6874: printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
6875: /* strcpy(pathimach,argv[0]); */
6876: /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
6877: split(pathtot,path,optionfile,optionfilext,optionfilefiname);
6878: printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
1.184 brouard 6879: #ifdef WIN32
6880: _chdir(path); /* Can be a relative path */
6881: if(_getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */
6882: #else
1.126 brouard 6883: chdir(path); /* Can be a relative path */
1.184 brouard 6884: if (getcwd(pathcd, MAXLINE) > 0) /* So pathcd is the full path */
6885: #endif
6886: printf("Current directory %s!\n",pathcd);
1.126 brouard 6887: strcpy(command,"mkdir ");
6888: strcat(command,optionfilefiname);
6889: if((outcmd=system(command)) != 0){
1.169 brouard 6890: printf("Directory already exists (or can't create it) %s%s, err=%d\n",path,optionfilefiname,outcmd);
1.126 brouard 6891: /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
6892: /* fclose(ficlog); */
6893: /* exit(1); */
6894: }
6895: /* if((imk=mkdir(optionfilefiname))<0){ */
6896: /* perror("mkdir"); */
6897: /* } */
6898:
6899: /*-------- arguments in the command line --------*/
6900:
1.186 brouard 6901: /* Main Log file */
1.126 brouard 6902: strcat(filelog, optionfilefiname);
6903: strcat(filelog,".log"); /* */
6904: if((ficlog=fopen(filelog,"w"))==NULL) {
6905: printf("Problem with logfile %s\n",filelog);
6906: goto end;
6907: }
6908: fprintf(ficlog,"Log filename:%s\n",filelog);
1.197 brouard 6909: fprintf(ficlog,"Version %s %s",version,fullversion);
1.126 brouard 6910: fprintf(ficlog,"\nEnter the parameter file name: \n");
6911: fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
6912: path=%s \n\
6913: optionfile=%s\n\
6914: optionfilext=%s\n\
1.156 brouard 6915: optionfilefiname='%s'\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
1.126 brouard 6916:
1.197 brouard 6917: syscompilerinfo(1);
1.167 brouard 6918:
1.126 brouard 6919: printf("Local time (at start):%s",strstart);
6920: fprintf(ficlog,"Local time (at start): %s",strstart);
6921: fflush(ficlog);
6922: /* (void) gettimeofday(&curr_time,&tzp); */
1.157 brouard 6923: /* printf("Elapsed time %d\n", asc_diff_time(curr_time.tm_sec-start_time.tm_sec,tmpout)); */
1.126 brouard 6924:
6925: /* */
6926: strcpy(fileres,"r");
6927: strcat(fileres, optionfilefiname);
1.201 brouard 6928: strcat(fileresu, optionfilefiname); /* Without r in front */
1.126 brouard 6929: strcat(fileres,".txt"); /* Other files have txt extension */
1.201 brouard 6930: strcat(fileresu,".txt"); /* Other files have txt extension */
1.126 brouard 6931:
1.186 brouard 6932: /* Main ---------arguments file --------*/
1.126 brouard 6933:
6934: if((ficpar=fopen(optionfile,"r"))==NULL) {
1.155 brouard 6935: printf("Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
6936: fprintf(ficlog,"Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
1.126 brouard 6937: fflush(ficlog);
1.149 brouard 6938: /* goto end; */
6939: exit(70);
1.126 brouard 6940: }
6941:
6942:
6943:
6944: strcpy(filereso,"o");
1.201 brouard 6945: strcat(filereso,fileresu);
1.126 brouard 6946: if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
6947: printf("Problem with Output resultfile: %s\n", filereso);
6948: fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
6949: fflush(ficlog);
6950: goto end;
6951: }
6952:
6953: /* Reads comments: lines beginning with '#' */
6954: numlinepar=0;
1.197 brouard 6955:
6956: /* First parameter line */
6957: while(fgets(line, MAXLINE, ficpar)) {
6958: /* If line starts with a # it is a comment */
6959: if (line[0] == '#') {
6960: numlinepar++;
6961: fputs(line,stdout);
6962: fputs(line,ficparo);
6963: fputs(line,ficlog);
6964: continue;
6965: }else
6966: break;
6967: }
6968: if((num_filled=sscanf(line,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", \
6969: title, datafile, &lastobs, &firstpass,&lastpass)) !=EOF){
6970: if (num_filled != 5) {
6971: printf("Should be 5 parameters\n");
6972: }
1.126 brouard 6973: numlinepar++;
1.197 brouard 6974: printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", title, datafile, lastobs, firstpass,lastpass);
6975: }
6976: /* Second parameter line */
6977: while(fgets(line, MAXLINE, ficpar)) {
6978: /* If line starts with a # it is a comment */
6979: if (line[0] == '#') {
6980: numlinepar++;
6981: fputs(line,stdout);
6982: fputs(line,ficparo);
6983: fputs(line,ficlog);
6984: continue;
6985: }else
6986: break;
6987: }
6988: if((num_filled=sscanf(line,"ftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\n", \
6989: &ftol, &stepm, &ncovcol, &nlstate, &ndeath, &maxwav, &mle, &weightopt)) !=EOF){
6990: if (num_filled != 8) {
1.209 ! brouard 6991: printf("Not 8 parameters, for example:ftol=1.e-8 stepm=12 ncovcol=2 nlstate=2 ndeath=1 maxwav=3 mle=1 weight=1\n");
! 6992: printf("but line=%s\n",line);
1.197 brouard 6993: }
6994: 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 6995: }
1.203 brouard 6996: /* ftolpl=6*ftol*1.e5; /\* 6.e-3 make convergences in less than 80 loops for the prevalence limit *\/ */
1.209 ! brouard 6997: /*ftolpl=6.e-4; *//* 6.e-3 make convergences in less than 80 loops for the prevalence limit */
1.197 brouard 6998: /* Third parameter line */
6999: while(fgets(line, MAXLINE, ficpar)) {
7000: /* If line starts with a # it is a comment */
7001: if (line[0] == '#') {
7002: numlinepar++;
7003: fputs(line,stdout);
7004: fputs(line,ficparo);
7005: fputs(line,ficlog);
7006: continue;
7007: }else
7008: break;
7009: }
1.201 brouard 7010: if((num_filled=sscanf(line,"model=1+age%[^.\n]", model)) !=EOF){
7011: if (num_filled == 0)
7012: model[0]='\0';
7013: else if (num_filled != 1){
1.197 brouard 7014: printf("ERROR %d: Model should be at minimum 'model=1+age.' %s\n",num_filled, line);
7015: fprintf(ficlog,"ERROR %d: Model should be at minimum 'model=1+age.' %s\n",num_filled, line);
7016: model[0]='\0';
7017: goto end;
7018: }
7019: else{
7020: if (model[0]=='+'){
7021: for(i=1; i<=strlen(model);i++)
7022: modeltemp[i-1]=model[i];
1.201 brouard 7023: strcpy(model,modeltemp);
1.197 brouard 7024: }
7025: }
1.199 brouard 7026: /* printf(" model=1+age%s modeltemp= %s, model=%s\n",model, modeltemp, model);fflush(stdout); */
1.203 brouard 7027: printf("model=1+age+%s\n",model);fflush(stdout);
1.197 brouard 7028: }
7029: /* 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); */
7030: /* numlinepar=numlinepar+3; /\* In general *\/ */
7031: /* 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 7032: 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);
7033: 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 7034: fflush(ficlog);
1.190 brouard 7035: /* if(model[0]=='#'|| model[0]== '\0'){ */
7036: if(model[0]=='#'){
1.187 brouard 7037: printf("Error in 'model' line: model should start with 'model=1+age+' and end with '.' \n \
7038: 'model=1+age+.' or 'model=1+age+V1.' or 'model=1+age+age*age+V1+V1*age.' or \n \
7039: 'model=1+age+V1+V2.' or 'model=1+age+V1+V2+V1*V2.' etc. \n"); \
7040: if(mle != -1){
7041: printf("Fix the model line and run imach with mle=-1 to get a correct template of the parameter file.\n");
7042: exit(1);
7043: }
7044: }
1.126 brouard 7045: while((c=getc(ficpar))=='#' && c!= EOF){
7046: ungetc(c,ficpar);
7047: fgets(line, MAXLINE, ficpar);
7048: numlinepar++;
1.195 brouard 7049: if(line[1]=='q'){ /* This #q will quit imach (the answer is q) */
7050: z[0]=line[1];
7051: }
7052: /* printf("****line [1] = %c \n",line[1]); */
1.141 brouard 7053: fputs(line, stdout);
7054: //puts(line);
1.126 brouard 7055: fputs(line,ficparo);
7056: fputs(line,ficlog);
7057: }
7058: ungetc(c,ficpar);
7059:
7060:
1.145 brouard 7061: covar=matrix(0,NCOVMAX,1,n); /**< used in readdata */
1.136 brouard 7062: cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement plus one, indepently of n in Vn*/
7063: /* v1+v2+v3+v2*v4+v5*age makes cptcovn = 5
7064: v1+v2*age+v2*v3 makes cptcovn = 3
7065: */
7066: if (strlen(model)>1)
1.187 brouard 7067: 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 7068: else
1.187 brouard 7069: ncovmodel=2; /* Constant and age */
1.133 brouard 7070: nforce= (nlstate+ndeath-1)*nlstate; /* Number of forces ij from state i to j */
7071: npar= nforce*ncovmodel; /* Number of parameters like aij*/
1.131 brouard 7072: if(npar >MAXPARM || nlstate >NLSTATEMAX || ndeath >NDEATHMAX || ncovmodel>NCOVMAX){
7073: 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);
7074: 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);
7075: fflush(stdout);
7076: fclose (ficlog);
7077: goto end;
7078: }
1.126 brouard 7079: delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
7080: delti=delti3[1][1];
7081: /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
7082: if(mle==-1){ /* Print a wizard for help writing covariance matrix */
7083: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
1.191 brouard 7084: printf(" You chose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
7085: fprintf(ficlog," You chose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
1.126 brouard 7086: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
7087: fclose (ficparo);
7088: fclose (ficlog);
7089: goto end;
7090: exit(0);
7091: }
1.186 brouard 7092: else if(mle==-3) { /* Main Wizard */
1.126 brouard 7093: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
1.192 brouard 7094: printf(" You chose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
7095: fprintf(ficlog," You chose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
1.126 brouard 7096: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
7097: matcov=matrix(1,npar,1,npar);
1.203 brouard 7098: hess=matrix(1,npar,1,npar);
1.126 brouard 7099: }
7100: else{
1.145 brouard 7101: /* Read guessed parameters */
1.126 brouard 7102: /* Reads comments: lines beginning with '#' */
7103: while((c=getc(ficpar))=='#' && c!= EOF){
7104: ungetc(c,ficpar);
7105: fgets(line, MAXLINE, ficpar);
7106: numlinepar++;
1.141 brouard 7107: fputs(line,stdout);
1.126 brouard 7108: fputs(line,ficparo);
7109: fputs(line,ficlog);
7110: }
7111: ungetc(c,ficpar);
7112:
7113: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
7114: for(i=1; i <=nlstate; i++){
7115: j=0;
7116: for(jj=1; jj <=nlstate+ndeath; jj++){
7117: if(jj==i) continue;
7118: j++;
7119: fscanf(ficpar,"%1d%1d",&i1,&j1);
1.193 brouard 7120: if ((i1 != i) || (j1 != jj)){
1.126 brouard 7121: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \
7122: It might be a problem of design; if ncovcol and the model are correct\n \
7123: run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1);
7124: exit(1);
7125: }
7126: fprintf(ficparo,"%1d%1d",i1,j1);
7127: if(mle==1)
1.193 brouard 7128: printf("%1d%1d",i,jj);
7129: fprintf(ficlog,"%1d%1d",i,jj);
1.126 brouard 7130: for(k=1; k<=ncovmodel;k++){
7131: fscanf(ficpar," %lf",¶m[i][j][k]);
7132: if(mle==1){
7133: printf(" %lf",param[i][j][k]);
7134: fprintf(ficlog," %lf",param[i][j][k]);
7135: }
7136: else
7137: fprintf(ficlog," %lf",param[i][j][k]);
7138: fprintf(ficparo," %lf",param[i][j][k]);
7139: }
7140: fscanf(ficpar,"\n");
7141: numlinepar++;
7142: if(mle==1)
7143: printf("\n");
7144: fprintf(ficlog,"\n");
7145: fprintf(ficparo,"\n");
7146: }
7147: }
7148: fflush(ficlog);
7149:
1.145 brouard 7150: /* Reads scales values */
1.126 brouard 7151: p=param[1][1];
7152:
7153: /* Reads comments: lines beginning with '#' */
7154: while((c=getc(ficpar))=='#' && c!= EOF){
7155: ungetc(c,ficpar);
7156: fgets(line, MAXLINE, ficpar);
7157: numlinepar++;
1.141 brouard 7158: fputs(line,stdout);
1.126 brouard 7159: fputs(line,ficparo);
7160: fputs(line,ficlog);
7161: }
7162: ungetc(c,ficpar);
7163:
7164: for(i=1; i <=nlstate; i++){
7165: for(j=1; j <=nlstate+ndeath-1; j++){
7166: fscanf(ficpar,"%1d%1d",&i1,&j1);
1.164 brouard 7167: if ( (i1-i) * (j1-j) != 0){
1.126 brouard 7168: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
7169: exit(1);
7170: }
7171: printf("%1d%1d",i,j);
7172: fprintf(ficparo,"%1d%1d",i1,j1);
7173: fprintf(ficlog,"%1d%1d",i1,j1);
7174: for(k=1; k<=ncovmodel;k++){
7175: fscanf(ficpar,"%le",&delti3[i][j][k]);
7176: printf(" %le",delti3[i][j][k]);
7177: fprintf(ficparo," %le",delti3[i][j][k]);
7178: fprintf(ficlog," %le",delti3[i][j][k]);
7179: }
7180: fscanf(ficpar,"\n");
7181: numlinepar++;
7182: printf("\n");
7183: fprintf(ficparo,"\n");
7184: fprintf(ficlog,"\n");
7185: }
7186: }
7187: fflush(ficlog);
7188:
1.145 brouard 7189: /* Reads covariance matrix */
1.126 brouard 7190: delti=delti3[1][1];
7191:
7192:
7193: /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
7194:
7195: /* Reads comments: lines beginning with '#' */
7196: while((c=getc(ficpar))=='#' && c!= EOF){
7197: ungetc(c,ficpar);
7198: fgets(line, MAXLINE, ficpar);
7199: numlinepar++;
1.141 brouard 7200: fputs(line,stdout);
1.126 brouard 7201: fputs(line,ficparo);
7202: fputs(line,ficlog);
7203: }
7204: ungetc(c,ficpar);
7205:
7206: matcov=matrix(1,npar,1,npar);
1.203 brouard 7207: hess=matrix(1,npar,1,npar);
1.131 brouard 7208: for(i=1; i <=npar; i++)
7209: for(j=1; j <=npar; j++) matcov[i][j]=0.;
7210:
1.194 brouard 7211: /* Scans npar lines */
1.126 brouard 7212: for(i=1; i <=npar; i++){
1.194 brouard 7213: count=fscanf(ficpar,"%1d%1d%1d",&i1,&j1,&jk);
7214: if(count != 3){
7215: printf("Error! Error in parameter file %s at line %d after line starting with %1d%1d%1d\n\
7216: This is probably because your covariance matrix doesn't \n contain exactly %d lines corresponding to your model line '1+age+%s'.\n\
7217: Please run with mle=-1 to get a correct covariance matrix.\n",optionfile,numlinepar, i1,j1,jk, npar, model);
7218: fprintf(ficlog,"Error! Error in parameter file %s at line %d after line starting with %1d%1d%1d\n\
7219: This is probably because your covariance matrix doesn't \n contain exactly %d lines corresponding to your model line '1+age+%s'.\n\
7220: Please run with mle=-1 to get a correct covariance matrix.\n",optionfile,numlinepar, i1,j1,jk, npar, model);
7221: exit(1);
7222: }else
1.126 brouard 7223: if(mle==1)
1.194 brouard 7224: printf("%1d%1d%1d",i1,j1,jk);
7225: fprintf(ficlog,"%1d%1d%1d",i1,j1,jk);
7226: fprintf(ficparo,"%1d%1d%1d",i1,j1,jk);
1.126 brouard 7227: for(j=1; j <=i; j++){
7228: fscanf(ficpar," %le",&matcov[i][j]);
7229: if(mle==1){
7230: printf(" %.5le",matcov[i][j]);
7231: }
7232: fprintf(ficlog," %.5le",matcov[i][j]);
7233: fprintf(ficparo," %.5le",matcov[i][j]);
7234: }
7235: fscanf(ficpar,"\n");
7236: numlinepar++;
7237: if(mle==1)
7238: printf("\n");
7239: fprintf(ficlog,"\n");
7240: fprintf(ficparo,"\n");
7241: }
1.194 brouard 7242: /* End of read covariance matrix npar lines */
1.126 brouard 7243: for(i=1; i <=npar; i++)
7244: for(j=i+1;j<=npar;j++)
7245: matcov[i][j]=matcov[j][i];
7246:
7247: if(mle==1)
7248: printf("\n");
7249: fprintf(ficlog,"\n");
7250:
7251: fflush(ficlog);
7252:
7253: /*-------- Rewriting parameter file ----------*/
7254: strcpy(rfileres,"r"); /* "Rparameterfile */
7255: strcat(rfileres,optionfilefiname); /* Parameter file first name*/
7256: strcat(rfileres,"."); /* */
7257: strcat(rfileres,optionfilext); /* Other files have txt extension */
7258: if((ficres =fopen(rfileres,"w"))==NULL) {
1.201 brouard 7259: printf("Problem writing new parameter file: %s\n", rfileres);goto end;
7260: fprintf(ficlog,"Problem writing new parameter file: %s\n", rfileres);goto end;
1.126 brouard 7261: }
7262: fprintf(ficres,"#%s\n",version);
7263: } /* End of mle != -3 */
7264:
1.186 brouard 7265: /* Main data
7266: */
1.126 brouard 7267: n= lastobs;
7268: num=lvector(1,n);
7269: moisnais=vector(1,n);
7270: annais=vector(1,n);
7271: moisdc=vector(1,n);
7272: andc=vector(1,n);
7273: agedc=vector(1,n);
7274: cod=ivector(1,n);
7275: weight=vector(1,n);
7276: for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
7277: mint=matrix(1,maxwav,1,n);
7278: anint=matrix(1,maxwav,1,n);
1.131 brouard 7279: s=imatrix(1,maxwav+1,1,n); /* s[i][j] health state for wave i and individual j */
1.126 brouard 7280: tab=ivector(1,NCOVMAX);
1.144 brouard 7281: ncodemax=ivector(1,NCOVMAX); /* Number of code per covariate; if O and 1 only, 2**ncov; V1+V2+V3+V4=>16 */
1.192 brouard 7282: 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 7283:
1.136 brouard 7284: /* Reads data from file datafile */
7285: if (readdata(datafile, firstobs, lastobs, &imx)==1)
7286: goto end;
7287:
7288: /* Calculation of the number of parameters from char model */
1.137 brouard 7289: /* modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4
7290: k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tag[cptcovage=1]=4
7291: k=3 V4 Tvar[k=3]= 4 (from V4)
7292: k=2 V1 Tvar[k=2]= 1 (from V1)
7293: k=1 Tvar[1]=2 (from V2)
7294: */
7295: Tvar=ivector(1,NCOVMAX); /* Was 15 changed to NCOVMAX. */
7296: /* V2+V1+V4+age*V3 is a model with 4 covariates (3 plus signs).
7297: For each model-covariate stores the data-covariate id. Tvar[1]=2, Tvar[2]=1, Tvar[3]=4,
7298: Tvar[4=age*V3] is 3 and 'age' is recorded in Tage.
7299: */
7300: /* For model-covariate k tells which data-covariate to use but
7301: because this model-covariate is a construction we invent a new column
7302: ncovcol + k1
7303: If already ncovcol=4 and model=V2+V1+V1*V4+age*V3
7304: Tvar[3=V1*V4]=4+1 etc */
1.145 brouard 7305: Tprod=ivector(1,NCOVMAX); /* Gives the position of a product */
1.137 brouard 7306: /* Tprod[k1=1]=3(=V1*V4) for V2+V1+V1*V4+age*V3
7307: if V2+V1+V1*V4+age*V3+V3*V2 TProd[k1=2]=5 (V3*V2)
7308: */
1.145 brouard 7309: Tvaraff=ivector(1,NCOVMAX); /* Unclear */
7310: 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 7311: * For V3*V2 (in V2+V1+V1*V4+age*V3+V3*V2), V3*V2 position is 2nd.
7312: * Tvard[k1=2][1]=3 (V3) Tvard[k1=2][2]=2(V2) */
1.145 brouard 7313: Tage=ivector(1,NCOVMAX); /* Gives the covariate id of covariates associated with age: V2 + V1 + age*V4 + V3*age
1.137 brouard 7314: 4 covariates (3 plus signs)
7315: Tage[1=V3*age]= 4; Tage[2=age*V4] = 3
7316: */
1.136 brouard 7317:
1.186 brouard 7318: /* Main decodemodel */
7319:
1.187 brouard 7320:
1.136 brouard 7321: if(decodemodel(model, lastobs) == 1)
7322: goto end;
7323:
1.137 brouard 7324: if((double)(lastobs-imx)/(double)imx > 1.10){
7325: nbwarn++;
7326: 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);
7327: 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);
7328: }
1.136 brouard 7329: /* if(mle==1){*/
1.137 brouard 7330: if (weightopt != 1) { /* Maximisation without weights. We can have weights different from 1 but want no weight*/
7331: for(i=1;i<=imx;i++) weight[i]=1.0; /* changed to imx */
1.136 brouard 7332: }
7333:
7334: /*-calculation of age at interview from date of interview and age at death -*/
7335: agev=matrix(1,maxwav,1,imx);
7336:
7337: if(calandcheckages(imx, maxwav, &agemin, &agemax, &nberr, &nbwarn) == 1)
7338: goto end;
7339:
1.126 brouard 7340:
1.136 brouard 7341: agegomp=(int)agemin;
7342: free_vector(moisnais,1,n);
7343: free_vector(annais,1,n);
1.126 brouard 7344: /* free_matrix(mint,1,maxwav,1,n);
7345: free_matrix(anint,1,maxwav,1,n);*/
7346: free_vector(moisdc,1,n);
7347: free_vector(andc,1,n);
1.145 brouard 7348: /* */
7349:
1.126 brouard 7350: wav=ivector(1,imx);
7351: dh=imatrix(1,lastpass-firstpass+1,1,imx);
7352: bh=imatrix(1,lastpass-firstpass+1,1,imx);
7353: mw=imatrix(1,lastpass-firstpass+1,1,imx);
7354:
7355: /* Concatenates waves */
7356: concatwav(wav, dh, bh, mw, s, agedc, agev, firstpass, lastpass, imx, nlstate, stepm);
1.145 brouard 7357: /* */
7358:
1.126 brouard 7359: /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
7360:
7361: nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
7362: ncodemax[1]=1;
1.145 brouard 7363: Ndum =ivector(-1,NCOVMAX);
1.187 brouard 7364: if (ncovmodel-nagesqr > 2 ) /* That is if covariate other than cst, age and age*age */
1.145 brouard 7365: tricode(Tvar,nbcode,imx, Ndum); /**< Fills nbcode[Tvar[j]][l]; */
1.186 brouard 7366: /* Nbcode gives the value of the lth modality of jth covariate, in
7367: V2+V1*age, there are 3 covariates Tvar[2]=1 (V1).*/
7368: /* 1 to ncodemax[j] is the maximum value of this jth covariate */
1.145 brouard 7369:
1.200 brouard 7370: /* codtab=imatrix(1,100,1,10);*/ /* codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) */
1.198 brouard 7371: /*printf(" codtab[1,1],codtab[100,10]=%d,%d\n", codtab[1][1],codtabm(100,10));*/
1.186 brouard 7372: /* codtab gives the value 1 or 2 of the hth combination of k covariates (1 or 2).*/
1.145 brouard 7373: h=0;
7374:
7375:
7376: /*if (cptcovn > 0) */
1.126 brouard 7377:
1.145 brouard 7378:
1.126 brouard 7379: m=pow(2,cptcoveff);
7380:
1.144 brouard 7381: /**< codtab(h,k) k = codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) + 1
1.186 brouard 7382: * For k=4 covariates, h goes from 1 to 2**k
7383: * codtabm(h,k)= 1 & (h-1) >> (k-1) ;
7384: * h\k 1 2 3 4
1.143 brouard 7385: *______________________________
7386: * 1 i=1 1 i=1 1 i=1 1 i=1 1
7387: * 2 2 1 1 1
7388: * 3 i=2 1 2 1 1
7389: * 4 2 2 1 1
7390: * 5 i=3 1 i=2 1 2 1
7391: * 6 2 1 2 1
7392: * 7 i=4 1 2 2 1
7393: * 8 2 2 2 1
1.197 brouard 7394: * 9 i=5 1 i=3 1 i=2 1 2
7395: * 10 2 1 1 2
7396: * 11 i=6 1 2 1 2
7397: * 12 2 2 1 2
7398: * 13 i=7 1 i=4 1 2 2
7399: * 14 2 1 2 2
7400: * 15 i=8 1 2 2 2
7401: * 16 2 2 2 2
1.143 brouard 7402: */
1.202 brouard 7403: /* /\* for(h=1; h <=100 ;h++){ *\/ */
7404: /* /\* printf("h=%2d ", h); *\/ */
7405: /* /\* for(k=1; k <=10; k++){ *\/ */
7406: /* /\* printf("k=%d %d ",k,codtabm(h,k)); *\/ */
7407: /* /\* codtab[h][k]=codtabm(h,k); *\/ */
7408: /* /\* } *\/ */
7409: /* /\* printf("\n"); *\/ */
7410: /* } */
1.197 brouard 7411: /* for(k=1;k<=cptcoveff; k++){ /\* scans any effective covariate *\/ */
7412: /* 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 *\/ */
7413: /* for(j=1; j <= ncodemax[k]; j++){ /\* For each modality of this covariate ncodemax=2*\/ */
7414: /* for(cpt=1; cpt <=pow(2,k-1); cpt++){ /\* cpt=1 to 8/2**(3+1-1 or 3+1-3) =1 or 4 *\/ */
7415: /* h++; */
7416: /* if (h>m) */
7417: /* h=1; */
7418: /* codtab[h][k]=j; */
7419: /* /\* codtab[12][3]=1; *\/ */
7420: /* /\*codtab[h][Tvar[k]]=j;*\/ */
7421: /* /\* 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]]); *\/ */
7422: /* } */
7423: /* } */
7424: /* } */
7425: /* } */
1.126 brouard 7426: /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);
7427: codtab[1][2]=1;codtab[2][2]=2; */
1.197 brouard 7428: /* for(i=1; i <=m ;i++){ */
7429: /* for(k=1; k <=cptcovn; k++){ */
7430: /* printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff); */
7431: /* } */
7432: /* printf("\n"); */
7433: /* } */
7434: /* scanf("%d",i);*/
1.145 brouard 7435:
7436: free_ivector(Ndum,-1,NCOVMAX);
7437:
7438:
1.126 brouard 7439:
1.186 brouard 7440: /* Initialisation of ----------- gnuplot -------------*/
1.126 brouard 7441: strcpy(optionfilegnuplot,optionfilefiname);
7442: if(mle==-3)
1.201 brouard 7443: strcat(optionfilegnuplot,"-MORT_");
1.126 brouard 7444: strcat(optionfilegnuplot,".gp");
7445:
7446: if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
7447: printf("Problem with file %s",optionfilegnuplot);
7448: }
7449: else{
1.204 brouard 7450: fprintf(ficgp,"\n# IMaCh-%s\n", version);
1.126 brouard 7451: fprintf(ficgp,"# %s\n", optionfilegnuplot);
1.141 brouard 7452: //fprintf(ficgp,"set missing 'NaNq'\n");
7453: fprintf(ficgp,"set datafile missing 'NaNq'\n");
1.126 brouard 7454: }
7455: /* fclose(ficgp);*/
1.186 brouard 7456:
7457:
7458: /* Initialisation of --------- index.htm --------*/
1.126 brouard 7459:
7460: strcpy(optionfilehtm,optionfilefiname); /* Main html file */
7461: if(mle==-3)
1.201 brouard 7462: strcat(optionfilehtm,"-MORT_");
1.126 brouard 7463: strcat(optionfilehtm,".htm");
7464: if((fichtm=fopen(optionfilehtm,"w"))==NULL) {
1.131 brouard 7465: printf("Problem with %s \n",optionfilehtm);
7466: exit(0);
1.126 brouard 7467: }
7468:
7469: strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
7470: strcat(optionfilehtmcov,"-cov.htm");
7471: if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL) {
7472: printf("Problem with %s \n",optionfilehtmcov), exit(0);
7473: }
7474: else{
7475: fprintf(fichtmcov,"<html><head>\n<title>IMaCh Cov %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
7476: <hr size=\"2\" color=\"#EC5E5E\"> \n\
1.204 brouard 7477: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n",\
1.126 brouard 7478: optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
7479: }
7480:
1.204 brouard 7481: 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> \
7482: <hr size=\"2\" color=\"#EC5E5E\"> \n\
7483: <font size=\"2\">IMaCh-%s <br> %s</font> \
1.126 brouard 7484: <hr size=\"2\" color=\"#EC5E5E\"> \n\
1.204 brouard 7485: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n\
1.126 brouard 7486: \n\
7487: <hr size=\"2\" color=\"#EC5E5E\">\
7488: <ul><li><h4>Parameter files</h4>\n\
7489: - Parameter file: <a href=\"%s.%s\">%s.%s</a><br>\n\
7490: - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
7491: - Log file of the run: <a href=\"%s\">%s</a><br>\n\
7492: - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
7493: - Date and time at start: %s</ul>\n",\
7494: optionfilehtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
7495: optionfilefiname,optionfilext,optionfilefiname,optionfilext,\
7496: fileres,fileres,\
7497: filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
7498: fflush(fichtm);
7499:
7500: strcpy(pathr,path);
7501: strcat(pathr,optionfilefiname);
1.184 brouard 7502: #ifdef WIN32
7503: _chdir(optionfilefiname); /* Move to directory named optionfile */
7504: #else
1.126 brouard 7505: chdir(optionfilefiname); /* Move to directory named optionfile */
1.184 brouard 7506: #endif
7507:
1.126 brouard 7508:
7509: /* Calculates basic frequencies. Computes observed prevalence at single age
7510: and prints on file fileres'p'. */
7511: freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart);
7512:
7513: fprintf(fichtm,"\n");
7514: fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
7515: Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
7516: Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
7517: imx,agemin,agemax,jmin,jmax,jmean);
7518: pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
7519: oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
7520: newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
7521: savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
7522: oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
7523:
7524:
7525: /* For Powell, parameters are in a vector p[] starting at p[1]
7526: so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
7527: p=param[1][1]; /* *(*(*(param +1)+1)+0) */
7528:
7529: globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
1.186 brouard 7530: /* For mortality only */
1.126 brouard 7531: if (mle==-3){
1.136 brouard 7532: ximort=matrix(1,NDIM,1,NDIM);
1.186 brouard 7533: /* ximort=gsl_matrix_alloc(1,NDIM,1,NDIM); */
1.126 brouard 7534: cens=ivector(1,n);
7535: ageexmed=vector(1,n);
7536: agecens=vector(1,n);
7537: dcwave=ivector(1,n);
7538:
7539: for (i=1; i<=imx; i++){
7540: dcwave[i]=-1;
7541: for (m=firstpass; m<=lastpass; m++)
7542: if (s[m][i]>nlstate) {
7543: dcwave[i]=m;
7544: /* printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
7545: break;
7546: }
7547: }
7548:
7549: for (i=1; i<=imx; i++) {
7550: if (wav[i]>0){
7551: ageexmed[i]=agev[mw[1][i]][i];
7552: j=wav[i];
7553: agecens[i]=1.;
7554:
7555: if (ageexmed[i]> 1 && wav[i] > 0){
7556: agecens[i]=agev[mw[j][i]][i];
7557: cens[i]= 1;
7558: }else if (ageexmed[i]< 1)
7559: cens[i]= -1;
7560: if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
7561: cens[i]=0 ;
7562: }
7563: else cens[i]=-1;
7564: }
7565:
7566: for (i=1;i<=NDIM;i++) {
7567: for (j=1;j<=NDIM;j++)
7568: ximort[i][j]=(i == j ? 1.0 : 0.0);
7569: }
7570:
1.145 brouard 7571: /*p[1]=0.0268; p[NDIM]=0.083;*/
1.126 brouard 7572: /*printf("%lf %lf", p[1], p[2]);*/
7573:
7574:
1.136 brouard 7575: #ifdef GSL
7576: printf("GSL optimization\n"); fprintf(ficlog,"Powell\n");
1.162 brouard 7577: #else
1.126 brouard 7578: printf("Powell\n"); fprintf(ficlog,"Powell\n");
1.136 brouard 7579: #endif
1.201 brouard 7580: strcpy(filerespow,"POW-MORT_");
7581: strcat(filerespow,fileresu);
1.126 brouard 7582: if((ficrespow=fopen(filerespow,"w"))==NULL) {
7583: printf("Problem with resultfile: %s\n", filerespow);
7584: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
7585: }
1.136 brouard 7586: #ifdef GSL
7587: fprintf(ficrespow,"# GSL optimization\n# iter -2*LL");
1.162 brouard 7588: #else
1.126 brouard 7589: fprintf(ficrespow,"# Powell\n# iter -2*LL");
1.136 brouard 7590: #endif
1.126 brouard 7591: /* for (i=1;i<=nlstate;i++)
7592: for(j=1;j<=nlstate+ndeath;j++)
7593: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
7594: */
7595: fprintf(ficrespow,"\n");
1.136 brouard 7596: #ifdef GSL
7597: /* gsl starts here */
7598: T = gsl_multimin_fminimizer_nmsimplex;
7599: gsl_multimin_fminimizer *sfm = NULL;
7600: gsl_vector *ss, *x;
7601: gsl_multimin_function minex_func;
7602:
7603: /* Initial vertex size vector */
7604: ss = gsl_vector_alloc (NDIM);
7605:
7606: if (ss == NULL){
7607: GSL_ERROR_VAL ("failed to allocate space for ss", GSL_ENOMEM, 0);
7608: }
7609: /* Set all step sizes to 1 */
7610: gsl_vector_set_all (ss, 0.001);
7611:
7612: /* Starting point */
1.126 brouard 7613:
1.136 brouard 7614: x = gsl_vector_alloc (NDIM);
7615:
7616: if (x == NULL){
7617: gsl_vector_free(ss);
7618: GSL_ERROR_VAL ("failed to allocate space for x", GSL_ENOMEM, 0);
7619: }
7620:
7621: /* Initialize method and iterate */
7622: /* p[1]=0.0268; p[NDIM]=0.083; */
1.186 brouard 7623: /* gsl_vector_set(x, 0, 0.0268); */
7624: /* gsl_vector_set(x, 1, 0.083); */
1.136 brouard 7625: gsl_vector_set(x, 0, p[1]);
7626: gsl_vector_set(x, 1, p[2]);
7627:
7628: minex_func.f = &gompertz_f;
7629: minex_func.n = NDIM;
7630: minex_func.params = (void *)&p; /* ??? */
7631:
7632: sfm = gsl_multimin_fminimizer_alloc (T, NDIM);
7633: gsl_multimin_fminimizer_set (sfm, &minex_func, x, ss);
7634:
7635: printf("Iterations beginning .....\n\n");
7636: printf("Iter. # Intercept Slope -Log Likelihood Simplex size\n");
7637:
7638: iteri=0;
7639: while (rval == GSL_CONTINUE){
7640: iteri++;
7641: status = gsl_multimin_fminimizer_iterate(sfm);
7642:
7643: if (status) printf("error: %s\n", gsl_strerror (status));
7644: fflush(0);
7645:
7646: if (status)
7647: break;
7648:
7649: rval = gsl_multimin_test_size (gsl_multimin_fminimizer_size (sfm), 1e-6);
7650: ssval = gsl_multimin_fminimizer_size (sfm);
7651:
7652: if (rval == GSL_SUCCESS)
7653: printf ("converged to a local maximum at\n");
7654:
7655: printf("%5d ", iteri);
7656: for (it = 0; it < NDIM; it++){
7657: printf ("%10.5f ", gsl_vector_get (sfm->x, it));
7658: }
7659: printf("f() = %-10.5f ssize = %.7f\n", sfm->fval, ssval);
7660: }
7661:
7662: printf("\n\n Please note: Program should be run many times with varying starting points to detemine global maximum\n\n");
7663:
7664: gsl_vector_free(x); /* initial values */
7665: gsl_vector_free(ss); /* inital step size */
7666: for (it=0; it<NDIM; it++){
7667: p[it+1]=gsl_vector_get(sfm->x,it);
7668: fprintf(ficrespow," %.12lf", p[it]);
7669: }
7670: gsl_multimin_fminimizer_free (sfm); /* p *(sfm.x.data) et p *(sfm.x.data+1) */
7671: #endif
7672: #ifdef POWELL
7673: powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
7674: #endif
1.126 brouard 7675: fclose(ficrespow);
7676:
1.203 brouard 7677: hesscov(matcov, hess, p, NDIM, delti, 1e-4, gompertz);
1.126 brouard 7678:
7679: for(i=1; i <=NDIM; i++)
7680: for(j=i+1;j<=NDIM;j++)
7681: matcov[i][j]=matcov[j][i];
7682:
7683: printf("\nCovariance matrix\n ");
1.203 brouard 7684: fprintf(ficlog,"\nCovariance matrix\n ");
1.126 brouard 7685: for(i=1; i <=NDIM; i++) {
7686: for(j=1;j<=NDIM;j++){
7687: printf("%f ",matcov[i][j]);
1.203 brouard 7688: fprintf(ficlog,"%f ",matcov[i][j]);
1.126 brouard 7689: }
1.203 brouard 7690: printf("\n "); fprintf(ficlog,"\n ");
1.126 brouard 7691: }
7692:
7693: printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
1.193 brouard 7694: for (i=1;i<=NDIM;i++) {
1.126 brouard 7695: printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
1.193 brouard 7696: fprintf(ficlog,"%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
7697: }
1.126 brouard 7698: lsurv=vector(1,AGESUP);
7699: lpop=vector(1,AGESUP);
7700: tpop=vector(1,AGESUP);
7701: lsurv[agegomp]=100000;
7702:
7703: for (k=agegomp;k<=AGESUP;k++) {
7704: agemortsup=k;
7705: if (p[1]*exp(p[2]*(k-agegomp))>1) break;
7706: }
7707:
7708: for (k=agegomp;k<agemortsup;k++)
7709: lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
7710:
7711: for (k=agegomp;k<agemortsup;k++){
7712: lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
7713: sumlpop=sumlpop+lpop[k];
7714: }
7715:
7716: tpop[agegomp]=sumlpop;
7717: for (k=agegomp;k<(agemortsup-3);k++){
7718: /* tpop[k+1]=2;*/
7719: tpop[k+1]=tpop[k]-lpop[k];
7720: }
7721:
7722:
7723: printf("\nAge lx qx dx Lx Tx e(x)\n");
7724: for (k=agegomp;k<(agemortsup-2);k++)
7725: 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]);
7726:
7727:
7728: replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
1.194 brouard 7729: if(ageminpar == AGEOVERFLOW ||agemaxpar == AGEOVERFLOW){
7730: printf("Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
7731: This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\
7732: Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
7733: fprintf(ficlog,"Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
7734: This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\
7735: Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
7736: }else
1.201 brouard 7737: printinggnuplotmort(fileresu, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
7738: printinghtmlmort(fileresu,title,datafile, firstpass, lastpass, \
1.126 brouard 7739: stepm, weightopt,\
7740: model,imx,p,matcov,agemortsup);
7741:
7742: free_vector(lsurv,1,AGESUP);
7743: free_vector(lpop,1,AGESUP);
7744: free_vector(tpop,1,AGESUP);
1.136 brouard 7745: #ifdef GSL
7746: free_ivector(cens,1,n);
7747: free_vector(agecens,1,n);
7748: free_ivector(dcwave,1,n);
7749: free_matrix(ximort,1,NDIM,1,NDIM);
7750: #endif
1.186 brouard 7751: } /* Endof if mle==-3 mortality only */
1.205 brouard 7752: /* Standard */
7753: else{ /* For mle !=- 3, could be 0 or 1 or 4 etc. */
7754: globpr=0;/* Computes sum of likelihood for globpr=1 and funcone */
7755: /* Computes likelihood for initial parameters, uses funcone to compute gpimx and gsw */
1.132 brouard 7756: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
1.126 brouard 7757: printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
7758: for (k=1; k<=npar;k++)
7759: printf(" %d %8.5f",k,p[k]);
7760: printf("\n");
1.205 brouard 7761: if(mle>=1){ /* Could be 1 or 2, Real Maximization */
7762: /* mlikeli uses func not funcone */
7763: mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
7764: }
7765: if(mle==0) {/* No optimization, will print the likelihoods for the datafile */
7766: globpr=0;/* Computes sum of likelihood for globpr=1 and funcone */
7767: /* Computes likelihood for initial parameters, uses funcone to compute gpimx and gsw */
7768: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
7769: }
7770: globpr=1; /* again, to print the individual contributions using computed gpimx and gsw */
1.126 brouard 7771: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
7772: printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
7773: for (k=1; k<=npar;k++)
7774: printf(" %d %8.5f",k,p[k]);
7775: printf("\n");
7776:
7777: /*--------- results files --------------*/
1.192 brouard 7778: 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 7779:
7780:
7781: fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
7782: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
7783: fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
7784: for(i=1,jk=1; i <=nlstate; i++){
7785: for(k=1; k <=(nlstate+ndeath); k++){
7786: if (k != i) {
7787: printf("%d%d ",i,k);
7788: fprintf(ficlog,"%d%d ",i,k);
7789: fprintf(ficres,"%1d%1d ",i,k);
7790: for(j=1; j <=ncovmodel; j++){
1.190 brouard 7791: printf("%12.7f ",p[jk]);
7792: fprintf(ficlog,"%12.7f ",p[jk]);
7793: fprintf(ficres,"%12.7f ",p[jk]);
1.126 brouard 7794: jk++;
7795: }
7796: printf("\n");
7797: fprintf(ficlog,"\n");
7798: fprintf(ficres,"\n");
7799: }
7800: }
7801: }
1.203 brouard 7802: if(mle != 0){
7803: /* Computing hessian and covariance matrix only at a peak of the Likelihood, that is after optimization */
1.126 brouard 7804: ftolhess=ftol; /* Usually correct */
1.203 brouard 7805: hesscov(matcov, hess, p, npar, delti, ftolhess, func);
7806: 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");
7807: 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");
7808: for(i=1,jk=1; i <=nlstate; i++){
7809: for(k=1; k <=(nlstate+ndeath); k++){
7810: if (k != i) {
7811: printf("%d%d ",i,k);
7812: fprintf(ficlog,"%d%d ",i,k);
7813: for(j=1; j <=ncovmodel; j++){
7814: 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]));
7815: 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]));
7816: jk++;
7817: }
7818: printf("\n");
7819: fprintf(ficlog,"\n");
1.193 brouard 7820: }
7821: }
7822: }
1.203 brouard 7823: } /* end of hesscov and Wald tests */
1.193 brouard 7824:
1.203 brouard 7825: /* */
1.126 brouard 7826: fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
7827: printf("# Scales (for hessian or gradient estimation)\n");
7828: fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
7829: for(i=1,jk=1; i <=nlstate; i++){
7830: for(j=1; j <=nlstate+ndeath; j++){
7831: if (j!=i) {
7832: fprintf(ficres,"%1d%1d",i,j);
7833: printf("%1d%1d",i,j);
7834: fprintf(ficlog,"%1d%1d",i,j);
7835: for(k=1; k<=ncovmodel;k++){
7836: printf(" %.5e",delti[jk]);
7837: fprintf(ficlog," %.5e",delti[jk]);
7838: fprintf(ficres," %.5e",delti[jk]);
7839: jk++;
7840: }
7841: printf("\n");
7842: fprintf(ficlog,"\n");
7843: fprintf(ficres,"\n");
7844: }
7845: }
7846: }
7847:
7848: 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 7849: if(mle >= 1) /* To big for the screen */
1.126 brouard 7850: 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");
7851: 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");
7852: /* # 121 Var(a12)\n\ */
7853: /* # 122 Cov(b12,a12) Var(b12)\n\ */
7854: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
7855: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
7856: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
7857: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
7858: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
7859: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
7860:
7861:
7862: /* Just to have a covariance matrix which will be more understandable
7863: even is we still don't want to manage dictionary of variables
7864: */
7865: for(itimes=1;itimes<=2;itimes++){
7866: jj=0;
7867: for(i=1; i <=nlstate; i++){
7868: for(j=1; j <=nlstate+ndeath; j++){
7869: if(j==i) continue;
7870: for(k=1; k<=ncovmodel;k++){
7871: jj++;
7872: ca[0]= k+'a'-1;ca[1]='\0';
7873: if(itimes==1){
7874: if(mle>=1)
7875: printf("#%1d%1d%d",i,j,k);
7876: fprintf(ficlog,"#%1d%1d%d",i,j,k);
7877: fprintf(ficres,"#%1d%1d%d",i,j,k);
7878: }else{
7879: if(mle>=1)
7880: printf("%1d%1d%d",i,j,k);
7881: fprintf(ficlog,"%1d%1d%d",i,j,k);
7882: fprintf(ficres,"%1d%1d%d",i,j,k);
7883: }
7884: ll=0;
7885: for(li=1;li <=nlstate; li++){
7886: for(lj=1;lj <=nlstate+ndeath; lj++){
7887: if(lj==li) continue;
7888: for(lk=1;lk<=ncovmodel;lk++){
7889: ll++;
7890: if(ll<=jj){
7891: cb[0]= lk +'a'-1;cb[1]='\0';
7892: if(ll<jj){
7893: if(itimes==1){
7894: if(mle>=1)
7895: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
7896: fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
7897: fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
7898: }else{
7899: if(mle>=1)
7900: printf(" %.5e",matcov[jj][ll]);
7901: fprintf(ficlog," %.5e",matcov[jj][ll]);
7902: fprintf(ficres," %.5e",matcov[jj][ll]);
7903: }
7904: }else{
7905: if(itimes==1){
7906: if(mle>=1)
7907: printf(" Var(%s%1d%1d)",ca,i,j);
7908: fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
7909: fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
7910: }else{
7911: if(mle>=1)
1.203 brouard 7912: printf(" %.7e",matcov[jj][ll]);
7913: fprintf(ficlog," %.7e",matcov[jj][ll]);
7914: fprintf(ficres," %.7e",matcov[jj][ll]);
1.126 brouard 7915: }
7916: }
7917: }
7918: } /* end lk */
7919: } /* end lj */
7920: } /* end li */
7921: if(mle>=1)
7922: printf("\n");
7923: fprintf(ficlog,"\n");
7924: fprintf(ficres,"\n");
7925: numlinepar++;
7926: } /* end k*/
7927: } /*end j */
7928: } /* end i */
7929: } /* end itimes */
7930:
7931: fflush(ficlog);
7932: fflush(ficres);
1.209 ! brouard 7933: while(fgets(line, MAXLINE, ficpar)) {
! 7934: /* If line starts with a # it is a comment */
! 7935: if (line[0] == '#') {
! 7936: numlinepar++;
1.141 brouard 7937: fputs(line,stdout);
1.126 brouard 7938: fputs(line,ficparo);
1.209 ! brouard 7939: fputs(line,ficlog);
! 7940: continue;
! 7941: }else
! 7942: break;
! 7943: }
! 7944:
! 7945: /* while((c=getc(ficpar))=='#' && c!= EOF){ */
! 7946: /* ungetc(c,ficpar); */
! 7947: /* fgets(line, MAXLINE, ficpar); */
! 7948: /* fputs(line,stdout); */
! 7949: /* fputs(line,ficparo); */
! 7950: /* } */
! 7951: /* ungetc(c,ficpar); */
1.126 brouard 7952:
7953: estepm=0;
1.209 ! brouard 7954: if((num_filled=sscanf(line,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d ftolpl=%lf\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm, &ftolpl)) !=EOF){
! 7955:
! 7956: if (num_filled != 6) {
! 7957: printf("Not 6 parameters in line, for example:agemin=60 agemax=95 bage=55 fage=95 estepm=24 ftolpl=6e-4\n");
! 7958: printf("but line=%s\n",line);
! 7959: goto end;
! 7960: }
! 7961: printf("agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d ftolpl=%lf\n",ageminpar,agemaxpar, bage, fage, estepm, ftolpl);
! 7962: }
! 7963: /* ftolpl=6*ftol*1.e5; /\* 6.e-3 make convergences in less than 80 loops for the prevalence limit *\/ */
! 7964: /*ftolpl=6.e-4;*/ /* 6.e-3 make convergences in less than 80 loops for the prevalence limit */
! 7965:
! 7966: /* fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d ftolpl=%\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm); */
1.126 brouard 7967: if (estepm==0 || estepm < stepm) estepm=stepm;
7968: if (fage <= 2) {
7969: bage = ageminpar;
7970: fage = agemaxpar;
7971: }
7972:
7973: fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
7974: fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
7975: fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
1.186 brouard 7976:
7977: /* Other stuffs, more or less useful */
1.126 brouard 7978: while((c=getc(ficpar))=='#' && c!= EOF){
7979: ungetc(c,ficpar);
7980: fgets(line, MAXLINE, ficpar);
1.141 brouard 7981: fputs(line,stdout);
1.126 brouard 7982: fputs(line,ficparo);
7983: }
7984: ungetc(c,ficpar);
7985:
7986: 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);
7987: 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);
7988: 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);
7989: printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
7990: 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);
7991:
7992: while((c=getc(ficpar))=='#' && c!= EOF){
7993: ungetc(c,ficpar);
7994: fgets(line, MAXLINE, ficpar);
1.141 brouard 7995: fputs(line,stdout);
1.126 brouard 7996: fputs(line,ficparo);
7997: }
7998: ungetc(c,ficpar);
7999:
8000:
8001: dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
8002: dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
8003:
8004: fscanf(ficpar,"pop_based=%d\n",&popbased);
1.193 brouard 8005: fprintf(ficlog,"pop_based=%d\n",popbased);
1.126 brouard 8006: fprintf(ficparo,"pop_based=%d\n",popbased);
8007: fprintf(ficres,"pop_based=%d\n",popbased);
8008:
8009: while((c=getc(ficpar))=='#' && c!= EOF){
8010: ungetc(c,ficpar);
8011: fgets(line, MAXLINE, ficpar);
1.141 brouard 8012: fputs(line,stdout);
1.126 brouard 8013: fputs(line,ficparo);
8014: }
8015: ungetc(c,ficpar);
8016:
8017: 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);
8018: 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);
8019: 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);
8020: 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);
8021: 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);
8022: /* day and month of proj2 are not used but only year anproj2.*/
8023:
8024:
8025:
1.145 brouard 8026: /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint); */
8027: /* ,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2); */
1.126 brouard 8028:
8029: replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
1.194 brouard 8030: if(ageminpar == AGEOVERFLOW ||agemaxpar == -AGEOVERFLOW){
8031: printf("Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
8032: This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\
8033: Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
8034: fprintf(ficlog,"Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
8035: This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\
8036: Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
8037: }else
1.201 brouard 8038: printinggnuplot(fileresu, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
1.126 brouard 8039:
1.201 brouard 8040: printinghtml(fileresu,title,datafile, firstpass, lastpass, stepm, weightopt,\
1.126 brouard 8041: model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
8042: jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
8043:
8044: /*------------ free_vector -------------*/
8045: /* chdir(path); */
8046:
8047: free_ivector(wav,1,imx);
8048: free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
8049: free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
8050: free_imatrix(mw,1,lastpass-firstpass+1,1,imx);
8051: free_lvector(num,1,n);
8052: free_vector(agedc,1,n);
8053: /*free_matrix(covar,0,NCOVMAX,1,n);*/
8054: /*free_matrix(covar,1,NCOVMAX,1,n);*/
8055: fclose(ficparo);
8056: fclose(ficres);
8057:
8058:
1.186 brouard 8059: /* Other results (useful)*/
8060:
8061:
1.126 brouard 8062: /*--------------- Prevalence limit (period or stable prevalence) --------------*/
1.180 brouard 8063: /*#include "prevlim.h"*/ /* Use ficrespl, ficlog */
8064: prlim=matrix(1,nlstate,1,nlstate);
1.209 ! brouard 8065: prevalence_limit(p, prlim, ageminpar, agemaxpar, ftolpl, &ncvyear);
1.126 brouard 8066: fclose(ficrespl);
8067:
1.145 brouard 8068: #ifdef FREEEXIT2
8069: #include "freeexit2.h"
8070: #endif
8071:
1.126 brouard 8072: /*------------- h Pij x at various ages ------------*/
1.180 brouard 8073: /*#include "hpijx.h"*/
8074: hPijx(p, bage, fage);
1.145 brouard 8075: fclose(ficrespij);
1.126 brouard 8076:
1.145 brouard 8077: /*-------------- Variance of one-step probabilities---*/
8078: k=1;
1.126 brouard 8079: varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
8080:
8081:
8082: probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
8083: for(i=1;i<=AGESUP;i++)
8084: for(j=1;j<=NCOVMAX;j++)
8085: for(k=1;k<=NCOVMAX;k++)
8086: probs[i][j][k]=0.;
8087:
8088: /*---------- Forecasting ------------------*/
8089: /*if((stepm == 1) && (strcmp(model,".")==0)){*/
8090: if(prevfcast==1){
8091: /* if(stepm ==1){*/
1.201 brouard 8092: prevforecast(fileresu, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
1.126 brouard 8093: /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
8094: /* } */
8095: /* else{ */
8096: /* erreur=108; */
8097: /* 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); */
8098: /* 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); */
8099: /* } */
8100: }
1.186 brouard 8101:
8102: /* ------ Other prevalence ratios------------ */
1.126 brouard 8103:
1.127 brouard 8104: /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
8105:
8106: prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
8107: /* 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",\
8108: ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
8109: */
1.126 brouard 8110:
1.127 brouard 8111: if (mobilav!=0) {
8112: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
8113: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
8114: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
8115: printf(" Error in movingaverage mobilav=%d\n",mobilav);
8116: }
1.126 brouard 8117: }
8118:
8119:
1.127 brouard 8120: /*---------- Health expectancies, no variances ------------*/
8121:
1.201 brouard 8122: strcpy(filerese,"E_");
8123: strcat(filerese,fileresu);
1.126 brouard 8124: if((ficreseij=fopen(filerese,"w"))==NULL) {
8125: printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
8126: fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
8127: }
1.208 brouard 8128: printf("Computing Health Expectancies: result on file '%s' ...", filerese);fflush(stdout);
8129: fprintf(ficlog,"Computing Health Expectancies: result on file '%s' ...", filerese);fflush(ficlog);
1.145 brouard 8130: /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
8131: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
8132:
8133: for (k=1; k <= (int) pow(2,cptcoveff); k++){
1.127 brouard 8134: fprintf(ficreseij,"\n#****** ");
8135: for(j=1;j<=cptcoveff;j++) {
1.200 brouard 8136: fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.127 brouard 8137: }
8138: fprintf(ficreseij,"******\n");
8139:
8140: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
8141: oldm=oldms;savm=savms;
8142: evsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart);
8143:
8144: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
1.145 brouard 8145: /*}*/
1.127 brouard 8146: }
8147: fclose(ficreseij);
1.208 brouard 8148: printf("done evsij\n");fflush(stdout);
8149: fprintf(ficlog,"done evsij\n");fflush(ficlog);
1.127 brouard 8150:
8151: /*---------- Health expectancies and variances ------------*/
8152:
8153:
1.201 brouard 8154: strcpy(filerest,"T_");
8155: strcat(filerest,fileresu);
1.127 brouard 8156: if((ficrest=fopen(filerest,"w"))==NULL) {
8157: printf("Problem with total LE resultfile: %s\n", filerest);goto end;
8158: fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
8159: }
1.208 brouard 8160: printf("Computing Total Life expectancies with their standard errors: file '%s' ...\n", filerest); fflush(stdout);
8161: fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' ...\n", filerest); fflush(ficlog);
1.127 brouard 8162:
1.126 brouard 8163:
1.201 brouard 8164: strcpy(fileresstde,"STDE_");
8165: strcat(fileresstde,fileresu);
1.126 brouard 8166: if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {
8167: printf("Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
8168: fprintf(ficlog,"Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
8169: }
1.208 brouard 8170: printf(" Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
8171: fprintf(ficlog," Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
1.126 brouard 8172:
1.201 brouard 8173: strcpy(filerescve,"CVE_");
8174: strcat(filerescve,fileresu);
1.126 brouard 8175: if((ficrescveij=fopen(filerescve,"w"))==NULL) {
8176: printf("Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
8177: fprintf(ficlog,"Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
8178: }
1.208 brouard 8179: printf(" Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
8180: fprintf(ficlog," Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
1.126 brouard 8181:
1.201 brouard 8182: strcpy(fileresv,"V_");
8183: strcat(fileresv,fileresu);
1.126 brouard 8184: if((ficresvij=fopen(fileresv,"w"))==NULL) {
8185: printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
8186: fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
8187: }
1.208 brouard 8188: printf(" Computing Variance-covariance of DFLEs: file '%s' ... ", fileresv);fflush(stdout);
8189: fprintf(ficlog," Computing Variance-covariance of DFLEs: file '%s' ... ", fileresv);fflush(ficlog);
1.126 brouard 8190:
1.145 brouard 8191: /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
8192: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
8193:
8194: for (k=1; k <= (int) pow(2,cptcoveff); k++){
1.208 brouard 8195: fprintf(ficrest,"\n#****** ");
8196: for(j=1;j<=cptcoveff;j++)
8197: fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
8198: fprintf(ficrest,"******\n");
8199:
8200: fprintf(ficresstdeij,"\n#****** ");
8201: fprintf(ficrescveij,"\n#****** ");
8202: for(j=1;j<=cptcoveff;j++) {
8203: fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
8204: fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
8205: }
8206: fprintf(ficresstdeij,"******\n");
8207: fprintf(ficrescveij,"******\n");
8208:
8209: fprintf(ficresvij,"\n#****** ");
8210: for(j=1;j<=cptcoveff;j++)
8211: fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
8212: fprintf(ficresvij,"******\n");
8213:
8214: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
8215: oldm=oldms;savm=savms;
8216: printf(" cvevsij %d, ",k);
8217: fprintf(ficlog, " cvevsij %d, ",k);
8218: cvevsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);
8219: printf(" end cvevsij \n ");
8220: fprintf(ficlog, " end cvevsij \n ");
8221:
8222: /*
8223: */
8224: /* goto endfree; */
8225:
8226: vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
8227: pstamp(ficrest);
8228:
8229:
8230: for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
8231: oldm=oldms;savm=savms; /* ZZ Segmentation fault */
8232: cptcod= 0; /* To be deleted */
8233: printf("varevsij %d \n",vpopbased);
8234: fprintf(ficlog, "varevsij %d \n",vpopbased);
1.209 ! brouard 8235: varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl, &ncvyear, k, estepm, cptcov,cptcod,vpopbased,mobilav, strstart); /* cptcod not initialized Intel */
1.208 brouard 8236: 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 ");
8237: if(vpopbased==1)
8238: 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);
8239: else
8240: fprintf(ficrest,"the age specific period (stable) prevalences in each health state \n");
8241: fprintf(ficrest,"# Age popbased mobilav e.. (std) ");
8242: for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
8243: fprintf(ficrest,"\n");
8244: /* printf("Which p?\n"); for(i=1;i<=npar;i++)printf("p[i=%d]=%lf,",i,p[i]);printf("\n"); */
8245: epj=vector(1,nlstate+1);
8246: printf("Computing age specific period (stable) prevalences in each health state \n");
8247: fprintf(ficlog,"Computing age specific period (stable) prevalences in each health state \n");
8248: for(age=bage; age <=fage ;age++){
1.209 ! brouard 8249: prevalim(prlim, nlstate, p, age, oldm, savm, ftolpl, &ncvyear, k); /*ZZ Is it the correct prevalim */
1.208 brouard 8250: if (vpopbased==1) {
8251: if(mobilav ==0){
8252: for(i=1; i<=nlstate;i++)
8253: prlim[i][i]=probs[(int)age][i][k];
8254: }else{ /* mobilav */
8255: for(i=1; i<=nlstate;i++)
8256: prlim[i][i]=mobaverage[(int)age][i][k];
1.126 brouard 8257: }
1.208 brouard 8258: }
8259:
8260: fprintf(ficrest," %4.0f %d %d",age, vpopbased, mobilav);
8261: /* fprintf(ficrest," %4.0f %d %d %d %d",age, vpopbased, mobilav,Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); */ /* to be done */
8262: /* printf(" age %4.0f ",age); */
8263: for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
8264: for(i=1, epj[j]=0.;i <=nlstate;i++) {
8265: epj[j] += prlim[i][i]*eij[i][j][(int)age];
8266: /*ZZZ printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
8267: /* printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]); */
1.126 brouard 8268: }
1.208 brouard 8269: epj[nlstate+1] +=epj[j];
8270: }
8271: /* printf(" age %4.0f \n",age); */
8272:
8273: for(i=1, vepp=0.;i <=nlstate;i++)
8274: for(j=1;j <=nlstate;j++)
8275: vepp += vareij[i][j][(int)age];
8276: fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
8277: for(j=1;j <=nlstate;j++){
8278: fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
1.126 brouard 8279: }
1.208 brouard 8280: fprintf(ficrest,"\n");
1.126 brouard 8281: }
1.208 brouard 8282: } /* End vpopbased */
8283: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
8284: free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
8285: free_vector(epj,1,nlstate+1);
8286: printf("done \n");fflush(stdout);
8287: fprintf(ficlog,"done\n");fflush(ficlog);
8288:
1.145 brouard 8289: /*}*/
1.208 brouard 8290: } /* End k */
1.126 brouard 8291: free_vector(weight,1,n);
1.145 brouard 8292: free_imatrix(Tvard,1,NCOVMAX,1,2);
1.126 brouard 8293: free_imatrix(s,1,maxwav+1,1,n);
8294: free_matrix(anint,1,maxwav,1,n);
8295: free_matrix(mint,1,maxwav,1,n);
8296: free_ivector(cod,1,n);
8297: free_ivector(tab,1,NCOVMAX);
8298: fclose(ficresstdeij);
8299: fclose(ficrescveij);
8300: fclose(ficresvij);
8301: fclose(ficrest);
1.208 brouard 8302: printf("done Health expectancies\n");fflush(stdout);
8303: fprintf(ficlog,"done Health expectancies\n");fflush(ficlog);
1.126 brouard 8304: fclose(ficpar);
8305:
8306: /*------- Variance of period (stable) prevalence------*/
8307:
1.201 brouard 8308: strcpy(fileresvpl,"VPL_");
8309: strcat(fileresvpl,fileresu);
1.126 brouard 8310: if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
8311: printf("Problem with variance of period (stable) prevalence resultfile: %s\n", fileresvpl);
8312: exit(0);
8313: }
1.208 brouard 8314: printf("Computing Variance-covariance of period (stable) prevalence: file '%s' ...", fileresvpl);fflush(stdout);
8315: fprintf(ficlog, "Computing Variance-covariance of period (stable) prevalence: file '%s' ...", fileresvpl);fflush(ficlog);
1.126 brouard 8316:
1.145 brouard 8317: /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
8318: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
8319:
8320: for (k=1; k <= (int) pow(2,cptcoveff); k++){
8321: fprintf(ficresvpl,"\n#****** ");
1.126 brouard 8322: for(j=1;j<=cptcoveff;j++)
1.200 brouard 8323: fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.126 brouard 8324: fprintf(ficresvpl,"******\n");
8325:
8326: varpl=matrix(1,nlstate,(int) bage, (int) fage);
8327: oldm=oldms;savm=savms;
1.209 ! brouard 8328: varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl, &ncvyear, k, strstart);
1.126 brouard 8329: free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
1.145 brouard 8330: /*}*/
1.126 brouard 8331: }
8332:
8333: fclose(ficresvpl);
1.208 brouard 8334: printf("done variance-covariance of period prevalence\n");fflush(stdout);
8335: fprintf(ficlog,"done variance-covariance of period prevalence\n");fflush(ficlog);
1.126 brouard 8336:
8337: /*---------- End : free ----------------*/
8338: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
8339: free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
8340: } /* mle==-3 arrives here for freeing */
1.164 brouard 8341: /* endfree:*/
1.141 brouard 8342: free_matrix(prlim,1,nlstate,1,nlstate); /*here or after loop ? */
1.126 brouard 8343: free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
8344: free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
8345: free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
8346: free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
8347: free_matrix(covar,0,NCOVMAX,1,n);
8348: free_matrix(matcov,1,npar,1,npar);
1.203 brouard 8349: free_matrix(hess,1,npar,1,npar);
1.126 brouard 8350: /*free_vector(delti,1,npar);*/
8351: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
8352: free_matrix(agev,1,maxwav,1,imx);
8353: free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
8354:
1.145 brouard 8355: free_ivector(ncodemax,1,NCOVMAX);
1.192 brouard 8356: free_ivector(ncodemaxwundef,1,NCOVMAX);
1.145 brouard 8357: free_ivector(Tvar,1,NCOVMAX);
8358: free_ivector(Tprod,1,NCOVMAX);
8359: free_ivector(Tvaraff,1,NCOVMAX);
8360: free_ivector(Tage,1,NCOVMAX);
1.126 brouard 8361:
8362: free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
1.200 brouard 8363: /* free_imatrix(codtab,1,100,1,10); */
1.126 brouard 8364: fflush(fichtm);
8365: fflush(ficgp);
8366:
8367:
8368: if((nberr >0) || (nbwarn>0)){
8369: printf("End of Imach with %d errors and/or %d warnings\n",nberr,nbwarn);
8370: fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
8371: }else{
8372: printf("End of Imach\n");
8373: fprintf(ficlog,"End of Imach\n");
8374: }
8375: printf("See log file on %s\n",filelog);
8376: /* gettimeofday(&end_time, (struct timezone*)0);*/ /* after time */
1.157 brouard 8377: /*(void) gettimeofday(&end_time,&tzp);*/
8378: rend_time = time(NULL);
8379: end_time = *localtime(&rend_time);
8380: /* tml = *localtime(&end_time.tm_sec); */
8381: strcpy(strtend,asctime(&end_time));
1.126 brouard 8382: printf("Local time at start %s\nLocal time at end %s",strstart, strtend);
8383: fprintf(ficlog,"Local time at start %s\nLocal time at end %s\n",strstart, strtend);
1.157 brouard 8384: printf("Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
1.126 brouard 8385:
1.157 brouard 8386: printf("Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
8387: fprintf(ficlog,"Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
8388: fprintf(ficlog,"Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
1.126 brouard 8389: /* printf("Total time was %d uSec.\n", total_usecs);*/
8390: /* if(fileappend(fichtm,optionfilehtm)){ */
8391: fprintf(fichtm,"<br>Local time at start %s<br>Local time at end %s<br>\n</body></html>",strstart, strtend);
8392: fclose(fichtm);
8393: fprintf(fichtmcov,"<br>Local time at start %s<br>Local time at end %s<br>\n</body></html>",strstart, strtend);
8394: fclose(fichtmcov);
8395: fclose(ficgp);
8396: fclose(ficlog);
8397: /*------ End -----------*/
8398:
8399:
8400: printf("Before Current directory %s!\n",pathcd);
1.184 brouard 8401: #ifdef WIN32
8402: if (_chdir(pathcd) != 0)
8403: printf("Can't move to directory %s!\n",path);
8404: if(_getcwd(pathcd,MAXLINE) > 0)
8405: #else
1.126 brouard 8406: if(chdir(pathcd) != 0)
1.184 brouard 8407: printf("Can't move to directory %s!\n", path);
8408: if (getcwd(pathcd, MAXLINE) > 0)
8409: #endif
1.126 brouard 8410: printf("Current directory %s!\n",pathcd);
8411: /*strcat(plotcmd,CHARSEPARATOR);*/
8412: sprintf(plotcmd,"gnuplot");
1.157 brouard 8413: #ifdef _WIN32
1.126 brouard 8414: sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
8415: #endif
8416: if(!stat(plotcmd,&info)){
1.158 brouard 8417: printf("Error or gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
1.126 brouard 8418: if(!stat(getenv("GNUPLOTBIN"),&info)){
1.158 brouard 8419: printf("Error or gnuplot program not found: '%s' Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);
1.126 brouard 8420: }else
8421: strcpy(pplotcmd,plotcmd);
1.157 brouard 8422: #ifdef __unix
1.126 brouard 8423: strcpy(plotcmd,GNUPLOTPROGRAM);
8424: if(!stat(plotcmd,&info)){
1.158 brouard 8425: printf("Error gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
1.126 brouard 8426: }else
8427: strcpy(pplotcmd,plotcmd);
8428: #endif
8429: }else
8430: strcpy(pplotcmd,plotcmd);
8431:
8432: sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
1.158 brouard 8433: printf("Starting graphs with: '%s'\n",plotcmd);fflush(stdout);
1.126 brouard 8434:
8435: if((outcmd=system(plotcmd)) != 0){
1.158 brouard 8436: printf("gnuplot command might not be in your path: '%s', err=%d\n", plotcmd, outcmd);
1.154 brouard 8437: printf("\n Trying if gnuplot resides on the same directory that IMaCh\n");
1.152 brouard 8438: sprintf(plotcmd,"%sgnuplot %s", pathimach, optionfilegnuplot);
1.150 brouard 8439: if((outcmd=system(plotcmd)) != 0)
1.153 brouard 8440: printf("\n Still a problem with gnuplot command %s, err=%d\n", plotcmd, outcmd);
1.126 brouard 8441: }
1.158 brouard 8442: printf(" Successful, please wait...");
1.126 brouard 8443: while (z[0] != 'q') {
8444: /* chdir(path); */
1.154 brouard 8445: printf("\nType e to edit results with your browser, g to graph again and q for exit: ");
1.126 brouard 8446: scanf("%s",z);
8447: /* if (z[0] == 'c') system("./imach"); */
8448: if (z[0] == 'e') {
1.158 brouard 8449: #ifdef __APPLE__
1.152 brouard 8450: sprintf(pplotcmd, "open %s", optionfilehtm);
1.157 brouard 8451: #elif __linux
8452: sprintf(pplotcmd, "xdg-open %s", optionfilehtm);
1.153 brouard 8453: #else
1.152 brouard 8454: sprintf(pplotcmd, "%s", optionfilehtm);
1.153 brouard 8455: #endif
8456: printf("Starting browser with: %s",pplotcmd);fflush(stdout);
8457: system(pplotcmd);
1.126 brouard 8458: }
8459: else if (z[0] == 'g') system(plotcmd);
8460: else if (z[0] == 'q') exit(0);
8461: }
8462: end:
8463: while (z[0] != 'q') {
1.195 brouard 8464: printf("\nType q for exiting: "); fflush(stdout);
1.126 brouard 8465: scanf("%s",z);
8466: }
8467: }
FreeBSD-CVSweb <freebsd-cvsweb@FreeBSD.org>
![[BACK]](/icons/small/back.gif){kind=icon}
Return to imach.c CVS log ![[TXT]](/icons/small/text.gif){kind=icon}
![[DIR]](/icons/small/dir.gif){kind=icon}
Up to [Local Repository] / imach / src