Annotation of imach/src/imach.c, revision 1.235
1.235 ! brouard 1: /* $Id: imach.c,v 1.234 2016/08/23 16:51:20 brouard Exp $
1.126 brouard 2: $State: Exp $
1.163 brouard 3: $Log: imach.c,v $
1.235 ! brouard 4: Revision 1.234 2016/08/23 16:51:20 brouard
! 5: *** empty log message ***
! 6:
1.234 brouard 7: Revision 1.233 2016/08/23 07:40:50 brouard
8: Summary: not working
9:
1.233 brouard 10: Revision 1.232 2016/08/22 14:20:21 brouard
11: Summary: not working
12:
1.232 brouard 13: Revision 1.231 2016/08/22 07:17:15 brouard
14: Summary: not working
15:
1.231 brouard 16: Revision 1.230 2016/08/22 06:55:53 brouard
17: Summary: Not working
18:
1.230 brouard 19: Revision 1.229 2016/07/23 09:45:53 brouard
20: Summary: Completing for func too
21:
1.229 brouard 22: Revision 1.228 2016/07/22 17:45:30 brouard
23: Summary: Fixing some arrays, still debugging
24:
1.227 brouard 25: Revision 1.226 2016/07/12 18:42:34 brouard
26: Summary: temp
27:
1.226 brouard 28: Revision 1.225 2016/07/12 08:40:03 brouard
29: Summary: saving but not running
30:
1.225 brouard 31: Revision 1.224 2016/07/01 13:16:01 brouard
32: Summary: Fixes
33:
1.224 brouard 34: Revision 1.223 2016/02/19 09:23:35 brouard
35: Summary: temporary
36:
1.223 brouard 37: Revision 1.222 2016/02/17 08:14:50 brouard
38: Summary: Probably last 0.98 stable version 0.98r6
39:
1.222 brouard 40: Revision 1.221 2016/02/15 23:35:36 brouard
41: Summary: minor bug
42:
1.220 brouard 43: Revision 1.219 2016/02/15 00:48:12 brouard
44: *** empty log message ***
45:
1.219 brouard 46: Revision 1.218 2016/02/12 11:29:23 brouard
47: Summary: 0.99 Back projections
48:
1.218 brouard 49: Revision 1.217 2015/12/23 17:18:31 brouard
50: Summary: Experimental backcast
51:
1.217 brouard 52: Revision 1.216 2015/12/18 17:32:11 brouard
53: Summary: 0.98r4 Warning and status=-2
54:
55: Version 0.98r4 is now:
56: - displaying an error when status is -1, date of interview unknown and date of death known;
57: - permitting a status -2 when the vital status is unknown at a known date of right truncation.
58: Older changes concerning s=-2, dating from 2005 have been supersed.
59:
1.216 brouard 60: Revision 1.215 2015/12/16 08:52:24 brouard
61: Summary: 0.98r4 working
62:
1.215 brouard 63: Revision 1.214 2015/12/16 06:57:54 brouard
64: Summary: temporary not working
65:
1.214 brouard 66: Revision 1.213 2015/12/11 18:22:17 brouard
67: Summary: 0.98r4
68:
1.213 brouard 69: Revision 1.212 2015/11/21 12:47:24 brouard
70: Summary: minor typo
71:
1.212 brouard 72: Revision 1.211 2015/11/21 12:41:11 brouard
73: Summary: 0.98r3 with some graph of projected cross-sectional
74:
75: Author: Nicolas Brouard
76:
1.211 brouard 77: Revision 1.210 2015/11/18 17:41:20 brouard
78: Summary: Start working on projected prevalences
79:
1.210 brouard 80: Revision 1.209 2015/11/17 22:12:03 brouard
81: Summary: Adding ftolpl parameter
82: Author: N Brouard
83:
84: We had difficulties to get smoothed confidence intervals. It was due
85: to the period prevalence which wasn't computed accurately. The inner
86: parameter ftolpl is now an outer parameter of the .imach parameter
87: file after estepm. If ftolpl is small 1.e-4 and estepm too,
88: computation are long.
89:
1.209 brouard 90: Revision 1.208 2015/11/17 14:31:57 brouard
91: Summary: temporary
92:
1.208 brouard 93: Revision 1.207 2015/10/27 17:36:57 brouard
94: *** empty log message ***
95:
1.207 brouard 96: Revision 1.206 2015/10/24 07:14:11 brouard
97: *** empty log message ***
98:
1.206 brouard 99: Revision 1.205 2015/10/23 15:50:53 brouard
100: Summary: 0.98r3 some clarification for graphs on likelihood contributions
101:
1.205 brouard 102: Revision 1.204 2015/10/01 16:20:26 brouard
103: Summary: Some new graphs of contribution to likelihood
104:
1.204 brouard 105: Revision 1.203 2015/09/30 17:45:14 brouard
106: Summary: looking at better estimation of the hessian
107:
108: Also a better criteria for convergence to the period prevalence And
109: therefore adding the number of years needed to converge. (The
110: prevalence in any alive state shold sum to one
111:
1.203 brouard 112: Revision 1.202 2015/09/22 19:45:16 brouard
113: Summary: Adding some overall graph on contribution to likelihood. Might change
114:
1.202 brouard 115: Revision 1.201 2015/09/15 17:34:58 brouard
116: Summary: 0.98r0
117:
118: - Some new graphs like suvival functions
119: - Some bugs fixed like model=1+age+V2.
120:
1.201 brouard 121: Revision 1.200 2015/09/09 16:53:55 brouard
122: Summary: Big bug thanks to Flavia
123:
124: Even model=1+age+V2. did not work anymore
125:
1.200 brouard 126: Revision 1.199 2015/09/07 14:09:23 brouard
127: Summary: 0.98q6 changing default small png format for graph to vectorized svg.
128:
1.199 brouard 129: Revision 1.198 2015/09/03 07:14:39 brouard
130: Summary: 0.98q5 Flavia
131:
1.198 brouard 132: Revision 1.197 2015/09/01 18:24:39 brouard
133: *** empty log message ***
134:
1.197 brouard 135: Revision 1.196 2015/08/18 23:17:52 brouard
136: Summary: 0.98q5
137:
1.196 brouard 138: Revision 1.195 2015/08/18 16:28:39 brouard
139: Summary: Adding a hack for testing purpose
140:
141: After reading the title, ftol and model lines, if the comment line has
142: a q, starting with #q, the answer at the end of the run is quit. It
143: permits to run test files in batch with ctest. The former workaround was
144: $ echo q | imach foo.imach
145:
1.195 brouard 146: Revision 1.194 2015/08/18 13:32:00 brouard
147: Summary: Adding error when the covariance matrix doesn't contain the exact number of lines required by the model line.
148:
1.194 brouard 149: Revision 1.193 2015/08/04 07:17:42 brouard
150: Summary: 0.98q4
151:
1.193 brouard 152: Revision 1.192 2015/07/16 16:49:02 brouard
153: Summary: Fixing some outputs
154:
1.192 brouard 155: Revision 1.191 2015/07/14 10:00:33 brouard
156: Summary: Some fixes
157:
1.191 brouard 158: Revision 1.190 2015/05/05 08:51:13 brouard
159: Summary: Adding digits in output parameters (7 digits instead of 6)
160:
161: Fix 1+age+.
162:
1.190 brouard 163: Revision 1.189 2015/04/30 14:45:16 brouard
164: Summary: 0.98q2
165:
1.189 brouard 166: Revision 1.188 2015/04/30 08:27:53 brouard
167: *** empty log message ***
168:
1.188 brouard 169: Revision 1.187 2015/04/29 09:11:15 brouard
170: *** empty log message ***
171:
1.187 brouard 172: Revision 1.186 2015/04/23 12:01:52 brouard
173: Summary: V1*age is working now, version 0.98q1
174:
175: Some codes had been disabled in order to simplify and Vn*age was
176: working in the optimization phase, ie, giving correct MLE parameters,
177: but, as usual, outputs were not correct and program core dumped.
178:
1.186 brouard 179: Revision 1.185 2015/03/11 13:26:42 brouard
180: Summary: Inclusion of compile and links command line for Intel Compiler
181:
1.185 brouard 182: Revision 1.184 2015/03/11 11:52:39 brouard
183: Summary: Back from Windows 8. Intel Compiler
184:
1.184 brouard 185: Revision 1.183 2015/03/10 20:34:32 brouard
186: Summary: 0.98q0, trying with directest, mnbrak fixed
187:
188: We use directest instead of original Powell test; probably no
189: incidence on the results, but better justifications;
190: We fixed Numerical Recipes mnbrak routine which was wrong and gave
191: wrong results.
192:
1.183 brouard 193: Revision 1.182 2015/02/12 08:19:57 brouard
194: Summary: Trying to keep directest which seems simpler and more general
195: Author: Nicolas Brouard
196:
1.182 brouard 197: Revision 1.181 2015/02/11 23:22:24 brouard
198: Summary: Comments on Powell added
199:
200: Author:
201:
1.181 brouard 202: Revision 1.180 2015/02/11 17:33:45 brouard
203: Summary: Finishing move from main to function (hpijx and prevalence_limit)
204:
1.180 brouard 205: Revision 1.179 2015/01/04 09:57:06 brouard
206: Summary: back to OS/X
207:
1.179 brouard 208: Revision 1.178 2015/01/04 09:35:48 brouard
209: *** empty log message ***
210:
1.178 brouard 211: Revision 1.177 2015/01/03 18:40:56 brouard
212: Summary: Still testing ilc32 on OSX
213:
1.177 brouard 214: Revision 1.176 2015/01/03 16:45:04 brouard
215: *** empty log message ***
216:
1.176 brouard 217: Revision 1.175 2015/01/03 16:33:42 brouard
218: *** empty log message ***
219:
1.175 brouard 220: Revision 1.174 2015/01/03 16:15:49 brouard
221: Summary: Still in cross-compilation
222:
1.174 brouard 223: Revision 1.173 2015/01/03 12:06:26 brouard
224: Summary: trying to detect cross-compilation
225:
1.173 brouard 226: Revision 1.172 2014/12/27 12:07:47 brouard
227: Summary: Back from Visual Studio and Intel, options for compiling for Windows XP
228:
1.172 brouard 229: Revision 1.171 2014/12/23 13:26:59 brouard
230: Summary: Back from Visual C
231:
232: Still problem with utsname.h on Windows
233:
1.171 brouard 234: Revision 1.170 2014/12/23 11:17:12 brouard
235: Summary: Cleaning some \%% back to %%
236:
237: The escape was mandatory for a specific compiler (which one?), but too many warnings.
238:
1.170 brouard 239: Revision 1.169 2014/12/22 23:08:31 brouard
240: Summary: 0.98p
241:
242: Outputs some informations on compiler used, OS etc. Testing on different platforms.
243:
1.169 brouard 244: Revision 1.168 2014/12/22 15:17:42 brouard
1.170 brouard 245: Summary: update
1.169 brouard 246:
1.168 brouard 247: Revision 1.167 2014/12/22 13:50:56 brouard
248: Summary: Testing uname and compiler version and if compiled 32 or 64
249:
250: Testing on Linux 64
251:
1.167 brouard 252: Revision 1.166 2014/12/22 11:40:47 brouard
253: *** empty log message ***
254:
1.166 brouard 255: Revision 1.165 2014/12/16 11:20:36 brouard
256: Summary: After compiling on Visual C
257:
258: * imach.c (Module): Merging 1.61 to 1.162
259:
1.165 brouard 260: Revision 1.164 2014/12/16 10:52:11 brouard
261: Summary: Merging with Visual C after suppressing some warnings for unused variables. Also fixing Saito's bug 0.98Xn
262:
263: * imach.c (Module): Merging 1.61 to 1.162
264:
1.164 brouard 265: Revision 1.163 2014/12/16 10:30:11 brouard
266: * imach.c (Module): Merging 1.61 to 1.162
267:
1.163 brouard 268: Revision 1.162 2014/09/25 11:43:39 brouard
269: Summary: temporary backup 0.99!
270:
1.162 brouard 271: Revision 1.1 2014/09/16 11:06:58 brouard
272: Summary: With some code (wrong) for nlopt
273:
274: Author:
275:
276: Revision 1.161 2014/09/15 20:41:41 brouard
277: Summary: Problem with macro SQR on Intel compiler
278:
1.161 brouard 279: Revision 1.160 2014/09/02 09:24:05 brouard
280: *** empty log message ***
281:
1.160 brouard 282: Revision 1.159 2014/09/01 10:34:10 brouard
283: Summary: WIN32
284: Author: Brouard
285:
1.159 brouard 286: Revision 1.158 2014/08/27 17:11:51 brouard
287: *** empty log message ***
288:
1.158 brouard 289: Revision 1.157 2014/08/27 16:26:55 brouard
290: Summary: Preparing windows Visual studio version
291: Author: Brouard
292:
293: In order to compile on Visual studio, time.h is now correct and time_t
294: and tm struct should be used. difftime should be used but sometimes I
295: just make the differences in raw time format (time(&now).
296: Trying to suppress #ifdef LINUX
297: Add xdg-open for __linux in order to open default browser.
298:
1.157 brouard 299: Revision 1.156 2014/08/25 20:10:10 brouard
300: *** empty log message ***
301:
1.156 brouard 302: Revision 1.155 2014/08/25 18:32:34 brouard
303: Summary: New compile, minor changes
304: Author: Brouard
305:
1.155 brouard 306: Revision 1.154 2014/06/20 17:32:08 brouard
307: Summary: Outputs now all graphs of convergence to period prevalence
308:
1.154 brouard 309: Revision 1.153 2014/06/20 16:45:46 brouard
310: Summary: If 3 live state, convergence to period prevalence on same graph
311: Author: Brouard
312:
1.153 brouard 313: Revision 1.152 2014/06/18 17:54:09 brouard
314: Summary: open browser, use gnuplot on same dir than imach if not found in the path
315:
1.152 brouard 316: Revision 1.151 2014/06/18 16:43:30 brouard
317: *** empty log message ***
318:
1.151 brouard 319: Revision 1.150 2014/06/18 16:42:35 brouard
320: Summary: If gnuplot is not in the path try on same directory than imach binary (OSX)
321: Author: brouard
322:
1.150 brouard 323: Revision 1.149 2014/06/18 15:51:14 brouard
324: Summary: Some fixes in parameter files errors
325: Author: Nicolas Brouard
326:
1.149 brouard 327: Revision 1.148 2014/06/17 17:38:48 brouard
328: Summary: Nothing new
329: Author: Brouard
330:
331: Just a new packaging for OS/X version 0.98nS
332:
1.148 brouard 333: Revision 1.147 2014/06/16 10:33:11 brouard
334: *** empty log message ***
335:
1.147 brouard 336: Revision 1.146 2014/06/16 10:20:28 brouard
337: Summary: Merge
338: Author: Brouard
339:
340: Merge, before building revised version.
341:
1.146 brouard 342: Revision 1.145 2014/06/10 21:23:15 brouard
343: Summary: Debugging with valgrind
344: Author: Nicolas Brouard
345:
346: Lot of changes in order to output the results with some covariates
347: After the Edimburgh REVES conference 2014, it seems mandatory to
348: improve the code.
349: No more memory valgrind error but a lot has to be done in order to
350: continue the work of splitting the code into subroutines.
351: Also, decodemodel has been improved. Tricode is still not
352: optimal. nbcode should be improved. Documentation has been added in
353: the source code.
354:
1.144 brouard 355: Revision 1.143 2014/01/26 09:45:38 brouard
356: Summary: Version 0.98nR (to be improved, but gives same optimization results as 0.98k. Nice, promising
357:
358: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
359: (Module): Version 0.98nR Running ok, but output format still only works for three covariates.
360:
1.143 brouard 361: Revision 1.142 2014/01/26 03:57:36 brouard
362: Summary: gnuplot changed plot w l 1 has to be changed to plot w l lt 2
363:
364: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
365:
1.142 brouard 366: Revision 1.141 2014/01/26 02:42:01 brouard
367: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
368:
1.141 brouard 369: Revision 1.140 2011/09/02 10:37:54 brouard
370: Summary: times.h is ok with mingw32 now.
371:
1.140 brouard 372: Revision 1.139 2010/06/14 07:50:17 brouard
373: After the theft of my laptop, I probably lost some lines of codes which were not uploaded to the CVS tree.
374: I remember having already fixed agemin agemax which are pointers now but not cvs saved.
375:
1.139 brouard 376: Revision 1.138 2010/04/30 18:19:40 brouard
377: *** empty log message ***
378:
1.138 brouard 379: Revision 1.137 2010/04/29 18:11:38 brouard
380: (Module): Checking covariates for more complex models
381: than V1+V2. A lot of change to be done. Unstable.
382:
1.137 brouard 383: Revision 1.136 2010/04/26 20:30:53 brouard
384: (Module): merging some libgsl code. Fixing computation
385: of likelione (using inter/intrapolation if mle = 0) in order to
386: get same likelihood as if mle=1.
387: Some cleaning of code and comments added.
388:
1.136 brouard 389: Revision 1.135 2009/10/29 15:33:14 brouard
390: (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
391:
1.135 brouard 392: Revision 1.134 2009/10/29 13:18:53 brouard
393: (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
394:
1.134 brouard 395: Revision 1.133 2009/07/06 10:21:25 brouard
396: just nforces
397:
1.133 brouard 398: Revision 1.132 2009/07/06 08:22:05 brouard
399: Many tings
400:
1.132 brouard 401: Revision 1.131 2009/06/20 16:22:47 brouard
402: Some dimensions resccaled
403:
1.131 brouard 404: Revision 1.130 2009/05/26 06:44:34 brouard
405: (Module): Max Covariate is now set to 20 instead of 8. A
406: lot of cleaning with variables initialized to 0. Trying to make
407: V2+V3*age+V1+V4 strb=V3*age+V1+V4 working better.
408:
1.130 brouard 409: Revision 1.129 2007/08/31 13:49:27 lievre
410: Modification of the way of exiting when the covariate is not binary in order to see on the window the error message before exiting
411:
1.129 lievre 412: Revision 1.128 2006/06/30 13:02:05 brouard
413: (Module): Clarifications on computing e.j
414:
1.128 brouard 415: Revision 1.127 2006/04/28 18:11:50 brouard
416: (Module): Yes the sum of survivors was wrong since
417: imach-114 because nhstepm was no more computed in the age
418: loop. Now we define nhstepma in the age loop.
419: (Module): In order to speed up (in case of numerous covariates) we
420: compute health expectancies (without variances) in a first step
421: and then all the health expectancies with variances or standard
422: deviation (needs data from the Hessian matrices) which slows the
423: computation.
424: In the future we should be able to stop the program is only health
425: expectancies and graph are needed without standard deviations.
426:
1.127 brouard 427: Revision 1.126 2006/04/28 17:23:28 brouard
428: (Module): Yes the sum of survivors was wrong since
429: imach-114 because nhstepm was no more computed in the age
430: loop. Now we define nhstepma in the age loop.
431: Version 0.98h
432:
1.126 brouard 433: Revision 1.125 2006/04/04 15:20:31 lievre
434: Errors in calculation of health expectancies. Age was not initialized.
435: Forecasting file added.
436:
437: Revision 1.124 2006/03/22 17:13:53 lievre
438: Parameters are printed with %lf instead of %f (more numbers after the comma).
439: The log-likelihood is printed in the log file
440:
441: Revision 1.123 2006/03/20 10:52:43 brouard
442: * imach.c (Module): <title> changed, corresponds to .htm file
443: name. <head> headers where missing.
444:
445: * imach.c (Module): Weights can have a decimal point as for
446: English (a comma might work with a correct LC_NUMERIC environment,
447: otherwise the weight is truncated).
448: Modification of warning when the covariates values are not 0 or
449: 1.
450: Version 0.98g
451:
452: Revision 1.122 2006/03/20 09:45:41 brouard
453: (Module): Weights can have a decimal point as for
454: English (a comma might work with a correct LC_NUMERIC environment,
455: otherwise the weight is truncated).
456: Modification of warning when the covariates values are not 0 or
457: 1.
458: Version 0.98g
459:
460: Revision 1.121 2006/03/16 17:45:01 lievre
461: * imach.c (Module): Comments concerning covariates added
462:
463: * imach.c (Module): refinements in the computation of lli if
464: status=-2 in order to have more reliable computation if stepm is
465: not 1 month. Version 0.98f
466:
467: Revision 1.120 2006/03/16 15:10:38 lievre
468: (Module): refinements in the computation of lli if
469: status=-2 in order to have more reliable computation if stepm is
470: not 1 month. Version 0.98f
471:
472: Revision 1.119 2006/03/15 17:42:26 brouard
473: (Module): Bug if status = -2, the loglikelihood was
474: computed as likelihood omitting the logarithm. Version O.98e
475:
476: Revision 1.118 2006/03/14 18:20:07 brouard
477: (Module): varevsij Comments added explaining the second
478: table of variances if popbased=1 .
479: (Module): Covariances of eij, ekl added, graphs fixed, new html link.
480: (Module): Function pstamp added
481: (Module): Version 0.98d
482:
483: Revision 1.117 2006/03/14 17:16:22 brouard
484: (Module): varevsij Comments added explaining the second
485: table of variances if popbased=1 .
486: (Module): Covariances of eij, ekl added, graphs fixed, new html link.
487: (Module): Function pstamp added
488: (Module): Version 0.98d
489:
490: Revision 1.116 2006/03/06 10:29:27 brouard
491: (Module): Variance-covariance wrong links and
492: varian-covariance of ej. is needed (Saito).
493:
494: Revision 1.115 2006/02/27 12:17:45 brouard
495: (Module): One freematrix added in mlikeli! 0.98c
496:
497: Revision 1.114 2006/02/26 12:57:58 brouard
498: (Module): Some improvements in processing parameter
499: filename with strsep.
500:
501: Revision 1.113 2006/02/24 14:20:24 brouard
502: (Module): Memory leaks checks with valgrind and:
503: datafile was not closed, some imatrix were not freed and on matrix
504: allocation too.
505:
506: Revision 1.112 2006/01/30 09:55:26 brouard
507: (Module): Back to gnuplot.exe instead of wgnuplot.exe
508:
509: Revision 1.111 2006/01/25 20:38:18 brouard
510: (Module): Lots of cleaning and bugs added (Gompertz)
511: (Module): Comments can be added in data file. Missing date values
512: can be a simple dot '.'.
513:
514: Revision 1.110 2006/01/25 00:51:50 brouard
515: (Module): Lots of cleaning and bugs added (Gompertz)
516:
517: Revision 1.109 2006/01/24 19:37:15 brouard
518: (Module): Comments (lines starting with a #) are allowed in data.
519:
520: Revision 1.108 2006/01/19 18:05:42 lievre
521: Gnuplot problem appeared...
522: To be fixed
523:
524: Revision 1.107 2006/01/19 16:20:37 brouard
525: Test existence of gnuplot in imach path
526:
527: Revision 1.106 2006/01/19 13:24:36 brouard
528: Some cleaning and links added in html output
529:
530: Revision 1.105 2006/01/05 20:23:19 lievre
531: *** empty log message ***
532:
533: Revision 1.104 2005/09/30 16:11:43 lievre
534: (Module): sump fixed, loop imx fixed, and simplifications.
535: (Module): If the status is missing at the last wave but we know
536: that the person is alive, then we can code his/her status as -2
537: (instead of missing=-1 in earlier versions) and his/her
538: contributions to the likelihood is 1 - Prob of dying from last
539: health status (= 1-p13= p11+p12 in the easiest case of somebody in
540: the healthy state at last known wave). Version is 0.98
541:
542: Revision 1.103 2005/09/30 15:54:49 lievre
543: (Module): sump fixed, loop imx fixed, and simplifications.
544:
545: Revision 1.102 2004/09/15 17:31:30 brouard
546: Add the possibility to read data file including tab characters.
547:
548: Revision 1.101 2004/09/15 10:38:38 brouard
549: Fix on curr_time
550:
551: Revision 1.100 2004/07/12 18:29:06 brouard
552: Add version for Mac OS X. Just define UNIX in Makefile
553:
554: Revision 1.99 2004/06/05 08:57:40 brouard
555: *** empty log message ***
556:
557: Revision 1.98 2004/05/16 15:05:56 brouard
558: New version 0.97 . First attempt to estimate force of mortality
559: directly from the data i.e. without the need of knowing the health
560: state at each age, but using a Gompertz model: log u =a + b*age .
561: This is the basic analysis of mortality and should be done before any
562: other analysis, in order to test if the mortality estimated from the
563: cross-longitudinal survey is different from the mortality estimated
564: from other sources like vital statistic data.
565:
566: The same imach parameter file can be used but the option for mle should be -3.
567:
1.133 brouard 568: Agnès, who wrote this part of the code, tried to keep most of the
1.126 brouard 569: former routines in order to include the new code within the former code.
570:
571: The output is very simple: only an estimate of the intercept and of
572: the slope with 95% confident intervals.
573:
574: Current limitations:
575: A) Even if you enter covariates, i.e. with the
576: model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
577: B) There is no computation of Life Expectancy nor Life Table.
578:
579: Revision 1.97 2004/02/20 13:25:42 lievre
580: Version 0.96d. Population forecasting command line is (temporarily)
581: suppressed.
582:
583: Revision 1.96 2003/07/15 15:38:55 brouard
584: * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
585: rewritten within the same printf. Workaround: many printfs.
586:
587: Revision 1.95 2003/07/08 07:54:34 brouard
588: * imach.c (Repository):
589: (Repository): Using imachwizard code to output a more meaningful covariance
590: matrix (cov(a12,c31) instead of numbers.
591:
592: Revision 1.94 2003/06/27 13:00:02 brouard
593: Just cleaning
594:
595: Revision 1.93 2003/06/25 16:33:55 brouard
596: (Module): On windows (cygwin) function asctime_r doesn't
597: exist so I changed back to asctime which exists.
598: (Module): Version 0.96b
599:
600: Revision 1.92 2003/06/25 16:30:45 brouard
601: (Module): On windows (cygwin) function asctime_r doesn't
602: exist so I changed back to asctime which exists.
603:
604: Revision 1.91 2003/06/25 15:30:29 brouard
605: * imach.c (Repository): Duplicated warning errors corrected.
606: (Repository): Elapsed time after each iteration is now output. It
607: helps to forecast when convergence will be reached. Elapsed time
608: is stamped in powell. We created a new html file for the graphs
609: concerning matrix of covariance. It has extension -cov.htm.
610:
611: Revision 1.90 2003/06/24 12:34:15 brouard
612: (Module): Some bugs corrected for windows. Also, when
613: mle=-1 a template is output in file "or"mypar.txt with the design
614: of the covariance matrix to be input.
615:
616: Revision 1.89 2003/06/24 12:30:52 brouard
617: (Module): Some bugs corrected for windows. Also, when
618: mle=-1 a template is output in file "or"mypar.txt with the design
619: of the covariance matrix to be input.
620:
621: Revision 1.88 2003/06/23 17:54:56 brouard
622: * 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.
623:
624: Revision 1.87 2003/06/18 12:26:01 brouard
625: Version 0.96
626:
627: Revision 1.86 2003/06/17 20:04:08 brouard
628: (Module): Change position of html and gnuplot routines and added
629: routine fileappend.
630:
631: Revision 1.85 2003/06/17 13:12:43 brouard
632: * imach.c (Repository): Check when date of death was earlier that
633: current date of interview. It may happen when the death was just
634: prior to the death. In this case, dh was negative and likelihood
635: was wrong (infinity). We still send an "Error" but patch by
636: assuming that the date of death was just one stepm after the
637: interview.
638: (Repository): Because some people have very long ID (first column)
639: we changed int to long in num[] and we added a new lvector for
640: memory allocation. But we also truncated to 8 characters (left
641: truncation)
642: (Repository): No more line truncation errors.
643:
644: Revision 1.84 2003/06/13 21:44:43 brouard
645: * imach.c (Repository): Replace "freqsummary" at a correct
646: place. It differs from routine "prevalence" which may be called
647: many times. Probs is memory consuming and must be used with
648: parcimony.
649: Version 0.95a3 (should output exactly the same maximization than 0.8a2)
650:
651: Revision 1.83 2003/06/10 13:39:11 lievre
652: *** empty log message ***
653:
654: Revision 1.82 2003/06/05 15:57:20 brouard
655: Add log in imach.c and fullversion number is now printed.
656:
657: */
658: /*
659: Interpolated Markov Chain
660:
661: Short summary of the programme:
662:
1.227 brouard 663: This program computes Healthy Life Expectancies or State-specific
664: (if states aren't health statuses) Expectancies from
665: cross-longitudinal data. Cross-longitudinal data consist in:
666:
667: -1- a first survey ("cross") where individuals from different ages
668: are interviewed on their health status or degree of disability (in
669: the case of a health survey which is our main interest)
670:
671: -2- at least a second wave of interviews ("longitudinal") which
672: measure each change (if any) in individual health status. Health
673: expectancies are computed from the time spent in each health state
674: according to a model. More health states you consider, more time is
675: necessary to reach the Maximum Likelihood of the parameters involved
676: in the model. The simplest model is the multinomial logistic model
677: where pij is the probability to be observed in state j at the second
678: wave conditional to be observed in state i at the first
679: wave. Therefore the model is: log(pij/pii)= aij + bij*age+ cij*sex +
680: etc , where 'age' is age and 'sex' is a covariate. If you want to
681: have a more complex model than "constant and age", you should modify
682: the program where the markup *Covariates have to be included here
683: again* invites you to do it. More covariates you add, slower the
1.126 brouard 684: convergence.
685:
686: The advantage of this computer programme, compared to a simple
687: multinomial logistic model, is clear when the delay between waves is not
688: identical for each individual. Also, if a individual missed an
689: intermediate interview, the information is lost, but taken into
690: account using an interpolation or extrapolation.
691:
692: hPijx is the probability to be observed in state i at age x+h
693: conditional to the observed state i at age x. The delay 'h' can be
694: split into an exact number (nh*stepm) of unobserved intermediate
695: states. This elementary transition (by month, quarter,
696: semester or year) is modelled as a multinomial logistic. The hPx
697: matrix is simply the matrix product of nh*stepm elementary matrices
698: and the contribution of each individual to the likelihood is simply
699: hPijx.
700:
701: Also this programme outputs the covariance matrix of the parameters but also
1.218 brouard 702: of the life expectancies. It also computes the period (stable) prevalence.
703:
704: Back prevalence and projections:
1.227 brouard 705:
706: - back_prevalence_limit(double *p, double **bprlim, double ageminpar,
707: double agemaxpar, double ftolpl, int *ncvyearp, double
708: dateprev1,double dateprev2, int firstpass, int lastpass, int
709: mobilavproj)
710:
711: Computes the back prevalence limit for any combination of
712: covariate values k at any age between ageminpar and agemaxpar and
713: returns it in **bprlim. In the loops,
714:
715: - **bprevalim(**bprlim, ***mobaverage, nlstate, *p, age, **oldm,
716: **savm, **dnewm, **doldm, **dsavm, ftolpl, ncvyearp, k);
717:
718: - hBijx Back Probability to be in state i at age x-h being in j at x
1.218 brouard 719: Computes for any combination of covariates k and any age between bage and fage
720: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
721: oldm=oldms;savm=savms;
1.227 brouard 722:
723: - hbxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
1.218 brouard 724: Computes the transition matrix starting at age 'age' over
725: 'nhstepm*hstepm*stepm' months (i.e. until
726: age (in years) age+nhstepm*hstepm*stepm/12) by multiplying
1.227 brouard 727: nhstepm*hstepm matrices.
728:
729: Returns p3mat[i][j][h] after calling
730: p3mat[i][j][h]=matprod2(newm,
731: bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent, dnewm, doldm,
732: dsavm,ij),\ 1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
733: oldm);
1.226 brouard 734:
735: Important routines
736:
737: - func (or funcone), computes logit (pij) distinguishing
738: o fixed variables (single or product dummies or quantitative);
739: o varying variables by:
740: (1) wave (single, product dummies, quantitative),
741: (2) by age (can be month) age (done), age*age (done), age*Vn where Vn can be:
742: % fixed dummy (treated) or quantitative (not done because time-consuming);
743: % varying dummy (not done) or quantitative (not done);
744: - Tricode which tests the modality of dummy variables (in order to warn with wrong or empty modalities)
745: and returns the number of efficient covariates cptcoveff and modalities nbcode[Tvar[k]][1]= 0 and nbcode[Tvar[k]][2]= 1 usually.
746: - printinghtml which outputs results like life expectancy in and from a state for a combination of modalities of dummy variables
747: o There are 2*cptcoveff combinations of (0,1) for cptcoveff variables. Outputting only combinations with people, éliminating 1 1 if
748: race White (0 0), Black vs White (1 0), Hispanic (0 1) and 1 1 being meaningless.
1.218 brouard 749:
1.226 brouard 750:
751:
1.133 brouard 752: Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
753: Institut national d'études démographiques, Paris.
1.126 brouard 754: This software have been partly granted by Euro-REVES, a concerted action
755: from the European Union.
756: It is copyrighted identically to a GNU software product, ie programme and
757: software can be distributed freely for non commercial use. Latest version
758: can be accessed at http://euroreves.ined.fr/imach .
759:
760: Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
761: or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
762:
763: **********************************************************************/
764: /*
765: main
766: read parameterfile
767: read datafile
768: concatwav
769: freqsummary
770: if (mle >= 1)
771: mlikeli
772: print results files
773: if mle==1
774: computes hessian
775: read end of parameter file: agemin, agemax, bage, fage, estepm
776: begin-prev-date,...
777: open gnuplot file
778: open html file
1.145 brouard 779: period (stable) prevalence | pl_nom 1-1 2-2 etc by covariate
780: for age prevalim() | #****** V1=0 V2=1 V3=1 V4=0 ******
781: | 65 1 0 2 1 3 1 4 0 0.96326 0.03674
782: freexexit2 possible for memory heap.
783:
784: h Pij x | pij_nom ficrestpij
785: # Cov Agex agex+h hpijx with i,j= 1-1 1-2 1-3 2-1 2-2 2-3
786: 1 85 85 1.00000 0.00000 0.00000 0.00000 1.00000 0.00000
787: 1 85 86 0.68299 0.22291 0.09410 0.71093 0.00000 0.28907
788:
789: 1 65 99 0.00364 0.00322 0.99314 0.00350 0.00310 0.99340
790: 1 65 100 0.00214 0.00204 0.99581 0.00206 0.00196 0.99597
791: variance of p one-step probabilities varprob | prob_nom ficresprob #One-step probabilities and stand. devi in ()
792: Standard deviation of one-step probabilities | probcor_nom ficresprobcor #One-step probabilities and correlation matrix
793: Matrix of variance covariance of one-step probabilities | probcov_nom ficresprobcov #One-step probabilities and covariance matrix
794:
1.126 brouard 795: forecasting if prevfcast==1 prevforecast call prevalence()
796: health expectancies
797: Variance-covariance of DFLE
798: prevalence()
799: movingaverage()
800: varevsij()
801: if popbased==1 varevsij(,popbased)
802: total life expectancies
803: Variance of period (stable) prevalence
804: end
805: */
806:
1.187 brouard 807: /* #define DEBUG */
808: /* #define DEBUGBRENT */
1.203 brouard 809: /* #define DEBUGLINMIN */
810: /* #define DEBUGHESS */
811: #define DEBUGHESSIJ
1.224 brouard 812: /* #define LINMINORIGINAL /\* Don't use loop on scale in linmin (accepting nan) *\/ */
1.165 brouard 813: #define POWELL /* Instead of NLOPT */
1.224 brouard 814: #define POWELLNOF3INFF1TEST /* Skip test */
1.186 brouard 815: /* #define POWELLORIGINAL /\* Don't use Directest to decide new direction but original Powell test *\/ */
816: /* #define MNBRAKORIGINAL /\* Don't use mnbrak fix *\/ */
1.126 brouard 817:
818: #include <math.h>
819: #include <stdio.h>
820: #include <stdlib.h>
821: #include <string.h>
1.226 brouard 822: #include <ctype.h>
1.159 brouard 823:
824: #ifdef _WIN32
825: #include <io.h>
1.172 brouard 826: #include <windows.h>
827: #include <tchar.h>
1.159 brouard 828: #else
1.126 brouard 829: #include <unistd.h>
1.159 brouard 830: #endif
1.126 brouard 831:
832: #include <limits.h>
833: #include <sys/types.h>
1.171 brouard 834:
835: #if defined(__GNUC__)
836: #include <sys/utsname.h> /* Doesn't work on Windows */
837: #endif
838:
1.126 brouard 839: #include <sys/stat.h>
840: #include <errno.h>
1.159 brouard 841: /* extern int errno; */
1.126 brouard 842:
1.157 brouard 843: /* #ifdef LINUX */
844: /* #include <time.h> */
845: /* #include "timeval.h" */
846: /* #else */
847: /* #include <sys/time.h> */
848: /* #endif */
849:
1.126 brouard 850: #include <time.h>
851:
1.136 brouard 852: #ifdef GSL
853: #include <gsl/gsl_errno.h>
854: #include <gsl/gsl_multimin.h>
855: #endif
856:
1.167 brouard 857:
1.162 brouard 858: #ifdef NLOPT
859: #include <nlopt.h>
860: typedef struct {
861: double (* function)(double [] );
862: } myfunc_data ;
863: #endif
864:
1.126 brouard 865: /* #include <libintl.h> */
866: /* #define _(String) gettext (String) */
867:
1.141 brouard 868: #define MAXLINE 1024 /* Was 256. Overflow with 312 with 2 states and 4 covariates. Should be ok */
1.126 brouard 869:
870: #define GNUPLOTPROGRAM "gnuplot"
871: /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
872: #define FILENAMELENGTH 132
873:
874: #define GLOCK_ERROR_NOPATH -1 /* empty path */
875: #define GLOCK_ERROR_GETCWD -2 /* cannot get cwd */
876:
1.144 brouard 877: #define MAXPARM 128 /**< Maximum number of parameters for the optimization */
878: #define NPARMAX 64 /**< (nlstate+ndeath-1)*nlstate*ncovmodel */
1.126 brouard 879:
880: #define NINTERVMAX 8
1.144 brouard 881: #define NLSTATEMAX 8 /**< Maximum number of live states (for func) */
882: #define NDEATHMAX 8 /**< Maximum number of dead states (for func) */
883: #define NCOVMAX 20 /**< Maximum number of covariates, including generated covariates V1*V2 */
1.197 brouard 884: #define codtabm(h,k) (1 & (h-1) >> (k-1))+1
1.211 brouard 885: /*#define decodtabm(h,k,cptcoveff)= (h <= (1<<cptcoveff)?(((h-1) >> (k-1)) & 1) +1 : -1)*/
886: #define decodtabm(h,k,cptcoveff) (((h-1) >> (k-1)) & 1) +1
1.126 brouard 887: #define MAXN 20000
1.144 brouard 888: #define YEARM 12. /**< Number of months per year */
1.218 brouard 889: /* #define AGESUP 130 */
890: #define AGESUP 150
891: #define AGEMARGE 25 /* Marge for agemin and agemax for(iage=agemin-AGEMARGE; iage <= agemax+3+AGEMARGE; iage++) */
1.126 brouard 892: #define AGEBASE 40
1.194 brouard 893: #define AGEOVERFLOW 1.e20
1.164 brouard 894: #define AGEGOMP 10 /**< Minimal age for Gompertz adjustment */
1.157 brouard 895: #ifdef _WIN32
896: #define DIRSEPARATOR '\\'
897: #define CHARSEPARATOR "\\"
898: #define ODIRSEPARATOR '/'
899: #else
1.126 brouard 900: #define DIRSEPARATOR '/'
901: #define CHARSEPARATOR "/"
902: #define ODIRSEPARATOR '\\'
903: #endif
904:
1.235 ! brouard 905: /* $Id: imach.c,v 1.234 2016/08/23 16:51:20 brouard Exp $ */
1.126 brouard 906: /* $State: Exp $ */
1.196 brouard 907: #include "version.h"
908: char version[]=__IMACH_VERSION__;
1.224 brouard 909: char copyright[]="February 2016,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121), Intel Software 2015-2018";
1.235 ! brouard 910: char fullversion[]="$Revision: 1.234 $ $Date: 2016/08/23 16:51:20 $";
1.126 brouard 911: char strstart[80];
912: char optionfilext[10], optionfilefiname[FILENAMELENGTH];
1.130 brouard 913: int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings */
1.187 brouard 914: int nagesqr=0, nforce=0; /* nagesqr=1 if model is including age*age, number of forces */
1.145 brouard 915: /* Number of covariates model=V2+V1+ V3*age+V2*V4 */
916: int cptcovn=0; /**< cptcovn number of covariates added in the model (excepting constant and age and age*product) */
917: int cptcovt=0; /**< cptcovt number of covariates added in the model (excepting constant and age) */
1.225 brouard 918: int cptcovs=0; /**< cptcovs number of simple covariates in the model V2+V1 =2 */
919: int cptcovsnq=0; /**< cptcovsnq number of simple covariates in the model but non quantitative V2+V1 =2 */
1.145 brouard 920: int cptcovage=0; /**< Number of covariates with age: V3*age only =1 */
921: int cptcovprodnoage=0; /**< Number of covariate products without age */
922: int cptcoveff=0; /* Total number of covariates to vary for printing results */
1.233 brouard 923: int ncovf=0; /* Total number of effective fixed covariates (dummy or quantitative) in the model */
924: int ncovv=0; /* Total number of effective (wave) varying covariates (dummy or quantitative) in the model */
1.232 brouard 925: int ncova=0; /* Total number of effective (wave and stepm) varying with age covariates (dummy of quantitative) in the model */
1.234 brouard 926: int nsd=0; /**< Total number of single dummy variables (output) */
927: int nsq=0; /**< Total number of single quantitative variables (output) */
1.232 brouard 928: int ncoveff=0; /* Total number of effective fixed dummy covariates in the model */
1.225 brouard 929: int nqfveff=0; /**< nqfveff Number of Quantitative Fixed Variables Effective */
1.224 brouard 930: int ntveff=0; /**< ntveff number of effective time varying variables */
931: int nqtveff=0; /**< ntqveff number of effective time varying quantitative variables */
1.145 brouard 932: int cptcov=0; /* Working variable */
1.218 brouard 933: int ncovcombmax=NCOVMAX; /* Maximum calculated number of covariate combination = pow(2, cptcoveff) */
1.126 brouard 934: int npar=NPARMAX;
935: int nlstate=2; /* Number of live states */
936: int ndeath=1; /* Number of dead states */
1.130 brouard 937: int ncovmodel=0, ncovcol=0; /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
1.223 brouard 938: int nqv=0, ntv=0, nqtv=0; /* Total number of quantitative variables, time variable (dummy), quantitative and time variable */
1.126 brouard 939: int popbased=0;
940:
941: int *wav; /* Number of waves for this individuual 0 is possible */
1.130 brouard 942: int maxwav=0; /* Maxim number of waves */
943: int jmin=0, jmax=0; /* min, max spacing between 2 waves */
944: int ijmin=0, ijmax=0; /* Individuals having jmin and jmax */
945: int gipmx=0, gsw=0; /* Global variables on the number of contributions
1.126 brouard 946: to the likelihood and the sum of weights (done by funcone)*/
1.130 brouard 947: int mle=1, weightopt=0;
1.126 brouard 948: int **mw; /* mw[mi][i] is number of the mi wave for this individual */
949: int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
950: int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
951: * wave mi and wave mi+1 is not an exact multiple of stepm. */
1.162 brouard 952: int countcallfunc=0; /* Count the number of calls to func */
1.230 brouard 953: int selected(int kvar); /* Is covariate kvar selected for printing results */
954:
1.130 brouard 955: double jmean=1; /* Mean space between 2 waves */
1.145 brouard 956: double **matprod2(); /* test */
1.126 brouard 957: double **oldm, **newm, **savm; /* Working pointers to matrices */
958: double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
1.218 brouard 959: double **ddnewms, **ddoldms, **ddsavms; /* for freeing later */
960:
1.136 brouard 961: /*FILE *fic ; */ /* Used in readdata only */
1.217 brouard 962: FILE *ficpar, *ficparo,*ficres, *ficresp, *ficresphtm, *ficresphtmfr, *ficrespl, *ficresplb,*ficrespij, *ficrespijb, *ficrest,*ficresf, *ficresfb,*ficrespop;
1.126 brouard 963: FILE *ficlog, *ficrespow;
1.130 brouard 964: int globpr=0; /* Global variable for printing or not */
1.126 brouard 965: double fretone; /* Only one call to likelihood */
1.130 brouard 966: long ipmx=0; /* Number of contributions */
1.126 brouard 967: double sw; /* Sum of weights */
968: char filerespow[FILENAMELENGTH];
969: char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
970: FILE *ficresilk;
971: FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
972: FILE *ficresprobmorprev;
973: FILE *fichtm, *fichtmcov; /* Html File */
974: FILE *ficreseij;
975: char filerese[FILENAMELENGTH];
976: FILE *ficresstdeij;
977: char fileresstde[FILENAMELENGTH];
978: FILE *ficrescveij;
979: char filerescve[FILENAMELENGTH];
980: FILE *ficresvij;
981: char fileresv[FILENAMELENGTH];
982: FILE *ficresvpl;
983: char fileresvpl[FILENAMELENGTH];
984: char title[MAXLINE];
1.234 brouard 985: char model[MAXLINE]; /**< The model line */
1.217 brouard 986: char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH], filerespl[FILENAMELENGTH], fileresplb[FILENAMELENGTH];
1.126 brouard 987: char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
988: char tmpout[FILENAMELENGTH], tmpout2[FILENAMELENGTH];
989: char command[FILENAMELENGTH];
990: int outcmd=0;
991:
1.217 brouard 992: char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filerespijb[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
1.202 brouard 993: char fileresu[FILENAMELENGTH]; /* fileres without r in front */
1.126 brouard 994: char filelog[FILENAMELENGTH]; /* Log file */
995: char filerest[FILENAMELENGTH];
996: char fileregp[FILENAMELENGTH];
997: char popfile[FILENAMELENGTH];
998:
999: char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
1000:
1.157 brouard 1001: /* struct timeval start_time, end_time, curr_time, last_time, forecast_time; */
1002: /* struct timezone tzp; */
1003: /* extern int gettimeofday(); */
1004: struct tm tml, *gmtime(), *localtime();
1005:
1006: extern time_t time();
1007:
1008: struct tm start_time, end_time, curr_time, last_time, forecast_time;
1009: time_t rstart_time, rend_time, rcurr_time, rlast_time, rforecast_time; /* raw time */
1010: struct tm tm;
1011:
1.126 brouard 1012: char strcurr[80], strfor[80];
1013:
1014: char *endptr;
1015: long lval;
1016: double dval;
1017:
1018: #define NR_END 1
1019: #define FREE_ARG char*
1020: #define FTOL 1.0e-10
1021:
1022: #define NRANSI
1023: #define ITMAX 200
1024:
1025: #define TOL 2.0e-4
1026:
1027: #define CGOLD 0.3819660
1028: #define ZEPS 1.0e-10
1029: #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);
1030:
1031: #define GOLD 1.618034
1032: #define GLIMIT 100.0
1033: #define TINY 1.0e-20
1034:
1035: static double maxarg1,maxarg2;
1036: #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
1037: #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
1038:
1039: #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
1040: #define rint(a) floor(a+0.5)
1.166 brouard 1041: /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/myutils_8h-source.html */
1.183 brouard 1042: #define mytinydouble 1.0e-16
1.166 brouard 1043: /* #define DEQUAL(a,b) (fabs((a)-(b))<mytinydouble) */
1044: /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/mynrutils_8h-source.html */
1045: /* static double dsqrarg; */
1046: /* #define DSQR(a) (DEQUAL((dsqrarg=(a)),0.0) ? 0.0 : dsqrarg*dsqrarg) */
1.126 brouard 1047: static double sqrarg;
1048: #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
1049: #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}
1050: int agegomp= AGEGOMP;
1051:
1052: int imx;
1053: int stepm=1;
1054: /* Stepm, step in month: minimum step interpolation*/
1055:
1056: int estepm;
1057: /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
1058:
1059: int m,nb;
1060: long *num;
1.197 brouard 1061: int firstpass=0, lastpass=4,*cod, *cens;
1.192 brouard 1062: int *ncodemax; /* ncodemax[j]= Number of modalities of the j th
1063: covariate for which somebody answered excluding
1064: undefined. Usually 2: 0 and 1. */
1065: int *ncodemaxwundef; /* ncodemax[j]= Number of modalities of the j th
1066: covariate for which somebody answered including
1067: undefined. Usually 3: -1, 0 and 1. */
1.126 brouard 1068: double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
1.218 brouard 1069: double **pmmij, ***probs; /* Global pointer */
1.219 brouard 1070: double ***mobaverage, ***mobaverages; /* New global variable */
1.126 brouard 1071: double *ageexmed,*agecens;
1072: double dateintmean=0;
1073:
1074: double *weight;
1075: int **s; /* Status */
1.141 brouard 1076: double *agedc;
1.145 brouard 1077: double **covar; /**< covar[j,i], value of jth covariate for individual i,
1.141 brouard 1078: * covar=matrix(0,NCOVMAX,1,n);
1.187 brouard 1079: * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*age; */
1.225 brouard 1080: double **coqvar; /* Fixed quantitative covariate iqv */
1081: double ***cotvar; /* Time varying covariate itv */
1082: double ***cotqvar; /* Time varying quantitative covariate itqv */
1.141 brouard 1083: double idx;
1084: int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */
1.234 brouard 1085: /* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
1086: /*k 1 2 3 4 5 6 7 8 9 */
1087: /*Tvar[k]= 5 4 3 6 5 2 7 1 1 */
1088: /* Tndvar[k] 1 2 3 4 5 */
1089: /*TDvar 4 3 6 7 1 */ /* For outputs only; combination of dummies fixed or varying */
1090: /* Tns[k] 1 2 2 4 5 */ /* Number of single cova */
1091: /* TvarsD[k] 1 2 3 */ /* Number of single dummy cova */
1092: /* TvarsDind 2 3 9 */ /* position K of single dummy cova */
1093: /* TvarsQ[k] 1 2 */ /* Number of single quantitative cova */
1094: /* TvarsQind 1 6 */ /* position K of single quantitative cova */
1095: /* Tprod[i]=k 4 7 */
1096: /* Tage[i]=k 5 8 */
1097: /* */
1098: /* Type */
1099: /* V 1 2 3 4 5 */
1100: /* F F V V V */
1101: /* D Q D D Q */
1102: /* */
1103: int *TvarsD;
1104: int *TvarsDind;
1105: int *TvarsQ;
1106: int *TvarsQind;
1107:
1.235 ! brouard 1108: #define MAXRESULTLINES 10
! 1109: int nresult=0;
! 1110: int TKresult[MAXRESULTLINES];
! 1111: double Tresult[MAXRESULTLINES][NCOVMAX];/* For dummy variable , value (output) */
! 1112: int Tvresult[MAXRESULTLINES][NCOVMAX]; /* For dummy variable , variable # (output) */
! 1113: double Tqresult[MAXRESULTLINES][NCOVMAX]; /* For quantitative variable , value (output) */
! 1114: int Tvqresult[MAXRESULTLINES][NCOVMAX]; /* For quantitative variable , variable # (output) */
! 1115:
1.234 brouard 1116: /* int *TDvar; /\**< TDvar[1]=4, TDvarF[2]=3, TDvar[3]=6 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 *\/ */
1.232 brouard 1117: int *TvarF; /**< TvarF[1]=Tvar[6]=2, TvarF[2]=Tvar[7]=7, TvarF[3]=Tvar[9]=1 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
1118: int *TvarFind; /**< TvarFind[1]=6, TvarFind[2]=7, Tvarind[3]=9 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
1119: int *TvarV; /**< TvarV[1]=Tvar[1]=5, TvarV[2]=Tvar[2]=4 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
1120: int *TvarVind; /**< TvarVind[1]=1, TvarVind[2]=2 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
1121: int *TvarA; /**< TvarA[1]=Tvar[5]=5, TvarA[2]=Tvar[8]=1 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
1122: int *TvarAind; /**< TvarindA[1]=5, TvarAind[2]=8 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
1.231 brouard 1123: int *TvarFD; /**< TvarFD[1]=V1 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
1124: int *TvarFDind; /* TvarFDind[1]=9 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
1125: int *TvarFQ; /* TvarFQ[1]=V2 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple fixed quantitative variable */
1126: int *TvarFQind; /* TvarFQind[1]=6 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple fixed quantitative variable */
1127: int *TvarVD; /* TvarVD[1]=V5 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple fixed quantitative variable */
1128: int *TvarVDind; /* TvarVDind[1]=1 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple fixed quantitative variable */
1129: int *TvarVQ; /* TvarVQ[1]=V5 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple time varying quantitative variable */
1130: int *TvarVQind; /* TvarVQind[1]=1 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple time varying quantitative variable */
1131:
1.230 brouard 1132: int *Tvarsel; /**< Selected covariates for output */
1133: double *Tvalsel; /**< Selected modality value of covariate for output */
1.226 brouard 1134: int *Typevar; /**< 0 for simple covariate (dummy, quantitative, fixed or varying), 1 for age product, 2 for product */
1.227 brouard 1135: int *Fixed; /** Fixed[k] 0=fixed, 1 varying, 2 fixed with age product, 3 varying with age product */
1136: int *Dummy; /** Dummy[k] 0=dummy (0 1), 1 quantitative (single or product without age), 2 dummy with age product, 3 quant with age product */
1.197 brouard 1137: int *Tage;
1.227 brouard 1138: int anyvaryingduminmodel=0; /**< Any varying dummy in Model=1 yes, 0 no, to avoid a loop on waves in freq */
1.228 brouard 1139: int *Tmodelind; /** Tmodelind[Tvaraff[3]]=9 for V1 position,Tvaraff[1]@9={4, 3, 1, 0, 0, 0, 0, 0, 0}, model=V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1*/
1.230 brouard 1140: int *TmodelInvind; /** Tmodelind[Tvaraff[3]]=9 for V1 position,Tvaraff[1]@9={4, 3, 1, 0, 0, 0, 0, 0, 0}, model=V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1*/
1141: int *TmodelInvQind; /** Tmodelqind[1]=1 for V5(quantitative varying) position,Tvaraff[1]@9={4, 3, 1, 0, 0, 0, 0, 0, 0}, model=V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
1.145 brouard 1142: int *Ndum; /** Freq of modality (tricode */
1.200 brouard 1143: /* int **codtab;*/ /**< codtab=imatrix(1,100,1,10); */
1.227 brouard 1144: int **Tvard;
1145: int *Tprod;/**< Gives the k position of the k1 product */
1146: int *Tposprod; /**< Gives the k1 product from the k position */
1147: /* Tprod[k1=1]=3(=V1*V4) for V2+V1+V1*V4+age*V3
1148: if V2+V1+V1*V4+age*V3+V3*V2 TProd[k1=2]=5 (V3*V2)
1149: Tposprod[k]=k1 , Tposprod[3]=1, Tposprod[5]=2
1150: */
1151: int cptcovprod, *Tvaraff, *invalidvarcomb;
1.126 brouard 1152: double *lsurv, *lpop, *tpop;
1153:
1.231 brouard 1154: #define FD 1; /* Fixed dummy covariate */
1155: #define FQ 2; /* Fixed quantitative covariate */
1156: #define FP 3; /* Fixed product covariate */
1157: #define FPDD 7; /* Fixed product dummy*dummy covariate */
1158: #define FPDQ 8; /* Fixed product dummy*quantitative covariate */
1159: #define FPQQ 9; /* Fixed product quantitative*quantitative covariate */
1160: #define VD 10; /* Varying dummy covariate */
1161: #define VQ 11; /* Varying quantitative covariate */
1162: #define VP 12; /* Varying product covariate */
1163: #define VPDD 13; /* Varying product dummy*dummy covariate */
1164: #define VPDQ 14; /* Varying product dummy*quantitative covariate */
1165: #define VPQQ 15; /* Varying product quantitative*quantitative covariate */
1166: #define APFD 16; /* Age product * fixed dummy covariate */
1167: #define APFQ 17; /* Age product * fixed quantitative covariate */
1168: #define APVD 18; /* Age product * varying dummy covariate */
1169: #define APVQ 19; /* Age product * varying quantitative covariate */
1170:
1171: #define FTYPE 1; /* Fixed covariate */
1172: #define VTYPE 2; /* Varying covariate (loop in wave) */
1173: #define ATYPE 2; /* Age product covariate (loop in dh within wave)*/
1174:
1175: struct kmodel{
1176: int maintype; /* main type */
1177: int subtype; /* subtype */
1178: };
1179: struct kmodel modell[NCOVMAX];
1180:
1.143 brouard 1181: double ftol=FTOL; /**< Tolerance for computing Max Likelihood */
1182: double ftolhess; /**< Tolerance for computing hessian */
1.126 brouard 1183:
1184: /**************** split *************************/
1185: static int split( char *path, char *dirc, char *name, char *ext, char *finame )
1186: {
1187: /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
1188: the name of the file (name), its extension only (ext) and its first part of the name (finame)
1189: */
1190: char *ss; /* pointer */
1.186 brouard 1191: int l1=0, l2=0; /* length counters */
1.126 brouard 1192:
1193: l1 = strlen(path ); /* length of path */
1194: if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
1195: ss= strrchr( path, DIRSEPARATOR ); /* find last / */
1196: if ( ss == NULL ) { /* no directory, so determine current directory */
1197: strcpy( name, path ); /* we got the fullname name because no directory */
1198: /*if(strrchr(path, ODIRSEPARATOR )==NULL)
1199: printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
1200: /* get current working directory */
1201: /* extern char* getcwd ( char *buf , int len);*/
1.184 brouard 1202: #ifdef WIN32
1203: if (_getcwd( dirc, FILENAME_MAX ) == NULL ) {
1204: #else
1205: if (getcwd(dirc, FILENAME_MAX) == NULL) {
1206: #endif
1.126 brouard 1207: return( GLOCK_ERROR_GETCWD );
1208: }
1209: /* got dirc from getcwd*/
1210: printf(" DIRC = %s \n",dirc);
1.205 brouard 1211: } else { /* strip directory from path */
1.126 brouard 1212: ss++; /* after this, the filename */
1213: l2 = strlen( ss ); /* length of filename */
1214: if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
1215: strcpy( name, ss ); /* save file name */
1216: strncpy( dirc, path, l1 - l2 ); /* now the directory */
1.186 brouard 1217: dirc[l1-l2] = '\0'; /* add zero */
1.126 brouard 1218: printf(" DIRC2 = %s \n",dirc);
1219: }
1220: /* We add a separator at the end of dirc if not exists */
1221: l1 = strlen( dirc ); /* length of directory */
1222: if( dirc[l1-1] != DIRSEPARATOR ){
1223: dirc[l1] = DIRSEPARATOR;
1224: dirc[l1+1] = 0;
1225: printf(" DIRC3 = %s \n",dirc);
1226: }
1227: ss = strrchr( name, '.' ); /* find last / */
1228: if (ss >0){
1229: ss++;
1230: strcpy(ext,ss); /* save extension */
1231: l1= strlen( name);
1232: l2= strlen(ss)+1;
1233: strncpy( finame, name, l1-l2);
1234: finame[l1-l2]= 0;
1235: }
1236:
1237: return( 0 ); /* we're done */
1238: }
1239:
1240:
1241: /******************************************/
1242:
1243: void replace_back_to_slash(char *s, char*t)
1244: {
1245: int i;
1246: int lg=0;
1247: i=0;
1248: lg=strlen(t);
1249: for(i=0; i<= lg; i++) {
1250: (s[i] = t[i]);
1251: if (t[i]== '\\') s[i]='/';
1252: }
1253: }
1254:
1.132 brouard 1255: char *trimbb(char *out, char *in)
1.137 brouard 1256: { /* Trim multiple blanks in line but keeps first blanks if line starts with blanks */
1.132 brouard 1257: char *s;
1258: s=out;
1259: while (*in != '\0'){
1.137 brouard 1260: while( *in == ' ' && *(in+1) == ' '){ /* && *(in+1) != '\0'){*/
1.132 brouard 1261: in++;
1262: }
1263: *out++ = *in++;
1264: }
1265: *out='\0';
1266: return s;
1267: }
1268:
1.187 brouard 1269: /* char *substrchaine(char *out, char *in, char *chain) */
1270: /* { */
1271: /* /\* Substract chain 'chain' from 'in', return and output 'out' *\/ */
1272: /* char *s, *t; */
1273: /* t=in;s=out; */
1274: /* while ((*in != *chain) && (*in != '\0')){ */
1275: /* *out++ = *in++; */
1276: /* } */
1277:
1278: /* /\* *in matches *chain *\/ */
1279: /* while ((*in++ == *chain++) && (*in != '\0')){ */
1280: /* printf("*in = %c, *out= %c *chain= %c \n", *in, *out, *chain); */
1281: /* } */
1282: /* in--; chain--; */
1283: /* while ( (*in != '\0')){ */
1284: /* printf("Bef *in = %c, *out= %c *chain= %c \n", *in, *out, *chain); */
1285: /* *out++ = *in++; */
1286: /* printf("Aft *in = %c, *out= %c *chain= %c \n", *in, *out, *chain); */
1287: /* } */
1288: /* *out='\0'; */
1289: /* out=s; */
1290: /* return out; */
1291: /* } */
1292: char *substrchaine(char *out, char *in, char *chain)
1293: {
1294: /* Substract chain 'chain' from 'in', return and output 'out' */
1295: /* in="V1+V1*age+age*age+V2", chain="age*age" */
1296:
1297: char *strloc;
1298:
1299: strcpy (out, in);
1300: strloc = strstr(out, chain); /* strloc points to out at age*age+V2 */
1301: printf("Bef strloc=%s chain=%s out=%s \n", strloc, chain, out);
1302: if(strloc != NULL){
1303: /* will affect out */ /* strloc+strlenc(chain)=+V2 */ /* Will also work in Unicode */
1304: memmove(strloc,strloc+strlen(chain), strlen(strloc+strlen(chain))+1);
1305: /* strcpy (strloc, strloc +strlen(chain));*/
1306: }
1307: printf("Aft strloc=%s chain=%s in=%s out=%s \n", strloc, chain, in, out);
1308: return out;
1309: }
1310:
1311:
1.145 brouard 1312: char *cutl(char *blocc, char *alocc, char *in, char occ)
1313: {
1.187 brouard 1314: /* cuts string in into blocc and alocc where blocc ends before FIRST occurence of char 'occ'
1.145 brouard 1315: and alocc starts after first occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
1.187 brouard 1316: gives blocc="abcdef" and alocc="ghi2j".
1.145 brouard 1317: If occ is not found blocc is null and alocc is equal to in. Returns blocc
1318: */
1.160 brouard 1319: char *s, *t;
1.145 brouard 1320: t=in;s=in;
1321: while ((*in != occ) && (*in != '\0')){
1322: *alocc++ = *in++;
1323: }
1324: if( *in == occ){
1325: *(alocc)='\0';
1326: s=++in;
1327: }
1328:
1329: if (s == t) {/* occ not found */
1330: *(alocc-(in-s))='\0';
1331: in=s;
1332: }
1333: while ( *in != '\0'){
1334: *blocc++ = *in++;
1335: }
1336:
1337: *blocc='\0';
1338: return t;
1339: }
1.137 brouard 1340: char *cutv(char *blocc, char *alocc, char *in, char occ)
1341: {
1.187 brouard 1342: /* cuts string in into blocc and alocc where blocc ends before LAST occurence of char 'occ'
1.137 brouard 1343: and alocc starts after last occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
1344: gives blocc="abcdef2ghi" and alocc="j".
1345: If occ is not found blocc is null and alocc is equal to in. Returns alocc
1346: */
1347: char *s, *t;
1348: t=in;s=in;
1349: while (*in != '\0'){
1350: while( *in == occ){
1351: *blocc++ = *in++;
1352: s=in;
1353: }
1354: *blocc++ = *in++;
1355: }
1356: if (s == t) /* occ not found */
1357: *(blocc-(in-s))='\0';
1358: else
1359: *(blocc-(in-s)-1)='\0';
1360: in=s;
1361: while ( *in != '\0'){
1362: *alocc++ = *in++;
1363: }
1364:
1365: *alocc='\0';
1366: return s;
1367: }
1368:
1.126 brouard 1369: int nbocc(char *s, char occ)
1370: {
1371: int i,j=0;
1372: int lg=20;
1373: i=0;
1374: lg=strlen(s);
1375: for(i=0; i<= lg; i++) {
1.234 brouard 1376: if (s[i] == occ ) j++;
1.126 brouard 1377: }
1378: return j;
1379: }
1380:
1.137 brouard 1381: /* void cutv(char *u,char *v, char*t, char occ) */
1382: /* { */
1383: /* /\* cuts string t into u and v where u ends before last occurence of char 'occ' */
1384: /* and v starts after last occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2') */
1385: /* gives u="abcdef2ghi" and v="j" *\/ */
1386: /* int i,lg,j,p=0; */
1387: /* i=0; */
1388: /* lg=strlen(t); */
1389: /* for(j=0; j<=lg-1; j++) { */
1390: /* if((t[j]!= occ) && (t[j+1]== occ)) p=j+1; */
1391: /* } */
1.126 brouard 1392:
1.137 brouard 1393: /* for(j=0; j<p; j++) { */
1394: /* (u[j] = t[j]); */
1395: /* } */
1396: /* u[p]='\0'; */
1.126 brouard 1397:
1.137 brouard 1398: /* for(j=0; j<= lg; j++) { */
1399: /* if (j>=(p+1))(v[j-p-1] = t[j]); */
1400: /* } */
1401: /* } */
1.126 brouard 1402:
1.160 brouard 1403: #ifdef _WIN32
1404: char * strsep(char **pp, const char *delim)
1405: {
1406: char *p, *q;
1407:
1408: if ((p = *pp) == NULL)
1409: return 0;
1410: if ((q = strpbrk (p, delim)) != NULL)
1411: {
1412: *pp = q + 1;
1413: *q = '\0';
1414: }
1415: else
1416: *pp = 0;
1417: return p;
1418: }
1419: #endif
1420:
1.126 brouard 1421: /********************** nrerror ********************/
1422:
1423: void nrerror(char error_text[])
1424: {
1425: fprintf(stderr,"ERREUR ...\n");
1426: fprintf(stderr,"%s\n",error_text);
1427: exit(EXIT_FAILURE);
1428: }
1429: /*********************** vector *******************/
1430: double *vector(int nl, int nh)
1431: {
1432: double *v;
1433: v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
1434: if (!v) nrerror("allocation failure in vector");
1435: return v-nl+NR_END;
1436: }
1437:
1438: /************************ free vector ******************/
1439: void free_vector(double*v, int nl, int nh)
1440: {
1441: free((FREE_ARG)(v+nl-NR_END));
1442: }
1443:
1444: /************************ivector *******************************/
1445: int *ivector(long nl,long nh)
1446: {
1447: int *v;
1448: v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
1449: if (!v) nrerror("allocation failure in ivector");
1450: return v-nl+NR_END;
1451: }
1452:
1453: /******************free ivector **************************/
1454: void free_ivector(int *v, long nl, long nh)
1455: {
1456: free((FREE_ARG)(v+nl-NR_END));
1457: }
1458:
1459: /************************lvector *******************************/
1460: long *lvector(long nl,long nh)
1461: {
1462: long *v;
1463: v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
1464: if (!v) nrerror("allocation failure in ivector");
1465: return v-nl+NR_END;
1466: }
1467:
1468: /******************free lvector **************************/
1469: void free_lvector(long *v, long nl, long nh)
1470: {
1471: free((FREE_ARG)(v+nl-NR_END));
1472: }
1473:
1474: /******************* imatrix *******************************/
1475: int **imatrix(long nrl, long nrh, long ncl, long nch)
1476: /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */
1477: {
1478: long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;
1479: int **m;
1480:
1481: /* allocate pointers to rows */
1482: m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));
1483: if (!m) nrerror("allocation failure 1 in matrix()");
1484: m += NR_END;
1485: m -= nrl;
1486:
1487:
1488: /* allocate rows and set pointers to them */
1489: m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));
1490: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
1491: m[nrl] += NR_END;
1492: m[nrl] -= ncl;
1493:
1494: for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;
1495:
1496: /* return pointer to array of pointers to rows */
1497: return m;
1498: }
1499:
1500: /****************** free_imatrix *************************/
1501: void free_imatrix(m,nrl,nrh,ncl,nch)
1502: int **m;
1503: long nch,ncl,nrh,nrl;
1504: /* free an int matrix allocated by imatrix() */
1505: {
1506: free((FREE_ARG) (m[nrl]+ncl-NR_END));
1507: free((FREE_ARG) (m+nrl-NR_END));
1508: }
1509:
1510: /******************* matrix *******************************/
1511: double **matrix(long nrl, long nrh, long ncl, long nch)
1512: {
1513: long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
1514: double **m;
1515:
1516: m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
1517: if (!m) nrerror("allocation failure 1 in matrix()");
1518: m += NR_END;
1519: m -= nrl;
1520:
1521: m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
1522: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
1523: m[nrl] += NR_END;
1524: m[nrl] -= ncl;
1525:
1526: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
1527: return m;
1.145 brouard 1528: /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) or &(m[1][0])
1529: m[i] = address of ith row of the table. &(m[i]) is its value which is another adress
1530: that of m[i][0]. In order to get the value p m[i][0] but it is unitialized.
1.126 brouard 1531: */
1532: }
1533:
1534: /*************************free matrix ************************/
1535: void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
1536: {
1537: free((FREE_ARG)(m[nrl]+ncl-NR_END));
1538: free((FREE_ARG)(m+nrl-NR_END));
1539: }
1540:
1541: /******************* ma3x *******************************/
1542: double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
1543: {
1544: long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
1545: double ***m;
1546:
1547: m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
1548: if (!m) nrerror("allocation failure 1 in matrix()");
1549: m += NR_END;
1550: m -= nrl;
1551:
1552: m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
1553: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
1554: m[nrl] += NR_END;
1555: m[nrl] -= ncl;
1556:
1557: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
1558:
1559: m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
1560: if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
1561: m[nrl][ncl] += NR_END;
1562: m[nrl][ncl] -= nll;
1563: for (j=ncl+1; j<=nch; j++)
1564: m[nrl][j]=m[nrl][j-1]+nlay;
1565:
1566: for (i=nrl+1; i<=nrh; i++) {
1567: m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
1568: for (j=ncl+1; j<=nch; j++)
1569: m[i][j]=m[i][j-1]+nlay;
1570: }
1571: return m;
1572: /* gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
1573: &(m[i][j][k]) <=> *((*(m+i) + j)+k)
1574: */
1575: }
1576:
1577: /*************************free ma3x ************************/
1578: void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
1579: {
1580: free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
1581: free((FREE_ARG)(m[nrl]+ncl-NR_END));
1582: free((FREE_ARG)(m+nrl-NR_END));
1583: }
1584:
1585: /*************** function subdirf ***********/
1586: char *subdirf(char fileres[])
1587: {
1588: /* Caution optionfilefiname is hidden */
1589: strcpy(tmpout,optionfilefiname);
1590: strcat(tmpout,"/"); /* Add to the right */
1591: strcat(tmpout,fileres);
1592: return tmpout;
1593: }
1594:
1595: /*************** function subdirf2 ***********/
1596: char *subdirf2(char fileres[], char *preop)
1597: {
1598:
1599: /* Caution optionfilefiname is hidden */
1600: strcpy(tmpout,optionfilefiname);
1601: strcat(tmpout,"/");
1602: strcat(tmpout,preop);
1603: strcat(tmpout,fileres);
1604: return tmpout;
1605: }
1606:
1607: /*************** function subdirf3 ***********/
1608: char *subdirf3(char fileres[], char *preop, char *preop2)
1609: {
1610:
1611: /* Caution optionfilefiname is hidden */
1612: strcpy(tmpout,optionfilefiname);
1613: strcat(tmpout,"/");
1614: strcat(tmpout,preop);
1615: strcat(tmpout,preop2);
1616: strcat(tmpout,fileres);
1617: return tmpout;
1618: }
1.213 brouard 1619:
1620: /*************** function subdirfext ***********/
1621: char *subdirfext(char fileres[], char *preop, char *postop)
1622: {
1623:
1624: strcpy(tmpout,preop);
1625: strcat(tmpout,fileres);
1626: strcat(tmpout,postop);
1627: return tmpout;
1628: }
1.126 brouard 1629:
1.213 brouard 1630: /*************** function subdirfext3 ***********/
1631: char *subdirfext3(char fileres[], char *preop, char *postop)
1632: {
1633:
1634: /* Caution optionfilefiname is hidden */
1635: strcpy(tmpout,optionfilefiname);
1636: strcat(tmpout,"/");
1637: strcat(tmpout,preop);
1638: strcat(tmpout,fileres);
1639: strcat(tmpout,postop);
1640: return tmpout;
1641: }
1642:
1.162 brouard 1643: char *asc_diff_time(long time_sec, char ascdiff[])
1644: {
1645: long sec_left, days, hours, minutes;
1646: days = (time_sec) / (60*60*24);
1647: sec_left = (time_sec) % (60*60*24);
1648: hours = (sec_left) / (60*60) ;
1649: sec_left = (sec_left) %(60*60);
1650: minutes = (sec_left) /60;
1651: sec_left = (sec_left) % (60);
1652: sprintf(ascdiff,"%ld day(s) %ld hour(s) %ld minute(s) %ld second(s)",days, hours, minutes, sec_left);
1653: return ascdiff;
1654: }
1655:
1.126 brouard 1656: /***************** f1dim *************************/
1657: extern int ncom;
1658: extern double *pcom,*xicom;
1659: extern double (*nrfunc)(double []);
1660:
1661: double f1dim(double x)
1662: {
1663: int j;
1664: double f;
1665: double *xt;
1666:
1667: xt=vector(1,ncom);
1668: for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];
1669: f=(*nrfunc)(xt);
1670: free_vector(xt,1,ncom);
1671: return f;
1672: }
1673:
1674: /*****************brent *************************/
1675: double brent(double ax, double bx, double cx, double (*f)(double), double tol, double *xmin)
1.187 brouard 1676: {
1677: /* Given a function f, and given a bracketing triplet of abscissas ax, bx, cx (such that bx is
1678: * between ax and cx, and f(bx) is less than both f(ax) and f(cx) ), this routine isolates
1679: * the minimum to a fractional precision of about tol using Brent’s method. The abscissa of
1680: * the minimum is returned as xmin, and the minimum function value is returned as brent , the
1681: * returned function value.
1682: */
1.126 brouard 1683: int iter;
1684: double a,b,d,etemp;
1.159 brouard 1685: double fu=0,fv,fw,fx;
1.164 brouard 1686: double ftemp=0.;
1.126 brouard 1687: double p,q,r,tol1,tol2,u,v,w,x,xm;
1688: double e=0.0;
1689:
1690: a=(ax < cx ? ax : cx);
1691: b=(ax > cx ? ax : cx);
1692: x=w=v=bx;
1693: fw=fv=fx=(*f)(x);
1694: for (iter=1;iter<=ITMAX;iter++) {
1695: xm=0.5*(a+b);
1696: tol2=2.0*(tol1=tol*fabs(x)+ZEPS);
1697: /* if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
1698: printf(".");fflush(stdout);
1699: fprintf(ficlog,".");fflush(ficlog);
1.162 brouard 1700: #ifdef DEBUGBRENT
1.126 brouard 1701: 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);
1702: 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);
1703: /* if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
1704: #endif
1705: if (fabs(x-xm) <= (tol2-0.5*(b-a))){
1706: *xmin=x;
1707: return fx;
1708: }
1709: ftemp=fu;
1710: if (fabs(e) > tol1) {
1711: r=(x-w)*(fx-fv);
1712: q=(x-v)*(fx-fw);
1713: p=(x-v)*q-(x-w)*r;
1714: q=2.0*(q-r);
1715: if (q > 0.0) p = -p;
1716: q=fabs(q);
1717: etemp=e;
1718: e=d;
1719: if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))
1.224 brouard 1720: d=CGOLD*(e=(x >= xm ? a-x : b-x));
1.126 brouard 1721: else {
1.224 brouard 1722: d=p/q;
1723: u=x+d;
1724: if (u-a < tol2 || b-u < tol2)
1725: d=SIGN(tol1,xm-x);
1.126 brouard 1726: }
1727: } else {
1728: d=CGOLD*(e=(x >= xm ? a-x : b-x));
1729: }
1730: u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));
1731: fu=(*f)(u);
1732: if (fu <= fx) {
1733: if (u >= x) a=x; else b=x;
1734: SHFT(v,w,x,u)
1.183 brouard 1735: SHFT(fv,fw,fx,fu)
1736: } else {
1737: if (u < x) a=u; else b=u;
1738: if (fu <= fw || w == x) {
1.224 brouard 1739: v=w;
1740: w=u;
1741: fv=fw;
1742: fw=fu;
1.183 brouard 1743: } else if (fu <= fv || v == x || v == w) {
1.224 brouard 1744: v=u;
1745: fv=fu;
1.183 brouard 1746: }
1747: }
1.126 brouard 1748: }
1749: nrerror("Too many iterations in brent");
1750: *xmin=x;
1751: return fx;
1752: }
1753:
1754: /****************** mnbrak ***********************/
1755:
1756: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,
1757: double (*func)(double))
1.183 brouard 1758: { /* Given a function func , and given distinct initial points ax and bx , this routine searches in
1759: the downhill direction (defined by the function as evaluated at the initial points) and returns
1760: new points ax , bx , cx that bracket a minimum of the function. Also returned are the function
1761: values at the three points, fa, fb , and fc such that fa > fb and fb < fc.
1762: */
1.126 brouard 1763: double ulim,u,r,q, dum;
1764: double fu;
1.187 brouard 1765:
1766: double scale=10.;
1767: int iterscale=0;
1768:
1769: *fa=(*func)(*ax); /* xta[j]=pcom[j]+(*ax)*xicom[j]; fa=f(xta[j])*/
1770: *fb=(*func)(*bx); /* xtb[j]=pcom[j]+(*bx)*xicom[j]; fb=f(xtb[j]) */
1771:
1772:
1773: /* while(*fb != *fb){ /\* *ax should be ok, reducing distance to *ax *\/ */
1774: /* printf("Warning mnbrak *fb = %lf, *bx=%lf *ax=%lf *fa==%lf iter=%d\n",*fb, *bx, *ax, *fa, iterscale++); */
1775: /* *bx = *ax - (*ax - *bx)/scale; */
1776: /* *fb=(*func)(*bx); /\* xtb[j]=pcom[j]+(*bx)*xicom[j]; fb=f(xtb[j]) *\/ */
1777: /* } */
1778:
1.126 brouard 1779: if (*fb > *fa) {
1780: SHFT(dum,*ax,*bx,dum)
1.183 brouard 1781: SHFT(dum,*fb,*fa,dum)
1782: }
1.126 brouard 1783: *cx=(*bx)+GOLD*(*bx-*ax);
1784: *fc=(*func)(*cx);
1.183 brouard 1785: #ifdef DEBUG
1.224 brouard 1786: printf("mnbrak0 a=%lf *fa=%lf, b=%lf *fb=%lf, c=%lf *fc=%lf\n",*ax,*fa,*bx,*fb,*cx, *fc);
1787: fprintf(ficlog,"mnbrak0 a=%lf *fa=%lf, b=%lf *fb=%lf, c=%lf *fc=%lf\n",*ax,*fa,*bx,*fb,*cx, *fc);
1.183 brouard 1788: #endif
1.224 brouard 1789: while (*fb > *fc) { /* Declining a,b,c with fa> fb > fc. If fc=inf it exits and if flat fb=fc it exits too.*/
1.126 brouard 1790: r=(*bx-*ax)*(*fb-*fc);
1.224 brouard 1791: q=(*bx-*cx)*(*fb-*fa); /* What if fa=inf */
1.126 brouard 1792: u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/
1.183 brouard 1793: (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); /* Minimum abscissa of a parabolic estimated from (a,fa), (b,fb) and (c,fc). */
1794: ulim=(*bx)+GLIMIT*(*cx-*bx); /* Maximum abscissa where function should be evaluated */
1795: if ((*bx-u)*(u-*cx) > 0.0) { /* if u_p is between b and c */
1.126 brouard 1796: fu=(*func)(u);
1.163 brouard 1797: #ifdef DEBUG
1798: /* f(x)=A(x-u)**2+f(u) */
1799: double A, fparabu;
1800: A= (*fb - *fa)/(*bx-*ax)/(*bx+*ax-2*u);
1801: fparabu= *fa - A*(*ax-u)*(*ax-u);
1.224 brouard 1802: printf("\nmnbrak (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf), (*u=%.12f, fu=%.12lf, fparabu=%.12f, q=%lf < %lf=r)\n",*ax,*fa,*bx,*fb,*cx,*fc,u,fu, fparabu,q,r);
1803: fprintf(ficlog,"\nmnbrak (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf), (*u=%.12f, fu=%.12lf, fparabu=%.12f, q=%lf < %lf=r)\n",*ax,*fa,*bx,*fb,*cx,*fc,u,fu, fparabu,q,r);
1.183 brouard 1804: /* And thus,it can be that fu > *fc even if fparabu < *fc */
1805: /* mnbrak (*ax=7.666299858533, *fa=299039.693133272231), (*bx=8.595447774979, *fb=298976.598289369489),
1806: (*cx=10.098840694817, *fc=298946.631474258087), (*u=9.852501168332, fu=298948.773013752128, fparabu=298945.434711494134) */
1807: /* In that case, there is no bracket in the output! Routine is wrong with many consequences.*/
1.163 brouard 1808: #endif
1.184 brouard 1809: #ifdef MNBRAKORIGINAL
1.183 brouard 1810: #else
1.191 brouard 1811: /* if (fu > *fc) { */
1812: /* #ifdef DEBUG */
1813: /* printf("mnbrak4 fu > fc \n"); */
1814: /* fprintf(ficlog, "mnbrak4 fu > fc\n"); */
1815: /* #endif */
1816: /* /\* 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 *\\/ *\/ */
1817: /* /\* SHFT(*fa,*fc,fu,*fc) /\\* (b, u, c) is a bracket while test fb > fc will be fu > fc will exit *\\/ *\/ */
1818: /* dum=u; /\* Shifting c and u *\/ */
1819: /* u = *cx; */
1820: /* *cx = dum; */
1821: /* dum = fu; */
1822: /* fu = *fc; */
1823: /* *fc =dum; */
1824: /* } else { /\* end *\/ */
1825: /* #ifdef DEBUG */
1826: /* printf("mnbrak3 fu < fc \n"); */
1827: /* fprintf(ficlog, "mnbrak3 fu < fc\n"); */
1828: /* #endif */
1829: /* dum=u; /\* Shifting c and u *\/ */
1830: /* u = *cx; */
1831: /* *cx = dum; */
1832: /* dum = fu; */
1833: /* fu = *fc; */
1834: /* *fc =dum; */
1835: /* } */
1.224 brouard 1836: #ifdef DEBUGMNBRAK
1837: double A, fparabu;
1838: A= (*fb - *fa)/(*bx-*ax)/(*bx+*ax-2*u);
1839: fparabu= *fa - A*(*ax-u)*(*ax-u);
1840: printf("\nmnbrak35 ax=%lf fa=%lf bx=%lf fb=%lf, u=%lf fp=%lf fu=%lf < or >= fc=%lf cx=%lf, q=%lf < %lf=r \n",*ax, *fa, *bx,*fb,u,fparabu,fu,*fc,*cx,q,r);
1841: fprintf(ficlog,"\nmnbrak35 ax=%lf fa=%lf bx=%lf fb=%lf, u=%lf fp=%lf fu=%lf < or >= fc=%lf cx=%lf, q=%lf < %lf=r \n",*ax, *fa, *bx,*fb,u,fparabu,fu,*fc,*cx,q,r);
1.183 brouard 1842: #endif
1.191 brouard 1843: dum=u; /* Shifting c and u */
1844: u = *cx;
1845: *cx = dum;
1846: dum = fu;
1847: fu = *fc;
1848: *fc =dum;
1.183 brouard 1849: #endif
1.162 brouard 1850: } else if ((*cx-u)*(u-ulim) > 0.0) { /* u is after c but before ulim */
1.183 brouard 1851: #ifdef DEBUG
1.224 brouard 1852: printf("\nmnbrak2 u=%lf after c=%lf but before ulim\n",u,*cx);
1853: fprintf(ficlog,"\nmnbrak2 u=%lf after c=%lf but before ulim\n",u,*cx);
1.183 brouard 1854: #endif
1.126 brouard 1855: fu=(*func)(u);
1856: if (fu < *fc) {
1.183 brouard 1857: #ifdef DEBUG
1.224 brouard 1858: printf("\nmnbrak2 u=%lf after c=%lf but before ulim=%lf AND fu=%lf < %lf=fc\n",u,*cx,ulim,fu, *fc);
1859: fprintf(ficlog,"\nmnbrak2 u=%lf after c=%lf but before ulim=%lf AND fu=%lf < %lf=fc\n",u,*cx,ulim,fu, *fc);
1860: #endif
1861: SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))
1862: SHFT(*fb,*fc,fu,(*func)(u))
1863: #ifdef DEBUG
1864: printf("\nmnbrak2 shift GOLD c=%lf",*cx+GOLD*(*cx-*bx));
1.183 brouard 1865: #endif
1866: }
1.162 brouard 1867: } else if ((u-ulim)*(ulim-*cx) >= 0.0) { /* u outside ulim (verifying that ulim is beyond c) */
1.183 brouard 1868: #ifdef DEBUG
1.224 brouard 1869: printf("\nmnbrak2 u=%lf outside ulim=%lf (verifying that ulim is beyond c=%lf)\n",u,ulim,*cx);
1870: fprintf(ficlog,"\nmnbrak2 u=%lf outside ulim=%lf (verifying that ulim is beyond c=%lf)\n",u,ulim,*cx);
1.183 brouard 1871: #endif
1.126 brouard 1872: u=ulim;
1873: fu=(*func)(u);
1.183 brouard 1874: } else { /* u could be left to b (if r > q parabola has a maximum) */
1875: #ifdef DEBUG
1.224 brouard 1876: printf("\nmnbrak2 u=%lf could be left to b=%lf (if r=%lf > q=%lf parabola has a maximum)\n",u,*bx,r,q);
1877: fprintf(ficlog,"\nmnbrak2 u=%lf could be left to b=%lf (if r=%lf > q=%lf parabola has a maximum)\n",u,*bx,r,q);
1.183 brouard 1878: #endif
1.126 brouard 1879: u=(*cx)+GOLD*(*cx-*bx);
1880: fu=(*func)(u);
1.224 brouard 1881: #ifdef DEBUG
1882: printf("\nmnbrak2 new u=%lf fu=%lf shifted gold left from c=%lf and b=%lf \n",u,fu,*cx,*bx);
1883: fprintf(ficlog,"\nmnbrak2 new u=%lf fu=%lf shifted gold left from c=%lf and b=%lf \n",u,fu,*cx,*bx);
1884: #endif
1.183 brouard 1885: } /* end tests */
1.126 brouard 1886: SHFT(*ax,*bx,*cx,u)
1.183 brouard 1887: SHFT(*fa,*fb,*fc,fu)
1888: #ifdef DEBUG
1.224 brouard 1889: printf("\nmnbrak2 shift (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf)\n",*ax,*fa,*bx,*fb,*cx,*fc);
1890: fprintf(ficlog, "\nmnbrak2 shift (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf)\n",*ax,*fa,*bx,*fb,*cx,*fc);
1.183 brouard 1891: #endif
1892: } /* 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 1893: }
1894:
1895: /*************** linmin ************************/
1.162 brouard 1896: /* Given an n -dimensional point p[1..n] and an n -dimensional direction xi[1..n] , moves and
1897: resets p to where the function func(p) takes on a minimum along the direction xi from p ,
1898: and replaces xi by the actual vector displacement that p was moved. Also returns as fret
1899: the value of func at the returned location p . This is actually all accomplished by calling the
1900: routines mnbrak and brent .*/
1.126 brouard 1901: int ncom;
1902: double *pcom,*xicom;
1903: double (*nrfunc)(double []);
1904:
1.224 brouard 1905: #ifdef LINMINORIGINAL
1.126 brouard 1906: void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))
1.224 brouard 1907: #else
1908: void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []), int *flat)
1909: #endif
1.126 brouard 1910: {
1911: double brent(double ax, double bx, double cx,
1912: double (*f)(double), double tol, double *xmin);
1913: double f1dim(double x);
1914: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,
1915: double *fc, double (*func)(double));
1916: int j;
1917: double xx,xmin,bx,ax;
1918: double fx,fb,fa;
1.187 brouard 1919:
1.203 brouard 1920: #ifdef LINMINORIGINAL
1921: #else
1922: double scale=10., axs, xxs; /* Scale added for infinity */
1923: #endif
1924:
1.126 brouard 1925: ncom=n;
1926: pcom=vector(1,n);
1927: xicom=vector(1,n);
1928: nrfunc=func;
1929: for (j=1;j<=n;j++) {
1930: pcom[j]=p[j];
1.202 brouard 1931: xicom[j]=xi[j]; /* Former scale xi[j] of currrent direction i */
1.126 brouard 1932: }
1.187 brouard 1933:
1.203 brouard 1934: #ifdef LINMINORIGINAL
1935: xx=1.;
1936: #else
1937: axs=0.0;
1938: xxs=1.;
1939: do{
1940: xx= xxs;
1941: #endif
1.187 brouard 1942: ax=0.;
1943: mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); /* Outputs: xtx[j]=pcom[j]+(*xx)*xicom[j]; fx=f(xtx[j]) */
1944: /* brackets with inputs ax=0 and xx=1, but points, pcom=p, and directions values, xicom=xi, are sent via f1dim(x) */
1945: /* 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)) */
1946: /* Outputs: fa=f(p(j)) and fx=f(p(j) + xxs * xi(j) ) and f(bx)= f(p(j)+ bx* xi(j)) */
1947: /* Given input ax=axs and xx=xxs, xx might be too far from ax to get a finite f(xx) */
1948: /* Searches on line, outputs (ax, xx, bx) such that fx < min(fa and fb) */
1949: /* 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 1950: #ifdef LINMINORIGINAL
1951: #else
1952: if (fx != fx){
1.224 brouard 1953: xxs=xxs/scale; /* Trying a smaller xx, closer to initial ax=0 */
1954: printf("|");
1955: fprintf(ficlog,"|");
1.203 brouard 1956: #ifdef DEBUGLINMIN
1.224 brouard 1957: 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);
1.203 brouard 1958: #endif
1959: }
1.224 brouard 1960: }while(fx != fx && xxs > 1.e-5);
1.203 brouard 1961: #endif
1962:
1.191 brouard 1963: #ifdef DEBUGLINMIN
1964: 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 1965: 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 1966: #endif
1.224 brouard 1967: #ifdef LINMINORIGINAL
1968: #else
1969: if(fb == fx){ /* Flat function in the direction */
1970: xmin=xx;
1971: *flat=1;
1972: }else{
1973: *flat=0;
1974: #endif
1975: /*Flat mnbrak2 shift (*ax=0.000000000000, *fa=51626.272983130431), (*bx=-1.618034000000, *fb=51590.149499362531), (*cx=-4.236068025156, *fc=51590.149499362531) */
1.187 brouard 1976: *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); /* Giving a bracketting triplet (ax, xx, bx), find a minimum, xmin, according to f1dim, *fret(xmin),*/
1977: /* fa = f(p[j] + ax * xi[j]), fx = f(p[j] + xx * xi[j]), fb = f(p[j] + bx * xi[j]) */
1978: /* fmin = f(p[j] + xmin * xi[j]) */
1979: /* P+lambda n in that direction (lambdamin), with TOL between abscisses */
1980: /* f1dim(xmin): for (j=1;j<=ncom;j++) xt[j]=pcom[j]+xmin*xicom[j]; */
1.126 brouard 1981: #ifdef DEBUG
1.224 brouard 1982: printf("retour brent from bracket (a=%lf fa=%lf, xx=%lf fx=%lf, b=%lf fb=%lf): fret=%lf xmin=%lf\n",ax,fa,xx,fx,bx,fb,*fret,xmin);
1983: fprintf(ficlog,"retour brent from bracket (a=%lf fa=%lf, xx=%lf fx=%lf, b=%lf fb=%lf): fret=%lf xmin=%lf\n",ax,fa,xx,fx,bx,fb,*fret,xmin);
1984: #endif
1985: #ifdef LINMINORIGINAL
1986: #else
1987: }
1.126 brouard 1988: #endif
1.191 brouard 1989: #ifdef DEBUGLINMIN
1990: printf("linmin end ");
1.202 brouard 1991: fprintf(ficlog,"linmin end ");
1.191 brouard 1992: #endif
1.126 brouard 1993: for (j=1;j<=n;j++) {
1.203 brouard 1994: #ifdef LINMINORIGINAL
1995: xi[j] *= xmin;
1996: #else
1997: #ifdef DEBUGLINMIN
1998: if(xxs <1.0)
1999: printf(" before xi[%d]=%12.8f", j,xi[j]);
2000: #endif
2001: 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) */
2002: #ifdef DEBUGLINMIN
2003: if(xxs <1.0)
2004: 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 );
2005: #endif
2006: #endif
1.187 brouard 2007: p[j] += xi[j]; /* Parameters values are updated accordingly */
1.126 brouard 2008: }
1.191 brouard 2009: #ifdef DEBUGLINMIN
1.203 brouard 2010: printf("\n");
1.191 brouard 2011: printf("Comparing last *frec(xmin=%12.8f)=%12.8f from Brent and frec(0.)=%12.8f \n", xmin, *fret, (*func)(p));
1.202 brouard 2012: 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 2013: for (j=1;j<=n;j++) {
1.202 brouard 2014: printf(" xi[%d]= %14.10f p[%d]= %12.7f",j,xi[j],j,p[j]);
2015: fprintf(ficlog," xi[%d]= %14.10f p[%d]= %12.7f",j,xi[j],j,p[j]);
2016: if(j % ncovmodel == 0){
1.191 brouard 2017: printf("\n");
1.202 brouard 2018: fprintf(ficlog,"\n");
2019: }
1.191 brouard 2020: }
1.203 brouard 2021: #else
1.191 brouard 2022: #endif
1.126 brouard 2023: free_vector(xicom,1,n);
2024: free_vector(pcom,1,n);
2025: }
2026:
2027:
2028: /*************** powell ************************/
1.162 brouard 2029: /*
2030: Minimization of a function func of n variables. Input consists of an initial starting point
2031: p[1..n] ; an initial matrix xi[1..n][1..n] , whose columns contain the initial set of di-
2032: rections (usually the n unit vectors); and ftol , the fractional tolerance in the function value
2033: such that failure to decrease by more than this amount on one iteration signals doneness. On
2034: output, p is set to the best point found, xi is the then-current direction set, fret is the returned
2035: function value at p , and iter is the number of iterations taken. The routine linmin is used.
2036: */
1.224 brouard 2037: #ifdef LINMINORIGINAL
2038: #else
2039: int *flatdir; /* Function is vanishing in that direction */
1.225 brouard 2040: int flat=0, flatd=0; /* Function is vanishing in that direction */
1.224 brouard 2041: #endif
1.126 brouard 2042: void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,
2043: double (*func)(double []))
2044: {
1.224 brouard 2045: #ifdef LINMINORIGINAL
2046: void linmin(double p[], double xi[], int n, double *fret,
1.126 brouard 2047: double (*func)(double []));
1.224 brouard 2048: #else
2049: void linmin(double p[], double xi[], int n, double *fret,
2050: double (*func)(double []),int *flat);
2051: #endif
1.126 brouard 2052: int i,ibig,j;
2053: double del,t,*pt,*ptt,*xit;
1.181 brouard 2054: double directest;
1.126 brouard 2055: double fp,fptt;
2056: double *xits;
2057: int niterf, itmp;
1.224 brouard 2058: #ifdef LINMINORIGINAL
2059: #else
2060:
2061: flatdir=ivector(1,n);
2062: for (j=1;j<=n;j++) flatdir[j]=0;
2063: #endif
1.126 brouard 2064:
2065: pt=vector(1,n);
2066: ptt=vector(1,n);
2067: xit=vector(1,n);
2068: xits=vector(1,n);
2069: *fret=(*func)(p);
2070: for (j=1;j<=n;j++) pt[j]=p[j];
1.202 brouard 2071: rcurr_time = time(NULL);
1.126 brouard 2072: for (*iter=1;;++(*iter)) {
1.187 brouard 2073: fp=(*fret); /* From former iteration or initial value */
1.126 brouard 2074: ibig=0;
2075: del=0.0;
1.157 brouard 2076: rlast_time=rcurr_time;
2077: /* (void) gettimeofday(&curr_time,&tzp); */
2078: rcurr_time = time(NULL);
2079: curr_time = *localtime(&rcurr_time);
2080: printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, rcurr_time-rlast_time, rcurr_time-rstart_time);fflush(stdout);
2081: fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret,rcurr_time-rlast_time, rcurr_time-rstart_time); fflush(ficlog);
2082: /* fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tm_sec-start_time.tm_sec); */
1.192 brouard 2083: for (i=1;i<=n;i++) {
1.126 brouard 2084: printf(" %d %.12f",i, p[i]);
2085: fprintf(ficlog," %d %.12lf",i, p[i]);
2086: fprintf(ficrespow," %.12lf", p[i]);
2087: }
2088: printf("\n");
2089: fprintf(ficlog,"\n");
2090: fprintf(ficrespow,"\n");fflush(ficrespow);
2091: if(*iter <=3){
1.157 brouard 2092: tml = *localtime(&rcurr_time);
2093: strcpy(strcurr,asctime(&tml));
2094: rforecast_time=rcurr_time;
1.126 brouard 2095: itmp = strlen(strcurr);
2096: if(strcurr[itmp-1]=='\n') /* Windows outputs with a new line */
1.224 brouard 2097: strcurr[itmp-1]='\0';
1.162 brouard 2098: printf("\nConsidering the time needed for the last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
1.157 brouard 2099: fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
1.126 brouard 2100: for(niterf=10;niterf<=30;niterf+=10){
1.224 brouard 2101: rforecast_time=rcurr_time+(niterf-*iter)*(rcurr_time-rlast_time);
2102: forecast_time = *localtime(&rforecast_time);
2103: strcpy(strfor,asctime(&forecast_time));
2104: itmp = strlen(strfor);
2105: if(strfor[itmp-1]=='\n')
2106: strfor[itmp-1]='\0';
2107: 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);
2108: 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 2109: }
2110: }
1.187 brouard 2111: for (i=1;i<=n;i++) { /* For each direction i */
2112: for (j=1;j<=n;j++) xit[j]=xi[j][i]; /* Directions stored from previous iteration with previous scales */
1.126 brouard 2113: fptt=(*fret);
2114: #ifdef DEBUG
1.203 brouard 2115: printf("fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
2116: fprintf(ficlog, "fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
1.126 brouard 2117: #endif
1.203 brouard 2118: printf("%d",i);fflush(stdout); /* print direction (parameter) i */
1.126 brouard 2119: fprintf(ficlog,"%d",i);fflush(ficlog);
1.224 brouard 2120: #ifdef LINMINORIGINAL
1.188 brouard 2121: linmin(p,xit,n,fret,func); /* Point p[n]. xit[n] has been loaded for direction i as input.*/
1.224 brouard 2122: #else
2123: linmin(p,xit,n,fret,func,&flat); /* Point p[n]. xit[n] has been loaded for direction i as input.*/
2124: flatdir[i]=flat; /* Function is vanishing in that direction i */
2125: #endif
2126: /* Outputs are fret(new point p) p is updated and xit rescaled */
1.188 brouard 2127: if (fabs(fptt-(*fret)) > del) { /* We are keeping the max gain on each of the n directions */
1.224 brouard 2128: /* because that direction will be replaced unless the gain del is small */
2129: /* in comparison with the 'probable' gain, mu^2, with the last average direction. */
2130: /* Unless the n directions are conjugate some gain in the determinant may be obtained */
2131: /* with the new direction. */
2132: del=fabs(fptt-(*fret));
2133: ibig=i;
1.126 brouard 2134: }
2135: #ifdef DEBUG
2136: printf("%d %.12e",i,(*fret));
2137: fprintf(ficlog,"%d %.12e",i,(*fret));
2138: for (j=1;j<=n;j++) {
1.224 brouard 2139: xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
2140: printf(" x(%d)=%.12e",j,xit[j]);
2141: fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
1.126 brouard 2142: }
2143: for(j=1;j<=n;j++) {
1.225 brouard 2144: printf(" p(%d)=%.12e",j,p[j]);
2145: fprintf(ficlog," p(%d)=%.12e",j,p[j]);
1.126 brouard 2146: }
2147: printf("\n");
2148: fprintf(ficlog,"\n");
2149: #endif
1.187 brouard 2150: } /* end loop on each direction i */
2151: /* Convergence test will use last linmin estimation (fret) and compare former iteration (fp) */
1.188 brouard 2152: /* But p and xit have been updated at the end of linmin, *fret corresponds to new p, xit */
1.187 brouard 2153: /* New value of last point Pn is not computed, P(n-1) */
1.224 brouard 2154: for(j=1;j<=n;j++) {
1.225 brouard 2155: if(flatdir[j] >0){
2156: printf(" p(%d)=%lf flat=%d ",j,p[j],flatdir[j]);
2157: fprintf(ficlog," p(%d)=%lf flat=%d ",j,p[j],flatdir[j]);
2158: }
2159: /* printf("\n"); */
2160: /* fprintf(ficlog,"\n"); */
2161: }
1.182 brouard 2162: if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) { /* Did we reach enough precision? */
1.188 brouard 2163: /* We could compare with a chi^2. chisquare(0.95,ddl=1)=3.84 */
2164: /* By adding age*age in a model, the new -2LL should be lower and the difference follows a */
2165: /* a chisquare statistics with 1 degree. To be significant at the 95% level, it should have */
2166: /* decreased of more than 3.84 */
2167: /* By adding age*age and V1*age the gain (-2LL) should be more than 5.99 (ddl=2) */
2168: /* By using V1+V2+V3, the gain should be 7.82, compared with basic 1+age. */
2169: /* By adding 10 parameters more the gain should be 18.31 */
1.224 brouard 2170:
1.188 brouard 2171: /* Starting the program with initial values given by a former maximization will simply change */
2172: /* the scales of the directions and the directions, because the are reset to canonical directions */
2173: /* Thus the first calls to linmin will give new points and better maximizations until fp-(*fret) is */
2174: /* under the tolerance value. If the tolerance is very small 1.e-9, it could last long. */
1.126 brouard 2175: #ifdef DEBUG
2176: int k[2],l;
2177: k[0]=1;
2178: k[1]=-1;
2179: printf("Max: %.12e",(*func)(p));
2180: fprintf(ficlog,"Max: %.12e",(*func)(p));
2181: for (j=1;j<=n;j++) {
2182: printf(" %.12e",p[j]);
2183: fprintf(ficlog," %.12e",p[j]);
2184: }
2185: printf("\n");
2186: fprintf(ficlog,"\n");
2187: for(l=0;l<=1;l++) {
2188: for (j=1;j<=n;j++) {
2189: ptt[j]=p[j]+(p[j]-pt[j])*k[l];
2190: printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
2191: fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
2192: }
2193: printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
2194: fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
2195: }
2196: #endif
2197:
1.224 brouard 2198: #ifdef LINMINORIGINAL
2199: #else
2200: free_ivector(flatdir,1,n);
2201: #endif
1.126 brouard 2202: free_vector(xit,1,n);
2203: free_vector(xits,1,n);
2204: free_vector(ptt,1,n);
2205: free_vector(pt,1,n);
2206: return;
1.192 brouard 2207: } /* enough precision */
1.126 brouard 2208: if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");
1.181 brouard 2209: for (j=1;j<=n;j++) { /* Computes the extrapolated point P_0 + 2 (P_n-P_0) */
1.126 brouard 2210: ptt[j]=2.0*p[j]-pt[j];
2211: xit[j]=p[j]-pt[j];
2212: pt[j]=p[j];
2213: }
1.181 brouard 2214: fptt=(*func)(ptt); /* f_3 */
1.224 brouard 2215: #ifdef NODIRECTIONCHANGEDUNTILNITER /* No change in drections until some iterations are done */
2216: if (*iter <=4) {
1.225 brouard 2217: #else
2218: #endif
1.224 brouard 2219: #ifdef POWELLNOF3INFF1TEST /* skips test F3 <F1 */
1.192 brouard 2220: #else
1.161 brouard 2221: if (fptt < fp) { /* If extrapolated point is better, decide if we keep that new direction or not */
1.192 brouard 2222: #endif
1.162 brouard 2223: /* (x1 f1=fp), (x2 f2=*fret), (x3 f3=fptt), (xm fm) */
1.161 brouard 2224: /* From x1 (P0) distance of x2 is at h and x3 is 2h */
1.162 brouard 2225: /* Let f"(x2) be the 2nd derivative equal everywhere. */
2226: /* Then the parabolic through (x1,f1), (x2,f2) and (x3,f3) */
2227: /* will reach at f3 = fm + h^2/2 f"m ; f" = (f1 -2f2 +f3 ) / h**2 */
1.224 brouard 2228: /* Conditional for using this new direction is that mu^2 = (f1-2f2+f3)^2 /2 < del or directest <0 */
2229: /* also lamda^2=(f1-f2)^2/mu² is a parasite solution of powell */
2230: /* For powell, inclusion of this average direction is only if t(del)<0 or del inbetween mu^2 and lambda^2 */
1.161 brouard 2231: /* t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); */
1.224 brouard 2232: /* Even if f3 <f1, directest can be negative and t >0 */
2233: /* mu² and del² are equal when f3=f1 */
2234: /* f3 < f1 : mu² < del <= lambda^2 both test are equivalent */
2235: /* f3 < f1 : mu² < lambda^2 < del then directtest is negative and powell t is positive */
2236: /* f3 > f1 : lambda² < mu^2 < del then t is negative and directest >0 */
2237: /* f3 > f1 : lambda² < del < mu^2 then t is positive and directest >0 */
1.183 brouard 2238: #ifdef NRCORIGINAL
2239: t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)- del*SQR(fp-fptt); /* Original Numerical Recipes in C*/
2240: #else
2241: 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 2242: t= t- del*SQR(fp-fptt);
1.183 brouard 2243: #endif
1.202 brouard 2244: directest = fp-2.0*(*fret)+fptt - 2.0 * del; /* If delta was big enough we change it for a new direction */
1.161 brouard 2245: #ifdef DEBUG
1.181 brouard 2246: 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);
2247: 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 2248: printf("t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
2249: (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
2250: fprintf(ficlog,"t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
2251: (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
2252: 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);
2253: 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);
2254: #endif
1.183 brouard 2255: #ifdef POWELLORIGINAL
2256: if (t < 0.0) { /* Then we use it for new direction */
2257: #else
1.182 brouard 2258: if (directest*t < 0.0) { /* Contradiction between both tests */
1.224 brouard 2259: 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 2260: printf("f1-2f2+f3= %.12lf, f1-f2-del= %.12lf, f1-f3= %.12lf\n",fp-2.0*(*fret)+fptt, fp -(*fret) -del, fp-fptt);
1.224 brouard 2261: fprintf(ficlog,"directest= %.12lf (if directest<0 or t<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 2262: fprintf(ficlog,"f1-2f2+f3= %.12lf, f1-f2-del= %.12lf, f1-f3= %.12lf\n",fp-2.0*(*fret)+fptt, fp -(*fret) -del, fp-fptt);
2263: }
1.181 brouard 2264: if (directest < 0.0) { /* Then we use it for new direction */
2265: #endif
1.191 brouard 2266: #ifdef DEBUGLINMIN
1.234 brouard 2267: printf("Before linmin in direction P%d-P0\n",n);
2268: for (j=1;j<=n;j++) {
2269: printf(" Before xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
2270: fprintf(ficlog," Before xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
2271: if(j % ncovmodel == 0){
2272: printf("\n");
2273: fprintf(ficlog,"\n");
2274: }
2275: }
1.224 brouard 2276: #endif
2277: #ifdef LINMINORIGINAL
1.234 brouard 2278: linmin(p,xit,n,fret,func); /* computes minimum on the extrapolated direction: changes p and rescales xit.*/
1.224 brouard 2279: #else
1.234 brouard 2280: linmin(p,xit,n,fret,func,&flat); /* computes minimum on the extrapolated direction: changes p and rescales xit.*/
2281: flatdir[i]=flat; /* Function is vanishing in that direction i */
1.191 brouard 2282: #endif
1.234 brouard 2283:
1.191 brouard 2284: #ifdef DEBUGLINMIN
1.234 brouard 2285: for (j=1;j<=n;j++) {
2286: printf("After xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
2287: fprintf(ficlog,"After xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
2288: if(j % ncovmodel == 0){
2289: printf("\n");
2290: fprintf(ficlog,"\n");
2291: }
2292: }
1.224 brouard 2293: #endif
1.234 brouard 2294: for (j=1;j<=n;j++) {
2295: xi[j][ibig]=xi[j][n]; /* Replace direction with biggest decrease by last direction n */
2296: xi[j][n]=xit[j]; /* and this nth direction by the by the average p_0 p_n */
2297: }
1.224 brouard 2298: #ifdef LINMINORIGINAL
2299: #else
1.234 brouard 2300: for (j=1, flatd=0;j<=n;j++) {
2301: if(flatdir[j]>0)
2302: flatd++;
2303: }
2304: if(flatd >0){
2305: printf("%d flat directions\n",flatd);
2306: fprintf(ficlog,"%d flat directions\n",flatd);
2307: for (j=1;j<=n;j++) {
2308: if(flatdir[j]>0){
2309: printf("%d ",j);
2310: fprintf(ficlog,"%d ",j);
2311: }
2312: }
2313: printf("\n");
2314: fprintf(ficlog,"\n");
2315: }
1.191 brouard 2316: #endif
1.234 brouard 2317: printf("Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
2318: fprintf(ficlog,"Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
2319:
1.126 brouard 2320: #ifdef DEBUG
1.234 brouard 2321: printf("Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
2322: fprintf(ficlog,"Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
2323: for(j=1;j<=n;j++){
2324: printf(" %lf",xit[j]);
2325: fprintf(ficlog," %lf",xit[j]);
2326: }
2327: printf("\n");
2328: fprintf(ficlog,"\n");
1.126 brouard 2329: #endif
1.192 brouard 2330: } /* end of t or directest negative */
1.224 brouard 2331: #ifdef POWELLNOF3INFF1TEST
1.192 brouard 2332: #else
1.234 brouard 2333: } /* end if (fptt < fp) */
1.192 brouard 2334: #endif
1.225 brouard 2335: #ifdef NODIRECTIONCHANGEDUNTILNITER /* No change in drections until some iterations are done */
1.234 brouard 2336: } /*NODIRECTIONCHANGEDUNTILNITER No change in drections until some iterations are done */
1.225 brouard 2337: #else
1.224 brouard 2338: #endif
1.234 brouard 2339: } /* loop iteration */
1.126 brouard 2340: }
1.234 brouard 2341:
1.126 brouard 2342: /**** Prevalence limit (stable or period prevalence) ****************/
1.234 brouard 2343:
1.235 ! brouard 2344: double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int *ncvyear, int ij, int nres)
1.234 brouard 2345: {
1.235 ! brouard 2346: /* Computes the prevalence limit in each live state at age x and for covariate combination ij
! 2347: (and selected quantitative values in nres)
! 2348: by left multiplying the unit
1.234 brouard 2349: matrix by transitions matrix until convergence is reached with precision ftolpl */
1.206 brouard 2350: /* Wx= Wx-1 Px-1= Wx-2 Px-2 Px-1 = Wx-n Px-n ... Px-2 Px-1 I */
2351: /* Wx is row vector: population in state 1, population in state 2, population dead */
2352: /* or prevalence in state 1, prevalence in state 2, 0 */
2353: /* newm is the matrix after multiplications, its rows are identical at a factor */
2354: /* Initial matrix pimij */
2355: /* {0.85204250825084937, 0.13044499163996345, 0.017512500109187184, */
2356: /* 0.090851990222114765, 0.88271245433047185, 0.026435555447413338, */
2357: /* 0, 0 , 1} */
2358: /*
2359: * and after some iteration: */
2360: /* {0.45504275246439968, 0.42731458730878791, 0.11764266022681241, */
2361: /* 0.45201005341706885, 0.42865420071559901, 0.11933574586733192, */
2362: /* 0, 0 , 1} */
2363: /* And prevalence by suppressing the deaths are close to identical rows in prlim: */
2364: /* {0.51571254859325999, 0.4842874514067399, */
2365: /* 0.51326036147820708, 0.48673963852179264} */
2366: /* If we start from prlim again, prlim tends to a constant matrix */
1.234 brouard 2367:
1.126 brouard 2368: int i, ii,j,k;
1.209 brouard 2369: double *min, *max, *meandiff, maxmax,sumnew=0.;
1.145 brouard 2370: /* double **matprod2(); */ /* test */
1.218 brouard 2371: double **out, cov[NCOVMAX+1], **pmij(); /* **pmmij is a global variable feeded with oldms etc */
1.126 brouard 2372: double **newm;
1.209 brouard 2373: double agefin, delaymax=200. ; /* 100 Max number of years to converge */
1.203 brouard 2374: int ncvloop=0;
1.169 brouard 2375:
1.209 brouard 2376: min=vector(1,nlstate);
2377: max=vector(1,nlstate);
2378: meandiff=vector(1,nlstate);
2379:
1.218 brouard 2380: /* Starting with matrix unity */
1.126 brouard 2381: for (ii=1;ii<=nlstate+ndeath;ii++)
2382: for (j=1;j<=nlstate+ndeath;j++){
2383: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2384: }
1.169 brouard 2385:
2386: cov[1]=1.;
2387:
2388: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
1.202 brouard 2389: /* Start at agefin= age, computes the matrix of passage and loops decreasing agefin until convergence is reached */
1.126 brouard 2390: for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
1.202 brouard 2391: ncvloop++;
1.126 brouard 2392: newm=savm;
2393: /* Covariates have to be included here again */
1.138 brouard 2394: cov[2]=agefin;
1.187 brouard 2395: if(nagesqr==1)
2396: cov[3]= agefin*agefin;;
1.234 brouard 2397: for (k=1; k<=nsd;k++) { /* For single dummy covariates only */
2398: /* Here comes the value of the covariate 'ij' after renumbering k with single dummy covariates */
2399: cov[2+nagesqr+TvarsDind[k]]=nbcode[TvarsD[k]][codtabm(ij,k)];
1.235 ! brouard 2400: /* printf("prevalim Dummy combi=%d k=%d TvarsD[%d]=V%d TvarsDind[%d]=%d nbcode=%d cov=%lf codtabm(%d,Tvar[%d])=%d \n",ij,k, k, TvarsD[k],k,TvarsDind[k],nbcode[TvarsD[k]][codtabm(ij,k)],cov[2+nagesqr+TvarsDind[k]], ij, k, codtabm(ij,k)); */
1.234 brouard 2401: }
2402: for (k=1; k<=nsq;k++) { /* For single varying covariates only */
2403: /* Here comes the value of quantitative after renumbering k with single quantitative covariates */
1.235 ! brouard 2404: cov[2+nagesqr+TvarsQind[k]]=Tqresult[nres][k];
! 2405: /* printf("prevalim Quantitative k=%d TvarsQind[%d]=%d, TvarsQ[%d]=V%d,Tqresult[%d][%d]=%f\n",k,k,TvarsQind[k],k,TvarsQ[k],nres,k,Tqresult[nres][k]); */
1.138 brouard 2406: }
1.234 brouard 2407: for (k=1; k<=cptcovage;k++){
2408: if(Dummy[Tvar[Tage[k]]]){
2409: cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
2410: } else{
1.235 ! brouard 2411: cov[2+nagesqr+Tage[k]]=Tqresult[nres][k];
1.234 brouard 2412: }
1.235 ! brouard 2413: /* printf("prevalim Age combi=%d k=%d Tage[%d]=V%d Tqresult[%d][%d]=%f\n",ij,k,k,Tage[k],nres,k,Tqresult[nres][k]); */
1.234 brouard 2414: }
2415: for (k=1; k<=cptcovprod;k++){ /* */
1.235 ! brouard 2416: /* printf("prevalim Prod ij=%d k=%d Tprod[%d]=%d Tvard[%d][1]=V%d, Tvard[%d][2]=V%d\n",ij,k,k,Tprod[k], k,Tvard[k][1], k,Tvard[k][2]); */
1.200 brouard 2417: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)];
1.234 brouard 2418: }
1.138 brouard 2419: /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
2420: /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
2421: /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
1.145 brouard 2422: /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
2423: /* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind *\/ */
1.218 brouard 2424: /* age and covariate values of ij are in 'cov' */
1.142 brouard 2425: out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /* Bug Valgrind */
1.138 brouard 2426:
1.126 brouard 2427: savm=oldm;
2428: oldm=newm;
1.209 brouard 2429:
2430: for(j=1; j<=nlstate; j++){
2431: max[j]=0.;
2432: min[j]=1.;
2433: }
2434: for(i=1;i<=nlstate;i++){
2435: sumnew=0;
2436: for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
2437: for(j=1; j<=nlstate; j++){
2438: prlim[i][j]= newm[i][j]/(1-sumnew);
2439: max[j]=FMAX(max[j],prlim[i][j]);
2440: min[j]=FMIN(min[j],prlim[i][j]);
2441: }
2442: }
2443:
1.126 brouard 2444: maxmax=0.;
1.209 brouard 2445: for(j=1; j<=nlstate; j++){
2446: meandiff[j]=(max[j]-min[j])/(max[j]+min[j])*2.; /* mean difference for each column */
2447: maxmax=FMAX(maxmax,meandiff[j]);
2448: /* 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 2449: } /* j loop */
1.203 brouard 2450: *ncvyear= (int)age- (int)agefin;
1.208 brouard 2451: /* 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 2452: if(maxmax < ftolpl){
1.209 brouard 2453: /* printf("maxmax=%lf ncvloop=%ld, age=%d, agefin=%d ncvyear=%d \n", maxmax, ncvloop, (int)age, (int)agefin, *ncvyear); */
2454: free_vector(min,1,nlstate);
2455: free_vector(max,1,nlstate);
2456: free_vector(meandiff,1,nlstate);
1.126 brouard 2457: return prlim;
2458: }
1.169 brouard 2459: } /* age loop */
1.208 brouard 2460: /* After some age loop it doesn't converge */
1.209 brouard 2461: 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 2462: 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 2463: /* 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); */
2464: free_vector(min,1,nlstate);
2465: free_vector(max,1,nlstate);
2466: free_vector(meandiff,1,nlstate);
1.208 brouard 2467:
1.169 brouard 2468: return prlim; /* should not reach here */
1.126 brouard 2469: }
2470:
1.217 brouard 2471:
2472: /**** Back Prevalence limit (stable or period prevalence) ****************/
2473:
1.218 brouard 2474: /* double **bprevalim(double **bprlim, double ***prevacurrent, int nlstate, double x[], double age, double ageminpar, double agemaxpar, double **oldm, double **savm, double **dnewm, double **doldm, double **dsavm, double ftolpl, int *ncvyear, int ij) */
2475: /* double **bprevalim(double **bprlim, double ***prevacurrent, int nlstate, double x[], double age, double **oldm, double **savm, double **dnewm, double **doldm, double **dsavm, double ftolpl, int *ncvyear, int ij) */
2476: double **bprevalim(double **bprlim, double ***prevacurrent, int nlstate, double x[], double age, double ftolpl, int *ncvyear, int ij)
1.217 brouard 2477: {
1.218 brouard 2478: /* Computes the prevalence limit in each live state at age x and covariate ij by left multiplying the unit
1.217 brouard 2479: matrix by transitions matrix until convergence is reached with precision ftolpl */
2480: /* Wx= Wx-1 Px-1= Wx-2 Px-2 Px-1 = Wx-n Px-n ... Px-2 Px-1 I */
2481: /* Wx is row vector: population in state 1, population in state 2, population dead */
2482: /* or prevalence in state 1, prevalence in state 2, 0 */
2483: /* newm is the matrix after multiplications, its rows are identical at a factor */
2484: /* Initial matrix pimij */
2485: /* {0.85204250825084937, 0.13044499163996345, 0.017512500109187184, */
2486: /* 0.090851990222114765, 0.88271245433047185, 0.026435555447413338, */
2487: /* 0, 0 , 1} */
2488: /*
2489: * and after some iteration: */
2490: /* {0.45504275246439968, 0.42731458730878791, 0.11764266022681241, */
2491: /* 0.45201005341706885, 0.42865420071559901, 0.11933574586733192, */
2492: /* 0, 0 , 1} */
2493: /* And prevalence by suppressing the deaths are close to identical rows in prlim: */
2494: /* {0.51571254859325999, 0.4842874514067399, */
2495: /* 0.51326036147820708, 0.48673963852179264} */
2496: /* If we start from prlim again, prlim tends to a constant matrix */
2497:
2498: int i, ii,j,k;
2499: double *min, *max, *meandiff, maxmax,sumnew=0.;
2500: /* double **matprod2(); */ /* test */
2501: double **out, cov[NCOVMAX+1], **bmij();
2502: double **newm;
1.218 brouard 2503: double **dnewm, **doldm, **dsavm; /* for use */
2504: double **oldm, **savm; /* for use */
2505:
1.217 brouard 2506: double agefin, delaymax=200. ; /* 100 Max number of years to converge */
2507: int ncvloop=0;
2508:
2509: min=vector(1,nlstate);
2510: max=vector(1,nlstate);
2511: meandiff=vector(1,nlstate);
2512:
1.218 brouard 2513: dnewm=ddnewms; doldm=ddoldms; dsavm=ddsavms;
2514: oldm=oldms; savm=savms;
2515:
2516: /* Starting with matrix unity */
2517: for (ii=1;ii<=nlstate+ndeath;ii++)
2518: for (j=1;j<=nlstate+ndeath;j++){
1.217 brouard 2519: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2520: }
2521:
2522: cov[1]=1.;
2523:
2524: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
2525: /* Start at agefin= age, computes the matrix of passage and loops decreasing agefin until convergence is reached */
1.218 brouard 2526: /* for(agefin=age+stepm/YEARM; agefin<=age+delaymax; agefin=agefin+stepm/YEARM){ /\* A changer en age *\/ */
2527: for(agefin=age; agefin<AGESUP; agefin=agefin+stepm/YEARM){ /* A changer en age */
1.217 brouard 2528: ncvloop++;
1.218 brouard 2529: newm=savm; /* oldm should be kept from previous iteration or unity at start */
2530: /* newm points to the allocated table savm passed by the function it can be written, savm could be reallocated */
1.217 brouard 2531: /* Covariates have to be included here again */
2532: cov[2]=agefin;
2533: if(nagesqr==1)
2534: cov[3]= agefin*agefin;;
2535: for (k=1; k<=cptcovn;k++) {
2536: /* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; */
2537: cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)];
2538: /* 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])]); */
2539: }
2540: for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtabm(ij,k)]*cov[2];
2541: for (k=1; k<=cptcovprod;k++) /* Useless */
2542: /* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])] * nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])]; */
2543: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)];
2544:
2545: /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
2546: /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
2547: /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
2548: /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
2549: /* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind *\/ */
1.218 brouard 2550: /* ij should be linked to the correct index of cov */
2551: /* age and covariate values ij are in 'cov', but we need to pass
2552: * ij for the observed prevalence at age and status and covariate
2553: * number: prevacurrent[(int)agefin][ii][ij]
2554: */
2555: /* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent, ageminpar, agemaxpar, dnewm, doldm, dsavm,ij)); /\* Bug Valgrind *\/ */
2556: /* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent, dnewm, doldm, dsavm,ij)); /\* Bug Valgrind *\/ */
2557: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent,ij)); /* Bug Valgrind */
1.217 brouard 2558: savm=oldm;
2559: oldm=newm;
2560: for(j=1; j<=nlstate; j++){
2561: max[j]=0.;
2562: min[j]=1.;
2563: }
2564: for(j=1; j<=nlstate; j++){
2565: for(i=1;i<=nlstate;i++){
1.234 brouard 2566: /* bprlim[i][j]= newm[i][j]/(1-sumnew); */
2567: bprlim[i][j]= newm[i][j];
2568: max[i]=FMAX(max[i],bprlim[i][j]); /* Max in line */
2569: min[i]=FMIN(min[i],bprlim[i][j]);
1.217 brouard 2570: }
2571: }
1.218 brouard 2572:
1.217 brouard 2573: maxmax=0.;
2574: for(i=1; i<=nlstate; i++){
2575: meandiff[i]=(max[i]-min[i])/(max[i]+min[i])*2.; /* mean difference for each column */
2576: maxmax=FMAX(maxmax,meandiff[i]);
2577: /* printf("Back age= %d meandiff[%d]=%f, agefin=%d max[%d]=%f min[%d]=%f maxmax=%f\n", (int)age, i, meandiff[i],(int)agefin, i, max[i], i, min[i],maxmax); */
2578: } /* j loop */
2579: *ncvyear= -( (int)age- (int)agefin);
1.218 brouard 2580: /* printf("Back maxmax=%lf ncvloop=%d, age=%d, agefin=%d ncvyear=%d \n", maxmax, ncvloop, (int)age, (int)agefin, *ncvyear);*/
1.217 brouard 2581: if(maxmax < ftolpl){
1.220 brouard 2582: /* printf("OK Back maxmax=%lf ncvloop=%d, age=%d, agefin=%d ncvyear=%d \n", maxmax, ncvloop, (int)age, (int)agefin, *ncvyear); */
1.217 brouard 2583: free_vector(min,1,nlstate);
2584: free_vector(max,1,nlstate);
2585: free_vector(meandiff,1,nlstate);
2586: return bprlim;
2587: }
2588: } /* age loop */
2589: /* After some age loop it doesn't converge */
2590: printf("Warning: the back stable prevalence at age %d did not converge with the required precision (%g > ftolpl=%g) within %.0f years. Try to lower 'ftolpl'. \n\
2591: Oldest 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);
2592: /* 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); */
2593: free_vector(min,1,nlstate);
2594: free_vector(max,1,nlstate);
2595: free_vector(meandiff,1,nlstate);
2596:
2597: return bprlim; /* should not reach here */
2598: }
2599:
1.126 brouard 2600: /*************** transition probabilities ***************/
2601:
2602: double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
2603: {
1.138 brouard 2604: /* According to parameters values stored in x and the covariate's values stored in cov,
2605: computes the probability to be observed in state j being in state i by appying the
2606: model to the ncovmodel covariates (including constant and age).
2607: lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc]
2608: and, according on how parameters are entered, the position of the coefficient xij(nc) of the
2609: ncth covariate in the global vector x is given by the formula:
2610: j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
2611: j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
2612: Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
2613: sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.
2614: Outputs ps[i][j] the probability to be observed in j being in j according to
2615: the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
2616: */
2617: double s1, lnpijopii;
1.126 brouard 2618: /*double t34;*/
1.164 brouard 2619: int i,j, nc, ii, jj;
1.126 brouard 2620:
1.223 brouard 2621: for(i=1; i<= nlstate; i++){
2622: for(j=1; j<i;j++){
2623: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
2624: /*lnpijopii += param[i][j][nc]*cov[nc];*/
2625: lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
2626: /* printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
2627: }
2628: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
2629: /* printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
2630: }
2631: for(j=i+1; j<=nlstate+ndeath;j++){
2632: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
2633: /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
2634: lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
2635: /* printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
2636: }
2637: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
2638: }
2639: }
1.218 brouard 2640:
1.223 brouard 2641: for(i=1; i<= nlstate; i++){
2642: s1=0;
2643: for(j=1; j<i; j++){
2644: s1+=exp(ps[i][j]); /* In fact sums pij/pii */
2645: /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
2646: }
2647: for(j=i+1; j<=nlstate+ndeath; j++){
2648: s1+=exp(ps[i][j]); /* In fact sums pij/pii */
2649: /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
2650: }
2651: /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
2652: ps[i][i]=1./(s1+1.);
2653: /* Computing other pijs */
2654: for(j=1; j<i; j++)
2655: ps[i][j]= exp(ps[i][j])*ps[i][i];
2656: for(j=i+1; j<=nlstate+ndeath; j++)
2657: ps[i][j]= exp(ps[i][j])*ps[i][i];
2658: /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
2659: } /* end i */
1.218 brouard 2660:
1.223 brouard 2661: for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
2662: for(jj=1; jj<= nlstate+ndeath; jj++){
2663: ps[ii][jj]=0;
2664: ps[ii][ii]=1;
2665: }
2666: }
1.218 brouard 2667:
2668:
1.223 brouard 2669: /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
2670: /* for(jj=1; jj<= nlstate+ndeath; jj++){ */
2671: /* printf(" pmij ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
2672: /* } */
2673: /* printf("\n "); */
2674: /* } */
2675: /* printf("\n ");printf("%lf ",cov[2]);*/
2676: /*
2677: for(i=1; i<= npar; i++) printf("%f ",x[i]);
1.218 brouard 2678: goto end;*/
1.223 brouard 2679: return ps;
1.126 brouard 2680: }
2681:
1.218 brouard 2682: /*************** backward transition probabilities ***************/
2683:
2684: /* double **bmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate, double ***prevacurrent, double ageminpar, double agemaxpar, double ***dnewm, double **doldm, double **dsavm, int ij ) */
2685: /* double **bmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate, double ***prevacurrent, double ***dnewm, double **doldm, double **dsavm, int ij ) */
2686: double **bmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate, double ***prevacurrent, int ij )
2687: {
1.222 brouard 2688: /* Computes the backward probability at age agefin and covariate ij
2689: * and returns in **ps as well as **bmij.
2690: */
1.218 brouard 2691: int i, ii, j,k;
1.222 brouard 2692:
2693: double **out, **pmij();
2694: double sumnew=0.;
1.218 brouard 2695: double agefin;
1.222 brouard 2696:
2697: double **dnewm, **dsavm, **doldm;
2698: double **bbmij;
2699:
1.218 brouard 2700: doldm=ddoldms; /* global pointers */
1.222 brouard 2701: dnewm=ddnewms;
2702: dsavm=ddsavms;
2703:
2704: agefin=cov[2];
2705: /* bmij *//* age is cov[2], ij is included in cov, but we need for
2706: the observed prevalence (with this covariate ij) */
2707: dsavm=pmij(pmmij,cov,ncovmodel,x,nlstate);
2708: /* We do have the matrix Px in savm and we need pij */
2709: for (j=1;j<=nlstate+ndeath;j++){
2710: sumnew=0.; /* w1 p11 + w2 p21 only on live states */
2711: for (ii=1;ii<=nlstate;ii++){
2712: sumnew+=dsavm[ii][j]*prevacurrent[(int)agefin][ii][ij];
2713: } /* sumnew is (N11+N21)/N..= N.1/N.. = sum on i of w_i pij */
2714: for (ii=1;ii<=nlstate+ndeath;ii++){
2715: if(sumnew >= 1.e-10){
2716: /* if(agefin >= agemaxpar && agefin <= agemaxpar+stepm/YEARM){ */
2717: /* doldm[ii][j]=(ii==j ? 1./sumnew : 0.0); */
2718: /* }else if(agefin >= agemaxpar+stepm/YEARM){ */
2719: /* doldm[ii][j]=(ii==j ? 1./sumnew : 0.0); */
2720: /* }else */
2721: doldm[ii][j]=(ii==j ? 1./sumnew : 0.0);
2722: }else{
2723: printf("ii=%d, i=%d, doldm=%lf dsavm=%lf, probs=%lf, sumnew=%lf,agefin=%d\n",ii,j,doldm[ii][j],dsavm[ii][j],prevacurrent[(int)agefin][ii][ij],sumnew, (int)agefin);
2724: }
2725: } /*End ii */
2726: } /* End j, At the end doldm is diag[1/(w_1p1i+w_2 p2i)] */
2727: /* left Product of this diag matrix by dsavm=Px (newm=dsavm*doldm) */
2728: bbmij=matprod2(dnewm, dsavm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, doldm); /* Bug Valgrind */
2729: /* dsavm=doldm; /\* dsavm is now diag [1/(w_1p1i+w_2 p2i)] but can be overwritten*\/ */
2730: /* doldm=dnewm; /\* doldm is now Px * diag [1/(w_1p1i+w_2 p2i)] *\/ */
2731: /* dnewm=dsavm; /\* doldm is now Px * diag [1/(w_1p1i+w_2 p2i)] *\/ */
2732: /* left Product of this matrix by diag matrix of prevalences (savm) */
2733: for (j=1;j<=nlstate+ndeath;j++){
2734: for (ii=1;ii<=nlstate+ndeath;ii++){
2735: dsavm[ii][j]=(ii==j ? prevacurrent[(int)agefin][ii][ij] : 0.0);
2736: }
2737: } /* End j, At the end oldm is diag[1/(w_1p1i+w_2 p2i)] */
2738: ps=matprod2(doldm, dsavm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, dnewm); /* Bug Valgrind */
2739: /* newm or out is now diag[w_i] * Px * diag [1/(w_1p1i+w_2 p2i)] */
2740: /* end bmij */
2741: return ps;
1.218 brouard 2742: }
1.217 brouard 2743: /*************** transition probabilities ***************/
2744:
1.218 brouard 2745: double **bpmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
1.217 brouard 2746: {
2747: /* According to parameters values stored in x and the covariate's values stored in cov,
2748: computes the probability to be observed in state j being in state i by appying the
2749: model to the ncovmodel covariates (including constant and age).
2750: lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc]
2751: and, according on how parameters are entered, the position of the coefficient xij(nc) of the
2752: ncth covariate in the global vector x is given by the formula:
2753: j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
2754: j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
2755: Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
2756: sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.
2757: Outputs ps[i][j] the probability to be observed in j being in j according to
2758: the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
2759: */
2760: double s1, lnpijopii;
2761: /*double t34;*/
2762: int i,j, nc, ii, jj;
2763:
1.234 brouard 2764: for(i=1; i<= nlstate; i++){
2765: for(j=1; j<i;j++){
2766: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
2767: /*lnpijopii += param[i][j][nc]*cov[nc];*/
2768: lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
2769: /* printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
2770: }
2771: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
2772: /* printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
2773: }
2774: for(j=i+1; j<=nlstate+ndeath;j++){
2775: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
2776: /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
2777: lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
2778: /* printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
2779: }
2780: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
2781: }
2782: }
2783:
2784: for(i=1; i<= nlstate; i++){
2785: s1=0;
2786: for(j=1; j<i; j++){
2787: s1+=exp(ps[i][j]); /* In fact sums pij/pii */
2788: /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
2789: }
2790: for(j=i+1; j<=nlstate+ndeath; j++){
2791: s1+=exp(ps[i][j]); /* In fact sums pij/pii */
2792: /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
2793: }
2794: /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
2795: ps[i][i]=1./(s1+1.);
2796: /* Computing other pijs */
2797: for(j=1; j<i; j++)
2798: ps[i][j]= exp(ps[i][j])*ps[i][i];
2799: for(j=i+1; j<=nlstate+ndeath; j++)
2800: ps[i][j]= exp(ps[i][j])*ps[i][i];
2801: /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
2802: } /* end i */
2803:
2804: for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
2805: for(jj=1; jj<= nlstate+ndeath; jj++){
2806: ps[ii][jj]=0;
2807: ps[ii][ii]=1;
2808: }
2809: }
2810: /* Added for backcast */ /* Transposed matrix too */
2811: for(jj=1; jj<= nlstate+ndeath; jj++){
2812: s1=0.;
2813: for(ii=1; ii<= nlstate+ndeath; ii++){
2814: s1+=ps[ii][jj];
2815: }
2816: for(ii=1; ii<= nlstate; ii++){
2817: ps[ii][jj]=ps[ii][jj]/s1;
2818: }
2819: }
2820: /* Transposition */
2821: for(jj=1; jj<= nlstate+ndeath; jj++){
2822: for(ii=jj; ii<= nlstate+ndeath; ii++){
2823: s1=ps[ii][jj];
2824: ps[ii][jj]=ps[jj][ii];
2825: ps[jj][ii]=s1;
2826: }
2827: }
2828: /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
2829: /* for(jj=1; jj<= nlstate+ndeath; jj++){ */
2830: /* printf(" pmij ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
2831: /* } */
2832: /* printf("\n "); */
2833: /* } */
2834: /* printf("\n ");printf("%lf ",cov[2]);*/
2835: /*
2836: for(i=1; i<= npar; i++) printf("%f ",x[i]);
2837: goto end;*/
2838: return ps;
1.217 brouard 2839: }
2840:
2841:
1.126 brouard 2842: /**************** Product of 2 matrices ******************/
2843:
1.145 brouard 2844: double **matprod2(double **out, double **in,int nrl, int nrh, int ncl, int nch, int ncolol, int ncoloh, double **b)
1.126 brouard 2845: {
2846: /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
2847: b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
2848: /* in, b, out are matrice of pointers which should have been initialized
2849: before: only the contents of out is modified. The function returns
2850: a pointer to pointers identical to out */
1.145 brouard 2851: int i, j, k;
1.126 brouard 2852: for(i=nrl; i<= nrh; i++)
1.145 brouard 2853: for(k=ncolol; k<=ncoloh; k++){
2854: out[i][k]=0.;
2855: for(j=ncl; j<=nch; j++)
2856: out[i][k] +=in[i][j]*b[j][k];
2857: }
1.126 brouard 2858: return out;
2859: }
2860:
2861:
2862: /************* Higher Matrix Product ***************/
2863:
1.235 ! brouard 2864: double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij, int nres )
1.126 brouard 2865: {
1.218 brouard 2866: /* Computes the transition matrix starting at age 'age' and combination of covariate values corresponding to ij over
1.126 brouard 2867: 'nhstepm*hstepm*stepm' months (i.e. until
2868: age (in years) age+nhstepm*hstepm*stepm/12) by multiplying
2869: nhstepm*hstepm matrices.
2870: Output is stored in matrix po[i][j][h] for h every 'hstepm' step
2871: (typically every 2 years instead of every month which is too big
2872: for the memory).
2873: Model is determined by parameters x and covariates have to be
2874: included manually here.
2875:
2876: */
2877:
2878: int i, j, d, h, k;
1.131 brouard 2879: double **out, cov[NCOVMAX+1];
1.126 brouard 2880: double **newm;
1.187 brouard 2881: double agexact;
1.214 brouard 2882: double agebegin, ageend;
1.126 brouard 2883:
2884: /* Hstepm could be zero and should return the unit matrix */
2885: for (i=1;i<=nlstate+ndeath;i++)
2886: for (j=1;j<=nlstate+ndeath;j++){
2887: oldm[i][j]=(i==j ? 1.0 : 0.0);
2888: po[i][j][0]=(i==j ? 1.0 : 0.0);
2889: }
2890: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
2891: for(h=1; h <=nhstepm; h++){
2892: for(d=1; d <=hstepm; d++){
2893: newm=savm;
2894: /* Covariates have to be included here again */
2895: cov[1]=1.;
1.214 brouard 2896: agexact=age+((h-1)*hstepm + (d-1))*stepm/YEARM; /* age just before transition */
1.187 brouard 2897: cov[2]=agexact;
2898: if(nagesqr==1)
1.227 brouard 2899: cov[3]= agexact*agexact;
1.235 ! brouard 2900: for (k=1; k<=nsd;k++) { /* For single dummy covariates only */
! 2901: /* Here comes the value of the covariate 'ij' after renumbering k with single dummy covariates */
! 2902: cov[2+nagesqr+TvarsDind[k]]=nbcode[TvarsD[k]][codtabm(ij,k)];
! 2903: /* printf("hpxij Dummy combi=%d k=%d TvarsD[%d]=V%d TvarsDind[%d]=%d nbcode=%d cov=%lf codtabm(%d,Tvar[%d])=%d \n",ij,k, k, TvarsD[k],k,TvarsDind[k],nbcode[TvarsD[k]][codtabm(ij,k)],cov[2+nagesqr+TvarsDind[k]], ij, k, codtabm(ij,k)); */
! 2904: }
! 2905: for (k=1; k<=nsq;k++) { /* For single varying covariates only */
! 2906: /* Here comes the value of quantitative after renumbering k with single quantitative covariates */
! 2907: cov[2+nagesqr+TvarsQind[k]]=Tqresult[nres][k];
! 2908: /* printf("hPxij Quantitative k=%d TvarsQind[%d]=%d, TvarsQ[%d]=V%d,Tqresult[%d][%d]=%f\n",k,k,TvarsQind[k],k,TvarsQ[k],nres,k,Tqresult[nres][k]); */
! 2909: }
! 2910: for (k=1; k<=cptcovage;k++){
! 2911: if(Dummy[Tvar[Tage[k]]]){
! 2912: cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
! 2913: } else{
! 2914: cov[2+nagesqr+Tage[k]]=Tqresult[nres][k];
! 2915: }
! 2916: /* printf("hPxij Age combi=%d k=%d Tage[%d]=V%d Tqresult[%d][%d]=%f\n",ij,k,k,Tage[k],nres,k,Tqresult[nres][k]); */
! 2917: }
! 2918: for (k=1; k<=cptcovprod;k++){ /* */
! 2919: /* printf("hPxij Prod ij=%d k=%d Tprod[%d]=%d Tvard[%d][1]=V%d, Tvard[%d][2]=V%d\n",ij,k,k,Tprod[k], k,Tvard[k][1], k,Tvard[k][2]); */
! 2920: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)];
! 2921: }
! 2922: /* for (k=1; k<=cptcovn;k++) */
! 2923: /* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)]; */
! 2924: /* for (k=1; k<=cptcovage;k++) /\* Should start at cptcovn+1 *\/ */
! 2925: /* cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2]; */
! 2926: /* for (k=1; k<=cptcovprod;k++) /\* Useless because included in cptcovn *\/ */
! 2927: /* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)]; */
1.227 brouard 2928:
2929:
1.126 brouard 2930: /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
2931: /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
1.218 brouard 2932: /* right multiplication of oldm by the current matrix */
1.126 brouard 2933: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
2934: pmij(pmmij,cov,ncovmodel,x,nlstate));
1.217 brouard 2935: /* if((int)age == 70){ */
2936: /* printf(" Forward hpxij age=%d agexact=%f d=%d nhstepm=%d hstepm=%d\n", (int) age, agexact, d, nhstepm, hstepm); */
2937: /* for(i=1; i<=nlstate+ndeath; i++) { */
2938: /* printf("%d pmmij ",i); */
2939: /* for(j=1;j<=nlstate+ndeath;j++) { */
2940: /* printf("%f ",pmmij[i][j]); */
2941: /* } */
2942: /* printf(" oldm "); */
2943: /* for(j=1;j<=nlstate+ndeath;j++) { */
2944: /* printf("%f ",oldm[i][j]); */
2945: /* } */
2946: /* printf("\n"); */
2947: /* } */
2948: /* } */
1.126 brouard 2949: savm=oldm;
2950: oldm=newm;
2951: }
2952: for(i=1; i<=nlstate+ndeath; i++)
2953: for(j=1;j<=nlstate+ndeath;j++) {
1.218 brouard 2954: po[i][j][h]=newm[i][j];
2955: /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
1.126 brouard 2956: }
1.128 brouard 2957: /*printf("h=%d ",h);*/
1.126 brouard 2958: } /* end h */
1.218 brouard 2959: /* printf("\n H=%d \n",h); */
1.126 brouard 2960: return po;
2961: }
2962:
1.217 brouard 2963: /************* Higher Back Matrix Product ***************/
1.218 brouard 2964: /* double ***hbxij(double ***po, int nhstepm, double age, int hstepm, double *x, double ***prevacurrent, int nlstate, int stepm, double **oldm, double **savm, double **dnewm, double **doldm, double **dsavm, int ij ) */
1.222 brouard 2965: double ***hbxij(double ***po, int nhstepm, double age, int hstepm, double *x, double ***prevacurrent, int nlstate, int stepm, int ij )
1.217 brouard 2966: {
1.218 brouard 2967: /* Computes the transition matrix starting at age 'age' over
1.217 brouard 2968: 'nhstepm*hstepm*stepm' months (i.e. until
1.218 brouard 2969: age (in years) age+nhstepm*hstepm*stepm/12) by multiplying
2970: nhstepm*hstepm matrices.
2971: Output is stored in matrix po[i][j][h] for h every 'hstepm' step
2972: (typically every 2 years instead of every month which is too big
1.217 brouard 2973: for the memory).
1.218 brouard 2974: Model is determined by parameters x and covariates have to be
2975: included manually here.
1.217 brouard 2976:
1.222 brouard 2977: */
1.217 brouard 2978:
2979: int i, j, d, h, k;
2980: double **out, cov[NCOVMAX+1];
2981: double **newm;
2982: double agexact;
2983: double agebegin, ageend;
1.222 brouard 2984: double **oldm, **savm;
1.217 brouard 2985:
1.222 brouard 2986: oldm=oldms;savm=savms;
1.217 brouard 2987: /* Hstepm could be zero and should return the unit matrix */
2988: for (i=1;i<=nlstate+ndeath;i++)
2989: for (j=1;j<=nlstate+ndeath;j++){
2990: oldm[i][j]=(i==j ? 1.0 : 0.0);
2991: po[i][j][0]=(i==j ? 1.0 : 0.0);
2992: }
2993: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
2994: for(h=1; h <=nhstepm; h++){
2995: for(d=1; d <=hstepm; d++){
2996: newm=savm;
2997: /* Covariates have to be included here again */
2998: cov[1]=1.;
2999: agexact=age-((h-1)*hstepm + (d-1))*stepm/YEARM; /* age just before transition */
3000: /* agexact=age+((h-1)*hstepm + (d-1))*stepm/YEARM; /\* age just before transition *\/ */
3001: cov[2]=agexact;
3002: if(nagesqr==1)
1.222 brouard 3003: cov[3]= agexact*agexact;
1.218 brouard 3004: for (k=1; k<=cptcovn;k++)
1.222 brouard 3005: cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)];
3006: /* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; */
1.217 brouard 3007: for (k=1; k<=cptcovage;k++) /* Should start at cptcovn+1 */
1.222 brouard 3008: /* cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
3009: cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
3010: /* cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,Tvar[Tage[k]])]*cov[2]; */
1.217 brouard 3011: for (k=1; k<=cptcovprod;k++) /* Useless because included in cptcovn */
1.222 brouard 3012: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)];
3013: /* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])]*nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])]; */
1.218 brouard 3014:
3015:
1.217 brouard 3016: /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
3017: /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
1.218 brouard 3018: /* Careful transposed matrix */
1.222 brouard 3019: /* age is in cov[2] */
1.218 brouard 3020: /* out=matprod2(newm, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent, dnewm, doldm, dsavm,ij),\ */
1.222 brouard 3021: /* 1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); */
1.218 brouard 3022: out=matprod2(newm, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent,ij),\
1.222 brouard 3023: 1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
1.217 brouard 3024: /* if((int)age == 70){ */
3025: /* printf(" Backward hbxij age=%d agexact=%f d=%d nhstepm=%d hstepm=%d\n", (int) age, agexact, d, nhstepm, hstepm); */
3026: /* for(i=1; i<=nlstate+ndeath; i++) { */
3027: /* printf("%d pmmij ",i); */
3028: /* for(j=1;j<=nlstate+ndeath;j++) { */
3029: /* printf("%f ",pmmij[i][j]); */
3030: /* } */
3031: /* printf(" oldm "); */
3032: /* for(j=1;j<=nlstate+ndeath;j++) { */
3033: /* printf("%f ",oldm[i][j]); */
3034: /* } */
3035: /* printf("\n"); */
3036: /* } */
3037: /* } */
3038: savm=oldm;
3039: oldm=newm;
3040: }
3041: for(i=1; i<=nlstate+ndeath; i++)
3042: for(j=1;j<=nlstate+ndeath;j++) {
1.222 brouard 3043: po[i][j][h]=newm[i][j];
3044: /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
1.217 brouard 3045: }
3046: /*printf("h=%d ",h);*/
3047: } /* end h */
1.222 brouard 3048: /* printf("\n H=%d \n",h); */
1.217 brouard 3049: return po;
3050: }
3051:
3052:
1.162 brouard 3053: #ifdef NLOPT
3054: double myfunc(unsigned n, const double *p1, double *grad, void *pd){
3055: double fret;
3056: double *xt;
3057: int j;
3058: myfunc_data *d2 = (myfunc_data *) pd;
3059: /* xt = (p1-1); */
3060: xt=vector(1,n);
3061: for (j=1;j<=n;j++) xt[j]=p1[j-1]; /* xt[1]=p1[0] */
3062:
3063: fret=(d2->function)(xt); /* p xt[1]@8 is fine */
3064: /* fret=(*func)(xt); /\* p xt[1]@8 is fine *\/ */
3065: printf("Function = %.12lf ",fret);
3066: for (j=1;j<=n;j++) printf(" %d %.8lf", j, xt[j]);
3067: printf("\n");
3068: free_vector(xt,1,n);
3069: return fret;
3070: }
3071: #endif
1.126 brouard 3072:
3073: /*************** log-likelihood *************/
3074: double func( double *x)
3075: {
1.226 brouard 3076: int i, ii, j, k, mi, d, kk;
3077: int ioffset=0;
3078: double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
3079: double **out;
3080: double lli; /* Individual log likelihood */
3081: int s1, s2;
1.228 brouard 3082: int iv=0, iqv=0, itv=0, iqtv=0 ; /* Index of varying covariate, fixed quantitative cov, time varying covariate, quantitative time varying covariate */
1.226 brouard 3083: double bbh, survp;
3084: long ipmx;
3085: double agexact;
3086: /*extern weight */
3087: /* We are differentiating ll according to initial status */
3088: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
3089: /*for(i=1;i<imx;i++)
3090: printf(" %d\n",s[4][i]);
3091: */
1.162 brouard 3092:
1.226 brouard 3093: ++countcallfunc;
1.162 brouard 3094:
1.226 brouard 3095: cov[1]=1.;
1.126 brouard 3096:
1.226 brouard 3097: for(k=1; k<=nlstate; k++) ll[k]=0.;
1.224 brouard 3098: ioffset=0;
1.226 brouard 3099: if(mle==1){
3100: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
3101: /* Computes the values of the ncovmodel covariates of the model
3102: depending if the covariates are fixed or varying (age dependent) and stores them in cov[]
3103: Then computes with function pmij which return a matrix p[i][j] giving the elementary probability
3104: to be observed in j being in i according to the model.
3105: */
3106: ioffset=2+nagesqr+cptcovage;
1.233 brouard 3107: /* Fixed */
1.234 brouard 3108: for (k=1; k<=ncovf;k++){ /* Simple and product fixed covariates without age* products */
3109: cov[ioffset+TvarFind[k]]=covar[Tvar[TvarFind[k]]][i];/* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, only V1 is fixed (k=6)*/
3110: }
1.226 brouard 3111: /* In model V2+V1*V4+age*V3+V3*V2 Tvar[1] is V2, Tvar[2=V1*V4]
3112: is 6, Tvar[3=age*V3] should not be computed because of age Tvar[4=V3*V2]
3113: has been calculated etc */
3114: /* For an individual i, wav[i] gives the number of effective waves */
3115: /* We compute the contribution to Likelihood of each effective transition
3116: mw[mi][i] is real wave of the mi th effectve wave */
3117: /* Then statuses are computed at each begin and end of an effective wave s1=s[ mw[mi][i] ][i];
3118: s2=s[mw[mi+1][i]][i];
3119: And the iv th varying covariate is the cotvar[mw[mi+1][i]][iv][i]
3120: But if the variable is not in the model TTvar[iv] is the real variable effective in the model:
3121: meaning that decodemodel should be used cotvar[mw[mi+1][i]][TTvar[iv]][i]
3122: */
3123: for(mi=1; mi<= wav[i]-1; mi++){
1.234 brouard 3124: for(k=1; k <= ncovv ; k++){ /* Varying covariates (single and product but no age )*/
3125: cov[ioffset+TvarVind[k]]=cotvar[mw[mi][i]][Tvar[TvarVind[k]]][i];
3126: }
3127: for (ii=1;ii<=nlstate+ndeath;ii++)
3128: for (j=1;j<=nlstate+ndeath;j++){
3129: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
3130: savm[ii][j]=(ii==j ? 1.0 : 0.0);
3131: }
3132: for(d=0; d<dh[mi][i]; d++){
3133: newm=savm;
3134: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
3135: cov[2]=agexact;
3136: if(nagesqr==1)
3137: cov[3]= agexact*agexact; /* Should be changed here */
3138: for (kk=1; kk<=cptcovage;kk++) {
3139: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact; /* Tage[kk] gives the data-covariate associated with age */
3140: }
3141: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
3142: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
3143: savm=oldm;
3144: oldm=newm;
3145: } /* end mult */
3146:
3147: /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
3148: /* But now since version 0.9 we anticipate for bias at large stepm.
3149: * If stepm is larger than one month (smallest stepm) and if the exact delay
3150: * (in months) between two waves is not a multiple of stepm, we rounded to
3151: * the nearest (and in case of equal distance, to the lowest) interval but now
3152: * we keep into memory the bias bh[mi][i] and also the previous matrix product
3153: * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
3154: * probability in order to take into account the bias as a fraction of the way
1.231 brouard 3155: * from savm to out if bh is negative or even beyond if bh is positive. bh varies
3156: * -stepm/2 to stepm/2 .
3157: * For stepm=1 the results are the same as for previous versions of Imach.
3158: * For stepm > 1 the results are less biased than in previous versions.
3159: */
1.234 brouard 3160: s1=s[mw[mi][i]][i];
3161: s2=s[mw[mi+1][i]][i];
3162: bbh=(double)bh[mi][i]/(double)stepm;
3163: /* bias bh is positive if real duration
3164: * is higher than the multiple of stepm and negative otherwise.
3165: */
3166: /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
3167: if( s2 > nlstate){
3168: /* i.e. if s2 is a death state and if the date of death is known
3169: then the contribution to the likelihood is the probability to
3170: die between last step unit time and current step unit time,
3171: which is also equal to probability to die before dh
3172: minus probability to die before dh-stepm .
3173: In version up to 0.92 likelihood was computed
3174: as if date of death was unknown. Death was treated as any other
3175: health state: the date of the interview describes the actual state
3176: and not the date of a change in health state. The former idea was
3177: to consider that at each interview the state was recorded
3178: (healthy, disable or death) and IMaCh was corrected; but when we
3179: introduced the exact date of death then we should have modified
3180: the contribution of an exact death to the likelihood. This new
3181: contribution is smaller and very dependent of the step unit
3182: stepm. It is no more the probability to die between last interview
3183: and month of death but the probability to survive from last
3184: interview up to one month before death multiplied by the
3185: probability to die within a month. Thanks to Chris
3186: Jackson for correcting this bug. Former versions increased
3187: mortality artificially. The bad side is that we add another loop
3188: which slows down the processing. The difference can be up to 10%
3189: lower mortality.
3190: */
3191: /* If, at the beginning of the maximization mostly, the
3192: cumulative probability or probability to be dead is
3193: constant (ie = 1) over time d, the difference is equal to
3194: 0. out[s1][3] = savm[s1][3]: probability, being at state
3195: s1 at precedent wave, to be dead a month before current
3196: wave is equal to probability, being at state s1 at
3197: precedent wave, to be dead at mont of the current
3198: wave. Then the observed probability (that this person died)
3199: is null according to current estimated parameter. In fact,
3200: it should be very low but not zero otherwise the log go to
3201: infinity.
3202: */
1.183 brouard 3203: /* #ifdef INFINITYORIGINAL */
3204: /* lli=log(out[s1][s2] - savm[s1][s2]); */
3205: /* #else */
3206: /* if ((out[s1][s2] - savm[s1][s2]) < mytinydouble) */
3207: /* lli=log(mytinydouble); */
3208: /* else */
3209: /* lli=log(out[s1][s2] - savm[s1][s2]); */
3210: /* #endif */
1.226 brouard 3211: lli=log(out[s1][s2] - savm[s1][s2]);
1.216 brouard 3212:
1.226 brouard 3213: } else if ( s2==-1 ) { /* alive */
3214: for (j=1,survp=0. ; j<=nlstate; j++)
3215: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
3216: /*survp += out[s1][j]; */
3217: lli= log(survp);
3218: }
3219: else if (s2==-4) {
3220: for (j=3,survp=0. ; j<=nlstate; j++)
3221: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
3222: lli= log(survp);
3223: }
3224: else if (s2==-5) {
3225: for (j=1,survp=0. ; j<=2; j++)
3226: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
3227: lli= log(survp);
3228: }
3229: else{
3230: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
3231: /* 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 */
3232: }
3233: /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
3234: /*if(lli ==000.0)*/
3235: /*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); */
3236: ipmx +=1;
3237: sw += weight[i];
3238: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
3239: /* if (lli < log(mytinydouble)){ */
3240: /* 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); */
3241: /* 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]); */
3242: /* } */
3243: } /* end of wave */
3244: } /* end of individual */
3245: } else if(mle==2){
3246: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
3247: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
3248: for(mi=1; mi<= wav[i]-1; mi++){
3249: for (ii=1;ii<=nlstate+ndeath;ii++)
3250: for (j=1;j<=nlstate+ndeath;j++){
3251: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
3252: savm[ii][j]=(ii==j ? 1.0 : 0.0);
3253: }
3254: for(d=0; d<=dh[mi][i]; d++){
3255: newm=savm;
3256: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
3257: cov[2]=agexact;
3258: if(nagesqr==1)
3259: cov[3]= agexact*agexact;
3260: for (kk=1; kk<=cptcovage;kk++) {
3261: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
3262: }
3263: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
3264: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
3265: savm=oldm;
3266: oldm=newm;
3267: } /* end mult */
3268:
3269: s1=s[mw[mi][i]][i];
3270: s2=s[mw[mi+1][i]][i];
3271: bbh=(double)bh[mi][i]/(double)stepm;
3272: 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 */
3273: ipmx +=1;
3274: sw += weight[i];
3275: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
3276: } /* end of wave */
3277: } /* end of individual */
3278: } else if(mle==3){ /* exponential inter-extrapolation */
3279: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
3280: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
3281: for(mi=1; mi<= wav[i]-1; mi++){
3282: for (ii=1;ii<=nlstate+ndeath;ii++)
3283: for (j=1;j<=nlstate+ndeath;j++){
3284: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
3285: savm[ii][j]=(ii==j ? 1.0 : 0.0);
3286: }
3287: for(d=0; d<dh[mi][i]; d++){
3288: newm=savm;
3289: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
3290: cov[2]=agexact;
3291: if(nagesqr==1)
3292: cov[3]= agexact*agexact;
3293: for (kk=1; kk<=cptcovage;kk++) {
3294: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
3295: }
3296: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
3297: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
3298: savm=oldm;
3299: oldm=newm;
3300: } /* end mult */
3301:
3302: s1=s[mw[mi][i]][i];
3303: s2=s[mw[mi+1][i]][i];
3304: bbh=(double)bh[mi][i]/(double)stepm;
3305: 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 */
3306: ipmx +=1;
3307: sw += weight[i];
3308: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
3309: } /* end of wave */
3310: } /* end of individual */
3311: }else if (mle==4){ /* ml=4 no inter-extrapolation */
3312: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
3313: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
3314: for(mi=1; mi<= wav[i]-1; mi++){
3315: for (ii=1;ii<=nlstate+ndeath;ii++)
3316: for (j=1;j<=nlstate+ndeath;j++){
3317: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
3318: savm[ii][j]=(ii==j ? 1.0 : 0.0);
3319: }
3320: for(d=0; d<dh[mi][i]; d++){
3321: newm=savm;
3322: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
3323: cov[2]=agexact;
3324: if(nagesqr==1)
3325: cov[3]= agexact*agexact;
3326: for (kk=1; kk<=cptcovage;kk++) {
3327: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
3328: }
1.126 brouard 3329:
1.226 brouard 3330: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
3331: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
3332: savm=oldm;
3333: oldm=newm;
3334: } /* end mult */
3335:
3336: s1=s[mw[mi][i]][i];
3337: s2=s[mw[mi+1][i]][i];
3338: if( s2 > nlstate){
3339: lli=log(out[s1][s2] - savm[s1][s2]);
3340: } else if ( s2==-1 ) { /* alive */
3341: for (j=1,survp=0. ; j<=nlstate; j++)
3342: survp += out[s1][j];
3343: lli= log(survp);
3344: }else{
3345: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
3346: }
3347: ipmx +=1;
3348: sw += weight[i];
3349: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1.126 brouard 3350: /* 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]); */
1.226 brouard 3351: } /* end of wave */
3352: } /* end of individual */
3353: }else{ /* ml=5 no inter-extrapolation no jackson =0.8a */
3354: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
3355: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
3356: for(mi=1; mi<= wav[i]-1; mi++){
3357: for (ii=1;ii<=nlstate+ndeath;ii++)
3358: for (j=1;j<=nlstate+ndeath;j++){
3359: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
3360: savm[ii][j]=(ii==j ? 1.0 : 0.0);
3361: }
3362: for(d=0; d<dh[mi][i]; d++){
3363: newm=savm;
3364: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
3365: cov[2]=agexact;
3366: if(nagesqr==1)
3367: cov[3]= agexact*agexact;
3368: for (kk=1; kk<=cptcovage;kk++) {
3369: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
3370: }
1.126 brouard 3371:
1.226 brouard 3372: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
3373: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
3374: savm=oldm;
3375: oldm=newm;
3376: } /* end mult */
3377:
3378: s1=s[mw[mi][i]][i];
3379: s2=s[mw[mi+1][i]][i];
3380: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
3381: ipmx +=1;
3382: sw += weight[i];
3383: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
3384: /*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]);*/
3385: } /* end of wave */
3386: } /* end of individual */
3387: } /* End of if */
3388: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
3389: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
3390: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
3391: return -l;
1.126 brouard 3392: }
3393:
3394: /*************** log-likelihood *************/
3395: double funcone( double *x)
3396: {
1.228 brouard 3397: /* Same as func but slower because of a lot of printf and if */
1.126 brouard 3398: int i, ii, j, k, mi, d, kk;
1.228 brouard 3399: int ioffset=0;
1.131 brouard 3400: double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
1.126 brouard 3401: double **out;
3402: double lli; /* Individual log likelihood */
3403: double llt;
3404: int s1, s2;
1.228 brouard 3405: int iv=0, iqv=0, itv=0, iqtv=0 ; /* Index of varying covariate, fixed quantitative cov, time varying covariate, quantitative time varying covariate */
3406:
1.126 brouard 3407: double bbh, survp;
1.187 brouard 3408: double agexact;
1.214 brouard 3409: double agebegin, ageend;
1.126 brouard 3410: /*extern weight */
3411: /* We are differentiating ll according to initial status */
3412: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
3413: /*for(i=1;i<imx;i++)
3414: printf(" %d\n",s[4][i]);
3415: */
3416: cov[1]=1.;
3417:
3418: for(k=1; k<=nlstate; k++) ll[k]=0.;
1.224 brouard 3419: ioffset=0;
3420: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1.225 brouard 3421: ioffset=2+nagesqr+cptcovage;
1.232 brouard 3422: /* Fixed */
1.224 brouard 3423: /* for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i]; */
1.232 brouard 3424: /* for (k=1; k<=ncoveff;k++){ /\* Simple and product fixed Dummy covariates without age* products *\/ */
3425: for (k=1; k<=ncovf;k++){ /* Simple and product fixed covariates without age* products */
3426: cov[ioffset+TvarFind[k]]=covar[Tvar[TvarFind[k]]][i];/* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, only V1 is fixed (k=6)*/
3427: /* cov[ioffset+TvarFind[1]]=covar[Tvar[TvarFind[1]]][i]; */
3428: /* cov[2+6]=covar[Tvar[6]][i]; */
3429: /* cov[2+6]=covar[2][i]; V2 */
3430: /* cov[TvarFind[2]]=covar[Tvar[TvarFind[2]]][i]; */
3431: /* cov[2+7]=covar[Tvar[7]][i]; */
3432: /* cov[2+7]=covar[7][i]; V7=V1*V2 */
3433: /* cov[TvarFind[3]]=covar[Tvar[TvarFind[3]]][i]; */
3434: /* cov[2+9]=covar[Tvar[9]][i]; */
3435: /* cov[2+9]=covar[1][i]; V1 */
1.225 brouard 3436: }
1.232 brouard 3437: /* for (k=1; k<=nqfveff;k++){ /\* Simple and product fixed Quantitative covariates without age* products *\/ */
3438: /* cov[++ioffset]=coqvar[TvarFQ[k]][i];/\* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, only V2 and V1*V2 is fixed (k=6 and 7?)*\/ */
3439: /* } */
1.231 brouard 3440: /* for(iqv=1; iqv <= nqfveff; iqv++){ /\* Quantitative fixed covariates *\/ */
3441: /* cov[++ioffset]=coqvar[Tvar[iqv]][i]; /\* Only V2 k=6 and V1*V2 7 *\/ */
3442: /* } */
1.225 brouard 3443:
1.233 brouard 3444:
3445: for(mi=1; mi<= wav[i]-1; mi++){ /* Varying with waves */
1.232 brouard 3446: /* Wave varying (but not age varying) */
3447: for(k=1; k <= ncovv ; k++){ /* Varying covariates (single and product but no age )*/
1.233 brouard 3448: cov[ioffset+TvarVind[k]]=cotvar[mw[mi][i]][Tvar[TvarVind[k]]][i];
1.232 brouard 3449: }
3450: /* for(itv=1; itv <= ntveff; itv++){ /\* Varying dummy covariates (single??)*\/ */
1.231 brouard 3451: /* iv= Tvar[Tmodelind[ioffset-2-nagesqr-cptcovage+itv]]-ncovcol-nqv; /\* Counting the # varying covariate from 1 to ntveff *\/ */
3452: /* cov[ioffset+iv]=cotvar[mw[mi][i]][iv][i]; */
1.232 brouard 3453: /* k=ioffset-2-nagesqr-cptcovage+itv; /\* position in simple model *\/ */
3454: /* cov[ioffset+itv]=cotvar[mw[mi][i]][TmodelInvind[itv]][i]; */
1.231 brouard 3455: /* printf(" i=%d,mi=%d,itv=%d,TmodelInvind[itv]=%d,cotvar[mw[mi][i]][TmodelInvind[itv]][i]=%f\n", i, mi, itv, TmodelInvind[itv],cotvar[mw[mi][i]][TmodelInvind[itv]][i]); */
1.232 brouard 3456: /* for(iqtv=1; iqtv <= nqtveff; iqtv++){ /\* Varying quantitatives covariates *\/ */
3457: /* iv=TmodelInvQind[iqtv]; /\* Counting the # varying covariate from 1 to ntveff *\/ */
3458: /* /\* printf(" i=%d,mi=%d,iqtv=%d,TmodelInvQind[iqtv]=%d,cotqvar[mw[mi][i]][TmodelInvQind[iqtv]][i]=%f\n", i, mi, iqtv, TmodelInvQind[iqtv],cotqvar[mw[mi][i]][TmodelInvQind[iqtv]][i]); *\/ */
3459: /* cov[ioffset+ntveff+iqtv]=cotqvar[mw[mi][i]][TmodelInvQind[iqtv]][i]; */
3460: /* } */
1.126 brouard 3461: for (ii=1;ii<=nlstate+ndeath;ii++)
1.231 brouard 3462: for (j=1;j<=nlstate+ndeath;j++){
3463: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
3464: savm[ii][j]=(ii==j ? 1.0 : 0.0);
3465: }
1.214 brouard 3466:
3467: agebegin=agev[mw[mi][i]][i]; /* Age at beginning of effective wave */
3468: ageend=agev[mw[mi][i]][i] + (dh[mi][i])*stepm/YEARM; /* Age at end of effective wave and at the end of transition */
3469: for(d=0; d<dh[mi][i]; d++){ /* Delay between two effective waves */
1.231 brouard 3470: /*dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
3471: and mw[mi+1][i]. dh depends on stepm.*/
3472: newm=savm;
3473: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
3474: cov[2]=agexact;
3475: if(nagesqr==1)
3476: cov[3]= agexact*agexact;
3477: for (kk=1; kk<=cptcovage;kk++) {
3478: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
3479: }
3480: /* printf("i=%d,mi=%d,d=%d,mw[mi][i]=%d\n",i, mi,d,mw[mi][i]); */
3481: /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
3482: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
3483: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
3484: /* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, */
3485: /* 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); */
3486: savm=oldm;
3487: oldm=newm;
1.126 brouard 3488: } /* end mult */
3489:
3490: s1=s[mw[mi][i]][i];
3491: s2=s[mw[mi+1][i]][i];
1.217 brouard 3492: /* if(s2==-1){ */
3493: /* printf(" s1=%d, s2=%d i=%d \n", s1, s2, i); */
3494: /* /\* exit(1); *\/ */
3495: /* } */
1.126 brouard 3496: bbh=(double)bh[mi][i]/(double)stepm;
3497: /* bias is positive if real duration
3498: * is higher than the multiple of stepm and negative otherwise.
3499: */
3500: if( s2 > nlstate && (mle <5) ){ /* Jackson */
1.232 brouard 3501: lli=log(out[s1][s2] - savm[s1][s2]);
1.216 brouard 3502: } else if ( s2==-1 ) { /* alive */
1.232 brouard 3503: for (j=1,survp=0. ; j<=nlstate; j++)
3504: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
3505: lli= log(survp);
1.126 brouard 3506: }else if (mle==1){
1.232 brouard 3507: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
1.126 brouard 3508: } else if(mle==2){
1.232 brouard 3509: 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 */
1.126 brouard 3510: } else if(mle==3){ /* exponential inter-extrapolation */
1.232 brouard 3511: 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 */
1.126 brouard 3512: } else if (mle==4){ /* mle=4 no inter-extrapolation */
1.232 brouard 3513: lli=log(out[s1][s2]); /* Original formula */
1.136 brouard 3514: } else{ /* mle=0 back to 1 */
1.232 brouard 3515: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
3516: /*lli=log(out[s1][s2]); */ /* Original formula */
1.126 brouard 3517: } /* End of if */
3518: ipmx +=1;
3519: sw += weight[i];
3520: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1.132 brouard 3521: /*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 3522: if(globpr){
1.232 brouard 3523: fprintf(ficresilk,"%9ld %6.1f %6.1f %6d %2d %2d %2d %2d %3d %15.6f %8.4f %8.3f\
1.126 brouard 3524: %11.6f %11.6f %11.6f ", \
1.232 brouard 3525: num[i], agebegin, ageend, i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],weight[i]*gipmx/gsw,
3526: 2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
3527: for(k=1,llt=0.,l=0.; k<=nlstate; k++){
3528: llt +=ll[k]*gipmx/gsw;
3529: fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
3530: }
3531: fprintf(ficresilk," %10.6f\n", -llt);
1.126 brouard 3532: }
1.232 brouard 3533: } /* end of wave */
3534: } /* end of individual */
3535: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
3536: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
3537: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
3538: if(globpr==0){ /* First time we count the contributions and weights */
3539: gipmx=ipmx;
3540: gsw=sw;
3541: }
3542: return -l;
1.126 brouard 3543: }
3544:
3545:
3546: /*************** function likelione ***********/
3547: void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
3548: {
3549: /* This routine should help understanding what is done with
3550: the selection of individuals/waves and
3551: to check the exact contribution to the likelihood.
3552: Plotting could be done.
3553: */
3554: int k;
3555:
3556: if(*globpri !=0){ /* Just counts and sums, no printings */
1.201 brouard 3557: strcpy(fileresilk,"ILK_");
1.202 brouard 3558: strcat(fileresilk,fileresu);
1.126 brouard 3559: if((ficresilk=fopen(fileresilk,"w"))==NULL) {
3560: printf("Problem with resultfile: %s\n", fileresilk);
3561: fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
3562: }
1.214 brouard 3563: fprintf(ficresilk, "#individual(line's_record) count ageb ageend s1 s2 wave# effective_wave# number_of_matrices_product pij weight weight/gpw -2ln(pij)*weight 0pij_x 0pij_(x-stepm) cumulating_loglikeli_by_health_state(reweighted=-2ll*weightXnumber_of_contribs/sum_of_weights) and_total\n");
3564: fprintf(ficresilk, "#num_i ageb agend i s1 s2 mi mw dh likeli weight %%weight 2wlli out sav ");
1.126 brouard 3565: /* i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
3566: for(k=1; k<=nlstate; k++)
3567: fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
3568: fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
3569: }
3570:
3571: *fretone=(*funcone)(p);
3572: if(*globpri !=0){
3573: fclose(ficresilk);
1.205 brouard 3574: if (mle ==0)
3575: fprintf(fichtm,"\n<br>File of contributions to the likelihood computed with initial parameters and mle = %d.",mle);
3576: else if(mle >=1)
3577: fprintf(fichtm,"\n<br>File of contributions to the likelihood computed with optimized parameters mle = %d.",mle);
3578: 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 3579:
1.208 brouard 3580:
3581: for (k=1; k<= nlstate ; k++) {
1.211 brouard 3582: fprintf(fichtm,"<br>- Probability p<sub>%dj</sub> by origin %d and destination j. Dot's sizes are related to corresponding weight: <a href=\"%s-p%dj.png\">%s-p%dj.png</a><br> \
1.208 brouard 3583: <img src=\"%s-p%dj.png\">",k,k,subdirf2(optionfilefiname,"ILK_"),k,subdirf2(optionfilefiname,"ILK_"),k,subdirf2(optionfilefiname,"ILK_"),k);
3584: }
1.207 brouard 3585: 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 3586: <img src=\"%s-ori.png\">",subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"));
1.207 brouard 3587: fprintf(fichtm,"<br>- and by state of destination <a href=\"%s-dest.png\">%s-dest.png</a><br> \
1.204 brouard 3588: <img src=\"%s-dest.png\">",subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"));
1.207 brouard 3589: fflush(fichtm);
1.205 brouard 3590: }
1.126 brouard 3591: return;
3592: }
3593:
3594:
3595: /*********** Maximum Likelihood Estimation ***************/
3596:
3597: void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
3598: {
1.165 brouard 3599: int i,j, iter=0;
1.126 brouard 3600: double **xi;
3601: double fret;
3602: double fretone; /* Only one call to likelihood */
3603: /* char filerespow[FILENAMELENGTH];*/
1.162 brouard 3604:
3605: #ifdef NLOPT
3606: int creturn;
3607: nlopt_opt opt;
3608: /* double lb[9] = { -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL }; /\* lower bounds *\/ */
3609: double *lb;
3610: double minf; /* the minimum objective value, upon return */
3611: double * p1; /* Shifted parameters from 0 instead of 1 */
3612: myfunc_data dinst, *d = &dinst;
3613: #endif
3614:
3615:
1.126 brouard 3616: xi=matrix(1,npar,1,npar);
3617: for (i=1;i<=npar;i++)
3618: for (j=1;j<=npar;j++)
3619: xi[i][j]=(i==j ? 1.0 : 0.0);
3620: printf("Powell\n"); fprintf(ficlog,"Powell\n");
1.201 brouard 3621: strcpy(filerespow,"POW_");
1.126 brouard 3622: strcat(filerespow,fileres);
3623: if((ficrespow=fopen(filerespow,"w"))==NULL) {
3624: printf("Problem with resultfile: %s\n", filerespow);
3625: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
3626: }
3627: fprintf(ficrespow,"# Powell\n# iter -2*LL");
3628: for (i=1;i<=nlstate;i++)
3629: for(j=1;j<=nlstate+ndeath;j++)
3630: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
3631: fprintf(ficrespow,"\n");
1.162 brouard 3632: #ifdef POWELL
1.126 brouard 3633: powell(p,xi,npar,ftol,&iter,&fret,func);
1.162 brouard 3634: #endif
1.126 brouard 3635:
1.162 brouard 3636: #ifdef NLOPT
3637: #ifdef NEWUOA
3638: opt = nlopt_create(NLOPT_LN_NEWUOA,npar);
3639: #else
3640: opt = nlopt_create(NLOPT_LN_BOBYQA,npar);
3641: #endif
3642: lb=vector(0,npar-1);
3643: for (i=0;i<npar;i++) lb[i]= -HUGE_VAL;
3644: nlopt_set_lower_bounds(opt, lb);
3645: nlopt_set_initial_step1(opt, 0.1);
3646:
3647: p1= (p+1); /* p *(p+1)@8 and p *(p1)@8 are equal p1[0]=p[1] */
3648: d->function = func;
3649: printf(" Func %.12lf \n",myfunc(npar,p1,NULL,d));
3650: nlopt_set_min_objective(opt, myfunc, d);
3651: nlopt_set_xtol_rel(opt, ftol);
3652: if ((creturn=nlopt_optimize(opt, p1, &minf)) < 0) {
3653: printf("nlopt failed! %d\n",creturn);
3654: }
3655: else {
3656: printf("found minimum after %d evaluations (NLOPT=%d)\n", countcallfunc ,NLOPT);
3657: printf("found minimum at f(%g,%g) = %0.10g\n", p[0], p[1], minf);
3658: iter=1; /* not equal */
3659: }
3660: nlopt_destroy(opt);
3661: #endif
1.126 brouard 3662: free_matrix(xi,1,npar,1,npar);
3663: fclose(ficrespow);
1.203 brouard 3664: printf("\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
3665: fprintf(ficlog,"\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
1.180 brouard 3666: fprintf(ficres,"#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
1.126 brouard 3667:
3668: }
3669:
3670: /**** Computes Hessian and covariance matrix ***/
1.203 brouard 3671: void hesscov(double **matcov, double **hess, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
1.126 brouard 3672: {
3673: double **a,**y,*x,pd;
1.203 brouard 3674: /* double **hess; */
1.164 brouard 3675: int i, j;
1.126 brouard 3676: int *indx;
3677:
3678: double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
1.203 brouard 3679: double hessij(double p[], double **hess, double delti[], int i, int j,double (*func)(double []),int npar);
1.126 brouard 3680: void lubksb(double **a, int npar, int *indx, double b[]) ;
3681: void ludcmp(double **a, int npar, int *indx, double *d) ;
3682: double gompertz(double p[]);
1.203 brouard 3683: /* hess=matrix(1,npar,1,npar); */
1.126 brouard 3684:
3685: printf("\nCalculation of the hessian matrix. Wait...\n");
3686: fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
3687: for (i=1;i<=npar;i++){
1.203 brouard 3688: printf("%d-",i);fflush(stdout);
3689: fprintf(ficlog,"%d-",i);fflush(ficlog);
1.126 brouard 3690:
3691: hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
3692:
3693: /* printf(" %f ",p[i]);
3694: printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
3695: }
3696:
3697: for (i=1;i<=npar;i++) {
3698: for (j=1;j<=npar;j++) {
3699: if (j>i) {
1.203 brouard 3700: printf(".%d-%d",i,j);fflush(stdout);
3701: fprintf(ficlog,".%d-%d",i,j);fflush(ficlog);
3702: hess[i][j]=hessij(p,hess, delti,i,j,func,npar);
1.126 brouard 3703:
3704: hess[j][i]=hess[i][j];
3705: /*printf(" %lf ",hess[i][j]);*/
3706: }
3707: }
3708: }
3709: printf("\n");
3710: fprintf(ficlog,"\n");
3711:
3712: printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
3713: fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
3714:
3715: a=matrix(1,npar,1,npar);
3716: y=matrix(1,npar,1,npar);
3717: x=vector(1,npar);
3718: indx=ivector(1,npar);
3719: for (i=1;i<=npar;i++)
3720: for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
3721: ludcmp(a,npar,indx,&pd);
3722:
3723: for (j=1;j<=npar;j++) {
3724: for (i=1;i<=npar;i++) x[i]=0;
3725: x[j]=1;
3726: lubksb(a,npar,indx,x);
3727: for (i=1;i<=npar;i++){
3728: matcov[i][j]=x[i];
3729: }
3730: }
3731:
3732: printf("\n#Hessian matrix#\n");
3733: fprintf(ficlog,"\n#Hessian matrix#\n");
3734: for (i=1;i<=npar;i++) {
3735: for (j=1;j<=npar;j++) {
1.203 brouard 3736: printf("%.6e ",hess[i][j]);
3737: fprintf(ficlog,"%.6e ",hess[i][j]);
1.126 brouard 3738: }
3739: printf("\n");
3740: fprintf(ficlog,"\n");
3741: }
3742:
1.203 brouard 3743: /* printf("\n#Covariance matrix#\n"); */
3744: /* fprintf(ficlog,"\n#Covariance matrix#\n"); */
3745: /* for (i=1;i<=npar;i++) { */
3746: /* for (j=1;j<=npar;j++) { */
3747: /* printf("%.6e ",matcov[i][j]); */
3748: /* fprintf(ficlog,"%.6e ",matcov[i][j]); */
3749: /* } */
3750: /* printf("\n"); */
3751: /* fprintf(ficlog,"\n"); */
3752: /* } */
3753:
1.126 brouard 3754: /* Recompute Inverse */
1.203 brouard 3755: /* for (i=1;i<=npar;i++) */
3756: /* for (j=1;j<=npar;j++) a[i][j]=matcov[i][j]; */
3757: /* ludcmp(a,npar,indx,&pd); */
3758:
3759: /* printf("\n#Hessian matrix recomputed#\n"); */
3760:
3761: /* for (j=1;j<=npar;j++) { */
3762: /* for (i=1;i<=npar;i++) x[i]=0; */
3763: /* x[j]=1; */
3764: /* lubksb(a,npar,indx,x); */
3765: /* for (i=1;i<=npar;i++){ */
3766: /* y[i][j]=x[i]; */
3767: /* printf("%.3e ",y[i][j]); */
3768: /* fprintf(ficlog,"%.3e ",y[i][j]); */
3769: /* } */
3770: /* printf("\n"); */
3771: /* fprintf(ficlog,"\n"); */
3772: /* } */
3773:
3774: /* Verifying the inverse matrix */
3775: #ifdef DEBUGHESS
3776: y=matprod2(y,hess,1,npar,1,npar,1,npar,matcov);
1.126 brouard 3777:
1.203 brouard 3778: printf("\n#Verification: multiplying the matrix of covariance by the Hessian matrix, should be unity:#\n");
3779: fprintf(ficlog,"\n#Verification: multiplying the matrix of covariance by the Hessian matrix. Should be unity:#\n");
1.126 brouard 3780:
3781: for (j=1;j<=npar;j++) {
3782: for (i=1;i<=npar;i++){
1.203 brouard 3783: printf("%.2f ",y[i][j]);
3784: fprintf(ficlog,"%.2f ",y[i][j]);
1.126 brouard 3785: }
3786: printf("\n");
3787: fprintf(ficlog,"\n");
3788: }
1.203 brouard 3789: #endif
1.126 brouard 3790:
3791: free_matrix(a,1,npar,1,npar);
3792: free_matrix(y,1,npar,1,npar);
3793: free_vector(x,1,npar);
3794: free_ivector(indx,1,npar);
1.203 brouard 3795: /* free_matrix(hess,1,npar,1,npar); */
1.126 brouard 3796:
3797:
3798: }
3799:
3800: /*************** hessian matrix ****************/
3801: double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
1.203 brouard 3802: { /* Around values of x, computes the function func and returns the scales delti and hessian */
1.126 brouard 3803: int i;
3804: int l=1, lmax=20;
1.203 brouard 3805: double k1,k2, res, fx;
1.132 brouard 3806: double p2[MAXPARM+1]; /* identical to x */
1.126 brouard 3807: double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
3808: int k=0,kmax=10;
3809: double l1;
3810:
3811: fx=func(x);
3812: for (i=1;i<=npar;i++) p2[i]=x[i];
1.145 brouard 3813: for(l=0 ; l <=lmax; l++){ /* Enlarging the zone around the Maximum */
1.126 brouard 3814: l1=pow(10,l);
3815: delts=delt;
3816: for(k=1 ; k <kmax; k=k+1){
3817: delt = delta*(l1*k);
3818: p2[theta]=x[theta] +delt;
1.145 brouard 3819: k1=func(p2)-fx; /* Might be negative if too close to the theoretical maximum */
1.126 brouard 3820: p2[theta]=x[theta]-delt;
3821: k2=func(p2)-fx;
3822: /*res= (k1-2.0*fx+k2)/delt/delt; */
1.203 brouard 3823: res= (k1+k2)/delt/delt/2.; /* Divided by 2 because L and not 2*L */
1.126 brouard 3824:
1.203 brouard 3825: #ifdef DEBUGHESSII
1.126 brouard 3826: 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);
3827: 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);
3828: #endif
3829: /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
3830: if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
3831: k=kmax;
3832: }
3833: else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
1.164 brouard 3834: k=kmax; l=lmax*10;
1.126 brouard 3835: }
3836: else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){
3837: delts=delt;
3838: }
1.203 brouard 3839: } /* End loop k */
1.126 brouard 3840: }
3841: delti[theta]=delts;
3842: return res;
3843:
3844: }
3845:
1.203 brouard 3846: double hessij( double x[], double **hess, double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
1.126 brouard 3847: {
3848: int i;
1.164 brouard 3849: int l=1, lmax=20;
1.126 brouard 3850: double k1,k2,k3,k4,res,fx;
1.132 brouard 3851: double p2[MAXPARM+1];
1.203 brouard 3852: int k, kmax=1;
3853: double v1, v2, cv12, lc1, lc2;
1.208 brouard 3854:
3855: int firstime=0;
1.203 brouard 3856:
1.126 brouard 3857: fx=func(x);
1.203 brouard 3858: for (k=1; k<=kmax; k=k+10) {
1.126 brouard 3859: for (i=1;i<=npar;i++) p2[i]=x[i];
1.203 brouard 3860: p2[thetai]=x[thetai]+delti[thetai]*k;
3861: p2[thetaj]=x[thetaj]+delti[thetaj]*k;
1.126 brouard 3862: k1=func(p2)-fx;
3863:
1.203 brouard 3864: p2[thetai]=x[thetai]+delti[thetai]*k;
3865: p2[thetaj]=x[thetaj]-delti[thetaj]*k;
1.126 brouard 3866: k2=func(p2)-fx;
3867:
1.203 brouard 3868: p2[thetai]=x[thetai]-delti[thetai]*k;
3869: p2[thetaj]=x[thetaj]+delti[thetaj]*k;
1.126 brouard 3870: k3=func(p2)-fx;
3871:
1.203 brouard 3872: p2[thetai]=x[thetai]-delti[thetai]*k;
3873: p2[thetaj]=x[thetaj]-delti[thetaj]*k;
1.126 brouard 3874: k4=func(p2)-fx;
1.203 brouard 3875: res=(k1-k2-k3+k4)/4.0/delti[thetai]/k/delti[thetaj]/k/2.; /* Because of L not 2*L */
3876: if(k1*k2*k3*k4 <0.){
1.208 brouard 3877: firstime=1;
1.203 brouard 3878: kmax=kmax+10;
1.208 brouard 3879: }
3880: if(kmax >=10 || firstime ==1){
1.218 brouard 3881: printf("Warning: directions %d-%d, you are not estimating the Hessian at the exact maximum likelihood; you may increase ftol=%.2e\n",thetai,thetaj, ftol);
3882: fprintf(ficlog,"Warning: directions %d-%d, you are not estimating the Hessian at the exact maximum likelihood; you may increase ftol=%.2e\n",thetai,thetaj, ftol);
1.203 brouard 3883: 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);
3884: 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);
3885: }
3886: #ifdef DEBUGHESSIJ
3887: v1=hess[thetai][thetai];
3888: v2=hess[thetaj][thetaj];
3889: cv12=res;
3890: /* Computing eigen value of Hessian matrix */
3891: lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
3892: lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
3893: if ((lc2 <0) || (lc1 <0) ){
3894: printf("Warning: sub Hessian matrix '%d%d' does not have positive eigen values \n",thetai,thetaj);
3895: fprintf(ficlog, "Warning: sub Hessian matrix '%d%d' does not have positive eigen values \n",thetai,thetaj);
3896: 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);
3897: 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);
3898: }
1.126 brouard 3899: #endif
3900: }
3901: return res;
3902: }
3903:
1.203 brouard 3904: /* Not done yet: Was supposed to fix if not exactly at the maximum */
3905: /* double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar) */
3906: /* { */
3907: /* int i; */
3908: /* int l=1, lmax=20; */
3909: /* double k1,k2,k3,k4,res,fx; */
3910: /* double p2[MAXPARM+1]; */
3911: /* double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4; */
3912: /* int k=0,kmax=10; */
3913: /* double l1; */
3914:
3915: /* fx=func(x); */
3916: /* for(l=0 ; l <=lmax; l++){ /\* Enlarging the zone around the Maximum *\/ */
3917: /* l1=pow(10,l); */
3918: /* delts=delt; */
3919: /* for(k=1 ; k <kmax; k=k+1){ */
3920: /* delt = delti*(l1*k); */
3921: /* for (i=1;i<=npar;i++) p2[i]=x[i]; */
3922: /* p2[thetai]=x[thetai]+delti[thetai]/k; */
3923: /* p2[thetaj]=x[thetaj]+delti[thetaj]/k; */
3924: /* k1=func(p2)-fx; */
3925:
3926: /* p2[thetai]=x[thetai]+delti[thetai]/k; */
3927: /* p2[thetaj]=x[thetaj]-delti[thetaj]/k; */
3928: /* k2=func(p2)-fx; */
3929:
3930: /* p2[thetai]=x[thetai]-delti[thetai]/k; */
3931: /* p2[thetaj]=x[thetaj]+delti[thetaj]/k; */
3932: /* k3=func(p2)-fx; */
3933:
3934: /* p2[thetai]=x[thetai]-delti[thetai]/k; */
3935: /* p2[thetaj]=x[thetaj]-delti[thetaj]/k; */
3936: /* k4=func(p2)-fx; */
3937: /* res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /\* Because of L not 2*L *\/ */
3938: /* #ifdef DEBUGHESSIJ */
3939: /* 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); */
3940: /* 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); */
3941: /* #endif */
3942: /* if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)|| (k4 <khi/nkhi/2.)|| (k4 <khi/nkhi/2.)){ */
3943: /* k=kmax; */
3944: /* } */
3945: /* else if((k1 >khi/nkhif) || (k2 >khi/nkhif) || (k4 >khi/nkhif) || (k4 >khi/nkhif)){ /\* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. *\/ */
3946: /* k=kmax; l=lmax*10; */
3947: /* } */
3948: /* else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ */
3949: /* delts=delt; */
3950: /* } */
3951: /* } /\* End loop k *\/ */
3952: /* } */
3953: /* delti[theta]=delts; */
3954: /* return res; */
3955: /* } */
3956:
3957:
1.126 brouard 3958: /************** Inverse of matrix **************/
3959: void ludcmp(double **a, int n, int *indx, double *d)
3960: {
3961: int i,imax,j,k;
3962: double big,dum,sum,temp;
3963: double *vv;
3964:
3965: vv=vector(1,n);
3966: *d=1.0;
3967: for (i=1;i<=n;i++) {
3968: big=0.0;
3969: for (j=1;j<=n;j++)
3970: if ((temp=fabs(a[i][j])) > big) big=temp;
3971: if (big == 0.0) nrerror("Singular matrix in routine ludcmp");
3972: vv[i]=1.0/big;
3973: }
3974: for (j=1;j<=n;j++) {
3975: for (i=1;i<j;i++) {
3976: sum=a[i][j];
3977: for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];
3978: a[i][j]=sum;
3979: }
3980: big=0.0;
3981: for (i=j;i<=n;i++) {
3982: sum=a[i][j];
3983: for (k=1;k<j;k++)
3984: sum -= a[i][k]*a[k][j];
3985: a[i][j]=sum;
3986: if ( (dum=vv[i]*fabs(sum)) >= big) {
3987: big=dum;
3988: imax=i;
3989: }
3990: }
3991: if (j != imax) {
3992: for (k=1;k<=n;k++) {
3993: dum=a[imax][k];
3994: a[imax][k]=a[j][k];
3995: a[j][k]=dum;
3996: }
3997: *d = -(*d);
3998: vv[imax]=vv[j];
3999: }
4000: indx[j]=imax;
4001: if (a[j][j] == 0.0) a[j][j]=TINY;
4002: if (j != n) {
4003: dum=1.0/(a[j][j]);
4004: for (i=j+1;i<=n;i++) a[i][j] *= dum;
4005: }
4006: }
4007: free_vector(vv,1,n); /* Doesn't work */
4008: ;
4009: }
4010:
4011: void lubksb(double **a, int n, int *indx, double b[])
4012: {
4013: int i,ii=0,ip,j;
4014: double sum;
4015:
4016: for (i=1;i<=n;i++) {
4017: ip=indx[i];
4018: sum=b[ip];
4019: b[ip]=b[i];
4020: if (ii)
4021: for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];
4022: else if (sum) ii=i;
4023: b[i]=sum;
4024: }
4025: for (i=n;i>=1;i--) {
4026: sum=b[i];
4027: for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];
4028: b[i]=sum/a[i][i];
4029: }
4030: }
4031:
4032: void pstamp(FILE *fichier)
4033: {
1.196 brouard 4034: fprintf(fichier,"# %s.%s\n#IMaCh version %s, %s\n#%s\n# %s", optionfilefiname,optionfilext,version,copyright, fullversion, strstart);
1.126 brouard 4035: }
4036:
4037: /************ Frequencies ********************/
1.226 brouard 4038: void freqsummary(char fileres[], int iagemin, int iagemax, int **s, double **agev, int nlstate, int imx, \
4039: int *Tvaraff, int *invalidvarcomb, int **nbcode, int *ncodemax,double **mint,double **anint, char strstart[], \
4040: int firstpass, int lastpass, int stepm, int weightopt, char model[])
4041: { /* Some frequencies */
4042:
1.227 brouard 4043: int i, m, jk, j1, bool, z1,j, k, iv;
1.226 brouard 4044: int iind=0, iage=0;
4045: int mi; /* Effective wave */
4046: int first;
4047: double ***freq; /* Frequencies */
4048: double *meanq;
4049: double **meanqt;
4050: double *pp, **prop, *posprop, *pospropt;
4051: double pos=0., posproptt=0., pospropta=0., k2, dateintsum=0,k2cpt=0;
4052: char fileresp[FILENAMELENGTH], fileresphtm[FILENAMELENGTH], fileresphtmfr[FILENAMELENGTH];
4053: double agebegin, ageend;
4054:
4055: pp=vector(1,nlstate);
4056: prop=matrix(1,nlstate,iagemin-AGEMARGE,iagemax+3+AGEMARGE);
4057: posprop=vector(1,nlstate); /* Counting the number of transition starting from a live state per age */
4058: pospropt=vector(1,nlstate); /* Counting the number of transition starting from a live state */
4059: /* prop=matrix(1,nlstate,iagemin,iagemax+3); */
4060: meanq=vector(1,nqfveff); /* Number of Quantitative Fixed Variables Effective */
4061: meanqt=matrix(1,lastpass,1,nqtveff);
4062: strcpy(fileresp,"P_");
4063: strcat(fileresp,fileresu);
4064: /*strcat(fileresphtm,fileresu);*/
4065: if((ficresp=fopen(fileresp,"w"))==NULL) {
4066: printf("Problem with prevalence resultfile: %s\n", fileresp);
4067: fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
4068: exit(0);
4069: }
1.214 brouard 4070:
1.226 brouard 4071: strcpy(fileresphtm,subdirfext(optionfilefiname,"PHTM_",".htm"));
4072: if((ficresphtm=fopen(fileresphtm,"w"))==NULL) {
4073: printf("Problem with prevalence HTM resultfile '%s' with errno='%s'\n",fileresphtm,strerror(errno));
4074: fprintf(ficlog,"Problem with prevalence HTM resultfile '%s' with errno='%s'\n",fileresphtm,strerror(errno));
4075: fflush(ficlog);
4076: exit(70);
4077: }
4078: else{
4079: fprintf(ficresphtm,"<html><head>\n<title>IMaCh PHTM_ %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
1.214 brouard 4080: <hr size=\"2\" color=\"#EC5E5E\"> \n\
4081: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n",\
1.226 brouard 4082: fileresphtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
4083: }
4084: fprintf(ficresphtm,"Current page is file <a href=\"%s\">%s</a><br>\n\n<h4>Frequencies and prevalence by age at begin of transition</h4>\n",fileresphtm, fileresphtm);
1.214 brouard 4085:
1.226 brouard 4086: strcpy(fileresphtmfr,subdirfext(optionfilefiname,"PHTMFR_",".htm"));
4087: if((ficresphtmfr=fopen(fileresphtmfr,"w"))==NULL) {
4088: printf("Problem with frequency table HTM resultfile '%s' with errno='%s'\n",fileresphtmfr,strerror(errno));
4089: fprintf(ficlog,"Problem with frequency table HTM resultfile '%s' with errno='%s'\n",fileresphtmfr,strerror(errno));
4090: fflush(ficlog);
4091: exit(70);
4092: }
4093: else{
4094: fprintf(ficresphtmfr,"<html><head>\n<title>IMaCh PHTM_Frequency table %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
1.214 brouard 4095: <hr size=\"2\" color=\"#EC5E5E\"> \n\
4096: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n",\
1.226 brouard 4097: fileresphtmfr,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
4098: }
4099: fprintf(ficresphtmfr,"Current page is file <a href=\"%s\">%s</a><br>\n\n<h4>Frequencies of all effective transitions by age at begin of transition </h4>Unknown status is -1<br/>\n",fileresphtmfr, fileresphtmfr);
1.214 brouard 4100:
1.226 brouard 4101: freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin-AGEMARGE,iagemax+3+AGEMARGE);
4102: j1=0;
1.126 brouard 4103:
1.227 brouard 4104: /* j=ncoveff; /\* Only fixed dummy covariates *\/ */
4105: j=cptcoveff; /* Only dummy covariates of the model */
1.226 brouard 4106: if (cptcovn<1) {j=1;ncodemax[1]=1;}
1.220 brouard 4107:
1.226 brouard 4108: first=1;
1.220 brouard 4109:
1.226 brouard 4110: /* Detects if a combination j1 is empty: for a multinomial variable like 3 education levels:
4111: reference=low_education V1=0,V2=0
4112: med_educ V1=1 V2=0,
4113: high_educ V1=0 V2=1
4114: Then V1=1 and V2=1 is a noisy combination that we want to exclude for the list 2**cptcoveff
4115: */
1.126 brouard 4116:
1.227 brouard 4117: for (j1 = 1; j1 <= (int) pow(2,j); j1++){ /* Loop on covariates combination in order of model, excluding quantitatives V4=0, V3=0 for example, fixed or varying covariates */
1.226 brouard 4118: posproptt=0.;
4119: /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
4120: scanf("%d", i);*/
4121: for (i=-5; i<=nlstate+ndeath; i++)
4122: for (jk=-5; jk<=nlstate+ndeath; jk++)
1.231 brouard 4123: for(m=iagemin; m <= iagemax+3; m++)
4124: freq[i][jk][m]=0;
4125:
1.226 brouard 4126: for (i=1; i<=nlstate; i++) {
4127: for(m=iagemin; m <= iagemax+3; m++)
1.231 brouard 4128: prop[i][m]=0;
1.226 brouard 4129: posprop[i]=0;
4130: pospropt[i]=0;
4131: }
1.227 brouard 4132: /* for (z1=1; z1<= nqfveff; z1++) { */
4133: /* meanq[z1]+=0.; */
4134: /* for(m=1;m<=lastpass;m++){ */
4135: /* meanqt[m][z1]=0.; */
4136: /* } */
4137: /* } */
1.231 brouard 4138:
1.226 brouard 4139: dateintsum=0;
4140: k2cpt=0;
1.227 brouard 4141: /* For that combination of covariate j1, we count and print the frequencies in one pass */
1.226 brouard 4142: for (iind=1; iind<=imx; iind++) { /* For each individual iind */
4143: bool=1;
1.227 brouard 4144: if(anyvaryingduminmodel==0){ /* If All fixed covariates */
1.234 brouard 4145: if (cptcoveff >0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
1.227 brouard 4146: /* for (z1=1; z1<= nqfveff; z1++) { */
4147: /* meanq[z1]+=coqvar[Tvar[z1]][iind]; /\* Computes mean of quantitative with selected filter *\/ */
4148: /* } */
1.234 brouard 4149: for (z1=1; z1<=cptcoveff; z1++) {
4150: /* if(Tvaraff[z1] ==-20){ */
4151: /* /\* sumnew+=cotvar[mw[mi][iind]][z1][iind]; *\/ */
4152: /* }else if(Tvaraff[z1] ==-10){ */
4153: /* /\* sumnew+=coqvar[z1][iind]; *\/ */
4154: /* }else */
4155: if (covar[Tvaraff[z1]][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]){
4156: /* Tests if this individual iind responded to j1 (V4=1 V3=0) */
4157: bool=0;
4158: /* 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",
4159: bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtabm(j1,z1),
4160: j1,z1,nbcode[Tvaraff[z1]][codtabm(j1,z1)],j1);*/
4161: /* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtabm(7,3)=1 and nbcde[3][?]=1*/
4162: } /* Onlyf fixed */
4163: } /* end z1 */
4164: } /* cptcovn > 0 */
1.227 brouard 4165: } /* end any */
4166: if (bool==1){ /* We selected an individual iind satisfying combination j1 or all fixed */
1.234 brouard 4167: /* for(m=firstpass; m<=lastpass; m++){ */
4168: for(mi=1; mi<wav[iind];mi++){ /* For that wave */
4169: m=mw[mi][iind];
4170: if(anyvaryingduminmodel==1){ /* Some are varying covariates */
4171: for (z1=1; z1<=cptcoveff; z1++) {
4172: if( Fixed[Tmodelind[z1]]==1){
4173: iv= Tvar[Tmodelind[z1]]-ncovcol-nqv;
4174: if (cotvar[m][iv][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]) /* iv=1 to ntv, right modality */
4175: bool=0;
4176: }else if( Fixed[Tmodelind[z1]]== 0) { /* fixed */
4177: if (covar[Tvaraff[z1]][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]) {
4178: bool=0;
4179: }
4180: }
4181: }
4182: }/* Some are varying covariates, we tried to speed up if all fixed covariates in the model, avoiding waves loop */
4183: /* bool =0 we keep that guy which corresponds to the combination of dummy values */
4184: if(bool==1){
4185: /* dh[m][iind] or dh[mw[mi][iind]][iind] is the delay between two effective (mi) waves m=mw[mi][iind]
4186: and mw[mi+1][iind]. dh depends on stepm. */
4187: agebegin=agev[m][iind]; /* Age at beginning of wave before transition*/
4188: ageend=agev[m][iind]+(dh[m][iind])*stepm/YEARM; /* Age at end of wave and transition */
4189: if(m >=firstpass && m <=lastpass){
4190: k2=anint[m][iind]+(mint[m][iind]/12.);
4191: /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
4192: if(agev[m][iind]==0) agev[m][iind]=iagemax+1; /* All ages equal to 0 are in iagemax+1 */
4193: if(agev[m][iind]==1) agev[m][iind]=iagemax+2; /* All ages equal to 1 are in iagemax+2 */
4194: if (s[m][iind]>0 && s[m][iind]<=nlstate) /* If status at wave m is known and a live state */
4195: prop[s[m][iind]][(int)agev[m][iind]] += weight[iind]; /* At age of beginning of transition, where status is known */
4196: if (m<lastpass) {
4197: /* if(s[m][iind]==4 && s[m+1][iind]==4) */
4198: /* printf(" num=%ld m=%d, iind=%d s1=%d s2=%d agev at m=%d\n", num[iind], m, iind,s[m][iind],s[m+1][iind], (int)agev[m][iind]); */
4199: if(s[m][iind]==-1)
4200: printf(" num=%ld m=%d, iind=%d s1=%d s2=%d agev at m=%d agebegin=%.2f ageend=%.2f, agemed=%d\n", num[iind], m, iind,s[m][iind],s[m+1][iind], (int)agev[m][iind],agebegin, ageend, (int)((agebegin+ageend)/2.));
4201: freq[s[m][iind]][s[m+1][iind]][(int)agev[m][iind]] += weight[iind]; /* At age of beginning of transition, where status is known */
4202: /* freq[s[m][iind]][s[m+1][iind]][(int)((agebegin+ageend)/2.)] += weight[iind]; */
4203: freq[s[m][iind]][s[m+1][iind]][iagemax+3] += weight[iind]; /* Total is in iagemax+3 *//* At age of beginning of transition, where status is known */
4204: }
4205: } /* end if between passes */
4206: if ((agev[m][iind]>1) && (agev[m][iind]< (iagemax+3)) && (anint[m][iind]!=9999) && (mint[m][iind]!=99)) {
4207: dateintsum=dateintsum+k2;
4208: k2cpt++;
4209: /* printf("iind=%ld dateintmean = %lf dateintsum=%lf k2cpt=%lf k2=%lf\n",iind, dateintsum/k2cpt, dateintsum,k2cpt, k2); */
4210: }
4211: } /* end bool 2 */
4212: } /* end m */
1.226 brouard 4213: } /* end bool */
4214: } /* end iind = 1 to imx */
4215: /* prop[s][age] is feeded for any initial and valid live state as well as
4216: freq[s1][s2][age] at single age of beginning the transition, for a combination j1 */
1.231 brouard 4217:
4218:
1.226 brouard 4219: /* fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
4220: pstamp(ficresp);
1.227 brouard 4221: /* if (ncoveff>0) { */
4222: if (cptcoveff>0) {
1.226 brouard 4223: fprintf(ficresp, "\n#********** Variable ");
4224: fprintf(ficresphtm, "\n<br/><br/><h3>********** Variable ");
4225: fprintf(ficresphtmfr, "\n<br/><br/><h3>********** Variable ");
1.227 brouard 4226: for (z1=1; z1<=cptcoveff; z1++){
1.234 brouard 4227: fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
4228: fprintf(ficresphtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
4229: fprintf(ficresphtmfr, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.226 brouard 4230: }
4231: fprintf(ficresp, "**********\n#");
4232: fprintf(ficresphtm, "**********</h3>\n");
4233: fprintf(ficresphtmfr, "**********</h3>\n");
4234: fprintf(ficlog, "\n#********** Variable ");
1.227 brouard 4235: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficlog, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.226 brouard 4236: fprintf(ficlog, "**********\n");
4237: }
4238: fprintf(ficresphtm,"<table style=\"text-align:center; border: 1px solid\">");
4239: for(i=1; i<=nlstate;i++) {
4240: fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
4241: fprintf(ficresphtm, "<th>Age</th><th>Prev(%d)</th><th>N(%d)</th><th>N</th>",i,i);
4242: }
4243: fprintf(ficresp, "\n");
4244: fprintf(ficresphtm, "\n");
1.231 brouard 4245:
1.226 brouard 4246: /* Header of frequency table by age */
4247: fprintf(ficresphtmfr,"<table style=\"text-align:center; border: 1px solid\">");
4248: fprintf(ficresphtmfr,"<th>Age</th> ");
4249: for(jk=-1; jk <=nlstate+ndeath; jk++){
4250: for(m=-1; m <=nlstate+ndeath; m++){
1.234 brouard 4251: if(jk!=0 && m!=0)
4252: fprintf(ficresphtmfr,"<th>%d%d</th> ",jk,m);
1.226 brouard 4253: }
4254: }
4255: fprintf(ficresphtmfr, "\n");
1.231 brouard 4256:
1.226 brouard 4257: /* For each age */
4258: for(iage=iagemin; iage <= iagemax+3; iage++){
4259: fprintf(ficresphtm,"<tr>");
4260: if(iage==iagemax+1){
1.231 brouard 4261: fprintf(ficlog,"1");
4262: fprintf(ficresphtmfr,"<tr><th>0</th> ");
1.226 brouard 4263: }else if(iage==iagemax+2){
1.231 brouard 4264: fprintf(ficlog,"0");
4265: fprintf(ficresphtmfr,"<tr><th>Unknown</th> ");
1.226 brouard 4266: }else if(iage==iagemax+3){
1.231 brouard 4267: fprintf(ficlog,"Total");
4268: fprintf(ficresphtmfr,"<tr><th>Total</th> ");
1.226 brouard 4269: }else{
1.231 brouard 4270: if(first==1){
4271: first=0;
4272: printf("See log file for details...\n");
4273: }
4274: fprintf(ficresphtmfr,"<tr><th>%d</th> ",iage);
4275: fprintf(ficlog,"Age %d", iage);
1.226 brouard 4276: }
4277: for(jk=1; jk <=nlstate ; jk++){
1.231 brouard 4278: for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
4279: pp[jk] += freq[jk][m][iage];
1.226 brouard 4280: }
4281: for(jk=1; jk <=nlstate ; jk++){
1.231 brouard 4282: for(m=-1, pos=0; m <=0 ; m++)
4283: pos += freq[jk][m][iage];
4284: if(pp[jk]>=1.e-10){
4285: if(first==1){
4286: printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
4287: }
4288: fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
4289: }else{
4290: if(first==1)
4291: printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
4292: fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
4293: }
1.226 brouard 4294: }
1.231 brouard 4295:
1.226 brouard 4296: for(jk=1; jk <=nlstate ; jk++){
1.231 brouard 4297: /* posprop[jk]=0; */
4298: for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)/* Summing on all ages */
4299: pp[jk] += freq[jk][m][iage];
1.226 brouard 4300: } /* pp[jk] is the total number of transitions starting from state jk and any ending status until this age */
1.231 brouard 4301:
1.226 brouard 4302: for(jk=1,pos=0, pospropta=0.; jk <=nlstate ; jk++){
1.231 brouard 4303: pos += pp[jk]; /* pos is the total number of transitions until this age */
4304: posprop[jk] += prop[jk][iage]; /* prop is the number of transitions from a live state
4305: from jk at age iage prop[s[m][iind]][(int)agev[m][iind]] += weight[iind] */
4306: pospropta += prop[jk][iage]; /* prop is the number of transitions from a live state
4307: from jk at age iage prop[s[m][iind]][(int)agev[m][iind]] += weight[iind] */
1.226 brouard 4308: }
4309: for(jk=1; jk <=nlstate ; jk++){
1.231 brouard 4310: if(pos>=1.e-5){
4311: if(first==1)
4312: printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
4313: fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
4314: }else{
4315: if(first==1)
4316: printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
4317: fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
4318: }
4319: if( iage <= iagemax){
4320: if(pos>=1.e-5){
4321: fprintf(ficresp," %d %.5f %.0f %.0f",iage,prop[jk][iage]/pospropta, prop[jk][iage],pospropta);
4322: fprintf(ficresphtm,"<th>%d</th><td>%.5f</td><td>%.0f</td><td>%.0f</td>",iage,prop[jk][iage]/pospropta, prop[jk][iage],pospropta);
4323: /*probs[iage][jk][j1]= pp[jk]/pos;*/
4324: /*printf("\niage=%d jk=%d j1=%d %.5f %.0f %.0f %f",iage,jk,j1,pp[jk]/pos, pp[jk],pos,probs[iage][jk][j1]);*/
4325: }
4326: else{
4327: fprintf(ficresp," %d NaNq %.0f %.0f",iage,prop[jk][iage],pospropta);
4328: fprintf(ficresphtm,"<th>%d</th><td>NaNq</td><td>%.0f</td><td>%.0f</td>",iage, prop[jk][iage],pospropta);
4329: }
4330: }
4331: pospropt[jk] +=posprop[jk];
1.226 brouard 4332: } /* end loop jk */
4333: /* pospropt=0.; */
4334: for(jk=-1; jk <=nlstate+ndeath; jk++){
1.231 brouard 4335: for(m=-1; m <=nlstate+ndeath; m++){
4336: if(freq[jk][m][iage] !=0 ) { /* minimizing output */
4337: if(first==1){
4338: printf(" %d%d=%.0f",jk,m,freq[jk][m][iage]);
4339: }
4340: fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][iage]);
4341: }
4342: if(jk!=0 && m!=0)
4343: fprintf(ficresphtmfr,"<td>%.0f</td> ",freq[jk][m][iage]);
4344: }
1.226 brouard 4345: } /* end loop jk */
4346: posproptt=0.;
4347: for(jk=1; jk <=nlstate; jk++){
1.231 brouard 4348: posproptt += pospropt[jk];
1.226 brouard 4349: }
4350: fprintf(ficresphtmfr,"</tr>\n ");
4351: if(iage <= iagemax){
1.231 brouard 4352: fprintf(ficresp,"\n");
4353: fprintf(ficresphtm,"</tr>\n");
1.226 brouard 4354: }
4355: if(first==1)
1.231 brouard 4356: printf("Others in log...\n");
1.226 brouard 4357: fprintf(ficlog,"\n");
4358: } /* end loop age iage */
4359: fprintf(ficresphtm,"<tr><th>Tot</th>");
4360: for(jk=1; jk <=nlstate ; jk++){
4361: if(posproptt < 1.e-5){
1.231 brouard 4362: fprintf(ficresphtm,"<td>Nanq</td><td>%.0f</td><td>%.0f</td>",pospropt[jk],posproptt);
1.226 brouard 4363: }else{
1.231 brouard 4364: fprintf(ficresphtm,"<td>%.5f</td><td>%.0f</td><td>%.0f</td>",pospropt[jk]/posproptt,pospropt[jk],posproptt);
1.226 brouard 4365: }
4366: }
4367: fprintf(ficresphtm,"</tr>\n");
4368: fprintf(ficresphtm,"</table>\n");
4369: fprintf(ficresphtmfr,"</table>\n");
4370: if(posproptt < 1.e-5){
4371: fprintf(ficresphtm,"\n <p><b> This combination (%d) is not valid and no result will be produced</b></p>",j1);
4372: fprintf(ficresphtmfr,"\n <p><b> This combination (%d) is not valid and no result will be produced</b></p>",j1);
4373: fprintf(ficres,"\n This combination (%d) is not valid and no result will be produced\n\n",j1);
4374: invalidvarcomb[j1]=1;
4375: }else{
4376: fprintf(ficresphtm,"\n <p> This combination (%d) is valid and result will be produced.</p>",j1);
4377: invalidvarcomb[j1]=0;
4378: }
4379: fprintf(ficresphtmfr,"</table>\n");
4380: } /* end selected combination of covariate j1 */
4381: dateintmean=dateintsum/k2cpt;
1.231 brouard 4382:
1.226 brouard 4383: fclose(ficresp);
4384: fclose(ficresphtm);
4385: fclose(ficresphtmfr);
4386: free_vector(meanq,1,nqfveff);
4387: free_matrix(meanqt,1,lastpass,1,nqtveff);
4388: free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin-AGEMARGE, iagemax+3+AGEMARGE);
4389: free_vector(pospropt,1,nlstate);
4390: free_vector(posprop,1,nlstate);
4391: free_matrix(prop,1,nlstate,iagemin-AGEMARGE, iagemax+3+AGEMARGE);
4392: free_vector(pp,1,nlstate);
4393: /* End of freqsummary */
4394: }
1.126 brouard 4395:
4396: /************ Prevalence ********************/
1.227 brouard 4397: 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)
4398: {
4399: /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
4400: in each health status at the date of interview (if between dateprev1 and dateprev2).
4401: We still use firstpass and lastpass as another selection.
4402: */
1.126 brouard 4403:
1.227 brouard 4404: int i, m, jk, j1, bool, z1,j, iv;
4405: int mi; /* Effective wave */
4406: int iage;
4407: double agebegin, ageend;
4408:
4409: double **prop;
4410: double posprop;
4411: double y2; /* in fractional years */
4412: int iagemin, iagemax;
4413: int first; /** to stop verbosity which is redirected to log file */
4414:
4415: iagemin= (int) agemin;
4416: iagemax= (int) agemax;
4417: /*pp=vector(1,nlstate);*/
4418: prop=matrix(1,nlstate,iagemin-AGEMARGE,iagemax+3+AGEMARGE);
4419: /* freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
4420: j1=0;
1.222 brouard 4421:
1.227 brouard 4422: /*j=cptcoveff;*/
4423: if (cptcovn<1) {j=1;ncodemax[1]=1;}
1.222 brouard 4424:
1.227 brouard 4425: first=1;
4426: for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){ /* For each combination of covariate */
4427: for (i=1; i<=nlstate; i++)
4428: for(iage=iagemin-AGEMARGE; iage <= iagemax+3+AGEMARGE; iage++)
4429: prop[i][iage]=0.0;
4430: printf("Prevalence combination of varying and fixed dummies %d\n",j1);
4431: /* fprintf(ficlog," V%d=%d ",Tvaraff[j1],nbcode[Tvaraff[j1]][codtabm(k,j1)]); */
4432: fprintf(ficlog,"Prevalence combination of varying and fixed dummies %d\n",j1);
4433:
4434: for (i=1; i<=imx; i++) { /* Each individual */
4435: bool=1;
4436: /* for(m=firstpass; m<=lastpass; m++){/\* Other selection (we can limit to certain interviews*\/ */
4437: for(mi=1; mi<wav[i];mi++){ /* For this wave too look where individual can be counted V4=0 V3=0 */
4438: m=mw[mi][i];
4439: /* Tmodelind[z1]=k is the position of the varying covariate in the model, but which # within 1 to ntv? */
4440: /* Tvar[Tmodelind[z1]] is the n of Vn; n-ncovcol-nqv is the first time varying covariate or iv */
4441: for (z1=1; z1<=cptcoveff; z1++){
4442: if( Fixed[Tmodelind[z1]]==1){
4443: iv= Tvar[Tmodelind[z1]]-ncovcol-nqv;
4444: if (cotvar[m][iv][i]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]) /* iv=1 to ntv, right modality */
4445: bool=0;
4446: }else if( Fixed[Tmodelind[z1]]== 0) /* fixed */
4447: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]) {
4448: bool=0;
4449: }
4450: }
4451: if(bool==1){ /* Otherwise we skip that wave/person */
4452: agebegin=agev[m][i]; /* Age at beginning of wave before transition*/
4453: /* ageend=agev[m][i]+(dh[m][i])*stepm/YEARM; /\* Age at end of wave and transition *\/ */
4454: if(m >=firstpass && m <=lastpass){
4455: y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
4456: if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
4457: if(agev[m][i]==0) agev[m][i]=iagemax+1;
4458: if(agev[m][i]==1) agev[m][i]=iagemax+2;
4459: if((int)agev[m][i] <iagemin-AGEMARGE || (int)agev[m][i] >iagemax+3+AGEMARGE){
4460: printf("Error on individual # %d agev[m][i]=%f <%d-%d or > %d+3+%d m=%d; either change agemin or agemax or fix data\n",i, agev[m][i],iagemin,AGEMARGE, iagemax,AGEMARGE,m);
4461: exit(1);
4462: }
4463: if (s[m][i]>0 && s[m][i]<=nlstate) {
4464: /*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]]);*/
4465: prop[s[m][i]][(int)agev[m][i]] += weight[i];/* At age of beginning of transition, where status is known */
4466: prop[s[m][i]][iagemax+3] += weight[i];
4467: } /* end valid statuses */
4468: } /* end selection of dates */
4469: } /* end selection of waves */
4470: } /* end bool */
4471: } /* end wave */
4472: } /* end individual */
4473: for(i=iagemin; i <= iagemax+3; i++){
4474: for(jk=1,posprop=0; jk <=nlstate ; jk++) {
4475: posprop += prop[jk][i];
4476: }
4477:
4478: for(jk=1; jk <=nlstate ; jk++){
4479: if( i <= iagemax){
4480: if(posprop>=1.e-5){
4481: probs[i][jk][j1]= prop[jk][i]/posprop;
4482: } else{
4483: if(first==1){
4484: first=0;
4485: printf("Warning Observed prevalence probs[%d][%d][%d]=%lf because of lack of cases\nSee others in log file...\n",jk,i,j1,probs[i][jk][j1]);
4486: }
4487: }
4488: }
4489: }/* end jk */
4490: }/* end i */
1.222 brouard 4491: /*} *//* end i1 */
1.227 brouard 4492: } /* end j1 */
1.222 brouard 4493:
1.227 brouard 4494: /* free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
4495: /*free_vector(pp,1,nlstate);*/
4496: free_matrix(prop,1,nlstate, iagemin-AGEMARGE,iagemax+3+AGEMARGE);
4497: } /* End of prevalence */
1.126 brouard 4498:
4499: /************* Waves Concatenation ***************/
4500:
4501: 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)
4502: {
4503: /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
4504: Death is a valid wave (if date is known).
4505: mw[mi][i] is the mi (mi=1 to wav[i]) effective wave of individual i
4506: dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
4507: and mw[mi+1][i]. dh depends on stepm.
1.227 brouard 4508: */
1.126 brouard 4509:
1.224 brouard 4510: int i=0, mi=0, m=0, mli=0;
1.126 brouard 4511: /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
4512: double sum=0., jmean=0.;*/
1.224 brouard 4513: int first=0, firstwo=0, firsthree=0, firstfour=0, firstfiv=0;
1.126 brouard 4514: int j, k=0,jk, ju, jl;
4515: double sum=0.;
4516: first=0;
1.214 brouard 4517: firstwo=0;
1.217 brouard 4518: firsthree=0;
1.218 brouard 4519: firstfour=0;
1.164 brouard 4520: jmin=100000;
1.126 brouard 4521: jmax=-1;
4522: jmean=0.;
1.224 brouard 4523:
4524: /* Treating live states */
1.214 brouard 4525: for(i=1; i<=imx; i++){ /* For simple cases and if state is death */
1.224 brouard 4526: mi=0; /* First valid wave */
1.227 brouard 4527: mli=0; /* Last valid wave */
1.126 brouard 4528: m=firstpass;
1.214 brouard 4529: while(s[m][i] <= nlstate){ /* a live state */
1.227 brouard 4530: if(m >firstpass && s[m][i]==s[m-1][i] && mint[m][i]==mint[m-1][i] && anint[m][i]==anint[m-1][i]){/* Two succesive identical information on wave m */
4531: mli=m-1;/* mw[++mi][i]=m-1; */
4532: }else if(s[m][i]>=1 || s[m][i]==-4 || s[m][i]==-5){ /* Since 0.98r4 if status=-2 vital status is really unknown, wave should be skipped */
4533: mw[++mi][i]=m;
4534: mli=m;
1.224 brouard 4535: } /* else might be a useless wave -1 and mi is not incremented and mw[mi] not updated */
4536: if(m < lastpass){ /* m < lastpass, standard case */
1.227 brouard 4537: m++; /* mi gives the "effective" current wave, m the current wave, go to next wave by incrementing m */
1.216 brouard 4538: }
1.227 brouard 4539: else{ /* m >= lastpass, eventual special issue with warning */
1.224 brouard 4540: #ifdef UNKNOWNSTATUSNOTCONTRIBUTING
1.227 brouard 4541: break;
1.224 brouard 4542: #else
1.227 brouard 4543: if(s[m][i]==-1 && (int) andc[i] == 9999 && (int)anint[m][i] != 9999){
4544: if(firsthree == 0){
4545: printf("Information! Unknown status for individual %ld line=%d occurred at last wave %d at known date %d/%d. Please, check if your unknown date of death %d/%d means a live state %d at wave %d. This case(%d)/wave(%d) contributes to the likelihood as pi. .\nOthers in log file only\n",num[i],i,lastpass,(int)mint[m][i],(int)anint[m][i], (int) moisdc[i], (int) andc[i], s[m][i], m, i, m);
4546: firsthree=1;
4547: }
4548: fprintf(ficlog,"Information! Unknown status for individual %ld line=%d occurred at last wave %d at known date %d/%d. Please, check if your unknown date of death %d/%d means a live state %d at wave %d. This case(%d)/wave(%d) contributes to the likelihood as pi. .\n",num[i],i,lastpass,(int)mint[m][i],(int)anint[m][i], (int) moisdc[i], (int) andc[i], s[m][i], m, i, m);
4549: mw[++mi][i]=m;
4550: mli=m;
4551: }
4552: if(s[m][i]==-2){ /* Vital status is really unknown */
4553: nbwarn++;
4554: if((int)anint[m][i] == 9999){ /* Has the vital status really been verified? */
4555: printf("Warning! Vital status for individual %ld (line=%d) at last wave %d interviewed at date %d/%d is unknown %d. Please, check if the vital status and the date of death %d/%d are really unknown. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\nOthers in log file only\n",num[i],i,lastpass,(int)mint[m][i],(int)anint[m][i], s[m][i], (int) moisdc[i], (int) andc[i], i, m);
4556: fprintf(ficlog,"Warning! Vital status for individual %ld (line=%d) at last wave %d interviewed at date %d/%d is unknown %d. Please, check if the vital status and the date of death %d/%d are really unknown. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\n",num[i],i,lastpass,(int)mint[m][i],(int)anint[m][i], s[m][i], (int) moisdc[i], (int) andc[i], i, m);
4557: }
4558: break;
4559: }
4560: break;
1.224 brouard 4561: #endif
1.227 brouard 4562: }/* End m >= lastpass */
1.126 brouard 4563: }/* end while */
1.224 brouard 4564:
1.227 brouard 4565: /* mi is the last effective wave, m is lastpass, mw[j][i] gives the # of j-th effective wave for individual i */
1.216 brouard 4566: /* After last pass */
1.224 brouard 4567: /* Treating death states */
1.214 brouard 4568: if (s[m][i] > nlstate){ /* In a death state */
1.227 brouard 4569: /* if( mint[m][i]==mdc[m][i] && anint[m][i]==andc[m][i]){ /\* same date of death and date of interview *\/ */
4570: /* } */
1.126 brouard 4571: mi++; /* Death is another wave */
4572: /* if(mi==0) never been interviewed correctly before death */
1.227 brouard 4573: /* Only death is a correct wave */
1.126 brouard 4574: mw[mi][i]=m;
1.224 brouard 4575: }
4576: #ifndef DISPATCHINGKNOWNDEATHAFTERLASTWAVE
1.227 brouard 4577: else if ((int) andc[i] != 9999) { /* Status is negative. A death occured after lastpass, we can't take it into account because of potential bias */
1.216 brouard 4578: /* m++; */
4579: /* mi++; */
4580: /* s[m][i]=nlstate+1; /\* We are setting the status to the last of non live state *\/ */
4581: /* mw[mi][i]=m; */
1.218 brouard 4582: if ((int)anint[m][i]!= 9999) { /* date of last interview is known */
1.227 brouard 4583: if((andc[i]+moisdc[i]/12.) <=(anint[m][i]+mint[m][i]/12.)){ /* death occured before last wave and status should have been death instead of -1 */
4584: nbwarn++;
4585: if(firstfiv==0){
4586: printf("Warning! Death for individual %ld line=%d occurred at %d/%d before last wave %d interviewed at %d/%d and should have been coded as death instead of '%d'. This case (%d)/wave (%d) is contributing to likelihood.\nOthers in log file only\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], s[m][i], i,m );
4587: firstfiv=1;
4588: }else{
4589: fprintf(ficlog,"Warning! Death for individual %ld line=%d occurred at %d/%d before last wave %d interviewed at %d/%d and should have been coded as death instead of '%d'. This case (%d)/wave (%d) is contributing to likelihood.\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], s[m][i], i,m );
4590: }
4591: }else{ /* Death occured afer last wave potential bias */
4592: nberr++;
4593: if(firstwo==0){
4594: printf("Error! Death for individual %ld line=%d occurred at %d/%d after last wave %d interviewed at %d/%d. Potential bias if other individuals are still alive at this date but ignored. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\nOthers in log file only\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], i,m );
4595: firstwo=1;
4596: }
4597: fprintf(ficlog,"Error! Death for individual %ld line=%d occurred at %d/%d after last wave %d interviewed at %d/%d. Potential bias if other individuals are still alive at this date but ignored. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], i,m );
4598: }
1.218 brouard 4599: }else{ /* end date of interview is known */
1.227 brouard 4600: /* death is known but not confirmed by death status at any wave */
4601: if(firstfour==0){
4602: printf("Error! Death for individual %ld line=%d occurred %d/%d but not confirmed by any death status for any wave, including last wave %d at unknown date %d/%d. Potential bias if other individuals are still alive at this date but ignored. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\nOthers in log file only\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], i,m );
4603: firstfour=1;
4604: }
4605: fprintf(ficlog,"Error! Death for individual %ld line=%d occurred %d/%d but not confirmed by any death status for any wave, including last wave %d at unknown date %d/%d. Potential bias if other individuals are still alive at this date but ignored. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], i,m );
1.214 brouard 4606: }
1.224 brouard 4607: } /* end if date of death is known */
4608: #endif
4609: wav[i]=mi; /* mi should be the last effective wave (or mli) */
4610: /* wav[i]=mw[mi][i]; */
1.126 brouard 4611: if(mi==0){
4612: nbwarn++;
4613: if(first==0){
1.227 brouard 4614: printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
4615: first=1;
1.126 brouard 4616: }
4617: if(first==1){
1.227 brouard 4618: fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
1.126 brouard 4619: }
4620: } /* end mi==0 */
4621: } /* End individuals */
1.214 brouard 4622: /* wav and mw are no more changed */
1.223 brouard 4623:
1.214 brouard 4624:
1.126 brouard 4625: for(i=1; i<=imx; i++){
4626: for(mi=1; mi<wav[i];mi++){
4627: if (stepm <=0)
1.227 brouard 4628: dh[mi][i]=1;
1.126 brouard 4629: else{
1.227 brouard 4630: if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
4631: if (agedc[i] < 2*AGESUP) {
4632: j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);
4633: if(j==0) j=1; /* Survives at least one month after exam */
4634: else if(j<0){
4635: nberr++;
4636: 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]);
4637: j=1; /* Temporary Dangerous patch */
4638: 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);
4639: 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]);
4640: 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);
4641: }
4642: k=k+1;
4643: if (j >= jmax){
4644: jmax=j;
4645: ijmax=i;
4646: }
4647: if (j <= jmin){
4648: jmin=j;
4649: ijmin=i;
4650: }
4651: sum=sum+j;
4652: /*if (j<0) printf("j=%d num=%d \n",j,i);*/
4653: /* printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
4654: }
4655: }
4656: else{
4657: j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
1.126 brouard 4658: /* 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]); */
1.223 brouard 4659:
1.227 brouard 4660: k=k+1;
4661: if (j >= jmax) {
4662: jmax=j;
4663: ijmax=i;
4664: }
4665: else if (j <= jmin){
4666: jmin=j;
4667: ijmin=i;
4668: }
4669: /* if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
4670: /*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]);*/
4671: if(j<0){
4672: nberr++;
4673: 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]);
4674: 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]);
4675: }
4676: sum=sum+j;
4677: }
4678: jk= j/stepm;
4679: jl= j -jk*stepm;
4680: ju= j -(jk+1)*stepm;
4681: if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
4682: if(jl==0){
4683: dh[mi][i]=jk;
4684: bh[mi][i]=0;
4685: }else{ /* We want a negative bias in order to only have interpolation ie
4686: * to avoid the price of an extra matrix product in likelihood */
4687: dh[mi][i]=jk+1;
4688: bh[mi][i]=ju;
4689: }
4690: }else{
4691: if(jl <= -ju){
4692: dh[mi][i]=jk;
4693: bh[mi][i]=jl; /* bias is positive if real duration
4694: * is higher than the multiple of stepm and negative otherwise.
4695: */
4696: }
4697: else{
4698: dh[mi][i]=jk+1;
4699: bh[mi][i]=ju;
4700: }
4701: if(dh[mi][i]==0){
4702: dh[mi][i]=1; /* At least one step */
4703: bh[mi][i]=ju; /* At least one step */
4704: /* 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);*/
4705: }
4706: } /* end if mle */
1.126 brouard 4707: }
4708: } /* end wave */
4709: }
4710: jmean=sum/k;
4711: 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 4712: 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);
1.227 brouard 4713: }
1.126 brouard 4714:
4715: /*********** Tricode ****************************/
1.220 brouard 4716: void tricode(int *cptcov, int *Tvar, int **nbcode, int imx, int *Ndum)
1.126 brouard 4717: {
1.144 brouard 4718: /**< Uses cptcovn+2*cptcovprod as the number of covariates */
4719: /* 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 4720: * Boring subroutine which should only output nbcode[Tvar[j]][k]
1.224 brouard 4721: * Tvar[5] in V2+V1+V3*age+V2*V4 is 4 (V4) even it is a time varying or quantitative variable
4722: * nbcode[Tvar[5]][1]= nbcode[4][1]=0, nbcode[4][2]=1 (usually);
1.144 brouard 4723: */
1.130 brouard 4724:
1.145 brouard 4725: int ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
1.136 brouard 4726: int modmaxcovj=0; /* Modality max of covariates j */
1.145 brouard 4727: int cptcode=0; /* Modality max of covariates j */
4728: int modmincovj=0; /* Modality min of covariates j */
4729:
4730:
1.220 brouard 4731: /* cptcoveff=0; */
1.224 brouard 4732: /* *cptcov=0; */
1.126 brouard 4733:
1.144 brouard 4734: for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */
1.126 brouard 4735:
1.224 brouard 4736: /* Loop on covariates without age and products and no quantitative variable */
4737: /* for (j=1; j<=(cptcovs); j++) { /\* From model V1 + V2*age+ V3 + V3*V4 keeps V1 + V3 = 2 only *\/ */
1.227 brouard 4738: for (k=1; k<=cptcovt; k++) { /* From model V1 + V2*age + V3 + V3*V4 keeps V1 + V3 = 2 only */
4739: for (j=-1; (j < maxncov); j++) Ndum[j]=0;
4740: if(Dummy[k]==0 && Typevar[k] !=1){ /* Dummy covariate and not age product */
4741: switch(Fixed[k]) {
4742: case 0: /* Testing on fixed dummy covariate, simple or product of fixed */
1.231 brouard 4743: for (i=1; i<=imx; i++) { /* Loop on individuals: reads the data file to get the maximum value of the modality of this covariate Vj*/
4744: ij=(int)(covar[Tvar[k]][i]);
4745: /* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i
4746: * If product of Vn*Vm, still boolean *:
4747: * If it was coded 1, 2, 3, 4 should be splitted into 3 boolean variables
4748: * 1 => 0 0 0, 2 => 0 0 1, 3 => 0 1 1, 4=1 0 0 */
4749: /* Finds for covariate j, n=Tvar[j] of Vn . ij is the
4750: modality of the nth covariate of individual i. */
4751: if (ij > modmaxcovj)
4752: modmaxcovj=ij;
4753: else if (ij < modmincovj)
4754: modmincovj=ij;
4755: if ((ij < -1) && (ij > NCOVMAX)){
4756: printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX );
4757: exit(1);
4758: }else
4759: Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/
4760: /* If coded 1, 2, 3 , counts the number of 1 Ndum[1], number of 2, Ndum[2], etc */
4761: /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
4762: /* getting the maximum value of the modality of the covariate
4763: (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and
4764: female ies 1, then modmaxcovj=1.
4765: */
4766: } /* end for loop on individuals i */
4767: printf(" Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", k, Tvar[k], modmincovj, modmaxcovj);
4768: fprintf(ficlog," Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", k, Tvar[k], modmincovj, modmaxcovj);
4769: cptcode=modmaxcovj;
4770: /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */
4771: /*for (i=0; i<=cptcode; i++) {*/
4772: for (j=modmincovj; j<=modmaxcovj; j++) { /* j=-1 ? 0 and 1*//* For each value j of the modality of model-cov k */
4773: printf("Frequencies of covariates %d ie V%d with value %d: %d\n", k, Tvar[k], j, Ndum[j]);
4774: fprintf(ficlog, "Frequencies of covariates %d ie V%d with value %d: %d\n", k, Tvar[k], j, Ndum[j]);
4775: if( Ndum[j] != 0 ){ /* Counts if nobody answered modality j ie empty modality, we skip it and reorder */
4776: if( j != -1){
4777: ncodemax[k]++; /* ncodemax[k]= Number of modalities of the k th
4778: covariate for which somebody answered excluding
4779: undefined. Usually 2: 0 and 1. */
4780: }
4781: ncodemaxwundef[k]++; /* ncodemax[j]= Number of modalities of the k th
4782: covariate for which somebody answered including
4783: undefined. Usually 3: -1, 0 and 1. */
4784: } /* In fact ncodemax[k]=2 (dichotom. variables only) but it could be more for
4785: * historical reasons: 3 if coded 1, 2, 3 and 4 and Ndum[2]=0 */
4786: } /* Ndum[-1] number of undefined modalities */
4787:
4788: /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */
4789: /* For covariate j, modalities could be 1, 2, 3, 4, 5, 6, 7. */
4790: /* If Ndum[1]=0, Ndum[2]=0, Ndum[3]= 635, Ndum[4]=0, Ndum[5]=0, Ndum[6]=27, Ndum[7]=125; */
4791: /* modmincovj=3; modmaxcovj = 7; */
4792: /* There are only 3 modalities non empty 3, 6, 7 (or 2 if 27 is too few) : ncodemax[j]=3; */
4793: /* which will be coded 0, 1, 2 which in binary on 2=3-1 digits are 0=00 1=01, 2=10; */
4794: /* defining two dummy variables: variables V1_1 and V1_2.*/
4795: /* nbcode[Tvar[j]][ij]=k; */
4796: /* nbcode[Tvar[j]][1]=0; */
4797: /* nbcode[Tvar[j]][2]=1; */
4798: /* nbcode[Tvar[j]][3]=2; */
4799: /* To be continued (not working yet). */
4800: ij=0; /* ij is similar to i but can jump over null modalities */
4801: 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*/
4802: if (Ndum[i] == 0) { /* If nobody responded to this modality k */
4803: break;
4804: }
4805: ij++;
4806: nbcode[Tvar[k]][ij]=i; /* stores the original value of modality i in an array nbcode, ij modality from 1 to last non-nul modality. nbcode[1][1]=0 nbcode[1][2]=1*/
4807: cptcode = ij; /* New max modality for covar j */
4808: } /* end of loop on modality i=-1 to 1 or more */
4809: break;
1.227 brouard 4810: case 1: /* Testing on varying covariate, could be simple and
4811: * should look at waves or product of fixed *
4812: * varying. No time to test -1, assuming 0 and 1 only */
1.231 brouard 4813: ij=0;
4814: for(i=0; i<=1;i++){
4815: nbcode[Tvar[k]][++ij]=i;
4816: }
4817: break;
1.227 brouard 4818: default:
1.231 brouard 4819: break;
1.227 brouard 4820: } /* end switch */
4821: } /* end dummy test */
1.225 brouard 4822:
1.192 brouard 4823: /* for (k=0; k<= cptcode; k++) { /\* k=-1 ? k=0 to 1 *\//\* Could be 1 to 4 *\//\* cptcode=modmaxcovj *\/ */
4824: /* /\*recode from 0 *\/ */
4825: /* k is a modality. If we have model=V1+V1*sex */
4826: /* then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
4827: /* But if some modality were not used, it is recoded from 0 to a newer modmaxcovj=cptcode *\/ */
4828: /* } */
4829: /* /\* cptcode = ij; *\/ /\* New max modality for covar j *\/ */
4830: /* if (ij > ncodemax[j]) { */
4831: /* printf( " Error ij=%d > ncodemax[%d]=%d\n", ij, j, ncodemax[j]); */
4832: /* fprintf(ficlog, " Error ij=%d > ncodemax[%d]=%d\n", ij, j, ncodemax[j]); */
4833: /* break; */
4834: /* } */
4835: /* } /\* end of loop on modality k *\/ */
1.137 brouard 4836: } /* end of loop on model-covariate j. nbcode[Tvarj][1]=0 and nbcode[Tvarj][2]=1 sets the value of covariate j*/
4837:
1.225 brouard 4838: for (k=-1; k< maxncov; k++) Ndum[k]=0;
1.227 brouard 4839: /* Look at fixed dummy (single or product) covariates to check empty modalities */
1.187 brouard 4840: for (i=1; i<=ncovmodel-2-nagesqr; i++) { /* -2, cste and age and eventually age*age */
1.225 brouard 4841: /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
1.227 brouard 4842: ij=Tvar[i]; /* Tvar 5,4,3,6,5,7,1,4 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V4*age */
4843: Ndum[ij]++; /* Count the # of 1, 2 etc: {1,1,1,2,2,1,1} because V1 once, V2 once, two V4 and V5 in above */
4844: /* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, {2, 1, 1, 1, 2, 1, 1, 0, 0} */
1.225 brouard 4845: } /* V4+V3+V5, Ndum[1]@5={0, 0, 1, 1, 1} */
4846:
4847: ij=0;
1.227 brouard 4848: /* for (i=0; i<= maxncov-1; i++) { /\* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) *\/ */
4849: for (k=1; k<= cptcovt; k++) { /* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) */
1.225 brouard 4850: /*printf("Ndum[%d]=%d\n",i, Ndum[i]);*/
1.227 brouard 4851: /* if((Ndum[i]!=0) && (i<=ncovcol)){ /\* Tvar[i] <= ncovmodel ? *\/ */
4852: if(Ndum[Tvar[k]]!=0 && Dummy[k] == 0 && Typevar[k]==0){ /* Only Dummy and non empty in the model */
4853: /* If product not in single variable we don't print results */
1.225 brouard 4854: /*printf("diff Ndum[%d]=%d\n",i, Ndum[i]);*/
1.230 brouard 4855: ++ij;/* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, */
4856: Tvaraff[ij]=Tvar[k]; /* For printing combination *//* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, Tvar {5, 4, 3, 6, 5, 2, 7, 1, 1} Tvaraff={4, 3, 1} V4, V3, V1*/
4857: Tmodelind[ij]=k; /* Tmodelind: index in model of dummies Tmodelind[1]=2 V4: pos=2; V3: pos=3, V1=9 {2, 3, 9, ?, ?,} */
1.231 brouard 4858: TmodelInvind[ij]=Tvar[k]- ncovcol-nqv; /* Inverse TmodelInvind[2=V4]=2 second dummy varying cov (V4)4-1-1 {0, 2, 1, } TmodelInvind[3]=1 */
1.227 brouard 4859: if(Fixed[k]!=0)
4860: anyvaryingduminmodel=1;
1.231 brouard 4861: /* }else if((Ndum[i]!=0) && (i<=ncovcol+nqv)){ */
4862: /* Tvaraff[++ij]=-10; /\* Dont'n know how to treat quantitative variables yet *\/ */
4863: /* }else if((Ndum[i]!=0) && (i<=ncovcol+nqv+ntv)){ */
4864: /* Tvaraff[++ij]=i; /\*For printing (unclear) *\/ */
4865: /* }else if((Ndum[i]!=0) && (i<=ncovcol+nqv+ntv+nqtv)){ */
4866: /* Tvaraff[++ij]=-20; /\* Dont'n know how to treat quantitative variables yet *\/ */
1.227 brouard 4867: }
1.225 brouard 4868: } /* Tvaraff[1]@5 {3, 4, -20, 0, 0} Very strange */
4869: /* ij--; */
4870: /* cptcoveff=ij; /\*Number of total covariates*\/ */
4871: *cptcov=ij; /*Number of total real effective covariates: effective
1.231 brouard 4872: * because they can be excluded from the model and real
4873: * if in the model but excluded because missing values, but how to get k from ij?*/
1.227 brouard 4874: for(j=ij+1; j<= cptcovt; j++){
4875: Tvaraff[j]=0;
4876: Tmodelind[j]=0;
4877: }
1.228 brouard 4878: for(j=ntveff+1; j<= cptcovt; j++){
4879: TmodelInvind[j]=0;
4880: }
1.227 brouard 4881: /* To be sorted */
4882: ;
1.126 brouard 4883: }
4884:
1.145 brouard 4885:
1.126 brouard 4886: /*********** Health Expectancies ****************/
4887:
1.235 ! brouard 4888: void evsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,char strstart[], int nres )
1.126 brouard 4889:
4890: {
4891: /* Health expectancies, no variances */
1.164 brouard 4892: int i, j, nhstepm, hstepm, h, nstepm;
1.126 brouard 4893: int nhstepma, nstepma; /* Decreasing with age */
4894: double age, agelim, hf;
4895: double ***p3mat;
4896: double eip;
4897:
4898: pstamp(ficreseij);
4899: fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
4900: fprintf(ficreseij,"# Age");
4901: for(i=1; i<=nlstate;i++){
4902: for(j=1; j<=nlstate;j++){
4903: fprintf(ficreseij," e%1d%1d ",i,j);
4904: }
4905: fprintf(ficreseij," e%1d. ",i);
4906: }
4907: fprintf(ficreseij,"\n");
4908:
4909:
4910: if(estepm < stepm){
4911: printf ("Problem %d lower than %d\n",estepm, stepm);
4912: }
4913: else hstepm=estepm;
4914: /* We compute the life expectancy from trapezoids spaced every estepm months
4915: * This is mainly to measure the difference between two models: for example
4916: * if stepm=24 months pijx are given only every 2 years and by summing them
4917: * we are calculating an estimate of the Life Expectancy assuming a linear
4918: * progression in between and thus overestimating or underestimating according
4919: * to the curvature of the survival function. If, for the same date, we
4920: * estimate the model with stepm=1 month, we can keep estepm to 24 months
4921: * to compare the new estimate of Life expectancy with the same linear
4922: * hypothesis. A more precise result, taking into account a more precise
4923: * curvature will be obtained if estepm is as small as stepm. */
4924:
4925: /* For example we decided to compute the life expectancy with the smallest unit */
4926: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
4927: nhstepm is the number of hstepm from age to agelim
4928: nstepm is the number of stepm from age to agelin.
4929: Look at hpijx to understand the reason of that which relies in memory size
4930: and note for a fixed period like estepm months */
4931: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
4932: survival function given by stepm (the optimization length). Unfortunately it
4933: means that if the survival funtion is printed only each two years of age and if
4934: you sum them up and add 1 year (area under the trapezoids) you won't get the same
4935: results. So we changed our mind and took the option of the best precision.
4936: */
4937: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
4938:
4939: agelim=AGESUP;
4940: /* If stepm=6 months */
4941: /* Computed by stepm unit matrices, product of hstepm matrices, stored
4942: in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
4943:
4944: /* nhstepm age range expressed in number of stepm */
4945: nstepm=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
4946: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
4947: /* if (stepm >= YEARM) hstepm=1;*/
4948: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
4949: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4950:
4951: for (age=bage; age<=fage; age ++){
4952: nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
4953: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
4954: /* if (stepm >= YEARM) hstepm=1;*/
4955: nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
4956:
4957: /* If stepm=6 months */
4958: /* Computed by stepm unit matrices, product of hstepma matrices, stored
4959: in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
4960:
1.235 ! brouard 4961: hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij, nres);
1.126 brouard 4962:
4963: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
4964:
4965: printf("%d|",(int)age);fflush(stdout);
4966: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
4967:
4968: /* Computing expectancies */
4969: for(i=1; i<=nlstate;i++)
4970: for(j=1; j<=nlstate;j++)
4971: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
4972: eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
4973:
4974: /* 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]);*/
4975:
4976: }
4977:
4978: fprintf(ficreseij,"%3.0f",age );
4979: for(i=1; i<=nlstate;i++){
4980: eip=0;
4981: for(j=1; j<=nlstate;j++){
4982: eip +=eij[i][j][(int)age];
4983: fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
4984: }
4985: fprintf(ficreseij,"%9.4f", eip );
4986: }
4987: fprintf(ficreseij,"\n");
4988:
4989: }
4990: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4991: printf("\n");
4992: fprintf(ficlog,"\n");
4993:
4994: }
4995:
1.235 ! brouard 4996: 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[], int nres )
1.126 brouard 4997:
4998: {
4999: /* Covariances of health expectancies eij and of total life expectancies according
1.222 brouard 5000: to initial status i, ei. .
1.126 brouard 5001: */
5002: int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
5003: int nhstepma, nstepma; /* Decreasing with age */
5004: double age, agelim, hf;
5005: double ***p3matp, ***p3matm, ***varhe;
5006: double **dnewm,**doldm;
5007: double *xp, *xm;
5008: double **gp, **gm;
5009: double ***gradg, ***trgradg;
5010: int theta;
5011:
5012: double eip, vip;
5013:
5014: varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
5015: xp=vector(1,npar);
5016: xm=vector(1,npar);
5017: dnewm=matrix(1,nlstate*nlstate,1,npar);
5018: doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
5019:
5020: pstamp(ficresstdeij);
5021: fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
5022: fprintf(ficresstdeij,"# Age");
5023: for(i=1; i<=nlstate;i++){
5024: for(j=1; j<=nlstate;j++)
5025: fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
5026: fprintf(ficresstdeij," e%1d. ",i);
5027: }
5028: fprintf(ficresstdeij,"\n");
5029:
5030: pstamp(ficrescveij);
5031: fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
5032: fprintf(ficrescveij,"# Age");
5033: for(i=1; i<=nlstate;i++)
5034: for(j=1; j<=nlstate;j++){
5035: cptj= (j-1)*nlstate+i;
5036: for(i2=1; i2<=nlstate;i2++)
5037: for(j2=1; j2<=nlstate;j2++){
5038: cptj2= (j2-1)*nlstate+i2;
5039: if(cptj2 <= cptj)
5040: fprintf(ficrescveij," %1d%1d,%1d%1d",i,j,i2,j2);
5041: }
5042: }
5043: fprintf(ficrescveij,"\n");
5044:
5045: if(estepm < stepm){
5046: printf ("Problem %d lower than %d\n",estepm, stepm);
5047: }
5048: else hstepm=estepm;
5049: /* We compute the life expectancy from trapezoids spaced every estepm months
5050: * This is mainly to measure the difference between two models: for example
5051: * if stepm=24 months pijx are given only every 2 years and by summing them
5052: * we are calculating an estimate of the Life Expectancy assuming a linear
5053: * progression in between and thus overestimating or underestimating according
5054: * to the curvature of the survival function. If, for the same date, we
5055: * estimate the model with stepm=1 month, we can keep estepm to 24 months
5056: * to compare the new estimate of Life expectancy with the same linear
5057: * hypothesis. A more precise result, taking into account a more precise
5058: * curvature will be obtained if estepm is as small as stepm. */
5059:
5060: /* For example we decided to compute the life expectancy with the smallest unit */
5061: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
5062: nhstepm is the number of hstepm from age to agelim
5063: nstepm is the number of stepm from age to agelin.
5064: Look at hpijx to understand the reason of that which relies in memory size
5065: and note for a fixed period like estepm months */
5066: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
5067: survival function given by stepm (the optimization length). Unfortunately it
5068: means that if the survival funtion is printed only each two years of age and if
5069: you sum them up and add 1 year (area under the trapezoids) you won't get the same
5070: results. So we changed our mind and took the option of the best precision.
5071: */
5072: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
5073:
5074: /* If stepm=6 months */
5075: /* nhstepm age range expressed in number of stepm */
5076: agelim=AGESUP;
5077: nstepm=(int) rint((agelim-bage)*YEARM/stepm);
5078: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
5079: /* if (stepm >= YEARM) hstepm=1;*/
5080: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
5081:
5082: p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5083: p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5084: gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
5085: trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
5086: gp=matrix(0,nhstepm,1,nlstate*nlstate);
5087: gm=matrix(0,nhstepm,1,nlstate*nlstate);
5088:
5089: for (age=bage; age<=fage; age ++){
5090: nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
5091: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
5092: /* if (stepm >= YEARM) hstepm=1;*/
5093: nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
1.218 brouard 5094:
1.126 brouard 5095: /* If stepm=6 months */
5096: /* Computed by stepm unit matrices, product of hstepma matrices, stored
5097: in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
5098:
5099: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
1.218 brouard 5100:
1.126 brouard 5101: /* Computing Variances of health expectancies */
5102: /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
5103: decrease memory allocation */
5104: for(theta=1; theta <=npar; theta++){
5105: for(i=1; i<=npar; i++){
1.222 brouard 5106: xp[i] = x[i] + (i==theta ?delti[theta]:0);
5107: xm[i] = x[i] - (i==theta ?delti[theta]:0);
1.126 brouard 5108: }
1.235 ! brouard 5109: hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij, nres);
! 5110: hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij, nres);
1.218 brouard 5111:
1.126 brouard 5112: for(j=1; j<= nlstate; j++){
1.222 brouard 5113: for(i=1; i<=nlstate; i++){
5114: for(h=0; h<=nhstepm-1; h++){
5115: gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
5116: gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
5117: }
5118: }
1.126 brouard 5119: }
1.218 brouard 5120:
1.126 brouard 5121: for(ij=1; ij<= nlstate*nlstate; ij++)
1.222 brouard 5122: for(h=0; h<=nhstepm-1; h++){
5123: gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
5124: }
1.126 brouard 5125: }/* End theta */
5126:
5127:
5128: for(h=0; h<=nhstepm-1; h++)
5129: for(j=1; j<=nlstate*nlstate;j++)
1.222 brouard 5130: for(theta=1; theta <=npar; theta++)
5131: trgradg[h][j][theta]=gradg[h][theta][j];
1.126 brouard 5132:
1.218 brouard 5133:
1.222 brouard 5134: for(ij=1;ij<=nlstate*nlstate;ij++)
1.126 brouard 5135: for(ji=1;ji<=nlstate*nlstate;ji++)
1.222 brouard 5136: varhe[ij][ji][(int)age] =0.;
1.218 brouard 5137:
1.222 brouard 5138: printf("%d|",(int)age);fflush(stdout);
5139: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
5140: for(h=0;h<=nhstepm-1;h++){
1.126 brouard 5141: for(k=0;k<=nhstepm-1;k++){
1.222 brouard 5142: matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
5143: matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
5144: for(ij=1;ij<=nlstate*nlstate;ij++)
5145: for(ji=1;ji<=nlstate*nlstate;ji++)
5146: varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
1.126 brouard 5147: }
5148: }
1.218 brouard 5149:
1.126 brouard 5150: /* Computing expectancies */
1.235 ! brouard 5151: hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij,nres);
1.126 brouard 5152: for(i=1; i<=nlstate;i++)
5153: for(j=1; j<=nlstate;j++)
1.222 brouard 5154: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
5155: eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
1.218 brouard 5156:
1.222 brouard 5157: /* 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]);*/
1.218 brouard 5158:
1.222 brouard 5159: }
1.218 brouard 5160:
1.126 brouard 5161: fprintf(ficresstdeij,"%3.0f",age );
5162: for(i=1; i<=nlstate;i++){
5163: eip=0.;
5164: vip=0.;
5165: for(j=1; j<=nlstate;j++){
1.222 brouard 5166: eip += eij[i][j][(int)age];
5167: for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
5168: vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
5169: fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
1.126 brouard 5170: }
5171: fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
5172: }
5173: fprintf(ficresstdeij,"\n");
1.218 brouard 5174:
1.126 brouard 5175: fprintf(ficrescveij,"%3.0f",age );
5176: for(i=1; i<=nlstate;i++)
5177: for(j=1; j<=nlstate;j++){
1.222 brouard 5178: cptj= (j-1)*nlstate+i;
5179: for(i2=1; i2<=nlstate;i2++)
5180: for(j2=1; j2<=nlstate;j2++){
5181: cptj2= (j2-1)*nlstate+i2;
5182: if(cptj2 <= cptj)
5183: fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
5184: }
1.126 brouard 5185: }
5186: fprintf(ficrescveij,"\n");
1.218 brouard 5187:
1.126 brouard 5188: }
5189: free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
5190: free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
5191: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
5192: free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
5193: free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5194: free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5195: printf("\n");
5196: fprintf(ficlog,"\n");
1.218 brouard 5197:
1.126 brouard 5198: free_vector(xm,1,npar);
5199: free_vector(xp,1,npar);
5200: free_matrix(dnewm,1,nlstate*nlstate,1,npar);
5201: free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
5202: free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
5203: }
1.218 brouard 5204:
1.126 brouard 5205: /************ Variance ******************/
1.235 ! brouard 5206: 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[], int nres)
1.218 brouard 5207: {
5208: /* Variance of health expectancies */
5209: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
5210: /* double **newm;*/
5211: /* int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav)*/
5212:
5213: /* int movingaverage(); */
5214: double **dnewm,**doldm;
5215: double **dnewmp,**doldmp;
5216: int i, j, nhstepm, hstepm, h, nstepm ;
5217: int k;
5218: double *xp;
5219: double **gp, **gm; /* for var eij */
5220: double ***gradg, ***trgradg; /*for var eij */
5221: double **gradgp, **trgradgp; /* for var p point j */
5222: double *gpp, *gmp; /* for var p point j */
5223: double **varppt; /* for var p point j nlstate to nlstate+ndeath */
5224: double ***p3mat;
5225: double age,agelim, hf;
5226: /* double ***mobaverage; */
5227: int theta;
5228: char digit[4];
5229: char digitp[25];
5230:
5231: char fileresprobmorprev[FILENAMELENGTH];
5232:
5233: if(popbased==1){
5234: if(mobilav!=0)
5235: strcpy(digitp,"-POPULBASED-MOBILAV_");
5236: else strcpy(digitp,"-POPULBASED-NOMOBIL_");
5237: }
5238: else
5239: strcpy(digitp,"-STABLBASED_");
1.126 brouard 5240:
1.218 brouard 5241: /* if (mobilav!=0) { */
5242: /* mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
5243: /* if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){ */
5244: /* fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav); */
5245: /* printf(" Error in movingaverage mobilav=%d\n",mobilav); */
5246: /* } */
5247: /* } */
5248:
5249: strcpy(fileresprobmorprev,"PRMORPREV-");
5250: sprintf(digit,"%-d",ij);
5251: /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
5252: strcat(fileresprobmorprev,digit); /* Tvar to be done */
5253: strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
5254: strcat(fileresprobmorprev,fileresu);
5255: if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
5256: printf("Problem with resultfile: %s\n", fileresprobmorprev);
5257: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
5258: }
5259: printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
5260: fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
5261: pstamp(ficresprobmorprev);
5262: 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);
5263: fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
5264: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
5265: fprintf(ficresprobmorprev," p.%-d SE",j);
5266: for(i=1; i<=nlstate;i++)
5267: fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
5268: }
5269: fprintf(ficresprobmorprev,"\n");
5270:
5271: fprintf(ficgp,"\n# Routine varevsij");
5272: fprintf(ficgp,"\nunset title \n");
5273: /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
5274: 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");
5275: fprintf(fichtm,"\n<br>%s <br>\n",digitp);
5276: /* } */
5277: varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
5278: pstamp(ficresvij);
5279: fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n# (weighted average of eij where weights are ");
5280: if(popbased==1)
5281: 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);
5282: else
5283: fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
5284: fprintf(ficresvij,"# Age");
5285: for(i=1; i<=nlstate;i++)
5286: for(j=1; j<=nlstate;j++)
5287: fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
5288: fprintf(ficresvij,"\n");
5289:
5290: xp=vector(1,npar);
5291: dnewm=matrix(1,nlstate,1,npar);
5292: doldm=matrix(1,nlstate,1,nlstate);
5293: dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
5294: doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
5295:
5296: gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
5297: gpp=vector(nlstate+1,nlstate+ndeath);
5298: gmp=vector(nlstate+1,nlstate+ndeath);
5299: trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
1.126 brouard 5300:
1.218 brouard 5301: if(estepm < stepm){
5302: printf ("Problem %d lower than %d\n",estepm, stepm);
5303: }
5304: else hstepm=estepm;
5305: /* For example we decided to compute the life expectancy with the smallest unit */
5306: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
5307: nhstepm is the number of hstepm from age to agelim
5308: nstepm is the number of stepm from age to agelim.
5309: Look at function hpijx to understand why because of memory size limitations,
5310: we decided (b) to get a life expectancy respecting the most precise curvature of the
5311: survival function given by stepm (the optimization length). Unfortunately it
5312: means that if the survival funtion is printed every two years of age and if
5313: you sum them up and add 1 year (area under the trapezoids) you won't get the same
5314: results. So we changed our mind and took the option of the best precision.
5315: */
5316: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
5317: agelim = AGESUP;
5318: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
5319: nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
5320: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
5321: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5322: gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
5323: gp=matrix(0,nhstepm,1,nlstate);
5324: gm=matrix(0,nhstepm,1,nlstate);
5325:
5326:
5327: for(theta=1; theta <=npar; theta++){
5328: for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
5329: xp[i] = x[i] + (i==theta ?delti[theta]:0);
5330: }
5331:
1.235 ! brouard 5332: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij, nresult);
1.218 brouard 5333:
5334: if (popbased==1) {
5335: if(mobilav ==0){
5336: for(i=1; i<=nlstate;i++)
5337: prlim[i][i]=probs[(int)age][i][ij];
5338: }else{ /* mobilav */
5339: for(i=1; i<=nlstate;i++)
5340: prlim[i][i]=mobaverage[(int)age][i][ij];
5341: }
5342: }
5343:
1.235 ! brouard 5344: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij,nres); /* Returns p3mat[i][j][h] for h=1 to nhstepm */
1.218 brouard 5345: for(j=1; j<= nlstate; j++){
5346: for(h=0; h<=nhstepm; h++){
5347: for(i=1, gp[h][j]=0.;i<=nlstate;i++)
5348: gp[h][j] += prlim[i][i]*p3mat[i][j][h];
5349: }
5350: }
5351: /* Next for computing probability of death (h=1 means
5352: computed over hstepm matrices product = hstepm*stepm months)
5353: as a weighted average of prlim.
5354: */
5355: for(j=nlstate+1;j<=nlstate+ndeath;j++){
5356: for(i=1,gpp[j]=0.; i<= nlstate; i++)
5357: gpp[j] += prlim[i][i]*p3mat[i][j][1];
5358: }
5359: /* end probability of death */
5360:
5361: for(i=1; i<=npar; i++) /* Computes gradient x - delta */
5362: xp[i] = x[i] - (i==theta ?delti[theta]:0);
5363:
1.235 ! brouard 5364: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp, ij, nresult);
1.218 brouard 5365:
5366: if (popbased==1) {
5367: if(mobilav ==0){
5368: for(i=1; i<=nlstate;i++)
5369: prlim[i][i]=probs[(int)age][i][ij];
5370: }else{ /* mobilav */
5371: for(i=1; i<=nlstate;i++)
5372: prlim[i][i]=mobaverage[(int)age][i][ij];
5373: }
5374: }
5375:
1.235 ! brouard 5376: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij,nres);
1.218 brouard 5377:
5378: for(j=1; j<= nlstate; j++){ /* Sum of wi * eij = e.j */
5379: for(h=0; h<=nhstepm; h++){
5380: for(i=1, gm[h][j]=0.;i<=nlstate;i++)
5381: gm[h][j] += prlim[i][i]*p3mat[i][j][h];
5382: }
5383: }
5384: /* This for computing probability of death (h=1 means
5385: computed over hstepm matrices product = hstepm*stepm months)
5386: as a weighted average of prlim.
5387: */
5388: for(j=nlstate+1;j<=nlstate+ndeath;j++){
5389: for(i=1,gmp[j]=0.; i<= nlstate; i++)
5390: gmp[j] += prlim[i][i]*p3mat[i][j][1];
5391: }
5392: /* end probability of death */
5393:
5394: for(j=1; j<= nlstate; j++) /* vareij */
5395: for(h=0; h<=nhstepm; h++){
5396: gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
5397: }
5398:
5399: for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
5400: gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
5401: }
5402:
5403: } /* End theta */
5404:
5405: trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
5406:
5407: for(h=0; h<=nhstepm; h++) /* veij */
5408: for(j=1; j<=nlstate;j++)
5409: for(theta=1; theta <=npar; theta++)
5410: trgradg[h][j][theta]=gradg[h][theta][j];
5411:
5412: for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
5413: for(theta=1; theta <=npar; theta++)
5414: trgradgp[j][theta]=gradgp[theta][j];
5415:
5416:
5417: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
5418: for(i=1;i<=nlstate;i++)
5419: for(j=1;j<=nlstate;j++)
5420: vareij[i][j][(int)age] =0.;
5421:
5422: for(h=0;h<=nhstepm;h++){
5423: for(k=0;k<=nhstepm;k++){
5424: matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
5425: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
5426: for(i=1;i<=nlstate;i++)
5427: for(j=1;j<=nlstate;j++)
5428: vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
5429: }
5430: }
5431:
5432: /* pptj */
5433: matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
5434: matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
5435: for(j=nlstate+1;j<=nlstate+ndeath;j++)
5436: for(i=nlstate+1;i<=nlstate+ndeath;i++)
5437: varppt[j][i]=doldmp[j][i];
5438: /* end ppptj */
5439: /* x centered again */
5440:
1.235 ! brouard 5441: prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ncvyearp,ij, nresult);
1.218 brouard 5442:
5443: if (popbased==1) {
5444: if(mobilav ==0){
5445: for(i=1; i<=nlstate;i++)
5446: prlim[i][i]=probs[(int)age][i][ij];
5447: }else{ /* mobilav */
5448: for(i=1; i<=nlstate;i++)
5449: prlim[i][i]=mobaverage[(int)age][i][ij];
5450: }
5451: }
5452:
5453: /* This for computing probability of death (h=1 means
5454: computed over hstepm (estepm) matrices product = hstepm*stepm months)
5455: as a weighted average of prlim.
5456: */
1.235 ! brouard 5457: hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij, nres);
1.218 brouard 5458: for(j=nlstate+1;j<=nlstate+ndeath;j++){
5459: for(i=1,gmp[j]=0.;i<= nlstate; i++)
5460: gmp[j] += prlim[i][i]*p3mat[i][j][1];
5461: }
5462: /* end probability of death */
5463:
5464: fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
5465: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
5466: fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
5467: for(i=1; i<=nlstate;i++){
5468: fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
5469: }
5470: }
5471: fprintf(ficresprobmorprev,"\n");
5472:
5473: fprintf(ficresvij,"%.0f ",age );
5474: for(i=1; i<=nlstate;i++)
5475: for(j=1; j<=nlstate;j++){
5476: fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
5477: }
5478: fprintf(ficresvij,"\n");
5479: free_matrix(gp,0,nhstepm,1,nlstate);
5480: free_matrix(gm,0,nhstepm,1,nlstate);
5481: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
5482: free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
5483: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5484: } /* End age */
5485: free_vector(gpp,nlstate+1,nlstate+ndeath);
5486: free_vector(gmp,nlstate+1,nlstate+ndeath);
5487: free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
5488: free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
5489: /* fprintf(ficgp,"\nunset parametric;unset label; set ter png small size 320, 240"); */
5490: fprintf(ficgp,"\nunset parametric;unset label; set ter svg size 640, 480");
5491: /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
5492: fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
5493: fprintf(ficgp,"\nset out \"%s%s.svg\";",subdirf3(optionfilefiname,"VARMUPTJGR-",digitp),digit);
5494: /* fprintf(ficgp,"\n plot \"%s\" u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
5495: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
5496: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
5497: fprintf(ficgp,"\n plot \"%s\" u 1:($3) not w l lt 1 ",subdirf(fileresprobmorprev));
5498: fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)) t \"95%% interval\" w l lt 2 ",subdirf(fileresprobmorprev));
5499: fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)) not w l lt 2 ",subdirf(fileresprobmorprev));
5500: fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
5501: 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);
5502: /* 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 5503: */
1.218 brouard 5504: /* fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.svg\";replot;",digitp,optionfilefiname,digit); */
5505: fprintf(ficgp,"\nset out;\nset out \"%s%s.svg\";replot;set out;\n",subdirf3(optionfilefiname,"VARMUPTJGR-",digitp),digit);
1.126 brouard 5506:
1.218 brouard 5507: free_vector(xp,1,npar);
5508: free_matrix(doldm,1,nlstate,1,nlstate);
5509: free_matrix(dnewm,1,nlstate,1,npar);
5510: free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
5511: free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
5512: free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
5513: /* if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
5514: fclose(ficresprobmorprev);
5515: fflush(ficgp);
5516: fflush(fichtm);
5517: } /* end varevsij */
1.126 brouard 5518:
5519: /************ Variance of prevlim ******************/
1.235 ! brouard 5520: 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[], int nres)
1.126 brouard 5521: {
1.205 brouard 5522: /* Variance of prevalence limit for each state ij using current parameters x[] and estimates of neighbourhood give by delti*/
1.126 brouard 5523: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
1.164 brouard 5524:
1.126 brouard 5525: double **dnewm,**doldm;
5526: int i, j, nhstepm, hstepm;
5527: double *xp;
5528: double *gp, *gm;
5529: double **gradg, **trgradg;
1.208 brouard 5530: double **mgm, **mgp;
1.126 brouard 5531: double age,agelim;
5532: int theta;
5533:
5534: pstamp(ficresvpl);
5535: fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
5536: fprintf(ficresvpl,"# Age");
5537: for(i=1; i<=nlstate;i++)
5538: fprintf(ficresvpl," %1d-%1d",i,i);
5539: fprintf(ficresvpl,"\n");
5540:
5541: xp=vector(1,npar);
5542: dnewm=matrix(1,nlstate,1,npar);
5543: doldm=matrix(1,nlstate,1,nlstate);
5544:
5545: hstepm=1*YEARM; /* Every year of age */
5546: hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
5547: agelim = AGESUP;
5548: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
5549: nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
5550: if (stepm >= YEARM) hstepm=1;
5551: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
5552: gradg=matrix(1,npar,1,nlstate);
1.208 brouard 5553: mgp=matrix(1,npar,1,nlstate);
5554: mgm=matrix(1,npar,1,nlstate);
1.126 brouard 5555: gp=vector(1,nlstate);
5556: gm=vector(1,nlstate);
5557:
5558: for(theta=1; theta <=npar; theta++){
5559: for(i=1; i<=npar; i++){ /* Computes gradient */
5560: xp[i] = x[i] + (i==theta ?delti[theta]:0);
5561: }
1.209 brouard 5562: if((int)age==79 ||(int)age== 80 ||(int)age== 81 )
1.235 ! brouard 5563: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij,nres);
1.209 brouard 5564: else
1.235 ! brouard 5565: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij,nres);
1.208 brouard 5566: for(i=1;i<=nlstate;i++){
1.126 brouard 5567: gp[i] = prlim[i][i];
1.208 brouard 5568: mgp[theta][i] = prlim[i][i];
5569: }
1.126 brouard 5570: for(i=1; i<=npar; i++) /* Computes gradient */
5571: xp[i] = x[i] - (i==theta ?delti[theta]:0);
1.209 brouard 5572: if((int)age==79 ||(int)age== 80 ||(int)age== 81 )
1.235 ! brouard 5573: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij,nres);
1.209 brouard 5574: else
1.235 ! brouard 5575: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij,nres);
1.208 brouard 5576: for(i=1;i<=nlstate;i++){
1.126 brouard 5577: gm[i] = prlim[i][i];
1.208 brouard 5578: mgm[theta][i] = prlim[i][i];
5579: }
1.126 brouard 5580: for(i=1;i<=nlstate;i++)
5581: gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
1.209 brouard 5582: /* gradg[theta][2]= -gradg[theta][1]; */ /* For testing if nlstate=2 */
1.126 brouard 5583: } /* End theta */
5584:
5585: trgradg =matrix(1,nlstate,1,npar);
5586:
5587: for(j=1; j<=nlstate;j++)
5588: for(theta=1; theta <=npar; theta++)
5589: trgradg[j][theta]=gradg[theta][j];
1.209 brouard 5590: /* if((int)age==79 ||(int)age== 80 ||(int)age== 81 ){ */
5591: /* printf("\nmgm mgp %d ",(int)age); */
5592: /* for(j=1; j<=nlstate;j++){ */
5593: /* printf(" %d ",j); */
5594: /* for(theta=1; theta <=npar; theta++) */
5595: /* printf(" %d %lf %lf",theta,mgm[theta][j],mgp[theta][j]); */
5596: /* printf("\n "); */
5597: /* } */
5598: /* } */
5599: /* if((int)age==79 ||(int)age== 80 ||(int)age== 81 ){ */
5600: /* printf("\n gradg %d ",(int)age); */
5601: /* for(j=1; j<=nlstate;j++){ */
5602: /* printf("%d ",j); */
5603: /* for(theta=1; theta <=npar; theta++) */
5604: /* printf("%d %lf ",theta,gradg[theta][j]); */
5605: /* printf("\n "); */
5606: /* } */
5607: /* } */
1.126 brouard 5608:
5609: for(i=1;i<=nlstate;i++)
5610: varpl[i][(int)age] =0.;
1.209 brouard 5611: if((int)age==79 ||(int)age== 80 ||(int)age== 81){
1.205 brouard 5612: matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
5613: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
5614: }else{
1.126 brouard 5615: matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
5616: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
1.205 brouard 5617: }
1.126 brouard 5618: for(i=1;i<=nlstate;i++)
5619: varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
5620:
5621: fprintf(ficresvpl,"%.0f ",age );
5622: for(i=1; i<=nlstate;i++)
5623: fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
5624: fprintf(ficresvpl,"\n");
5625: free_vector(gp,1,nlstate);
5626: free_vector(gm,1,nlstate);
1.208 brouard 5627: free_matrix(mgm,1,npar,1,nlstate);
5628: free_matrix(mgp,1,npar,1,nlstate);
1.126 brouard 5629: free_matrix(gradg,1,npar,1,nlstate);
5630: free_matrix(trgradg,1,nlstate,1,npar);
5631: } /* End age */
5632:
5633: free_vector(xp,1,npar);
5634: free_matrix(doldm,1,nlstate,1,npar);
5635: free_matrix(dnewm,1,nlstate,1,nlstate);
5636:
5637: }
5638:
5639: /************ Variance of one-step probabilities ******************/
5640: 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[])
1.222 brouard 5641: {
5642: int i, j=0, k1, l1, tj;
5643: int k2, l2, j1, z1;
5644: int k=0, l;
5645: int first=1, first1, first2;
5646: double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
5647: double **dnewm,**doldm;
5648: double *xp;
5649: double *gp, *gm;
5650: double **gradg, **trgradg;
5651: double **mu;
5652: double age, cov[NCOVMAX+1];
5653: double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
5654: int theta;
5655: char fileresprob[FILENAMELENGTH];
5656: char fileresprobcov[FILENAMELENGTH];
5657: char fileresprobcor[FILENAMELENGTH];
5658: double ***varpij;
5659:
5660: strcpy(fileresprob,"PROB_");
5661: strcat(fileresprob,fileres);
5662: if((ficresprob=fopen(fileresprob,"w"))==NULL) {
5663: printf("Problem with resultfile: %s\n", fileresprob);
5664: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
5665: }
5666: strcpy(fileresprobcov,"PROBCOV_");
5667: strcat(fileresprobcov,fileresu);
5668: if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
5669: printf("Problem with resultfile: %s\n", fileresprobcov);
5670: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
5671: }
5672: strcpy(fileresprobcor,"PROBCOR_");
5673: strcat(fileresprobcor,fileresu);
5674: if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
5675: printf("Problem with resultfile: %s\n", fileresprobcor);
5676: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
5677: }
5678: printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
5679: fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
5680: printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
5681: fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
5682: printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
5683: fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
5684: pstamp(ficresprob);
5685: fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
5686: fprintf(ficresprob,"# Age");
5687: pstamp(ficresprobcov);
5688: fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
5689: fprintf(ficresprobcov,"# Age");
5690: pstamp(ficresprobcor);
5691: fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
5692: fprintf(ficresprobcor,"# Age");
1.126 brouard 5693:
5694:
1.222 brouard 5695: for(i=1; i<=nlstate;i++)
5696: for(j=1; j<=(nlstate+ndeath);j++){
5697: fprintf(ficresprob," p%1d-%1d (SE)",i,j);
5698: fprintf(ficresprobcov," p%1d-%1d ",i,j);
5699: fprintf(ficresprobcor," p%1d-%1d ",i,j);
5700: }
5701: /* fprintf(ficresprob,"\n");
5702: fprintf(ficresprobcov,"\n");
5703: fprintf(ficresprobcor,"\n");
5704: */
5705: xp=vector(1,npar);
5706: dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
5707: doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
5708: mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
5709: varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
5710: first=1;
5711: fprintf(ficgp,"\n# Routine varprob");
5712: fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
5713: fprintf(fichtm,"\n");
5714:
5715: 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);
5716: 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);
5717: fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated \
1.126 brouard 5718: and drawn. It helps understanding how is the covariance between two incidences.\
5719: They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
1.222 brouard 5720: 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. \
1.126 brouard 5721: It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
5722: would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
5723: standard deviations wide on each axis. <br>\
5724: Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
5725: and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
5726: To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
5727:
1.222 brouard 5728: cov[1]=1;
5729: /* tj=cptcoveff; */
1.225 brouard 5730: tj = (int) pow(2,cptcoveff);
1.222 brouard 5731: if (cptcovn<1) {tj=1;ncodemax[1]=1;}
5732: j1=0;
1.224 brouard 5733: for(j1=1; j1<=tj;j1++){ /* For each valid combination of covariates or only once*/
1.222 brouard 5734: if (cptcovn>0) {
5735: fprintf(ficresprob, "\n#********** Variable ");
1.225 brouard 5736: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.222 brouard 5737: fprintf(ficresprob, "**********\n#\n");
5738: fprintf(ficresprobcov, "\n#********** Variable ");
1.225 brouard 5739: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.222 brouard 5740: fprintf(ficresprobcov, "**********\n#\n");
1.220 brouard 5741:
1.222 brouard 5742: fprintf(ficgp, "\n#********** Variable ");
1.225 brouard 5743: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.222 brouard 5744: fprintf(ficgp, "**********\n#\n");
1.220 brouard 5745:
5746:
1.222 brouard 5747: fprintf(fichtmcov, "\n<hr size=\"2\" color=\"#EC5E5E\">********** Variable ");
1.225 brouard 5748: for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.222 brouard 5749: fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
1.220 brouard 5750:
1.222 brouard 5751: fprintf(ficresprobcor, "\n#********** Variable ");
1.225 brouard 5752: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.222 brouard 5753: fprintf(ficresprobcor, "**********\n#");
5754: if(invalidvarcomb[j1]){
5755: fprintf(ficgp,"\n#Combination (%d) ignored because no cases \n",j1);
5756: fprintf(fichtmcov,"\n<h3>Combination (%d) ignored because no cases </h3>\n",j1);
5757: continue;
5758: }
5759: }
5760: gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
5761: trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
5762: gp=vector(1,(nlstate)*(nlstate+ndeath));
5763: gm=vector(1,(nlstate)*(nlstate+ndeath));
5764: for (age=bage; age<=fage; age ++){
5765: cov[2]=age;
5766: if(nagesqr==1)
5767: cov[3]= age*age;
5768: for (k=1; k<=cptcovn;k++) {
5769: cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(j1,k)];
5770: /*cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(j1,Tvar[k])];*//* j1 1 2 3 4
5771: * 1 1 1 1 1
5772: * 2 2 1 1 1
5773: * 3 1 2 1 1
5774: */
5775: /* nbcode[1][1]=0 nbcode[1][2]=1;*/
5776: }
5777: /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
5778: for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
5779: for (k=1; k<=cptcovprod;k++)
5780: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)];
1.220 brouard 5781:
5782:
1.222 brouard 5783: for(theta=1; theta <=npar; theta++){
5784: for(i=1; i<=npar; i++)
5785: xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
1.220 brouard 5786:
1.222 brouard 5787: pmij(pmmij,cov,ncovmodel,xp,nlstate);
1.220 brouard 5788:
1.222 brouard 5789: k=0;
5790: for(i=1; i<= (nlstate); i++){
5791: for(j=1; j<=(nlstate+ndeath);j++){
5792: k=k+1;
5793: gp[k]=pmmij[i][j];
5794: }
5795: }
1.220 brouard 5796:
1.222 brouard 5797: for(i=1; i<=npar; i++)
5798: xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
1.220 brouard 5799:
1.222 brouard 5800: pmij(pmmij,cov,ncovmodel,xp,nlstate);
5801: k=0;
5802: for(i=1; i<=(nlstate); i++){
5803: for(j=1; j<=(nlstate+ndeath);j++){
5804: k=k+1;
5805: gm[k]=pmmij[i][j];
5806: }
5807: }
1.220 brouard 5808:
1.222 brouard 5809: for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)
5810: gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];
5811: }
1.126 brouard 5812:
1.222 brouard 5813: for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
5814: for(theta=1; theta <=npar; theta++)
5815: trgradg[j][theta]=gradg[theta][j];
1.220 brouard 5816:
1.222 brouard 5817: matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);
5818: matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
1.220 brouard 5819:
1.222 brouard 5820: pmij(pmmij,cov,ncovmodel,x,nlstate);
1.220 brouard 5821:
1.222 brouard 5822: k=0;
5823: for(i=1; i<=(nlstate); i++){
5824: for(j=1; j<=(nlstate+ndeath);j++){
5825: k=k+1;
5826: mu[k][(int) age]=pmmij[i][j];
5827: }
5828: }
5829: for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
5830: for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
5831: varpij[i][j][(int)age] = doldm[i][j];
1.220 brouard 5832:
1.222 brouard 5833: /*printf("\n%d ",(int)age);
5834: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
5835: printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
5836: fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
5837: }*/
1.220 brouard 5838:
1.222 brouard 5839: fprintf(ficresprob,"\n%d ",(int)age);
5840: fprintf(ficresprobcov,"\n%d ",(int)age);
5841: fprintf(ficresprobcor,"\n%d ",(int)age);
1.220 brouard 5842:
1.222 brouard 5843: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
5844: fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
5845: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
5846: fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
5847: fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
5848: }
5849: i=0;
5850: for (k=1; k<=(nlstate);k++){
5851: for (l=1; l<=(nlstate+ndeath);l++){
5852: i++;
5853: fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
5854: fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
5855: for (j=1; j<=i;j++){
5856: /* printf(" k=%d l=%d i=%d j=%d\n",k,l,i,j);fflush(stdout); */
5857: fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
5858: fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
5859: }
5860: }
5861: }/* end of loop for state */
5862: } /* end of loop for age */
5863: free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
5864: free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
5865: free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
5866: free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
5867:
5868: /* Confidence intervalle of pij */
5869: /*
5870: fprintf(ficgp,"\nunset parametric;unset label");
5871: fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
5872: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
5873: 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);
5874: fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
5875: fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
5876: fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
5877: */
5878:
5879: /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
5880: first1=1;first2=2;
5881: for (k2=1; k2<=(nlstate);k2++){
5882: for (l2=1; l2<=(nlstate+ndeath);l2++){
5883: if(l2==k2) continue;
5884: j=(k2-1)*(nlstate+ndeath)+l2;
5885: for (k1=1; k1<=(nlstate);k1++){
5886: for (l1=1; l1<=(nlstate+ndeath);l1++){
5887: if(l1==k1) continue;
5888: i=(k1-1)*(nlstate+ndeath)+l1;
5889: if(i<=j) continue;
5890: for (age=bage; age<=fage; age ++){
5891: if ((int)age %5==0){
5892: v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
5893: v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
5894: cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
5895: mu1=mu[i][(int) age]/stepm*YEARM ;
5896: mu2=mu[j][(int) age]/stepm*YEARM;
5897: c12=cv12/sqrt(v1*v2);
5898: /* Computing eigen value of matrix of covariance */
5899: lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
5900: lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
5901: if ((lc2 <0) || (lc1 <0) ){
5902: if(first2==1){
5903: first1=0;
5904: 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);
5905: }
5906: 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);
5907: /* lc1=fabs(lc1); */ /* If we want to have them positive */
5908: /* lc2=fabs(lc2); */
5909: }
1.220 brouard 5910:
1.222 brouard 5911: /* Eigen vectors */
5912: v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
5913: /*v21=sqrt(1.-v11*v11); *//* error */
5914: v21=(lc1-v1)/cv12*v11;
5915: v12=-v21;
5916: v22=v11;
5917: tnalp=v21/v11;
5918: if(first1==1){
5919: first1=0;
5920: 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);
5921: }
5922: 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);
5923: /*printf(fignu*/
5924: /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
5925: /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
5926: if(first==1){
5927: first=0;
5928: fprintf(ficgp,"\n# Ellipsoids of confidence\n#\n");
5929: fprintf(ficgp,"\nset parametric;unset label");
5930: 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);
5931: fprintf(ficgp,"\nset ter svg size 640, 480");
5932: fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
1.220 brouard 5933: :<a href=\"%s_%d%1d%1d-%1d%1d.svg\"> \
1.201 brouard 5934: %s_%d%1d%1d-%1d%1d.svg</A>, ",k1,l1,k2,l2,\
1.222 brouard 5935: subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2, \
5936: subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
5937: fprintf(fichtmcov,"\n<br><img src=\"%s_%d%1d%1d-%1d%1d.svg\"> ",subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
5938: fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
5939: fprintf(ficgp,"\nset out \"%s_%d%1d%1d-%1d%1d.svg\"",subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
5940: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
5941: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
5942: 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", \
5943: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2), \
5944: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
5945: }else{
5946: first=0;
5947: fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
5948: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
5949: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
5950: 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", \
5951: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2), \
5952: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
5953: }/* if first */
5954: } /* age mod 5 */
5955: } /* end loop age */
5956: fprintf(ficgp,"\nset out;\nset out \"%s_%d%1d%1d-%1d%1d.svg\";replot;set out;",subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
5957: first=1;
5958: } /*l12 */
5959: } /* k12 */
5960: } /*l1 */
5961: }/* k1 */
5962: } /* loop on combination of covariates j1 */
5963: free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
5964: free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
5965: free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
5966: free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
5967: free_vector(xp,1,npar);
5968: fclose(ficresprob);
5969: fclose(ficresprobcov);
5970: fclose(ficresprobcor);
5971: fflush(ficgp);
5972: fflush(fichtmcov);
5973: }
1.126 brouard 5974:
5975:
5976: /******************* Printing html file ***********/
1.201 brouard 5977: void printinghtml(char fileresu[], char title[], char datafile[], int firstpass, \
1.126 brouard 5978: int lastpass, int stepm, int weightopt, char model[],\
5979: int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
1.217 brouard 5980: int popforecast, int prevfcast, int backcast, int estepm , \
1.213 brouard 5981: double jprev1, double mprev1,double anprev1, double dateprev1, \
5982: double jprev2, double mprev2,double anprev2, double dateprev2){
1.126 brouard 5983: int jj1, k1, i1, cpt;
5984:
5985: fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
5986: <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
5987: </ul>");
1.214 brouard 5988: fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n");
5989: fprintf(fichtm,"<li>- Observed frequency between two states (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> (html file)<br/>\n",
5990: jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirfext3(optionfilefiname,"PHTMFR_",".htm"),subdirfext3(optionfilefiname,"PHTMFR_",".htm"));
5991: fprintf(fichtm,"<li> - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> (html file) ",
1.213 brouard 5992: jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirfext3(optionfilefiname,"PHTM_",".htm"),subdirfext3(optionfilefiname,"PHTM_",".htm"));
5993: fprintf(fichtm,", <a href=\"%s\">%s</a> (text file) <br>\n",subdirf2(fileresu,"P_"),subdirf2(fileresu,"P_"));
1.126 brouard 5994: fprintf(fichtm,"\
5995: - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
1.201 brouard 5996: stepm,subdirf2(fileresu,"PIJ_"),subdirf2(fileresu,"PIJ_"));
1.126 brouard 5997: fprintf(fichtm,"\
1.217 brouard 5998: - Estimated back transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
5999: stepm,subdirf2(fileresu,"PIJB_"),subdirf2(fileresu,"PIJB_"));
6000: fprintf(fichtm,"\
1.126 brouard 6001: - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
1.201 brouard 6002: subdirf2(fileresu,"PL_"),subdirf2(fileresu,"PL_"));
1.126 brouard 6003: fprintf(fichtm,"\
1.217 brouard 6004: - Period (stable) back prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
6005: subdirf2(fileresu,"PLB_"),subdirf2(fileresu,"PLB_"));
6006: fprintf(fichtm,"\
1.211 brouard 6007: - (a) Life expectancies by health status at initial age, e<sub>i.</sub> (b) health expectancies by health status at initial age, e<sub>ij</sub> . If one or more covariates are included, specific tables for each value of the covariate are output in sequences within the same file (estepm=%2d months): \
1.126 brouard 6008: <a href=\"%s\">%s</a> <br>\n",
1.201 brouard 6009: estepm,subdirf2(fileresu,"E_"),subdirf2(fileresu,"E_"));
1.211 brouard 6010: if(prevfcast==1){
6011: fprintf(fichtm,"\
6012: - Prevalence projections by age and states: \
1.201 brouard 6013: <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileresu,"F_"),subdirf2(fileresu,"F_"));
1.211 brouard 6014: }
1.126 brouard 6015:
1.222 brouard 6016: fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
1.126 brouard 6017:
1.225 brouard 6018: m=pow(2,cptcoveff);
1.222 brouard 6019: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
1.126 brouard 6020:
1.222 brouard 6021: jj1=0;
6022: for(k1=1; k1<=m;k1++){
1.220 brouard 6023:
1.222 brouard 6024: /* for(i1=1; i1<=ncodemax[k1];i1++){ */
6025: jj1++;
6026: if (cptcovn > 0) {
6027: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
1.225 brouard 6028: for (cpt=1; cpt<=cptcoveff;cpt++){
1.222 brouard 6029: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]);
6030: printf(" V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]);fflush(stdout);
6031: }
1.230 brouard 6032: /* if(nqfveff+nqtveff 0) */ /* Test to be done */
1.222 brouard 6033: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
6034: if(invalidvarcomb[k1]){
6035: fprintf(fichtm,"\n<h3>Combination (%d) ignored because no cases </h3>\n",k1);
6036: printf("\nCombination (%d) ignored because no cases \n",k1);
6037: continue;
6038: }
6039: }
6040: /* aij, bij */
6041: fprintf(fichtm,"<br>- Logit model (yours is: 1+age+%s), for example: logit(pij)=log(pij/pii)= aij+ bij age + V1 age + etc. as a function of age: <a href=\"%s_%d-1.svg\">%s_%d-1.svg</a><br> \
1.211 brouard 6042: <img src=\"%s_%d-1.svg\">",model,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1);
1.222 brouard 6043: /* Pij */
6044: fprintf(fichtm,"<br>\n- P<sub>ij</sub> or conditional probabilities to be observed in state j being in state i, %d (stepm) months before: <a href=\"%s_%d-2.svg\">%s_%d-2.svg</a><br> \
1.201 brouard 6045: <img src=\"%s_%d-2.svg\">",stepm,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1);
1.222 brouard 6046: /* Quasi-incidences */
6047: fprintf(fichtm,"<br>\n- I<sub>ij</sub> or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
1.220 brouard 6048: before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too, \
1.211 brouard 6049: incidence (rates) are the limit when h tends to zero of the ratio of the probability <sub>h</sub>P<sub>ij</sub> \
6050: divided by h: <sub>h</sub>P<sub>ij</sub>/h : <a href=\"%s_%d-3.svg\">%s_%d-3.svg</a><br> \
1.201 brouard 6051: <img src=\"%s_%d-3.svg\">",stepm,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1);
1.222 brouard 6052: /* Survival functions (period) in state j */
6053: for(cpt=1; cpt<=nlstate;cpt++){
6054: 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> \
1.201 brouard 6055: <img src=\"%s_%d-%d.svg\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"LIJ_"),cpt,jj1,subdirf2(optionfilefiname,"LIJ_"),cpt,jj1,subdirf2(optionfilefiname,"LIJ_"),cpt,jj1);
1.222 brouard 6056: }
6057: /* State specific survival functions (period) */
6058: for(cpt=1; cpt<=nlstate;cpt++){
6059: fprintf(fichtm,"<br>\n- Survival functions from state %d in each live state and total.\
1.220 brouard 6060: Or probability to survive in various states (1 to %d) being in state %d at different ages. \
1.201 brouard 6061: <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);
1.222 brouard 6062: }
6063: /* Period (stable) prevalence in each health state */
6064: for(cpt=1; cpt<=nlstate;cpt++){
6065: 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> \
1.201 brouard 6066: <img src=\"%s_%d-%d.svg\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"P_"),cpt,jj1,subdirf2(optionfilefiname,"P_"),cpt,jj1,subdirf2(optionfilefiname,"P_"),cpt,jj1);
1.222 brouard 6067: }
6068: if(backcast==1){
6069: /* Period (stable) back prevalence in each health state */
6070: for(cpt=1; cpt<=nlstate;cpt++){
6071: fprintf(fichtm,"<br>\n- Convergence to period (stable) back prevalence in state %d. Or probability to be in state %d being in state (1 to %d) at different ages. <a href=\"%s_%d-%d.svg\">%s_%d-%d.svg</a><br> \
1.217 brouard 6072: <img src=\"%s_%d-%d.svg\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"PB_"),cpt,jj1,subdirf2(optionfilefiname,"PB_"),cpt,jj1,subdirf2(optionfilefiname,"PB_"),cpt,jj1);
1.222 brouard 6073: }
1.217 brouard 6074: }
1.222 brouard 6075: if(prevfcast==1){
6076: /* Projection of prevalence up to period (stable) prevalence in each health state */
6077: for(cpt=1; cpt<=nlstate;cpt++){
6078: fprintf(fichtm,"<br>\n- Projection of cross-sectional prevalence (estimated with cases observed from %.1f to %.1f) up to period (stable) prevalence in state %d. Or probability to be in state %d being in state (1 to %d) at different ages. <a href=\"%s%d_%d.svg\">%s%d_%d.svg</a><br> \
1.213 brouard 6079: <img src=\"%s_%d-%d.svg\">", dateprev1, dateprev2, cpt, cpt, nlstate, subdirf2(optionfilefiname,"PROJ_"),cpt,jj1,subdirf2(optionfilefiname,"PROJ_"),cpt,jj1,subdirf2(optionfilefiname,"PROJ_"),cpt,jj1);
1.222 brouard 6080: }
6081: }
1.220 brouard 6082:
1.222 brouard 6083: for(cpt=1; cpt<=nlstate;cpt++) {
6084: 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 6085: <img src=\"%s_%d%d.svg\">",cpt,nlstate,subdirf2(optionfilefiname,"EXP_"),cpt,jj1,subdirf2(optionfilefiname,"EXP_"),cpt,jj1,subdirf2(optionfilefiname,"EXP_"),cpt,jj1);
1.222 brouard 6086: }
6087: /* } /\* end i1 *\/ */
6088: }/* End k1 */
6089: fprintf(fichtm,"</ul>");
1.126 brouard 6090:
1.222 brouard 6091: fprintf(fichtm,"\
1.126 brouard 6092: \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
1.193 brouard 6093: - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br> \
1.203 brouard 6094: - 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 6095: But because parameters are usually highly correlated (a higher incidence of disability \
6096: and a higher incidence of recovery can give very close observed transition) it might \
6097: be very useful to look not only at linear confidence intervals estimated from the \
6098: variances but at the covariance matrix. And instead of looking at the estimated coefficients \
6099: (parameters) of the logistic regression, it might be more meaningful to visualize the \
6100: covariance matrix of the one-step probabilities. \
6101: See page 'Matrix of variance-covariance of one-step probabilities' below. \n", rfileres,rfileres);
1.126 brouard 6102:
1.222 brouard 6103: fprintf(fichtm," - Standard deviation of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
6104: subdirf2(fileresu,"PROB_"),subdirf2(fileresu,"PROB_"));
6105: fprintf(fichtm,"\
1.126 brouard 6106: - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
1.222 brouard 6107: subdirf2(fileresu,"PROBCOV_"),subdirf2(fileresu,"PROBCOV_"));
1.126 brouard 6108:
1.222 brouard 6109: fprintf(fichtm,"\
1.126 brouard 6110: - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
1.222 brouard 6111: subdirf2(fileresu,"PROBCOR_"),subdirf2(fileresu,"PROBCOR_"));
6112: fprintf(fichtm,"\
1.126 brouard 6113: - 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): \
6114: <a href=\"%s\">%s</a> <br>\n</li>",
1.201 brouard 6115: estepm,subdirf2(fileresu,"CVE_"),subdirf2(fileresu,"CVE_"));
1.222 brouard 6116: fprintf(fichtm,"\
1.126 brouard 6117: - (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): \
6118: <a href=\"%s\">%s</a> <br>\n</li>",
1.201 brouard 6119: estepm,subdirf2(fileresu,"STDE_"),subdirf2(fileresu,"STDE_"));
1.222 brouard 6120: fprintf(fichtm,"\
1.128 brouard 6121: - 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",
1.222 brouard 6122: estepm, subdirf2(fileresu,"V_"),subdirf2(fileresu,"V_"));
6123: fprintf(fichtm,"\
1.128 brouard 6124: - 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",
1.222 brouard 6125: estepm, subdirf2(fileresu,"T_"),subdirf2(fileresu,"T_"));
6126: fprintf(fichtm,"\
1.126 brouard 6127: - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
1.222 brouard 6128: subdirf2(fileresu,"VPL_"),subdirf2(fileresu,"VPL_"));
1.126 brouard 6129:
6130: /* if(popforecast==1) fprintf(fichtm,"\n */
6131: /* - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
6132: /* - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
6133: /* <br>",fileres,fileres,fileres,fileres); */
6134: /* else */
6135: /* 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); */
1.222 brouard 6136: fflush(fichtm);
6137: fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
1.126 brouard 6138:
1.225 brouard 6139: m=pow(2,cptcoveff);
1.222 brouard 6140: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
1.126 brouard 6141:
1.222 brouard 6142: jj1=0;
6143: for(k1=1; k1<=m;k1++){
6144: /* for(i1=1; i1<=ncodemax[k1];i1++){ */
6145: jj1++;
1.126 brouard 6146: if (cptcovn > 0) {
6147: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
1.225 brouard 6148: for (cpt=1; cpt<=cptcoveff;cpt++) /**< cptcoveff number of variables */
1.222 brouard 6149: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]);
1.126 brouard 6150: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
1.220 brouard 6151:
1.222 brouard 6152: if(invalidvarcomb[k1]){
6153: fprintf(fichtm,"\n<h4>Combination (%d) ignored because no cases </h4>\n",k1);
6154: continue;
6155: }
1.126 brouard 6156: }
6157: for(cpt=1; cpt<=nlstate;cpt++) {
1.218 brouard 6158: fprintf(fichtm,"\n<br>- Observed (cross-sectional) and period (incidence based) \
6159: prevalence (with 95%% confidence interval) in state (%d): <a href=\"%s_%d-%d.svg\"> %s_%d-%d.svg</a>\n <br>\
1.205 brouard 6160: <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 6161: }
6162: fprintf(fichtm,"\n<br>- Total life expectancy by age and \
1.128 brouard 6163: health expectancies in states (1) and (2). If popbased=1 the smooth (due to the model) \
6164: true period expectancies (those weighted with period prevalences are also\
6165: drawn in addition to the population based expectancies computed using\
1.218 brouard 6166: observed and cahotic prevalences: <a href=\"%s_%d.svg\">%s_%d.svg</a>\n<br>\
1.205 brouard 6167: <img src=\"%s_%d.svg\">",subdirf2(optionfilefiname,"E_"),jj1,subdirf2(optionfilefiname,"E_"),jj1,subdirf2(optionfilefiname,"E_"),jj1);
1.222 brouard 6168: /* } /\* end i1 *\/ */
6169: }/* End k1 */
6170: fprintf(fichtm,"</ul>");
6171: fflush(fichtm);
1.126 brouard 6172: }
6173:
6174: /******************* Gnuplot file **************/
1.223 brouard 6175: void printinggnuplot(char fileresu[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , int prevfcast, int backcast, char pathc[], double p[]){
1.126 brouard 6176:
6177: char dirfileres[132],optfileres[132];
1.223 brouard 6178: char gplotcondition[132];
1.235 ! brouard 6179: int cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,k4=0,ij=0,l=0;
1.211 brouard 6180: int lv=0, vlv=0, kl=0;
1.130 brouard 6181: int ng=0;
1.201 brouard 6182: int vpopbased;
1.223 brouard 6183: int ioffset; /* variable offset for columns */
1.235 ! brouard 6184: int nres=0; /* Index of resultline */
1.219 brouard 6185:
1.126 brouard 6186: /* if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
6187: /* printf("Problem with file %s",optionfilegnuplot); */
6188: /* fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
6189: /* } */
6190:
6191: /*#ifdef windows */
6192: fprintf(ficgp,"cd \"%s\" \n",pathc);
1.223 brouard 6193: /*#endif */
1.225 brouard 6194: m=pow(2,cptcoveff);
1.126 brouard 6195:
1.202 brouard 6196: /* Contribution to likelihood */
6197: /* Plot the probability implied in the likelihood */
1.223 brouard 6198: fprintf(ficgp,"\n# Contributions to the Likelihood, mle >=1. For mle=4 no interpolation, pure matrix products.\n#\n");
6199: fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Likelihood (-2Log(L))\";");
6200: /* fprintf(ficgp,"\nset ter svg size 640, 480"); */ /* Too big for svg */
6201: fprintf(ficgp,"\nset ter pngcairo size 640, 480");
1.204 brouard 6202: /* nice for mle=4 plot by number of matrix products.
1.202 brouard 6203: replot "rrtest1/toto.txt" u 2:($4 == 1 && $5==2 ? $9 : 1/0):5 t "p12" with point lc 1 */
6204: /* replot exp(p1+p2*x)/(1+exp(p1+p2*x)+exp(p3+p4*x)+exp(p5+p6*x)) t "p12(x)" */
1.223 brouard 6205: /* fprintf(ficgp,"\nset out \"%s.svg\";",subdirf2(optionfilefiname,"ILK_")); */
6206: fprintf(ficgp,"\nset out \"%s-dest.png\";",subdirf2(optionfilefiname,"ILK_"));
6207: fprintf(ficgp,"\nset log y;plot \"%s\" u 2:(-$13):6 t \"All sample, transitions colored by destination\" with dots lc variable; set out;\n",subdirf(fileresilk));
6208: fprintf(ficgp,"\nset out \"%s-ori.png\";",subdirf2(optionfilefiname,"ILK_"));
6209: fprintf(ficgp,"\nset log y;plot \"%s\" u 2:(-$13):5 t \"All sample, transitions colored by origin\" with dots lc variable; set out;\n\n",subdirf(fileresilk));
6210: for (i=1; i<= nlstate ; i ++) {
6211: fprintf(ficgp,"\nset out \"%s-p%dj.png\";set ylabel \"Probability for each individual/wave\";",subdirf2(optionfilefiname,"ILK_"),i);
6212: fprintf(ficgp,"unset log;\n# plot weighted, mean weight should have point size of 0.5\n plot \"%s\"",subdirf(fileresilk));
6213: fprintf(ficgp," u 2:($5 == %d && $6==%d ? $10 : 1/0):($12/4.):6 t \"p%d%d\" with points pointtype 7 ps variable lc variable \\\n",i,1,i,1);
6214: for (j=2; j<= nlstate+ndeath ; j ++) {
6215: fprintf(ficgp,",\\\n \"\" u 2:($5 == %d && $6==%d ? $10 : 1/0):($12/4.):6 t \"p%d%d\" with points pointtype 7 ps variable lc variable ",i,j,i,j);
6216: }
6217: fprintf(ficgp,";\nset out; unset ylabel;\n");
6218: }
6219: /* 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 */
6220: /* fprintf(ficgp,"\nset log y;plot \"%s\" u 2:(-$11):3 t \"All sample, all transitions\" with dots lc variable",subdirf(fileresilk)); */
6221: /* fprintf(ficgp,"\nreplot \"%s\" u 2:($3 <= 3 ? -$11 : 1/0):3 t \"First 3 individuals\" with line lc variable", subdirf(fileresilk)); */
6222: fprintf(ficgp,"\nset out;unset log\n");
6223: /* fprintf(ficgp,"\nset out \"%s.svg\"; replot; set out; # bug gnuplot",subdirf2(optionfilefiname,"ILK_")); */
1.202 brouard 6224:
1.126 brouard 6225: strcpy(dirfileres,optionfilefiname);
6226: strcpy(optfileres,"vpl");
1.223 brouard 6227: /* 1eme*/
1.211 brouard 6228: for (cpt=1; cpt<= nlstate ; cpt ++) { /* For each live state */
1.235 ! brouard 6229: for(nres=1; nres <= nresult; nres++) /* For each resultline */
! 6230: for (k1=1; k1<= m ; k1 ++) { /* For each valid combination of covariate */
! 6231: /* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */
! 6232: if(TKresult[nres]!= k1)
! 6233: continue;
! 6234: /* We are interested in selected combination by the resultline */
! 6235: printf("\n# 1st: Period (stable) prevalence with CI: 'VPL_' files and live state =%d ", cpt);
! 6236: fprintf(ficgp,"\n# 1st: Period (stable) prevalence with CI: 'VPL_' files and live state =%d ", cpt);
1.225 brouard 6237: for (k=1; k<=cptcoveff; k++){ /* For each covariate k get corresponding value lv for combination k1 */
6238: lv= decodtabm(k1,k,cptcoveff); /* Should be the value of the covariate corresponding to k1 combination */
1.223 brouard 6239: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
6240: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
6241: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
6242: vlv= nbcode[Tvaraff[k]][lv]; /* vlv is the value of the covariate lv, 0 or 1 */
6243: /* For each combination of covariate k1 (V1=1, V3=0), we printed the current covariate k and its value vlv */
1.235 ! brouard 6244: printf(" V%d=%d ",Tvaraff[k],vlv);
1.223 brouard 6245: fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
1.211 brouard 6246: }
1.235 ! brouard 6247: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
! 6248: printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
! 6249: fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
! 6250: }
! 6251: printf("\n#\n");
1.211 brouard 6252: fprintf(ficgp,"\n#\n");
1.223 brouard 6253: if(invalidvarcomb[k1]){
6254: fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
6255: continue;
6256: }
1.235 ! brouard 6257:
1.223 brouard 6258: fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"V_"),cpt,k1);
6259: fprintf(ficgp,"\n#set out \"V_%s_%d-%d.svg\" \n",optionfilefiname,cpt,k1);
6260: fprintf(ficgp,"set xlabel \"Age\" \n\
1.235 ! brouard 6261: set ylabel \"Probability\" \n \
! 6262: set ter svg size 640, 480\n \
1.201 brouard 6263: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"%%lf",ageminpar,fage,subdirf2(fileresu,"VPL_"),k1-1,k1-1);
1.235 ! brouard 6264:
1.223 brouard 6265: for (i=1; i<= nlstate ; i ++) {
6266: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
6267: else fprintf(ficgp," %%*lf (%%*lf)");
6268: }
6269: 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);
6270: for (i=1; i<= nlstate ; i ++) {
6271: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
6272: else fprintf(ficgp," %%*lf (%%*lf)");
6273: }
6274: fprintf(ficgp,"\" t\"95%% CI\" w l lt 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"%%lf",subdirf2(fileresu,"VPL_"),k1-1,k1-1);
6275: for (i=1; i<= nlstate ; i ++) {
6276: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
6277: else fprintf(ficgp," %%*lf (%%*lf)");
6278: }
6279: fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence\" w l lt 2",subdirf2(fileresu,"P_"),k1-1,k1-1,2+4*(cpt-1));
6280: if(backcast==1){ /* We need to get the corresponding values of the covariates involved in this combination k1 */
6281: /* fprintf(ficgp,",\"%s\" every :::%d::%d u 1:($%d) t\"Backward stable prevalence\" w l lt 3",subdirf2(fileresu,"PLB_"),k1-1,k1-1,1+cpt); */
6282: fprintf(ficgp,",\"%s\" u 1:((",subdirf2(fileresu,"PLB_")); /* Age is in 1 */
1.225 brouard 6283: if(cptcoveff ==0){
1.223 brouard 6284: fprintf(ficgp,"$%d)) t 'Backward prevalence in state %d' with line ", 2+(cpt-1), cpt );
6285: }else{
6286: kl=0;
1.225 brouard 6287: for (k=1; k<=cptcoveff; k++){ /* For each combination of covariate */
6288: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */
1.223 brouard 6289: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
6290: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
6291: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
6292: vlv= nbcode[Tvaraff[k]][lv];
6293: kl++;
6294: /* kl=6+(cpt-1)*(nlstate+1)+1+(i-1); /\* 6+(1-1)*(2+1)+1+(1-1)=7, 6+(2-1)(2+1)+1+(1-1)=10 *\/ */
6295: /*6+(cpt-1)*(nlstate+1)+1+(i-1)+(nlstate+1)*nlstate; 6+(1-1)*(2+1)+1+(1-1) +(2+1)*2=13 */
6296: /*6+1+(i-1)+(nlstate+1)*nlstate; 6+1+(1-1) +(2+1)*2=13 */
6297: /* '' u 6:(($1==1 && $2==0 && $3==2 && $4==0)? $9/(1.-$15) : 1/0):($5==2000? 3:2) t 'p.1' with line lc variable*/
1.225 brouard 6298: if(k==cptcoveff){
1.227 brouard 6299: fprintf(ficgp,"$%d==%d && $%d==%d)? $%d : 1/0) t 'Backward prevalence in state %d' ",kl+1, Tvaraff[k],kl+1+1,nbcode[Tvaraff[k]][lv], \
6300: 4+(cpt-1), cpt ); /* 4 or 6 ?*/
1.223 brouard 6301: }else{
6302: fprintf(ficgp,"$%d==%d && $%d==%d && ",kl+1, Tvaraff[k],kl+1+1,nbcode[Tvaraff[k]][lv]);
6303: kl++;
6304: }
6305: } /* end covariate */
6306: } /* end if no covariate */
6307: } /* end if backcast */
6308: fprintf(ficgp,"\nset out \n");
1.201 brouard 6309: } /* k1 */
6310: } /* cpt */
1.235 ! brouard 6311:
! 6312:
1.126 brouard 6313: /*2 eme*/
6314: for (k1=1; k1<= m ; k1 ++) {
1.223 brouard 6315: fprintf(ficgp,"\n# 2nd: Total life expectancy with CI: 't' files ");
1.235 ! brouard 6316: for(nres=1; nres <= nresult; nres++) /* For each resultline */
1.225 brouard 6317: for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */
1.235 ! brouard 6318: if(TKresult[nres]!= k)
! 6319: continue;
1.225 brouard 6320: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
1.223 brouard 6321: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
6322: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
6323: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
6324: vlv= nbcode[Tvaraff[k]][lv];
6325: fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
1.235 ! brouard 6326: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
! 6327: printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
! 6328: fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
! 6329: }
1.223 brouard 6330: }
6331: fprintf(ficgp,"\n#\n");
6332: if(invalidvarcomb[k1]){
6333: fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
6334: continue;
6335: }
1.219 brouard 6336:
1.223 brouard 6337: fprintf(ficgp,"\nset out \"%s_%d.svg\" \n",subdirf2(optionfilefiname,"E_"),k1);
6338: for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
6339: if(vpopbased==0)
6340: fprintf(ficgp,"set ylabel \"Years\" \nset ter svg size 640, 480\nplot [%.f:%.f] ",ageminpar,fage);
6341: else
6342: fprintf(ficgp,"\nreplot ");
6343: for (i=1; i<= nlstate+1 ; i ++) {
6344: k=2*i;
6345: 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);
6346: for (j=1; j<= nlstate+1 ; j ++) {
6347: if (j==i) fprintf(ficgp," %%lf (%%lf)");
6348: else fprintf(ficgp," %%*lf (%%*lf)");
6349: }
6350: if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l lt %d, \\\n",i);
6351: else fprintf(ficgp,"\" t\"LE in state (%d)\" w l lt %d, \\\n",i-1,i+1);
6352: 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);
6353: for (j=1; j<= nlstate+1 ; j ++) {
6354: if (j==i) fprintf(ficgp," %%lf (%%lf)");
6355: else fprintf(ficgp," %%*lf (%%*lf)");
6356: }
6357: fprintf(ficgp,"\" t\"\" w l lt 0,");
6358: 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);
6359: for (j=1; j<= nlstate+1 ; j ++) {
6360: if (j==i) fprintf(ficgp," %%lf (%%lf)");
6361: else fprintf(ficgp," %%*lf (%%*lf)");
6362: }
6363: if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l lt 0");
6364: else fprintf(ficgp,"\" t\"\" w l lt 0,\\\n");
6365: } /* state */
6366: } /* vpopbased */
6367: fprintf(ficgp,"\nset out;set out \"%s_%d.svg\"; replot; set out; \n",subdirf2(optionfilefiname,"E_"),k1); /* Buggy gnuplot */
1.235 ! brouard 6368: } /* k1 end 2 eme*/
1.219 brouard 6369:
6370:
1.126 brouard 6371: /*3eme*/
6372: for (k1=1; k1<= m ; k1 ++) {
1.220 brouard 6373:
1.126 brouard 6374: for (cpt=1; cpt<= nlstate ; cpt ++) {
1.211 brouard 6375: fprintf(ficgp,"\n# 3d: Life expectancy with EXP_ files: cov=%d state=%d",k1, cpt);
1.235 ! brouard 6376: for(nres=1; nres <= nresult; nres++) /* For each resultline */
1.225 brouard 6377: for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */
1.235 ! brouard 6378: if(TKresult[nres]!= k)
! 6379: continue;
1.225 brouard 6380: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
1.223 brouard 6381: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
6382: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
6383: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
6384: vlv= nbcode[Tvaraff[k]][lv];
6385: fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
1.235 ! brouard 6386: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
! 6387: printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
! 6388: fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
! 6389: }
1.211 brouard 6390: }
6391: fprintf(ficgp,"\n#\n");
1.223 brouard 6392: if(invalidvarcomb[k1]){
6393: fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
6394: continue;
6395: }
1.219 brouard 6396:
1.126 brouard 6397: /* k=2+nlstate*(2*cpt-2); */
6398: k=2+(nlstate+1)*(cpt-1);
1.201 brouard 6399: fprintf(ficgp,"\nset out \"%s_%d%d.svg\" \n",subdirf2(optionfilefiname,"EXP_"),cpt,k1);
1.199 brouard 6400: fprintf(ficgp,"set ter svg size 640, 480\n\
1.201 brouard 6401: 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 6402: /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
1.223 brouard 6403: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
6404: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
6405: fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
6406: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
6407: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
1.219 brouard 6408:
1.126 brouard 6409: */
6410: for (i=1; i< nlstate ; i ++) {
1.223 brouard 6411: 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);
6412: /* 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);*/
1.219 brouard 6413:
1.126 brouard 6414: }
1.201 brouard 6415: 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 6416: }
6417: }
6418:
1.223 brouard 6419: /* 4eme */
1.201 brouard 6420: /* Survival functions (period) from state i in state j by initial state i */
6421: for (k1=1; k1<= m ; k1 ++) { /* For each multivariate if any */
1.220 brouard 6422:
1.201 brouard 6423: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
1.211 brouard 6424: fprintf(ficgp,"\n#\n#\n# Survival functions in state j : 'LIJ_' files, cov=%d state=%d",k1, cpt);
1.225 brouard 6425: for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */
6426: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
1.223 brouard 6427: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
6428: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
6429: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
6430: vlv= nbcode[Tvaraff[k]][lv];
6431: fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
1.211 brouard 6432: }
6433: fprintf(ficgp,"\n#\n");
1.223 brouard 6434: if(invalidvarcomb[k1]){
6435: fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
6436: continue;
6437: }
1.220 brouard 6438:
1.201 brouard 6439: fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"LIJ_"),cpt,k1);
6440: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability to be alive\" \n\
1.220 brouard 6441: set ter svg size 640, 480\n \
6442: unset log y\n \
1.201 brouard 6443: plot [%.f:%.f] ", ageminpar, agemaxpar);
1.211 brouard 6444: k=3;
1.201 brouard 6445: for (i=1; i<= nlstate ; i ++){
1.223 brouard 6446: if(i==1){
6447: fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
6448: }else{
6449: fprintf(ficgp,", '' ");
6450: }
6451: l=(nlstate+ndeath)*(i-1)+1;
6452: fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
6453: for (j=2; j<= nlstate+ndeath ; j ++)
6454: fprintf(ficgp,"+$%d",k+l+j-1);
6455: fprintf(ficgp,")) t \"l(%d,%d)\" w l",i,cpt);
1.201 brouard 6456: } /* nlstate */
6457: fprintf(ficgp,"\nset out\n");
6458: } /* end cpt state*/
6459: } /* end covariate */
1.220 brouard 6460:
6461: /* 5eme */
1.201 brouard 6462: /* Survival functions (period) from state i in state j by final state j */
1.202 brouard 6463: for (k1=1; k1<= m ; k1 ++) { /* For each covariate if any */
1.201 brouard 6464: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each inital state */
1.223 brouard 6465:
1.201 brouard 6466: fprintf(ficgp,"\n#\n#\n# Survival functions in state j and all livestates from state i by final state j: 'lij' files, cov=%d state=%d",k1, cpt);
1.225 brouard 6467: for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */
1.227 brouard 6468: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
6469: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
6470: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
6471: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
6472: vlv= nbcode[Tvaraff[k]][lv];
6473: fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
1.211 brouard 6474: }
6475: fprintf(ficgp,"\n#\n");
1.223 brouard 6476: if(invalidvarcomb[k1]){
1.227 brouard 6477: fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
6478: continue;
1.223 brouard 6479: }
1.227 brouard 6480:
1.201 brouard 6481: fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"LIJT_"),cpt,k1);
6482: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability to be alive\" \n\
1.227 brouard 6483: set ter svg size 640, 480\n \
6484: unset log y\n \
1.201 brouard 6485: plot [%.f:%.f] ", ageminpar, agemaxpar);
1.211 brouard 6486: k=3;
1.201 brouard 6487: for (j=1; j<= nlstate ; j ++){ /* Lived in state j */
1.227 brouard 6488: if(j==1)
6489: fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
6490: else
6491: fprintf(ficgp,", '' ");
6492: l=(nlstate+ndeath)*(cpt-1) +j;
6493: fprintf(ficgp," u (($1==%d && (floor($2)%%5 == 0)) ? ($3):1/0):($%d",k1,k+l);
6494: /* for (i=2; i<= nlstate+ndeath ; i ++) */
6495: /* fprintf(ficgp,"+$%d",k+l+i-1); */
6496: fprintf(ficgp,") t \"l(%d,%d)\" w l",cpt,j);
1.201 brouard 6497: } /* nlstate */
6498: fprintf(ficgp,", '' ");
6499: fprintf(ficgp," u (($1==%d && (floor($2)%%5 == 0)) ? ($3):1/0):(",k1);
6500: for (j=1; j<= nlstate ; j ++){ /* Lived in state j */
1.227 brouard 6501: l=(nlstate+ndeath)*(cpt-1) +j;
6502: if(j < nlstate)
6503: fprintf(ficgp,"$%d +",k+l);
6504: else
6505: fprintf(ficgp,"$%d) t\"l(%d,.)\" w l",k+l,cpt);
1.201 brouard 6506: }
6507: fprintf(ficgp,"\nset out\n");
6508: } /* end cpt state*/
6509: } /* end covariate */
1.227 brouard 6510:
1.220 brouard 6511: /* 6eme */
1.202 brouard 6512: /* CV preval stable (period) for each covariate */
1.211 brouard 6513: for (k1=1; k1<= m ; k1 ++) { /* For each covariate combination (1 to m=2**k), if any covariate is present */
1.153 brouard 6514: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
1.227 brouard 6515:
1.211 brouard 6516: fprintf(ficgp,"\n#\n#\n#CV preval stable (period): 'pij' files, covariatecombination#=%d state=%d",k1, cpt);
1.225 brouard 6517: for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */
1.227 brouard 6518: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
6519: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
6520: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
6521: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
6522: vlv= nbcode[Tvaraff[k]][lv];
6523: fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
1.211 brouard 6524: }
6525: fprintf(ficgp,"\n#\n");
1.223 brouard 6526: if(invalidvarcomb[k1]){
1.227 brouard 6527: fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
6528: continue;
1.223 brouard 6529: }
1.227 brouard 6530:
1.201 brouard 6531: fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"P_"),cpt,k1);
1.126 brouard 6532: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
1.227 brouard 6533: set ter svg size 640, 480\n \
6534: unset log y\n \
1.153 brouard 6535: plot [%.f:%.f] ", ageminpar, agemaxpar);
1.211 brouard 6536: k=3; /* Offset */
1.153 brouard 6537: for (i=1; i<= nlstate ; i ++){
1.227 brouard 6538: if(i==1)
6539: fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
6540: else
6541: fprintf(ficgp,", '' ");
6542: l=(nlstate+ndeath)*(i-1)+1;
6543: fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
6544: for (j=2; j<= nlstate ; j ++)
6545: fprintf(ficgp,"+$%d",k+l+j-1);
6546: fprintf(ficgp,")) t \"prev(%d,%d)\" w l",i,cpt);
1.153 brouard 6547: } /* nlstate */
1.201 brouard 6548: fprintf(ficgp,"\nset out\n");
1.153 brouard 6549: } /* end cpt state*/
6550: } /* end covariate */
1.227 brouard 6551:
6552:
1.220 brouard 6553: /* 7eme */
1.218 brouard 6554: if(backcast == 1){
1.217 brouard 6555: /* CV back preval stable (period) for each covariate */
1.218 brouard 6556: for (k1=1; k1<= m ; k1 ++) { /* For each covariate combination (1 to m=2**k), if any covariate is present */
6557: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
1.227 brouard 6558: fprintf(ficgp,"\n#\n#\n#CV Back preval stable (period): 'pij' files, covariatecombination#=%d state=%d",k1, cpt);
6559: for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */
6560: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
6561: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
6562: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
1.223 brouard 6563: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
1.227 brouard 6564: vlv= nbcode[Tvaraff[k]][lv];
6565: fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
6566: }
6567: fprintf(ficgp,"\n#\n");
6568: if(invalidvarcomb[k1]){
6569: fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
6570: continue;
6571: }
6572:
6573: fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"PB_"),cpt,k1);
6574: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
6575: set ter svg size 640, 480\n \
6576: unset log y\n \
1.218 brouard 6577: plot [%.f:%.f] ", ageminpar, agemaxpar);
1.227 brouard 6578: k=3; /* Offset */
6579: for (i=1; i<= nlstate ; i ++){
6580: if(i==1)
6581: fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJB_"));
6582: else
6583: fprintf(ficgp,", '' ");
6584: /* l=(nlstate+ndeath)*(i-1)+1; */
6585: l=(nlstate+ndeath)*(cpt-1)+1;
6586: /* fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l); /\* a vérifier *\/ */
6587: /* fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l+(cpt-1)+i-1); /\* a vérifier *\/ */
6588: fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d",k1,k+l+(cpt-1)+i-1); /* a vérifier */
6589: /* for (j=2; j<= nlstate ; j ++) */
6590: /* fprintf(ficgp,"+$%d",k+l+j-1); */
6591: /* /\* fprintf(ficgp,"+$%d",k+l+j-1); *\/ */
6592: fprintf(ficgp,") t \"bprev(%d,%d)\" w l",i,cpt);
6593: } /* nlstate */
6594: fprintf(ficgp,"\nset out\n");
1.218 brouard 6595: } /* end cpt state*/
6596: } /* end covariate */
6597: } /* End if backcast */
6598:
1.223 brouard 6599: /* 8eme */
1.218 brouard 6600: if(prevfcast==1){
6601: /* Projection from cross-sectional to stable (period) for each covariate */
6602:
6603: for (k1=1; k1<= m ; k1 ++) { /* For each covariate combination (1 to m=2**k), if any covariate is present */
1.211 brouard 6604: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
1.227 brouard 6605: fprintf(ficgp,"\n#\n#\n#Projection of prevalence to stable (period): 'PROJ_' files, covariatecombination#=%d state=%d",k1, cpt);
6606: for (k=1; k<=cptcoveff; k++){ /* For each correspondig covariate value */
6607: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */
6608: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
6609: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
6610: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
6611: vlv= nbcode[Tvaraff[k]][lv];
6612: fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
6613: }
6614: fprintf(ficgp,"\n#\n");
6615: if(invalidvarcomb[k1]){
6616: fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
6617: continue;
6618: }
6619:
6620: fprintf(ficgp,"# hpijx=probability over h years, hp.jx is weighted by observed prev\n ");
6621: fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"PROJ_"),cpt,k1);
6622: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Prevalence\" \n\
6623: set ter svg size 640, 480\n \
6624: unset log y\n \
1.219 brouard 6625: plot [%.f:%.f] ", ageminpar, agemaxpar);
1.227 brouard 6626: for (i=1; i<= nlstate+1 ; i ++){ /* nlstate +1 p11 p21 p.1 */
6627: /*# V1 = 1 V2 = 0 yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
6628: /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 */
6629: /*# yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
6630: /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 */
6631: if(i==1){
6632: fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"F_"));
6633: }else{
6634: fprintf(ficgp,",\\\n '' ");
6635: }
6636: if(cptcoveff ==0){ /* No covariate */
6637: ioffset=2; /* Age is in 2 */
6638: /*# yearproj age p11 p21 p31 p.1 p12 p22 p32 p.2 p13 p23 p33 p.3 p14 p24 p34 p.4*/
6639: /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 */
6640: /*# V1 = 1 yearproj age p11 p21 p31 p.1 p12 p22 p32 p.2 p13 p23 p33 p.3 p14 p24 p34 p.4*/
6641: /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 */
6642: fprintf(ficgp," u %d:(", ioffset);
6643: if(i==nlstate+1)
6644: fprintf(ficgp," $%d/(1.-$%d)) t 'pw.%d' with line ", \
6645: ioffset+(cpt-1)*(nlstate+1)+1+(i-1), ioffset+1+(i-1)+(nlstate+1)*nlstate,cpt );
6646: else
6647: fprintf(ficgp," $%d/(1.-$%d)) t 'p%d%d' with line ", \
6648: ioffset+(cpt-1)*(nlstate+1)+1+(i-1), ioffset+1+(i-1)+(nlstate+1)*nlstate,i,cpt );
6649: }else{ /* more than 2 covariates */
6650: if(cptcoveff ==1){
6651: ioffset=4; /* Age is in 4 */
6652: }else{
6653: ioffset=6; /* Age is in 6 */
6654: /*# V1 = 1 V2 = 0 yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
6655: /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 */
6656: }
6657: fprintf(ficgp," u %d:(",ioffset);
6658: kl=0;
6659: strcpy(gplotcondition,"(");
6660: for (k=1; k<=cptcoveff; k++){ /* For each covariate writing the chain of conditions */
6661: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to combination k1 and covariate k */
6662: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
6663: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
6664: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
6665: vlv= nbcode[Tvaraff[k]][lv]; /* Value of the modality of Tvaraff[k] */
6666: kl++;
6667: sprintf(gplotcondition+strlen(gplotcondition),"$%d==%d && $%d==%d " ,kl,Tvaraff[k], kl+1, nbcode[Tvaraff[k]][lv]);
6668: kl++;
6669: if(k <cptcoveff && cptcoveff>1)
6670: sprintf(gplotcondition+strlen(gplotcondition)," && ");
6671: }
6672: strcpy(gplotcondition+strlen(gplotcondition),")");
6673: /* kl=6+(cpt-1)*(nlstate+1)+1+(i-1); /\* 6+(1-1)*(2+1)+1+(1-1)=7, 6+(2-1)(2+1)+1+(1-1)=10 *\/ */
6674: /*6+(cpt-1)*(nlstate+1)+1+(i-1)+(nlstate+1)*nlstate; 6+(1-1)*(2+1)+1+(1-1) +(2+1)*2=13 */
6675: /*6+1+(i-1)+(nlstate+1)*nlstate; 6+1+(1-1) +(2+1)*2=13 */
6676: /* '' u 6:(($1==1 && $2==0 && $3==2 && $4==0)? $9/(1.-$15) : 1/0):($5==2000? 3:2) t 'p.1' with line lc variable*/
6677: if(i==nlstate+1){
6678: fprintf(ficgp,"%s ? $%d/(1.-$%d) : 1/0) t 'p.%d' with line ", gplotcondition, \
6679: ioffset+(cpt-1)*(nlstate+1)+1+(i-1), ioffset+1+(i-1)+(nlstate+1)*nlstate,cpt );
6680: }else{
6681: fprintf(ficgp,"%s ? $%d/(1.-$%d) : 1/0) t 'p%d%d' with line ", gplotcondition, \
6682: ioffset+(cpt-1)*(nlstate+1)+1+(i-1), ioffset +1+(i-1)+(nlstate+1)*nlstate,i,cpt );
6683: }
6684: } /* end if covariate */
6685: } /* nlstate */
6686: fprintf(ficgp,"\nset out\n");
1.223 brouard 6687: } /* end cpt state*/
6688: } /* end covariate */
6689: } /* End if prevfcast */
1.227 brouard 6690:
6691:
1.223 brouard 6692: /* proba elementaires */
6693: fprintf(ficgp,"\n##############\n#MLE estimated parameters\n#############\n");
1.126 brouard 6694: for(i=1,jk=1; i <=nlstate; i++){
1.187 brouard 6695: fprintf(ficgp,"# initial state %d\n",i);
1.126 brouard 6696: for(k=1; k <=(nlstate+ndeath); k++){
6697: if (k != i) {
1.227 brouard 6698: fprintf(ficgp,"# current state %d\n",k);
6699: for(j=1; j <=ncovmodel; j++){
6700: fprintf(ficgp,"p%d=%f; ",jk,p[jk]);
6701: jk++;
6702: }
6703: fprintf(ficgp,"\n");
1.126 brouard 6704: }
6705: }
1.223 brouard 6706: }
1.187 brouard 6707: fprintf(ficgp,"##############\n#\n");
1.227 brouard 6708:
1.145 brouard 6709: /*goto avoid;*/
1.200 brouard 6710: fprintf(ficgp,"\n##############\n#Graphics of probabilities or incidences\n#############\n");
1.187 brouard 6711: fprintf(ficgp,"# logi(p12/p11)=a12+b12*age+c12age*age+d12*V1+e12*V1*age\n");
6712: fprintf(ficgp,"# logi(p12/p11)=p1 +p2*age +p3*age*age+ p4*V1+ p5*V1*age\n");
6713: fprintf(ficgp,"# logi(p13/p11)=a13+b13*age+c13age*age+d13*V1+e13*V1*age\n");
6714: fprintf(ficgp,"# logi(p13/p11)=p6 +p7*age +p8*age*age+ p9*V1+ p10*V1*age\n");
6715: fprintf(ficgp,"# p12+p13+p14+p11=1=p11(1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n");
6716: fprintf(ficgp,"# +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age)+...)\n");
6717: fprintf(ficgp,"# p11=1/(1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n");
6718: fprintf(ficgp,"# +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age)+...)\n");
6719: fprintf(ficgp,"# p12=exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)/\n");
6720: fprintf(ficgp,"# (1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n");
6721: fprintf(ficgp,"# +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age))\n");
6722: fprintf(ficgp,"# +exp(a14+b14*age+c14age*age+d14*V1+e14*V1*age)+...)\n");
6723: fprintf(ficgp,"#\n");
1.223 brouard 6724: for(ng=1; ng<=3;ng++){ /* Number of graphics: first is logit, 2nd is probabilities, third is incidences per year*/
6725: fprintf(ficgp,"# ng=%d\n",ng);
1.225 brouard 6726: fprintf(ficgp,"# jk=1 to 2^%d=%d\n",cptcoveff,m);
1.223 brouard 6727: for(jk=1; jk <=m; jk++) {
6728: fprintf(ficgp,"# jk=%d\n",jk);
6729: fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" ",subdirf2(optionfilefiname,"PE_"),jk,ng);
6730: fprintf(ficgp,"\nset ter svg size 640, 480 ");
6731: if (ng==1){
6732: fprintf(ficgp,"\nset ylabel \"Value of the logit of the model\"\n"); /* exp(a12+b12*x) could be nice */
6733: fprintf(ficgp,"\nunset log y");
6734: }else if (ng==2){
6735: fprintf(ficgp,"\nset ylabel \"Probability\"\n");
6736: fprintf(ficgp,"\nset log y");
6737: }else if (ng==3){
6738: fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
6739: fprintf(ficgp,"\nset log y");
6740: }else
6741: fprintf(ficgp,"\nunset title ");
6742: fprintf(ficgp,"\nplot [%.f:%.f] ",ageminpar,agemaxpar);
6743: i=1;
6744: for(k2=1; k2<=nlstate; k2++) {
6745: k3=i;
6746: for(k=1; k<=(nlstate+ndeath); k++) {
6747: if (k != k2){
6748: switch( ng) {
6749: case 1:
6750: if(nagesqr==0)
6751: fprintf(ficgp," p%d+p%d*x",i,i+1);
6752: else /* nagesqr =1 */
6753: fprintf(ficgp," p%d+p%d*x+p%d*x*x",i,i+1,i+1+nagesqr);
6754: break;
6755: case 2: /* ng=2 */
6756: if(nagesqr==0)
6757: fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
6758: else /* nagesqr =1 */
6759: fprintf(ficgp," exp(p%d+p%d*x+p%d*x*x",i,i+1,i+1+nagesqr);
6760: break;
6761: case 3:
6762: if(nagesqr==0)
6763: fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
6764: else /* nagesqr =1 */
6765: fprintf(ficgp," %f*exp(p%d+p%d*x+p%d*x*x",YEARM/stepm,i,i+1,i+1+nagesqr);
6766: break;
6767: }
6768: ij=1;/* To be checked else nbcode[0][0] wrong */
6769: for(j=3; j <=ncovmodel-nagesqr; j++) {
6770: /* printf("Tage[%d]=%d, j=%d\n", ij, Tage[ij], j); */
6771: if(ij <=cptcovage) { /* Bug valgrind */
6772: if((j-2)==Tage[ij]) { /* Bug valgrind */
6773: fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);
6774: /* fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(jk,Tvar[j-2])]); */
6775: ij++;
6776: }
6777: }
6778: else
1.227 brouard 6779: fprintf(ficgp,"+p%d*%d",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(jk,j-2)]); /* Valgrind bug nbcode */
1.223 brouard 6780: }
6781: }else{
6782: i=i-ncovmodel;
6783: if(ng !=1 ) /* For logit formula of log p11 is more difficult to get */
6784: fprintf(ficgp," (1.");
6785: }
1.227 brouard 6786:
1.223 brouard 6787: if(ng != 1){
6788: fprintf(ficgp,")/(1");
1.227 brouard 6789:
1.223 brouard 6790: for(k1=1; k1 <=nlstate; k1++){
6791: if(nagesqr==0)
6792: fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
6793: else /* nagesqr =1 */
6794: 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);
1.217 brouard 6795:
1.223 brouard 6796: ij=1;
6797: for(j=3; j <=ncovmodel-nagesqr; j++){
6798: if(ij <=cptcovage) { /* Bug valgrind */
6799: if((j-2)==Tage[ij]) { /* Bug valgrind */
6800: fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);
6801: /* fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(jk,Tvar[j-2])]); */
6802: ij++;
6803: }
6804: }
6805: else
1.225 brouard 6806: fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);/* Valgrind bug nbcode */
1.223 brouard 6807: }
6808: fprintf(ficgp,")");
6809: }
6810: fprintf(ficgp,")");
6811: if(ng ==2)
6812: fprintf(ficgp," t \"p%d%d\" ", k2,k);
6813: else /* ng= 3 */
6814: fprintf(ficgp," t \"i%d%d\" ", k2,k);
6815: }else{ /* end ng <> 1 */
6816: if( k !=k2) /* logit p11 is hard to draw */
6817: fprintf(ficgp," t \"logit(p%d%d)\" ", k2,k);
6818: }
6819: if ((k+k2)!= (nlstate*2+ndeath) && ng != 1)
6820: fprintf(ficgp,",");
6821: if (ng == 1 && k!=k2 && (k+k2)!= (nlstate*2+ndeath))
6822: fprintf(ficgp,",");
6823: i=i+ncovmodel;
6824: } /* end k */
6825: } /* end k2 */
6826: fprintf(ficgp,"\n set out\n");
6827: } /* end jk */
6828: } /* end ng */
6829: /* avoid: */
6830: fflush(ficgp);
1.126 brouard 6831: } /* end gnuplot */
6832:
6833:
6834: /*************** Moving average **************/
1.219 brouard 6835: /* int movingaverage(double ***probs, double bage, double fage, double ***mobaverage, int mobilav, double bageout, double fageout){ */
1.222 brouard 6836: int movingaverage(double ***probs, double bage, double fage, double ***mobaverage, int mobilav){
1.218 brouard 6837:
1.222 brouard 6838: int i, cpt, cptcod;
6839: int modcovmax =1;
6840: int mobilavrange, mob;
6841: int iage=0;
6842:
6843: double sum=0.;
6844: double age;
6845: double *sumnewp, *sumnewm;
6846: double *agemingood, *agemaxgood; /* Currently identical for all covariates */
6847:
6848:
1.225 brouard 6849: /* modcovmax=2*cptcoveff;/\* Max number of modalities. We suppose */
1.222 brouard 6850: /* a covariate has 2 modalities, should be equal to ncovcombmax *\/ */
6851:
6852: sumnewp = vector(1,ncovcombmax);
6853: sumnewm = vector(1,ncovcombmax);
6854: agemingood = vector(1,ncovcombmax);
6855: agemaxgood = vector(1,ncovcombmax);
6856:
6857: for (cptcod=1;cptcod<=ncovcombmax;cptcod++){
6858: sumnewm[cptcod]=0.;
6859: sumnewp[cptcod]=0.;
6860: agemingood[cptcod]=0;
6861: agemaxgood[cptcod]=0;
6862: }
6863: if (cptcovn<1) ncovcombmax=1; /* At least 1 pass */
6864:
6865: if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
6866: if(mobilav==1) mobilavrange=5; /* default */
6867: else mobilavrange=mobilav;
6868: for (age=bage; age<=fage; age++)
6869: for (i=1; i<=nlstate;i++)
6870: for (cptcod=1;cptcod<=ncovcombmax;cptcod++)
6871: mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
6872: /* We keep the original values on the extreme ages bage, fage and for
6873: fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
6874: we use a 5 terms etc. until the borders are no more concerned.
6875: */
6876: for (mob=3;mob <=mobilavrange;mob=mob+2){
6877: for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
6878: for (i=1; i<=nlstate;i++){
6879: for (cptcod=1;cptcod<=ncovcombmax;cptcod++){
6880: mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
6881: for (cpt=1;cpt<=(mob-1)/2;cpt++){
6882: mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
6883: mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
6884: }
6885: mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
6886: }
6887: }
6888: }/* end age */
6889: }/* end mob */
6890: }else
6891: return -1;
6892: for (cptcod=1;cptcod<=ncovcombmax;cptcod++){
6893: /* for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){ */
6894: if(invalidvarcomb[cptcod]){
6895: printf("\nCombination (%d) ignored because no cases \n",cptcod);
6896: continue;
6897: }
1.219 brouard 6898:
1.222 brouard 6899: agemingood[cptcod]=fage-(mob-1)/2;
6900: for (age=fage-(mob-1)/2; age>=bage; age--){/* From oldest to youngest, finding the youngest wrong */
6901: sumnewm[cptcod]=0.;
6902: for (i=1; i<=nlstate;i++){
6903: sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];
6904: }
6905: if(fabs(sumnewm[cptcod] - 1.) <= 1.e-3) { /* good */
6906: agemingood[cptcod]=age;
6907: }else{ /* bad */
6908: for (i=1; i<=nlstate;i++){
6909: mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemingood[cptcod]][i][cptcod];
6910: } /* i */
6911: } /* end bad */
6912: }/* age */
6913: sum=0.;
6914: for (i=1; i<=nlstate;i++){
6915: sum+=mobaverage[(int)agemingood[cptcod]][i][cptcod];
6916: }
6917: if(fabs(sum - 1.) > 1.e-3) { /* bad */
6918: printf("For this combination of covariate cptcod=%d, we can't get a smoothed prevalence which sums to one at any descending age!\n",cptcod);
6919: /* for (i=1; i<=nlstate;i++){ */
6920: /* mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemingood[cptcod]][i][cptcod]; */
6921: /* } /\* i *\/ */
6922: } /* end bad */
6923: /* else{ /\* We found some ages summing to one, we will smooth the oldest *\/ */
6924: /* From youngest, finding the oldest wrong */
6925: agemaxgood[cptcod]=bage+(mob-1)/2;
6926: for (age=bage+(mob-1)/2; age<=fage; age++){
6927: sumnewm[cptcod]=0.;
6928: for (i=1; i<=nlstate;i++){
6929: sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];
6930: }
6931: if(fabs(sumnewm[cptcod] - 1.) <= 1.e-3) { /* good */
6932: agemaxgood[cptcod]=age;
6933: }else{ /* bad */
6934: for (i=1; i<=nlstate;i++){
6935: mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemaxgood[cptcod]][i][cptcod];
6936: } /* i */
6937: } /* end bad */
6938: }/* age */
6939: sum=0.;
6940: for (i=1; i<=nlstate;i++){
6941: sum+=mobaverage[(int)agemaxgood[cptcod]][i][cptcod];
6942: }
6943: if(fabs(sum - 1.) > 1.e-3) { /* bad */
6944: printf("For this combination of covariate cptcod=%d, we can't get a smoothed prevalence which sums to one at any ascending age!\n",cptcod);
6945: /* for (i=1; i<=nlstate;i++){ */
6946: /* mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemingood[cptcod]][i][cptcod]; */
6947: /* } /\* i *\/ */
6948: } /* end bad */
6949:
6950: for (age=bage; age<=fage; age++){
1.235 ! brouard 6951: /* printf("%d %d ", cptcod, (int)age); */
1.222 brouard 6952: sumnewp[cptcod]=0.;
6953: sumnewm[cptcod]=0.;
6954: for (i=1; i<=nlstate;i++){
6955: sumnewp[cptcod]+=probs[(int)age][i][cptcod];
6956: sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];
6957: /* printf("%.4f %.4f ",probs[(int)age][i][cptcod], mobaverage[(int)age][i][cptcod]); */
6958: }
6959: /* printf("%.4f %.4f \n",sumnewp[cptcod], sumnewm[cptcod]); */
6960: }
6961: /* printf("\n"); */
6962: /* } */
6963: /* brutal averaging */
6964: for (i=1; i<=nlstate;i++){
6965: for (age=1; age<=bage; age++){
6966: mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemingood[cptcod]][i][cptcod];
6967: /* printf("age=%d i=%d cptcod=%d mobaverage=%.4f \n",(int)age,i, cptcod, mobaverage[(int)age][i][cptcod]); */
6968: }
6969: for (age=fage; age<=AGESUP; age++){
6970: mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemaxgood[cptcod]][i][cptcod];
6971: /* printf("age=%d i=%d cptcod=%d mobaverage=%.4f \n",(int)age,i, cptcod, mobaverage[(int)age][i][cptcod]); */
6972: }
6973: } /* end i status */
6974: for (i=nlstate+1; i<=nlstate+ndeath;i++){
6975: for (age=1; age<=AGESUP; age++){
6976: /*printf("i=%d, age=%d, cptcod=%d\n",i, (int)age, cptcod);*/
6977: mobaverage[(int)age][i][cptcod]=0.;
6978: }
6979: }
6980: }/* end cptcod */
6981: free_vector(sumnewm,1, ncovcombmax);
6982: free_vector(sumnewp,1, ncovcombmax);
6983: free_vector(agemaxgood,1, ncovcombmax);
6984: free_vector(agemingood,1, ncovcombmax);
6985: return 0;
6986: }/* End movingaverage */
1.218 brouard 6987:
1.126 brouard 6988:
6989: /************** Forecasting ******************/
1.235 ! brouard 6990: 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 6991: /* proj1, year, month, day of starting projection
6992: agemin, agemax range of age
6993: dateprev1 dateprev2 range of dates during which prevalence is computed
6994: anproj2 year of en of projection (same day and month as proj1).
6995: */
1.235 ! brouard 6996: int yearp, stepsize, hstepm, nhstepm, j, k, cptcod, i, h, i1, k4, nres=0;
1.126 brouard 6997: double agec; /* generic age */
6998: double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
6999: double *popeffectif,*popcount;
7000: double ***p3mat;
1.218 brouard 7001: /* double ***mobaverage; */
1.126 brouard 7002: char fileresf[FILENAMELENGTH];
7003:
7004: agelim=AGESUP;
1.211 brouard 7005: /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
7006: in each health status at the date of interview (if between dateprev1 and dateprev2).
7007: We still use firstpass and lastpass as another selection.
7008: */
1.214 brouard 7009: /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart,\ */
7010: /* firstpass, lastpass, stepm, weightopt, model); */
1.126 brouard 7011:
1.201 brouard 7012: strcpy(fileresf,"F_");
7013: strcat(fileresf,fileresu);
1.126 brouard 7014: if((ficresf=fopen(fileresf,"w"))==NULL) {
7015: printf("Problem with forecast resultfile: %s\n", fileresf);
7016: fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
7017: }
1.235 ! brouard 7018: printf("\nComputing forecasting: result on file '%s', please wait... \n", fileresf);
! 7019: fprintf(ficlog,"\nComputing forecasting: result on file '%s', please wait... \n", fileresf);
1.126 brouard 7020:
1.225 brouard 7021: if (cptcoveff==0) ncodemax[cptcoveff]=1;
1.126 brouard 7022:
7023:
7024: stepsize=(int) (stepm+YEARM-1)/YEARM;
7025: if (stepm<=12) stepsize=1;
7026: if(estepm < stepm){
7027: printf ("Problem %d lower than %d\n",estepm, stepm);
7028: }
7029: else hstepm=estepm;
7030:
7031: hstepm=hstepm/stepm;
7032: yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp and
7033: fractional in yp1 */
7034: anprojmean=yp;
7035: yp2=modf((yp1*12),&yp);
7036: mprojmean=yp;
7037: yp1=modf((yp2*30.5),&yp);
7038: jprojmean=yp;
7039: if(jprojmean==0) jprojmean=1;
7040: if(mprojmean==0) jprojmean=1;
7041:
1.227 brouard 7042: i1=pow(2,cptcoveff);
1.126 brouard 7043: if (cptcovn < 1){i1=1;}
7044:
7045: fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);
7046:
7047: fprintf(ficresf,"#****** Routine prevforecast **\n");
1.227 brouard 7048:
1.126 brouard 7049: /* if (h==(int)(YEARM*yearp)){ */
1.235 ! brouard 7050: for(nres=1; nres <= nresult; nres++) /* For each resultline */
! 7051: for(k=1; k<=i1;k++){
! 7052: if(TKresult[nres]!= k)
! 7053: continue;
1.227 brouard 7054: if(invalidvarcomb[k]){
7055: printf("\nCombination (%d) projection ignored because no cases \n",k);
7056: continue;
7057: }
7058: fprintf(ficresf,"\n#****** hpijx=probability over h years, hp.jx is weighted by observed prev \n#");
7059: for(j=1;j<=cptcoveff;j++) {
7060: fprintf(ficresf," V%d (=) %d",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
7061: }
1.235 ! brouard 7062: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
! 7063: printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
! 7064: fprintf(ficlog," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
! 7065: }
1.227 brouard 7066: fprintf(ficresf," yearproj age");
7067: for(j=1; j<=nlstate+ndeath;j++){
7068: for(i=1; i<=nlstate;i++)
7069: fprintf(ficresf," p%d%d",i,j);
7070: fprintf(ficresf," wp.%d",j);
7071: }
7072: for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {
7073: fprintf(ficresf,"\n");
7074: fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);
7075: for (agec=fage; agec>=(ageminpar-1); agec--){
7076: nhstepm=(int) rint((agelim-agec)*YEARM/stepm);
7077: nhstepm = nhstepm/hstepm;
7078: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
7079: oldm=oldms;savm=savms;
1.235 ! brouard 7080: hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k,nres);
1.227 brouard 7081:
7082: for (h=0; h<=nhstepm; h++){
7083: if (h*hstepm/YEARM*stepm ==yearp) {
7084: fprintf(ficresf,"\n");
7085: for(j=1;j<=cptcoveff;j++)
7086: fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
7087: fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
7088: }
7089: for(j=1; j<=nlstate+ndeath;j++) {
7090: ppij=0.;
7091: for(i=1; i<=nlstate;i++) {
7092: if (mobilav==1)
7093: ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][k];
7094: else {
7095: ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][k];
7096: }
7097: if (h*hstepm/YEARM*stepm== yearp) {
7098: fprintf(ficresf," %.3f", p3mat[i][j][h]);
7099: }
7100: } /* end i */
7101: if (h*hstepm/YEARM*stepm==yearp) {
7102: fprintf(ficresf," %.3f", ppij);
7103: }
7104: }/* end j */
7105: } /* end h */
7106: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
7107: } /* end agec */
7108: } /* end yearp */
7109: } /* end k */
1.219 brouard 7110:
1.126 brouard 7111: fclose(ficresf);
1.215 brouard 7112: printf("End of Computing forecasting \n");
7113: fprintf(ficlog,"End of Computing forecasting\n");
7114:
1.126 brouard 7115: }
7116:
1.218 brouard 7117: /* /\************** Back Forecasting ******************\/ */
1.225 brouard 7118: /* void prevbackforecast(char fileres[], double anback1, double mback1, double jback1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double anback2, double p[], int cptcoveff){ */
1.218 brouard 7119: /* /\* back1, year, month, day of starting backection */
7120: /* agemin, agemax range of age */
7121: /* dateprev1 dateprev2 range of dates during which prevalence is computed */
7122: /* anback2 year of en of backection (same day and month as back1). */
7123: /* *\/ */
7124: /* int yearp, stepsize, hstepm, nhstepm, j, k, cptcod, i, h, i1; */
7125: /* double agec; /\* generic age *\/ */
7126: /* double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean; */
7127: /* double *popeffectif,*popcount; */
7128: /* double ***p3mat; */
7129: /* /\* double ***mobaverage; *\/ */
7130: /* char fileresfb[FILENAMELENGTH]; */
7131:
7132: /* agelim=AGESUP; */
7133: /* /\* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people */
7134: /* in each health status at the date of interview (if between dateprev1 and dateprev2). */
7135: /* We still use firstpass and lastpass as another selection. */
7136: /* *\/ */
7137: /* /\* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart,\ *\/ */
7138: /* /\* firstpass, lastpass, stepm, weightopt, model); *\/ */
7139: /* prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass); */
7140:
7141: /* strcpy(fileresfb,"FB_"); */
7142: /* strcat(fileresfb,fileresu); */
7143: /* if((ficresfb=fopen(fileresfb,"w"))==NULL) { */
7144: /* printf("Problem with back forecast resultfile: %s\n", fileresfb); */
7145: /* fprintf(ficlog,"Problem with back forecast resultfile: %s\n", fileresfb); */
7146: /* } */
7147: /* printf("Computing back forecasting: result on file '%s', please wait... \n", fileresfb); */
7148: /* fprintf(ficlog,"Computing back forecasting: result on file '%s', please wait... \n", fileresfb); */
7149:
1.225 brouard 7150: /* if (cptcoveff==0) ncodemax[cptcoveff]=1; */
1.218 brouard 7151:
7152: /* /\* if (mobilav!=0) { *\/ */
7153: /* /\* mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); *\/ */
7154: /* /\* if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){ *\/ */
7155: /* /\* fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav); *\/ */
7156: /* /\* printf(" Error in movingaverage mobilav=%d\n",mobilav); *\/ */
7157: /* /\* } *\/ */
7158: /* /\* } *\/ */
7159:
7160: /* stepsize=(int) (stepm+YEARM-1)/YEARM; */
7161: /* if (stepm<=12) stepsize=1; */
7162: /* if(estepm < stepm){ */
7163: /* printf ("Problem %d lower than %d\n",estepm, stepm); */
7164: /* } */
7165: /* else hstepm=estepm; */
7166:
7167: /* hstepm=hstepm/stepm; */
7168: /* yp1=modf(dateintmean,&yp);/\* extracts integral of datemean in yp and */
7169: /* fractional in yp1 *\/ */
7170: /* anprojmean=yp; */
7171: /* yp2=modf((yp1*12),&yp); */
7172: /* mprojmean=yp; */
7173: /* yp1=modf((yp2*30.5),&yp); */
7174: /* jprojmean=yp; */
7175: /* if(jprojmean==0) jprojmean=1; */
7176: /* if(mprojmean==0) jprojmean=1; */
7177:
1.225 brouard 7178: /* i1=cptcoveff; */
1.218 brouard 7179: /* if (cptcovn < 1){i1=1;} */
1.217 brouard 7180:
1.218 brouard 7181: /* fprintf(ficresfb,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2); */
1.217 brouard 7182:
1.218 brouard 7183: /* fprintf(ficresfb,"#****** Routine prevbackforecast **\n"); */
7184:
7185: /* /\* if (h==(int)(YEARM*yearp)){ *\/ */
7186: /* for(cptcov=1, k=0;cptcov<=i1;cptcov++){ */
1.225 brouard 7187: /* for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){ */
1.218 brouard 7188: /* k=k+1; */
7189: /* fprintf(ficresfb,"\n#****** hbijx=probability over h years, hp.jx is weighted by observed prev \n#"); */
1.225 brouard 7190: /* for(j=1;j<=cptcoveff;j++) { */
1.218 brouard 7191: /* fprintf(ficresfb," V%d (=) %d",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); */
7192: /* } */
7193: /* fprintf(ficresfb," yearbproj age"); */
7194: /* for(j=1; j<=nlstate+ndeath;j++){ */
7195: /* for(i=1; i<=nlstate;i++) */
7196: /* fprintf(ficresfb," p%d%d",i,j); */
7197: /* fprintf(ficresfb," p.%d",j); */
7198: /* } */
7199: /* for (yearp=0; yearp>=(anback2-anback1);yearp -=stepsize) { */
7200: /* /\* for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) { *\/ */
7201: /* fprintf(ficresfb,"\n"); */
7202: /* fprintf(ficresfb,"\n# Back Forecasting at date %.lf/%.lf/%.lf ",jback1,mback1,anback1+yearp); */
7203: /* for (agec=fage; agec>=(ageminpar-1); agec--){ */
7204: /* nhstepm=(int) rint((agelim-agec)*YEARM/stepm); */
7205: /* nhstepm = nhstepm/hstepm; */
7206: /* p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); */
7207: /* oldm=oldms;savm=savms; */
7208: /* hbxij(p3mat,nhstepm,agec,hstepm,p,prevacurrent,nlstate,stepm,oldm,savm,oldm,savm, dnewm, doldm, dsavm, k); */
7209: /* for (h=0; h<=nhstepm; h++){ */
7210: /* if (h*hstepm/YEARM*stepm ==yearp) { */
7211: /* fprintf(ficresfb,"\n"); */
1.225 brouard 7212: /* for(j=1;j<=cptcoveff;j++) */
1.218 brouard 7213: /* fprintf(ficresfb,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); */
7214: /* fprintf(ficresfb,"%.f %.f ",anback1+yearp,agec+h*hstepm/YEARM*stepm); */
7215: /* } */
7216: /* for(j=1; j<=nlstate+ndeath;j++) { */
7217: /* ppij=0.; */
7218: /* for(i=1; i<=nlstate;i++) { */
7219: /* if (mobilav==1) */
7220: /* ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod]; */
7221: /* else { */
7222: /* ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod]; */
7223: /* } */
7224: /* if (h*hstepm/YEARM*stepm== yearp) { */
7225: /* fprintf(ficresfb," %.3f", p3mat[i][j][h]); */
7226: /* } */
7227: /* } /\* end i *\/ */
7228: /* if (h*hstepm/YEARM*stepm==yearp) { */
7229: /* fprintf(ficresfb," %.3f", ppij); */
7230: /* } */
7231: /* }/\* end j *\/ */
7232: /* } /\* end h *\/ */
7233: /* free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); */
7234: /* } /\* end agec *\/ */
7235: /* } /\* end yearp *\/ */
7236: /* } /\* end cptcod *\/ */
7237: /* } /\* end cptcov *\/ */
7238:
7239: /* /\* if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); *\/ */
7240:
7241: /* fclose(ficresfb); */
7242: /* printf("End of Computing Back forecasting \n"); */
7243: /* fprintf(ficlog,"End of Computing Back forecasting\n"); */
1.217 brouard 7244:
1.218 brouard 7245: /* } */
1.217 brouard 7246:
1.126 brouard 7247: /************** Forecasting *****not tested NB*************/
1.227 brouard 7248: /* void populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2s, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){ */
1.126 brouard 7249:
1.227 brouard 7250: /* int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h; */
7251: /* int *popage; */
7252: /* double calagedatem, agelim, kk1, kk2; */
7253: /* double *popeffectif,*popcount; */
7254: /* double ***p3mat,***tabpop,***tabpopprev; */
7255: /* /\* double ***mobaverage; *\/ */
7256: /* char filerespop[FILENAMELENGTH]; */
1.126 brouard 7257:
1.227 brouard 7258: /* tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
7259: /* tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
7260: /* agelim=AGESUP; */
7261: /* calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM; */
1.126 brouard 7262:
1.227 brouard 7263: /* prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass); */
1.126 brouard 7264:
7265:
1.227 brouard 7266: /* strcpy(filerespop,"POP_"); */
7267: /* strcat(filerespop,fileresu); */
7268: /* if((ficrespop=fopen(filerespop,"w"))==NULL) { */
7269: /* printf("Problem with forecast resultfile: %s\n", filerespop); */
7270: /* fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop); */
7271: /* } */
7272: /* printf("Computing forecasting: result on file '%s' \n", filerespop); */
7273: /* fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop); */
1.126 brouard 7274:
1.227 brouard 7275: /* if (cptcoveff==0) ncodemax[cptcoveff]=1; */
1.126 brouard 7276:
1.227 brouard 7277: /* /\* if (mobilav!=0) { *\/ */
7278: /* /\* mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); *\/ */
7279: /* /\* if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){ *\/ */
7280: /* /\* fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav); *\/ */
7281: /* /\* printf(" Error in movingaverage mobilav=%d\n",mobilav); *\/ */
7282: /* /\* } *\/ */
7283: /* /\* } *\/ */
1.126 brouard 7284:
1.227 brouard 7285: /* stepsize=(int) (stepm+YEARM-1)/YEARM; */
7286: /* if (stepm<=12) stepsize=1; */
1.126 brouard 7287:
1.227 brouard 7288: /* agelim=AGESUP; */
1.126 brouard 7289:
1.227 brouard 7290: /* hstepm=1; */
7291: /* hstepm=hstepm/stepm; */
1.218 brouard 7292:
1.227 brouard 7293: /* if (popforecast==1) { */
7294: /* if((ficpop=fopen(popfile,"r"))==NULL) { */
7295: /* printf("Problem with population file : %s\n",popfile);exit(0); */
7296: /* fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0); */
7297: /* } */
7298: /* popage=ivector(0,AGESUP); */
7299: /* popeffectif=vector(0,AGESUP); */
7300: /* popcount=vector(0,AGESUP); */
1.126 brouard 7301:
1.227 brouard 7302: /* i=1; */
7303: /* while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1; */
1.218 brouard 7304:
1.227 brouard 7305: /* imx=i; */
7306: /* for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i]; */
7307: /* } */
1.218 brouard 7308:
1.227 brouard 7309: /* for(cptcov=1,k=0;cptcov<=i2;cptcov++){ */
7310: /* for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){ */
7311: /* k=k+1; */
7312: /* fprintf(ficrespop,"\n#******"); */
7313: /* for(j=1;j<=cptcoveff;j++) { */
7314: /* fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); */
7315: /* } */
7316: /* fprintf(ficrespop,"******\n"); */
7317: /* fprintf(ficrespop,"# Age"); */
7318: /* for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j); */
7319: /* if (popforecast==1) fprintf(ficrespop," [Population]"); */
1.126 brouard 7320:
1.227 brouard 7321: /* for (cpt=0; cpt<=0;cpt++) { */
7322: /* fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt); */
1.126 brouard 7323:
1.227 brouard 7324: /* for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ */
7325: /* nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); */
7326: /* nhstepm = nhstepm/hstepm; */
1.126 brouard 7327:
1.227 brouard 7328: /* p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); */
7329: /* oldm=oldms;savm=savms; */
7330: /* hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k); */
1.218 brouard 7331:
1.227 brouard 7332: /* for (h=0; h<=nhstepm; h++){ */
7333: /* if (h==(int) (calagedatem+YEARM*cpt)) { */
7334: /* fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm); */
7335: /* } */
7336: /* for(j=1; j<=nlstate+ndeath;j++) { */
7337: /* kk1=0.;kk2=0; */
7338: /* for(i=1; i<=nlstate;i++) { */
7339: /* if (mobilav==1) */
7340: /* kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod]; */
7341: /* else { */
7342: /* kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod]; */
7343: /* } */
7344: /* } */
7345: /* if (h==(int)(calagedatem+12*cpt)){ */
7346: /* tabpop[(int)(agedeb)][j][cptcod]=kk1; */
7347: /* /\*fprintf(ficrespop," %.3f", kk1); */
7348: /* if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*\/ */
7349: /* } */
7350: /* } */
7351: /* for(i=1; i<=nlstate;i++){ */
7352: /* kk1=0.; */
7353: /* for(j=1; j<=nlstate;j++){ */
7354: /* kk1= kk1+tabpop[(int)(agedeb)][j][cptcod]; */
7355: /* } */
7356: /* tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)]; */
7357: /* } */
1.218 brouard 7358:
1.227 brouard 7359: /* if (h==(int)(calagedatem+12*cpt)) */
7360: /* for(j=1; j<=nlstate;j++) */
7361: /* fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]); */
7362: /* } */
7363: /* free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); */
7364: /* } */
7365: /* } */
1.218 brouard 7366:
1.227 brouard 7367: /* /\******\/ */
1.218 brouard 7368:
1.227 brouard 7369: /* for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) { */
7370: /* fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt); */
7371: /* for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ */
7372: /* nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); */
7373: /* nhstepm = nhstepm/hstepm; */
1.126 brouard 7374:
1.227 brouard 7375: /* p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); */
7376: /* oldm=oldms;savm=savms; */
7377: /* hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k); */
7378: /* for (h=0; h<=nhstepm; h++){ */
7379: /* if (h==(int) (calagedatem+YEARM*cpt)) { */
7380: /* fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm); */
7381: /* } */
7382: /* for(j=1; j<=nlstate+ndeath;j++) { */
7383: /* kk1=0.;kk2=0; */
7384: /* for(i=1; i<=nlstate;i++) { */
7385: /* kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod]; */
7386: /* } */
7387: /* if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1); */
7388: /* } */
7389: /* } */
7390: /* free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); */
7391: /* } */
7392: /* } */
7393: /* } */
7394: /* } */
1.218 brouard 7395:
1.227 brouard 7396: /* /\* if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); *\/ */
1.218 brouard 7397:
1.227 brouard 7398: /* if (popforecast==1) { */
7399: /* free_ivector(popage,0,AGESUP); */
7400: /* free_vector(popeffectif,0,AGESUP); */
7401: /* free_vector(popcount,0,AGESUP); */
7402: /* } */
7403: /* free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
7404: /* free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
7405: /* fclose(ficrespop); */
7406: /* } /\* End of popforecast *\/ */
1.218 brouard 7407:
1.126 brouard 7408: int fileappend(FILE *fichier, char *optionfich)
7409: {
7410: if((fichier=fopen(optionfich,"a"))==NULL) {
7411: printf("Problem with file: %s\n", optionfich);
7412: fprintf(ficlog,"Problem with file: %s\n", optionfich);
7413: return (0);
7414: }
7415: fflush(fichier);
7416: return (1);
7417: }
7418:
7419:
7420: /**************** function prwizard **********************/
7421: void prwizard(int ncovmodel, int nlstate, int ndeath, char model[], FILE *ficparo)
7422: {
7423:
7424: /* Wizard to print covariance matrix template */
7425:
1.164 brouard 7426: char ca[32], cb[32];
7427: int i,j, k, li, lj, lk, ll, jj, npar, itimes;
1.126 brouard 7428: int numlinepar;
7429:
7430: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
7431: fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
7432: for(i=1; i <=nlstate; i++){
7433: jj=0;
7434: for(j=1; j <=nlstate+ndeath; j++){
7435: if(j==i) continue;
7436: jj++;
7437: /*ca[0]= k+'a'-1;ca[1]='\0';*/
7438: printf("%1d%1d",i,j);
7439: fprintf(ficparo,"%1d%1d",i,j);
7440: for(k=1; k<=ncovmodel;k++){
7441: /* printf(" %lf",param[i][j][k]); */
7442: /* fprintf(ficparo," %lf",param[i][j][k]); */
7443: printf(" 0.");
7444: fprintf(ficparo," 0.");
7445: }
7446: printf("\n");
7447: fprintf(ficparo,"\n");
7448: }
7449: }
7450: printf("# Scales (for hessian or gradient estimation)\n");
7451: fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
7452: npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
7453: for(i=1; i <=nlstate; i++){
7454: jj=0;
7455: for(j=1; j <=nlstate+ndeath; j++){
7456: if(j==i) continue;
7457: jj++;
7458: fprintf(ficparo,"%1d%1d",i,j);
7459: printf("%1d%1d",i,j);
7460: fflush(stdout);
7461: for(k=1; k<=ncovmodel;k++){
7462: /* printf(" %le",delti3[i][j][k]); */
7463: /* fprintf(ficparo," %le",delti3[i][j][k]); */
7464: printf(" 0.");
7465: fprintf(ficparo," 0.");
7466: }
7467: numlinepar++;
7468: printf("\n");
7469: fprintf(ficparo,"\n");
7470: }
7471: }
7472: printf("# Covariance matrix\n");
7473: /* # 121 Var(a12)\n\ */
7474: /* # 122 Cov(b12,a12) Var(b12)\n\ */
7475: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
7476: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
7477: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
7478: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
7479: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
7480: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
7481: fflush(stdout);
7482: fprintf(ficparo,"# Covariance matrix\n");
7483: /* # 121 Var(a12)\n\ */
7484: /* # 122 Cov(b12,a12) Var(b12)\n\ */
7485: /* # ...\n\ */
7486: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
7487:
7488: for(itimes=1;itimes<=2;itimes++){
7489: jj=0;
7490: for(i=1; i <=nlstate; i++){
7491: for(j=1; j <=nlstate+ndeath; j++){
7492: if(j==i) continue;
7493: for(k=1; k<=ncovmodel;k++){
7494: jj++;
7495: ca[0]= k+'a'-1;ca[1]='\0';
7496: if(itimes==1){
7497: printf("#%1d%1d%d",i,j,k);
7498: fprintf(ficparo,"#%1d%1d%d",i,j,k);
7499: }else{
7500: printf("%1d%1d%d",i,j,k);
7501: fprintf(ficparo,"%1d%1d%d",i,j,k);
7502: /* printf(" %.5le",matcov[i][j]); */
7503: }
7504: ll=0;
7505: for(li=1;li <=nlstate; li++){
7506: for(lj=1;lj <=nlstate+ndeath; lj++){
7507: if(lj==li) continue;
7508: for(lk=1;lk<=ncovmodel;lk++){
7509: ll++;
7510: if(ll<=jj){
7511: cb[0]= lk +'a'-1;cb[1]='\0';
7512: if(ll<jj){
7513: if(itimes==1){
7514: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
7515: fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
7516: }else{
7517: printf(" 0.");
7518: fprintf(ficparo," 0.");
7519: }
7520: }else{
7521: if(itimes==1){
7522: printf(" Var(%s%1d%1d)",ca,i,j);
7523: fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
7524: }else{
7525: printf(" 0.");
7526: fprintf(ficparo," 0.");
7527: }
7528: }
7529: }
7530: } /* end lk */
7531: } /* end lj */
7532: } /* end li */
7533: printf("\n");
7534: fprintf(ficparo,"\n");
7535: numlinepar++;
7536: } /* end k*/
7537: } /*end j */
7538: } /* end i */
7539: } /* end itimes */
7540:
7541: } /* end of prwizard */
7542: /******************* Gompertz Likelihood ******************************/
7543: double gompertz(double x[])
7544: {
7545: double A,B,L=0.0,sump=0.,num=0.;
7546: int i,n=0; /* n is the size of the sample */
7547:
1.220 brouard 7548: for (i=1;i<=imx ; i++) {
1.126 brouard 7549: sump=sump+weight[i];
7550: /* sump=sump+1;*/
7551: num=num+1;
7552: }
7553:
7554:
7555: /* for (i=0; i<=imx; i++)
7556: 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]);*/
7557:
7558: for (i=1;i<=imx ; i++)
7559: {
7560: if (cens[i] == 1 && wav[i]>1)
7561: A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
7562:
7563: if (cens[i] == 0 && wav[i]>1)
7564: A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
7565: +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);
7566:
7567: /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
7568: if (wav[i] > 1 ) { /* ??? */
7569: L=L+A*weight[i];
7570: /* 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]);*/
7571: }
7572: }
7573:
7574: /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
7575:
7576: return -2*L*num/sump;
7577: }
7578:
1.136 brouard 7579: #ifdef GSL
7580: /******************* Gompertz_f Likelihood ******************************/
7581: double gompertz_f(const gsl_vector *v, void *params)
7582: {
7583: double A,B,LL=0.0,sump=0.,num=0.;
7584: double *x= (double *) v->data;
7585: int i,n=0; /* n is the size of the sample */
7586:
7587: for (i=0;i<=imx-1 ; i++) {
7588: sump=sump+weight[i];
7589: /* sump=sump+1;*/
7590: num=num+1;
7591: }
7592:
7593:
7594: /* for (i=0; i<=imx; i++)
7595: 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]);*/
7596: printf("x[0]=%lf x[1]=%lf\n",x[0],x[1]);
7597: for (i=1;i<=imx ; i++)
7598: {
7599: if (cens[i] == 1 && wav[i]>1)
7600: A=-x[0]/(x[1])*(exp(x[1]*(agecens[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)));
7601:
7602: if (cens[i] == 0 && wav[i]>1)
7603: A=-x[0]/(x[1])*(exp(x[1]*(agedc[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)))
7604: +log(x[0]/YEARM)+x[1]*(agedc[i]-agegomp)+log(YEARM);
7605:
7606: /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
7607: if (wav[i] > 1 ) { /* ??? */
7608: LL=LL+A*weight[i];
7609: /* 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]);*/
7610: }
7611: }
7612:
7613: /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
7614: printf("x[0]=%lf x[1]=%lf -2*LL*num/sump=%lf\n",x[0],x[1],-2*LL*num/sump);
7615:
7616: return -2*LL*num/sump;
7617: }
7618: #endif
7619:
1.126 brouard 7620: /******************* Printing html file ***********/
1.201 brouard 7621: void printinghtmlmort(char fileresu[], char title[], char datafile[], int firstpass, \
1.126 brouard 7622: int lastpass, int stepm, int weightopt, char model[],\
7623: int imx, double p[],double **matcov,double agemortsup){
7624: int i,k;
7625:
7626: fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
7627: fprintf(fichtm," mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
7628: for (i=1;i<=2;i++)
7629: 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 7630: fprintf(fichtm,"<br><br><img src=\"graphmort.svg\">");
1.126 brouard 7631: fprintf(fichtm,"</ul>");
7632:
7633: fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
7634:
7635: 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>");
7636:
7637: for (k=agegomp;k<(agemortsup-2);k++)
7638: 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]);
7639:
7640:
7641: fflush(fichtm);
7642: }
7643:
7644: /******************* Gnuplot file **************/
1.201 brouard 7645: void printinggnuplotmort(char fileresu[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
1.126 brouard 7646:
7647: char dirfileres[132],optfileres[132];
1.164 brouard 7648:
1.126 brouard 7649: int ng;
7650:
7651:
7652: /*#ifdef windows */
7653: fprintf(ficgp,"cd \"%s\" \n",pathc);
7654: /*#endif */
7655:
7656:
7657: strcpy(dirfileres,optionfilefiname);
7658: strcpy(optfileres,"vpl");
1.199 brouard 7659: fprintf(ficgp,"set out \"graphmort.svg\"\n ");
1.126 brouard 7660: fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n ");
1.199 brouard 7661: fprintf(ficgp, "set ter svg size 640, 480\n set log y\n");
1.145 brouard 7662: /* fprintf(ficgp, "set size 0.65,0.65\n"); */
1.126 brouard 7663: fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
7664:
7665: }
7666:
1.136 brouard 7667: int readdata(char datafile[], int firstobs, int lastobs, int *imax)
7668: {
1.126 brouard 7669:
1.136 brouard 7670: /*-------- data file ----------*/
7671: FILE *fic;
7672: char dummy[]=" ";
1.223 brouard 7673: int i=0, j=0, n=0, iv=0;
7674: int lstra;
1.136 brouard 7675: int linei, month, year,iout;
7676: char line[MAXLINE], linetmp[MAXLINE];
1.164 brouard 7677: char stra[MAXLINE], strb[MAXLINE];
1.136 brouard 7678: char *stratrunc;
1.223 brouard 7679:
1.126 brouard 7680:
7681:
1.136 brouard 7682: if((fic=fopen(datafile,"r"))==NULL) {
1.218 brouard 7683: printf("Problem while opening datafile: %s with errno='%s'\n", datafile,strerror(errno));fflush(stdout);
7684: fprintf(ficlog,"Problem while opening datafile: %s with errno='%s'\n", datafile,strerror(errno));fflush(ficlog);return 1;
1.136 brouard 7685: }
1.126 brouard 7686:
1.136 brouard 7687: i=1;
7688: linei=0;
7689: while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
7690: linei=linei+1;
7691: for(j=strlen(line); j>=0;j--){ /* Untabifies line */
7692: if(line[j] == '\t')
7693: line[j] = ' ';
7694: }
7695: for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){
7696: ;
7697: };
7698: line[j+1]=0; /* Trims blanks at end of line */
7699: if(line[0]=='#'){
7700: fprintf(ficlog,"Comment line\n%s\n",line);
7701: printf("Comment line\n%s\n",line);
7702: continue;
7703: }
7704: trimbb(linetmp,line); /* Trims multiple blanks in line */
1.164 brouard 7705: strcpy(line, linetmp);
1.223 brouard 7706:
7707: /* Loops on waves */
7708: for (j=maxwav;j>=1;j--){
7709: for (iv=nqtv;iv>=1;iv--){ /* Loop on time varying quantitative variables */
1.232 brouard 7710: cutv(stra, strb, line, ' ');
7711: if(strb[0]=='.') { /* Missing value */
7712: lval=-1;
7713: cotqvar[j][iv][i]=-1; /* 0.0/0.0 */
7714: cotvar[j][ntv+iv][i]=-1; /* For performance reasons */
7715: if(isalpha(strb[1])) { /* .m or .d Really Missing value */
7716: printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be the %d th quantitative value out of %d measured at wave %d. If missing, you should remove this individual or impute a value. Exiting.\n", strb, linei,i,line,iv, nqtv, j);
7717: fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be the %d th quantitative value out of %d measured at wave %d. If missing, you should remove this individual or impute a value. Exiting.\n", strb, linei,i,line,iv, nqtv, j);fflush(ficlog);
7718: return 1;
7719: }
7720: }else{
7721: errno=0;
7722: /* what_kind_of_number(strb); */
7723: dval=strtod(strb,&endptr);
7724: /* if( strb[0]=='\0' || (*endptr != '\0')){ */
7725: /* if(strb != endptr && *endptr == '\0') */
7726: /* dval=dlval; */
7727: /* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN)) */
7728: if( strb[0]=='\0' || (*endptr != '\0')){
7729: printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be the %d th quantitative value out of %d measured at wave %d. Setting maxwav=%d might be wrong. Exiting.\n", strb, linei,i,line,iv, nqtv, j,maxwav);
7730: fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be the %d th quantitative value out of %d measured at wave %d. Setting maxwav=%d might be wrong. Exiting.\n", strb, linei,i,line, iv, nqtv, j,maxwav);fflush(ficlog);
7731: return 1;
7732: }
7733: cotqvar[j][iv][i]=dval;
7734: cotvar[j][ntv+iv][i]=dval;
7735: }
7736: strcpy(line,stra);
1.223 brouard 7737: }/* end loop ntqv */
1.225 brouard 7738:
1.223 brouard 7739: for (iv=ntv;iv>=1;iv--){ /* Loop on time varying dummies */
1.232 brouard 7740: cutv(stra, strb, line, ' ');
7741: if(strb[0]=='.') { /* Missing value */
7742: lval=-1;
7743: }else{
7744: errno=0;
7745: lval=strtol(strb,&endptr,10);
7746: /* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
7747: if( strb[0]=='\0' || (*endptr != '\0')){
7748: printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be the %d th dummy covariate out of %d measured at wave %d. Setting maxwav=%d might be wrong. Exiting.\n", strb, linei,i,line,iv, ntv, j,maxwav);
7749: fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be the %d dummy covariate out of %d measured wave %d. Setting maxwav=%d might be wrong. Exiting.\n", strb, linei,i,line,iv, ntv,j,maxwav);fflush(ficlog);
7750: return 1;
7751: }
7752: }
7753: if(lval <-1 || lval >1){
7754: printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
1.223 brouard 7755: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
7756: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
1.232 brouard 7757: For example, for multinomial values like 1, 2 and 3,\n \
7758: build V1=0 V2=0 for the reference value (1),\n \
7759: V1=1 V2=0 for (2) \n \
1.223 brouard 7760: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
1.232 brouard 7761: output of IMaCh is often meaningless.\n \
1.223 brouard 7762: Exiting.\n",lval,linei, i,line,j);
1.232 brouard 7763: fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
1.223 brouard 7764: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
7765: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
1.232 brouard 7766: For example, for multinomial values like 1, 2 and 3,\n \
7767: build V1=0 V2=0 for the reference value (1),\n \
7768: V1=1 V2=0 for (2) \n \
1.223 brouard 7769: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
1.232 brouard 7770: output of IMaCh is often meaningless.\n \
1.223 brouard 7771: Exiting.\n",lval,linei, i,line,j);fflush(ficlog);
1.232 brouard 7772: return 1;
7773: }
7774: cotvar[j][iv][i]=(double)(lval);
7775: strcpy(line,stra);
1.223 brouard 7776: }/* end loop ntv */
1.225 brouard 7777:
1.223 brouard 7778: /* Statuses at wave */
1.137 brouard 7779: cutv(stra, strb, line, ' ');
1.223 brouard 7780: if(strb[0]=='.') { /* Missing value */
1.232 brouard 7781: lval=-1;
1.136 brouard 7782: }else{
1.232 brouard 7783: errno=0;
7784: lval=strtol(strb,&endptr,10);
7785: /* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
7786: if( strb[0]=='\0' || (*endptr != '\0')){
7787: 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);
7788: 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);
7789: return 1;
7790: }
1.136 brouard 7791: }
1.225 brouard 7792:
1.136 brouard 7793: s[j][i]=lval;
1.225 brouard 7794:
1.223 brouard 7795: /* Date of Interview */
1.136 brouard 7796: strcpy(line,stra);
7797: cutv(stra, strb,line,' ');
1.169 brouard 7798: if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
1.136 brouard 7799: }
1.169 brouard 7800: else if( (iout=sscanf(strb,"%s.",dummy)) != 0){
1.225 brouard 7801: month=99;
7802: year=9999;
1.136 brouard 7803: }else{
1.225 brouard 7804: 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);
7805: 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);
7806: return 1;
1.136 brouard 7807: }
7808: anint[j][i]= (double) year;
7809: mint[j][i]= (double)month;
7810: strcpy(line,stra);
1.223 brouard 7811: } /* End loop on waves */
1.225 brouard 7812:
1.223 brouard 7813: /* Date of death */
1.136 brouard 7814: cutv(stra, strb,line,' ');
1.169 brouard 7815: if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
1.136 brouard 7816: }
1.169 brouard 7817: else if( (iout=sscanf(strb,"%s.",dummy)) != 0){
1.136 brouard 7818: month=99;
7819: year=9999;
7820: }else{
1.141 brouard 7821: 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);
1.225 brouard 7822: 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);
7823: return 1;
1.136 brouard 7824: }
7825: andc[i]=(double) year;
7826: moisdc[i]=(double) month;
7827: strcpy(line,stra);
7828:
1.223 brouard 7829: /* Date of birth */
1.136 brouard 7830: cutv(stra, strb,line,' ');
1.169 brouard 7831: if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
1.136 brouard 7832: }
1.169 brouard 7833: else if( (iout=sscanf(strb,"%s.", dummy)) != 0){
1.136 brouard 7834: month=99;
7835: year=9999;
7836: }else{
1.141 brouard 7837: 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);
7838: 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);
1.225 brouard 7839: return 1;
1.136 brouard 7840: }
7841: if (year==9999) {
1.141 brouard 7842: 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);
7843: 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);
1.225 brouard 7844: return 1;
7845:
1.136 brouard 7846: }
7847: annais[i]=(double)(year);
7848: moisnais[i]=(double)(month);
7849: strcpy(line,stra);
1.225 brouard 7850:
1.223 brouard 7851: /* Sample weight */
1.136 brouard 7852: cutv(stra, strb,line,' ');
7853: errno=0;
7854: dval=strtod(strb,&endptr);
7855: if( strb[0]=='\0' || (*endptr != '\0')){
1.141 brouard 7856: printf("Error reading data around '%f' at line number %d, \"%s\" for individual %d\nShould be a weight. Exiting.\n",dval, i,line,linei);
7857: 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 7858: fflush(ficlog);
7859: return 1;
7860: }
7861: weight[i]=dval;
7862: strcpy(line,stra);
1.225 brouard 7863:
1.223 brouard 7864: for (iv=nqv;iv>=1;iv--){ /* Loop on fixed quantitative variables */
7865: cutv(stra, strb, line, ' ');
7866: if(strb[0]=='.') { /* Missing value */
1.225 brouard 7867: lval=-1;
1.223 brouard 7868: }else{
1.225 brouard 7869: errno=0;
7870: /* what_kind_of_number(strb); */
7871: dval=strtod(strb,&endptr);
7872: /* if(strb != endptr && *endptr == '\0') */
7873: /* dval=dlval; */
7874: /* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN)) */
7875: if( strb[0]=='\0' || (*endptr != '\0')){
7876: printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be the %d th quantitative value (out of %d) constant for all waves. Setting maxwav=%d might be wrong. Exiting.\n", strb, linei,i,line, iv, nqv, maxwav);
7877: fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be the %d th quantitative value (out of %d) constant for all waves. Setting maxwav=%d might be wrong. Exiting.\n", strb, linei,i,line, iv, nqv, maxwav);fflush(ficlog);
7878: return 1;
7879: }
7880: coqvar[iv][i]=dval;
1.226 brouard 7881: covar[ncovcol+iv][i]=dval; /* including qvar in standard covar for performance reasons */
1.223 brouard 7882: }
7883: strcpy(line,stra);
7884: }/* end loop nqv */
1.136 brouard 7885:
1.223 brouard 7886: /* Covariate values */
1.136 brouard 7887: for (j=ncovcol;j>=1;j--){
7888: cutv(stra, strb,line,' ');
1.223 brouard 7889: if(strb[0]=='.') { /* Missing covariate value */
1.225 brouard 7890: lval=-1;
1.136 brouard 7891: }else{
1.225 brouard 7892: errno=0;
7893: lval=strtol(strb,&endptr,10);
7894: if( strb[0]=='\0' || (*endptr != '\0')){
7895: 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);
7896: 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);
7897: return 1;
7898: }
1.136 brouard 7899: }
7900: if(lval <-1 || lval >1){
1.225 brouard 7901: printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
1.136 brouard 7902: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
7903: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
1.225 brouard 7904: For example, for multinomial values like 1, 2 and 3,\n \
7905: build V1=0 V2=0 for the reference value (1),\n \
7906: V1=1 V2=0 for (2) \n \
1.136 brouard 7907: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
1.225 brouard 7908: output of IMaCh is often meaningless.\n \
1.136 brouard 7909: Exiting.\n",lval,linei, i,line,j);
1.225 brouard 7910: fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
1.136 brouard 7911: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
7912: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
1.225 brouard 7913: For example, for multinomial values like 1, 2 and 3,\n \
7914: build V1=0 V2=0 for the reference value (1),\n \
7915: V1=1 V2=0 for (2) \n \
1.136 brouard 7916: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
1.225 brouard 7917: output of IMaCh is often meaningless.\n \
1.136 brouard 7918: Exiting.\n",lval,linei, i,line,j);fflush(ficlog);
1.225 brouard 7919: return 1;
1.136 brouard 7920: }
7921: covar[j][i]=(double)(lval);
7922: strcpy(line,stra);
7923: }
7924: lstra=strlen(stra);
1.225 brouard 7925:
1.136 brouard 7926: if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
7927: stratrunc = &(stra[lstra-9]);
7928: num[i]=atol(stratrunc);
7929: }
7930: else
7931: num[i]=atol(stra);
7932: /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
7933: 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;}*/
7934:
7935: i=i+1;
7936: } /* End loop reading data */
1.225 brouard 7937:
1.136 brouard 7938: *imax=i-1; /* Number of individuals */
7939: fclose(fic);
1.225 brouard 7940:
1.136 brouard 7941: return (0);
1.164 brouard 7942: /* endread: */
1.225 brouard 7943: printf("Exiting readdata: ");
7944: fclose(fic);
7945: return (1);
1.223 brouard 7946: }
1.126 brouard 7947:
1.234 brouard 7948: void removefirstspace(char **stri){/*, char stro[]) {*/
1.230 brouard 7949: char *p1 = *stri, *p2 = *stri;
1.235 ! brouard 7950: while (*p2 == ' ')
1.234 brouard 7951: p2++;
7952: /* while ((*p1++ = *p2++) !=0) */
7953: /* ; */
7954: /* do */
7955: /* while (*p2 == ' ') */
7956: /* p2++; */
7957: /* while (*p1++ == *p2++); */
7958: *stri=p2;
1.145 brouard 7959: }
7960:
1.235 ! brouard 7961: int decoderesult ( char resultline[], int nres)
1.230 brouard 7962: /**< This routine decode one result line and returns the combination # of dummy covariates only **/
7963: {
1.235 ! brouard 7964: int j=0, k=0, k1=0, k2=0, k3=0, k4=0, match=0, k2q=0, k3q=0, k4q=0;
1.230 brouard 7965: char resultsav[MAXLINE];
1.234 brouard 7966: int resultmodel[MAXLINE];
7967: int modelresult[MAXLINE];
1.230 brouard 7968: char stra[80], strb[80], strc[80], strd[80],stre[80];
7969:
1.234 brouard 7970: removefirstspace(&resultline);
1.233 brouard 7971: printf("decoderesult:%s\n",resultline);
1.230 brouard 7972:
7973: if (strstr(resultline,"v") !=0){
7974: printf("Error. 'v' must be in upper case 'V' result: %s ",resultline);
7975: fprintf(ficlog,"Error. 'v' must be in upper case result: %s ",resultline);fflush(ficlog);
7976: return 1;
7977: }
7978: trimbb(resultsav, resultline);
7979: if (strlen(resultsav) >1){
7980: j=nbocc(resultsav,'='); /**< j=Number of covariate values'=' */
7981: }
1.234 brouard 7982: if( j != cptcovs ){ /* Be careful if a variable is in a product but not single */
7983: printf("ERROR: the number of variable in the resultline, %d, differs from the number of variable used in the model line, %d.\n",j, cptcovs);
7984: fprintf(ficlog,"ERROR: the number of variable in the resultline, %d, differs from the number of variable used in the model line, %d.\n",j, cptcovs);
7985: }
7986: for(k=1; k<=j;k++){ /* Loop on any covariate of the result line */
7987: if(nbocc(resultsav,'=') >1){
7988: cutl(stra,strb,resultsav,' '); /* keeps in strb after the first ' '
7989: resultsav= V4=1 V5=25.1 V3=0 strb=V3=0 stra= V4=1 V5=25.1 */
7990: cutl(strc,strd,strb,'='); /* strb:V4=1 strc=1 strd=V4 */
7991: }else
7992: cutl(strc,strd,resultsav,'=');
1.230 brouard 7993: Tvalsel[k]=atof(strc); /* 1 */
1.234 brouard 7994:
1.230 brouard 7995: cutl(strc,stre,strd,'V'); /* strd='V4' strc=4 stre='V' */;
7996: Tvarsel[k]=atoi(strc);
7997: /* Typevarsel[k]=1; /\* 1 for age product *\/ */
7998: /* cptcovsel++; */
7999: if (nbocc(stra,'=') >0)
8000: strcpy(resultsav,stra); /* and analyzes it */
8001: }
1.235 ! brouard 8002: /* Checking for missing or useless values in comparison of current model needs */
1.234 brouard 8003: for(k1=1; k1<= cptcovt ;k1++){ /* model line */
8004: if(Typevar[k1]==0){
8005: match=0;
8006: for(k2=1; k2 <=j;k2++){
8007: if(Tvar[k1]==Tvarsel[k2]) {
8008: modelresult[k2]=k1;
8009: match=1;
8010: break;
8011: }
8012: }
8013: if(match == 0){
8014: printf("Error in result line: %d value missing; result: %s, model=%s\n",k1, resultline, model);
8015: }
8016: }
8017: }
1.235 ! brouard 8018: /* Checking for missing or useless values in comparison of current model needs */
! 8019: for(k2=1; k2 <=j;k2++){ /* result line V4=1 V5=24.1 V3=1 V2=8 V1=0 */
1.234 brouard 8020: match=0;
1.235 ! brouard 8021: for(k1=1; k1<= cptcovt ;k1++){ /* model line V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
! 8022: if(Typevar[k1]==0){ /* Single */
! 8023: if(Tvar[k1]==Tvarsel[k2]) { /* Tvar[2]=5 == Tvarsel[1]=4 */
! 8024: resultmodel[k1]=k2; /* resultmodel[2]=1 resultmodel[1]=2 resultmodel[3]=3 resultmodel[6]=4 resultmodel[9]=5 */
1.234 brouard 8025: ++match;
8026: }
8027: }
8028: }
8029: if(match == 0){
8030: printf("Error in result line: %d value missing; result: %s, model=%s\n",k1, resultline, model);
8031: }else if(match > 1){
8032: printf("Error in result line: %d doubled; result: %s, model=%s\n",k2, resultline, model);
8033: }
8034: }
1.235 ! brouard 8035:
1.234 brouard 8036: /* We need to deduce which combination number is chosen and save quantitative values */
1.235 ! brouard 8037: /* model line V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
! 8038: /* result line V4=1 V5=25.1 V3=0 V2=8 V1=1 */
! 8039: /* should give a combination of dummy V4=1, V3=0, V1=1 => V4*2**(0) + V3*2**(1) + V1*2**(2) = 5 + (1offset) = 6*/
! 8040: /* result line V4=1 V5=24.1 V3=1 V2=8 V1=0 */
! 8041: /* should give a combination of dummy V4=1, V3=1, V1=0 => V4*2**(0) + V3*2**(1) + V1*2**(2) = 3 + (1offset) = 4*/
! 8042: /* 1 0 0 0 */
! 8043: /* 2 1 0 0 */
! 8044: /* 3 0 1 0 */
! 8045: /* 4 1 1 0 */ /* V4=1, V3=1, V1=0 */
! 8046: /* 5 0 0 1 */
! 8047: /* 6 1 0 1 */ /* V4=1, V3=0, V1=1 */
! 8048: /* 7 0 1 1 */
! 8049: /* 8 1 1 1 */
! 8050: for(k1=1, k=0, k4=0, k4q=0; k1 <=cptcovt;k1++){ /* model line */
! 8051: if( Dummy[k1]==0 && Typevar[k1]==0 ){ /* Single dummy */
! 8052: k3= resultmodel[k1]; /* resultmodel[2] = 1=k3 */
! 8053: k2=(int)Tvarsel[k3]; /* Tvarsel[resultmodel[2]]= Tvarsel[1] = 4=k2 */
! 8054: k+=Tvalsel[k3]*pow(2,k4); /* Tvalsel[1]=1 */
! 8055: Tresult[nres][k4+1]=Tvalsel[k3];
! 8056: Tvresult[nres][k4+1]=(int)Tvarsel[k3];
! 8057: printf("Decoderesult Dummy k=%d, V(k2=V%d)= Tvalsel[%d]=%d, 2**(%d)\n",k, k2, k3, (int)Tvalsel[k3], k4);
! 8058: k4++;;
! 8059: } else if( Dummy[k1]==1 && Typevar[k1]==0 ){ /* Single quantitative */
! 8060: k3q= resultmodel[k1]; /* resultmodel[2] = 1=k3 */
! 8061: k2q=(int)Tvarsel[k3q]; /* Tvarsel[resultmodel[2]]= Tvarsel[1] = 4=k2 */
! 8062: Tqresult[nres][k4q+1]=Tvalsel[k3q];
! 8063: Tvqresult[nres][k4q+1]=(int)Tvarsel[k3q];
! 8064: printf("Decoderesult Quantitative nres=%d, V(k2q=V%d)= Tvalsel[%d]=%d, Tvarsel[%d]=%f\n",nres, k2q, k3q, Tvarsel[k3q], k3q, Tvalsel[k3q]);
! 8065: k4q++;;
! 8066: }
! 8067: }
1.234 brouard 8068:
1.235 ! brouard 8069: TKresult[nres]=++k; /* Combination for the nresult and the model */
1.230 brouard 8070: return (0);
8071: }
1.235 ! brouard 8072:
1.230 brouard 8073: int decodemodel( char model[], int lastobs)
8074: /**< This routine decodes the model and returns:
1.224 brouard 8075: * Model V1+V2+V3+V8+V7*V8+V5*V6+V8*age+V3*age+age*age
8076: * - nagesqr = 1 if age*age in the model, otherwise 0.
8077: * - cptcovt total number of covariates of the model nbocc(+)+1 = 8 excepting constant and age and age*age
8078: * - cptcovn or number of covariates k of the models excluding age*products =6 and age*age
8079: * - cptcovage number of covariates with age*products =2
8080: * - cptcovs number of simple covariates
8081: * - 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
8082: * which is a new column after the 9 (ncovcol) variables.
8083: * - if k is a product Vn*Vm covar[k][i] is filled with correct values for each individual
8084: * - Tprod[l] gives the kth covariates of the product Vn*Vm l=1 to cptcovprod-cptcovage
8085: * Tprod[1]@2 {5, 6}: position of first product V7*V8 is 5, and second V5*V6 is 6.
8086: * - Tvard[k] p Tvard[1][1]@4 {7, 8, 5, 6} for V7*V8 and V5*V6 .
8087: */
1.136 brouard 8088: {
1.145 brouard 8089: int i, j, k, ks;
1.227 brouard 8090: int j1, k1, k2, k3, k4;
1.136 brouard 8091: char modelsav[80];
1.145 brouard 8092: char stra[80], strb[80], strc[80], strd[80],stre[80];
1.187 brouard 8093: char *strpt;
1.136 brouard 8094:
1.145 brouard 8095: /*removespace(model);*/
1.136 brouard 8096: if (strlen(model) >1){ /* If there is at least 1 covariate */
1.145 brouard 8097: j=0, j1=0, k1=0, k2=-1, ks=0, cptcovn=0;
1.137 brouard 8098: if (strstr(model,"AGE") !=0){
1.192 brouard 8099: printf("Error. AGE must be in lower case 'age' model=1+age+%s. ",model);
8100: fprintf(ficlog,"Error. AGE must be in lower case model=1+age+%s. ",model);fflush(ficlog);
1.136 brouard 8101: return 1;
8102: }
1.141 brouard 8103: if (strstr(model,"v") !=0){
8104: printf("Error. 'v' must be in upper case 'V' model=%s ",model);
8105: fprintf(ficlog,"Error. 'v' must be in upper case model=%s ",model);fflush(ficlog);
8106: return 1;
8107: }
1.187 brouard 8108: strcpy(modelsav,model);
8109: if ((strpt=strstr(model,"age*age")) !=0){
8110: printf(" strpt=%s, model=%s\n",strpt, model);
8111: if(strpt != model){
1.234 brouard 8112: printf("Error in model: 'model=%s'; 'age*age' should in first place before other covariates\n \
1.192 brouard 8113: 'model=1+age+age*age+V1.' or 'model=1+age+age*age+V1+V1*age.', please swap as well as \n \
1.187 brouard 8114: corresponding column of parameters.\n",model);
1.234 brouard 8115: fprintf(ficlog,"Error in model: 'model=%s'; 'age*age' should in first place before other covariates\n \
1.192 brouard 8116: 'model=1+age+age*age+V1.' or 'model=1+age+age*age+V1+V1*age.', please swap as well as \n \
1.187 brouard 8117: corresponding column of parameters.\n",model); fflush(ficlog);
1.234 brouard 8118: return 1;
1.225 brouard 8119: }
1.187 brouard 8120: nagesqr=1;
8121: if (strstr(model,"+age*age") !=0)
1.234 brouard 8122: substrchaine(modelsav, model, "+age*age");
1.187 brouard 8123: else if (strstr(model,"age*age+") !=0)
1.234 brouard 8124: substrchaine(modelsav, model, "age*age+");
1.187 brouard 8125: else
1.234 brouard 8126: substrchaine(modelsav, model, "age*age");
1.187 brouard 8127: }else
8128: nagesqr=0;
8129: if (strlen(modelsav) >1){
8130: j=nbocc(modelsav,'+'); /**< j=Number of '+' */
8131: j1=nbocc(modelsav,'*'); /**< j1=Number of '*' */
1.224 brouard 8132: cptcovs=j+1-j1; /**< Number of simple covariates V1+V1*age+V3 +V3*V4+age*age=> V1 + V3 =5-3=2 */
1.187 brouard 8133: cptcovt= j+1; /* Number of total covariates in the model, not including
1.225 brouard 8134: * cst, age and age*age
8135: * V1+V1*age+ V3 + V3*V4+age*age=> 3+1=4*/
8136: /* including age products which are counted in cptcovage.
8137: * but the covariates which are products must be treated
8138: * separately: ncovn=4- 2=2 (V1+V3). */
1.187 brouard 8139: cptcovprod=j1; /**< Number of products V1*V2 +v3*age = 2 */
8140: cptcovprodnoage=0; /**< Number of covariate products without age: V3*V4 =1 */
1.225 brouard 8141:
8142:
1.187 brouard 8143: /* Design
8144: * V1 V2 V3 V4 V5 V6 V7 V8 V9 Weight
8145: * < ncovcol=8 >
8146: * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8
8147: * k= 1 2 3 4 5 6 7 8
8148: * cptcovn number of covariates (not including constant and age ) = # of + plus 1 = 7+1=8
8149: * covar[k,i], value of kth covariate if not including age for individual i:
1.224 brouard 8150: * covar[1][i]= (V1), covar[4][i]=(V4), covar[8][i]=(V8)
8151: * Tvar[k] # of the kth covariate: Tvar[1]=2 Tvar[2]=1 Tvar[4]=3 Tvar[8]=8
1.187 brouard 8152: * if multiplied by age: V3*age Tvar[3=V3*age]=3 (V3) Tvar[7]=8 and
8153: * Tage[++cptcovage]=k
8154: * if products, new covar are created after ncovcol with k1
8155: * Tvar[k]=ncovcol+k1; # of the kth covariate product: Tvar[5]=ncovcol+1=10 Tvar[6]=ncovcol+1=11
8156: * Tprod[k1]=k; Tprod[1]=5 Tprod[2]= 6; gives the position of the k1th product
8157: * 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
8158: * Tvar[cptcovn+k2]=Tvard[k1][1];Tvar[cptcovn+k2+1]=Tvard[k1][2];
8159: * Tvar[8+1]=5;Tvar[8+2]=6;Tvar[8+3]=7;Tvar[8+4]=8 inverted
8160: * V1 V2 V3 V4 V5 V6 V7 V8 V9 V10 V11
8161: * < ncovcol=8 >
8162: * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8 d1 d1 d2 d2
8163: * k= 1 2 3 4 5 6 7 8 9 10 11 12
8164: * Tvar[k]= 2 1 3 3 10 11 8 8 5 6 7 8
8165: * p Tvar[1]@12={2, 1, 3, 3, 11, 10, 8, 8, 7, 8, 5, 6}
8166: * p Tprod[1]@2={ 6, 5}
8167: *p Tvard[1][1]@4= {7, 8, 5, 6}
8168: * covar[k][i]= V2 V1 ? V3 V5*V6? V7*V8? ? V8
8169: * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
8170: *How to reorganize?
8171: * Model V1 + V2 + V3 + V8 + V5*V6 + V7*V8 + V3*age + V8*age
8172: * Tvars {2, 1, 3, 3, 11, 10, 8, 8, 7, 8, 5, 6}
8173: * {2, 1, 4, 8, 5, 6, 3, 7}
8174: * Struct []
8175: */
1.225 brouard 8176:
1.187 brouard 8177: /* This loop fills the array Tvar from the string 'model'.*/
8178: /* j is the number of + signs in the model V1+V2+V3 j=2 i=3 to 1 */
8179: /* modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4 */
8180: /* k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tage[cptcovage=1]=4 */
8181: /* k=3 V4 Tvar[k=3]= 4 (from V4) */
8182: /* k=2 V1 Tvar[k=2]= 1 (from V1) */
8183: /* k=1 Tvar[1]=2 (from V2) */
8184: /* k=5 Tvar[5] */
8185: /* for (k=1; k<=cptcovn;k++) { */
1.198 brouard 8186: /* cov[2+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; */
1.187 brouard 8187: /* } */
1.198 brouard 8188: /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,Tvar[Tage[k])]]*cov[2]; */
1.187 brouard 8189: /*
8190: * Treating invertedly V2+V1+V3*age+V2*V4 is as if written V2*V4 +V3*age + V1 + V2 */
1.227 brouard 8191: for(k=cptcovt; k>=1;k--){ /**< Number of covariates not including constant and age, neither age*age*/
8192: Tvar[k]=0; Tprod[k]=0; Tposprod[k]=0;
8193: }
1.187 brouard 8194: cptcovage=0;
8195: for(k=1; k<=cptcovt;k++){ /* Loop on total covariates of the model */
1.234 brouard 8196: cutl(stra,strb,modelsav,'+'); /* keeps in strb after the first '+'
1.225 brouard 8197: modelsav==V2+V1+V4+V3*age strb=V3*age stra=V2+V1+V4 */
1.234 brouard 8198: if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
8199: /* printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
8200: /*scanf("%d",i);*/
8201: if (strchr(strb,'*')) { /**< Model includes a product V2+V1+V4+V3*age strb=V3*age */
8202: cutl(strc,strd,strb,'*'); /**< strd*strc Vm*Vn: strb=V3*age(input) strc=age strd=V3 ; V3*V2 strc=V2, strd=V3 */
8203: if (strcmp(strc,"age")==0) { /**< Model includes age: Vn*age */
8204: /* covar is not filled and then is empty */
8205: cptcovprod--;
8206: cutl(stre,strb,strd,'V'); /* strd=V3(input): stre="3" */
8207: Tvar[k]=atoi(stre); /* V2+V1+V4+V3*age Tvar[4]=3 ; V1+V2*age Tvar[2]=2; V1+V1*age Tvar[2]=1 */
8208: Typevar[k]=1; /* 1 for age product */
8209: cptcovage++; /* Sums the number of covariates which include age as a product */
8210: Tage[cptcovage]=k; /* Tvar[4]=3, Tage[1] = 4 or V1+V1*age Tvar[2]=1, Tage[1]=2 */
8211: /*printf("stre=%s ", stre);*/
8212: } else if (strcmp(strd,"age")==0) { /* or age*Vn */
8213: cptcovprod--;
8214: cutl(stre,strb,strc,'V');
8215: Tvar[k]=atoi(stre);
8216: Typevar[k]=1; /* 1 for age product */
8217: cptcovage++;
8218: Tage[cptcovage]=k;
8219: } else { /* Age is not in the model product V2+V1+V1*V4+V3*age+V3*V2 strb=V3*V2*/
8220: /* loops on k1=1 (V3*V2) and k1=2 V4*V3 */
8221: cptcovn++;
8222: cptcovprodnoage++;k1++;
8223: cutl(stre,strb,strc,'V'); /* strc= Vn, stre is n; strb=V3*V2 stre=3 strc=*/
8224: Tvar[k]=ncovcol+nqv+ntv+nqtv+k1; /* For model-covariate k tells which data-covariate to use but
8225: because this model-covariate is a construction we invent a new column
8226: which is after existing variables ncovcol+nqv+ntv+nqtv + k1
8227: If already ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2
8228: Tvar[3=V1*V4]=4+1 Tvar[5=V3*V2]=4 + 2= 6, etc */
8229: Typevar[k]=2; /* 2 for double fixed dummy covariates */
8230: cutl(strc,strb,strd,'V'); /* strd was Vm, strc is m */
8231: Tprod[k1]=k; /* Tprod[1]=3(=V1*V4) for V2+V1+V1*V4+age*V3+V3*V2 */
8232: Tposprod[k]=k1; /* Tpsprod[3]=1, Tposprod[2]=5 */
8233: Tvard[k1][1] =atoi(strc); /* m 1 for V1*/
8234: Tvard[k1][2] =atoi(stre); /* n 4 for V4*/
8235: k2=k2+2; /* k2 is initialize to -1, We want to store the n and m in Vn*Vm at the end of Tvar */
8236: /* Tvar[cptcovt+k2]=Tvard[k1][1]; /\* Tvar[(cptcovt=4+k2=1)=5]= 1 (V1) *\/ */
8237: /* Tvar[cptcovt+k2+1]=Tvard[k1][2]; /\* Tvar[(cptcovt=4+(k2=1)+1)=6]= 4 (V4) *\/ */
1.225 brouard 8238: /*ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2, Tvar[3]=5, Tvar[4]=6, cptcovt=5 */
1.234 brouard 8239: /* 1 2 3 4 5 | Tvar[5+1)=1, Tvar[7]=2 */
8240: for (i=1; i<=lastobs;i++){
8241: /* Computes the new covariate which is a product of
8242: covar[n][i]* covar[m][i] and stores it at ncovol+k1 May not be defined */
8243: covar[ncovcol+k1][i]=covar[atoi(stre)][i]*covar[atoi(strc)][i];
8244: }
8245: } /* End age is not in the model */
8246: } /* End if model includes a product */
8247: else { /* no more sum */
8248: /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
8249: /* scanf("%d",i);*/
8250: cutl(strd,strc,strb,'V');
8251: ks++; /**< Number of simple covariates dummy or quantitative, fixe or varying */
8252: cptcovn++; /** V4+V3+V5: V4 and V3 timevarying dummy covariates, V5 timevarying quantitative */
8253: Tvar[k]=atoi(strd);
8254: Typevar[k]=0; /* 0 for simple covariates */
8255: }
8256: strcpy(modelsav,stra); /* modelsav=V2+V1+V4 stra=V2+V1+V4 */
1.223 brouard 8257: /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
1.225 brouard 8258: scanf("%d",i);*/
1.187 brouard 8259: } /* end of loop + on total covariates */
8260: } /* end if strlen(modelsave == 0) age*age might exist */
8261: } /* end if strlen(model == 0) */
1.136 brouard 8262:
8263: /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
8264: If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
1.225 brouard 8265:
1.136 brouard 8266: /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
1.225 brouard 8267: printf("cptcovprod=%d ", cptcovprod);
8268: fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
8269: scanf("%d ",i);*/
8270:
8271:
1.230 brouard 8272: /* Until here, decodemodel knows only the grammar (simple, product, age*) of the model but not what kind
8273: of variable (dummy vs quantitative, fixed vs time varying) is behind. But we know the # of each. */
1.226 brouard 8274: /* ncovcol= 1, nqv=1 | ntv=2, nqtv= 1 = 5 possible variables data: 2 fixed 3, varying
8275: model= V5 + V4 +V3 + V4*V3 + V5*age + V2 + V1*V2 + V1*age + V5*age, V1 is not used saving its place
8276: k = 1 2 3 4 5 6 7 8 9
8277: Tvar[k]= 5 4 3 1+1+2+1+1=6 5 2 7 1 5
8278: Typevar[k]= 0 0 0 2 1 0 2 1 1
1.227 brouard 8279: Fixed[k] 1 1 1 1 3 0 0 or 2 2 3
8280: Dummy[k] 1 0 0 0 3 1 1 2 3
8281: Tmodelind[combination of covar]=k;
1.225 brouard 8282: */
8283: /* Dispatching between quantitative and time varying covariates */
1.226 brouard 8284: /* If Tvar[k] >ncovcol it is a product */
1.225 brouard 8285: /* Tvar[k] is the value n of Vn with n varying for 1 to nvcol, or p Vp=Vn*Vm for product */
1.226 brouard 8286: /* Computing effective variables, ie used by the model, that is from the cptcovt variables */
1.227 brouard 8287: printf("Model=%s\n\
8288: Typevar: 0 for simple covariate (dummy, quantitative, fixed or varying), 1 for age product, 2 for product \n\
8289: Fixed[k] 0=fixed (product or simple), 1 varying, 2 fixed with age product, 3 varying with age product \n\
8290: Dummy[k] 0=dummy (0 1), 1 quantitative (single or product without age), 2 dummy with age product, 3 quant with age product\n",model);
8291: fprintf(ficlog,"Model=%s\n\
8292: Typevar: 0 for simple covariate (dummy, quantitative, fixed or varying), 1 for age product, 2 for product \n\
8293: Fixed[k] 0=fixed (product or simple), 1 varying, 2 fixed with age product, 3 varying with age product \n\
8294: Dummy[k] 0=dummy (0 1), 1 quantitative (single or product without age), 2 dummy with age product, 3 quant with age product\n",model);
8295:
1.234 brouard 8296: for(k=1, ncovf=0, nsd=0, nsq=0, ncovv=0, ncova=0, ncoveff=0, nqfveff=0, ntveff=0, nqtveff=0;k<=cptcovt; k++){ /* or cptocvt */
8297: if (Tvar[k] <=ncovcol && Typevar[k]==0 ){ /* Simple fixed dummy (<=ncovcol) covariates */
1.227 brouard 8298: Fixed[k]= 0;
8299: Dummy[k]= 0;
1.225 brouard 8300: ncoveff++;
1.232 brouard 8301: ncovf++;
1.234 brouard 8302: nsd++;
8303: modell[k].maintype= FTYPE;
8304: TvarsD[nsd]=Tvar[k];
8305: TvarsDind[nsd]=k;
8306: TvarF[ncovf]=Tvar[k];
8307: TvarFind[ncovf]=k;
8308: TvarFD[ncoveff]=Tvar[k]; /* TvarFD[1]=V1 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
8309: TvarFDind[ncoveff]=k; /* TvarFDind[1]=9 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
8310: }else if( Tvar[k] <=ncovcol && Typevar[k]==2){ /* Product of fixed dummy (<=ncovcol) covariates */
8311: Fixed[k]= 0;
8312: Dummy[k]= 0;
8313: ncoveff++;
8314: ncovf++;
8315: modell[k].maintype= FTYPE;
8316: TvarF[ncovf]=Tvar[k];
8317: TvarFind[ncovf]=k;
1.230 brouard 8318: TvarFD[ncoveff]=Tvar[k]; /* TvarFD[1]=V1 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
1.231 brouard 8319: TvarFDind[ncoveff]=k; /* TvarFDind[1]=9 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
8320: }else if( Tvar[k] <=ncovcol+nqv && Typevar[k]==0){ /* Remind that product Vn*Vm are added in k*/ /* Only simple fixed quantitative variable */
1.227 brouard 8321: Fixed[k]= 0;
8322: Dummy[k]= 1;
1.230 brouard 8323: nqfveff++;
1.234 brouard 8324: modell[k].maintype= FTYPE;
8325: modell[k].subtype= FQ;
8326: nsq++;
8327: TvarsQ[nsq]=Tvar[k];
8328: TvarsQind[nsq]=k;
1.232 brouard 8329: ncovf++;
1.234 brouard 8330: TvarF[ncovf]=Tvar[k];
8331: TvarFind[ncovf]=k;
1.231 brouard 8332: TvarFQ[nqfveff]=Tvar[k]-ncovcol; /* TvarFQ[1]=V2-1=1st in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple fixed quantitative variable */
1.230 brouard 8333: TvarFQind[nqfveff]=k; /* TvarFQind[1]=6 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple fixed quantitative variable */
1.234 brouard 8334: }else if( Tvar[k] <=ncovcol+nqv+ntv && Typevar[k]==0){/* Only simple time varying variables */
1.227 brouard 8335: Fixed[k]= 1;
8336: Dummy[k]= 0;
1.225 brouard 8337: ntveff++; /* Only simple time varying dummy variable */
1.234 brouard 8338: modell[k].maintype= VTYPE;
8339: modell[k].subtype= VD;
8340: nsd++;
8341: TvarsD[nsd]=Tvar[k];
8342: TvarsDind[nsd]=k;
8343: ncovv++; /* Only simple time varying variables */
8344: TvarV[ncovv]=Tvar[k];
8345: TvarVind[ncovv]=k;
1.231 brouard 8346: TvarVD[ntveff]=Tvar[k]; /* TvarVD[1]=V4 TvarVD[2]=V3 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple time varying dummy variable */
8347: TvarVDind[ntveff]=k; /* TvarVDind[1]=2 TvarVDind[2]=3 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple time varying dummy variable */
1.228 brouard 8348: printf("Quasi Tmodelind[%d]=%d,Tvar[Tmodelind[%d]]=V%d, ncovcol=%d, nqv=%d,Tvar[k]- ncovcol-nqv=%d\n",ntveff,k,ntveff,Tvar[k], ncovcol, nqv,Tvar[k]- ncovcol-nqv);
8349: printf("Quasi TmodelInvind[%d]=%d\n",k,Tvar[k]- ncovcol-nqv);
1.231 brouard 8350: }else if( Tvar[k] <=ncovcol+nqv+ntv+nqtv && Typevar[k]==0){ /* Only simple time varying quantitative variable V5*/
1.234 brouard 8351: Fixed[k]= 1;
8352: Dummy[k]= 1;
8353: nqtveff++;
8354: modell[k].maintype= VTYPE;
8355: modell[k].subtype= VQ;
8356: ncovv++; /* Only simple time varying variables */
8357: nsq++;
8358: TvarsQ[nsq]=Tvar[k];
8359: TvarsQind[nsq]=k;
8360: TvarV[ncovv]=Tvar[k];
8361: TvarVind[ncovv]=k;
1.231 brouard 8362: TvarVQ[nqtveff]=Tvar[k]; /* TvarVQ[1]=V5 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple time varying quantitative variable */
8363: TvarVQind[nqtveff]=k; /* TvarVQind[1]=1 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple time varying quantitative variable */
1.234 brouard 8364: TmodelInvQind[nqtveff]=Tvar[k]- ncovcol-nqv-ntv;/* Only simple time varying quantitative variable */
8365: /* Tmodeliqind[k]=nqtveff;/\* Only simple time varying quantitative variable *\/ */
8366: printf("Quasi TmodelQind[%d]=%d,Tvar[TmodelQind[%d]]=V%d, ncovcol=%d, nqv=%d, ntv=%d,Tvar[k]- ncovcol-nqv-ntv=%d\n",nqtveff,k,nqtveff,Tvar[k], ncovcol, nqv, ntv, Tvar[k]- ncovcol-nqv-ntv);
1.228 brouard 8367: printf("Quasi TmodelInvQind[%d]=%d\n",k,Tvar[k]- ncovcol-nqv-ntv);
1.227 brouard 8368: }else if (Typevar[k] == 1) { /* product with age */
1.234 brouard 8369: ncova++;
8370: TvarA[ncova]=Tvar[k];
8371: TvarAind[ncova]=k;
1.231 brouard 8372: if (Tvar[k] <=ncovcol ){ /* Product age with fixed dummy covariatee */
1.234 brouard 8373: Fixed[k]= 2;
8374: Dummy[k]= 2;
8375: modell[k].maintype= ATYPE;
8376: modell[k].subtype= APFD;
8377: /* ncoveff++; */
1.227 brouard 8378: }else if( Tvar[k] <=ncovcol+nqv) { /* Remind that product Vn*Vm are added in k*/
1.234 brouard 8379: Fixed[k]= 2;
8380: Dummy[k]= 3;
8381: modell[k].maintype= ATYPE;
8382: modell[k].subtype= APFQ; /* Product age * fixed quantitative */
8383: /* nqfveff++; /\* Only simple fixed quantitative variable *\/ */
1.227 brouard 8384: }else if( Tvar[k] <=ncovcol+nqv+ntv ){
1.234 brouard 8385: Fixed[k]= 3;
8386: Dummy[k]= 2;
8387: modell[k].maintype= ATYPE;
8388: modell[k].subtype= APVD; /* Product age * varying dummy */
8389: /* ntveff++; /\* Only simple time varying dummy variable *\/ */
1.227 brouard 8390: }else if( Tvar[k] <=ncovcol+nqv+ntv+nqtv){
1.234 brouard 8391: Fixed[k]= 3;
8392: Dummy[k]= 3;
8393: modell[k].maintype= ATYPE;
8394: modell[k].subtype= APVQ; /* Product age * varying quantitative */
8395: /* nqtveff++;/\* Only simple time varying quantitative variable *\/ */
1.227 brouard 8396: }
8397: }else if (Typevar[k] == 2) { /* product without age */
8398: k1=Tposprod[k];
8399: if(Tvard[k1][1] <=ncovcol){
1.234 brouard 8400: if(Tvard[k1][2] <=ncovcol){
8401: Fixed[k]= 1;
8402: Dummy[k]= 0;
8403: modell[k].maintype= FTYPE;
8404: modell[k].subtype= FPDD; /* Product fixed dummy * fixed dummy */
8405: ncovf++; /* Fixed variables without age */
8406: TvarF[ncovf]=Tvar[k];
8407: TvarFind[ncovf]=k;
8408: }else if(Tvard[k1][2] <=ncovcol+nqv){
8409: Fixed[k]= 0; /* or 2 ?*/
8410: Dummy[k]= 1;
8411: modell[k].maintype= FTYPE;
8412: modell[k].subtype= FPDQ; /* Product fixed dummy * fixed quantitative */
8413: ncovf++; /* Varying variables without age */
8414: TvarF[ncovf]=Tvar[k];
8415: TvarFind[ncovf]=k;
8416: }else if(Tvard[k1][2] <=ncovcol+nqv+ntv){
8417: Fixed[k]= 1;
8418: Dummy[k]= 0;
8419: modell[k].maintype= VTYPE;
8420: modell[k].subtype= VPDD; /* Product fixed dummy * varying dummy */
8421: ncovv++; /* Varying variables without age */
8422: TvarV[ncovv]=Tvar[k];
8423: TvarVind[ncovv]=k;
8424: }else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){
8425: Fixed[k]= 1;
8426: Dummy[k]= 1;
8427: modell[k].maintype= VTYPE;
8428: modell[k].subtype= VPDQ; /* Product fixed dummy * varying quantitative */
8429: ncovv++; /* Varying variables without age */
8430: TvarV[ncovv]=Tvar[k];
8431: TvarVind[ncovv]=k;
8432: }
1.227 brouard 8433: }else if(Tvard[k1][1] <=ncovcol+nqv){
1.234 brouard 8434: if(Tvard[k1][2] <=ncovcol){
8435: Fixed[k]= 0; /* or 2 ?*/
8436: Dummy[k]= 1;
8437: modell[k].maintype= FTYPE;
8438: modell[k].subtype= FPDQ; /* Product fixed quantitative * fixed dummy */
8439: ncovf++; /* Fixed variables without age */
8440: TvarF[ncovf]=Tvar[k];
8441: TvarFind[ncovf]=k;
8442: }else if(Tvard[k1][2] <=ncovcol+nqv+ntv){
8443: Fixed[k]= 1;
8444: Dummy[k]= 1;
8445: modell[k].maintype= VTYPE;
8446: modell[k].subtype= VPDQ; /* Product fixed quantitative * varying dummy */
8447: ncovv++; /* Varying variables without age */
8448: TvarV[ncovv]=Tvar[k];
8449: TvarVind[ncovv]=k;
8450: }else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){
8451: Fixed[k]= 1;
8452: Dummy[k]= 1;
8453: modell[k].maintype= VTYPE;
8454: modell[k].subtype= VPQQ; /* Product fixed quantitative * varying quantitative */
8455: ncovv++; /* Varying variables without age */
8456: TvarV[ncovv]=Tvar[k];
8457: TvarVind[ncovv]=k;
8458: ncovv++; /* Varying variables without age */
8459: TvarV[ncovv]=Tvar[k];
8460: TvarVind[ncovv]=k;
8461: }
1.227 brouard 8462: }else if(Tvard[k1][1] <=ncovcol+nqv+ntv){
1.234 brouard 8463: if(Tvard[k1][2] <=ncovcol){
8464: Fixed[k]= 1;
8465: Dummy[k]= 1;
8466: modell[k].maintype= VTYPE;
8467: modell[k].subtype= VPDD; /* Product time varying dummy * fixed dummy */
8468: ncovv++; /* Varying variables without age */
8469: TvarV[ncovv]=Tvar[k];
8470: TvarVind[ncovv]=k;
8471: }else if(Tvard[k1][2] <=ncovcol+nqv){
8472: Fixed[k]= 1;
8473: Dummy[k]= 1;
8474: modell[k].maintype= VTYPE;
8475: modell[k].subtype= VPDQ; /* Product time varying dummy * fixed quantitative */
8476: ncovv++; /* Varying variables without age */
8477: TvarV[ncovv]=Tvar[k];
8478: TvarVind[ncovv]=k;
8479: }else if(Tvard[k1][2] <=ncovcol+nqv+ntv){
8480: Fixed[k]= 1;
8481: Dummy[k]= 0;
8482: modell[k].maintype= VTYPE;
8483: modell[k].subtype= VPDD; /* Product time varying dummy * time varying dummy */
8484: ncovv++; /* Varying variables without age */
8485: TvarV[ncovv]=Tvar[k];
8486: TvarVind[ncovv]=k;
8487: }else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){
8488: Fixed[k]= 1;
8489: Dummy[k]= 1;
8490: modell[k].maintype= VTYPE;
8491: modell[k].subtype= VPDQ; /* Product time varying dummy * time varying quantitative */
8492: ncovv++; /* Varying variables without age */
8493: TvarV[ncovv]=Tvar[k];
8494: TvarVind[ncovv]=k;
8495: }
1.227 brouard 8496: }else if(Tvard[k1][1] <=ncovcol+nqv+ntv+nqtv){
1.234 brouard 8497: if(Tvard[k1][2] <=ncovcol){
8498: Fixed[k]= 1;
8499: Dummy[k]= 1;
8500: modell[k].maintype= VTYPE;
8501: modell[k].subtype= VPDQ; /* Product time varying quantitative * fixed dummy */
8502: ncovv++; /* Varying variables without age */
8503: TvarV[ncovv]=Tvar[k];
8504: TvarVind[ncovv]=k;
8505: }else if(Tvard[k1][2] <=ncovcol+nqv){
8506: Fixed[k]= 1;
8507: Dummy[k]= 1;
8508: modell[k].maintype= VTYPE;
8509: modell[k].subtype= VPQQ; /* Product time varying quantitative * fixed quantitative */
8510: ncovv++; /* Varying variables without age */
8511: TvarV[ncovv]=Tvar[k];
8512: TvarVind[ncovv]=k;
8513: }else if(Tvard[k1][2] <=ncovcol+nqv+ntv){
8514: Fixed[k]= 1;
8515: Dummy[k]= 1;
8516: modell[k].maintype= VTYPE;
8517: modell[k].subtype= VPDQ; /* Product time varying quantitative * time varying dummy */
8518: ncovv++; /* Varying variables without age */
8519: TvarV[ncovv]=Tvar[k];
8520: TvarVind[ncovv]=k;
8521: }else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){
8522: Fixed[k]= 1;
8523: Dummy[k]= 1;
8524: modell[k].maintype= VTYPE;
8525: modell[k].subtype= VPQQ; /* Product time varying quantitative * time varying quantitative */
8526: ncovv++; /* Varying variables without age */
8527: TvarV[ncovv]=Tvar[k];
8528: TvarVind[ncovv]=k;
8529: }
1.227 brouard 8530: }else{
1.234 brouard 8531: printf("Error unknown type of covariate: Tvard[%d][1]=%d,Tvard[%d][2]=%d\n",k1,Tvard[k1][1],k1,Tvard[k1][2]);
8532: fprintf(ficlog,"Error unknown type of covariate: Tvard[%d][1]=%d,Tvard[%d][2]=%d\n",k1,Tvard[k1][1],k1,Tvard[k1][2]);
1.226 brouard 8533: } /* end k1 */
1.225 brouard 8534: }else{
1.226 brouard 8535: printf("Error, current version can't treat for performance reasons, Tvar[%d]=%d, Typevar[%d]=%d\n", k, Tvar[k], k, Typevar[k]);
8536: fprintf(ficlog,"Error, current version can't treat for performance reasons, Tvar[%d]=%d, Typevar[%d]=%d\n", k, Tvar[k], k, Typevar[k]);
1.225 brouard 8537: }
1.227 brouard 8538: printf("Decodemodel, k=%d, Tvar[%d]=V%d,Typevar=%d, Fixed=%d, Dummy=%d\n",k, k,Tvar[k],Typevar[k],Fixed[k],Dummy[k]);
1.231 brouard 8539: printf(" modell[%d].maintype=%d, modell[%d].subtype=%d\n",k,modell[k].maintype,k,modell[k].subtype);
1.227 brouard 8540: fprintf(ficlog,"Decodemodel, k=%d, Tvar[%d]=V%d,Typevar=%d, Fixed=%d, Dummy=%d\n",k, k,Tvar[k],Typevar[k],Fixed[k],Dummy[k]);
8541: }
8542: /* Searching for doublons in the model */
8543: for(k1=1; k1<= cptcovt;k1++){
8544: for(k2=1; k2 <k1;k2++){
8545: if((Typevar[k1]==Typevar[k2]) && (Fixed[Tvar[k1]]==Fixed[Tvar[k2]]) && (Dummy[Tvar[k1]]==Dummy[Tvar[k2]] )){
1.234 brouard 8546: if((Typevar[k1] == 0 || Typevar[k1] == 1)){ /* Simple or age product */
8547: if(Tvar[k1]==Tvar[k2]){
8548: printf("Error duplication in the model=%s at positions (+) %d and %d, Tvar[%d]=V%d, Tvar[%d]=V%d, Typevar=%d, Fixed=%d, Dummy=%d\n", model, k1,k2, k1, Tvar[k1], k2, Tvar[k2],Typevar[k1],Fixed[Tvar[k1]],Dummy[Tvar[k1]]);
8549: fprintf(ficlog,"Error duplication in the model=%s at positions (+) %d and %d, Tvar[%d]=V%d, Tvar[%d]=V%d, Typevar=%d, Fixed=%d, Dummy=%d\n", model, k1,k2, k1, Tvar[k1], k2, Tvar[k2],Typevar[k1],Fixed[Tvar[k1]],Dummy[Tvar[k1]]); fflush(ficlog);
8550: return(1);
8551: }
8552: }else if (Typevar[k1] ==2){
8553: k3=Tposprod[k1];
8554: k4=Tposprod[k2];
8555: if( ((Tvard[k3][1]== Tvard[k4][1])&&(Tvard[k3][2]== Tvard[k4][2])) || ((Tvard[k3][1]== Tvard[k4][2])&&(Tvard[k3][2]== Tvard[k4][1])) ){
8556: printf("Error duplication in the model=%s at positions (+) %d and %d, V%d*V%d, Typevar=%d, Fixed=%d, Dummy=%d\n",model, k1,k2, Tvard[k3][1], Tvard[k3][2],Typevar[k1],Fixed[Tvar[k1]],Dummy[Tvar[k1]]);
8557: fprintf(ficlog,"Error duplication in the model=%s at positions (+) %d and %d, V%d*V%d, Typevar=%d, Fixed=%d, Dummy=%d\n",model, k1,k2, Tvard[k3][1], Tvard[k3][2],Typevar[k1],Fixed[Tvar[k1]],Dummy[Tvar[k1]]); fflush(ficlog);
8558: return(1);
8559: }
8560: }
1.227 brouard 8561: }
8562: }
1.225 brouard 8563: }
8564: printf("ncoveff=%d, nqfveff=%d, ntveff=%d, nqtveff=%d, cptcovn=%d\n",ncoveff,nqfveff,ntveff,nqtveff,cptcovn);
8565: fprintf(ficlog,"ncoveff=%d, nqfveff=%d, ntveff=%d, nqtveff=%d, cptcovn=%d\n",ncoveff,nqfveff,ntveff,nqtveff,cptcovn);
1.234 brouard 8566: printf("ncovf=%d, ncovv=%d, ncova=%d, nsd=%d, nsq=%d\n",ncovf,ncovv,ncova,nsd,nsq);
8567: fprintf(ficlog,"ncovf=%d, ncovv=%d, ncova=%d, nsd=%d, nsq=%d\n",ncovf,ncovv,ncova,nsd, nsq);
1.137 brouard 8568: return (0); /* with covar[new additional covariate if product] and Tage if age */
1.164 brouard 8569: /*endread:*/
1.225 brouard 8570: printf("Exiting decodemodel: ");
8571: return (1);
1.136 brouard 8572: }
8573:
1.169 brouard 8574: int calandcheckages(int imx, int maxwav, double *agemin, double *agemax, int *nberr, int *nbwarn )
1.136 brouard 8575: {
8576: int i, m;
1.218 brouard 8577: int firstone=0;
8578:
1.136 brouard 8579: for (i=1; i<=imx; i++) {
8580: for(m=2; (m<= maxwav); m++) {
8581: if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
8582: anint[m][i]=9999;
1.216 brouard 8583: if (s[m][i] != -2) /* Keeping initial status of unknown vital status */
8584: s[m][i]=-1;
1.136 brouard 8585: }
8586: if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
1.169 brouard 8587: *nberr = *nberr + 1;
1.218 brouard 8588: if(firstone == 0){
8589: firstone=1;
8590: 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 can be biased (%d) because status is a death state %d at wave %d. Wave dropped.\nOther similar cases in log file\n",(int)moisdc[i],(int)andc[i],num[i],i, *nberr,s[m][i],m);
8591: }
8592: 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 can be biased (%d) because status is a death state %d at wave %d. Wave dropped.\n",(int)moisdc[i],(int)andc[i],num[i],i, *nberr,s[m][i],m);
1.136 brouard 8593: s[m][i]=-1;
8594: }
8595: if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
1.169 brouard 8596: (*nberr)++;
1.136 brouard 8597: 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]);
8598: 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]);
8599: s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
8600: }
8601: }
8602: }
8603:
8604: for (i=1; i<=imx; i++) {
8605: agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
8606: for(m=firstpass; (m<= lastpass); m++){
1.214 brouard 8607: if(s[m][i] >0 || s[m][i]==-1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){ /* What if s[m][i]=-1 */
1.136 brouard 8608: if (s[m][i] >= nlstate+1) {
1.169 brouard 8609: if(agedc[i]>0){
8610: if((int)moisdc[i]!=99 && (int)andc[i]!=9999){
1.136 brouard 8611: agev[m][i]=agedc[i];
1.214 brouard 8612: /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
1.169 brouard 8613: }else {
1.136 brouard 8614: if ((int)andc[i]!=9999){
8615: nbwarn++;
8616: printf("Warning negative age at death: %ld line:%d\n",num[i],i);
8617: fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
8618: agev[m][i]=-1;
8619: }
8620: }
1.169 brouard 8621: } /* agedc > 0 */
1.214 brouard 8622: } /* end if */
1.136 brouard 8623: else if(s[m][i] !=9){ /* Standard case, age in fractional
8624: years but with the precision of a month */
8625: agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
8626: if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
8627: agev[m][i]=1;
8628: else if(agev[m][i] < *agemin){
8629: *agemin=agev[m][i];
8630: printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], *agemin);
8631: }
8632: else if(agev[m][i] >*agemax){
8633: *agemax=agev[m][i];
1.156 brouard 8634: /* printf(" Max anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.2f\n",m,i,anint[m][i], i,annais[i], *agemax);*/
1.136 brouard 8635: }
8636: /*agev[m][i]=anint[m][i]-annais[i];*/
8637: /* agev[m][i] = age[i]+2*m;*/
1.214 brouard 8638: } /* en if 9*/
1.136 brouard 8639: else { /* =9 */
1.214 brouard 8640: /* printf("Debug num[%d]=%ld s[%d][%d]=%d\n",i,num[i], m,i, s[m][i]); */
1.136 brouard 8641: agev[m][i]=1;
8642: s[m][i]=-1;
8643: }
8644: }
1.214 brouard 8645: else if(s[m][i]==0) /*= 0 Unknown */
1.136 brouard 8646: agev[m][i]=1;
1.214 brouard 8647: else{
8648: printf("Warning, num[%d]=%ld, s[%d][%d]=%d\n", i, num[i], m, i,s[m][i]);
8649: fprintf(ficlog, "Warning, num[%d]=%ld, s[%d][%d]=%d\n", i, num[i], m, i,s[m][i]);
8650: agev[m][i]=0;
8651: }
8652: } /* End for lastpass */
8653: }
1.136 brouard 8654:
8655: for (i=1; i<=imx; i++) {
8656: for(m=firstpass; (m<=lastpass); m++){
8657: if (s[m][i] > (nlstate+ndeath)) {
1.169 brouard 8658: (*nberr)++;
1.136 brouard 8659: 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);
8660: 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);
8661: return 1;
8662: }
8663: }
8664: }
8665:
8666: /*for (i=1; i<=imx; i++){
8667: for (m=firstpass; (m<lastpass); m++){
8668: printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
8669: }
8670:
8671: }*/
8672:
8673:
1.139 brouard 8674: printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
8675: fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
1.136 brouard 8676:
8677: return (0);
1.164 brouard 8678: /* endread:*/
1.136 brouard 8679: printf("Exiting calandcheckages: ");
8680: return (1);
8681: }
8682:
1.172 brouard 8683: #if defined(_MSC_VER)
8684: /*printf("Visual C++ compiler: %s \n;", _MSC_FULL_VER);*/
8685: /*fprintf(ficlog, "Visual C++ compiler: %s \n;", _MSC_FULL_VER);*/
8686: //#include "stdafx.h"
8687: //#include <stdio.h>
8688: //#include <tchar.h>
8689: //#include <windows.h>
8690: //#include <iostream>
8691: typedef BOOL(WINAPI *LPFN_ISWOW64PROCESS) (HANDLE, PBOOL);
8692:
8693: LPFN_ISWOW64PROCESS fnIsWow64Process;
8694:
8695: BOOL IsWow64()
8696: {
8697: BOOL bIsWow64 = FALSE;
8698:
8699: //typedef BOOL (APIENTRY *LPFN_ISWOW64PROCESS)
8700: // (HANDLE, PBOOL);
8701:
8702: //LPFN_ISWOW64PROCESS fnIsWow64Process;
8703:
8704: HMODULE module = GetModuleHandle(_T("kernel32"));
8705: const char funcName[] = "IsWow64Process";
8706: fnIsWow64Process = (LPFN_ISWOW64PROCESS)
8707: GetProcAddress(module, funcName);
8708:
8709: if (NULL != fnIsWow64Process)
8710: {
8711: if (!fnIsWow64Process(GetCurrentProcess(),
8712: &bIsWow64))
8713: //throw std::exception("Unknown error");
8714: printf("Unknown error\n");
8715: }
8716: return bIsWow64 != FALSE;
8717: }
8718: #endif
1.177 brouard 8719:
1.191 brouard 8720: void syscompilerinfo(int logged)
1.167 brouard 8721: {
8722: /* #include "syscompilerinfo.h"*/
1.185 brouard 8723: /* command line Intel compiler 32bit windows, XP compatible:*/
8724: /* /GS /W3 /Gy
8725: /Zc:wchar_t /Zi /O2 /Fd"Release\vc120.pdb" /D "WIN32" /D "NDEBUG" /D
8726: "_CONSOLE" /D "_LIB" /D "_USING_V110_SDK71_" /D "_UNICODE" /D
8727: "UNICODE" /Qipo /Zc:forScope /Gd /Oi /MT /Fa"Release\" /EHsc /nologo
1.186 brouard 8728: /Fo"Release\" /Qprof-dir "Release\" /Fp"Release\IMaCh.pch"
8729: */
8730: /* 64 bits */
1.185 brouard 8731: /*
8732: /GS /W3 /Gy
8733: /Zc:wchar_t /Zi /O2 /Fd"x64\Release\vc120.pdb" /D "WIN32" /D "NDEBUG"
8734: /D "_CONSOLE" /D "_LIB" /D "_UNICODE" /D "UNICODE" /Qipo /Zc:forScope
8735: /Oi /MD /Fa"x64\Release\" /EHsc /nologo /Fo"x64\Release\" /Qprof-dir
8736: "x64\Release\" /Fp"x64\Release\IMaCh.pch" */
8737: /* Optimization are useless and O3 is slower than O2 */
8738: /*
8739: /GS /W3 /Gy /Zc:wchar_t /Zi /O3 /Fd"x64\Release\vc120.pdb" /D "WIN32"
8740: /D "NDEBUG" /D "_CONSOLE" /D "_LIB" /D "_UNICODE" /D "UNICODE" /Qipo
8741: /Zc:forScope /Oi /MD /Fa"x64\Release\" /EHsc /nologo /Qparallel
8742: /Fo"x64\Release\" /Qprof-dir "x64\Release\" /Fp"x64\Release\IMaCh.pch"
8743: */
1.186 brouard 8744: /* Link is */ /* /OUT:"visual studio
1.185 brouard 8745: 2013\Projects\IMaCh\Release\IMaCh.exe" /MANIFEST /NXCOMPAT
8746: /PDB:"visual studio
8747: 2013\Projects\IMaCh\Release\IMaCh.pdb" /DYNAMICBASE
8748: "kernel32.lib" "user32.lib" "gdi32.lib" "winspool.lib"
8749: "comdlg32.lib" "advapi32.lib" "shell32.lib" "ole32.lib"
8750: "oleaut32.lib" "uuid.lib" "odbc32.lib" "odbccp32.lib"
8751: /MACHINE:X86 /OPT:REF /SAFESEH /INCREMENTAL:NO
8752: /SUBSYSTEM:CONSOLE",5.01" /MANIFESTUAC:"level='asInvoker'
8753: uiAccess='false'"
8754: /ManifestFile:"Release\IMaCh.exe.intermediate.manifest" /OPT:ICF
8755: /NOLOGO /TLBID:1
8756: */
1.177 brouard 8757: #if defined __INTEL_COMPILER
1.178 brouard 8758: #if defined(__GNUC__)
8759: struct utsname sysInfo; /* For Intel on Linux and OS/X */
8760: #endif
1.177 brouard 8761: #elif defined(__GNUC__)
1.179 brouard 8762: #ifndef __APPLE__
1.174 brouard 8763: #include <gnu/libc-version.h> /* Only on gnu */
1.179 brouard 8764: #endif
1.177 brouard 8765: struct utsname sysInfo;
1.178 brouard 8766: int cross = CROSS;
8767: if (cross){
8768: printf("Cross-");
1.191 brouard 8769: if(logged) fprintf(ficlog, "Cross-");
1.178 brouard 8770: }
1.174 brouard 8771: #endif
8772:
1.171 brouard 8773: #include <stdint.h>
1.178 brouard 8774:
1.191 brouard 8775: printf("Compiled with:");if(logged)fprintf(ficlog,"Compiled with:");
1.169 brouard 8776: #if defined(__clang__)
1.191 brouard 8777: printf(" Clang/LLVM");if(logged)fprintf(ficlog," Clang/LLVM"); /* Clang/LLVM. ---------------------------------------------- */
1.169 brouard 8778: #endif
8779: #if defined(__ICC) || defined(__INTEL_COMPILER)
1.191 brouard 8780: printf(" Intel ICC/ICPC");if(logged)fprintf(ficlog," Intel ICC/ICPC");/* Intel ICC/ICPC. ------------------------------------------ */
1.169 brouard 8781: #endif
8782: #if defined(__GNUC__) || defined(__GNUG__)
1.191 brouard 8783: printf(" GNU GCC/G++");if(logged)fprintf(ficlog," GNU GCC/G++");/* GNU GCC/G++. --------------------------------------------- */
1.169 brouard 8784: #endif
8785: #if defined(__HP_cc) || defined(__HP_aCC)
1.191 brouard 8786: printf(" Hewlett-Packard C/aC++");if(logged)fprintf(fcilog," Hewlett-Packard C/aC++"); /* Hewlett-Packard C/aC++. ---------------------------------- */
1.169 brouard 8787: #endif
8788: #if defined(__IBMC__) || defined(__IBMCPP__)
1.191 brouard 8789: printf(" IBM XL C/C++"); if(logged) fprintf(ficlog," IBM XL C/C++");/* IBM XL C/C++. -------------------------------------------- */
1.169 brouard 8790: #endif
8791: #if defined(_MSC_VER)
1.191 brouard 8792: printf(" Microsoft Visual Studio");if(logged)fprintf(ficlog," Microsoft Visual Studio");/* Microsoft Visual Studio. --------------------------------- */
1.169 brouard 8793: #endif
8794: #if defined(__PGI)
1.191 brouard 8795: printf(" Portland Group PGCC/PGCPP");if(logged) fprintf(ficlog," Portland Group PGCC/PGCPP");/* Portland Group PGCC/PGCPP. ------------------------------- */
1.169 brouard 8796: #endif
8797: #if defined(__SUNPRO_C) || defined(__SUNPRO_CC)
1.191 brouard 8798: printf(" Oracle Solaris Studio");if(logged)fprintf(ficlog," Oracle Solaris Studio\n");/* Oracle Solaris Studio. ----------------------------------- */
1.167 brouard 8799: #endif
1.191 brouard 8800: printf(" for "); if (logged) fprintf(ficlog, " for ");
1.169 brouard 8801:
1.167 brouard 8802: // http://stackoverflow.com/questions/4605842/how-to-identify-platform-compiler-from-preprocessor-macros
8803: #ifdef _WIN32 // note the underscore: without it, it's not msdn official!
8804: // Windows (x64 and x86)
1.191 brouard 8805: printf("Windows (x64 and x86) ");if(logged) fprintf(ficlog,"Windows (x64 and x86) ");
1.167 brouard 8806: #elif __unix__ // all unices, not all compilers
8807: // Unix
1.191 brouard 8808: printf("Unix ");if(logged) fprintf(ficlog,"Unix ");
1.167 brouard 8809: #elif __linux__
8810: // linux
1.191 brouard 8811: printf("linux ");if(logged) fprintf(ficlog,"linux ");
1.167 brouard 8812: #elif __APPLE__
1.174 brouard 8813: // Mac OS, not sure if this is covered by __posix__ and/or __unix__ though..
1.191 brouard 8814: printf("Mac OS ");if(logged) fprintf(ficlog,"Mac OS ");
1.167 brouard 8815: #endif
8816:
8817: /* __MINGW32__ */
8818: /* __CYGWIN__ */
8819: /* __MINGW64__ */
8820: // http://msdn.microsoft.com/en-us/library/b0084kay.aspx
8821: /* _MSC_VER //the Visual C++ compiler is 17.00.51106.1, the _MSC_VER macro evaluates to 1700. Type cl /? */
8822: /* _MSC_FULL_VER //the Visual C++ compiler is 15.00.20706.01, the _MSC_FULL_VER macro evaluates to 150020706 */
8823: /* _WIN64 // Defined for applications for Win64. */
8824: /* _M_X64 // Defined for compilations that target x64 processors. */
8825: /* _DEBUG // Defined when you compile with /LDd, /MDd, and /MTd. */
1.171 brouard 8826:
1.167 brouard 8827: #if UINTPTR_MAX == 0xffffffff
1.191 brouard 8828: printf(" 32-bit"); if(logged) fprintf(ficlog," 32-bit");/* 32-bit */
1.167 brouard 8829: #elif UINTPTR_MAX == 0xffffffffffffffff
1.191 brouard 8830: printf(" 64-bit"); if(logged) fprintf(ficlog," 64-bit");/* 64-bit */
1.167 brouard 8831: #else
1.191 brouard 8832: printf(" wtf-bit"); if(logged) fprintf(ficlog," wtf-bit");/* wtf */
1.167 brouard 8833: #endif
8834:
1.169 brouard 8835: #if defined(__GNUC__)
8836: # if defined(__GNUC_PATCHLEVEL__)
8837: # define __GNUC_VERSION__ (__GNUC__ * 10000 \
8838: + __GNUC_MINOR__ * 100 \
8839: + __GNUC_PATCHLEVEL__)
8840: # else
8841: # define __GNUC_VERSION__ (__GNUC__ * 10000 \
8842: + __GNUC_MINOR__ * 100)
8843: # endif
1.174 brouard 8844: printf(" using GNU C version %d.\n", __GNUC_VERSION__);
1.191 brouard 8845: if(logged) fprintf(ficlog, " using GNU C version %d.\n", __GNUC_VERSION__);
1.176 brouard 8846:
8847: if (uname(&sysInfo) != -1) {
8848: printf("Running on: %s %s %s %s %s\n",sysInfo.sysname, sysInfo.nodename, sysInfo.release, sysInfo.version, sysInfo.machine);
1.191 brouard 8849: 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 8850: }
8851: else
8852: perror("uname() error");
1.179 brouard 8853: //#ifndef __INTEL_COMPILER
8854: #if !defined (__INTEL_COMPILER) && !defined(__APPLE__)
1.174 brouard 8855: printf("GNU libc version: %s\n", gnu_get_libc_version());
1.191 brouard 8856: if(logged) fprintf(ficlog,"GNU libc version: %s\n", gnu_get_libc_version());
1.177 brouard 8857: #endif
1.169 brouard 8858: #endif
1.172 brouard 8859:
8860: // void main()
8861: // {
1.169 brouard 8862: #if defined(_MSC_VER)
1.174 brouard 8863: if (IsWow64()){
1.191 brouard 8864: printf("\nThe program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n");
8865: if (logged) fprintf(ficlog, "\nThe program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n");
1.174 brouard 8866: }
8867: else{
1.191 brouard 8868: printf("\nThe program is not running under WOW64 (i.e probably on a 64bit Windows).\n");
8869: if (logged) fprintf(ficlog, "\nThe programm is not running under WOW64 (i.e probably on a 64bit Windows).\n");
1.174 brouard 8870: }
1.172 brouard 8871: // printf("\nPress Enter to continue...");
8872: // getchar();
8873: // }
8874:
1.169 brouard 8875: #endif
8876:
1.167 brouard 8877:
1.219 brouard 8878: }
1.136 brouard 8879:
1.219 brouard 8880: int prevalence_limit(double *p, double **prlim, double ageminpar, double agemaxpar, double ftolpl, int *ncvyearp){
1.180 brouard 8881: /*--------------- Prevalence limit (period or stable prevalence) --------------*/
1.235 ! brouard 8882: int i, j, k, i1, k4=0, nres=0 ;
1.202 brouard 8883: /* double ftolpl = 1.e-10; */
1.180 brouard 8884: double age, agebase, agelim;
1.203 brouard 8885: double tot;
1.180 brouard 8886:
1.202 brouard 8887: strcpy(filerespl,"PL_");
8888: strcat(filerespl,fileresu);
8889: if((ficrespl=fopen(filerespl,"w"))==NULL) {
8890: printf("Problem with period (stable) prevalence resultfile: %s\n", filerespl);return 1;
8891: fprintf(ficlog,"Problem with period (stable) prevalence resultfile: %s\n", filerespl);return 1;
8892: }
1.227 brouard 8893: printf("\nComputing period (stable) prevalence: result on file '%s' \n", filerespl);
8894: fprintf(ficlog,"\nComputing period (stable) prevalence: result on file '%s' \n", filerespl);
1.202 brouard 8895: pstamp(ficrespl);
1.203 brouard 8896: fprintf(ficrespl,"# Period (stable) prevalence. Precision given by ftolpl=%g \n", ftolpl);
1.202 brouard 8897: fprintf(ficrespl,"#Age ");
8898: for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
8899: fprintf(ficrespl,"\n");
1.180 brouard 8900:
1.219 brouard 8901: /* prlim=matrix(1,nlstate,1,nlstate);*/ /* back in main */
1.180 brouard 8902:
1.219 brouard 8903: agebase=ageminpar;
8904: agelim=agemaxpar;
1.180 brouard 8905:
1.227 brouard 8906: /* i1=pow(2,ncoveff); */
1.234 brouard 8907: i1=pow(2,cptcoveff); /* Number of combination of dummy covariates */
1.219 brouard 8908: if (cptcovn < 1){i1=1;}
1.180 brouard 8909:
1.235 ! brouard 8910: for(nres=1; nres <= nresult; nres++) /* For each resultline */
1.220 brouard 8911: for(k=1; k<=i1;k++){
1.235 ! brouard 8912: if(TKresult[nres]!= k)
! 8913: continue;
! 8914:
1.220 brouard 8915: /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */
1.180 brouard 8916: /* for(cptcov=1,k=0;cptcov<=1;cptcov++){ */
1.219 brouard 8917: //for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
1.220 brouard 8918: /* k=k+1; */
1.219 brouard 8919: /* to clean */
8920: //printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtabm(cptcod,cptcov));
8921: fprintf(ficrespl,"#******");
8922: printf("#******");
8923: fprintf(ficlog,"#******");
1.227 brouard 8924: for(j=1;j<=cptcoveff ;j++) {/* all covariates */
8925: fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); /* Here problem for varying dummy*/
1.219 brouard 8926: printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
8927: fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
8928: }
1.235 ! brouard 8929: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
! 8930: printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
! 8931: fprintf(ficlog," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
! 8932: }
1.219 brouard 8933: fprintf(ficrespl,"******\n");
8934: printf("******\n");
8935: fprintf(ficlog,"******\n");
1.227 brouard 8936: if(invalidvarcomb[k]){
8937: printf("\nCombination (%d) ignored because no case \n",k);
8938: fprintf(ficrespl,"#Combination (%d) ignored because no case \n",k);
8939: fprintf(ficlog,"\nCombination (%d) ignored because no case \n",k);
1.220 brouard 8940: continue;
1.227 brouard 8941: }
1.219 brouard 8942:
8943: fprintf(ficrespl,"#Age ");
1.227 brouard 8944: for(j=1;j<=cptcoveff;j++) {
1.219 brouard 8945: fprintf(ficrespl,"V%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
8946: }
8947: for(i=1; i<=nlstate;i++) fprintf(ficrespl," %d-%d ",i,i);
8948: fprintf(ficrespl,"Total Years_to_converge\n");
1.227 brouard 8949:
1.219 brouard 8950: for (age=agebase; age<=agelim; age++){
8951: /* for (age=agebase; age<=agebase; age++){ */
1.235 ! brouard 8952: prevalim(prlim, nlstate, p, age, oldm, savm, ftolpl, ncvyearp, k, nres);
1.219 brouard 8953: fprintf(ficrespl,"%.0f ",age );
1.227 brouard 8954: for(j=1;j<=cptcoveff;j++)
8955: fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.219 brouard 8956: tot=0.;
8957: for(i=1; i<=nlstate;i++){
1.227 brouard 8958: tot += prlim[i][i];
8959: fprintf(ficrespl," %.5f", prlim[i][i]);
1.219 brouard 8960: }
8961: fprintf(ficrespl," %.3f %d\n", tot, *ncvyearp);
8962: } /* Age */
8963: /* was end of cptcod */
8964: } /* cptcov */
8965: return 0;
1.180 brouard 8966: }
8967:
1.218 brouard 8968: int back_prevalence_limit(double *p, double **bprlim, double ageminpar, double agemaxpar, double ftolpl, int *ncvyearp, double dateprev1,double dateprev2, int firstpass, int lastpass, int mobilavproj){
8969: /*--------------- Back Prevalence limit (period or stable prevalence) --------------*/
8970:
8971: /* Computes the back prevalence limit for any combination of covariate values
8972: * at any age between ageminpar and agemaxpar
8973: */
1.235 ! brouard 8974: int i, j, k, i1, nres=0 ;
1.217 brouard 8975: /* double ftolpl = 1.e-10; */
8976: double age, agebase, agelim;
8977: double tot;
1.218 brouard 8978: /* double ***mobaverage; */
8979: /* double **dnewm, **doldm, **dsavm; /\* for use *\/ */
1.217 brouard 8980:
8981: strcpy(fileresplb,"PLB_");
8982: strcat(fileresplb,fileresu);
8983: if((ficresplb=fopen(fileresplb,"w"))==NULL) {
8984: printf("Problem with period (stable) back prevalence resultfile: %s\n", fileresplb);return 1;
8985: fprintf(ficlog,"Problem with period (stable) back prevalence resultfile: %s\n", fileresplb);return 1;
8986: }
8987: printf("Computing period (stable) back prevalence: result on file '%s' \n", fileresplb);
8988: fprintf(ficlog,"Computing period (stable) back prevalence: result on file '%s' \n", fileresplb);
8989: pstamp(ficresplb);
8990: fprintf(ficresplb,"# Period (stable) back prevalence. Precision given by ftolpl=%g \n", ftolpl);
8991: fprintf(ficresplb,"#Age ");
8992: for(i=1; i<=nlstate;i++) fprintf(ficresplb,"%d-%d ",i,i);
8993: fprintf(ficresplb,"\n");
8994:
1.218 brouard 8995:
8996: /* prlim=matrix(1,nlstate,1,nlstate);*/ /* back in main */
8997:
8998: agebase=ageminpar;
8999: agelim=agemaxpar;
9000:
9001:
1.227 brouard 9002: i1=pow(2,cptcoveff);
1.218 brouard 9003: if (cptcovn < 1){i1=1;}
1.227 brouard 9004:
1.235 ! brouard 9005: for(nres=1; nres <= nresult; nres++) /* For each resultline */
! 9006: for(k=1; k<=i1;k++){ /* For any combination of dummy covariates, fixed and varying */
! 9007: if(TKresult[nres]!= k)
! 9008: continue;
1.218 brouard 9009: //printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtabm(cptcod,cptcov));
9010: fprintf(ficresplb,"#******");
9011: printf("#******");
9012: fprintf(ficlog,"#******");
1.227 brouard 9013: for(j=1;j<=cptcoveff ;j++) {/* all covariates */
1.218 brouard 9014: fprintf(ficresplb," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
9015: printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
9016: fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
9017: }
1.235 ! brouard 9018: for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
! 9019: printf(" V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
! 9020: fprintf(ficresplb," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
! 9021: fprintf(ficlog," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
! 9022: }
1.218 brouard 9023: fprintf(ficresplb,"******\n");
9024: printf("******\n");
9025: fprintf(ficlog,"******\n");
1.227 brouard 9026: if(invalidvarcomb[k]){
9027: printf("\nCombination (%d) ignored because no cases \n",k);
9028: fprintf(ficresplb,"#Combination (%d) ignored because no cases \n",k);
9029: fprintf(ficlog,"\nCombination (%d) ignored because no cases \n",k);
9030: continue;
9031: }
1.218 brouard 9032:
9033: fprintf(ficresplb,"#Age ");
1.227 brouard 9034: for(j=1;j<=cptcoveff;j++) {
1.218 brouard 9035: fprintf(ficresplb,"V%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
9036: }
9037: for(i=1; i<=nlstate;i++) fprintf(ficresplb," %d-%d ",i,i);
9038: fprintf(ficresplb,"Total Years_to_converge\n");
9039:
9040:
9041: for (age=agebase; age<=agelim; age++){
9042: /* for (age=agebase; age<=agebase; age++){ */
9043: if(mobilavproj > 0){
9044: /* bprevalim(bprlim, mobaverage, nlstate, p, age, ageminpar, agemaxpar, oldm, savm, doldm, dsavm, ftolpl, ncvyearp, k); */
9045: /* bprevalim(bprlim, mobaverage, nlstate, p, age, oldm, savm, dnewm, doldm, dsavm, ftolpl, ncvyearp, k); */
1.227 brouard 9046: bprevalim(bprlim, mobaverage, nlstate, p, age, ftolpl, ncvyearp, k);
1.218 brouard 9047: }else if (mobilavproj == 0){
1.227 brouard 9048: printf("There is no chance to get back prevalence limit if data aren't non zero and summing to 1, please try a non null mobil_average(=%d) parameter or mobil_average=-1 if you want to try at your own risk.\n",mobilavproj);
9049: fprintf(ficlog,"There is no chance to get back prevalence limit if data aren't non zero and summing to 1, please try a non null mobil_average(=%d) parameter or mobil_average=-1 if you want to try at your own risk.\n",mobilavproj);
9050: exit(1);
1.218 brouard 9051: }else{
1.227 brouard 9052: /* bprevalim(bprlim, probs, nlstate, p, age, oldm, savm, dnewm, doldm, dsavm, ftolpl, ncvyearp, k); */
9053: bprevalim(bprlim, probs, nlstate, p, age, ftolpl, ncvyearp, k);
1.218 brouard 9054: }
9055: fprintf(ficresplb,"%.0f ",age );
1.227 brouard 9056: for(j=1;j<=cptcoveff;j++)
9057: fprintf(ficresplb,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.218 brouard 9058: tot=0.;
9059: for(i=1; i<=nlstate;i++){
1.227 brouard 9060: tot += bprlim[i][i];
9061: fprintf(ficresplb," %.5f", bprlim[i][i]);
1.218 brouard 9062: }
9063: fprintf(ficresplb," %.3f %d\n", tot, *ncvyearp);
9064: } /* Age */
9065: /* was end of cptcod */
9066: } /* cptcov */
9067:
9068: /* hBijx(p, bage, fage); */
9069: /* fclose(ficrespijb); */
9070:
9071: return 0;
1.217 brouard 9072: }
1.218 brouard 9073:
1.180 brouard 9074: int hPijx(double *p, int bage, int fage){
9075: /*------------- h Pij x at various ages ------------*/
9076:
9077: int stepsize;
9078: int agelim;
9079: int hstepm;
9080: int nhstepm;
1.235 ! brouard 9081: int h, i, i1, j, k, k4, nres=0;
1.180 brouard 9082:
9083: double agedeb;
9084: double ***p3mat;
9085:
1.201 brouard 9086: strcpy(filerespij,"PIJ_"); strcat(filerespij,fileresu);
1.180 brouard 9087: if((ficrespij=fopen(filerespij,"w"))==NULL) {
9088: printf("Problem with Pij resultfile: %s\n", filerespij); return 1;
9089: fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij); return 1;
9090: }
9091: printf("Computing pij: result on file '%s' \n", filerespij);
9092: fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
9093:
9094: stepsize=(int) (stepm+YEARM-1)/YEARM;
9095: /*if (stepm<=24) stepsize=2;*/
9096:
9097: agelim=AGESUP;
9098: hstepm=stepsize*YEARM; /* Every year of age */
9099: hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
1.218 brouard 9100:
1.180 brouard 9101: /* hstepm=1; aff par mois*/
9102: pstamp(ficrespij);
9103: fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
1.227 brouard 9104: i1= pow(2,cptcoveff);
1.218 brouard 9105: /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */
9106: /* /\*for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*\/ */
9107: /* k=k+1; */
1.235 ! brouard 9108: for(nres=1; nres <= nresult; nres++) /* For each resultline */
! 9109: for(k=1; k<=i1;k++){
! 9110: if(TKresult[nres]!= k)
! 9111: continue;
1.183 brouard 9112: fprintf(ficrespij,"\n#****** ");
1.227 brouard 9113: for(j=1;j<=cptcoveff;j++)
1.198 brouard 9114: fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.235 ! brouard 9115: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
! 9116: printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
! 9117: fprintf(ficrespij," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
! 9118: }
1.183 brouard 9119: fprintf(ficrespij,"******\n");
9120:
9121: for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
9122: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
9123: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
9124:
9125: /* nhstepm=nhstepm*YEARM; aff par mois*/
1.180 brouard 9126:
1.183 brouard 9127: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
9128: oldm=oldms;savm=savms;
1.235 ! brouard 9129: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k, nres);
1.183 brouard 9130: fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
9131: for(i=1; i<=nlstate;i++)
9132: for(j=1; j<=nlstate+ndeath;j++)
9133: fprintf(ficrespij," %1d-%1d",i,j);
9134: fprintf(ficrespij,"\n");
9135: for (h=0; h<=nhstepm; h++){
9136: /*agedebphstep = agedeb + h*hstepm/YEARM*stepm;*/
9137: fprintf(ficrespij,"%d %3.f %3.f",k, agedeb, agedeb + h*hstepm/YEARM*stepm );
1.180 brouard 9138: for(i=1; i<=nlstate;i++)
9139: for(j=1; j<=nlstate+ndeath;j++)
1.183 brouard 9140: fprintf(ficrespij," %.5f", p3mat[i][j][h]);
1.180 brouard 9141: fprintf(ficrespij,"\n");
9142: }
1.183 brouard 9143: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
9144: fprintf(ficrespij,"\n");
9145: }
1.180 brouard 9146: /*}*/
9147: }
1.218 brouard 9148: return 0;
1.180 brouard 9149: }
1.218 brouard 9150:
9151: int hBijx(double *p, int bage, int fage, double ***prevacurrent){
1.217 brouard 9152: /*------------- h Bij x at various ages ------------*/
9153:
9154: int stepsize;
1.218 brouard 9155: /* int agelim; */
9156: int ageminl;
1.217 brouard 9157: int hstepm;
9158: int nhstepm;
9159: int h, i, i1, j, k;
1.218 brouard 9160:
1.217 brouard 9161: double agedeb;
9162: double ***p3mat;
1.218 brouard 9163:
9164: strcpy(filerespijb,"PIJB_"); strcat(filerespijb,fileresu);
9165: if((ficrespijb=fopen(filerespijb,"w"))==NULL) {
9166: printf("Problem with Pij back resultfile: %s\n", filerespijb); return 1;
9167: fprintf(ficlog,"Problem with Pij back resultfile: %s\n", filerespijb); return 1;
9168: }
9169: printf("Computing pij back: result on file '%s' \n", filerespijb);
9170: fprintf(ficlog,"Computing pij back: result on file '%s' \n", filerespijb);
9171:
9172: stepsize=(int) (stepm+YEARM-1)/YEARM;
9173: /*if (stepm<=24) stepsize=2;*/
1.217 brouard 9174:
1.218 brouard 9175: /* agelim=AGESUP; */
9176: ageminl=30;
9177: hstepm=stepsize*YEARM; /* Every year of age */
9178: hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
9179:
9180: /* hstepm=1; aff par mois*/
9181: pstamp(ficrespijb);
9182: fprintf(ficrespijb,"#****** h Pij x Back Probability to be in state i at age x-h being in j at x ");
1.227 brouard 9183: i1= pow(2,cptcoveff);
1.218 brouard 9184: /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */
9185: /* /\*for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*\/ */
9186: /* k=k+1; */
1.227 brouard 9187: for (k=1; k <= (int) pow(2,cptcoveff); k++){
1.218 brouard 9188: fprintf(ficrespijb,"\n#****** ");
1.227 brouard 9189: for(j=1;j<=cptcoveff;j++)
1.218 brouard 9190: fprintf(ficrespijb,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
9191: fprintf(ficrespijb,"******\n");
1.222 brouard 9192: if(invalidvarcomb[k]){
9193: fprintf(ficrespijb,"\n#Combination (%d) ignored because no cases \n",k);
9194: continue;
9195: }
1.218 brouard 9196:
9197: /* for (agedeb=fage; agedeb>=bage; agedeb--){ /\* If stepm=6 months *\/ */
9198: for (agedeb=bage; agedeb<=fage; agedeb++){ /* If stepm=6 months and estepm=24 (2 years) */
9199: /* nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /\* Typically 20 years = 20*12/6=40 *\/ */
9200: nhstepm=(int) rint((agedeb-ageminl)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
9201: nhstepm = nhstepm/hstepm; /* Typically 40/4=10, because estepm=24 stepm=6 => hstepm=24/6=4 */
9202:
9203: /* nhstepm=nhstepm*YEARM; aff par mois*/
9204:
9205: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
9206: /* oldm=oldms;savm=savms; */
9207: /* hbxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k); */
9208: hbxij(p3mat,nhstepm,agedeb,hstepm,p,prevacurrent,nlstate,stepm, k);
9209: /* hbxij(p3mat,nhstepm,agedeb,hstepm,p,prevacurrent,nlstate,stepm,oldm,savm, dnewm, doldm, dsavm, k); */
9210: fprintf(ficrespijb,"# Cov Agex agex-h hpijx with i,j=");
9211: for(i=1; i<=nlstate;i++)
9212: for(j=1; j<=nlstate+ndeath;j++)
9213: fprintf(ficrespijb," %1d-%1d",i,j);
9214: fprintf(ficrespijb,"\n");
9215: for (h=0; h<=nhstepm; h++){
9216: /*agedebphstep = agedeb + h*hstepm/YEARM*stepm;*/
9217: fprintf(ficrespijb,"%d %3.f %3.f",k, agedeb, agedeb - h*hstepm/YEARM*stepm );
9218: /* fprintf(ficrespijb,"%d %3.f %3.f",k, agedeb, agedeb + h*hstepm/YEARM*stepm ); */
1.217 brouard 9219: for(i=1; i<=nlstate;i++)
9220: for(j=1; j<=nlstate+ndeath;j++)
1.218 brouard 9221: fprintf(ficrespijb," %.5f", p3mat[i][j][h]);
1.217 brouard 9222: fprintf(ficrespijb,"\n");
9223: }
1.218 brouard 9224: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
9225: fprintf(ficrespijb,"\n");
1.217 brouard 9226: }
1.218 brouard 9227: /*}*/
9228: }
9229: return 0;
9230: } /* hBijx */
1.217 brouard 9231:
1.180 brouard 9232:
1.136 brouard 9233: /***********************************************/
9234: /**************** Main Program *****************/
9235: /***********************************************/
9236:
9237: int main(int argc, char *argv[])
9238: {
9239: #ifdef GSL
9240: const gsl_multimin_fminimizer_type *T;
9241: size_t iteri = 0, it;
9242: int rval = GSL_CONTINUE;
9243: int status = GSL_SUCCESS;
9244: double ssval;
9245: #endif
9246: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
1.164 brouard 9247: int i,j, k, n=MAXN,iter=0,m,size=100, cptcod;
1.209 brouard 9248: int ncvyear=0; /* Number of years needed for the period prevalence to converge */
1.164 brouard 9249: int jj, ll, li, lj, lk;
1.136 brouard 9250: int numlinepar=0; /* Current linenumber of parameter file */
1.197 brouard 9251: int num_filled;
1.136 brouard 9252: int itimes;
9253: int NDIM=2;
9254: int vpopbased=0;
1.235 ! brouard 9255: int nres=0;
1.136 brouard 9256:
1.164 brouard 9257: char ca[32], cb[32];
1.136 brouard 9258: /* FILE *fichtm; *//* Html File */
9259: /* FILE *ficgp;*/ /*Gnuplot File */
9260: struct stat info;
1.191 brouard 9261: double agedeb=0.;
1.194 brouard 9262:
9263: double ageminpar=AGEOVERFLOW,agemin=AGEOVERFLOW, agemaxpar=-AGEOVERFLOW, agemax=-AGEOVERFLOW;
1.219 brouard 9264: double ageminout=-AGEOVERFLOW,agemaxout=AGEOVERFLOW; /* Smaller Age range redefined after movingaverage */
1.136 brouard 9265:
1.165 brouard 9266: double fret;
1.191 brouard 9267: double dum=0.; /* Dummy variable */
1.136 brouard 9268: double ***p3mat;
1.218 brouard 9269: /* double ***mobaverage; */
1.164 brouard 9270:
9271: char line[MAXLINE];
1.197 brouard 9272: char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE];
9273:
1.234 brouard 9274: char modeltemp[MAXLINE];
1.230 brouard 9275: char resultline[MAXLINE];
9276:
1.136 brouard 9277: char pathr[MAXLINE], pathimach[MAXLINE];
1.164 brouard 9278: char *tok, *val; /* pathtot */
1.136 brouard 9279: int firstobs=1, lastobs=10;
1.195 brouard 9280: int c, h , cpt, c2;
1.191 brouard 9281: int jl=0;
9282: int i1, j1, jk, stepsize=0;
1.194 brouard 9283: int count=0;
9284:
1.164 brouard 9285: int *tab;
1.136 brouard 9286: int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
1.217 brouard 9287: int backcast=0;
1.136 brouard 9288: int mobilav=0,popforecast=0;
1.191 brouard 9289: int hstepm=0, nhstepm=0;
1.136 brouard 9290: int agemortsup;
9291: float sumlpop=0.;
9292: double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
9293: double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
9294:
1.191 brouard 9295: double bage=0, fage=110., age, agelim=0., agebase=0.;
1.136 brouard 9296: double ftolpl=FTOL;
9297: double **prlim;
1.217 brouard 9298: double **bprlim;
1.136 brouard 9299: double ***param; /* Matrix of parameters */
9300: double *p;
9301: double **matcov; /* Matrix of covariance */
1.203 brouard 9302: double **hess; /* Hessian matrix */
1.136 brouard 9303: double ***delti3; /* Scale */
9304: double *delti; /* Scale */
9305: double ***eij, ***vareij;
9306: double **varpl; /* Variances of prevalence limits by age */
9307: double *epj, vepp;
1.164 brouard 9308:
1.136 brouard 9309: double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
1.217 brouard 9310: double jback1=1,mback1=1,anback1=2000,jback2=1,mback2=1,anback2=2000;
9311:
1.136 brouard 9312: double **ximort;
1.145 brouard 9313: char *alph[]={"a","a","b","c","d","e"}, str[4]="1234";
1.136 brouard 9314: int *dcwave;
9315:
1.164 brouard 9316: char z[1]="c";
1.136 brouard 9317:
9318: /*char *strt;*/
9319: char strtend[80];
1.126 brouard 9320:
1.164 brouard 9321:
1.126 brouard 9322: /* setlocale (LC_ALL, ""); */
9323: /* bindtextdomain (PACKAGE, LOCALEDIR); */
9324: /* textdomain (PACKAGE); */
9325: /* setlocale (LC_CTYPE, ""); */
9326: /* setlocale (LC_MESSAGES, ""); */
9327:
9328: /* gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
1.157 brouard 9329: rstart_time = time(NULL);
9330: /* (void) gettimeofday(&start_time,&tzp);*/
9331: start_time = *localtime(&rstart_time);
1.126 brouard 9332: curr_time=start_time;
1.157 brouard 9333: /*tml = *localtime(&start_time.tm_sec);*/
9334: /* strcpy(strstart,asctime(&tml)); */
9335: strcpy(strstart,asctime(&start_time));
1.126 brouard 9336:
9337: /* printf("Localtime (at start)=%s",strstart); */
1.157 brouard 9338: /* tp.tm_sec = tp.tm_sec +86400; */
9339: /* tm = *localtime(&start_time.tm_sec); */
1.126 brouard 9340: /* tmg.tm_year=tmg.tm_year +dsign*dyear; */
9341: /* tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
9342: /* tmg.tm_hour=tmg.tm_hour + 1; */
1.157 brouard 9343: /* tp.tm_sec = mktime(&tmg); */
1.126 brouard 9344: /* strt=asctime(&tmg); */
9345: /* printf("Time(after) =%s",strstart); */
9346: /* (void) time (&time_value);
9347: * printf("time=%d,t-=%d\n",time_value,time_value-86400);
9348: * tm = *localtime(&time_value);
9349: * strstart=asctime(&tm);
9350: * printf("tim_value=%d,asctime=%s\n",time_value,strstart);
9351: */
9352:
9353: nberr=0; /* Number of errors and warnings */
9354: nbwarn=0;
1.184 brouard 9355: #ifdef WIN32
9356: _getcwd(pathcd, size);
9357: #else
1.126 brouard 9358: getcwd(pathcd, size);
1.184 brouard 9359: #endif
1.191 brouard 9360: syscompilerinfo(0);
1.196 brouard 9361: printf("\nIMaCh version %s, %s\n%s",version, copyright, fullversion);
1.126 brouard 9362: if(argc <=1){
9363: printf("\nEnter the parameter file name: ");
1.205 brouard 9364: if(!fgets(pathr,FILENAMELENGTH,stdin)){
9365: printf("ERROR Empty parameter file name\n");
9366: goto end;
9367: }
1.126 brouard 9368: i=strlen(pathr);
9369: if(pathr[i-1]=='\n')
9370: pathr[i-1]='\0';
1.156 brouard 9371: i=strlen(pathr);
1.205 brouard 9372: if(i >= 1 && pathr[i-1]==' ') {/* This may happen when dragging on oS/X! */
1.156 brouard 9373: pathr[i-1]='\0';
1.205 brouard 9374: }
9375: i=strlen(pathr);
9376: if( i==0 ){
9377: printf("ERROR Empty parameter file name\n");
9378: goto end;
9379: }
9380: for (tok = pathr; tok != NULL; ){
1.126 brouard 9381: printf("Pathr |%s|\n",pathr);
9382: while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
9383: printf("val= |%s| pathr=%s\n",val,pathr);
9384: strcpy (pathtot, val);
9385: if(pathr[0] == '\0') break; /* Dirty */
9386: }
9387: }
9388: else{
9389: strcpy(pathtot,argv[1]);
9390: }
9391: /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
9392: /*cygwin_split_path(pathtot,path,optionfile);
9393: printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
9394: /* cutv(path,optionfile,pathtot,'\\');*/
9395:
9396: /* Split argv[0], imach program to get pathimach */
9397: printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
9398: split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
9399: printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
9400: /* strcpy(pathimach,argv[0]); */
9401: /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
9402: split(pathtot,path,optionfile,optionfilext,optionfilefiname);
9403: printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
1.184 brouard 9404: #ifdef WIN32
9405: _chdir(path); /* Can be a relative path */
9406: if(_getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */
9407: #else
1.126 brouard 9408: chdir(path); /* Can be a relative path */
1.184 brouard 9409: if (getcwd(pathcd, MAXLINE) > 0) /* So pathcd is the full path */
9410: #endif
9411: printf("Current directory %s!\n",pathcd);
1.126 brouard 9412: strcpy(command,"mkdir ");
9413: strcat(command,optionfilefiname);
9414: if((outcmd=system(command)) != 0){
1.169 brouard 9415: printf("Directory already exists (or can't create it) %s%s, err=%d\n",path,optionfilefiname,outcmd);
1.126 brouard 9416: /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
9417: /* fclose(ficlog); */
9418: /* exit(1); */
9419: }
9420: /* if((imk=mkdir(optionfilefiname))<0){ */
9421: /* perror("mkdir"); */
9422: /* } */
9423:
9424: /*-------- arguments in the command line --------*/
9425:
1.186 brouard 9426: /* Main Log file */
1.126 brouard 9427: strcat(filelog, optionfilefiname);
9428: strcat(filelog,".log"); /* */
9429: if((ficlog=fopen(filelog,"w"))==NULL) {
9430: printf("Problem with logfile %s\n",filelog);
9431: goto end;
9432: }
9433: fprintf(ficlog,"Log filename:%s\n",filelog);
1.197 brouard 9434: fprintf(ficlog,"Version %s %s",version,fullversion);
1.126 brouard 9435: fprintf(ficlog,"\nEnter the parameter file name: \n");
9436: fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
9437: path=%s \n\
9438: optionfile=%s\n\
9439: optionfilext=%s\n\
1.156 brouard 9440: optionfilefiname='%s'\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
1.126 brouard 9441:
1.197 brouard 9442: syscompilerinfo(1);
1.167 brouard 9443:
1.126 brouard 9444: printf("Local time (at start):%s",strstart);
9445: fprintf(ficlog,"Local time (at start): %s",strstart);
9446: fflush(ficlog);
9447: /* (void) gettimeofday(&curr_time,&tzp); */
1.157 brouard 9448: /* printf("Elapsed time %d\n", asc_diff_time(curr_time.tm_sec-start_time.tm_sec,tmpout)); */
1.126 brouard 9449:
9450: /* */
9451: strcpy(fileres,"r");
9452: strcat(fileres, optionfilefiname);
1.201 brouard 9453: strcat(fileresu, optionfilefiname); /* Without r in front */
1.126 brouard 9454: strcat(fileres,".txt"); /* Other files have txt extension */
1.201 brouard 9455: strcat(fileresu,".txt"); /* Other files have txt extension */
1.126 brouard 9456:
1.186 brouard 9457: /* Main ---------arguments file --------*/
1.126 brouard 9458:
9459: if((ficpar=fopen(optionfile,"r"))==NULL) {
1.155 brouard 9460: printf("Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
9461: fprintf(ficlog,"Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
1.126 brouard 9462: fflush(ficlog);
1.149 brouard 9463: /* goto end; */
9464: exit(70);
1.126 brouard 9465: }
9466:
9467:
9468:
9469: strcpy(filereso,"o");
1.201 brouard 9470: strcat(filereso,fileresu);
1.126 brouard 9471: if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
9472: printf("Problem with Output resultfile: %s\n", filereso);
9473: fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
9474: fflush(ficlog);
9475: goto end;
9476: }
9477:
9478: /* Reads comments: lines beginning with '#' */
9479: numlinepar=0;
1.197 brouard 9480:
9481: /* First parameter line */
9482: while(fgets(line, MAXLINE, ficpar)) {
9483: /* If line starts with a # it is a comment */
9484: if (line[0] == '#') {
9485: numlinepar++;
9486: fputs(line,stdout);
9487: fputs(line,ficparo);
9488: fputs(line,ficlog);
9489: continue;
9490: }else
9491: break;
9492: }
9493: if((num_filled=sscanf(line,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", \
9494: title, datafile, &lastobs, &firstpass,&lastpass)) !=EOF){
9495: if (num_filled != 5) {
9496: printf("Should be 5 parameters\n");
9497: }
1.126 brouard 9498: numlinepar++;
1.197 brouard 9499: printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", title, datafile, lastobs, firstpass,lastpass);
9500: }
9501: /* Second parameter line */
9502: while(fgets(line, MAXLINE, ficpar)) {
9503: /* If line starts with a # it is a comment */
9504: if (line[0] == '#') {
9505: numlinepar++;
9506: fputs(line,stdout);
9507: fputs(line,ficparo);
9508: fputs(line,ficlog);
9509: continue;
9510: }else
9511: break;
9512: }
1.223 brouard 9513: if((num_filled=sscanf(line,"ftol=%lf stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\n", \
9514: &ftol, &stepm, &ncovcol, &nqv, &ntv, &nqtv, &nlstate, &ndeath, &maxwav, &mle, &weightopt)) !=EOF){
9515: if (num_filled != 11) {
9516: printf("Not 11 parameters, for example:ftol=1.e-8 stepm=12 ncovcol=2 nqv=1 ntv=2 nqtv=1 nlstate=2 ndeath=1 maxwav=3 mle=1 weight=1\n");
1.209 brouard 9517: printf("but line=%s\n",line);
1.197 brouard 9518: }
1.223 brouard 9519: printf("ftol=%e stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\n",ftol, stepm, ncovcol, nqv, ntv, nqtv, nlstate, ndeath, maxwav, mle, weightopt);
1.126 brouard 9520: }
1.203 brouard 9521: /* ftolpl=6*ftol*1.e5; /\* 6.e-3 make convergences in less than 80 loops for the prevalence limit *\/ */
1.209 brouard 9522: /*ftolpl=6.e-4; *//* 6.e-3 make convergences in less than 80 loops for the prevalence limit */
1.197 brouard 9523: /* Third parameter line */
9524: while(fgets(line, MAXLINE, ficpar)) {
9525: /* If line starts with a # it is a comment */
9526: if (line[0] == '#') {
9527: numlinepar++;
9528: fputs(line,stdout);
9529: fputs(line,ficparo);
9530: fputs(line,ficlog);
9531: continue;
9532: }else
9533: break;
9534: }
1.201 brouard 9535: if((num_filled=sscanf(line,"model=1+age%[^.\n]", model)) !=EOF){
9536: if (num_filled == 0)
9537: model[0]='\0';
9538: else if (num_filled != 1){
1.197 brouard 9539: printf("ERROR %d: Model should be at minimum 'model=1+age.' %s\n",num_filled, line);
9540: fprintf(ficlog,"ERROR %d: Model should be at minimum 'model=1+age.' %s\n",num_filled, line);
9541: model[0]='\0';
9542: goto end;
9543: }
9544: else{
9545: if (model[0]=='+'){
9546: for(i=1; i<=strlen(model);i++)
9547: modeltemp[i-1]=model[i];
1.201 brouard 9548: strcpy(model,modeltemp);
1.197 brouard 9549: }
9550: }
1.199 brouard 9551: /* printf(" model=1+age%s modeltemp= %s, model=%s\n",model, modeltemp, model);fflush(stdout); */
1.203 brouard 9552: printf("model=1+age+%s\n",model);fflush(stdout);
1.197 brouard 9553: }
9554: /* 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); */
9555: /* numlinepar=numlinepar+3; /\* In general *\/ */
9556: /* 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); */
1.223 brouard 9557: fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=1+age+%s.\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol, nqv, ntv, nqtv, nlstate,ndeath,maxwav, mle, weightopt,model);
9558: fprintf(ficlog,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=1+age+%s.\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol, nqv, ntv, nqtv, nlstate,ndeath,maxwav, mle, weightopt,model);
1.126 brouard 9559: fflush(ficlog);
1.190 brouard 9560: /* if(model[0]=='#'|| model[0]== '\0'){ */
9561: if(model[0]=='#'){
1.187 brouard 9562: printf("Error in 'model' line: model should start with 'model=1+age+' and end with '.' \n \
9563: 'model=1+age+.' or 'model=1+age+V1.' or 'model=1+age+age*age+V1+V1*age.' or \n \
9564: 'model=1+age+V1+V2.' or 'model=1+age+V1+V2+V1*V2.' etc. \n"); \
9565: if(mle != -1){
9566: printf("Fix the model line and run imach with mle=-1 to get a correct template of the parameter file.\n");
9567: exit(1);
9568: }
9569: }
1.126 brouard 9570: while((c=getc(ficpar))=='#' && c!= EOF){
9571: ungetc(c,ficpar);
9572: fgets(line, MAXLINE, ficpar);
9573: numlinepar++;
1.195 brouard 9574: if(line[1]=='q'){ /* This #q will quit imach (the answer is q) */
9575: z[0]=line[1];
9576: }
9577: /* printf("****line [1] = %c \n",line[1]); */
1.141 brouard 9578: fputs(line, stdout);
9579: //puts(line);
1.126 brouard 9580: fputs(line,ficparo);
9581: fputs(line,ficlog);
9582: }
9583: ungetc(c,ficpar);
9584:
9585:
1.145 brouard 9586: covar=matrix(0,NCOVMAX,1,n); /**< used in readdata */
1.225 brouard 9587: coqvar=matrix(1,nqv,1,n); /**< Fixed quantitative covariate */
1.233 brouard 9588: cotvar=ma3x(1,maxwav,1,ntv+nqtv,1,n); /**< Time varying covariate (dummy and quantitative)*/
1.225 brouard 9589: cotqvar=ma3x(1,maxwav,1,nqtv,1,n); /**< Time varying quantitative covariate */
1.136 brouard 9590: cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement plus one, indepently of n in Vn*/
9591: /* v1+v2+v3+v2*v4+v5*age makes cptcovn = 5
9592: v1+v2*age+v2*v3 makes cptcovn = 3
9593: */
9594: if (strlen(model)>1)
1.187 brouard 9595: 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 9596: else
1.187 brouard 9597: ncovmodel=2; /* Constant and age */
1.133 brouard 9598: nforce= (nlstate+ndeath-1)*nlstate; /* Number of forces ij from state i to j */
9599: npar= nforce*ncovmodel; /* Number of parameters like aij*/
1.131 brouard 9600: if(npar >MAXPARM || nlstate >NLSTATEMAX || ndeath >NDEATHMAX || ncovmodel>NCOVMAX){
9601: 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);
9602: 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);
9603: fflush(stdout);
9604: fclose (ficlog);
9605: goto end;
9606: }
1.126 brouard 9607: delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
9608: delti=delti3[1][1];
9609: /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
9610: if(mle==-1){ /* Print a wizard for help writing covariance matrix */
9611: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
1.191 brouard 9612: printf(" You chose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
9613: fprintf(ficlog," You chose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
1.126 brouard 9614: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
9615: fclose (ficparo);
9616: fclose (ficlog);
9617: goto end;
9618: exit(0);
1.220 brouard 9619: } else if(mle==-5) { /* Main Wizard */
1.126 brouard 9620: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
1.192 brouard 9621: printf(" You chose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
9622: fprintf(ficlog," You chose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
1.126 brouard 9623: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
9624: matcov=matrix(1,npar,1,npar);
1.203 brouard 9625: hess=matrix(1,npar,1,npar);
1.220 brouard 9626: } else{ /* Begin of mle != -1 or -5 */
1.145 brouard 9627: /* Read guessed parameters */
1.126 brouard 9628: /* Reads comments: lines beginning with '#' */
9629: while((c=getc(ficpar))=='#' && c!= EOF){
9630: ungetc(c,ficpar);
9631: fgets(line, MAXLINE, ficpar);
9632: numlinepar++;
1.141 brouard 9633: fputs(line,stdout);
1.126 brouard 9634: fputs(line,ficparo);
9635: fputs(line,ficlog);
9636: }
9637: ungetc(c,ficpar);
9638:
9639: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
9640: for(i=1; i <=nlstate; i++){
1.234 brouard 9641: j=0;
1.126 brouard 9642: for(jj=1; jj <=nlstate+ndeath; jj++){
1.234 brouard 9643: if(jj==i) continue;
9644: j++;
9645: fscanf(ficpar,"%1d%1d",&i1,&j1);
9646: if ((i1 != i) || (j1 != jj)){
9647: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \
1.126 brouard 9648: It might be a problem of design; if ncovcol and the model are correct\n \
9649: run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1);
1.234 brouard 9650: exit(1);
9651: }
9652: fprintf(ficparo,"%1d%1d",i1,j1);
9653: if(mle==1)
9654: printf("%1d%1d",i,jj);
9655: fprintf(ficlog,"%1d%1d",i,jj);
9656: for(k=1; k<=ncovmodel;k++){
9657: fscanf(ficpar," %lf",¶m[i][j][k]);
9658: if(mle==1){
9659: printf(" %lf",param[i][j][k]);
9660: fprintf(ficlog," %lf",param[i][j][k]);
9661: }
9662: else
9663: fprintf(ficlog," %lf",param[i][j][k]);
9664: fprintf(ficparo," %lf",param[i][j][k]);
9665: }
9666: fscanf(ficpar,"\n");
9667: numlinepar++;
9668: if(mle==1)
9669: printf("\n");
9670: fprintf(ficlog,"\n");
9671: fprintf(ficparo,"\n");
1.126 brouard 9672: }
9673: }
9674: fflush(ficlog);
1.234 brouard 9675:
1.145 brouard 9676: /* Reads scales values */
1.126 brouard 9677: p=param[1][1];
9678:
9679: /* Reads comments: lines beginning with '#' */
9680: while((c=getc(ficpar))=='#' && c!= EOF){
9681: ungetc(c,ficpar);
9682: fgets(line, MAXLINE, ficpar);
9683: numlinepar++;
1.141 brouard 9684: fputs(line,stdout);
1.126 brouard 9685: fputs(line,ficparo);
9686: fputs(line,ficlog);
9687: }
9688: ungetc(c,ficpar);
9689:
9690: for(i=1; i <=nlstate; i++){
9691: for(j=1; j <=nlstate+ndeath-1; j++){
1.234 brouard 9692: fscanf(ficpar,"%1d%1d",&i1,&j1);
9693: if ( (i1-i) * (j1-j) != 0){
9694: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
9695: exit(1);
9696: }
9697: printf("%1d%1d",i,j);
9698: fprintf(ficparo,"%1d%1d",i1,j1);
9699: fprintf(ficlog,"%1d%1d",i1,j1);
9700: for(k=1; k<=ncovmodel;k++){
9701: fscanf(ficpar,"%le",&delti3[i][j][k]);
9702: printf(" %le",delti3[i][j][k]);
9703: fprintf(ficparo," %le",delti3[i][j][k]);
9704: fprintf(ficlog," %le",delti3[i][j][k]);
9705: }
9706: fscanf(ficpar,"\n");
9707: numlinepar++;
9708: printf("\n");
9709: fprintf(ficparo,"\n");
9710: fprintf(ficlog,"\n");
1.126 brouard 9711: }
9712: }
9713: fflush(ficlog);
1.234 brouard 9714:
1.145 brouard 9715: /* Reads covariance matrix */
1.126 brouard 9716: delti=delti3[1][1];
1.220 brouard 9717:
9718:
1.126 brouard 9719: /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
1.220 brouard 9720:
1.126 brouard 9721: /* Reads comments: lines beginning with '#' */
9722: while((c=getc(ficpar))=='#' && c!= EOF){
9723: ungetc(c,ficpar);
9724: fgets(line, MAXLINE, ficpar);
9725: numlinepar++;
1.141 brouard 9726: fputs(line,stdout);
1.126 brouard 9727: fputs(line,ficparo);
9728: fputs(line,ficlog);
9729: }
9730: ungetc(c,ficpar);
1.220 brouard 9731:
1.126 brouard 9732: matcov=matrix(1,npar,1,npar);
1.203 brouard 9733: hess=matrix(1,npar,1,npar);
1.131 brouard 9734: for(i=1; i <=npar; i++)
9735: for(j=1; j <=npar; j++) matcov[i][j]=0.;
1.220 brouard 9736:
1.194 brouard 9737: /* Scans npar lines */
1.126 brouard 9738: for(i=1; i <=npar; i++){
1.226 brouard 9739: count=fscanf(ficpar,"%1d%1d%d",&i1,&j1,&jk);
1.194 brouard 9740: if(count != 3){
1.226 brouard 9741: printf("Error! Error in parameter file %s at line %d after line starting with %1d%1d%1d\n\
1.194 brouard 9742: This is probably because your covariance matrix doesn't \n contain exactly %d lines corresponding to your model line '1+age+%s'.\n\
9743: Please run with mle=-1 to get a correct covariance matrix.\n",optionfile,numlinepar, i1,j1,jk, npar, model);
1.226 brouard 9744: fprintf(ficlog,"Error! Error in parameter file %s at line %d after line starting with %1d%1d%1d\n\
1.194 brouard 9745: This is probably because your covariance matrix doesn't \n contain exactly %d lines corresponding to your model line '1+age+%s'.\n\
9746: Please run with mle=-1 to get a correct covariance matrix.\n",optionfile,numlinepar, i1,j1,jk, npar, model);
1.226 brouard 9747: exit(1);
1.220 brouard 9748: }else{
1.226 brouard 9749: if(mle==1)
9750: printf("%1d%1d%d",i1,j1,jk);
9751: }
9752: fprintf(ficlog,"%1d%1d%d",i1,j1,jk);
9753: fprintf(ficparo,"%1d%1d%d",i1,j1,jk);
1.126 brouard 9754: for(j=1; j <=i; j++){
1.226 brouard 9755: fscanf(ficpar," %le",&matcov[i][j]);
9756: if(mle==1){
9757: printf(" %.5le",matcov[i][j]);
9758: }
9759: fprintf(ficlog," %.5le",matcov[i][j]);
9760: fprintf(ficparo," %.5le",matcov[i][j]);
1.126 brouard 9761: }
9762: fscanf(ficpar,"\n");
9763: numlinepar++;
9764: if(mle==1)
1.220 brouard 9765: printf("\n");
1.126 brouard 9766: fprintf(ficlog,"\n");
9767: fprintf(ficparo,"\n");
9768: }
1.194 brouard 9769: /* End of read covariance matrix npar lines */
1.126 brouard 9770: for(i=1; i <=npar; i++)
9771: for(j=i+1;j<=npar;j++)
1.226 brouard 9772: matcov[i][j]=matcov[j][i];
1.126 brouard 9773:
9774: if(mle==1)
9775: printf("\n");
9776: fprintf(ficlog,"\n");
9777:
9778: fflush(ficlog);
9779:
9780: /*-------- Rewriting parameter file ----------*/
9781: strcpy(rfileres,"r"); /* "Rparameterfile */
9782: strcat(rfileres,optionfilefiname); /* Parameter file first name*/
9783: strcat(rfileres,"."); /* */
9784: strcat(rfileres,optionfilext); /* Other files have txt extension */
9785: if((ficres =fopen(rfileres,"w"))==NULL) {
1.201 brouard 9786: printf("Problem writing new parameter file: %s\n", rfileres);goto end;
9787: fprintf(ficlog,"Problem writing new parameter file: %s\n", rfileres);goto end;
1.126 brouard 9788: }
9789: fprintf(ficres,"#%s\n",version);
9790: } /* End of mle != -3 */
1.218 brouard 9791:
1.186 brouard 9792: /* Main data
9793: */
1.126 brouard 9794: n= lastobs;
9795: num=lvector(1,n);
9796: moisnais=vector(1,n);
9797: annais=vector(1,n);
9798: moisdc=vector(1,n);
9799: andc=vector(1,n);
1.220 brouard 9800: weight=vector(1,n);
1.126 brouard 9801: agedc=vector(1,n);
9802: cod=ivector(1,n);
1.220 brouard 9803: for(i=1;i<=n;i++){
1.234 brouard 9804: num[i]=0;
9805: moisnais[i]=0;
9806: annais[i]=0;
9807: moisdc[i]=0;
9808: andc[i]=0;
9809: agedc[i]=0;
9810: cod[i]=0;
9811: weight[i]=1.0; /* Equal weights, 1 by default */
9812: }
1.126 brouard 9813: mint=matrix(1,maxwav,1,n);
9814: anint=matrix(1,maxwav,1,n);
1.131 brouard 9815: s=imatrix(1,maxwav+1,1,n); /* s[i][j] health state for wave i and individual j */
1.126 brouard 9816: tab=ivector(1,NCOVMAX);
1.144 brouard 9817: ncodemax=ivector(1,NCOVMAX); /* Number of code per covariate; if O and 1 only, 2**ncov; V1+V2+V3+V4=>16 */
1.192 brouard 9818: 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 9819:
1.136 brouard 9820: /* Reads data from file datafile */
9821: if (readdata(datafile, firstobs, lastobs, &imx)==1)
9822: goto end;
9823:
9824: /* Calculation of the number of parameters from char model */
1.234 brouard 9825: /* modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4
1.137 brouard 9826: k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tag[cptcovage=1]=4
9827: k=3 V4 Tvar[k=3]= 4 (from V4)
9828: k=2 V1 Tvar[k=2]= 1 (from V1)
9829: k=1 Tvar[1]=2 (from V2)
1.234 brouard 9830: */
9831:
9832: Tvar=ivector(1,NCOVMAX); /* Was 15 changed to NCOVMAX. */
9833: TvarsDind=ivector(1,NCOVMAX); /* */
9834: TvarsD=ivector(1,NCOVMAX); /* */
9835: TvarsQind=ivector(1,NCOVMAX); /* */
9836: TvarsQ=ivector(1,NCOVMAX); /* */
1.232 brouard 9837: TvarF=ivector(1,NCOVMAX); /* */
9838: TvarFind=ivector(1,NCOVMAX); /* */
9839: TvarV=ivector(1,NCOVMAX); /* */
9840: TvarVind=ivector(1,NCOVMAX); /* */
9841: TvarA=ivector(1,NCOVMAX); /* */
9842: TvarAind=ivector(1,NCOVMAX); /* */
1.231 brouard 9843: TvarFD=ivector(1,NCOVMAX); /* */
9844: TvarFDind=ivector(1,NCOVMAX); /* */
9845: TvarFQ=ivector(1,NCOVMAX); /* */
9846: TvarFQind=ivector(1,NCOVMAX); /* */
9847: TvarVD=ivector(1,NCOVMAX); /* */
9848: TvarVDind=ivector(1,NCOVMAX); /* */
9849: TvarVQ=ivector(1,NCOVMAX); /* */
9850: TvarVQind=ivector(1,NCOVMAX); /* */
9851:
1.230 brouard 9852: Tvalsel=vector(1,NCOVMAX); /* */
1.233 brouard 9853: Tvarsel=ivector(1,NCOVMAX); /* */
1.226 brouard 9854: Typevar=ivector(-1,NCOVMAX); /* -1 to 2 */
9855: Fixed=ivector(-1,NCOVMAX); /* -1 to 3 */
9856: Dummy=ivector(-1,NCOVMAX); /* -1 to 3 */
1.137 brouard 9857: /* V2+V1+V4+age*V3 is a model with 4 covariates (3 plus signs).
9858: For each model-covariate stores the data-covariate id. Tvar[1]=2, Tvar[2]=1, Tvar[3]=4,
9859: Tvar[4=age*V3] is 3 and 'age' is recorded in Tage.
9860: */
9861: /* For model-covariate k tells which data-covariate to use but
9862: because this model-covariate is a construction we invent a new column
9863: ncovcol + k1
9864: If already ncovcol=4 and model=V2+V1+V1*V4+age*V3
9865: Tvar[3=V1*V4]=4+1 etc */
1.227 brouard 9866: Tprod=ivector(1,NCOVMAX); /* Gives the k position of the k1 product */
9867: Tposprod=ivector(1,NCOVMAX); /* Gives the k1 product from the k position */
1.137 brouard 9868: /* Tprod[k1=1]=3(=V1*V4) for V2+V1+V1*V4+age*V3
9869: if V2+V1+V1*V4+age*V3+V3*V2 TProd[k1=2]=5 (V3*V2)
1.227 brouard 9870: Tposprod[k]=k1 , Tposprod[3]=1, Tposprod[5]=2
1.137 brouard 9871: */
1.145 brouard 9872: Tvaraff=ivector(1,NCOVMAX); /* Unclear */
9873: 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 9874: * For V3*V2 (in V2+V1+V1*V4+age*V3+V3*V2), V3*V2 position is 2nd.
9875: * Tvard[k1=2][1]=3 (V3) Tvard[k1=2][2]=2(V2) */
1.145 brouard 9876: Tage=ivector(1,NCOVMAX); /* Gives the covariate id of covariates associated with age: V2 + V1 + age*V4 + V3*age
1.137 brouard 9877: 4 covariates (3 plus signs)
9878: Tage[1=V3*age]= 4; Tage[2=age*V4] = 3
9879: */
1.230 brouard 9880: Tmodelind=ivector(1,NCOVMAX);/** gives the k model position of an
1.227 brouard 9881: * individual dummy, fixed or varying:
9882: * Tmodelind[Tvaraff[3]]=9,Tvaraff[1]@9={4,
9883: * 3, 1, 0, 0, 0, 0, 0, 0},
1.230 brouard 9884: * model=V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 ,
9885: * V1 df, V2 qf, V3 & V4 dv, V5 qv
9886: * Tmodelind[1]@9={9,0,3,2,}*/
9887: TmodelInvind=ivector(1,NCOVMAX); /* TmodelInvind=Tvar[k]- ncovcol-nqv={5-2-1=2,*/
9888: TmodelInvQind=ivector(1,NCOVMAX);/** gives the k model position of an
1.228 brouard 9889: * individual quantitative, fixed or varying:
9890: * Tmodelqind[1]=1,Tvaraff[1]@9={4,
9891: * 3, 1, 0, 0, 0, 0, 0, 0},
9892: * model=V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1*/
1.186 brouard 9893: /* Main decodemodel */
9894:
1.187 brouard 9895:
1.223 brouard 9896: if(decodemodel(model, lastobs) == 1) /* In order to get Tvar[k] V4+V3+V5 p Tvar[1]@3 = {4, 3, 5}*/
1.136 brouard 9897: goto end;
9898:
1.137 brouard 9899: if((double)(lastobs-imx)/(double)imx > 1.10){
9900: nbwarn++;
9901: 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);
9902: 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);
9903: }
1.136 brouard 9904: /* if(mle==1){*/
1.137 brouard 9905: if (weightopt != 1) { /* Maximisation without weights. We can have weights different from 1 but want no weight*/
9906: for(i=1;i<=imx;i++) weight[i]=1.0; /* changed to imx */
1.136 brouard 9907: }
9908:
9909: /*-calculation of age at interview from date of interview and age at death -*/
9910: agev=matrix(1,maxwav,1,imx);
9911:
9912: if(calandcheckages(imx, maxwav, &agemin, &agemax, &nberr, &nbwarn) == 1)
9913: goto end;
9914:
1.126 brouard 9915:
1.136 brouard 9916: agegomp=(int)agemin;
9917: free_vector(moisnais,1,n);
9918: free_vector(annais,1,n);
1.126 brouard 9919: /* free_matrix(mint,1,maxwav,1,n);
9920: free_matrix(anint,1,maxwav,1,n);*/
1.215 brouard 9921: /* free_vector(moisdc,1,n); */
9922: /* free_vector(andc,1,n); */
1.145 brouard 9923: /* */
9924:
1.126 brouard 9925: wav=ivector(1,imx);
1.214 brouard 9926: /* dh=imatrix(1,lastpass-firstpass+1,1,imx); */
9927: /* bh=imatrix(1,lastpass-firstpass+1,1,imx); */
9928: /* mw=imatrix(1,lastpass-firstpass+1,1,imx); */
9929: dh=imatrix(1,lastpass-firstpass+2,1,imx); /* We are adding a wave if status is unknown at last wave but death occurs after last wave.*/
9930: bh=imatrix(1,lastpass-firstpass+2,1,imx);
9931: mw=imatrix(1,lastpass-firstpass+2,1,imx);
1.126 brouard 9932:
9933: /* Concatenates waves */
1.214 brouard 9934: /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
9935: Death is a valid wave (if date is known).
9936: mw[mi][i] is the number of (mi=1 to wav[i]) effective wave out of mi of individual i
9937: dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
9938: and mw[mi+1][i]. dh depends on stepm.
9939: */
9940:
1.126 brouard 9941: concatwav(wav, dh, bh, mw, s, agedc, agev, firstpass, lastpass, imx, nlstate, stepm);
1.145 brouard 9942: /* */
9943:
1.215 brouard 9944: free_vector(moisdc,1,n);
9945: free_vector(andc,1,n);
9946:
1.126 brouard 9947: /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
9948: nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
9949: ncodemax[1]=1;
1.145 brouard 9950: Ndum =ivector(-1,NCOVMAX);
1.225 brouard 9951: cptcoveff=0;
1.220 brouard 9952: if (ncovmodel-nagesqr > 2 ){ /* That is if covariate other than cst, age and age*age */
9953: tricode(&cptcoveff,Tvar,nbcode,imx, Ndum); /**< Fills nbcode[Tvar[j]][l]; */
1.227 brouard 9954: }
9955:
9956: ncovcombmax=pow(2,cptcoveff);
9957: invalidvarcomb=ivector(1, ncovcombmax);
9958: for(i=1;i<ncovcombmax;i++)
9959: invalidvarcomb[i]=0;
9960:
1.211 brouard 9961: /* Nbcode gives the value of the lth modality (currently 1 to 2) of jth covariate, in
1.186 brouard 9962: V2+V1*age, there are 3 covariates Tvar[2]=1 (V1).*/
1.211 brouard 9963: /* 1 to ncodemax[j] which is the maximum value of this jth covariate */
1.227 brouard 9964:
1.200 brouard 9965: /* codtab=imatrix(1,100,1,10);*/ /* codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) */
1.198 brouard 9966: /*printf(" codtab[1,1],codtab[100,10]=%d,%d\n", codtab[1][1],codtabm(100,10));*/
1.186 brouard 9967: /* codtab gives the value 1 or 2 of the hth combination of k covariates (1 or 2).*/
1.211 brouard 9968: /* nbcode[Tvaraff[j]][codtabm(h,j)]) : if there are only 2 modalities for a covariate j,
9969: * codtabm(h,j) gives its value classified at position h and nbcode gives how it is coded
9970: * (currently 0 or 1) in the data.
9971: * In a loop on h=1 to 2**k, and a loop on j (=1 to k), we get the value of
9972: * corresponding modality (h,j).
9973: */
9974:
1.145 brouard 9975: h=0;
9976: /*if (cptcovn > 0) */
1.126 brouard 9977: m=pow(2,cptcoveff);
9978:
1.144 brouard 9979: /**< codtab(h,k) k = codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) + 1
1.211 brouard 9980: * For k=4 covariates, h goes from 1 to m=2**k
9981: * codtabm(h,k)= (1 & (h-1) >> (k-1)) + 1;
9982: * #define codtabm(h,k) (1 & (h-1) >> (k-1))+1
1.186 brouard 9983: * h\k 1 2 3 4
1.143 brouard 9984: *______________________________
9985: * 1 i=1 1 i=1 1 i=1 1 i=1 1
9986: * 2 2 1 1 1
9987: * 3 i=2 1 2 1 1
9988: * 4 2 2 1 1
9989: * 5 i=3 1 i=2 1 2 1
9990: * 6 2 1 2 1
9991: * 7 i=4 1 2 2 1
9992: * 8 2 2 2 1
1.197 brouard 9993: * 9 i=5 1 i=3 1 i=2 1 2
9994: * 10 2 1 1 2
9995: * 11 i=6 1 2 1 2
9996: * 12 2 2 1 2
9997: * 13 i=7 1 i=4 1 2 2
9998: * 14 2 1 2 2
9999: * 15 i=8 1 2 2 2
10000: * 16 2 2 2 2
1.143 brouard 10001: */
1.212 brouard 10002: /* How to do the opposite? From combination h (=1 to 2**k) how to get the value on the covariates? */
1.211 brouard 10003: /* from h=5 and m, we get then number of covariates k=log(m)/log(2)=4
10004: * and the value of each covariate?
10005: * V1=1, V2=1, V3=2, V4=1 ?
10006: * h-1=4 and 4 is 0100 or reverse 0010, and +1 is 1121 ok.
10007: * h=6, 6-1=5, 5 is 0101, 1010, 2121, V1=2nd, V2=1st, V3=2nd, V4=1st.
10008: * In order to get the real value in the data, we use nbcode
10009: * nbcode[Tvar[3][2nd]]=1 and nbcode[Tvar[4][1]]=0
10010: * We are keeping this crazy system in order to be able (in the future?)
10011: * to have more than 2 values (0 or 1) for a covariate.
10012: * #define codtabm(h,k) (1 & (h-1) >> (k-1))+1
10013: * h=6, k=2? h-1=5=0101, reverse 1010, +1=2121, k=2nd position: value is 1: codtabm(6,2)=1
10014: * bbbbbbbb
10015: * 76543210
10016: * h-1 00000101 (6-1=5)
1.219 brouard 10017: *(h-1)>>(k-1)= 00000010 >> (2-1) = 1 right shift
1.211 brouard 10018: * &
10019: * 1 00000001 (1)
1.219 brouard 10020: * 00000000 = 1 & ((h-1) >> (k-1))
10021: * +1= 00000001 =1
1.211 brouard 10022: *
10023: * h=14, k=3 => h'=h-1=13, k'=k-1=2
10024: * h' 1101 =2^3+2^2+0x2^1+2^0
10025: * >>k' 11
10026: * & 00000001
10027: * = 00000001
10028: * +1 = 00000010=2 = codtabm(14,3)
10029: * Reverse h=6 and m=16?
10030: * cptcoveff=log(16)/log(2)=4 covariate: 6-1=5=0101 reversed=1010 +1=2121 =>V1=2, V2=1, V3=2, V4=1.
10031: * for (j=1 to cptcoveff) Vj=decodtabm(j,h,cptcoveff)
10032: * decodtabm(h,j,cptcoveff)= (((h-1) >> (j-1)) & 1) +1
10033: * decodtabm(h,j,cptcoveff)= (h <= (1<<cptcoveff)?(((h-1) >> (j-1)) & 1) +1 : -1)
10034: * V3=decodtabm(14,3,2**4)=2
10035: * h'=13 1101 =2^3+2^2+0x2^1+2^0
10036: *(h-1) >> (j-1) 0011 =13 >> 2
10037: * &1 000000001
10038: * = 000000001
10039: * +1= 000000010 =2
10040: * 2211
10041: * V1=1+1, V2=0+1, V3=1+1, V4=1+1
10042: * V3=2
1.220 brouard 10043: * codtabm and decodtabm are identical
1.211 brouard 10044: */
10045:
1.145 brouard 10046:
10047: free_ivector(Ndum,-1,NCOVMAX);
10048:
10049:
1.126 brouard 10050:
1.186 brouard 10051: /* Initialisation of ----------- gnuplot -------------*/
1.126 brouard 10052: strcpy(optionfilegnuplot,optionfilefiname);
10053: if(mle==-3)
1.201 brouard 10054: strcat(optionfilegnuplot,"-MORT_");
1.126 brouard 10055: strcat(optionfilegnuplot,".gp");
10056:
10057: if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
10058: printf("Problem with file %s",optionfilegnuplot);
10059: }
10060: else{
1.204 brouard 10061: fprintf(ficgp,"\n# IMaCh-%s\n", version);
1.126 brouard 10062: fprintf(ficgp,"# %s\n", optionfilegnuplot);
1.141 brouard 10063: //fprintf(ficgp,"set missing 'NaNq'\n");
10064: fprintf(ficgp,"set datafile missing 'NaNq'\n");
1.126 brouard 10065: }
10066: /* fclose(ficgp);*/
1.186 brouard 10067:
10068:
10069: /* Initialisation of --------- index.htm --------*/
1.126 brouard 10070:
10071: strcpy(optionfilehtm,optionfilefiname); /* Main html file */
10072: if(mle==-3)
1.201 brouard 10073: strcat(optionfilehtm,"-MORT_");
1.126 brouard 10074: strcat(optionfilehtm,".htm");
10075: if((fichtm=fopen(optionfilehtm,"w"))==NULL) {
1.131 brouard 10076: printf("Problem with %s \n",optionfilehtm);
10077: exit(0);
1.126 brouard 10078: }
10079:
10080: strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
10081: strcat(optionfilehtmcov,"-cov.htm");
10082: if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL) {
10083: printf("Problem with %s \n",optionfilehtmcov), exit(0);
10084: }
10085: else{
10086: fprintf(fichtmcov,"<html><head>\n<title>IMaCh Cov %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
10087: <hr size=\"2\" color=\"#EC5E5E\"> \n\
1.204 brouard 10088: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n",\
1.126 brouard 10089: optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
10090: }
10091:
1.213 brouard 10092: fprintf(fichtm,"<html><head>\n<head>\n<meta charset=\"utf-8\"/><meta http-equiv=\"Content-Type\" content=\"text/html; charset=utf-8\" />\n<title>IMaCh %s</title></head>\n <body><font size=\"7\"><a href=http:/euroreves.ined.fr/imach>IMaCh for Interpolated Markov Chain</a> </font><br>\n<font size=\"3\">Sponsored by Copyright (C) 2002-2015 <a href=http://www.ined.fr>INED</a>-EUROREVES-Institut de longévité-2013-2016-Japan Society for the Promotion of Sciences 日本学術振興会 (<a href=https://www.jsps.go.jp/english/e-grants/>Grant-in-Aid for Scientific Research 25293121</a>) - <a href=https://software.intel.com/en-us>Intel Software 2015-2018</a></font><br> \
1.204 brouard 10093: <hr size=\"2\" color=\"#EC5E5E\"> \n\
10094: <font size=\"2\">IMaCh-%s <br> %s</font> \
1.126 brouard 10095: <hr size=\"2\" color=\"#EC5E5E\"> \n\
1.204 brouard 10096: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n\
1.126 brouard 10097: \n\
10098: <hr size=\"2\" color=\"#EC5E5E\">\
10099: <ul><li><h4>Parameter files</h4>\n\
10100: - Parameter file: <a href=\"%s.%s\">%s.%s</a><br>\n\
10101: - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
10102: - Log file of the run: <a href=\"%s\">%s</a><br>\n\
10103: - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
10104: - Date and time at start: %s</ul>\n",\
10105: optionfilehtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
10106: optionfilefiname,optionfilext,optionfilefiname,optionfilext,\
10107: fileres,fileres,\
10108: filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
10109: fflush(fichtm);
10110:
10111: strcpy(pathr,path);
10112: strcat(pathr,optionfilefiname);
1.184 brouard 10113: #ifdef WIN32
10114: _chdir(optionfilefiname); /* Move to directory named optionfile */
10115: #else
1.126 brouard 10116: chdir(optionfilefiname); /* Move to directory named optionfile */
1.184 brouard 10117: #endif
10118:
1.126 brouard 10119:
1.220 brouard 10120: /* Calculates basic frequencies. Computes observed prevalence at single age
10121: and for any valid combination of covariates
1.126 brouard 10122: and prints on file fileres'p'. */
1.227 brouard 10123: freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx, Tvaraff, invalidvarcomb, nbcode, ncodemax,mint,anint,strstart, \
10124: firstpass, lastpass, stepm, weightopt, model);
1.126 brouard 10125:
10126: fprintf(fichtm,"\n");
10127: fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
10128: Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
10129: Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
10130: imx,agemin,agemax,jmin,jmax,jmean);
10131: pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
1.220 brouard 10132: oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
10133: newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
10134: savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
10135: oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
1.218 brouard 10136:
1.126 brouard 10137: /* For Powell, parameters are in a vector p[] starting at p[1]
10138: so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
10139: p=param[1][1]; /* *(*(*(param +1)+1)+0) */
10140:
10141: globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
1.186 brouard 10142: /* For mortality only */
1.126 brouard 10143: if (mle==-3){
1.136 brouard 10144: ximort=matrix(1,NDIM,1,NDIM);
1.220 brouard 10145: for(i=1;i<=NDIM;i++)
10146: for(j=1;j<=NDIM;j++)
10147: ximort[i][j]=0.;
1.186 brouard 10148: /* ximort=gsl_matrix_alloc(1,NDIM,1,NDIM); */
1.126 brouard 10149: cens=ivector(1,n);
10150: ageexmed=vector(1,n);
10151: agecens=vector(1,n);
10152: dcwave=ivector(1,n);
1.223 brouard 10153:
1.126 brouard 10154: for (i=1; i<=imx; i++){
10155: dcwave[i]=-1;
10156: for (m=firstpass; m<=lastpass; m++)
1.226 brouard 10157: if (s[m][i]>nlstate) {
10158: dcwave[i]=m;
10159: /* printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
10160: break;
10161: }
1.126 brouard 10162: }
1.226 brouard 10163:
1.126 brouard 10164: for (i=1; i<=imx; i++) {
10165: if (wav[i]>0){
1.226 brouard 10166: ageexmed[i]=agev[mw[1][i]][i];
10167: j=wav[i];
10168: agecens[i]=1.;
10169:
10170: if (ageexmed[i]> 1 && wav[i] > 0){
10171: agecens[i]=agev[mw[j][i]][i];
10172: cens[i]= 1;
10173: }else if (ageexmed[i]< 1)
10174: cens[i]= -1;
10175: if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
10176: cens[i]=0 ;
1.126 brouard 10177: }
10178: else cens[i]=-1;
10179: }
10180:
10181: for (i=1;i<=NDIM;i++) {
10182: for (j=1;j<=NDIM;j++)
1.226 brouard 10183: ximort[i][j]=(i == j ? 1.0 : 0.0);
1.126 brouard 10184: }
10185:
1.145 brouard 10186: /*p[1]=0.0268; p[NDIM]=0.083;*/
1.126 brouard 10187: /*printf("%lf %lf", p[1], p[2]);*/
10188:
10189:
1.136 brouard 10190: #ifdef GSL
10191: printf("GSL optimization\n"); fprintf(ficlog,"Powell\n");
1.162 brouard 10192: #else
1.126 brouard 10193: printf("Powell\n"); fprintf(ficlog,"Powell\n");
1.136 brouard 10194: #endif
1.201 brouard 10195: strcpy(filerespow,"POW-MORT_");
10196: strcat(filerespow,fileresu);
1.126 brouard 10197: if((ficrespow=fopen(filerespow,"w"))==NULL) {
10198: printf("Problem with resultfile: %s\n", filerespow);
10199: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
10200: }
1.136 brouard 10201: #ifdef GSL
10202: fprintf(ficrespow,"# GSL optimization\n# iter -2*LL");
1.162 brouard 10203: #else
1.126 brouard 10204: fprintf(ficrespow,"# Powell\n# iter -2*LL");
1.136 brouard 10205: #endif
1.126 brouard 10206: /* for (i=1;i<=nlstate;i++)
10207: for(j=1;j<=nlstate+ndeath;j++)
10208: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
10209: */
10210: fprintf(ficrespow,"\n");
1.136 brouard 10211: #ifdef GSL
10212: /* gsl starts here */
10213: T = gsl_multimin_fminimizer_nmsimplex;
10214: gsl_multimin_fminimizer *sfm = NULL;
10215: gsl_vector *ss, *x;
10216: gsl_multimin_function minex_func;
10217:
10218: /* Initial vertex size vector */
10219: ss = gsl_vector_alloc (NDIM);
10220:
10221: if (ss == NULL){
10222: GSL_ERROR_VAL ("failed to allocate space for ss", GSL_ENOMEM, 0);
10223: }
10224: /* Set all step sizes to 1 */
10225: gsl_vector_set_all (ss, 0.001);
10226:
10227: /* Starting point */
1.126 brouard 10228:
1.136 brouard 10229: x = gsl_vector_alloc (NDIM);
10230:
10231: if (x == NULL){
10232: gsl_vector_free(ss);
10233: GSL_ERROR_VAL ("failed to allocate space for x", GSL_ENOMEM, 0);
10234: }
10235:
10236: /* Initialize method and iterate */
10237: /* p[1]=0.0268; p[NDIM]=0.083; */
1.186 brouard 10238: /* gsl_vector_set(x, 0, 0.0268); */
10239: /* gsl_vector_set(x, 1, 0.083); */
1.136 brouard 10240: gsl_vector_set(x, 0, p[1]);
10241: gsl_vector_set(x, 1, p[2]);
10242:
10243: minex_func.f = &gompertz_f;
10244: minex_func.n = NDIM;
10245: minex_func.params = (void *)&p; /* ??? */
10246:
10247: sfm = gsl_multimin_fminimizer_alloc (T, NDIM);
10248: gsl_multimin_fminimizer_set (sfm, &minex_func, x, ss);
10249:
10250: printf("Iterations beginning .....\n\n");
10251: printf("Iter. # Intercept Slope -Log Likelihood Simplex size\n");
10252:
10253: iteri=0;
10254: while (rval == GSL_CONTINUE){
10255: iteri++;
10256: status = gsl_multimin_fminimizer_iterate(sfm);
10257:
10258: if (status) printf("error: %s\n", gsl_strerror (status));
10259: fflush(0);
10260:
10261: if (status)
10262: break;
10263:
10264: rval = gsl_multimin_test_size (gsl_multimin_fminimizer_size (sfm), 1e-6);
10265: ssval = gsl_multimin_fminimizer_size (sfm);
10266:
10267: if (rval == GSL_SUCCESS)
10268: printf ("converged to a local maximum at\n");
10269:
10270: printf("%5d ", iteri);
10271: for (it = 0; it < NDIM; it++){
10272: printf ("%10.5f ", gsl_vector_get (sfm->x, it));
10273: }
10274: printf("f() = %-10.5f ssize = %.7f\n", sfm->fval, ssval);
10275: }
10276:
10277: printf("\n\n Please note: Program should be run many times with varying starting points to detemine global maximum\n\n");
10278:
10279: gsl_vector_free(x); /* initial values */
10280: gsl_vector_free(ss); /* inital step size */
10281: for (it=0; it<NDIM; it++){
10282: p[it+1]=gsl_vector_get(sfm->x,it);
10283: fprintf(ficrespow," %.12lf", p[it]);
10284: }
10285: gsl_multimin_fminimizer_free (sfm); /* p *(sfm.x.data) et p *(sfm.x.data+1) */
10286: #endif
10287: #ifdef POWELL
10288: powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
10289: #endif
1.126 brouard 10290: fclose(ficrespow);
10291:
1.203 brouard 10292: hesscov(matcov, hess, p, NDIM, delti, 1e-4, gompertz);
1.126 brouard 10293:
10294: for(i=1; i <=NDIM; i++)
10295: for(j=i+1;j<=NDIM;j++)
1.220 brouard 10296: matcov[i][j]=matcov[j][i];
1.126 brouard 10297:
10298: printf("\nCovariance matrix\n ");
1.203 brouard 10299: fprintf(ficlog,"\nCovariance matrix\n ");
1.126 brouard 10300: for(i=1; i <=NDIM; i++) {
10301: for(j=1;j<=NDIM;j++){
1.220 brouard 10302: printf("%f ",matcov[i][j]);
10303: fprintf(ficlog,"%f ",matcov[i][j]);
1.126 brouard 10304: }
1.203 brouard 10305: printf("\n "); fprintf(ficlog,"\n ");
1.126 brouard 10306: }
10307:
10308: printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
1.193 brouard 10309: for (i=1;i<=NDIM;i++) {
1.126 brouard 10310: printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
1.193 brouard 10311: fprintf(ficlog,"%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
10312: }
1.126 brouard 10313: lsurv=vector(1,AGESUP);
10314: lpop=vector(1,AGESUP);
10315: tpop=vector(1,AGESUP);
10316: lsurv[agegomp]=100000;
10317:
10318: for (k=agegomp;k<=AGESUP;k++) {
10319: agemortsup=k;
10320: if (p[1]*exp(p[2]*(k-agegomp))>1) break;
10321: }
10322:
10323: for (k=agegomp;k<agemortsup;k++)
10324: lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
10325:
10326: for (k=agegomp;k<agemortsup;k++){
10327: lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
10328: sumlpop=sumlpop+lpop[k];
10329: }
10330:
10331: tpop[agegomp]=sumlpop;
10332: for (k=agegomp;k<(agemortsup-3);k++){
10333: /* tpop[k+1]=2;*/
10334: tpop[k+1]=tpop[k]-lpop[k];
10335: }
10336:
10337:
10338: printf("\nAge lx qx dx Lx Tx e(x)\n");
10339: for (k=agegomp;k<(agemortsup-2);k++)
10340: 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]);
10341:
10342:
10343: replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
1.220 brouard 10344: ageminpar=50;
10345: agemaxpar=100;
1.194 brouard 10346: if(ageminpar == AGEOVERFLOW ||agemaxpar == AGEOVERFLOW){
10347: printf("Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
10348: This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\
10349: Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
10350: fprintf(ficlog,"Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
10351: This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\
10352: Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
1.220 brouard 10353: }else{
10354: printf("Warning! ageminpar %f and agemaxpar %f have been fixed because for simplification until it is fixed...\n\n",ageminpar,agemaxpar);
10355: fprintf(ficlog,"Warning! ageminpar %f and agemaxpar %f have been fixed because for simplification until it is fixed...\n\n",ageminpar,agemaxpar);
1.201 brouard 10356: printinggnuplotmort(fileresu, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
1.220 brouard 10357: }
1.201 brouard 10358: printinghtmlmort(fileresu,title,datafile, firstpass, lastpass, \
1.126 brouard 10359: stepm, weightopt,\
10360: model,imx,p,matcov,agemortsup);
10361:
10362: free_vector(lsurv,1,AGESUP);
10363: free_vector(lpop,1,AGESUP);
10364: free_vector(tpop,1,AGESUP);
1.220 brouard 10365: free_matrix(ximort,1,NDIM,1,NDIM);
1.136 brouard 10366: free_ivector(cens,1,n);
10367: free_vector(agecens,1,n);
10368: free_ivector(dcwave,1,n);
1.220 brouard 10369: #ifdef GSL
1.136 brouard 10370: #endif
1.186 brouard 10371: } /* Endof if mle==-3 mortality only */
1.205 brouard 10372: /* Standard */
10373: else{ /* For mle !=- 3, could be 0 or 1 or 4 etc. */
10374: globpr=0;/* Computes sum of likelihood for globpr=1 and funcone */
10375: /* Computes likelihood for initial parameters, uses funcone to compute gpimx and gsw */
1.132 brouard 10376: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
1.126 brouard 10377: printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
10378: for (k=1; k<=npar;k++)
10379: printf(" %d %8.5f",k,p[k]);
10380: printf("\n");
1.205 brouard 10381: if(mle>=1){ /* Could be 1 or 2, Real Maximization */
10382: /* mlikeli uses func not funcone */
10383: mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
10384: }
10385: if(mle==0) {/* No optimization, will print the likelihoods for the datafile */
10386: globpr=0;/* Computes sum of likelihood for globpr=1 and funcone */
10387: /* Computes likelihood for initial parameters, uses funcone to compute gpimx and gsw */
10388: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
10389: }
10390: globpr=1; /* again, to print the individual contributions using computed gpimx and gsw */
1.126 brouard 10391: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
10392: printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
10393: for (k=1; k<=npar;k++)
10394: printf(" %d %8.5f",k,p[k]);
10395: printf("\n");
10396:
10397: /*--------- results files --------------*/
1.224 brouard 10398: fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=1+age+%s.\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nqv, ntv, nqtv, nlstate, ndeath, maxwav, weightopt,model);
1.126 brouard 10399:
10400:
10401: fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
10402: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
10403: fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
10404: for(i=1,jk=1; i <=nlstate; i++){
10405: for(k=1; k <=(nlstate+ndeath); k++){
1.225 brouard 10406: if (k != i) {
10407: printf("%d%d ",i,k);
10408: fprintf(ficlog,"%d%d ",i,k);
10409: fprintf(ficres,"%1d%1d ",i,k);
10410: for(j=1; j <=ncovmodel; j++){
10411: printf("%12.7f ",p[jk]);
10412: fprintf(ficlog,"%12.7f ",p[jk]);
10413: fprintf(ficres,"%12.7f ",p[jk]);
10414: jk++;
10415: }
10416: printf("\n");
10417: fprintf(ficlog,"\n");
10418: fprintf(ficres,"\n");
10419: }
1.126 brouard 10420: }
10421: }
1.203 brouard 10422: if(mle != 0){
10423: /* Computing hessian and covariance matrix only at a peak of the Likelihood, that is after optimization */
1.126 brouard 10424: ftolhess=ftol; /* Usually correct */
1.203 brouard 10425: hesscov(matcov, hess, p, npar, delti, ftolhess, func);
10426: 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");
10427: 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");
10428: for(i=1,jk=1; i <=nlstate; i++){
1.225 brouard 10429: for(k=1; k <=(nlstate+ndeath); k++){
10430: if (k != i) {
10431: printf("%d%d ",i,k);
10432: fprintf(ficlog,"%d%d ",i,k);
10433: for(j=1; j <=ncovmodel; j++){
10434: 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]));
10435: 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]));
10436: jk++;
10437: }
10438: printf("\n");
10439: fprintf(ficlog,"\n");
10440: }
10441: }
1.193 brouard 10442: }
1.203 brouard 10443: } /* end of hesscov and Wald tests */
1.225 brouard 10444:
1.203 brouard 10445: /* */
1.126 brouard 10446: fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
10447: printf("# Scales (for hessian or gradient estimation)\n");
10448: fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
10449: for(i=1,jk=1; i <=nlstate; i++){
10450: for(j=1; j <=nlstate+ndeath; j++){
1.225 brouard 10451: if (j!=i) {
10452: fprintf(ficres,"%1d%1d",i,j);
10453: printf("%1d%1d",i,j);
10454: fprintf(ficlog,"%1d%1d",i,j);
10455: for(k=1; k<=ncovmodel;k++){
10456: printf(" %.5e",delti[jk]);
10457: fprintf(ficlog," %.5e",delti[jk]);
10458: fprintf(ficres," %.5e",delti[jk]);
10459: jk++;
10460: }
10461: printf("\n");
10462: fprintf(ficlog,"\n");
10463: fprintf(ficres,"\n");
10464: }
1.126 brouard 10465: }
10466: }
10467:
10468: 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 10469: if(mle >= 1) /* To big for the screen */
1.126 brouard 10470: 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");
10471: 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");
10472: /* # 121 Var(a12)\n\ */
10473: /* # 122 Cov(b12,a12) Var(b12)\n\ */
10474: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
10475: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
10476: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
10477: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
10478: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
10479: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
10480:
10481:
10482: /* Just to have a covariance matrix which will be more understandable
10483: even is we still don't want to manage dictionary of variables
10484: */
10485: for(itimes=1;itimes<=2;itimes++){
10486: jj=0;
10487: for(i=1; i <=nlstate; i++){
1.225 brouard 10488: for(j=1; j <=nlstate+ndeath; j++){
10489: if(j==i) continue;
10490: for(k=1; k<=ncovmodel;k++){
10491: jj++;
10492: ca[0]= k+'a'-1;ca[1]='\0';
10493: if(itimes==1){
10494: if(mle>=1)
10495: printf("#%1d%1d%d",i,j,k);
10496: fprintf(ficlog,"#%1d%1d%d",i,j,k);
10497: fprintf(ficres,"#%1d%1d%d",i,j,k);
10498: }else{
10499: if(mle>=1)
10500: printf("%1d%1d%d",i,j,k);
10501: fprintf(ficlog,"%1d%1d%d",i,j,k);
10502: fprintf(ficres,"%1d%1d%d",i,j,k);
10503: }
10504: ll=0;
10505: for(li=1;li <=nlstate; li++){
10506: for(lj=1;lj <=nlstate+ndeath; lj++){
10507: if(lj==li) continue;
10508: for(lk=1;lk<=ncovmodel;lk++){
10509: ll++;
10510: if(ll<=jj){
10511: cb[0]= lk +'a'-1;cb[1]='\0';
10512: if(ll<jj){
10513: if(itimes==1){
10514: if(mle>=1)
10515: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
10516: fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
10517: fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
10518: }else{
10519: if(mle>=1)
10520: printf(" %.5e",matcov[jj][ll]);
10521: fprintf(ficlog," %.5e",matcov[jj][ll]);
10522: fprintf(ficres," %.5e",matcov[jj][ll]);
10523: }
10524: }else{
10525: if(itimes==1){
10526: if(mle>=1)
10527: printf(" Var(%s%1d%1d)",ca,i,j);
10528: fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
10529: fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
10530: }else{
10531: if(mle>=1)
10532: printf(" %.7e",matcov[jj][ll]);
10533: fprintf(ficlog," %.7e",matcov[jj][ll]);
10534: fprintf(ficres," %.7e",matcov[jj][ll]);
10535: }
10536: }
10537: }
10538: } /* end lk */
10539: } /* end lj */
10540: } /* end li */
10541: if(mle>=1)
10542: printf("\n");
10543: fprintf(ficlog,"\n");
10544: fprintf(ficres,"\n");
10545: numlinepar++;
10546: } /* end k*/
10547: } /*end j */
1.126 brouard 10548: } /* end i */
10549: } /* end itimes */
10550:
10551: fflush(ficlog);
10552: fflush(ficres);
1.225 brouard 10553: while(fgets(line, MAXLINE, ficpar)) {
10554: /* If line starts with a # it is a comment */
10555: if (line[0] == '#') {
10556: numlinepar++;
10557: fputs(line,stdout);
10558: fputs(line,ficparo);
10559: fputs(line,ficlog);
10560: continue;
10561: }else
10562: break;
10563: }
10564:
1.209 brouard 10565: /* while((c=getc(ficpar))=='#' && c!= EOF){ */
10566: /* ungetc(c,ficpar); */
10567: /* fgets(line, MAXLINE, ficpar); */
10568: /* fputs(line,stdout); */
10569: /* fputs(line,ficparo); */
10570: /* } */
10571: /* ungetc(c,ficpar); */
1.126 brouard 10572:
10573: estepm=0;
1.209 brouard 10574: 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){
1.225 brouard 10575:
10576: if (num_filled != 6) {
10577: printf("Error: Not 6 parameters in line, for example:agemin=60 agemax=95 bage=55 fage=95 estepm=24 ftolpl=6e-4\n, your line=%s . Probably you are running an older format.\n",line);
10578: fprintf(ficlog,"Error: Not 6 parameters in line, for example:agemin=60 agemax=95 bage=55 fage=95 estepm=24 ftolpl=6e-4\n, your line=%s . Probably you are running an older format.\n",line);
10579: goto end;
10580: }
10581: printf("agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d ftolpl=%lf\n",ageminpar,agemaxpar, bage, fage, estepm, ftolpl);
10582: }
10583: /* ftolpl=6*ftol*1.e5; /\* 6.e-3 make convergences in less than 80 loops for the prevalence limit *\/ */
10584: /*ftolpl=6.e-4;*/ /* 6.e-3 make convergences in less than 80 loops for the prevalence limit */
10585:
1.209 brouard 10586: /* fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d ftolpl=%\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm); */
1.126 brouard 10587: if (estepm==0 || estepm < stepm) estepm=stepm;
10588: if (fage <= 2) {
10589: bage = ageminpar;
10590: fage = agemaxpar;
10591: }
10592:
10593: fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
1.211 brouard 10594: fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d ftolpl=%e\n",ageminpar,agemaxpar,bage,fage, estepm, ftolpl);
10595: fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d, ftolpl=%e\n",ageminpar,agemaxpar,bage,fage, estepm, ftolpl);
1.220 brouard 10596:
1.186 brouard 10597: /* Other stuffs, more or less useful */
1.126 brouard 10598: while((c=getc(ficpar))=='#' && c!= EOF){
10599: ungetc(c,ficpar);
10600: fgets(line, MAXLINE, ficpar);
1.141 brouard 10601: fputs(line,stdout);
1.126 brouard 10602: fputs(line,ficparo);
10603: }
10604: ungetc(c,ficpar);
10605:
10606: 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);
10607: 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);
10608: 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);
10609: printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
10610: 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);
10611:
10612: while((c=getc(ficpar))=='#' && c!= EOF){
10613: ungetc(c,ficpar);
10614: fgets(line, MAXLINE, ficpar);
1.141 brouard 10615: fputs(line,stdout);
1.126 brouard 10616: fputs(line,ficparo);
10617: }
10618: ungetc(c,ficpar);
10619:
10620:
10621: dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
10622: dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
10623:
10624: fscanf(ficpar,"pop_based=%d\n",&popbased);
1.193 brouard 10625: fprintf(ficlog,"pop_based=%d\n",popbased);
1.126 brouard 10626: fprintf(ficparo,"pop_based=%d\n",popbased);
10627: fprintf(ficres,"pop_based=%d\n",popbased);
10628:
10629: while((c=getc(ficpar))=='#' && c!= EOF){
10630: ungetc(c,ficpar);
10631: fgets(line, MAXLINE, ficpar);
1.141 brouard 10632: fputs(line,stdout);
1.126 brouard 10633: fputs(line,ficparo);
10634: }
10635: ungetc(c,ficpar);
10636:
10637: 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);
10638: 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);
10639: 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);
10640: 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);
10641: 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);
10642: /* day and month of proj2 are not used but only year anproj2.*/
10643:
1.217 brouard 10644: while((c=getc(ficpar))=='#' && c!= EOF){
10645: ungetc(c,ficpar);
10646: fgets(line, MAXLINE, ficpar);
10647: fputs(line,stdout);
10648: fputs(line,ficparo);
10649: }
10650: ungetc(c,ficpar);
10651:
10652: fscanf(ficpar,"backcast=%d starting-back-date=%lf/%lf/%lf final-back-date=%lf/%lf/%lf mobil_average=%d\n",&backcast,&jback1,&mback1,&anback1,&jback2,&mback2,&anback2,&mobilavproj);
1.223 brouard 10653: fprintf(ficparo,"backcast=%d starting-back-date=%.lf/%.lf/%.lf final-back-date=%.lf/%.lf/%.lf mobil_average=%d\n",backcast,jback1,mback1,anback1,jback2,mback2,anback2,mobilavproj);
10654: fprintf(ficlog,"backcast=%d starting-back-date=%.lf/%.lf/%.lf final-back-date=%.lf/%.lf/%.lf mobil_average=%d\n",backcast,jback1,mback1,anback1,jback2,mback2,anback2,mobilavproj);
10655: fprintf(ficres,"backcast=%d starting-back-date=%.lf/%.lf/%.lf final-back-date=%.lf/%.lf/%.lf mobil_average=%d\n",backcast,jback1,mback1,anback1,jback2,mback2,anback2,mobilavproj);
1.217 brouard 10656: /* day and month of proj2 are not used but only year anproj2.*/
1.126 brouard 10657:
1.230 brouard 10658: /* Results */
1.235 ! brouard 10659: nresult=0;
1.230 brouard 10660: while(fgets(line, MAXLINE, ficpar)) {
10661: /* If line starts with a # it is a comment */
10662: if (line[0] == '#') {
10663: numlinepar++;
10664: fputs(line,stdout);
10665: fputs(line,ficparo);
10666: fputs(line,ficlog);
10667: continue;
10668: }else
10669: break;
10670: }
10671: while((num_filled=sscanf(line,"result:%[^\n]\n",resultline)) !=EOF){
10672: if (num_filled == 0)
10673: resultline[0]='\0';
10674: else if (num_filled != 1){
10675: printf("ERROR %d: result line should be at minimum 'result=' %s\n",num_filled, line);
10676: }
1.235 ! brouard 10677: nresult++; /* Sum of resultlines */
! 10678: printf("Result %d: result=%s\n",nresult, resultline);
! 10679: if(nresult > MAXRESULTLINES){
! 10680: printf("ERROR: Current version of IMaCh limits the number of resultlines to %d, you used %d\n",MAXRESULTLINES,nresult);
! 10681: fprintf(ficlog,"ERROR: Current version of IMaCh limits the number of resultlines to %d, you used %d\n",MAXRESULTLINES,nresult);
! 10682: goto end;
! 10683: }
! 10684: decoderesult(resultline, nresult); /* Fills TKresult[nresult] combination and Tresult[nresult][k4+1] combination values */
1.230 brouard 10685: while(fgets(line, MAXLINE, ficpar)) {
10686: /* If line starts with a # it is a comment */
10687: if (line[0] == '#') {
10688: numlinepar++;
10689: fputs(line,stdout);
10690: fputs(line,ficparo);
10691: fputs(line,ficlog);
10692: continue;
10693: }else
10694: break;
10695: }
10696: if (feof(ficpar))
10697: break;
10698: else{ /* Processess output results for this combination of covariate values */
10699: }
10700: }
10701:
10702:
1.126 brouard 10703:
1.230 brouard 10704: /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint); */
1.145 brouard 10705: /* ,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2); */
1.126 brouard 10706:
10707: replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
1.194 brouard 10708: if(ageminpar == AGEOVERFLOW ||agemaxpar == -AGEOVERFLOW){
1.230 brouard 10709: printf("Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
1.194 brouard 10710: This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\
10711: Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
1.230 brouard 10712: fprintf(ficlog,"Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
1.194 brouard 10713: This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\
10714: Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
1.220 brouard 10715: }else{
1.218 brouard 10716: printinggnuplot(fileresu, optionfilefiname,ageminpar,agemaxpar,fage, prevfcast, backcast, pathc,p);
1.220 brouard 10717: }
10718: printinghtml(fileresu,title,datafile, firstpass, lastpass, stepm, weightopt, \
1.225 brouard 10719: model,imx,jmin,jmax,jmean,rfileres,popforecast,prevfcast,backcast, estepm, \
10720: jprev1,mprev1,anprev1,dateprev1,jprev2,mprev2,anprev2,dateprev2);
1.220 brouard 10721:
1.225 brouard 10722: /*------------ free_vector -------------*/
10723: /* chdir(path); */
1.220 brouard 10724:
1.215 brouard 10725: /* free_ivector(wav,1,imx); */ /* Moved after last prevalence call */
10726: /* free_imatrix(dh,1,lastpass-firstpass+2,1,imx); */
10727: /* free_imatrix(bh,1,lastpass-firstpass+2,1,imx); */
10728: /* free_imatrix(mw,1,lastpass-firstpass+2,1,imx); */
1.126 brouard 10729: free_lvector(num,1,n);
10730: free_vector(agedc,1,n);
10731: /*free_matrix(covar,0,NCOVMAX,1,n);*/
10732: /*free_matrix(covar,1,NCOVMAX,1,n);*/
10733: fclose(ficparo);
10734: fclose(ficres);
1.220 brouard 10735:
10736:
1.186 brouard 10737: /* Other results (useful)*/
1.220 brouard 10738:
10739:
1.126 brouard 10740: /*--------------- Prevalence limit (period or stable prevalence) --------------*/
1.180 brouard 10741: /*#include "prevlim.h"*/ /* Use ficrespl, ficlog */
10742: prlim=matrix(1,nlstate,1,nlstate);
1.209 brouard 10743: prevalence_limit(p, prlim, ageminpar, agemaxpar, ftolpl, &ncvyear);
1.126 brouard 10744: fclose(ficrespl);
10745:
10746: /*------------- h Pij x at various ages ------------*/
1.180 brouard 10747: /*#include "hpijx.h"*/
10748: hPijx(p, bage, fage);
1.145 brouard 10749: fclose(ficrespij);
1.227 brouard 10750:
1.220 brouard 10751: /* ncovcombmax= pow(2,cptcoveff); */
1.219 brouard 10752: /*-------------- Variance of one-step probabilities---*/
1.145 brouard 10753: k=1;
1.126 brouard 10754: varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
1.227 brouard 10755:
1.219 brouard 10756: /* Prevalence for each covariates in probs[age][status][cov] */
1.218 brouard 10757: probs= ma3x(1,AGESUP,1,nlstate+ndeath, 1,ncovcombmax);
1.126 brouard 10758: for(i=1;i<=AGESUP;i++)
1.219 brouard 10759: for(j=1;j<=nlstate+ndeath;j++) /* ndeath is useless but a necessity to be compared with mobaverages */
1.225 brouard 10760: for(k=1;k<=ncovcombmax;k++)
10761: probs[i][j][k]=0.;
1.219 brouard 10762: prevalence(probs, ageminpar, agemaxpar, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
10763: if (mobilav!=0 ||mobilavproj !=0 ) {
10764: mobaverages= ma3x(1, AGESUP,1,nlstate+ndeath, 1,ncovcombmax);
1.227 brouard 10765: for(i=1;i<=AGESUP;i++)
10766: for(j=1;j<=nlstate;j++)
10767: for(k=1;k<=ncovcombmax;k++)
10768: mobaverages[i][j][k]=0.;
1.219 brouard 10769: mobaverage=mobaverages;
10770: if (mobilav!=0) {
1.235 ! brouard 10771: printf("Movingaveraging observed prevalence\n");
1.227 brouard 10772: if (movingaverage(probs, ageminpar, agemaxpar, mobaverage, mobilav)!=0){
10773: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
10774: printf(" Error in movingaverage mobilav=%d\n",mobilav);
10775: }
1.219 brouard 10776: }
10777: /* /\* Prevalence for each covariates in probs[age][status][cov] *\/ */
10778: /* prevalence(probs, ageminpar, agemaxpar, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass); */
10779: else if (mobilavproj !=0) {
1.235 ! brouard 10780: printf("Movingaveraging projected observed prevalence\n");
1.227 brouard 10781: if (movingaverage(probs, ageminpar, agemaxpar, mobaverage, mobilavproj)!=0){
10782: fprintf(ficlog," Error in movingaverage mobilavproj=%d\n",mobilavproj);
10783: printf(" Error in movingaverage mobilavproj=%d\n",mobilavproj);
10784: }
1.219 brouard 10785: }
10786: }/* end if moving average */
1.227 brouard 10787:
1.126 brouard 10788: /*---------- Forecasting ------------------*/
10789: /*if((stepm == 1) && (strcmp(model,".")==0)){*/
10790: if(prevfcast==1){
10791: /* if(stepm ==1){*/
1.225 brouard 10792: prevforecast(fileresu, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
1.126 brouard 10793: }
1.217 brouard 10794: if(backcast==1){
1.219 brouard 10795: ddnewms=matrix(1,nlstate+ndeath,1,nlstate+ndeath);
10796: ddoldms=matrix(1,nlstate+ndeath,1,nlstate+ndeath);
10797: ddsavms=matrix(1,nlstate+ndeath,1,nlstate+ndeath);
10798:
10799: /*--------------- Back Prevalence limit (period or stable prevalence) --------------*/
10800:
10801: bprlim=matrix(1,nlstate,1,nlstate);
10802: back_prevalence_limit(p, bprlim, ageminpar, agemaxpar, ftolpl, &ncvyear, dateprev1, dateprev2, firstpass, lastpass, mobilavproj);
10803: fclose(ficresplb);
10804:
1.222 brouard 10805: hBijx(p, bage, fage, mobaverage);
10806: fclose(ficrespijb);
1.219 brouard 10807: free_matrix(bprlim,1,nlstate,1,nlstate); /*here or after loop ? */
10808:
10809: /* prevbackforecast(fileresu, anback1, mback1, jback1, agemin, agemax, dateprev1, dateprev2, mobilavproj,
1.225 brouard 10810: bage, fage, firstpass, lastpass, anback2, p, cptcoveff); */
1.219 brouard 10811: free_matrix(ddnewms, 1, nlstate+ndeath, 1, nlstate+ndeath);
10812: free_matrix(ddsavms, 1, nlstate+ndeath, 1, nlstate+ndeath);
10813: free_matrix(ddoldms, 1, nlstate+ndeath, 1, nlstate+ndeath);
10814: }
1.217 brouard 10815:
1.186 brouard 10816:
10817: /* ------ Other prevalence ratios------------ */
1.126 brouard 10818:
1.215 brouard 10819: free_ivector(wav,1,imx);
10820: free_imatrix(dh,1,lastpass-firstpass+2,1,imx);
10821: free_imatrix(bh,1,lastpass-firstpass+2,1,imx);
10822: free_imatrix(mw,1,lastpass-firstpass+2,1,imx);
1.218 brouard 10823:
10824:
1.127 brouard 10825: /*---------- Health expectancies, no variances ------------*/
1.218 brouard 10826:
1.201 brouard 10827: strcpy(filerese,"E_");
10828: strcat(filerese,fileresu);
1.126 brouard 10829: if((ficreseij=fopen(filerese,"w"))==NULL) {
10830: printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
10831: fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
10832: }
1.208 brouard 10833: printf("Computing Health Expectancies: result on file '%s' ...", filerese);fflush(stdout);
10834: fprintf(ficlog,"Computing Health Expectancies: result on file '%s' ...", filerese);fflush(ficlog);
1.219 brouard 10835:
1.235 ! brouard 10836: i1=pow(2,cptcoveff); /* Number of combination of dummy covariates */
! 10837: if (cptcovn < 1){i1=1;}
! 10838:
! 10839: for(nres=1; nres <= nresult; nres++) /* For each resultline */
! 10840: for(k=1; k<=i1;k++){ /* For any combination of dummy covariates, fixed and varying */
! 10841: if(TKresult[nres]!= k)
! 10842: continue;
1.219 brouard 10843: fprintf(ficreseij,"\n#****** ");
1.235 ! brouard 10844: printf("\n#****** ");
1.225 brouard 10845: for(j=1;j<=cptcoveff;j++) {
1.227 brouard 10846: fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.235 ! brouard 10847: printf("V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
! 10848: }
! 10849: for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
! 10850: printf(" V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
! 10851: fprintf(ficreseij," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
1.219 brouard 10852: }
10853: fprintf(ficreseij,"******\n");
1.235 ! brouard 10854: printf("******\n");
1.219 brouard 10855:
10856: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
10857: oldm=oldms;savm=savms;
1.235 ! brouard 10858: evsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart, nres);
1.127 brouard 10859:
1.219 brouard 10860: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
1.127 brouard 10861: }
10862: fclose(ficreseij);
1.208 brouard 10863: printf("done evsij\n");fflush(stdout);
10864: fprintf(ficlog,"done evsij\n");fflush(ficlog);
1.218 brouard 10865:
1.227 brouard 10866: /*---------- State-specific expectancies and variances ------------*/
1.218 brouard 10867:
10868:
1.201 brouard 10869: strcpy(filerest,"T_");
10870: strcat(filerest,fileresu);
1.127 brouard 10871: if((ficrest=fopen(filerest,"w"))==NULL) {
10872: printf("Problem with total LE resultfile: %s\n", filerest);goto end;
10873: fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
10874: }
1.208 brouard 10875: printf("Computing Total Life expectancies with their standard errors: file '%s' ...\n", filerest); fflush(stdout);
10876: fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' ...\n", filerest); fflush(ficlog);
1.218 brouard 10877:
1.126 brouard 10878:
1.201 brouard 10879: strcpy(fileresstde,"STDE_");
10880: strcat(fileresstde,fileresu);
1.126 brouard 10881: if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {
1.227 brouard 10882: printf("Problem with State specific Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
10883: fprintf(ficlog,"Problem with State specific Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
1.126 brouard 10884: }
1.227 brouard 10885: printf(" Computing State-specific Expectancies and standard errors: result on file '%s' \n", fileresstde);
10886: fprintf(ficlog," Computing State-specific Expectancies and standard errors: result on file '%s' \n", fileresstde);
1.126 brouard 10887:
1.201 brouard 10888: strcpy(filerescve,"CVE_");
10889: strcat(filerescve,fileresu);
1.126 brouard 10890: if((ficrescveij=fopen(filerescve,"w"))==NULL) {
1.227 brouard 10891: printf("Problem with Covar. State-specific Exp. resultfile: %s\n", filerescve); exit(0);
10892: fprintf(ficlog,"Problem with Covar. State-specific Exp. resultfile: %s\n", filerescve); exit(0);
1.126 brouard 10893: }
1.227 brouard 10894: printf(" Computing Covar. of State-specific Expectancies: result on file '%s' \n", filerescve);
10895: fprintf(ficlog," Computing Covar. of State-specific Expectancies: result on file '%s' \n", filerescve);
1.126 brouard 10896:
1.201 brouard 10897: strcpy(fileresv,"V_");
10898: strcat(fileresv,fileresu);
1.126 brouard 10899: if((ficresvij=fopen(fileresv,"w"))==NULL) {
10900: printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
10901: fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
10902: }
1.227 brouard 10903: printf(" Computing Variance-covariance of State-specific Expectancies: file '%s' ... ", fileresv);fflush(stdout);
10904: fprintf(ficlog," Computing Variance-covariance of State-specific Expectancies: file '%s' ... ", fileresv);fflush(ficlog);
1.126 brouard 10905:
1.145 brouard 10906: /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
10907: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
10908:
1.235 ! brouard 10909: i1=pow(2,cptcoveff); /* Number of combination of dummy covariates */
! 10910: if (cptcovn < 1){i1=1;}
! 10911:
! 10912: for(nres=1; nres <= nresult; nres++) /* For each resultline */
! 10913: for(k=1; k<=i1;k++){ /* For any combination of dummy covariates, fixed and varying */
! 10914: if(TKresult[nres]!= k)
! 10915: continue;
! 10916: printf("\n#****** Selected:");
! 10917: fprintf(ficrest,"\n#****** Selected:");
! 10918: fprintf(ficlog,"\n#****** Selected:");
1.227 brouard 10919: for(j=1;j<=cptcoveff;j++){
10920: printf("V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
10921: fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
10922: fprintf(ficlog,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
10923: }
1.235 ! brouard 10924: for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
! 10925: printf(" V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
! 10926: fprintf(ficrest," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
! 10927: fprintf(ficlog," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
! 10928: }
1.208 brouard 10929: fprintf(ficrest,"******\n");
1.227 brouard 10930: fprintf(ficlog,"******\n");
10931: printf("******\n");
1.208 brouard 10932:
10933: fprintf(ficresstdeij,"\n#****** ");
10934: fprintf(ficrescveij,"\n#****** ");
1.225 brouard 10935: for(j=1;j<=cptcoveff;j++) {
1.227 brouard 10936: fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
10937: fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.208 brouard 10938: }
1.235 ! brouard 10939: for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
! 10940: fprintf(ficresstdeij," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
! 10941: fprintf(ficrescveij," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
! 10942: }
1.208 brouard 10943: fprintf(ficresstdeij,"******\n");
10944: fprintf(ficrescveij,"******\n");
10945:
10946: fprintf(ficresvij,"\n#****** ");
1.225 brouard 10947: for(j=1;j<=cptcoveff;j++)
1.227 brouard 10948: fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.235 ! brouard 10949: for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
! 10950: fprintf(ficresvij," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
! 10951: }
1.208 brouard 10952: fprintf(ficresvij,"******\n");
10953:
10954: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
10955: oldm=oldms;savm=savms;
1.235 ! brouard 10956: printf(" cvevsij ");
! 10957: fprintf(ficlog, " cvevsij ");
! 10958: cvevsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart, nres);
1.208 brouard 10959: printf(" end cvevsij \n ");
10960: fprintf(ficlog, " end cvevsij \n ");
10961:
10962: /*
10963: */
10964: /* goto endfree; */
10965:
10966: vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
10967: pstamp(ficrest);
10968:
10969:
10970: for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
1.227 brouard 10971: oldm=oldms;savm=savms; /* ZZ Segmentation fault */
10972: cptcod= 0; /* To be deleted */
10973: printf("varevsij vpopbased=%d \n",vpopbased);
10974: fprintf(ficlog, "varevsij vpopbased=%d \n",vpopbased);
1.235 ! brouard 10975: varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl, &ncvyear, k, estepm, cptcov,cptcod,vpopbased,mobilav, strstart, nres); /* cptcod not initialized Intel */
1.227 brouard 10976: 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 ");
10977: if(vpopbased==1)
10978: 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);
10979: else
10980: fprintf(ficrest,"the age specific period (stable) prevalences in each health state \n");
10981: fprintf(ficrest,"# Age popbased mobilav e.. (std) ");
10982: for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
10983: fprintf(ficrest,"\n");
10984: /* printf("Which p?\n"); for(i=1;i<=npar;i++)printf("p[i=%d]=%lf,",i,p[i]);printf("\n"); */
10985: epj=vector(1,nlstate+1);
10986: printf("Computing age specific period (stable) prevalences in each health state \n");
10987: fprintf(ficlog,"Computing age specific period (stable) prevalences in each health state \n");
10988: for(age=bage; age <=fage ;age++){
1.235 ! brouard 10989: prevalim(prlim, nlstate, p, age, oldm, savm, ftolpl, &ncvyear, k, nres); /*ZZ Is it the correct prevalim */
1.227 brouard 10990: if (vpopbased==1) {
10991: if(mobilav ==0){
10992: for(i=1; i<=nlstate;i++)
10993: prlim[i][i]=probs[(int)age][i][k];
10994: }else{ /* mobilav */
10995: for(i=1; i<=nlstate;i++)
10996: prlim[i][i]=mobaverage[(int)age][i][k];
10997: }
10998: }
1.219 brouard 10999:
1.227 brouard 11000: fprintf(ficrest," %4.0f %d %d",age, vpopbased, mobilav);
11001: /* fprintf(ficrest," %4.0f %d %d %d %d",age, vpopbased, mobilav,Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); */ /* to be done */
11002: /* printf(" age %4.0f ",age); */
11003: for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
11004: for(i=1, epj[j]=0.;i <=nlstate;i++) {
11005: epj[j] += prlim[i][i]*eij[i][j][(int)age];
11006: /*ZZZ printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
11007: /* printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]); */
11008: }
11009: epj[nlstate+1] +=epj[j];
11010: }
11011: /* printf(" age %4.0f \n",age); */
1.219 brouard 11012:
1.227 brouard 11013: for(i=1, vepp=0.;i <=nlstate;i++)
11014: for(j=1;j <=nlstate;j++)
11015: vepp += vareij[i][j][(int)age];
11016: fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
11017: for(j=1;j <=nlstate;j++){
11018: fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
11019: }
11020: fprintf(ficrest,"\n");
11021: }
1.208 brouard 11022: } /* End vpopbased */
11023: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
11024: free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
11025: free_vector(epj,1,nlstate+1);
1.235 ! brouard 11026: printf("done selection\n");fflush(stdout);
! 11027: fprintf(ficlog,"done selection\n");fflush(ficlog);
1.208 brouard 11028:
1.145 brouard 11029: /*}*/
1.235 ! brouard 11030: } /* End k selection */
1.227 brouard 11031:
11032: printf("done State-specific expectancies\n");fflush(stdout);
11033: fprintf(ficlog,"done State-specific expectancies\n");fflush(ficlog);
11034:
1.126 brouard 11035: /*------- Variance of period (stable) prevalence------*/
1.227 brouard 11036:
1.201 brouard 11037: strcpy(fileresvpl,"VPL_");
11038: strcat(fileresvpl,fileresu);
1.126 brouard 11039: if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
11040: printf("Problem with variance of period (stable) prevalence resultfile: %s\n", fileresvpl);
11041: exit(0);
11042: }
1.208 brouard 11043: printf("Computing Variance-covariance of period (stable) prevalence: file '%s' ...", fileresvpl);fflush(stdout);
11044: fprintf(ficlog, "Computing Variance-covariance of period (stable) prevalence: file '%s' ...", fileresvpl);fflush(ficlog);
1.227 brouard 11045:
1.145 brouard 11046: /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
11047: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
1.227 brouard 11048:
1.235 ! brouard 11049: i1=pow(2,cptcoveff);
! 11050: if (cptcovn < 1){i1=1;}
! 11051:
! 11052: for(nres=1; nres <= nresult; nres++) /* For each resultline */
! 11053: for(k=1; k<=i1;k++){
! 11054: if(TKresult[nres]!= k)
! 11055: continue;
1.227 brouard 11056: fprintf(ficresvpl,"\n#****** ");
11057: printf("\n#****** ");
11058: fprintf(ficlog,"\n#****** ");
11059: for(j=1;j<=cptcoveff;j++) {
11060: fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
11061: fprintf(ficlog,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
11062: printf("V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
11063: }
1.235 ! brouard 11064: for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
! 11065: printf(" V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
! 11066: fprintf(ficresvpl," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
! 11067: fprintf(ficlog," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
! 11068: }
1.227 brouard 11069: fprintf(ficresvpl,"******\n");
11070: printf("******\n");
11071: fprintf(ficlog,"******\n");
11072:
11073: varpl=matrix(1,nlstate,(int) bage, (int) fage);
11074: oldm=oldms;savm=savms;
1.235 ! brouard 11075: varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl, &ncvyear, k, strstart, nres);
1.227 brouard 11076: free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
1.145 brouard 11077: /*}*/
1.126 brouard 11078: }
1.227 brouard 11079:
1.126 brouard 11080: fclose(ficresvpl);
1.208 brouard 11081: printf("done variance-covariance of period prevalence\n");fflush(stdout);
11082: fprintf(ficlog,"done variance-covariance of period prevalence\n");fflush(ficlog);
1.227 brouard 11083:
11084: free_vector(weight,1,n);
11085: free_imatrix(Tvard,1,NCOVMAX,1,2);
11086: free_imatrix(s,1,maxwav+1,1,n);
11087: free_matrix(anint,1,maxwav,1,n);
11088: free_matrix(mint,1,maxwav,1,n);
11089: free_ivector(cod,1,n);
11090: free_ivector(tab,1,NCOVMAX);
11091: fclose(ficresstdeij);
11092: fclose(ficrescveij);
11093: fclose(ficresvij);
11094: fclose(ficrest);
11095: fclose(ficpar);
11096:
11097:
1.126 brouard 11098: /*---------- End : free ----------------*/
1.219 brouard 11099: if (mobilav!=0 ||mobilavproj !=0)
11100: free_ma3x(mobaverages,1, AGESUP,1,nlstate+ndeath, 1,ncovcombmax); /* We need to have a squared matrix with prevalence of the dead! */
1.218 brouard 11101: free_ma3x(probs,1,AGESUP,1,nlstate+ndeath, 1,ncovcombmax);
1.220 brouard 11102: free_matrix(prlim,1,nlstate,1,nlstate); /*here or after loop ? */
11103: free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
1.126 brouard 11104: } /* mle==-3 arrives here for freeing */
1.227 brouard 11105: /* endfree:*/
11106: free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
11107: free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
11108: free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
11109: free_ma3x(cotqvar,1,maxwav,1,nqtv,1,n);
1.233 brouard 11110: free_ma3x(cotvar,1,maxwav,1,ntv+nqtv,1,n);
1.227 brouard 11111: free_matrix(coqvar,1,maxwav,1,n);
11112: free_matrix(covar,0,NCOVMAX,1,n);
11113: free_matrix(matcov,1,npar,1,npar);
11114: free_matrix(hess,1,npar,1,npar);
11115: /*free_vector(delti,1,npar);*/
11116: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
11117: free_matrix(agev,1,maxwav,1,imx);
11118: free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
11119:
11120: free_ivector(ncodemax,1,NCOVMAX);
11121: free_ivector(ncodemaxwundef,1,NCOVMAX);
11122: free_ivector(Dummy,-1,NCOVMAX);
11123: free_ivector(Fixed,-1,NCOVMAX);
11124: free_ivector(Typevar,-1,NCOVMAX);
11125: free_ivector(Tvar,1,NCOVMAX);
1.234 brouard 11126: free_ivector(TvarsQ,1,NCOVMAX);
11127: free_ivector(TvarsQind,1,NCOVMAX);
11128: free_ivector(TvarsD,1,NCOVMAX);
11129: free_ivector(TvarsDind,1,NCOVMAX);
1.231 brouard 11130: free_ivector(TvarFD,1,NCOVMAX);
11131: free_ivector(TvarFDind,1,NCOVMAX);
1.232 brouard 11132: free_ivector(TvarF,1,NCOVMAX);
11133: free_ivector(TvarFind,1,NCOVMAX);
11134: free_ivector(TvarV,1,NCOVMAX);
11135: free_ivector(TvarVind,1,NCOVMAX);
11136: free_ivector(TvarA,1,NCOVMAX);
11137: free_ivector(TvarAind,1,NCOVMAX);
1.231 brouard 11138: free_ivector(TvarFQ,1,NCOVMAX);
11139: free_ivector(TvarFQind,1,NCOVMAX);
11140: free_ivector(TvarVD,1,NCOVMAX);
11141: free_ivector(TvarVDind,1,NCOVMAX);
11142: free_ivector(TvarVQ,1,NCOVMAX);
11143: free_ivector(TvarVQind,1,NCOVMAX);
1.230 brouard 11144: free_ivector(Tvarsel,1,NCOVMAX);
11145: free_vector(Tvalsel,1,NCOVMAX);
1.227 brouard 11146: free_ivector(Tposprod,1,NCOVMAX);
11147: free_ivector(Tprod,1,NCOVMAX);
11148: free_ivector(Tvaraff,1,NCOVMAX);
11149: free_ivector(invalidvarcomb,1,ncovcombmax);
11150: free_ivector(Tage,1,NCOVMAX);
11151: free_ivector(Tmodelind,1,NCOVMAX);
1.228 brouard 11152: free_ivector(TmodelInvind,1,NCOVMAX);
11153: free_ivector(TmodelInvQind,1,NCOVMAX);
1.227 brouard 11154:
11155: free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
11156: /* free_imatrix(codtab,1,100,1,10); */
1.126 brouard 11157: fflush(fichtm);
11158: fflush(ficgp);
11159:
1.227 brouard 11160:
1.126 brouard 11161: if((nberr >0) || (nbwarn>0)){
1.216 brouard 11162: printf("End of Imach with %d errors and/or %d warnings. Please look at the log file for details.\n",nberr,nbwarn);
11163: fprintf(ficlog,"End of Imach with %d errors and/or warnings %d. Please look at the log file for details.\n",nberr,nbwarn);
1.126 brouard 11164: }else{
11165: printf("End of Imach\n");
11166: fprintf(ficlog,"End of Imach\n");
11167: }
11168: printf("See log file on %s\n",filelog);
11169: /* gettimeofday(&end_time, (struct timezone*)0);*/ /* after time */
1.157 brouard 11170: /*(void) gettimeofday(&end_time,&tzp);*/
11171: rend_time = time(NULL);
11172: end_time = *localtime(&rend_time);
11173: /* tml = *localtime(&end_time.tm_sec); */
11174: strcpy(strtend,asctime(&end_time));
1.126 brouard 11175: printf("Local time at start %s\nLocal time at end %s",strstart, strtend);
11176: fprintf(ficlog,"Local time at start %s\nLocal time at end %s\n",strstart, strtend);
1.157 brouard 11177: printf("Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
1.227 brouard 11178:
1.157 brouard 11179: printf("Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
11180: fprintf(ficlog,"Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
11181: fprintf(ficlog,"Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
1.126 brouard 11182: /* printf("Total time was %d uSec.\n", total_usecs);*/
11183: /* if(fileappend(fichtm,optionfilehtm)){ */
11184: fprintf(fichtm,"<br>Local time at start %s<br>Local time at end %s<br>\n</body></html>",strstart, strtend);
11185: fclose(fichtm);
11186: fprintf(fichtmcov,"<br>Local time at start %s<br>Local time at end %s<br>\n</body></html>",strstart, strtend);
11187: fclose(fichtmcov);
11188: fclose(ficgp);
11189: fclose(ficlog);
11190: /*------ End -----------*/
1.227 brouard 11191:
11192:
11193: printf("Before Current directory %s!\n",pathcd);
1.184 brouard 11194: #ifdef WIN32
1.227 brouard 11195: if (_chdir(pathcd) != 0)
11196: printf("Can't move to directory %s!\n",path);
11197: if(_getcwd(pathcd,MAXLINE) > 0)
1.184 brouard 11198: #else
1.227 brouard 11199: if(chdir(pathcd) != 0)
11200: printf("Can't move to directory %s!\n", path);
11201: if (getcwd(pathcd, MAXLINE) > 0)
1.184 brouard 11202: #endif
1.126 brouard 11203: printf("Current directory %s!\n",pathcd);
11204: /*strcat(plotcmd,CHARSEPARATOR);*/
11205: sprintf(plotcmd,"gnuplot");
1.157 brouard 11206: #ifdef _WIN32
1.126 brouard 11207: sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
11208: #endif
11209: if(!stat(plotcmd,&info)){
1.158 brouard 11210: printf("Error or gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
1.126 brouard 11211: if(!stat(getenv("GNUPLOTBIN"),&info)){
1.158 brouard 11212: printf("Error or gnuplot program not found: '%s' Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);
1.126 brouard 11213: }else
11214: strcpy(pplotcmd,plotcmd);
1.157 brouard 11215: #ifdef __unix
1.126 brouard 11216: strcpy(plotcmd,GNUPLOTPROGRAM);
11217: if(!stat(plotcmd,&info)){
1.158 brouard 11218: printf("Error gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
1.126 brouard 11219: }else
11220: strcpy(pplotcmd,plotcmd);
11221: #endif
11222: }else
11223: strcpy(pplotcmd,plotcmd);
11224:
11225: sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
1.158 brouard 11226: printf("Starting graphs with: '%s'\n",plotcmd);fflush(stdout);
1.227 brouard 11227:
1.126 brouard 11228: if((outcmd=system(plotcmd)) != 0){
1.158 brouard 11229: printf("gnuplot command might not be in your path: '%s', err=%d\n", plotcmd, outcmd);
1.154 brouard 11230: printf("\n Trying if gnuplot resides on the same directory that IMaCh\n");
1.152 brouard 11231: sprintf(plotcmd,"%sgnuplot %s", pathimach, optionfilegnuplot);
1.150 brouard 11232: if((outcmd=system(plotcmd)) != 0)
1.153 brouard 11233: printf("\n Still a problem with gnuplot command %s, err=%d\n", plotcmd, outcmd);
1.126 brouard 11234: }
1.158 brouard 11235: printf(" Successful, please wait...");
1.126 brouard 11236: while (z[0] != 'q') {
11237: /* chdir(path); */
1.154 brouard 11238: printf("\nType e to edit results with your browser, g to graph again and q for exit: ");
1.126 brouard 11239: scanf("%s",z);
11240: /* if (z[0] == 'c') system("./imach"); */
11241: if (z[0] == 'e') {
1.158 brouard 11242: #ifdef __APPLE__
1.152 brouard 11243: sprintf(pplotcmd, "open %s", optionfilehtm);
1.157 brouard 11244: #elif __linux
11245: sprintf(pplotcmd, "xdg-open %s", optionfilehtm);
1.153 brouard 11246: #else
1.152 brouard 11247: sprintf(pplotcmd, "%s", optionfilehtm);
1.153 brouard 11248: #endif
11249: printf("Starting browser with: %s",pplotcmd);fflush(stdout);
11250: system(pplotcmd);
1.126 brouard 11251: }
11252: else if (z[0] == 'g') system(plotcmd);
11253: else if (z[0] == 'q') exit(0);
11254: }
1.227 brouard 11255: end:
1.126 brouard 11256: while (z[0] != 'q') {
1.195 brouard 11257: printf("\nType q for exiting: "); fflush(stdout);
1.126 brouard 11258: scanf("%s",z);
11259: }
11260: }
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