Annotation of imach/src/imach.c, revision 1.196
1.196 ! brouard 1: /* $Id: imach.c,v 1.195 2015/08/18 16:28:39 brouard Exp $
1.126 brouard 2: $State: Exp $
1.163 brouard 3: $Log: imach.c,v $
1.196 ! brouard 4: Revision 1.195 2015/08/18 16:28:39 brouard
! 5: Summary: Adding a hack for testing purpose
! 6:
! 7: After reading the title, ftol and model lines, if the comment line has
! 8: a q, starting with #q, the answer at the end of the run is quit. It
! 9: permits to run test files in batch with ctest. The former workaround was
! 10: $ echo q | imach foo.imach
! 11:
1.195 brouard 12: Revision 1.194 2015/08/18 13:32:00 brouard
13: Summary: Adding error when the covariance matrix doesn't contain the exact number of lines required by the model line.
14:
1.194 brouard 15: Revision 1.193 2015/08/04 07:17:42 brouard
16: Summary: 0.98q4
17:
1.193 brouard 18: Revision 1.192 2015/07/16 16:49:02 brouard
19: Summary: Fixing some outputs
20:
1.192 brouard 21: Revision 1.191 2015/07/14 10:00:33 brouard
22: Summary: Some fixes
23:
1.191 brouard 24: Revision 1.190 2015/05/05 08:51:13 brouard
25: Summary: Adding digits in output parameters (7 digits instead of 6)
26:
27: Fix 1+age+.
28:
1.190 brouard 29: Revision 1.189 2015/04/30 14:45:16 brouard
30: Summary: 0.98q2
31:
1.189 brouard 32: Revision 1.188 2015/04/30 08:27:53 brouard
33: *** empty log message ***
34:
1.188 brouard 35: Revision 1.187 2015/04/29 09:11:15 brouard
36: *** empty log message ***
37:
1.187 brouard 38: Revision 1.186 2015/04/23 12:01:52 brouard
39: Summary: V1*age is working now, version 0.98q1
40:
41: Some codes had been disabled in order to simplify and Vn*age was
42: working in the optimization phase, ie, giving correct MLE parameters,
43: but, as usual, outputs were not correct and program core dumped.
44:
1.186 brouard 45: Revision 1.185 2015/03/11 13:26:42 brouard
46: Summary: Inclusion of compile and links command line for Intel Compiler
47:
1.185 brouard 48: Revision 1.184 2015/03/11 11:52:39 brouard
49: Summary: Back from Windows 8. Intel Compiler
50:
1.184 brouard 51: Revision 1.183 2015/03/10 20:34:32 brouard
52: Summary: 0.98q0, trying with directest, mnbrak fixed
53:
54: We use directest instead of original Powell test; probably no
55: incidence on the results, but better justifications;
56: We fixed Numerical Recipes mnbrak routine which was wrong and gave
57: wrong results.
58:
1.183 brouard 59: Revision 1.182 2015/02/12 08:19:57 brouard
60: Summary: Trying to keep directest which seems simpler and more general
61: Author: Nicolas Brouard
62:
1.182 brouard 63: Revision 1.181 2015/02/11 23:22:24 brouard
64: Summary: Comments on Powell added
65:
66: Author:
67:
1.181 brouard 68: Revision 1.180 2015/02/11 17:33:45 brouard
69: Summary: Finishing move from main to function (hpijx and prevalence_limit)
70:
1.180 brouard 71: Revision 1.179 2015/01/04 09:57:06 brouard
72: Summary: back to OS/X
73:
1.179 brouard 74: Revision 1.178 2015/01/04 09:35:48 brouard
75: *** empty log message ***
76:
1.178 brouard 77: Revision 1.177 2015/01/03 18:40:56 brouard
78: Summary: Still testing ilc32 on OSX
79:
1.177 brouard 80: Revision 1.176 2015/01/03 16:45:04 brouard
81: *** empty log message ***
82:
1.176 brouard 83: Revision 1.175 2015/01/03 16:33:42 brouard
84: *** empty log message ***
85:
1.175 brouard 86: Revision 1.174 2015/01/03 16:15:49 brouard
87: Summary: Still in cross-compilation
88:
1.174 brouard 89: Revision 1.173 2015/01/03 12:06:26 brouard
90: Summary: trying to detect cross-compilation
91:
1.173 brouard 92: Revision 1.172 2014/12/27 12:07:47 brouard
93: Summary: Back from Visual Studio and Intel, options for compiling for Windows XP
94:
1.172 brouard 95: Revision 1.171 2014/12/23 13:26:59 brouard
96: Summary: Back from Visual C
97:
98: Still problem with utsname.h on Windows
99:
1.171 brouard 100: Revision 1.170 2014/12/23 11:17:12 brouard
101: Summary: Cleaning some \%% back to %%
102:
103: The escape was mandatory for a specific compiler (which one?), but too many warnings.
104:
1.170 brouard 105: Revision 1.169 2014/12/22 23:08:31 brouard
106: Summary: 0.98p
107:
108: Outputs some informations on compiler used, OS etc. Testing on different platforms.
109:
1.169 brouard 110: Revision 1.168 2014/12/22 15:17:42 brouard
1.170 brouard 111: Summary: update
1.169 brouard 112:
1.168 brouard 113: Revision 1.167 2014/12/22 13:50:56 brouard
114: Summary: Testing uname and compiler version and if compiled 32 or 64
115:
116: Testing on Linux 64
117:
1.167 brouard 118: Revision 1.166 2014/12/22 11:40:47 brouard
119: *** empty log message ***
120:
1.166 brouard 121: Revision 1.165 2014/12/16 11:20:36 brouard
122: Summary: After compiling on Visual C
123:
124: * imach.c (Module): Merging 1.61 to 1.162
125:
1.165 brouard 126: Revision 1.164 2014/12/16 10:52:11 brouard
127: Summary: Merging with Visual C after suppressing some warnings for unused variables. Also fixing Saito's bug 0.98Xn
128:
129: * imach.c (Module): Merging 1.61 to 1.162
130:
1.164 brouard 131: Revision 1.163 2014/12/16 10:30:11 brouard
132: * imach.c (Module): Merging 1.61 to 1.162
133:
1.163 brouard 134: Revision 1.162 2014/09/25 11:43:39 brouard
135: Summary: temporary backup 0.99!
136:
1.162 brouard 137: Revision 1.1 2014/09/16 11:06:58 brouard
138: Summary: With some code (wrong) for nlopt
139:
140: Author:
141:
142: Revision 1.161 2014/09/15 20:41:41 brouard
143: Summary: Problem with macro SQR on Intel compiler
144:
1.161 brouard 145: Revision 1.160 2014/09/02 09:24:05 brouard
146: *** empty log message ***
147:
1.160 brouard 148: Revision 1.159 2014/09/01 10:34:10 brouard
149: Summary: WIN32
150: Author: Brouard
151:
1.159 brouard 152: Revision 1.158 2014/08/27 17:11:51 brouard
153: *** empty log message ***
154:
1.158 brouard 155: Revision 1.157 2014/08/27 16:26:55 brouard
156: Summary: Preparing windows Visual studio version
157: Author: Brouard
158:
159: In order to compile on Visual studio, time.h is now correct and time_t
160: and tm struct should be used. difftime should be used but sometimes I
161: just make the differences in raw time format (time(&now).
162: Trying to suppress #ifdef LINUX
163: Add xdg-open for __linux in order to open default browser.
164:
1.157 brouard 165: Revision 1.156 2014/08/25 20:10:10 brouard
166: *** empty log message ***
167:
1.156 brouard 168: Revision 1.155 2014/08/25 18:32:34 brouard
169: Summary: New compile, minor changes
170: Author: Brouard
171:
1.155 brouard 172: Revision 1.154 2014/06/20 17:32:08 brouard
173: Summary: Outputs now all graphs of convergence to period prevalence
174:
1.154 brouard 175: Revision 1.153 2014/06/20 16:45:46 brouard
176: Summary: If 3 live state, convergence to period prevalence on same graph
177: Author: Brouard
178:
1.153 brouard 179: Revision 1.152 2014/06/18 17:54:09 brouard
180: Summary: open browser, use gnuplot on same dir than imach if not found in the path
181:
1.152 brouard 182: Revision 1.151 2014/06/18 16:43:30 brouard
183: *** empty log message ***
184:
1.151 brouard 185: Revision 1.150 2014/06/18 16:42:35 brouard
186: Summary: If gnuplot is not in the path try on same directory than imach binary (OSX)
187: Author: brouard
188:
1.150 brouard 189: Revision 1.149 2014/06/18 15:51:14 brouard
190: Summary: Some fixes in parameter files errors
191: Author: Nicolas Brouard
192:
1.149 brouard 193: Revision 1.148 2014/06/17 17:38:48 brouard
194: Summary: Nothing new
195: Author: Brouard
196:
197: Just a new packaging for OS/X version 0.98nS
198:
1.148 brouard 199: Revision 1.147 2014/06/16 10:33:11 brouard
200: *** empty log message ***
201:
1.147 brouard 202: Revision 1.146 2014/06/16 10:20:28 brouard
203: Summary: Merge
204: Author: Brouard
205:
206: Merge, before building revised version.
207:
1.146 brouard 208: Revision 1.145 2014/06/10 21:23:15 brouard
209: Summary: Debugging with valgrind
210: Author: Nicolas Brouard
211:
212: Lot of changes in order to output the results with some covariates
213: After the Edimburgh REVES conference 2014, it seems mandatory to
214: improve the code.
215: No more memory valgrind error but a lot has to be done in order to
216: continue the work of splitting the code into subroutines.
217: Also, decodemodel has been improved. Tricode is still not
218: optimal. nbcode should be improved. Documentation has been added in
219: the source code.
220:
1.144 brouard 221: Revision 1.143 2014/01/26 09:45:38 brouard
222: Summary: Version 0.98nR (to be improved, but gives same optimization results as 0.98k. Nice, promising
223:
224: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
225: (Module): Version 0.98nR Running ok, but output format still only works for three covariates.
226:
1.143 brouard 227: Revision 1.142 2014/01/26 03:57:36 brouard
228: Summary: gnuplot changed plot w l 1 has to be changed to plot w l lt 2
229:
230: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
231:
1.142 brouard 232: Revision 1.141 2014/01/26 02:42:01 brouard
233: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
234:
1.141 brouard 235: Revision 1.140 2011/09/02 10:37:54 brouard
236: Summary: times.h is ok with mingw32 now.
237:
1.140 brouard 238: Revision 1.139 2010/06/14 07:50:17 brouard
239: After the theft of my laptop, I probably lost some lines of codes which were not uploaded to the CVS tree.
240: I remember having already fixed agemin agemax which are pointers now but not cvs saved.
241:
1.139 brouard 242: Revision 1.138 2010/04/30 18:19:40 brouard
243: *** empty log message ***
244:
1.138 brouard 245: Revision 1.137 2010/04/29 18:11:38 brouard
246: (Module): Checking covariates for more complex models
247: than V1+V2. A lot of change to be done. Unstable.
248:
1.137 brouard 249: Revision 1.136 2010/04/26 20:30:53 brouard
250: (Module): merging some libgsl code. Fixing computation
251: of likelione (using inter/intrapolation if mle = 0) in order to
252: get same likelihood as if mle=1.
253: Some cleaning of code and comments added.
254:
1.136 brouard 255: Revision 1.135 2009/10/29 15:33:14 brouard
256: (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
257:
1.135 brouard 258: Revision 1.134 2009/10/29 13:18:53 brouard
259: (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
260:
1.134 brouard 261: Revision 1.133 2009/07/06 10:21:25 brouard
262: just nforces
263:
1.133 brouard 264: Revision 1.132 2009/07/06 08:22:05 brouard
265: Many tings
266:
1.132 brouard 267: Revision 1.131 2009/06/20 16:22:47 brouard
268: Some dimensions resccaled
269:
1.131 brouard 270: Revision 1.130 2009/05/26 06:44:34 brouard
271: (Module): Max Covariate is now set to 20 instead of 8. A
272: lot of cleaning with variables initialized to 0. Trying to make
273: V2+V3*age+V1+V4 strb=V3*age+V1+V4 working better.
274:
1.130 brouard 275: Revision 1.129 2007/08/31 13:49:27 lievre
276: Modification of the way of exiting when the covariate is not binary in order to see on the window the error message before exiting
277:
1.129 lievre 278: Revision 1.128 2006/06/30 13:02:05 brouard
279: (Module): Clarifications on computing e.j
280:
1.128 brouard 281: Revision 1.127 2006/04/28 18:11:50 brouard
282: (Module): Yes the sum of survivors was wrong since
283: imach-114 because nhstepm was no more computed in the age
284: loop. Now we define nhstepma in the age loop.
285: (Module): In order to speed up (in case of numerous covariates) we
286: compute health expectancies (without variances) in a first step
287: and then all the health expectancies with variances or standard
288: deviation (needs data from the Hessian matrices) which slows the
289: computation.
290: In the future we should be able to stop the program is only health
291: expectancies and graph are needed without standard deviations.
292:
1.127 brouard 293: Revision 1.126 2006/04/28 17:23:28 brouard
294: (Module): Yes the sum of survivors was wrong since
295: imach-114 because nhstepm was no more computed in the age
296: loop. Now we define nhstepma in the age loop.
297: Version 0.98h
298:
1.126 brouard 299: Revision 1.125 2006/04/04 15:20:31 lievre
300: Errors in calculation of health expectancies. Age was not initialized.
301: Forecasting file added.
302:
303: Revision 1.124 2006/03/22 17:13:53 lievre
304: Parameters are printed with %lf instead of %f (more numbers after the comma).
305: The log-likelihood is printed in the log file
306:
307: Revision 1.123 2006/03/20 10:52:43 brouard
308: * imach.c (Module): <title> changed, corresponds to .htm file
309: name. <head> headers where missing.
310:
311: * imach.c (Module): Weights can have a decimal point as for
312: English (a comma might work with a correct LC_NUMERIC environment,
313: otherwise the weight is truncated).
314: Modification of warning when the covariates values are not 0 or
315: 1.
316: Version 0.98g
317:
318: Revision 1.122 2006/03/20 09:45:41 brouard
319: (Module): Weights can have a decimal point as for
320: English (a comma might work with a correct LC_NUMERIC environment,
321: otherwise the weight is truncated).
322: Modification of warning when the covariates values are not 0 or
323: 1.
324: Version 0.98g
325:
326: Revision 1.121 2006/03/16 17:45:01 lievre
327: * imach.c (Module): Comments concerning covariates added
328:
329: * imach.c (Module): refinements in the computation of lli if
330: status=-2 in order to have more reliable computation if stepm is
331: not 1 month. Version 0.98f
332:
333: Revision 1.120 2006/03/16 15:10:38 lievre
334: (Module): refinements in the computation of lli if
335: status=-2 in order to have more reliable computation if stepm is
336: not 1 month. Version 0.98f
337:
338: Revision 1.119 2006/03/15 17:42:26 brouard
339: (Module): Bug if status = -2, the loglikelihood was
340: computed as likelihood omitting the logarithm. Version O.98e
341:
342: Revision 1.118 2006/03/14 18:20:07 brouard
343: (Module): varevsij Comments added explaining the second
344: table of variances if popbased=1 .
345: (Module): Covariances of eij, ekl added, graphs fixed, new html link.
346: (Module): Function pstamp added
347: (Module): Version 0.98d
348:
349: Revision 1.117 2006/03/14 17:16:22 brouard
350: (Module): varevsij Comments added explaining the second
351: table of variances if popbased=1 .
352: (Module): Covariances of eij, ekl added, graphs fixed, new html link.
353: (Module): Function pstamp added
354: (Module): Version 0.98d
355:
356: Revision 1.116 2006/03/06 10:29:27 brouard
357: (Module): Variance-covariance wrong links and
358: varian-covariance of ej. is needed (Saito).
359:
360: Revision 1.115 2006/02/27 12:17:45 brouard
361: (Module): One freematrix added in mlikeli! 0.98c
362:
363: Revision 1.114 2006/02/26 12:57:58 brouard
364: (Module): Some improvements in processing parameter
365: filename with strsep.
366:
367: Revision 1.113 2006/02/24 14:20:24 brouard
368: (Module): Memory leaks checks with valgrind and:
369: datafile was not closed, some imatrix were not freed and on matrix
370: allocation too.
371:
372: Revision 1.112 2006/01/30 09:55:26 brouard
373: (Module): Back to gnuplot.exe instead of wgnuplot.exe
374:
375: Revision 1.111 2006/01/25 20:38:18 brouard
376: (Module): Lots of cleaning and bugs added (Gompertz)
377: (Module): Comments can be added in data file. Missing date values
378: can be a simple dot '.'.
379:
380: Revision 1.110 2006/01/25 00:51:50 brouard
381: (Module): Lots of cleaning and bugs added (Gompertz)
382:
383: Revision 1.109 2006/01/24 19:37:15 brouard
384: (Module): Comments (lines starting with a #) are allowed in data.
385:
386: Revision 1.108 2006/01/19 18:05:42 lievre
387: Gnuplot problem appeared...
388: To be fixed
389:
390: Revision 1.107 2006/01/19 16:20:37 brouard
391: Test existence of gnuplot in imach path
392:
393: Revision 1.106 2006/01/19 13:24:36 brouard
394: Some cleaning and links added in html output
395:
396: Revision 1.105 2006/01/05 20:23:19 lievre
397: *** empty log message ***
398:
399: Revision 1.104 2005/09/30 16:11:43 lievre
400: (Module): sump fixed, loop imx fixed, and simplifications.
401: (Module): If the status is missing at the last wave but we know
402: that the person is alive, then we can code his/her status as -2
403: (instead of missing=-1 in earlier versions) and his/her
404: contributions to the likelihood is 1 - Prob of dying from last
405: health status (= 1-p13= p11+p12 in the easiest case of somebody in
406: the healthy state at last known wave). Version is 0.98
407:
408: Revision 1.103 2005/09/30 15:54:49 lievre
409: (Module): sump fixed, loop imx fixed, and simplifications.
410:
411: Revision 1.102 2004/09/15 17:31:30 brouard
412: Add the possibility to read data file including tab characters.
413:
414: Revision 1.101 2004/09/15 10:38:38 brouard
415: Fix on curr_time
416:
417: Revision 1.100 2004/07/12 18:29:06 brouard
418: Add version for Mac OS X. Just define UNIX in Makefile
419:
420: Revision 1.99 2004/06/05 08:57:40 brouard
421: *** empty log message ***
422:
423: Revision 1.98 2004/05/16 15:05:56 brouard
424: New version 0.97 . First attempt to estimate force of mortality
425: directly from the data i.e. without the need of knowing the health
426: state at each age, but using a Gompertz model: log u =a + b*age .
427: This is the basic analysis of mortality and should be done before any
428: other analysis, in order to test if the mortality estimated from the
429: cross-longitudinal survey is different from the mortality estimated
430: from other sources like vital statistic data.
431:
432: The same imach parameter file can be used but the option for mle should be -3.
433:
1.133 brouard 434: Agnès, who wrote this part of the code, tried to keep most of the
1.126 brouard 435: former routines in order to include the new code within the former code.
436:
437: The output is very simple: only an estimate of the intercept and of
438: the slope with 95% confident intervals.
439:
440: Current limitations:
441: A) Even if you enter covariates, i.e. with the
442: model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
443: B) There is no computation of Life Expectancy nor Life Table.
444:
445: Revision 1.97 2004/02/20 13:25:42 lievre
446: Version 0.96d. Population forecasting command line is (temporarily)
447: suppressed.
448:
449: Revision 1.96 2003/07/15 15:38:55 brouard
450: * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
451: rewritten within the same printf. Workaround: many printfs.
452:
453: Revision 1.95 2003/07/08 07:54:34 brouard
454: * imach.c (Repository):
455: (Repository): Using imachwizard code to output a more meaningful covariance
456: matrix (cov(a12,c31) instead of numbers.
457:
458: Revision 1.94 2003/06/27 13:00:02 brouard
459: Just cleaning
460:
461: Revision 1.93 2003/06/25 16:33:55 brouard
462: (Module): On windows (cygwin) function asctime_r doesn't
463: exist so I changed back to asctime which exists.
464: (Module): Version 0.96b
465:
466: Revision 1.92 2003/06/25 16:30:45 brouard
467: (Module): On windows (cygwin) function asctime_r doesn't
468: exist so I changed back to asctime which exists.
469:
470: Revision 1.91 2003/06/25 15:30:29 brouard
471: * imach.c (Repository): Duplicated warning errors corrected.
472: (Repository): Elapsed time after each iteration is now output. It
473: helps to forecast when convergence will be reached. Elapsed time
474: is stamped in powell. We created a new html file for the graphs
475: concerning matrix of covariance. It has extension -cov.htm.
476:
477: Revision 1.90 2003/06/24 12:34:15 brouard
478: (Module): Some bugs corrected for windows. Also, when
479: mle=-1 a template is output in file "or"mypar.txt with the design
480: of the covariance matrix to be input.
481:
482: Revision 1.89 2003/06/24 12:30:52 brouard
483: (Module): Some bugs corrected for windows. Also, when
484: mle=-1 a template is output in file "or"mypar.txt with the design
485: of the covariance matrix to be input.
486:
487: Revision 1.88 2003/06/23 17:54:56 brouard
488: * 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.
489:
490: Revision 1.87 2003/06/18 12:26:01 brouard
491: Version 0.96
492:
493: Revision 1.86 2003/06/17 20:04:08 brouard
494: (Module): Change position of html and gnuplot routines and added
495: routine fileappend.
496:
497: Revision 1.85 2003/06/17 13:12:43 brouard
498: * imach.c (Repository): Check when date of death was earlier that
499: current date of interview. It may happen when the death was just
500: prior to the death. In this case, dh was negative and likelihood
501: was wrong (infinity). We still send an "Error" but patch by
502: assuming that the date of death was just one stepm after the
503: interview.
504: (Repository): Because some people have very long ID (first column)
505: we changed int to long in num[] and we added a new lvector for
506: memory allocation. But we also truncated to 8 characters (left
507: truncation)
508: (Repository): No more line truncation errors.
509:
510: Revision 1.84 2003/06/13 21:44:43 brouard
511: * imach.c (Repository): Replace "freqsummary" at a correct
512: place. It differs from routine "prevalence" which may be called
513: many times. Probs is memory consuming and must be used with
514: parcimony.
515: Version 0.95a3 (should output exactly the same maximization than 0.8a2)
516:
517: Revision 1.83 2003/06/10 13:39:11 lievre
518: *** empty log message ***
519:
520: Revision 1.82 2003/06/05 15:57:20 brouard
521: Add log in imach.c and fullversion number is now printed.
522:
523: */
524: /*
525: Interpolated Markov Chain
526:
527: Short summary of the programme:
528:
529: This program computes Healthy Life Expectancies from
530: cross-longitudinal data. Cross-longitudinal data consist in: -1- a
531: first survey ("cross") where individuals from different ages are
532: interviewed on their health status or degree of disability (in the
533: case of a health survey which is our main interest) -2- at least a
534: second wave of interviews ("longitudinal") which measure each change
535: (if any) in individual health status. Health expectancies are
536: computed from the time spent in each health state according to a
537: model. More health states you consider, more time is necessary to reach the
538: Maximum Likelihood of the parameters involved in the model. The
539: simplest model is the multinomial logistic model where pij is the
540: probability to be observed in state j at the second wave
541: conditional to be observed in state i at the first wave. Therefore
542: the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
543: 'age' is age and 'sex' is a covariate. If you want to have a more
544: complex model than "constant and age", you should modify the program
545: where the markup *Covariates have to be included here again* invites
546: you to do it. More covariates you add, slower the
547: convergence.
548:
549: The advantage of this computer programme, compared to a simple
550: multinomial logistic model, is clear when the delay between waves is not
551: identical for each individual. Also, if a individual missed an
552: intermediate interview, the information is lost, but taken into
553: account using an interpolation or extrapolation.
554:
555: hPijx is the probability to be observed in state i at age x+h
556: conditional to the observed state i at age x. The delay 'h' can be
557: split into an exact number (nh*stepm) of unobserved intermediate
558: states. This elementary transition (by month, quarter,
559: semester or year) is modelled as a multinomial logistic. The hPx
560: matrix is simply the matrix product of nh*stepm elementary matrices
561: and the contribution of each individual to the likelihood is simply
562: hPijx.
563:
564: Also this programme outputs the covariance matrix of the parameters but also
565: of the life expectancies. It also computes the period (stable) prevalence.
566:
1.133 brouard 567: Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
568: Institut national d'études démographiques, Paris.
1.126 brouard 569: This software have been partly granted by Euro-REVES, a concerted action
570: from the European Union.
571: It is copyrighted identically to a GNU software product, ie programme and
572: software can be distributed freely for non commercial use. Latest version
573: can be accessed at http://euroreves.ined.fr/imach .
574:
575: Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
576: or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
577:
578: **********************************************************************/
579: /*
580: main
581: read parameterfile
582: read datafile
583: concatwav
584: freqsummary
585: if (mle >= 1)
586: mlikeli
587: print results files
588: if mle==1
589: computes hessian
590: read end of parameter file: agemin, agemax, bage, fage, estepm
591: begin-prev-date,...
592: open gnuplot file
593: open html file
1.145 brouard 594: period (stable) prevalence | pl_nom 1-1 2-2 etc by covariate
595: for age prevalim() | #****** V1=0 V2=1 V3=1 V4=0 ******
596: | 65 1 0 2 1 3 1 4 0 0.96326 0.03674
597: freexexit2 possible for memory heap.
598:
599: h Pij x | pij_nom ficrestpij
600: # Cov Agex agex+h hpijx with i,j= 1-1 1-2 1-3 2-1 2-2 2-3
601: 1 85 85 1.00000 0.00000 0.00000 0.00000 1.00000 0.00000
602: 1 85 86 0.68299 0.22291 0.09410 0.71093 0.00000 0.28907
603:
604: 1 65 99 0.00364 0.00322 0.99314 0.00350 0.00310 0.99340
605: 1 65 100 0.00214 0.00204 0.99581 0.00206 0.00196 0.99597
606: variance of p one-step probabilities varprob | prob_nom ficresprob #One-step probabilities and stand. devi in ()
607: Standard deviation of one-step probabilities | probcor_nom ficresprobcor #One-step probabilities and correlation matrix
608: Matrix of variance covariance of one-step probabilities | probcov_nom ficresprobcov #One-step probabilities and covariance matrix
609:
1.126 brouard 610: forecasting if prevfcast==1 prevforecast call prevalence()
611: health expectancies
612: Variance-covariance of DFLE
613: prevalence()
614: movingaverage()
615: varevsij()
616: if popbased==1 varevsij(,popbased)
617: total life expectancies
618: Variance of period (stable) prevalence
619: end
620: */
621:
1.187 brouard 622: /* #define DEBUG */
623: /* #define DEBUGBRENT */
1.165 brouard 624: #define POWELL /* Instead of NLOPT */
1.192 brouard 625: #define POWELLF1F3 /* Skip test */
1.186 brouard 626: /* #define POWELLORIGINAL /\* Don't use Directest to decide new direction but original Powell test *\/ */
627: /* #define MNBRAKORIGINAL /\* Don't use mnbrak fix *\/ */
1.126 brouard 628:
629: #include <math.h>
630: #include <stdio.h>
631: #include <stdlib.h>
632: #include <string.h>
1.159 brouard 633:
634: #ifdef _WIN32
635: #include <io.h>
1.172 brouard 636: #include <windows.h>
637: #include <tchar.h>
1.159 brouard 638: #else
1.126 brouard 639: #include <unistd.h>
1.159 brouard 640: #endif
1.126 brouard 641:
642: #include <limits.h>
643: #include <sys/types.h>
1.171 brouard 644:
645: #if defined(__GNUC__)
646: #include <sys/utsname.h> /* Doesn't work on Windows */
647: #endif
648:
1.126 brouard 649: #include <sys/stat.h>
650: #include <errno.h>
1.159 brouard 651: /* extern int errno; */
1.126 brouard 652:
1.157 brouard 653: /* #ifdef LINUX */
654: /* #include <time.h> */
655: /* #include "timeval.h" */
656: /* #else */
657: /* #include <sys/time.h> */
658: /* #endif */
659:
1.126 brouard 660: #include <time.h>
661:
1.136 brouard 662: #ifdef GSL
663: #include <gsl/gsl_errno.h>
664: #include <gsl/gsl_multimin.h>
665: #endif
666:
1.167 brouard 667:
1.162 brouard 668: #ifdef NLOPT
669: #include <nlopt.h>
670: typedef struct {
671: double (* function)(double [] );
672: } myfunc_data ;
673: #endif
674:
1.126 brouard 675: /* #include <libintl.h> */
676: /* #define _(String) gettext (String) */
677:
1.141 brouard 678: #define MAXLINE 1024 /* Was 256. Overflow with 312 with 2 states and 4 covariates. Should be ok */
1.126 brouard 679:
680: #define GNUPLOTPROGRAM "gnuplot"
681: /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
682: #define FILENAMELENGTH 132
683:
684: #define GLOCK_ERROR_NOPATH -1 /* empty path */
685: #define GLOCK_ERROR_GETCWD -2 /* cannot get cwd */
686:
1.144 brouard 687: #define MAXPARM 128 /**< Maximum number of parameters for the optimization */
688: #define NPARMAX 64 /**< (nlstate+ndeath-1)*nlstate*ncovmodel */
1.126 brouard 689:
690: #define NINTERVMAX 8
1.144 brouard 691: #define NLSTATEMAX 8 /**< Maximum number of live states (for func) */
692: #define NDEATHMAX 8 /**< Maximum number of dead states (for func) */
693: #define NCOVMAX 20 /**< Maximum number of covariates, including generated covariates V1*V2 */
1.145 brouard 694: #define codtabm(h,k) 1 & (h-1) >> (k-1) ;
1.126 brouard 695: #define MAXN 20000
1.144 brouard 696: #define YEARM 12. /**< Number of months per year */
1.126 brouard 697: #define AGESUP 130
698: #define AGEBASE 40
1.194 brouard 699: #define AGEOVERFLOW 1.e20
1.164 brouard 700: #define AGEGOMP 10 /**< Minimal age for Gompertz adjustment */
1.157 brouard 701: #ifdef _WIN32
702: #define DIRSEPARATOR '\\'
703: #define CHARSEPARATOR "\\"
704: #define ODIRSEPARATOR '/'
705: #else
1.126 brouard 706: #define DIRSEPARATOR '/'
707: #define CHARSEPARATOR "/"
708: #define ODIRSEPARATOR '\\'
709: #endif
710:
1.196 ! brouard 711: /* $Id: imach.c,v 1.195 2015/08/18 16:28:39 brouard Exp $ */
1.126 brouard 712: /* $State: Exp $ */
1.196 ! brouard 713: #include "version.h"
! 714: char version[]=__IMACH_VERSION__;
! 715: char copyright[]="August 2015,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121), Intel Software 2015";
! 716: char fullversion[]="$Revision: 1.195 $ $Date: 2015/08/18 16:28:39 $";
1.126 brouard 717: char strstart[80];
718: char optionfilext[10], optionfilefiname[FILENAMELENGTH];
1.130 brouard 719: int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings */
1.187 brouard 720: int nagesqr=0, nforce=0; /* nagesqr=1 if model is including age*age, number of forces */
1.145 brouard 721: /* Number of covariates model=V2+V1+ V3*age+V2*V4 */
722: int cptcovn=0; /**< cptcovn number of covariates added in the model (excepting constant and age and age*product) */
723: int cptcovt=0; /**< cptcovt number of covariates added in the model (excepting constant and age) */
724: int cptcovs=0; /**< cptcovs number of simple covariates V2+V1 =2 */
725: int cptcovage=0; /**< Number of covariates with age: V3*age only =1 */
726: int cptcovprodnoage=0; /**< Number of covariate products without age */
727: int cptcoveff=0; /* Total number of covariates to vary for printing results */
728: int cptcov=0; /* Working variable */
1.126 brouard 729: int npar=NPARMAX;
730: int nlstate=2; /* Number of live states */
731: int ndeath=1; /* Number of dead states */
1.130 brouard 732: int ncovmodel=0, ncovcol=0; /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
1.126 brouard 733: int popbased=0;
734:
735: int *wav; /* Number of waves for this individuual 0 is possible */
1.130 brouard 736: int maxwav=0; /* Maxim number of waves */
737: int jmin=0, jmax=0; /* min, max spacing between 2 waves */
738: int ijmin=0, ijmax=0; /* Individuals having jmin and jmax */
739: int gipmx=0, gsw=0; /* Global variables on the number of contributions
1.126 brouard 740: to the likelihood and the sum of weights (done by funcone)*/
1.130 brouard 741: int mle=1, weightopt=0;
1.126 brouard 742: int **mw; /* mw[mi][i] is number of the mi wave for this individual */
743: int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
744: int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
745: * wave mi and wave mi+1 is not an exact multiple of stepm. */
1.162 brouard 746: int countcallfunc=0; /* Count the number of calls to func */
1.130 brouard 747: double jmean=1; /* Mean space between 2 waves */
1.145 brouard 748: double **matprod2(); /* test */
1.126 brouard 749: double **oldm, **newm, **savm; /* Working pointers to matrices */
750: double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
1.136 brouard 751: /*FILE *fic ; */ /* Used in readdata only */
752: FILE *ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
1.126 brouard 753: FILE *ficlog, *ficrespow;
1.130 brouard 754: int globpr=0; /* Global variable for printing or not */
1.126 brouard 755: double fretone; /* Only one call to likelihood */
1.130 brouard 756: long ipmx=0; /* Number of contributions */
1.126 brouard 757: double sw; /* Sum of weights */
758: char filerespow[FILENAMELENGTH];
759: char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
760: FILE *ficresilk;
761: FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
762: FILE *ficresprobmorprev;
763: FILE *fichtm, *fichtmcov; /* Html File */
764: FILE *ficreseij;
765: char filerese[FILENAMELENGTH];
766: FILE *ficresstdeij;
767: char fileresstde[FILENAMELENGTH];
768: FILE *ficrescveij;
769: char filerescve[FILENAMELENGTH];
770: FILE *ficresvij;
771: char fileresv[FILENAMELENGTH];
772: FILE *ficresvpl;
773: char fileresvpl[FILENAMELENGTH];
774: char title[MAXLINE];
775: char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH], filerespl[FILENAMELENGTH];
776: char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
777: char tmpout[FILENAMELENGTH], tmpout2[FILENAMELENGTH];
778: char command[FILENAMELENGTH];
779: int outcmd=0;
780:
781: char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
782:
783: char filelog[FILENAMELENGTH]; /* Log file */
784: char filerest[FILENAMELENGTH];
785: char fileregp[FILENAMELENGTH];
786: char popfile[FILENAMELENGTH];
787:
788: char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
789:
1.157 brouard 790: /* struct timeval start_time, end_time, curr_time, last_time, forecast_time; */
791: /* struct timezone tzp; */
792: /* extern int gettimeofday(); */
793: struct tm tml, *gmtime(), *localtime();
794:
795: extern time_t time();
796:
797: struct tm start_time, end_time, curr_time, last_time, forecast_time;
798: time_t rstart_time, rend_time, rcurr_time, rlast_time, rforecast_time; /* raw time */
799: struct tm tm;
800:
1.126 brouard 801: char strcurr[80], strfor[80];
802:
803: char *endptr;
804: long lval;
805: double dval;
806:
807: #define NR_END 1
808: #define FREE_ARG char*
809: #define FTOL 1.0e-10
810:
811: #define NRANSI
812: #define ITMAX 200
813:
814: #define TOL 2.0e-4
815:
816: #define CGOLD 0.3819660
817: #define ZEPS 1.0e-10
818: #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);
819:
820: #define GOLD 1.618034
821: #define GLIMIT 100.0
822: #define TINY 1.0e-20
823:
824: static double maxarg1,maxarg2;
825: #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
826: #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
827:
828: #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
829: #define rint(a) floor(a+0.5)
1.166 brouard 830: /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/myutils_8h-source.html */
1.183 brouard 831: #define mytinydouble 1.0e-16
1.166 brouard 832: /* #define DEQUAL(a,b) (fabs((a)-(b))<mytinydouble) */
833: /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/mynrutils_8h-source.html */
834: /* static double dsqrarg; */
835: /* #define DSQR(a) (DEQUAL((dsqrarg=(a)),0.0) ? 0.0 : dsqrarg*dsqrarg) */
1.126 brouard 836: static double sqrarg;
837: #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
838: #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}
839: int agegomp= AGEGOMP;
840:
841: int imx;
842: int stepm=1;
843: /* Stepm, step in month: minimum step interpolation*/
844:
845: int estepm;
846: /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
847:
848: int m,nb;
849: long *num;
1.192 brouard 850: int firstpass=0, lastpass=4,*cod, *Tage,*cens;
851: int *ncodemax; /* ncodemax[j]= Number of modalities of the j th
852: covariate for which somebody answered excluding
853: undefined. Usually 2: 0 and 1. */
854: int *ncodemaxwundef; /* ncodemax[j]= Number of modalities of the j th
855: covariate for which somebody answered including
856: undefined. Usually 3: -1, 0 and 1. */
1.126 brouard 857: double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
858: double **pmmij, ***probs;
859: double *ageexmed,*agecens;
860: double dateintmean=0;
861:
862: double *weight;
863: int **s; /* Status */
1.141 brouard 864: double *agedc;
1.145 brouard 865: double **covar; /**< covar[j,i], value of jth covariate for individual i,
1.141 brouard 866: * covar=matrix(0,NCOVMAX,1,n);
1.187 brouard 867: * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*age; */
1.141 brouard 868: double idx;
869: int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */
1.145 brouard 870: int *Ndum; /** Freq of modality (tricode */
1.141 brouard 871: int **codtab; /**< codtab=imatrix(1,100,1,10); */
872: int **Tvard, *Tprod, cptcovprod, *Tvaraff;
1.126 brouard 873: double *lsurv, *lpop, *tpop;
874:
1.143 brouard 875: double ftol=FTOL; /**< Tolerance for computing Max Likelihood */
876: double ftolhess; /**< Tolerance for computing hessian */
1.126 brouard 877:
878: /**************** split *************************/
879: static int split( char *path, char *dirc, char *name, char *ext, char *finame )
880: {
881: /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
882: the name of the file (name), its extension only (ext) and its first part of the name (finame)
883: */
884: char *ss; /* pointer */
1.186 brouard 885: int l1=0, l2=0; /* length counters */
1.126 brouard 886:
887: l1 = strlen(path ); /* length of path */
888: if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
889: ss= strrchr( path, DIRSEPARATOR ); /* find last / */
890: if ( ss == NULL ) { /* no directory, so determine current directory */
891: strcpy( name, path ); /* we got the fullname name because no directory */
892: /*if(strrchr(path, ODIRSEPARATOR )==NULL)
893: printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
894: /* get current working directory */
895: /* extern char* getcwd ( char *buf , int len);*/
1.184 brouard 896: #ifdef WIN32
897: if (_getcwd( dirc, FILENAME_MAX ) == NULL ) {
898: #else
899: if (getcwd(dirc, FILENAME_MAX) == NULL) {
900: #endif
1.126 brouard 901: return( GLOCK_ERROR_GETCWD );
902: }
903: /* got dirc from getcwd*/
904: printf(" DIRC = %s \n",dirc);
905: } else { /* strip direcotry from path */
906: ss++; /* after this, the filename */
907: l2 = strlen( ss ); /* length of filename */
908: if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
909: strcpy( name, ss ); /* save file name */
910: strncpy( dirc, path, l1 - l2 ); /* now the directory */
1.186 brouard 911: dirc[l1-l2] = '\0'; /* add zero */
1.126 brouard 912: printf(" DIRC2 = %s \n",dirc);
913: }
914: /* We add a separator at the end of dirc if not exists */
915: l1 = strlen( dirc ); /* length of directory */
916: if( dirc[l1-1] != DIRSEPARATOR ){
917: dirc[l1] = DIRSEPARATOR;
918: dirc[l1+1] = 0;
919: printf(" DIRC3 = %s \n",dirc);
920: }
921: ss = strrchr( name, '.' ); /* find last / */
922: if (ss >0){
923: ss++;
924: strcpy(ext,ss); /* save extension */
925: l1= strlen( name);
926: l2= strlen(ss)+1;
927: strncpy( finame, name, l1-l2);
928: finame[l1-l2]= 0;
929: }
930:
931: return( 0 ); /* we're done */
932: }
933:
934:
935: /******************************************/
936:
937: void replace_back_to_slash(char *s, char*t)
938: {
939: int i;
940: int lg=0;
941: i=0;
942: lg=strlen(t);
943: for(i=0; i<= lg; i++) {
944: (s[i] = t[i]);
945: if (t[i]== '\\') s[i]='/';
946: }
947: }
948:
1.132 brouard 949: char *trimbb(char *out, char *in)
1.137 brouard 950: { /* Trim multiple blanks in line but keeps first blanks if line starts with blanks */
1.132 brouard 951: char *s;
952: s=out;
953: while (*in != '\0'){
1.137 brouard 954: while( *in == ' ' && *(in+1) == ' '){ /* && *(in+1) != '\0'){*/
1.132 brouard 955: in++;
956: }
957: *out++ = *in++;
958: }
959: *out='\0';
960: return s;
961: }
962:
1.187 brouard 963: /* char *substrchaine(char *out, char *in, char *chain) */
964: /* { */
965: /* /\* Substract chain 'chain' from 'in', return and output 'out' *\/ */
966: /* char *s, *t; */
967: /* t=in;s=out; */
968: /* while ((*in != *chain) && (*in != '\0')){ */
969: /* *out++ = *in++; */
970: /* } */
971:
972: /* /\* *in matches *chain *\/ */
973: /* while ((*in++ == *chain++) && (*in != '\0')){ */
974: /* printf("*in = %c, *out= %c *chain= %c \n", *in, *out, *chain); */
975: /* } */
976: /* in--; chain--; */
977: /* while ( (*in != '\0')){ */
978: /* printf("Bef *in = %c, *out= %c *chain= %c \n", *in, *out, *chain); */
979: /* *out++ = *in++; */
980: /* printf("Aft *in = %c, *out= %c *chain= %c \n", *in, *out, *chain); */
981: /* } */
982: /* *out='\0'; */
983: /* out=s; */
984: /* return out; */
985: /* } */
986: char *substrchaine(char *out, char *in, char *chain)
987: {
988: /* Substract chain 'chain' from 'in', return and output 'out' */
989: /* in="V1+V1*age+age*age+V2", chain="age*age" */
990:
991: char *strloc;
992:
993: strcpy (out, in);
994: strloc = strstr(out, chain); /* strloc points to out at age*age+V2 */
995: printf("Bef strloc=%s chain=%s out=%s \n", strloc, chain, out);
996: if(strloc != NULL){
997: /* will affect out */ /* strloc+strlenc(chain)=+V2 */ /* Will also work in Unicode */
998: memmove(strloc,strloc+strlen(chain), strlen(strloc+strlen(chain))+1);
999: /* strcpy (strloc, strloc +strlen(chain));*/
1000: }
1001: printf("Aft strloc=%s chain=%s in=%s out=%s \n", strloc, chain, in, out);
1002: return out;
1003: }
1004:
1005:
1.145 brouard 1006: char *cutl(char *blocc, char *alocc, char *in, char occ)
1007: {
1.187 brouard 1008: /* cuts string in into blocc and alocc where blocc ends before FIRST occurence of char 'occ'
1.145 brouard 1009: and alocc starts after first occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
1.187 brouard 1010: gives blocc="abcdef" and alocc="ghi2j".
1.145 brouard 1011: If occ is not found blocc is null and alocc is equal to in. Returns blocc
1012: */
1.160 brouard 1013: char *s, *t;
1.145 brouard 1014: t=in;s=in;
1015: while ((*in != occ) && (*in != '\0')){
1016: *alocc++ = *in++;
1017: }
1018: if( *in == occ){
1019: *(alocc)='\0';
1020: s=++in;
1021: }
1022:
1023: if (s == t) {/* occ not found */
1024: *(alocc-(in-s))='\0';
1025: in=s;
1026: }
1027: while ( *in != '\0'){
1028: *blocc++ = *in++;
1029: }
1030:
1031: *blocc='\0';
1032: return t;
1033: }
1.137 brouard 1034: char *cutv(char *blocc, char *alocc, char *in, char occ)
1035: {
1.187 brouard 1036: /* cuts string in into blocc and alocc where blocc ends before LAST occurence of char 'occ'
1.137 brouard 1037: and alocc starts after last occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
1038: gives blocc="abcdef2ghi" and alocc="j".
1039: If occ is not found blocc is null and alocc is equal to in. Returns alocc
1040: */
1041: char *s, *t;
1042: t=in;s=in;
1043: while (*in != '\0'){
1044: while( *in == occ){
1045: *blocc++ = *in++;
1046: s=in;
1047: }
1048: *blocc++ = *in++;
1049: }
1050: if (s == t) /* occ not found */
1051: *(blocc-(in-s))='\0';
1052: else
1053: *(blocc-(in-s)-1)='\0';
1054: in=s;
1055: while ( *in != '\0'){
1056: *alocc++ = *in++;
1057: }
1058:
1059: *alocc='\0';
1060: return s;
1061: }
1062:
1.126 brouard 1063: int nbocc(char *s, char occ)
1064: {
1065: int i,j=0;
1066: int lg=20;
1067: i=0;
1068: lg=strlen(s);
1069: for(i=0; i<= lg; i++) {
1070: if (s[i] == occ ) j++;
1071: }
1072: return j;
1073: }
1074:
1.137 brouard 1075: /* void cutv(char *u,char *v, char*t, char occ) */
1076: /* { */
1077: /* /\* cuts string t into u and v where u ends before last occurence of char 'occ' */
1078: /* and v starts after last occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2') */
1079: /* gives u="abcdef2ghi" and v="j" *\/ */
1080: /* int i,lg,j,p=0; */
1081: /* i=0; */
1082: /* lg=strlen(t); */
1083: /* for(j=0; j<=lg-1; j++) { */
1084: /* if((t[j]!= occ) && (t[j+1]== occ)) p=j+1; */
1085: /* } */
1.126 brouard 1086:
1.137 brouard 1087: /* for(j=0; j<p; j++) { */
1088: /* (u[j] = t[j]); */
1089: /* } */
1090: /* u[p]='\0'; */
1.126 brouard 1091:
1.137 brouard 1092: /* for(j=0; j<= lg; j++) { */
1093: /* if (j>=(p+1))(v[j-p-1] = t[j]); */
1094: /* } */
1095: /* } */
1.126 brouard 1096:
1.160 brouard 1097: #ifdef _WIN32
1098: char * strsep(char **pp, const char *delim)
1099: {
1100: char *p, *q;
1101:
1102: if ((p = *pp) == NULL)
1103: return 0;
1104: if ((q = strpbrk (p, delim)) != NULL)
1105: {
1106: *pp = q + 1;
1107: *q = '\0';
1108: }
1109: else
1110: *pp = 0;
1111: return p;
1112: }
1113: #endif
1114:
1.126 brouard 1115: /********************** nrerror ********************/
1116:
1117: void nrerror(char error_text[])
1118: {
1119: fprintf(stderr,"ERREUR ...\n");
1120: fprintf(stderr,"%s\n",error_text);
1121: exit(EXIT_FAILURE);
1122: }
1123: /*********************** vector *******************/
1124: double *vector(int nl, int nh)
1125: {
1126: double *v;
1127: v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
1128: if (!v) nrerror("allocation failure in vector");
1129: return v-nl+NR_END;
1130: }
1131:
1132: /************************ free vector ******************/
1133: void free_vector(double*v, int nl, int nh)
1134: {
1135: free((FREE_ARG)(v+nl-NR_END));
1136: }
1137:
1138: /************************ivector *******************************/
1139: int *ivector(long nl,long nh)
1140: {
1141: int *v;
1142: v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
1143: if (!v) nrerror("allocation failure in ivector");
1144: return v-nl+NR_END;
1145: }
1146:
1147: /******************free ivector **************************/
1148: void free_ivector(int *v, long nl, long nh)
1149: {
1150: free((FREE_ARG)(v+nl-NR_END));
1151: }
1152:
1153: /************************lvector *******************************/
1154: long *lvector(long nl,long nh)
1155: {
1156: long *v;
1157: v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
1158: if (!v) nrerror("allocation failure in ivector");
1159: return v-nl+NR_END;
1160: }
1161:
1162: /******************free lvector **************************/
1163: void free_lvector(long *v, long nl, long nh)
1164: {
1165: free((FREE_ARG)(v+nl-NR_END));
1166: }
1167:
1168: /******************* imatrix *******************************/
1169: int **imatrix(long nrl, long nrh, long ncl, long nch)
1170: /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */
1171: {
1172: long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;
1173: int **m;
1174:
1175: /* allocate pointers to rows */
1176: m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));
1177: if (!m) nrerror("allocation failure 1 in matrix()");
1178: m += NR_END;
1179: m -= nrl;
1180:
1181:
1182: /* allocate rows and set pointers to them */
1183: m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));
1184: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
1185: m[nrl] += NR_END;
1186: m[nrl] -= ncl;
1187:
1188: for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;
1189:
1190: /* return pointer to array of pointers to rows */
1191: return m;
1192: }
1193:
1194: /****************** free_imatrix *************************/
1195: void free_imatrix(m,nrl,nrh,ncl,nch)
1196: int **m;
1197: long nch,ncl,nrh,nrl;
1198: /* free an int matrix allocated by imatrix() */
1199: {
1200: free((FREE_ARG) (m[nrl]+ncl-NR_END));
1201: free((FREE_ARG) (m+nrl-NR_END));
1202: }
1203:
1204: /******************* matrix *******************************/
1205: double **matrix(long nrl, long nrh, long ncl, long nch)
1206: {
1207: long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
1208: double **m;
1209:
1210: m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
1211: if (!m) nrerror("allocation failure 1 in matrix()");
1212: m += NR_END;
1213: m -= nrl;
1214:
1215: m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
1216: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
1217: m[nrl] += NR_END;
1218: m[nrl] -= ncl;
1219:
1220: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
1221: return m;
1.145 brouard 1222: /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) or &(m[1][0])
1223: m[i] = address of ith row of the table. &(m[i]) is its value which is another adress
1224: that of m[i][0]. In order to get the value p m[i][0] but it is unitialized.
1.126 brouard 1225: */
1226: }
1227:
1228: /*************************free matrix ************************/
1229: void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
1230: {
1231: free((FREE_ARG)(m[nrl]+ncl-NR_END));
1232: free((FREE_ARG)(m+nrl-NR_END));
1233: }
1234:
1235: /******************* ma3x *******************************/
1236: double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
1237: {
1238: long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
1239: double ***m;
1240:
1241: m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
1242: if (!m) nrerror("allocation failure 1 in matrix()");
1243: m += NR_END;
1244: m -= nrl;
1245:
1246: m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
1247: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
1248: m[nrl] += NR_END;
1249: m[nrl] -= ncl;
1250:
1251: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
1252:
1253: m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
1254: if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
1255: m[nrl][ncl] += NR_END;
1256: m[nrl][ncl] -= nll;
1257: for (j=ncl+1; j<=nch; j++)
1258: m[nrl][j]=m[nrl][j-1]+nlay;
1259:
1260: for (i=nrl+1; i<=nrh; i++) {
1261: m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
1262: for (j=ncl+1; j<=nch; j++)
1263: m[i][j]=m[i][j-1]+nlay;
1264: }
1265: return m;
1266: /* gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
1267: &(m[i][j][k]) <=> *((*(m+i) + j)+k)
1268: */
1269: }
1270:
1271: /*************************free ma3x ************************/
1272: void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
1273: {
1274: free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
1275: free((FREE_ARG)(m[nrl]+ncl-NR_END));
1276: free((FREE_ARG)(m+nrl-NR_END));
1277: }
1278:
1279: /*************** function subdirf ***********/
1280: char *subdirf(char fileres[])
1281: {
1282: /* Caution optionfilefiname is hidden */
1283: strcpy(tmpout,optionfilefiname);
1284: strcat(tmpout,"/"); /* Add to the right */
1285: strcat(tmpout,fileres);
1286: return tmpout;
1287: }
1288:
1289: /*************** function subdirf2 ***********/
1290: char *subdirf2(char fileres[], char *preop)
1291: {
1292:
1293: /* Caution optionfilefiname is hidden */
1294: strcpy(tmpout,optionfilefiname);
1295: strcat(tmpout,"/");
1296: strcat(tmpout,preop);
1297: strcat(tmpout,fileres);
1298: return tmpout;
1299: }
1300:
1301: /*************** function subdirf3 ***********/
1302: char *subdirf3(char fileres[], char *preop, char *preop2)
1303: {
1304:
1305: /* Caution optionfilefiname is hidden */
1306: strcpy(tmpout,optionfilefiname);
1307: strcat(tmpout,"/");
1308: strcat(tmpout,preop);
1309: strcat(tmpout,preop2);
1310: strcat(tmpout,fileres);
1311: return tmpout;
1312: }
1313:
1.162 brouard 1314: char *asc_diff_time(long time_sec, char ascdiff[])
1315: {
1316: long sec_left, days, hours, minutes;
1317: days = (time_sec) / (60*60*24);
1318: sec_left = (time_sec) % (60*60*24);
1319: hours = (sec_left) / (60*60) ;
1320: sec_left = (sec_left) %(60*60);
1321: minutes = (sec_left) /60;
1322: sec_left = (sec_left) % (60);
1323: sprintf(ascdiff,"%ld day(s) %ld hour(s) %ld minute(s) %ld second(s)",days, hours, minutes, sec_left);
1324: return ascdiff;
1325: }
1326:
1.126 brouard 1327: /***************** f1dim *************************/
1328: extern int ncom;
1329: extern double *pcom,*xicom;
1330: extern double (*nrfunc)(double []);
1331:
1332: double f1dim(double x)
1333: {
1334: int j;
1335: double f;
1336: double *xt;
1337:
1338: xt=vector(1,ncom);
1339: for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];
1340: f=(*nrfunc)(xt);
1341: free_vector(xt,1,ncom);
1342: return f;
1343: }
1344:
1345: /*****************brent *************************/
1346: double brent(double ax, double bx, double cx, double (*f)(double), double tol, double *xmin)
1.187 brouard 1347: {
1348: /* Given a function f, and given a bracketing triplet of abscissas ax, bx, cx (such that bx is
1349: * between ax and cx, and f(bx) is less than both f(ax) and f(cx) ), this routine isolates
1350: * the minimum to a fractional precision of about tol using Brent’s method. The abscissa of
1351: * the minimum is returned as xmin, and the minimum function value is returned as brent , the
1352: * returned function value.
1353: */
1.126 brouard 1354: int iter;
1355: double a,b,d,etemp;
1.159 brouard 1356: double fu=0,fv,fw,fx;
1.164 brouard 1357: double ftemp=0.;
1.126 brouard 1358: double p,q,r,tol1,tol2,u,v,w,x,xm;
1359: double e=0.0;
1360:
1361: a=(ax < cx ? ax : cx);
1362: b=(ax > cx ? ax : cx);
1363: x=w=v=bx;
1364: fw=fv=fx=(*f)(x);
1365: for (iter=1;iter<=ITMAX;iter++) {
1366: xm=0.5*(a+b);
1367: tol2=2.0*(tol1=tol*fabs(x)+ZEPS);
1368: /* if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
1369: printf(".");fflush(stdout);
1370: fprintf(ficlog,".");fflush(ficlog);
1.162 brouard 1371: #ifdef DEBUGBRENT
1.126 brouard 1372: 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);
1373: 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);
1374: /* if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
1375: #endif
1376: if (fabs(x-xm) <= (tol2-0.5*(b-a))){
1377: *xmin=x;
1378: return fx;
1379: }
1380: ftemp=fu;
1381: if (fabs(e) > tol1) {
1382: r=(x-w)*(fx-fv);
1383: q=(x-v)*(fx-fw);
1384: p=(x-v)*q-(x-w)*r;
1385: q=2.0*(q-r);
1386: if (q > 0.0) p = -p;
1387: q=fabs(q);
1388: etemp=e;
1389: e=d;
1390: if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))
1391: d=CGOLD*(e=(x >= xm ? a-x : b-x));
1392: else {
1393: d=p/q;
1394: u=x+d;
1395: if (u-a < tol2 || b-u < tol2)
1396: d=SIGN(tol1,xm-x);
1397: }
1398: } else {
1399: d=CGOLD*(e=(x >= xm ? a-x : b-x));
1400: }
1401: u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));
1402: fu=(*f)(u);
1403: if (fu <= fx) {
1404: if (u >= x) a=x; else b=x;
1405: SHFT(v,w,x,u)
1.183 brouard 1406: SHFT(fv,fw,fx,fu)
1407: } else {
1408: if (u < x) a=u; else b=u;
1409: if (fu <= fw || w == x) {
1410: v=w;
1411: w=u;
1412: fv=fw;
1413: fw=fu;
1414: } else if (fu <= fv || v == x || v == w) {
1415: v=u;
1416: fv=fu;
1417: }
1418: }
1.126 brouard 1419: }
1420: nrerror("Too many iterations in brent");
1421: *xmin=x;
1422: return fx;
1423: }
1424:
1425: /****************** mnbrak ***********************/
1426:
1427: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,
1428: double (*func)(double))
1.183 brouard 1429: { /* Given a function func , and given distinct initial points ax and bx , this routine searches in
1430: the downhill direction (defined by the function as evaluated at the initial points) and returns
1431: new points ax , bx , cx that bracket a minimum of the function. Also returned are the function
1432: values at the three points, fa, fb , and fc such that fa > fb and fb < fc.
1433: */
1.126 brouard 1434: double ulim,u,r,q, dum;
1435: double fu;
1.187 brouard 1436:
1437: double scale=10.;
1438: int iterscale=0;
1439:
1440: *fa=(*func)(*ax); /* xta[j]=pcom[j]+(*ax)*xicom[j]; fa=f(xta[j])*/
1441: *fb=(*func)(*bx); /* xtb[j]=pcom[j]+(*bx)*xicom[j]; fb=f(xtb[j]) */
1442:
1443:
1444: /* while(*fb != *fb){ /\* *ax should be ok, reducing distance to *ax *\/ */
1445: /* printf("Warning mnbrak *fb = %lf, *bx=%lf *ax=%lf *fa==%lf iter=%d\n",*fb, *bx, *ax, *fa, iterscale++); */
1446: /* *bx = *ax - (*ax - *bx)/scale; */
1447: /* *fb=(*func)(*bx); /\* xtb[j]=pcom[j]+(*bx)*xicom[j]; fb=f(xtb[j]) *\/ */
1448: /* } */
1449:
1.126 brouard 1450: if (*fb > *fa) {
1451: SHFT(dum,*ax,*bx,dum)
1.183 brouard 1452: SHFT(dum,*fb,*fa,dum)
1453: }
1.126 brouard 1454: *cx=(*bx)+GOLD*(*bx-*ax);
1455: *fc=(*func)(*cx);
1.183 brouard 1456: #ifdef DEBUG
1457: printf("mnbrak0 *fb=%.12e *fc=%.12e\n",*fb,*fc);
1458: fprintf(ficlog,"mnbrak0 *fb=%.12e *fc=%.12e\n",*fb,*fc);
1459: #endif
1460: while (*fb > *fc) { /* Declining a,b,c with fa> fb > fc */
1.126 brouard 1461: r=(*bx-*ax)*(*fb-*fc);
1462: q=(*bx-*cx)*(*fb-*fa);
1463: u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/
1.183 brouard 1464: (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); /* Minimum abscissa of a parabolic estimated from (a,fa), (b,fb) and (c,fc). */
1465: ulim=(*bx)+GLIMIT*(*cx-*bx); /* Maximum abscissa where function should be evaluated */
1466: if ((*bx-u)*(u-*cx) > 0.0) { /* if u_p is between b and c */
1.126 brouard 1467: fu=(*func)(u);
1.163 brouard 1468: #ifdef DEBUG
1469: /* f(x)=A(x-u)**2+f(u) */
1470: double A, fparabu;
1471: A= (*fb - *fa)/(*bx-*ax)/(*bx+*ax-2*u);
1472: fparabu= *fa - A*(*ax-u)*(*ax-u);
1473: printf("mnbrak (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf), (*u=%.12f, fu=%.12lf, fparabu=%.12f)\n",*ax,*fa,*bx,*fb,*cx,*fc,u,fu, fparabu);
1474: fprintf(ficlog, "mnbrak (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf), (*u=%.12f, fu=%.12lf, fparabu=%.12f)\n",*ax,*fa,*bx,*fb,*cx,*fc,u,fu, fparabu);
1.183 brouard 1475: /* And thus,it can be that fu > *fc even if fparabu < *fc */
1476: /* mnbrak (*ax=7.666299858533, *fa=299039.693133272231), (*bx=8.595447774979, *fb=298976.598289369489),
1477: (*cx=10.098840694817, *fc=298946.631474258087), (*u=9.852501168332, fu=298948.773013752128, fparabu=298945.434711494134) */
1478: /* In that case, there is no bracket in the output! Routine is wrong with many consequences.*/
1.163 brouard 1479: #endif
1.184 brouard 1480: #ifdef MNBRAKORIGINAL
1.183 brouard 1481: #else
1.191 brouard 1482: /* if (fu > *fc) { */
1483: /* #ifdef DEBUG */
1484: /* printf("mnbrak4 fu > fc \n"); */
1485: /* fprintf(ficlog, "mnbrak4 fu > fc\n"); */
1486: /* #endif */
1487: /* /\* 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 *\\/ *\/ */
1488: /* /\* SHFT(*fa,*fc,fu,*fc) /\\* (b, u, c) is a bracket while test fb > fc will be fu > fc will exit *\\/ *\/ */
1489: /* dum=u; /\* Shifting c and u *\/ */
1490: /* u = *cx; */
1491: /* *cx = dum; */
1492: /* dum = fu; */
1493: /* fu = *fc; */
1494: /* *fc =dum; */
1495: /* } else { /\* end *\/ */
1496: /* #ifdef DEBUG */
1497: /* printf("mnbrak3 fu < fc \n"); */
1498: /* fprintf(ficlog, "mnbrak3 fu < fc\n"); */
1499: /* #endif */
1500: /* dum=u; /\* Shifting c and u *\/ */
1501: /* u = *cx; */
1502: /* *cx = dum; */
1503: /* dum = fu; */
1504: /* fu = *fc; */
1505: /* *fc =dum; */
1506: /* } */
1.183 brouard 1507: #ifdef DEBUG
1.191 brouard 1508: printf("mnbrak34 fu < or >= fc \n");
1509: fprintf(ficlog, "mnbrak34 fu < fc\n");
1.183 brouard 1510: #endif
1.191 brouard 1511: dum=u; /* Shifting c and u */
1512: u = *cx;
1513: *cx = dum;
1514: dum = fu;
1515: fu = *fc;
1516: *fc =dum;
1.183 brouard 1517: #endif
1.162 brouard 1518: } else if ((*cx-u)*(u-ulim) > 0.0) { /* u is after c but before ulim */
1.183 brouard 1519: #ifdef DEBUG
1520: printf("mnbrak2 u after c but before ulim\n");
1521: fprintf(ficlog, "mnbrak2 u after c but before ulim\n");
1522: #endif
1.126 brouard 1523: fu=(*func)(u);
1524: if (fu < *fc) {
1.183 brouard 1525: #ifdef DEBUG
1526: printf("mnbrak2 u after c but before ulim AND fu < fc\n");
1527: fprintf(ficlog, "mnbrak2 u after c but before ulim AND fu <fc \n");
1528: #endif
1.126 brouard 1529: SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))
1.183 brouard 1530: SHFT(*fb,*fc,fu,(*func)(u))
1531: }
1.162 brouard 1532: } else if ((u-ulim)*(ulim-*cx) >= 0.0) { /* u outside ulim (verifying that ulim is beyond c) */
1.183 brouard 1533: #ifdef DEBUG
1534: printf("mnbrak2 u outside ulim (verifying that ulim is beyond c)\n");
1535: fprintf(ficlog, "mnbrak2 u outside ulim (verifying that ulim is beyond c)\n");
1536: #endif
1.126 brouard 1537: u=ulim;
1538: fu=(*func)(u);
1.183 brouard 1539: } else { /* u could be left to b (if r > q parabola has a maximum) */
1540: #ifdef DEBUG
1541: printf("mnbrak2 u could be left to b (if r > q parabola has a maximum)\n");
1542: fprintf(ficlog, "mnbrak2 u could be left to b (if r > q parabola has a maximum)\n");
1543: #endif
1.126 brouard 1544: u=(*cx)+GOLD*(*cx-*bx);
1545: fu=(*func)(u);
1.183 brouard 1546: } /* end tests */
1.126 brouard 1547: SHFT(*ax,*bx,*cx,u)
1.183 brouard 1548: SHFT(*fa,*fb,*fc,fu)
1549: #ifdef DEBUG
1550: printf("mnbrak2 (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf), (*u=%.12f, fu=%.12lf)\n",*ax,*fa,*bx,*fb,*cx,*fc,u,fu);
1551: fprintf(ficlog, "mnbrak2 (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf), (*u=%.12f, fu=%.12lf)\n",*ax,*fa,*bx,*fb,*cx,*fc,u,fu);
1552: #endif
1553: } /* 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 1554: }
1555:
1556: /*************** linmin ************************/
1.162 brouard 1557: /* Given an n -dimensional point p[1..n] and an n -dimensional direction xi[1..n] , moves and
1558: resets p to where the function func(p) takes on a minimum along the direction xi from p ,
1559: and replaces xi by the actual vector displacement that p was moved. Also returns as fret
1560: the value of func at the returned location p . This is actually all accomplished by calling the
1561: routines mnbrak and brent .*/
1.126 brouard 1562: int ncom;
1563: double *pcom,*xicom;
1564: double (*nrfunc)(double []);
1565:
1566: void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))
1567: {
1568: double brent(double ax, double bx, double cx,
1569: double (*f)(double), double tol, double *xmin);
1570: double f1dim(double x);
1571: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,
1572: double *fc, double (*func)(double));
1573: int j;
1574: double xx,xmin,bx,ax;
1575: double fx,fb,fa;
1.187 brouard 1576:
1577: double scale=10., axs, xxs, xxss; /* Scale added for infinity */
1.126 brouard 1578:
1579: ncom=n;
1580: pcom=vector(1,n);
1581: xicom=vector(1,n);
1582: nrfunc=func;
1583: for (j=1;j<=n;j++) {
1584: pcom[j]=p[j];
1585: xicom[j]=xi[j];
1586: }
1.187 brouard 1587:
1.192 brouard 1588: /* axs=0.0; */
1589: /* xxss=1; /\* 1 and using scale *\/ */
1.187 brouard 1590: xxs=1;
1.192 brouard 1591: /* do{ */
1.187 brouard 1592: ax=0.;
1593: xx= xxs;
1594: mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); /* Outputs: xtx[j]=pcom[j]+(*xx)*xicom[j]; fx=f(xtx[j]) */
1595: /* brackets with inputs ax=0 and xx=1, but points, pcom=p, and directions values, xicom=xi, are sent via f1dim(x) */
1596: /* 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)) */
1597: /* Outputs: fa=f(p(j)) and fx=f(p(j) + xxs * xi(j) ) and f(bx)= f(p(j)+ bx* xi(j)) */
1598: /* Given input ax=axs and xx=xxs, xx might be too far from ax to get a finite f(xx) */
1599: /* Searches on line, outputs (ax, xx, bx) such that fx < min(fa and fb) */
1600: /* 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]]*/
1.192 brouard 1601: /* if (fx != fx){ */
1602: /* xxs=xxs/scale; /\* Trying a smaller xx, closer to initial ax=0 *\/ */
1603: /* 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); */
1604: /* } */
1605: /* }while(fx != fx); */
1.187 brouard 1606:
1.191 brouard 1607: #ifdef DEBUGLINMIN
1608: 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);
1609: #endif
1.187 brouard 1610: *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); /* Giving a bracketting triplet (ax, xx, bx), find a minimum, xmin, according to f1dim, *fret(xmin),*/
1611: /* fa = f(p[j] + ax * xi[j]), fx = f(p[j] + xx * xi[j]), fb = f(p[j] + bx * xi[j]) */
1612: /* fmin = f(p[j] + xmin * xi[j]) */
1613: /* P+lambda n in that direction (lambdamin), with TOL between abscisses */
1614: /* f1dim(xmin): for (j=1;j<=ncom;j++) xt[j]=pcom[j]+xmin*xicom[j]; */
1.126 brouard 1615: #ifdef DEBUG
1616: printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
1617: fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
1618: #endif
1.191 brouard 1619: #ifdef DEBUGLINMIN
1620: printf("linmin end ");
1621: #endif
1.126 brouard 1622: for (j=1;j<=n;j++) {
1.188 brouard 1623: /* printf(" before xi[%d]=%12.8f", j,xi[j]); */
1.187 brouard 1624: xi[j] *= xmin; /* xi rescaled by xmin: if xmin=-1.237 and xi=(1,0,...,0) xi=(-1.237,0,...,0) */
1.189 brouard 1625: /* if(xxs <1.0) */
1626: /* 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 ); */
1.187 brouard 1627: p[j] += xi[j]; /* Parameters values are updated accordingly */
1.126 brouard 1628: }
1.189 brouard 1629: /* printf("\n"); */
1.191 brouard 1630: #ifdef DEBUGLINMIN
1631: printf("Comparing last *frec(xmin=%12.8f)=%12.8f from Brent and frec(0.)=%12.8f \n", xmin, *fret, (*func)(p));
1632: for (j=1;j<=n;j++) {
1633: printf(" xi[%d]= %12.7f p[%d]= %12.7f",j,xi[j],j,p[j]);
1634: if(j % ncovmodel == 0)
1635: printf("\n");
1636: }
1637: #endif
1.126 brouard 1638: free_vector(xicom,1,n);
1639: free_vector(pcom,1,n);
1640: }
1641:
1642:
1643: /*************** powell ************************/
1.162 brouard 1644: /*
1645: Minimization of a function func of n variables. Input consists of an initial starting point
1646: p[1..n] ; an initial matrix xi[1..n][1..n] , whose columns contain the initial set of di-
1647: rections (usually the n unit vectors); and ftol , the fractional tolerance in the function value
1648: such that failure to decrease by more than this amount on one iteration signals doneness. On
1649: output, p is set to the best point found, xi is the then-current direction set, fret is the returned
1650: function value at p , and iter is the number of iterations taken. The routine linmin is used.
1651: */
1.126 brouard 1652: void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,
1653: double (*func)(double []))
1654: {
1655: void linmin(double p[], double xi[], int n, double *fret,
1656: double (*func)(double []));
1657: int i,ibig,j;
1658: double del,t,*pt,*ptt,*xit;
1.181 brouard 1659: double directest;
1.126 brouard 1660: double fp,fptt;
1661: double *xits;
1662: int niterf, itmp;
1663:
1664: pt=vector(1,n);
1665: ptt=vector(1,n);
1666: xit=vector(1,n);
1667: xits=vector(1,n);
1668: *fret=(*func)(p);
1669: for (j=1;j<=n;j++) pt[j]=p[j];
1.157 brouard 1670: rcurr_time = time(NULL);
1.126 brouard 1671: for (*iter=1;;++(*iter)) {
1.187 brouard 1672: fp=(*fret); /* From former iteration or initial value */
1.126 brouard 1673: ibig=0;
1674: del=0.0;
1.157 brouard 1675: rlast_time=rcurr_time;
1676: /* (void) gettimeofday(&curr_time,&tzp); */
1677: rcurr_time = time(NULL);
1678: curr_time = *localtime(&rcurr_time);
1679: printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, rcurr_time-rlast_time, rcurr_time-rstart_time);fflush(stdout);
1680: fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret,rcurr_time-rlast_time, rcurr_time-rstart_time); fflush(ficlog);
1681: /* fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tm_sec-start_time.tm_sec); */
1.192 brouard 1682: for (i=1;i<=n;i++) {
1.126 brouard 1683: printf(" %d %.12f",i, p[i]);
1684: fprintf(ficlog," %d %.12lf",i, p[i]);
1685: fprintf(ficrespow," %.12lf", p[i]);
1686: }
1687: printf("\n");
1688: fprintf(ficlog,"\n");
1689: fprintf(ficrespow,"\n");fflush(ficrespow);
1690: if(*iter <=3){
1.157 brouard 1691: tml = *localtime(&rcurr_time);
1692: strcpy(strcurr,asctime(&tml));
1693: rforecast_time=rcurr_time;
1.126 brouard 1694: itmp = strlen(strcurr);
1695: if(strcurr[itmp-1]=='\n') /* Windows outputs with a new line */
1696: strcurr[itmp-1]='\0';
1.162 brouard 1697: printf("\nConsidering the time needed for the last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
1.157 brouard 1698: fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
1.126 brouard 1699: for(niterf=10;niterf<=30;niterf+=10){
1.157 brouard 1700: rforecast_time=rcurr_time+(niterf-*iter)*(rcurr_time-rlast_time);
1701: forecast_time = *localtime(&rforecast_time);
1702: strcpy(strfor,asctime(&forecast_time));
1.126 brouard 1703: itmp = strlen(strfor);
1704: if(strfor[itmp-1]=='\n')
1705: strfor[itmp-1]='\0';
1.157 brouard 1706: 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);
1707: 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 1708: }
1709: }
1.187 brouard 1710: for (i=1;i<=n;i++) { /* For each direction i */
1711: for (j=1;j<=n;j++) xit[j]=xi[j][i]; /* Directions stored from previous iteration with previous scales */
1.126 brouard 1712: fptt=(*fret);
1713: #ifdef DEBUG
1.164 brouard 1714: printf("fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
1715: fprintf(ficlog, "fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
1.126 brouard 1716: #endif
1.187 brouard 1717: printf("%d",i);fflush(stdout); /* print direction (parameter) i */
1.126 brouard 1718: fprintf(ficlog,"%d",i);fflush(ficlog);
1.188 brouard 1719: linmin(p,xit,n,fret,func); /* Point p[n]. xit[n] has been loaded for direction i as input.*/
1720: /* Outputs are fret(new point p) p is updated and xit rescaled */
1721: if (fabs(fptt-(*fret)) > del) { /* We are keeping the max gain on each of the n directions */
1722: /* because that direction will be replaced unless the gain del is small */
1723: /* in comparison with the 'probable' gain, mu^2, with the last average direction. */
1724: /* Unless the n directions are conjugate some gain in the determinant may be obtained */
1725: /* with the new direction. */
1.126 brouard 1726: del=fabs(fptt-(*fret));
1727: ibig=i;
1728: }
1729: #ifdef DEBUG
1730: printf("%d %.12e",i,(*fret));
1731: fprintf(ficlog,"%d %.12e",i,(*fret));
1732: for (j=1;j<=n;j++) {
1733: xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
1734: printf(" x(%d)=%.12e",j,xit[j]);
1735: fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
1736: }
1737: for(j=1;j<=n;j++) {
1.162 brouard 1738: printf(" p(%d)=%.12e",j,p[j]);
1739: fprintf(ficlog," p(%d)=%.12e",j,p[j]);
1.126 brouard 1740: }
1741: printf("\n");
1742: fprintf(ficlog,"\n");
1743: #endif
1.187 brouard 1744: } /* end loop on each direction i */
1745: /* Convergence test will use last linmin estimation (fret) and compare former iteration (fp) */
1.188 brouard 1746: /* But p and xit have been updated at the end of linmin, *fret corresponds to new p, xit */
1.187 brouard 1747: /* New value of last point Pn is not computed, P(n-1) */
1.182 brouard 1748: if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) { /* Did we reach enough precision? */
1.188 brouard 1749: /* We could compare with a chi^2. chisquare(0.95,ddl=1)=3.84 */
1750: /* By adding age*age in a model, the new -2LL should be lower and the difference follows a */
1751: /* a chisquare statistics with 1 degree. To be significant at the 95% level, it should have */
1752: /* decreased of more than 3.84 */
1753: /* By adding age*age and V1*age the gain (-2LL) should be more than 5.99 (ddl=2) */
1754: /* By using V1+V2+V3, the gain should be 7.82, compared with basic 1+age. */
1755: /* By adding 10 parameters more the gain should be 18.31 */
1756:
1757: /* Starting the program with initial values given by a former maximization will simply change */
1758: /* the scales of the directions and the directions, because the are reset to canonical directions */
1759: /* Thus the first calls to linmin will give new points and better maximizations until fp-(*fret) is */
1760: /* under the tolerance value. If the tolerance is very small 1.e-9, it could last long. */
1.126 brouard 1761: #ifdef DEBUG
1762: int k[2],l;
1763: k[0]=1;
1764: k[1]=-1;
1765: printf("Max: %.12e",(*func)(p));
1766: fprintf(ficlog,"Max: %.12e",(*func)(p));
1767: for (j=1;j<=n;j++) {
1768: printf(" %.12e",p[j]);
1769: fprintf(ficlog," %.12e",p[j]);
1770: }
1771: printf("\n");
1772: fprintf(ficlog,"\n");
1773: for(l=0;l<=1;l++) {
1774: for (j=1;j<=n;j++) {
1775: ptt[j]=p[j]+(p[j]-pt[j])*k[l];
1776: printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
1777: fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
1778: }
1779: printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
1780: fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
1781: }
1782: #endif
1783:
1784:
1785: free_vector(xit,1,n);
1786: free_vector(xits,1,n);
1787: free_vector(ptt,1,n);
1788: free_vector(pt,1,n);
1789: return;
1.192 brouard 1790: } /* enough precision */
1.126 brouard 1791: if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");
1.181 brouard 1792: for (j=1;j<=n;j++) { /* Computes the extrapolated point P_0 + 2 (P_n-P_0) */
1.126 brouard 1793: ptt[j]=2.0*p[j]-pt[j];
1794: xit[j]=p[j]-pt[j];
1795: pt[j]=p[j];
1796: }
1.181 brouard 1797: fptt=(*func)(ptt); /* f_3 */
1.192 brouard 1798: #ifdef POWELLF1F3
1799: #else
1.161 brouard 1800: if (fptt < fp) { /* If extrapolated point is better, decide if we keep that new direction or not */
1.192 brouard 1801: #endif
1.162 brouard 1802: /* (x1 f1=fp), (x2 f2=*fret), (x3 f3=fptt), (xm fm) */
1.161 brouard 1803: /* From x1 (P0) distance of x2 is at h and x3 is 2h */
1.162 brouard 1804: /* Let f"(x2) be the 2nd derivative equal everywhere. */
1805: /* Then the parabolic through (x1,f1), (x2,f2) and (x3,f3) */
1806: /* will reach at f3 = fm + h^2/2 f"m ; f" = (f1 -2f2 +f3 ) / h**2 */
1.181 brouard 1807: /* Conditional for using this new direction is that mu^2 = (f1-2f2+f3)^2 /2 < del */
1.161 brouard 1808: /* t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); */
1.183 brouard 1809: #ifdef NRCORIGINAL
1810: t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)- del*SQR(fp-fptt); /* Original Numerical Recipes in C*/
1811: #else
1812: 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 1813: t= t- del*SQR(fp-fptt);
1.183 brouard 1814: #endif
1.182 brouard 1815: directest = fp-2.0*(*fret)+fptt - 2.0 * del; /* If del was big enough we change it for a new direction */
1.161 brouard 1816: #ifdef DEBUG
1.181 brouard 1817: 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);
1818: 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 1819: printf("t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
1820: (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
1821: fprintf(ficlog,"t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
1822: (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
1823: 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);
1824: 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);
1825: #endif
1.183 brouard 1826: #ifdef POWELLORIGINAL
1827: if (t < 0.0) { /* Then we use it for new direction */
1828: #else
1.182 brouard 1829: if (directest*t < 0.0) { /* Contradiction between both tests */
1.192 brouard 1830: printf("directest= %.12lf, t= %.12lf, f1= %.12lf,f2= %.12lf,f3= %.12lf, del= %.12lf\n",directest, t, fp,(*fret),fptt,del);
1831: printf("f1-2f2+f3= %.12lf, f1-f2-del= %.12lf, f1-f3= %.12lf\n",fp-2.0*(*fret)+fptt, fp -(*fret) -del, fp-fptt);
1832: fprintf(ficlog,"directest= %.12lf, t= %.12lf, f1= %.12lf,f2= %.12lf,f3= %.12lf, del= %.12lf\n",directest, t, fp,(*fret),fptt, del);
1833: fprintf(ficlog,"f1-2f2+f3= %.12lf, f1-f2-del= %.12lf, f1-f3= %.12lf\n",fp-2.0*(*fret)+fptt, fp -(*fret) -del, fp-fptt);
1834: }
1.181 brouard 1835: if (directest < 0.0) { /* Then we use it for new direction */
1836: #endif
1.191 brouard 1837: #ifdef DEBUGLINMIN
1838: printf("Before linmin in direction P%d-P0\n",n);
1839: for (j=1;j<=n;j++) {
1840: printf("Before xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
1841: if(j % ncovmodel == 0)
1842: printf("\n");
1843: }
1844: #endif
1.187 brouard 1845: linmin(p,xit,n,fret,func); /* computes minimum on the extrapolated direction: changes p and rescales xit.*/
1.191 brouard 1846: #ifdef DEBUGLINMIN
1847: for (j=1;j<=n;j++) {
1848: printf("After xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
1849: if(j % ncovmodel == 0)
1850: printf("\n");
1851: }
1852: #endif
1.126 brouard 1853: for (j=1;j<=n;j++) {
1.181 brouard 1854: xi[j][ibig]=xi[j][n]; /* Replace direction with biggest decrease by last direction n */
1855: xi[j][n]=xit[j]; /* and this nth direction by the by the average p_0 p_n */
1.126 brouard 1856: }
1.181 brouard 1857: printf("Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
1858: fprintf(ficlog,"Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
1.161 brouard 1859:
1.126 brouard 1860: #ifdef DEBUG
1.164 brouard 1861: printf("Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
1862: fprintf(ficlog,"Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
1.126 brouard 1863: for(j=1;j<=n;j++){
1864: printf(" %.12e",xit[j]);
1865: fprintf(ficlog," %.12e",xit[j]);
1866: }
1867: printf("\n");
1868: fprintf(ficlog,"\n");
1869: #endif
1.192 brouard 1870: } /* end of t or directest negative */
1871: #ifdef POWELLF1F3
1872: #else
1.162 brouard 1873: } /* end if (fptt < fp) */
1.192 brouard 1874: #endif
1875: } /* loop iteration */
1.126 brouard 1876: }
1877:
1878: /**** Prevalence limit (stable or period prevalence) ****************/
1879:
1880: double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
1881: {
1882: /* Computes the prevalence limit in each live state at age x by left multiplying the unit
1883: matrix by transitions matrix until convergence is reached */
1.169 brouard 1884:
1.126 brouard 1885: int i, ii,j,k;
1886: double min, max, maxmin, maxmax,sumnew=0.;
1.145 brouard 1887: /* double **matprod2(); */ /* test */
1.131 brouard 1888: double **out, cov[NCOVMAX+1], **pmij();
1.126 brouard 1889: double **newm;
1890: double agefin, delaymax=50 ; /* Max number of years to converge */
1.169 brouard 1891:
1.126 brouard 1892: for (ii=1;ii<=nlstate+ndeath;ii++)
1893: for (j=1;j<=nlstate+ndeath;j++){
1894: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1895: }
1.169 brouard 1896:
1897: cov[1]=1.;
1898:
1899: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
1.126 brouard 1900: for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
1901: newm=savm;
1902: /* Covariates have to be included here again */
1.138 brouard 1903: cov[2]=agefin;
1.187 brouard 1904: if(nagesqr==1)
1905: cov[3]= agefin*agefin;;
1.138 brouard 1906: for (k=1; k<=cptcovn;k++) {
1.187 brouard 1907: cov[2+nagesqr+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
1.145 brouard 1908: /*printf("prevalim ij=%d k=%d Tvar[%d]=%d nbcode=%d cov=%lf codtab[%d][Tvar[%d]]=%d \n",ij,k, k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], ij, k, codtab[ij][Tvar[k]]);*/
1.138 brouard 1909: }
1.186 brouard 1910: /*wrong? for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
1.187 brouard 1911: for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]]*cov[2];
1.186 brouard 1912: for (k=1; k<=cptcovprod;k++) /* Useless */
1.187 brouard 1913: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]] * nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
1.138 brouard 1914:
1915: /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
1916: /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
1917: /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
1.145 brouard 1918: /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
1919: /* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind *\/ */
1.142 brouard 1920: out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /* Bug Valgrind */
1.138 brouard 1921:
1.126 brouard 1922: savm=oldm;
1923: oldm=newm;
1924: maxmax=0.;
1925: for(j=1;j<=nlstate;j++){
1926: min=1.;
1927: max=0.;
1928: for(i=1; i<=nlstate; i++) {
1929: sumnew=0;
1930: for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
1931: prlim[i][j]= newm[i][j]/(1-sumnew);
1.145 brouard 1932: /*printf(" prevalim i=%d, j=%d, prmlim[%d][%d]=%f, agefin=%d \n", i, j, i, j, prlim[i][j],(int)agefin);*/
1.126 brouard 1933: max=FMAX(max,prlim[i][j]);
1934: min=FMIN(min,prlim[i][j]);
1935: }
1936: maxmin=max-min;
1937: maxmax=FMAX(maxmax,maxmin);
1.169 brouard 1938: } /* j loop */
1.126 brouard 1939: if(maxmax < ftolpl){
1940: return prlim;
1941: }
1.169 brouard 1942: } /* age loop */
1943: return prlim; /* should not reach here */
1.126 brouard 1944: }
1945:
1946: /*************** transition probabilities ***************/
1947:
1948: double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
1949: {
1.138 brouard 1950: /* According to parameters values stored in x and the covariate's values stored in cov,
1951: computes the probability to be observed in state j being in state i by appying the
1952: model to the ncovmodel covariates (including constant and age).
1953: lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc]
1954: and, according on how parameters are entered, the position of the coefficient xij(nc) of the
1955: ncth covariate in the global vector x is given by the formula:
1956: j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
1957: j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
1958: Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
1959: sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.
1960: Outputs ps[i][j] the probability to be observed in j being in j according to
1961: the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
1962: */
1963: double s1, lnpijopii;
1.126 brouard 1964: /*double t34;*/
1.164 brouard 1965: int i,j, nc, ii, jj;
1.126 brouard 1966:
1967: for(i=1; i<= nlstate; i++){
1968: for(j=1; j<i;j++){
1.138 brouard 1969: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
1970: /*lnpijopii += param[i][j][nc]*cov[nc];*/
1971: lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
1972: /* printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
1.126 brouard 1973: }
1.138 brouard 1974: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
1975: /* printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
1.126 brouard 1976: }
1977: for(j=i+1; j<=nlstate+ndeath;j++){
1.138 brouard 1978: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
1979: /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
1980: lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
1981: /* printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
1.126 brouard 1982: }
1.138 brouard 1983: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
1.126 brouard 1984: }
1985: }
1986:
1987: for(i=1; i<= nlstate; i++){
1988: s1=0;
1.131 brouard 1989: for(j=1; j<i; j++){
1.138 brouard 1990: s1+=exp(ps[i][j]); /* In fact sums pij/pii */
1.131 brouard 1991: /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
1992: }
1993: for(j=i+1; j<=nlstate+ndeath; j++){
1.138 brouard 1994: s1+=exp(ps[i][j]); /* In fact sums pij/pii */
1.131 brouard 1995: /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
1996: }
1.138 brouard 1997: /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
1.126 brouard 1998: ps[i][i]=1./(s1+1.);
1.138 brouard 1999: /* Computing other pijs */
1.126 brouard 2000: for(j=1; j<i; j++)
2001: ps[i][j]= exp(ps[i][j])*ps[i][i];
2002: for(j=i+1; j<=nlstate+ndeath; j++)
2003: ps[i][j]= exp(ps[i][j])*ps[i][i];
2004: /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
2005: } /* end i */
2006:
2007: for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
2008: for(jj=1; jj<= nlstate+ndeath; jj++){
2009: ps[ii][jj]=0;
2010: ps[ii][ii]=1;
2011: }
2012: }
2013:
1.145 brouard 2014:
2015: /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
2016: /* for(jj=1; jj<= nlstate+ndeath; jj++){ */
2017: /* printf(" pmij ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
2018: /* } */
2019: /* printf("\n "); */
2020: /* } */
2021: /* printf("\n ");printf("%lf ",cov[2]);*/
2022: /*
1.126 brouard 2023: for(i=1; i<= npar; i++) printf("%f ",x[i]);
2024: goto end;*/
2025: return ps;
2026: }
2027:
2028: /**************** Product of 2 matrices ******************/
2029:
1.145 brouard 2030: double **matprod2(double **out, double **in,int nrl, int nrh, int ncl, int nch, int ncolol, int ncoloh, double **b)
1.126 brouard 2031: {
2032: /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
2033: b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
2034: /* in, b, out are matrice of pointers which should have been initialized
2035: before: only the contents of out is modified. The function returns
2036: a pointer to pointers identical to out */
1.145 brouard 2037: int i, j, k;
1.126 brouard 2038: for(i=nrl; i<= nrh; i++)
1.145 brouard 2039: for(k=ncolol; k<=ncoloh; k++){
2040: out[i][k]=0.;
2041: for(j=ncl; j<=nch; j++)
2042: out[i][k] +=in[i][j]*b[j][k];
2043: }
1.126 brouard 2044: return out;
2045: }
2046:
2047:
2048: /************* Higher Matrix Product ***************/
2049:
2050: double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
2051: {
2052: /* Computes the transition matrix starting at age 'age' over
2053: 'nhstepm*hstepm*stepm' months (i.e. until
2054: age (in years) age+nhstepm*hstepm*stepm/12) by multiplying
2055: nhstepm*hstepm matrices.
2056: Output is stored in matrix po[i][j][h] for h every 'hstepm' step
2057: (typically every 2 years instead of every month which is too big
2058: for the memory).
2059: Model is determined by parameters x and covariates have to be
2060: included manually here.
2061:
2062: */
2063:
2064: int i, j, d, h, k;
1.131 brouard 2065: double **out, cov[NCOVMAX+1];
1.126 brouard 2066: double **newm;
1.187 brouard 2067: double agexact;
1.126 brouard 2068:
2069: /* Hstepm could be zero and should return the unit matrix */
2070: for (i=1;i<=nlstate+ndeath;i++)
2071: for (j=1;j<=nlstate+ndeath;j++){
2072: oldm[i][j]=(i==j ? 1.0 : 0.0);
2073: po[i][j][0]=(i==j ? 1.0 : 0.0);
2074: }
2075: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
2076: for(h=1; h <=nhstepm; h++){
2077: for(d=1; d <=hstepm; d++){
2078: newm=savm;
2079: /* Covariates have to be included here again */
2080: cov[1]=1.;
1.187 brouard 2081: agexact=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
2082: cov[2]=agexact;
2083: if(nagesqr==1)
2084: cov[3]= agexact*agexact;
1.131 brouard 2085: for (k=1; k<=cptcovn;k++)
1.187 brouard 2086: cov[2+nagesqr+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
1.186 brouard 2087: for (k=1; k<=cptcovage;k++) /* Should start at cptcovn+1 */
2088: /* cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
1.187 brouard 2089: cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtab[ij][Tvar[Tage[k]]]]*cov[2];
1.145 brouard 2090: for (k=1; k<=cptcovprod;k++) /* Useless because included in cptcovn */
1.187 brouard 2091: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
1.126 brouard 2092:
2093:
2094: /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
2095: /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
2096: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
2097: pmij(pmmij,cov,ncovmodel,x,nlstate));
2098: savm=oldm;
2099: oldm=newm;
2100: }
2101: for(i=1; i<=nlstate+ndeath; i++)
2102: for(j=1;j<=nlstate+ndeath;j++) {
2103: po[i][j][h]=newm[i][j];
1.128 brouard 2104: /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
1.126 brouard 2105: }
1.128 brouard 2106: /*printf("h=%d ",h);*/
1.126 brouard 2107: } /* end h */
1.128 brouard 2108: /* printf("\n H=%d \n",h); */
1.126 brouard 2109: return po;
2110: }
2111:
1.162 brouard 2112: #ifdef NLOPT
2113: double myfunc(unsigned n, const double *p1, double *grad, void *pd){
2114: double fret;
2115: double *xt;
2116: int j;
2117: myfunc_data *d2 = (myfunc_data *) pd;
2118: /* xt = (p1-1); */
2119: xt=vector(1,n);
2120: for (j=1;j<=n;j++) xt[j]=p1[j-1]; /* xt[1]=p1[0] */
2121:
2122: fret=(d2->function)(xt); /* p xt[1]@8 is fine */
2123: /* fret=(*func)(xt); /\* p xt[1]@8 is fine *\/ */
2124: printf("Function = %.12lf ",fret);
2125: for (j=1;j<=n;j++) printf(" %d %.8lf", j, xt[j]);
2126: printf("\n");
2127: free_vector(xt,1,n);
2128: return fret;
2129: }
2130: #endif
1.126 brouard 2131:
2132: /*************** log-likelihood *************/
2133: double func( double *x)
2134: {
2135: int i, ii, j, k, mi, d, kk;
1.131 brouard 2136: double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
1.126 brouard 2137: double **out;
2138: double sw; /* Sum of weights */
2139: double lli; /* Individual log likelihood */
2140: int s1, s2;
2141: double bbh, survp;
2142: long ipmx;
1.187 brouard 2143: double agexact;
1.126 brouard 2144: /*extern weight */
2145: /* We are differentiating ll according to initial status */
2146: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
2147: /*for(i=1;i<imx;i++)
2148: printf(" %d\n",s[4][i]);
2149: */
1.162 brouard 2150:
2151: ++countcallfunc;
2152:
1.126 brouard 2153: cov[1]=1.;
2154:
2155: for(k=1; k<=nlstate; k++) ll[k]=0.;
2156:
2157: if(mle==1){
2158: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1.138 brouard 2159: /* Computes the values of the ncovmodel covariates of the model
2160: depending if the covariates are fixed or variying (age dependent) and stores them in cov[]
2161: Then computes with function pmij which return a matrix p[i][j] giving the elementary probability
2162: to be observed in j being in i according to the model.
2163: */
1.145 brouard 2164: for (k=1; k<=cptcovn;k++){ /* Simple and product covariates without age* products */
1.187 brouard 2165: cov[2+nagesqr+k]=covar[Tvar[k]][i];
1.145 brouard 2166: }
1.137 brouard 2167: /* In model V2+V1*V4+age*V3+V3*V2 Tvar[1] is V2, Tvar[2=V1*V4]
1.138 brouard 2168: is 6, Tvar[3=age*V3] should not be computed because of age Tvar[4=V3*V2]
1.137 brouard 2169: has been calculated etc */
1.126 brouard 2170: for(mi=1; mi<= wav[i]-1; mi++){
2171: for (ii=1;ii<=nlstate+ndeath;ii++)
2172: for (j=1;j<=nlstate+ndeath;j++){
2173: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2174: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2175: }
2176: for(d=0; d<dh[mi][i]; d++){
2177: newm=savm;
1.187 brouard 2178: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
2179: cov[2]=agexact;
2180: if(nagesqr==1)
2181: cov[3]= agexact*agexact;
1.126 brouard 2182: for (kk=1; kk<=cptcovage;kk++) {
1.187 brouard 2183: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact; /* Tage[kk] gives the data-covariate associated with age */
1.126 brouard 2184: }
2185: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2186: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
2187: savm=oldm;
2188: oldm=newm;
2189: } /* end mult */
2190:
2191: /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
2192: /* But now since version 0.9 we anticipate for bias at large stepm.
2193: * If stepm is larger than one month (smallest stepm) and if the exact delay
2194: * (in months) between two waves is not a multiple of stepm, we rounded to
2195: * the nearest (and in case of equal distance, to the lowest) interval but now
2196: * we keep into memory the bias bh[mi][i] and also the previous matrix product
2197: * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
2198: * probability in order to take into account the bias as a fraction of the way
2199: * from savm to out if bh is negative or even beyond if bh is positive. bh varies
2200: * -stepm/2 to stepm/2 .
2201: * For stepm=1 the results are the same as for previous versions of Imach.
2202: * For stepm > 1 the results are less biased than in previous versions.
2203: */
2204: s1=s[mw[mi][i]][i];
2205: s2=s[mw[mi+1][i]][i];
2206: bbh=(double)bh[mi][i]/(double)stepm;
2207: /* bias bh is positive if real duration
2208: * is higher than the multiple of stepm and negative otherwise.
2209: */
2210: /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
2211: if( s2 > nlstate){
2212: /* i.e. if s2 is a death state and if the date of death is known
2213: then the contribution to the likelihood is the probability to
2214: die between last step unit time and current step unit time,
2215: which is also equal to probability to die before dh
2216: minus probability to die before dh-stepm .
2217: In version up to 0.92 likelihood was computed
2218: as if date of death was unknown. Death was treated as any other
2219: health state: the date of the interview describes the actual state
2220: and not the date of a change in health state. The former idea was
2221: to consider that at each interview the state was recorded
2222: (healthy, disable or death) and IMaCh was corrected; but when we
2223: introduced the exact date of death then we should have modified
2224: the contribution of an exact death to the likelihood. This new
2225: contribution is smaller and very dependent of the step unit
2226: stepm. It is no more the probability to die between last interview
2227: and month of death but the probability to survive from last
2228: interview up to one month before death multiplied by the
2229: probability to die within a month. Thanks to Chris
2230: Jackson for correcting this bug. Former versions increased
2231: mortality artificially. The bad side is that we add another loop
2232: which slows down the processing. The difference can be up to 10%
2233: lower mortality.
2234: */
1.183 brouard 2235: /* If, at the beginning of the maximization mostly, the
2236: cumulative probability or probability to be dead is
2237: constant (ie = 1) over time d, the difference is equal to
2238: 0. out[s1][3] = savm[s1][3]: probability, being at state
2239: s1 at precedent wave, to be dead a month before current
2240: wave is equal to probability, being at state s1 at
2241: precedent wave, to be dead at mont of the current
2242: wave. Then the observed probability (that this person died)
2243: is null according to current estimated parameter. In fact,
2244: it should be very low but not zero otherwise the log go to
2245: infinity.
2246: */
2247: /* #ifdef INFINITYORIGINAL */
2248: /* lli=log(out[s1][s2] - savm[s1][s2]); */
2249: /* #else */
2250: /* if ((out[s1][s2] - savm[s1][s2]) < mytinydouble) */
2251: /* lli=log(mytinydouble); */
2252: /* else */
2253: /* lli=log(out[s1][s2] - savm[s1][s2]); */
2254: /* #endif */
2255: lli=log(out[s1][s2] - savm[s1][s2]);
1.126 brouard 2256:
2257: } else if (s2==-2) {
2258: for (j=1,survp=0. ; j<=nlstate; j++)
2259: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
2260: /*survp += out[s1][j]; */
2261: lli= log(survp);
2262: }
2263:
2264: else if (s2==-4) {
2265: for (j=3,survp=0. ; j<=nlstate; j++)
2266: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
2267: lli= log(survp);
2268: }
2269:
2270: else if (s2==-5) {
2271: for (j=1,survp=0. ; j<=2; j++)
2272: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
2273: lli= log(survp);
2274: }
2275:
2276: else{
2277: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
2278: /* 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 */
2279: }
2280: /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
2281: /*if(lli ==000.0)*/
2282: /*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); */
2283: ipmx +=1;
2284: sw += weight[i];
2285: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1.183 brouard 2286: /* if (lli < log(mytinydouble)){ */
2287: /* 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); */
2288: /* 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]); */
2289: /* } */
1.126 brouard 2290: } /* end of wave */
2291: } /* end of individual */
2292: } else if(mle==2){
2293: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1.187 brouard 2294: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
1.126 brouard 2295: for(mi=1; mi<= wav[i]-1; mi++){
2296: for (ii=1;ii<=nlstate+ndeath;ii++)
2297: for (j=1;j<=nlstate+ndeath;j++){
2298: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2299: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2300: }
2301: for(d=0; d<=dh[mi][i]; d++){
2302: newm=savm;
1.187 brouard 2303: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
2304: cov[2]=agexact;
2305: if(nagesqr==1)
2306: cov[3]= agexact*agexact;
1.126 brouard 2307: for (kk=1; kk<=cptcovage;kk++) {
1.187 brouard 2308: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
1.126 brouard 2309: }
2310: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2311: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
2312: savm=oldm;
2313: oldm=newm;
2314: } /* end mult */
2315:
2316: s1=s[mw[mi][i]][i];
2317: s2=s[mw[mi+1][i]][i];
2318: bbh=(double)bh[mi][i]/(double)stepm;
2319: 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 */
2320: ipmx +=1;
2321: sw += weight[i];
2322: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
2323: } /* end of wave */
2324: } /* end of individual */
2325: } else if(mle==3){ /* exponential inter-extrapolation */
2326: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1.187 brouard 2327: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
1.126 brouard 2328: for(mi=1; mi<= wav[i]-1; mi++){
2329: for (ii=1;ii<=nlstate+ndeath;ii++)
2330: for (j=1;j<=nlstate+ndeath;j++){
2331: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2332: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2333: }
2334: for(d=0; d<dh[mi][i]; d++){
2335: newm=savm;
1.187 brouard 2336: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
2337: cov[2]=agexact;
2338: if(nagesqr==1)
2339: cov[3]= agexact*agexact;
1.126 brouard 2340: for (kk=1; kk<=cptcovage;kk++) {
1.187 brouard 2341: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
1.126 brouard 2342: }
2343: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2344: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
2345: savm=oldm;
2346: oldm=newm;
2347: } /* end mult */
2348:
2349: s1=s[mw[mi][i]][i];
2350: s2=s[mw[mi+1][i]][i];
2351: bbh=(double)bh[mi][i]/(double)stepm;
2352: 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 */
2353: ipmx +=1;
2354: sw += weight[i];
2355: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
2356: } /* end of wave */
2357: } /* end of individual */
2358: }else if (mle==4){ /* ml=4 no inter-extrapolation */
2359: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1.187 brouard 2360: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
1.126 brouard 2361: for(mi=1; mi<= wav[i]-1; mi++){
2362: for (ii=1;ii<=nlstate+ndeath;ii++)
2363: for (j=1;j<=nlstate+ndeath;j++){
2364: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2365: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2366: }
2367: for(d=0; d<dh[mi][i]; d++){
2368: newm=savm;
1.187 brouard 2369: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
2370: cov[2]=agexact;
2371: if(nagesqr==1)
2372: cov[3]= agexact*agexact;
1.126 brouard 2373: for (kk=1; kk<=cptcovage;kk++) {
1.187 brouard 2374: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
1.126 brouard 2375: }
2376:
2377: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2378: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
2379: savm=oldm;
2380: oldm=newm;
2381: } /* end mult */
2382:
2383: s1=s[mw[mi][i]][i];
2384: s2=s[mw[mi+1][i]][i];
2385: if( s2 > nlstate){
2386: lli=log(out[s1][s2] - savm[s1][s2]);
2387: }else{
2388: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
2389: }
2390: ipmx +=1;
2391: sw += weight[i];
2392: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
2393: /* 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]); */
2394: } /* end of wave */
2395: } /* end of individual */
2396: }else{ /* ml=5 no inter-extrapolation no jackson =0.8a */
2397: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1.187 brouard 2398: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
1.126 brouard 2399: for(mi=1; mi<= wav[i]-1; mi++){
2400: for (ii=1;ii<=nlstate+ndeath;ii++)
2401: for (j=1;j<=nlstate+ndeath;j++){
2402: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2403: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2404: }
2405: for(d=0; d<dh[mi][i]; d++){
2406: newm=savm;
1.187 brouard 2407: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
2408: cov[2]=agexact;
2409: if(nagesqr==1)
2410: cov[3]= agexact*agexact;
1.126 brouard 2411: for (kk=1; kk<=cptcovage;kk++) {
1.187 brouard 2412: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
1.126 brouard 2413: }
2414:
2415: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2416: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
2417: savm=oldm;
2418: oldm=newm;
2419: } /* end mult */
2420:
2421: s1=s[mw[mi][i]][i];
2422: s2=s[mw[mi+1][i]][i];
2423: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
2424: ipmx +=1;
2425: sw += weight[i];
2426: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
2427: /*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]);*/
2428: } /* end of wave */
2429: } /* end of individual */
2430: } /* End of if */
2431: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
2432: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
2433: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
2434: return -l;
2435: }
2436:
2437: /*************** log-likelihood *************/
2438: double funcone( double *x)
2439: {
2440: /* Same as likeli but slower because of a lot of printf and if */
2441: int i, ii, j, k, mi, d, kk;
1.131 brouard 2442: double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
1.126 brouard 2443: double **out;
2444: double lli; /* Individual log likelihood */
2445: double llt;
2446: int s1, s2;
2447: double bbh, survp;
1.187 brouard 2448: double agexact;
1.126 brouard 2449: /*extern weight */
2450: /* We are differentiating ll according to initial status */
2451: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
2452: /*for(i=1;i<imx;i++)
2453: printf(" %d\n",s[4][i]);
2454: */
2455: cov[1]=1.;
2456:
2457: for(k=1; k<=nlstate; k++) ll[k]=0.;
2458:
2459: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1.187 brouard 2460: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
1.126 brouard 2461: for(mi=1; mi<= wav[i]-1; mi++){
2462: for (ii=1;ii<=nlstate+ndeath;ii++)
2463: for (j=1;j<=nlstate+ndeath;j++){
2464: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2465: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2466: }
2467: for(d=0; d<dh[mi][i]; d++){
2468: newm=savm;
1.187 brouard 2469: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
2470: cov[2]=agexact;
2471: if(nagesqr==1)
2472: cov[3]= agexact*agexact;
1.126 brouard 2473: for (kk=1; kk<=cptcovage;kk++) {
1.187 brouard 2474: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
1.126 brouard 2475: }
1.187 brouard 2476:
1.145 brouard 2477: /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
1.126 brouard 2478: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2479: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1.145 brouard 2480: /* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, */
2481: /* 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); */
1.126 brouard 2482: savm=oldm;
2483: oldm=newm;
2484: } /* end mult */
2485:
2486: s1=s[mw[mi][i]][i];
2487: s2=s[mw[mi+1][i]][i];
2488: bbh=(double)bh[mi][i]/(double)stepm;
2489: /* bias is positive if real duration
2490: * is higher than the multiple of stepm and negative otherwise.
2491: */
2492: if( s2 > nlstate && (mle <5) ){ /* Jackson */
2493: lli=log(out[s1][s2] - savm[s1][s2]);
2494: } else if (s2==-2) {
2495: for (j=1,survp=0. ; j<=nlstate; j++)
2496: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
2497: lli= log(survp);
2498: }else if (mle==1){
2499: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
2500: } else if(mle==2){
2501: 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 */
2502: } else if(mle==3){ /* exponential inter-extrapolation */
2503: 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 */
2504: } else if (mle==4){ /* mle=4 no inter-extrapolation */
2505: lli=log(out[s1][s2]); /* Original formula */
1.136 brouard 2506: } else{ /* mle=0 back to 1 */
2507: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
2508: /*lli=log(out[s1][s2]); */ /* Original formula */
1.126 brouard 2509: } /* End of if */
2510: ipmx +=1;
2511: sw += weight[i];
2512: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1.132 brouard 2513: /*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 2514: if(globpr){
1.141 brouard 2515: fprintf(ficresilk,"%9ld %6d %2d %2d %1d %1d %3d %11.6f %8.4f\
1.126 brouard 2516: %11.6f %11.6f %11.6f ", \
2517: num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
2518: 2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
2519: for(k=1,llt=0.,l=0.; k<=nlstate; k++){
2520: llt +=ll[k]*gipmx/gsw;
2521: fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
2522: }
2523: fprintf(ficresilk," %10.6f\n", -llt);
2524: }
2525: } /* end of wave */
2526: } /* end of individual */
2527: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
2528: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
2529: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
2530: if(globpr==0){ /* First time we count the contributions and weights */
2531: gipmx=ipmx;
2532: gsw=sw;
2533: }
2534: return -l;
2535: }
2536:
2537:
2538: /*************** function likelione ***********/
2539: void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
2540: {
2541: /* This routine should help understanding what is done with
2542: the selection of individuals/waves and
2543: to check the exact contribution to the likelihood.
2544: Plotting could be done.
2545: */
2546: int k;
2547:
2548: if(*globpri !=0){ /* Just counts and sums, no printings */
2549: strcpy(fileresilk,"ilk");
2550: strcat(fileresilk,fileres);
2551: if((ficresilk=fopen(fileresilk,"w"))==NULL) {
2552: printf("Problem with resultfile: %s\n", fileresilk);
2553: fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
2554: }
2555: fprintf(ficresilk, "#individual(line's_record) s1 s2 wave# effective_wave# number_of_matrices_product pij weight -2ln(pij)*weight 0pij_x 0pij_(x-stepm) cumulating_loglikeli_by_health_state(reweighted=-2ll*weightXnumber_of_contribs/sum_of_weights) and_total\n");
2556: fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
2557: /* i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
2558: for(k=1; k<=nlstate; k++)
2559: fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
2560: fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
2561: }
2562:
2563: *fretone=(*funcone)(p);
2564: if(*globpri !=0){
2565: fclose(ficresilk);
2566: fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
2567: fflush(fichtm);
2568: }
2569: return;
2570: }
2571:
2572:
2573: /*********** Maximum Likelihood Estimation ***************/
2574:
2575: void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
2576: {
1.165 brouard 2577: int i,j, iter=0;
1.126 brouard 2578: double **xi;
2579: double fret;
2580: double fretone; /* Only one call to likelihood */
2581: /* char filerespow[FILENAMELENGTH];*/
1.162 brouard 2582:
2583: #ifdef NLOPT
2584: int creturn;
2585: nlopt_opt opt;
2586: /* double lb[9] = { -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL }; /\* lower bounds *\/ */
2587: double *lb;
2588: double minf; /* the minimum objective value, upon return */
2589: double * p1; /* Shifted parameters from 0 instead of 1 */
2590: myfunc_data dinst, *d = &dinst;
2591: #endif
2592:
2593:
1.126 brouard 2594: xi=matrix(1,npar,1,npar);
2595: for (i=1;i<=npar;i++)
2596: for (j=1;j<=npar;j++)
2597: xi[i][j]=(i==j ? 1.0 : 0.0);
2598: printf("Powell\n"); fprintf(ficlog,"Powell\n");
2599: strcpy(filerespow,"pow");
2600: strcat(filerespow,fileres);
2601: if((ficrespow=fopen(filerespow,"w"))==NULL) {
2602: printf("Problem with resultfile: %s\n", filerespow);
2603: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
2604: }
2605: fprintf(ficrespow,"# Powell\n# iter -2*LL");
2606: for (i=1;i<=nlstate;i++)
2607: for(j=1;j<=nlstate+ndeath;j++)
2608: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
2609: fprintf(ficrespow,"\n");
1.162 brouard 2610: #ifdef POWELL
1.126 brouard 2611: powell(p,xi,npar,ftol,&iter,&fret,func);
1.162 brouard 2612: #endif
1.126 brouard 2613:
1.162 brouard 2614: #ifdef NLOPT
2615: #ifdef NEWUOA
2616: opt = nlopt_create(NLOPT_LN_NEWUOA,npar);
2617: #else
2618: opt = nlopt_create(NLOPT_LN_BOBYQA,npar);
2619: #endif
2620: lb=vector(0,npar-1);
2621: for (i=0;i<npar;i++) lb[i]= -HUGE_VAL;
2622: nlopt_set_lower_bounds(opt, lb);
2623: nlopt_set_initial_step1(opt, 0.1);
2624:
2625: p1= (p+1); /* p *(p+1)@8 and p *(p1)@8 are equal p1[0]=p[1] */
2626: d->function = func;
2627: printf(" Func %.12lf \n",myfunc(npar,p1,NULL,d));
2628: nlopt_set_min_objective(opt, myfunc, d);
2629: nlopt_set_xtol_rel(opt, ftol);
2630: if ((creturn=nlopt_optimize(opt, p1, &minf)) < 0) {
2631: printf("nlopt failed! %d\n",creturn);
2632: }
2633: else {
2634: printf("found minimum after %d evaluations (NLOPT=%d)\n", countcallfunc ,NLOPT);
2635: printf("found minimum at f(%g,%g) = %0.10g\n", p[0], p[1], minf);
2636: iter=1; /* not equal */
2637: }
2638: nlopt_destroy(opt);
2639: #endif
1.126 brouard 2640: free_matrix(xi,1,npar,1,npar);
2641: fclose(ficrespow);
1.180 brouard 2642: printf("#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
2643: fprintf(ficlog,"#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
2644: fprintf(ficres,"#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
1.126 brouard 2645:
2646: }
2647:
2648: /**** Computes Hessian and covariance matrix ***/
2649: void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
2650: {
2651: double **a,**y,*x,pd;
2652: double **hess;
1.164 brouard 2653: int i, j;
1.126 brouard 2654: int *indx;
2655:
2656: double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
2657: double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
2658: void lubksb(double **a, int npar, int *indx, double b[]) ;
2659: void ludcmp(double **a, int npar, int *indx, double *d) ;
2660: double gompertz(double p[]);
2661: hess=matrix(1,npar,1,npar);
2662:
2663: printf("\nCalculation of the hessian matrix. Wait...\n");
2664: fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
2665: for (i=1;i<=npar;i++){
2666: printf("%d",i);fflush(stdout);
2667: fprintf(ficlog,"%d",i);fflush(ficlog);
2668:
2669: hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
2670:
2671: /* printf(" %f ",p[i]);
2672: printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
2673: }
2674:
2675: for (i=1;i<=npar;i++) {
2676: for (j=1;j<=npar;j++) {
2677: if (j>i) {
2678: printf(".%d%d",i,j);fflush(stdout);
2679: fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
2680: hess[i][j]=hessij(p,delti,i,j,func,npar);
2681:
2682: hess[j][i]=hess[i][j];
2683: /*printf(" %lf ",hess[i][j]);*/
2684: }
2685: }
2686: }
2687: printf("\n");
2688: fprintf(ficlog,"\n");
2689:
2690: printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
2691: fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
2692:
2693: a=matrix(1,npar,1,npar);
2694: y=matrix(1,npar,1,npar);
2695: x=vector(1,npar);
2696: indx=ivector(1,npar);
2697: for (i=1;i<=npar;i++)
2698: for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
2699: ludcmp(a,npar,indx,&pd);
2700:
2701: for (j=1;j<=npar;j++) {
2702: for (i=1;i<=npar;i++) x[i]=0;
2703: x[j]=1;
2704: lubksb(a,npar,indx,x);
2705: for (i=1;i<=npar;i++){
2706: matcov[i][j]=x[i];
2707: }
2708: }
2709:
2710: printf("\n#Hessian matrix#\n");
2711: fprintf(ficlog,"\n#Hessian matrix#\n");
2712: for (i=1;i<=npar;i++) {
2713: for (j=1;j<=npar;j++) {
2714: printf("%.3e ",hess[i][j]);
2715: fprintf(ficlog,"%.3e ",hess[i][j]);
2716: }
2717: printf("\n");
2718: fprintf(ficlog,"\n");
2719: }
2720:
2721: /* Recompute Inverse */
2722: for (i=1;i<=npar;i++)
2723: for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
2724: ludcmp(a,npar,indx,&pd);
2725:
2726: /* printf("\n#Hessian matrix recomputed#\n");
2727:
2728: for (j=1;j<=npar;j++) {
2729: for (i=1;i<=npar;i++) x[i]=0;
2730: x[j]=1;
2731: lubksb(a,npar,indx,x);
2732: for (i=1;i<=npar;i++){
2733: y[i][j]=x[i];
2734: printf("%.3e ",y[i][j]);
2735: fprintf(ficlog,"%.3e ",y[i][j]);
2736: }
2737: printf("\n");
2738: fprintf(ficlog,"\n");
2739: }
2740: */
2741:
2742: free_matrix(a,1,npar,1,npar);
2743: free_matrix(y,1,npar,1,npar);
2744: free_vector(x,1,npar);
2745: free_ivector(indx,1,npar);
2746: free_matrix(hess,1,npar,1,npar);
2747:
2748:
2749: }
2750:
2751: /*************** hessian matrix ****************/
2752: double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
2753: {
2754: int i;
2755: int l=1, lmax=20;
2756: double k1,k2;
1.132 brouard 2757: double p2[MAXPARM+1]; /* identical to x */
1.126 brouard 2758: double res;
2759: double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
2760: double fx;
2761: int k=0,kmax=10;
2762: double l1;
2763:
2764: fx=func(x);
2765: for (i=1;i<=npar;i++) p2[i]=x[i];
1.145 brouard 2766: for(l=0 ; l <=lmax; l++){ /* Enlarging the zone around the Maximum */
1.126 brouard 2767: l1=pow(10,l);
2768: delts=delt;
2769: for(k=1 ; k <kmax; k=k+1){
2770: delt = delta*(l1*k);
2771: p2[theta]=x[theta] +delt;
1.145 brouard 2772: k1=func(p2)-fx; /* Might be negative if too close to the theoretical maximum */
1.126 brouard 2773: p2[theta]=x[theta]-delt;
2774: k2=func(p2)-fx;
2775: /*res= (k1-2.0*fx+k2)/delt/delt; */
2776: res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
2777:
1.132 brouard 2778: #ifdef DEBUGHESS
1.126 brouard 2779: 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);
2780: 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);
2781: #endif
2782: /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
2783: if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
2784: k=kmax;
2785: }
2786: else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
1.164 brouard 2787: k=kmax; l=lmax*10;
1.126 brouard 2788: }
2789: else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){
2790: delts=delt;
2791: }
2792: }
2793: }
2794: delti[theta]=delts;
2795: return res;
2796:
2797: }
2798:
2799: double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
2800: {
2801: int i;
1.164 brouard 2802: int l=1, lmax=20;
1.126 brouard 2803: double k1,k2,k3,k4,res,fx;
1.132 brouard 2804: double p2[MAXPARM+1];
1.126 brouard 2805: int k;
2806:
2807: fx=func(x);
2808: for (k=1; k<=2; k++) {
2809: for (i=1;i<=npar;i++) p2[i]=x[i];
2810: p2[thetai]=x[thetai]+delti[thetai]/k;
2811: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
2812: k1=func(p2)-fx;
2813:
2814: p2[thetai]=x[thetai]+delti[thetai]/k;
2815: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
2816: k2=func(p2)-fx;
2817:
2818: p2[thetai]=x[thetai]-delti[thetai]/k;
2819: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
2820: k3=func(p2)-fx;
2821:
2822: p2[thetai]=x[thetai]-delti[thetai]/k;
2823: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
2824: k4=func(p2)-fx;
2825: res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
2826: #ifdef DEBUG
2827: 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);
2828: 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);
2829: #endif
2830: }
2831: return res;
2832: }
2833:
2834: /************** Inverse of matrix **************/
2835: void ludcmp(double **a, int n, int *indx, double *d)
2836: {
2837: int i,imax,j,k;
2838: double big,dum,sum,temp;
2839: double *vv;
2840:
2841: vv=vector(1,n);
2842: *d=1.0;
2843: for (i=1;i<=n;i++) {
2844: big=0.0;
2845: for (j=1;j<=n;j++)
2846: if ((temp=fabs(a[i][j])) > big) big=temp;
2847: if (big == 0.0) nrerror("Singular matrix in routine ludcmp");
2848: vv[i]=1.0/big;
2849: }
2850: for (j=1;j<=n;j++) {
2851: for (i=1;i<j;i++) {
2852: sum=a[i][j];
2853: for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];
2854: a[i][j]=sum;
2855: }
2856: big=0.0;
2857: for (i=j;i<=n;i++) {
2858: sum=a[i][j];
2859: for (k=1;k<j;k++)
2860: sum -= a[i][k]*a[k][j];
2861: a[i][j]=sum;
2862: if ( (dum=vv[i]*fabs(sum)) >= big) {
2863: big=dum;
2864: imax=i;
2865: }
2866: }
2867: if (j != imax) {
2868: for (k=1;k<=n;k++) {
2869: dum=a[imax][k];
2870: a[imax][k]=a[j][k];
2871: a[j][k]=dum;
2872: }
2873: *d = -(*d);
2874: vv[imax]=vv[j];
2875: }
2876: indx[j]=imax;
2877: if (a[j][j] == 0.0) a[j][j]=TINY;
2878: if (j != n) {
2879: dum=1.0/(a[j][j]);
2880: for (i=j+1;i<=n;i++) a[i][j] *= dum;
2881: }
2882: }
2883: free_vector(vv,1,n); /* Doesn't work */
2884: ;
2885: }
2886:
2887: void lubksb(double **a, int n, int *indx, double b[])
2888: {
2889: int i,ii=0,ip,j;
2890: double sum;
2891:
2892: for (i=1;i<=n;i++) {
2893: ip=indx[i];
2894: sum=b[ip];
2895: b[ip]=b[i];
2896: if (ii)
2897: for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];
2898: else if (sum) ii=i;
2899: b[i]=sum;
2900: }
2901: for (i=n;i>=1;i--) {
2902: sum=b[i];
2903: for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];
2904: b[i]=sum/a[i][i];
2905: }
2906: }
2907:
2908: void pstamp(FILE *fichier)
2909: {
1.196 ! brouard 2910: fprintf(fichier,"# %s.%s\n#IMaCh version %s, %s\n#%s\n# %s", optionfilefiname,optionfilext,version,copyright, fullversion, strstart);
1.126 brouard 2911: }
2912:
2913: /************ Frequencies ********************/
2914: void freqsummary(char fileres[], int iagemin, int iagemax, int **s, double **agev, int nlstate, int imx, int *Tvaraff, int **nbcode, int *ncodemax,double **mint,double **anint, char strstart[])
2915: { /* Some frequencies */
2916:
1.164 brouard 2917: int i, m, jk, j1, bool, z1,j;
1.126 brouard 2918: int first;
2919: double ***freq; /* Frequencies */
2920: double *pp, **prop;
2921: double pos,posprop, k2, dateintsum=0,k2cpt=0;
2922: char fileresp[FILENAMELENGTH];
2923:
2924: pp=vector(1,nlstate);
2925: prop=matrix(1,nlstate,iagemin,iagemax+3);
2926: strcpy(fileresp,"p");
2927: strcat(fileresp,fileres);
2928: if((ficresp=fopen(fileresp,"w"))==NULL) {
2929: printf("Problem with prevalence resultfile: %s\n", fileresp);
2930: fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
2931: exit(0);
2932: }
2933: freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
2934: j1=0;
2935:
2936: j=cptcoveff;
2937: if (cptcovn<1) {j=1;ncodemax[1]=1;}
2938:
2939: first=1;
2940:
1.169 brouard 2941: /* for(k1=1; k1<=j ; k1++){ */ /* Loop on covariates */
2942: /* for(i1=1; i1<=ncodemax[k1];i1++){ */ /* Now it is 2 */
2943: /* j1++; */
1.145 brouard 2944: for (j1 = 1; j1 <= (int) pow(2,cptcoveff); j1++){
1.126 brouard 2945: /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
2946: scanf("%d", i);*/
2947: for (i=-5; i<=nlstate+ndeath; i++)
2948: for (jk=-5; jk<=nlstate+ndeath; jk++)
2949: for(m=iagemin; m <= iagemax+3; m++)
2950: freq[i][jk][m]=0;
1.143 brouard 2951:
2952: for (i=1; i<=nlstate; i++)
2953: for(m=iagemin; m <= iagemax+3; m++)
2954: prop[i][m]=0;
1.126 brouard 2955:
2956: dateintsum=0;
2957: k2cpt=0;
2958: for (i=1; i<=imx; i++) {
2959: bool=1;
1.144 brouard 2960: if (cptcovn>0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
2961: for (z1=1; z1<=cptcoveff; z1++)
2962: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]){
1.145 brouard 2963: /* Tests if the value of each of the covariates of i is equal to filter j1 */
1.144 brouard 2964: bool=0;
1.145 brouard 2965: /* printf("bool=%d i=%d, z1=%d, Tvaraff[%d]=%d, covar[Tvarff][%d]=%2f, codtab[%d][%d]=%d, nbcode[Tvaraff][codtab[%d][%d]=%d, j1=%d\n",
2966: bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtab[j1][z1],
2967: j1,z1,nbcode[Tvaraff[z1]][codtab[j1][z1]],j1);*/
1.144 brouard 2968: /* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtab[7][3]=1 and nbcde[3][?]=1*/
2969: }
1.126 brouard 2970: }
1.144 brouard 2971:
1.126 brouard 2972: if (bool==1){
2973: for(m=firstpass; m<=lastpass; m++){
2974: k2=anint[m][i]+(mint[m][i]/12.);
2975: /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
2976: if(agev[m][i]==0) agev[m][i]=iagemax+1;
2977: if(agev[m][i]==1) agev[m][i]=iagemax+2;
2978: if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
2979: if (m<lastpass) {
2980: freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
2981: freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
2982: }
2983:
2984: if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
2985: dateintsum=dateintsum+k2;
2986: k2cpt++;
2987: }
2988: /*}*/
2989: }
2990: }
1.145 brouard 2991: } /* end i */
1.126 brouard 2992:
2993: /* fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
2994: pstamp(ficresp);
2995: if (cptcovn>0) {
2996: fprintf(ficresp, "\n#********** Variable ");
2997: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
2998: fprintf(ficresp, "**********\n#");
1.143 brouard 2999: fprintf(ficlog, "\n#********** Variable ");
3000: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficlog, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3001: fprintf(ficlog, "**********\n#");
1.126 brouard 3002: }
3003: for(i=1; i<=nlstate;i++)
3004: fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
3005: fprintf(ficresp, "\n");
3006:
3007: for(i=iagemin; i <= iagemax+3; i++){
3008: if(i==iagemax+3){
3009: fprintf(ficlog,"Total");
3010: }else{
3011: if(first==1){
3012: first=0;
3013: printf("See log file for details...\n");
3014: }
3015: fprintf(ficlog,"Age %d", i);
3016: }
3017: for(jk=1; jk <=nlstate ; jk++){
3018: for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
3019: pp[jk] += freq[jk][m][i];
3020: }
3021: for(jk=1; jk <=nlstate ; jk++){
3022: for(m=-1, pos=0; m <=0 ; m++)
3023: pos += freq[jk][m][i];
3024: if(pp[jk]>=1.e-10){
3025: if(first==1){
1.132 brouard 3026: printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
1.126 brouard 3027: }
3028: fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
3029: }else{
3030: if(first==1)
3031: printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
3032: fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
3033: }
3034: }
3035:
3036: for(jk=1; jk <=nlstate ; jk++){
3037: for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
3038: pp[jk] += freq[jk][m][i];
3039: }
3040: for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
3041: pos += pp[jk];
3042: posprop += prop[jk][i];
3043: }
3044: for(jk=1; jk <=nlstate ; jk++){
3045: if(pos>=1.e-5){
3046: if(first==1)
3047: printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
3048: fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
3049: }else{
3050: if(first==1)
3051: printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
3052: fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
3053: }
3054: if( i <= iagemax){
3055: if(pos>=1.e-5){
3056: fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
3057: /*probs[i][jk][j1]= pp[jk]/pos;*/
3058: /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
3059: }
3060: else
3061: fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
3062: }
3063: }
3064:
3065: for(jk=-1; jk <=nlstate+ndeath; jk++)
3066: for(m=-1; m <=nlstate+ndeath; m++)
3067: if(freq[jk][m][i] !=0 ) {
3068: if(first==1)
3069: printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
3070: fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
3071: }
3072: if(i <= iagemax)
3073: fprintf(ficresp,"\n");
3074: if(first==1)
3075: printf("Others in log...\n");
3076: fprintf(ficlog,"\n");
3077: }
1.145 brouard 3078: /*}*/
1.126 brouard 3079: }
3080: dateintmean=dateintsum/k2cpt;
3081:
3082: fclose(ficresp);
3083: free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
3084: free_vector(pp,1,nlstate);
3085: free_matrix(prop,1,nlstate,iagemin, iagemax+3);
3086: /* End of Freq */
3087: }
3088:
3089: /************ Prevalence ********************/
3090: 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)
3091: {
3092: /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
3093: in each health status at the date of interview (if between dateprev1 and dateprev2).
3094: We still use firstpass and lastpass as another selection.
3095: */
3096:
1.164 brouard 3097: int i, m, jk, j1, bool, z1,j;
3098:
3099: double **prop;
3100: double posprop;
1.126 brouard 3101: double y2; /* in fractional years */
3102: int iagemin, iagemax;
1.145 brouard 3103: int first; /** to stop verbosity which is redirected to log file */
1.126 brouard 3104:
3105: iagemin= (int) agemin;
3106: iagemax= (int) agemax;
3107: /*pp=vector(1,nlstate);*/
3108: prop=matrix(1,nlstate,iagemin,iagemax+3);
3109: /* freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
3110: j1=0;
3111:
1.145 brouard 3112: /*j=cptcoveff;*/
1.126 brouard 3113: if (cptcovn<1) {j=1;ncodemax[1]=1;}
3114:
1.145 brouard 3115: first=1;
3116: for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){
3117: /*for(i1=1; i1<=ncodemax[k1];i1++){
3118: j1++;*/
1.126 brouard 3119:
3120: for (i=1; i<=nlstate; i++)
3121: for(m=iagemin; m <= iagemax+3; m++)
3122: prop[i][m]=0.0;
3123:
3124: for (i=1; i<=imx; i++) { /* Each individual */
3125: bool=1;
3126: if (cptcovn>0) {
3127: for (z1=1; z1<=cptcoveff; z1++)
3128: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
3129: bool=0;
3130: }
3131: if (bool==1) {
3132: for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
3133: y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
3134: if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
3135: if(agev[m][i]==0) agev[m][i]=iagemax+1;
3136: if(agev[m][i]==1) agev[m][i]=iagemax+2;
3137: if((int)agev[m][i] <iagemin || (int)agev[m][i] >iagemax+3) printf("Error on individual =%d agev[m][i]=%f m=%d\n",i, agev[m][i],m);
3138: if (s[m][i]>0 && s[m][i]<=nlstate) {
3139: /*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]]);*/
3140: prop[s[m][i]][(int)agev[m][i]] += weight[i];
3141: prop[s[m][i]][iagemax+3] += weight[i];
3142: }
3143: }
3144: } /* end selection of waves */
3145: }
3146: }
3147: for(i=iagemin; i <= iagemax+3; i++){
3148: for(jk=1,posprop=0; jk <=nlstate ; jk++) {
3149: posprop += prop[jk][i];
3150: }
1.145 brouard 3151:
1.126 brouard 3152: for(jk=1; jk <=nlstate ; jk++){
3153: if( i <= iagemax){
3154: if(posprop>=1.e-5){
3155: probs[i][jk][j1]= prop[jk][i]/posprop;
1.145 brouard 3156: } else{
3157: if(first==1){
3158: first=0;
3159: printf("Warning Observed prevalence probs[%d][%d][%d]=%lf because of lack of cases\nSee others on log file...\n",jk,i,j1,probs[i][jk][j1]);
3160: }
3161: }
1.126 brouard 3162: }
3163: }/* end jk */
3164: }/* end i */
1.145 brouard 3165: /*} *//* end i1 */
3166: } /* end j1 */
1.126 brouard 3167:
3168: /* free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
3169: /*free_vector(pp,1,nlstate);*/
3170: free_matrix(prop,1,nlstate, iagemin,iagemax+3);
3171: } /* End of prevalence */
3172:
3173: /************* Waves Concatenation ***************/
3174:
3175: 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)
3176: {
3177: /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
3178: Death is a valid wave (if date is known).
3179: mw[mi][i] is the mi (mi=1 to wav[i]) effective wave of individual i
3180: dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
3181: and mw[mi+1][i]. dh depends on stepm.
3182: */
3183:
3184: int i, mi, m;
3185: /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
3186: double sum=0., jmean=0.;*/
3187: int first;
3188: int j, k=0,jk, ju, jl;
3189: double sum=0.;
3190: first=0;
1.164 brouard 3191: jmin=100000;
1.126 brouard 3192: jmax=-1;
3193: jmean=0.;
3194: for(i=1; i<=imx; i++){
3195: mi=0;
3196: m=firstpass;
3197: while(s[m][i] <= nlstate){
3198: if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
3199: mw[++mi][i]=m;
3200: if(m >=lastpass)
3201: break;
3202: else
3203: m++;
3204: }/* end while */
3205: if (s[m][i] > nlstate){
3206: mi++; /* Death is another wave */
3207: /* if(mi==0) never been interviewed correctly before death */
3208: /* Only death is a correct wave */
3209: mw[mi][i]=m;
3210: }
3211:
3212: wav[i]=mi;
3213: if(mi==0){
3214: nbwarn++;
3215: if(first==0){
3216: printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
3217: first=1;
3218: }
3219: if(first==1){
3220: fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
3221: }
3222: } /* end mi==0 */
3223: } /* End individuals */
3224:
3225: for(i=1; i<=imx; i++){
3226: for(mi=1; mi<wav[i];mi++){
3227: if (stepm <=0)
3228: dh[mi][i]=1;
3229: else{
3230: if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
3231: if (agedc[i] < 2*AGESUP) {
3232: j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);
3233: if(j==0) j=1; /* Survives at least one month after exam */
3234: else if(j<0){
3235: nberr++;
3236: 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]);
3237: j=1; /* Temporary Dangerous patch */
3238: 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);
3239: 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]);
3240: 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);
3241: }
3242: k=k+1;
3243: if (j >= jmax){
3244: jmax=j;
3245: ijmax=i;
3246: }
3247: if (j <= jmin){
3248: jmin=j;
3249: ijmin=i;
3250: }
3251: sum=sum+j;
3252: /*if (j<0) printf("j=%d num=%d \n",j,i);*/
3253: /* printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
3254: }
3255: }
3256: else{
3257: j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
3258: /* 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]); */
3259:
3260: k=k+1;
3261: if (j >= jmax) {
3262: jmax=j;
3263: ijmax=i;
3264: }
3265: else if (j <= jmin){
3266: jmin=j;
3267: ijmin=i;
3268: }
3269: /* if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
3270: /*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]);*/
3271: if(j<0){
3272: nberr++;
3273: 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]);
3274: 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]);
3275: }
3276: sum=sum+j;
3277: }
3278: jk= j/stepm;
3279: jl= j -jk*stepm;
3280: ju= j -(jk+1)*stepm;
3281: if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
3282: if(jl==0){
3283: dh[mi][i]=jk;
3284: bh[mi][i]=0;
3285: }else{ /* We want a negative bias in order to only have interpolation ie
1.136 brouard 3286: * to avoid the price of an extra matrix product in likelihood */
1.126 brouard 3287: dh[mi][i]=jk+1;
3288: bh[mi][i]=ju;
3289: }
3290: }else{
3291: if(jl <= -ju){
3292: dh[mi][i]=jk;
3293: bh[mi][i]=jl; /* bias is positive if real duration
3294: * is higher than the multiple of stepm and negative otherwise.
3295: */
3296: }
3297: else{
3298: dh[mi][i]=jk+1;
3299: bh[mi][i]=ju;
3300: }
3301: if(dh[mi][i]==0){
3302: dh[mi][i]=1; /* At least one step */
3303: bh[mi][i]=ju; /* At least one step */
3304: /* 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);*/
3305: }
3306: } /* end if mle */
3307: }
3308: } /* end wave */
3309: }
3310: jmean=sum/k;
3311: 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 3312: fprintf(ficlog,"Delay (in months) between two waves Min=%d (for indiviudal %d) Max=%d (%d) Mean=%f\n\n ",jmin, ijmin, jmax, ijmax, jmean);
1.126 brouard 3313: }
3314:
3315: /*********** Tricode ****************************/
1.145 brouard 3316: void tricode(int *Tvar, int **nbcode, int imx, int *Ndum)
1.126 brouard 3317: {
1.144 brouard 3318: /**< Uses cptcovn+2*cptcovprod as the number of covariates */
3319: /* 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 3320: * Boring subroutine which should only output nbcode[Tvar[j]][k]
1.145 brouard 3321: * Tvar[5] in V2+V1+V3*age+V2*V4 is 2 (V2)
1.169 brouard 3322: * nbcode[Tvar[j]][1]=
1.144 brouard 3323: */
1.130 brouard 3324:
1.145 brouard 3325: int ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
1.136 brouard 3326: int modmaxcovj=0; /* Modality max of covariates j */
1.145 brouard 3327: int cptcode=0; /* Modality max of covariates j */
3328: int modmincovj=0; /* Modality min of covariates j */
3329:
3330:
1.126 brouard 3331: cptcoveff=0;
3332:
1.144 brouard 3333: for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */
1.126 brouard 3334:
1.145 brouard 3335: /* Loop on covariates without age and products */
1.186 brouard 3336: for (j=1; j<=(cptcovs); j++) { /* From model V1 + V2*age+ V3 + V3*V4 keeps V1 + V3 = 2 only */
1.192 brouard 3337: for (k=-1; k < maxncov; k++) Ndum[k]=0;
1.186 brouard 3338: for (i=1; i<=imx; i++) { /* Loop on individuals: reads the data file to get the maximum value of the
1.136 brouard 3339: modality of this covariate Vj*/
1.145 brouard 3340: ij=(int)(covar[Tvar[j]][i]); /* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i
3341: * If product of Vn*Vm, still boolean *:
3342: * If it was coded 1, 2, 3, 4 should be splitted into 3 boolean variables
3343: * 1 => 0 0 0, 2 => 0 0 1, 3 => 0 1 1, 4=1 0 0 */
3344: /* Finds for covariate j, n=Tvar[j] of Vn . ij is the
1.136 brouard 3345: modality of the nth covariate of individual i. */
1.145 brouard 3346: if (ij > modmaxcovj)
3347: modmaxcovj=ij;
3348: else if (ij < modmincovj)
3349: modmincovj=ij;
3350: if ((ij < -1) && (ij > NCOVMAX)){
3351: printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX );
3352: exit(1);
3353: }else
1.136 brouard 3354: Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/
1.145 brouard 3355: /* If coded 1, 2, 3 , counts the number of 1 Ndum[1], number of 2, Ndum[2], etc */
1.126 brouard 3356: /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
1.136 brouard 3357: /* getting the maximum value of the modality of the covariate
3358: (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and
3359: female is 1, then modmaxcovj=1.*/
1.192 brouard 3360: } /* end for loop on individuals i */
1.145 brouard 3361: printf(" Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", j, Tvar[j], modmincovj, modmaxcovj);
1.192 brouard 3362: fprintf(ficlog," Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", j, Tvar[j], modmincovj, modmaxcovj);
1.145 brouard 3363: cptcode=modmaxcovj;
1.137 brouard 3364: /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */
1.145 brouard 3365: /*for (i=0; i<=cptcode; i++) {*/
1.192 brouard 3366: for (k=modmincovj; k<=modmaxcovj; k++) { /* k=-1 ? 0 and 1*//* For each value k of the modality of model-cov j */
3367: printf("Frequencies of covariates %d ie V%d with value %d: %d\n", j, Tvar[j], k, Ndum[k]);
3368: fprintf(ficlog, "Frequencies of covariates %d ie V%d with value %d: %d\n", j, Tvar[j], k, Ndum[k]);
3369: if( Ndum[k] != 0 ){ /* Counts if nobody answered modality k ie empty modality, we skip it and reorder */
3370: if( k != -1){
3371: ncodemax[j]++; /* ncodemax[j]= Number of modalities of the j th
3372: covariate for which somebody answered excluding
3373: undefined. Usually 2: 0 and 1. */
3374: }
3375: ncodemaxwundef[j]++; /* ncodemax[j]= Number of modalities of the j th
3376: covariate for which somebody answered including
3377: undefined. Usually 3: -1, 0 and 1. */
1.145 brouard 3378: }
3379: /* In fact ncodemax[j]=2 (dichotom. variables only) but it could be more for
3380: historical reasons: 3 if coded 1, 2, 3 and 4 and Ndum[2]=0 */
1.131 brouard 3381: } /* Ndum[-1] number of undefined modalities */
1.126 brouard 3382:
1.136 brouard 3383: /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */
1.186 brouard 3384: /* For covariate j, modalities could be 1, 2, 3, 4, 5, 6, 7.
3385: If Ndum[1]=0, Ndum[2]=0, Ndum[3]= 635, Ndum[4]=0, Ndum[5]=0, Ndum[6]=27, Ndum[7]=125;
1.145 brouard 3386: modmincovj=3; modmaxcovj = 7;
1.186 brouard 3387: There are only 3 modalities non empty 3, 6, 7 (or 2 if 27 is too few) : ncodemax[j]=3;
3388: which will be coded 0, 1, 2 which in binary on 2=3-1 digits are 0=00 1=01, 2=10;
3389: defining two dummy variables: variables V1_1 and V1_2.
1.145 brouard 3390: nbcode[Tvar[j]][ij]=k;
3391: nbcode[Tvar[j]][1]=0;
3392: nbcode[Tvar[j]][2]=1;
3393: nbcode[Tvar[j]][3]=2;
3394: */
1.192 brouard 3395: ij=0; /* ij is similar to i but can jumps over null modalities */
3396: for (i=modmincovj; i<=modmaxcovj; i++) { /* i= 1 to 2 for dichotomous, or from 1 to 3 or from -1 to 1*/
3397: if (Ndum[i] == 0) { /* If at least one individual responded to this modality k */
3398: break;
3399: }
3400: ij++;
3401: nbcode[Tvar[j]][ij]=i; /* stores the original modality i in an array nbcode, ij modality from 1 to last non-nul modality.*/
3402: cptcode = ij; /* New max modality for covar j */
3403: } /* end of loop on modality i=-1 to 1 or more */
3404:
3405: /* for (k=0; k<= cptcode; k++) { /\* k=-1 ? k=0 to 1 *\//\* Could be 1 to 4 *\//\* cptcode=modmaxcovj *\/ */
3406: /* /\*recode from 0 *\/ */
3407: /* k is a modality. If we have model=V1+V1*sex */
3408: /* then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
3409: /* But if some modality were not used, it is recoded from 0 to a newer modmaxcovj=cptcode *\/ */
3410: /* } */
3411: /* /\* cptcode = ij; *\/ /\* New max modality for covar j *\/ */
3412: /* if (ij > ncodemax[j]) { */
3413: /* printf( " Error ij=%d > ncodemax[%d]=%d\n", ij, j, ncodemax[j]); */
3414: /* fprintf(ficlog, " Error ij=%d > ncodemax[%d]=%d\n", ij, j, ncodemax[j]); */
3415: /* break; */
3416: /* } */
3417: /* } /\* end of loop on modality k *\/ */
1.137 brouard 3418: } /* end of loop on model-covariate j. nbcode[Tvarj][1]=0 and nbcode[Tvarj][2]=1 sets the value of covariate j*/
3419:
1.145 brouard 3420: for (k=-1; k< maxncov; k++) Ndum[k]=0;
1.137 brouard 3421:
1.187 brouard 3422: for (i=1; i<=ncovmodel-2-nagesqr; i++) { /* -2, cste and age and eventually age*age */
1.145 brouard 3423: /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
3424: ij=Tvar[i]; /* Tvar might be -1 if status was unknown */
1.187 brouard 3425: Ndum[ij]++; /* Might be supersed V1 + V1*age */
1.145 brouard 3426: }
1.126 brouard 3427:
1.192 brouard 3428: ij=0;
1.145 brouard 3429: for (i=0; i<= maxncov-1; i++) { /* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) */
3430: /*printf("Ndum[%d]=%d\n",i, Ndum[i]);*/
1.126 brouard 3431: if((Ndum[i]!=0) && (i<=ncovcol)){
1.192 brouard 3432: ij++;
1.145 brouard 3433: /*printf("diff Ndum[%d]=%d\n",i, Ndum[i]);*/
3434: Tvaraff[ij]=i; /*For printing (unclear) */
1.192 brouard 3435: }else{
3436: /* Tvaraff[ij]=0; */
3437: }
1.126 brouard 3438: }
1.192 brouard 3439: /* ij--; */
1.144 brouard 3440: cptcoveff=ij; /*Number of total covariates*/
1.145 brouard 3441:
1.126 brouard 3442: }
3443:
1.145 brouard 3444:
1.126 brouard 3445: /*********** Health Expectancies ****************/
3446:
1.127 brouard 3447: void evsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,char strstart[] )
1.126 brouard 3448:
3449: {
3450: /* Health expectancies, no variances */
1.164 brouard 3451: int i, j, nhstepm, hstepm, h, nstepm;
1.126 brouard 3452: int nhstepma, nstepma; /* Decreasing with age */
3453: double age, agelim, hf;
3454: double ***p3mat;
3455: double eip;
3456:
3457: pstamp(ficreseij);
3458: fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
3459: fprintf(ficreseij,"# Age");
3460: for(i=1; i<=nlstate;i++){
3461: for(j=1; j<=nlstate;j++){
3462: fprintf(ficreseij," e%1d%1d ",i,j);
3463: }
3464: fprintf(ficreseij," e%1d. ",i);
3465: }
3466: fprintf(ficreseij,"\n");
3467:
3468:
3469: if(estepm < stepm){
3470: printf ("Problem %d lower than %d\n",estepm, stepm);
3471: }
3472: else hstepm=estepm;
3473: /* We compute the life expectancy from trapezoids spaced every estepm months
3474: * This is mainly to measure the difference between two models: for example
3475: * if stepm=24 months pijx are given only every 2 years and by summing them
3476: * we are calculating an estimate of the Life Expectancy assuming a linear
3477: * progression in between and thus overestimating or underestimating according
3478: * to the curvature of the survival function. If, for the same date, we
3479: * estimate the model with stepm=1 month, we can keep estepm to 24 months
3480: * to compare the new estimate of Life expectancy with the same linear
3481: * hypothesis. A more precise result, taking into account a more precise
3482: * curvature will be obtained if estepm is as small as stepm. */
3483:
3484: /* For example we decided to compute the life expectancy with the smallest unit */
3485: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
3486: nhstepm is the number of hstepm from age to agelim
3487: nstepm is the number of stepm from age to agelin.
3488: Look at hpijx to understand the reason of that which relies in memory size
3489: and note for a fixed period like estepm months */
3490: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
3491: survival function given by stepm (the optimization length). Unfortunately it
3492: means that if the survival funtion is printed only each two years of age and if
3493: you sum them up and add 1 year (area under the trapezoids) you won't get the same
3494: results. So we changed our mind and took the option of the best precision.
3495: */
3496: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
3497:
3498: agelim=AGESUP;
3499: /* If stepm=6 months */
3500: /* Computed by stepm unit matrices, product of hstepm matrices, stored
3501: in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
3502:
3503: /* nhstepm age range expressed in number of stepm */
3504: nstepm=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
3505: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
3506: /* if (stepm >= YEARM) hstepm=1;*/
3507: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
3508: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3509:
3510: for (age=bage; age<=fage; age ++){
3511: nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
3512: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
3513: /* if (stepm >= YEARM) hstepm=1;*/
3514: nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
3515:
3516: /* If stepm=6 months */
3517: /* Computed by stepm unit matrices, product of hstepma matrices, stored
3518: in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
3519:
3520: hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
3521:
3522: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
3523:
3524: printf("%d|",(int)age);fflush(stdout);
3525: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
3526:
3527: /* Computing expectancies */
3528: for(i=1; i<=nlstate;i++)
3529: for(j=1; j<=nlstate;j++)
3530: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
3531: eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
3532:
3533: /* 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]);*/
3534:
3535: }
3536:
3537: fprintf(ficreseij,"%3.0f",age );
3538: for(i=1; i<=nlstate;i++){
3539: eip=0;
3540: for(j=1; j<=nlstate;j++){
3541: eip +=eij[i][j][(int)age];
3542: fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
3543: }
3544: fprintf(ficreseij,"%9.4f", eip );
3545: }
3546: fprintf(ficreseij,"\n");
3547:
3548: }
3549: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3550: printf("\n");
3551: fprintf(ficlog,"\n");
3552:
3553: }
3554:
1.127 brouard 3555: void cvevsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,double delti[],double **matcov,char strstart[] )
1.126 brouard 3556:
3557: {
3558: /* Covariances of health expectancies eij and of total life expectancies according
3559: to initial status i, ei. .
3560: */
3561: int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
3562: int nhstepma, nstepma; /* Decreasing with age */
3563: double age, agelim, hf;
3564: double ***p3matp, ***p3matm, ***varhe;
3565: double **dnewm,**doldm;
3566: double *xp, *xm;
3567: double **gp, **gm;
3568: double ***gradg, ***trgradg;
3569: int theta;
3570:
3571: double eip, vip;
3572:
3573: varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
3574: xp=vector(1,npar);
3575: xm=vector(1,npar);
3576: dnewm=matrix(1,nlstate*nlstate,1,npar);
3577: doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
3578:
3579: pstamp(ficresstdeij);
3580: fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
3581: fprintf(ficresstdeij,"# Age");
3582: for(i=1; i<=nlstate;i++){
3583: for(j=1; j<=nlstate;j++)
3584: fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
3585: fprintf(ficresstdeij," e%1d. ",i);
3586: }
3587: fprintf(ficresstdeij,"\n");
3588:
3589: pstamp(ficrescveij);
3590: fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
3591: fprintf(ficrescveij,"# Age");
3592: for(i=1; i<=nlstate;i++)
3593: for(j=1; j<=nlstate;j++){
3594: cptj= (j-1)*nlstate+i;
3595: for(i2=1; i2<=nlstate;i2++)
3596: for(j2=1; j2<=nlstate;j2++){
3597: cptj2= (j2-1)*nlstate+i2;
3598: if(cptj2 <= cptj)
3599: fprintf(ficrescveij," %1d%1d,%1d%1d",i,j,i2,j2);
3600: }
3601: }
3602: fprintf(ficrescveij,"\n");
3603:
3604: if(estepm < stepm){
3605: printf ("Problem %d lower than %d\n",estepm, stepm);
3606: }
3607: else hstepm=estepm;
3608: /* We compute the life expectancy from trapezoids spaced every estepm months
3609: * This is mainly to measure the difference between two models: for example
3610: * if stepm=24 months pijx are given only every 2 years and by summing them
3611: * we are calculating an estimate of the Life Expectancy assuming a linear
3612: * progression in between and thus overestimating or underestimating according
3613: * to the curvature of the survival function. If, for the same date, we
3614: * estimate the model with stepm=1 month, we can keep estepm to 24 months
3615: * to compare the new estimate of Life expectancy with the same linear
3616: * hypothesis. A more precise result, taking into account a more precise
3617: * curvature will be obtained if estepm is as small as stepm. */
3618:
3619: /* For example we decided to compute the life expectancy with the smallest unit */
3620: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
3621: nhstepm is the number of hstepm from age to agelim
3622: nstepm is the number of stepm from age to agelin.
3623: Look at hpijx to understand the reason of that which relies in memory size
3624: and note for a fixed period like estepm months */
3625: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
3626: survival function given by stepm (the optimization length). Unfortunately it
3627: means that if the survival funtion is printed only each two years of age and if
3628: you sum them up and add 1 year (area under the trapezoids) you won't get the same
3629: results. So we changed our mind and took the option of the best precision.
3630: */
3631: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
3632:
3633: /* If stepm=6 months */
3634: /* nhstepm age range expressed in number of stepm */
3635: agelim=AGESUP;
3636: nstepm=(int) rint((agelim-bage)*YEARM/stepm);
3637: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
3638: /* if (stepm >= YEARM) hstepm=1;*/
3639: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
3640:
3641: p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3642: p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3643: gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
3644: trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
3645: gp=matrix(0,nhstepm,1,nlstate*nlstate);
3646: gm=matrix(0,nhstepm,1,nlstate*nlstate);
3647:
3648: for (age=bage; age<=fage; age ++){
3649: nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
3650: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
3651: /* if (stepm >= YEARM) hstepm=1;*/
3652: nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
3653:
3654: /* If stepm=6 months */
3655: /* Computed by stepm unit matrices, product of hstepma matrices, stored
3656: in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
3657:
3658: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
3659:
3660: /* Computing Variances of health expectancies */
3661: /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
3662: decrease memory allocation */
3663: for(theta=1; theta <=npar; theta++){
3664: for(i=1; i<=npar; i++){
3665: xp[i] = x[i] + (i==theta ?delti[theta]:0);
3666: xm[i] = x[i] - (i==theta ?delti[theta]:0);
3667: }
3668: hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);
3669: hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);
3670:
3671: for(j=1; j<= nlstate; j++){
3672: for(i=1; i<=nlstate; i++){
3673: for(h=0; h<=nhstepm-1; h++){
3674: gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
3675: gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
3676: }
3677: }
3678: }
3679:
3680: for(ij=1; ij<= nlstate*nlstate; ij++)
3681: for(h=0; h<=nhstepm-1; h++){
3682: gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
3683: }
3684: }/* End theta */
3685:
3686:
3687: for(h=0; h<=nhstepm-1; h++)
3688: for(j=1; j<=nlstate*nlstate;j++)
3689: for(theta=1; theta <=npar; theta++)
3690: trgradg[h][j][theta]=gradg[h][theta][j];
3691:
3692:
3693: for(ij=1;ij<=nlstate*nlstate;ij++)
3694: for(ji=1;ji<=nlstate*nlstate;ji++)
3695: varhe[ij][ji][(int)age] =0.;
3696:
3697: printf("%d|",(int)age);fflush(stdout);
3698: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
3699: for(h=0;h<=nhstepm-1;h++){
3700: for(k=0;k<=nhstepm-1;k++){
3701: matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
3702: matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
3703: for(ij=1;ij<=nlstate*nlstate;ij++)
3704: for(ji=1;ji<=nlstate*nlstate;ji++)
3705: varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
3706: }
3707: }
3708:
3709: /* Computing expectancies */
3710: hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
3711: for(i=1; i<=nlstate;i++)
3712: for(j=1; j<=nlstate;j++)
3713: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
3714: eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
3715:
3716: /* 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]);*/
3717:
3718: }
3719:
3720: fprintf(ficresstdeij,"%3.0f",age );
3721: for(i=1; i<=nlstate;i++){
3722: eip=0.;
3723: vip=0.;
3724: for(j=1; j<=nlstate;j++){
3725: eip += eij[i][j][(int)age];
3726: for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
3727: vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
3728: fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
3729: }
3730: fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
3731: }
3732: fprintf(ficresstdeij,"\n");
3733:
3734: fprintf(ficrescveij,"%3.0f",age );
3735: for(i=1; i<=nlstate;i++)
3736: for(j=1; j<=nlstate;j++){
3737: cptj= (j-1)*nlstate+i;
3738: for(i2=1; i2<=nlstate;i2++)
3739: for(j2=1; j2<=nlstate;j2++){
3740: cptj2= (j2-1)*nlstate+i2;
3741: if(cptj2 <= cptj)
3742: fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
3743: }
3744: }
3745: fprintf(ficrescveij,"\n");
3746:
3747: }
3748: free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
3749: free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
3750: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
3751: free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
3752: free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3753: free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3754: printf("\n");
3755: fprintf(ficlog,"\n");
3756:
3757: free_vector(xm,1,npar);
3758: free_vector(xp,1,npar);
3759: free_matrix(dnewm,1,nlstate*nlstate,1,npar);
3760: free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
3761: free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
3762: }
3763:
3764: /************ Variance ******************/
3765: 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 ij, int estepm, int cptcov, int cptcod, int popbased, int mobilav, char strstart[])
3766: {
3767: /* Variance of health expectancies */
3768: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
3769: /* double **newm;*/
1.169 brouard 3770: /* int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav)*/
3771:
3772: int movingaverage();
1.126 brouard 3773: double **dnewm,**doldm;
3774: double **dnewmp,**doldmp;
3775: int i, j, nhstepm, hstepm, h, nstepm ;
1.164 brouard 3776: int k;
1.126 brouard 3777: double *xp;
3778: double **gp, **gm; /* for var eij */
3779: double ***gradg, ***trgradg; /*for var eij */
3780: double **gradgp, **trgradgp; /* for var p point j */
3781: double *gpp, *gmp; /* for var p point j */
3782: double **varppt; /* for var p point j nlstate to nlstate+ndeath */
3783: double ***p3mat;
3784: double age,agelim, hf;
3785: double ***mobaverage;
3786: int theta;
3787: char digit[4];
3788: char digitp[25];
3789:
3790: char fileresprobmorprev[FILENAMELENGTH];
3791:
3792: if(popbased==1){
3793: if(mobilav!=0)
3794: strcpy(digitp,"-populbased-mobilav-");
3795: else strcpy(digitp,"-populbased-nomobil-");
3796: }
3797: else
3798: strcpy(digitp,"-stablbased-");
3799:
3800: if (mobilav!=0) {
3801: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3802: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
3803: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
3804: printf(" Error in movingaverage mobilav=%d\n",mobilav);
3805: }
3806: }
3807:
3808: strcpy(fileresprobmorprev,"prmorprev");
3809: sprintf(digit,"%-d",ij);
3810: /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
3811: strcat(fileresprobmorprev,digit); /* Tvar to be done */
3812: strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
3813: strcat(fileresprobmorprev,fileres);
3814: if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
3815: printf("Problem with resultfile: %s\n", fileresprobmorprev);
3816: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
3817: }
3818: printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
3819:
3820: fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
3821: pstamp(ficresprobmorprev);
3822: 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);
3823: fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
3824: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
3825: fprintf(ficresprobmorprev," p.%-d SE",j);
3826: for(i=1; i<=nlstate;i++)
3827: fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
3828: }
3829: fprintf(ficresprobmorprev,"\n");
3830: fprintf(ficgp,"\n# Routine varevsij");
3831: /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
3832: 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");
3833: fprintf(fichtm,"\n<br>%s <br>\n",digitp);
3834: /* } */
3835: varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
3836: pstamp(ficresvij);
3837: fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n# (weighted average of eij where weights are ");
3838: if(popbased==1)
1.128 brouard 3839: fprintf(ficresvij,"the age specific prevalence observed (cross-sectionally) in the population i.e cross-sectionally\n in each health state (popbased=1) (mobilav=%d\n",mobilav);
1.126 brouard 3840: else
3841: fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
3842: fprintf(ficresvij,"# Age");
3843: for(i=1; i<=nlstate;i++)
3844: for(j=1; j<=nlstate;j++)
3845: fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
3846: fprintf(ficresvij,"\n");
3847:
3848: xp=vector(1,npar);
3849: dnewm=matrix(1,nlstate,1,npar);
3850: doldm=matrix(1,nlstate,1,nlstate);
3851: dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
3852: doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
3853:
3854: gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
3855: gpp=vector(nlstate+1,nlstate+ndeath);
3856: gmp=vector(nlstate+1,nlstate+ndeath);
3857: trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
3858:
3859: if(estepm < stepm){
3860: printf ("Problem %d lower than %d\n",estepm, stepm);
3861: }
3862: else hstepm=estepm;
3863: /* For example we decided to compute the life expectancy with the smallest unit */
3864: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
3865: nhstepm is the number of hstepm from age to agelim
3866: nstepm is the number of stepm from age to agelin.
1.128 brouard 3867: Look at function hpijx to understand why (it is linked to memory size questions) */
1.126 brouard 3868: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
3869: survival function given by stepm (the optimization length). Unfortunately it
3870: means that if the survival funtion is printed every two years of age and if
3871: you sum them up and add 1 year (area under the trapezoids) you won't get the same
3872: results. So we changed our mind and took the option of the best precision.
3873: */
3874: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
3875: agelim = AGESUP;
3876: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
3877: nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
3878: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
3879: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3880: gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
3881: gp=matrix(0,nhstepm,1,nlstate);
3882: gm=matrix(0,nhstepm,1,nlstate);
3883:
3884:
3885: for(theta=1; theta <=npar; theta++){
3886: for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
3887: xp[i] = x[i] + (i==theta ?delti[theta]:0);
3888: }
3889: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
3890: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
3891:
3892: if (popbased==1) {
3893: if(mobilav ==0){
3894: for(i=1; i<=nlstate;i++)
3895: prlim[i][i]=probs[(int)age][i][ij];
3896: }else{ /* mobilav */
3897: for(i=1; i<=nlstate;i++)
3898: prlim[i][i]=mobaverage[(int)age][i][ij];
3899: }
3900: }
3901:
3902: for(j=1; j<= nlstate; j++){
3903: for(h=0; h<=nhstepm; h++){
3904: for(i=1, gp[h][j]=0.;i<=nlstate;i++)
3905: gp[h][j] += prlim[i][i]*p3mat[i][j][h];
3906: }
3907: }
3908: /* This for computing probability of death (h=1 means
3909: computed over hstepm matrices product = hstepm*stepm months)
3910: as a weighted average of prlim.
3911: */
3912: for(j=nlstate+1;j<=nlstate+ndeath;j++){
3913: for(i=1,gpp[j]=0.; i<= nlstate; i++)
3914: gpp[j] += prlim[i][i]*p3mat[i][j][1];
3915: }
3916: /* end probability of death */
3917:
3918: for(i=1; i<=npar; i++) /* Computes gradient x - delta */
3919: xp[i] = x[i] - (i==theta ?delti[theta]:0);
3920: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
3921: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
3922:
3923: if (popbased==1) {
3924: if(mobilav ==0){
3925: for(i=1; i<=nlstate;i++)
3926: prlim[i][i]=probs[(int)age][i][ij];
3927: }else{ /* mobilav */
3928: for(i=1; i<=nlstate;i++)
3929: prlim[i][i]=mobaverage[(int)age][i][ij];
3930: }
3931: }
3932:
1.128 brouard 3933: for(j=1; j<= nlstate; j++){ /* Sum of wi * eij = e.j */
1.126 brouard 3934: for(h=0; h<=nhstepm; h++){
3935: for(i=1, gm[h][j]=0.;i<=nlstate;i++)
3936: gm[h][j] += prlim[i][i]*p3mat[i][j][h];
3937: }
3938: }
3939: /* This for computing probability of death (h=1 means
3940: computed over hstepm matrices product = hstepm*stepm months)
3941: as a weighted average of prlim.
3942: */
3943: for(j=nlstate+1;j<=nlstate+ndeath;j++){
3944: for(i=1,gmp[j]=0.; i<= nlstate; i++)
3945: gmp[j] += prlim[i][i]*p3mat[i][j][1];
3946: }
3947: /* end probability of death */
3948:
3949: for(j=1; j<= nlstate; j++) /* vareij */
3950: for(h=0; h<=nhstepm; h++){
3951: gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
3952: }
3953:
3954: for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
3955: gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
3956: }
3957:
3958: } /* End theta */
3959:
3960: trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
3961:
3962: for(h=0; h<=nhstepm; h++) /* veij */
3963: for(j=1; j<=nlstate;j++)
3964: for(theta=1; theta <=npar; theta++)
3965: trgradg[h][j][theta]=gradg[h][theta][j];
3966:
3967: for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
3968: for(theta=1; theta <=npar; theta++)
3969: trgradgp[j][theta]=gradgp[theta][j];
3970:
3971:
3972: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
3973: for(i=1;i<=nlstate;i++)
3974: for(j=1;j<=nlstate;j++)
3975: vareij[i][j][(int)age] =0.;
3976:
3977: for(h=0;h<=nhstepm;h++){
3978: for(k=0;k<=nhstepm;k++){
3979: matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
3980: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
3981: for(i=1;i<=nlstate;i++)
3982: for(j=1;j<=nlstate;j++)
3983: vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
3984: }
3985: }
3986:
3987: /* pptj */
3988: matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
3989: matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
3990: for(j=nlstate+1;j<=nlstate+ndeath;j++)
3991: for(i=nlstate+1;i<=nlstate+ndeath;i++)
3992: varppt[j][i]=doldmp[j][i];
3993: /* end ppptj */
3994: /* x centered again */
3995: hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);
3996: prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
3997:
3998: if (popbased==1) {
3999: if(mobilav ==0){
4000: for(i=1; i<=nlstate;i++)
4001: prlim[i][i]=probs[(int)age][i][ij];
4002: }else{ /* mobilav */
4003: for(i=1; i<=nlstate;i++)
4004: prlim[i][i]=mobaverage[(int)age][i][ij];
4005: }
4006: }
4007:
4008: /* This for computing probability of death (h=1 means
4009: computed over hstepm (estepm) matrices product = hstepm*stepm months)
4010: as a weighted average of prlim.
4011: */
4012: for(j=nlstate+1;j<=nlstate+ndeath;j++){
4013: for(i=1,gmp[j]=0.;i<= nlstate; i++)
4014: gmp[j] += prlim[i][i]*p3mat[i][j][1];
4015: }
4016: /* end probability of death */
4017:
4018: fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
4019: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
4020: fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
4021: for(i=1; i<=nlstate;i++){
4022: fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
4023: }
4024: }
4025: fprintf(ficresprobmorprev,"\n");
4026:
4027: fprintf(ficresvij,"%.0f ",age );
4028: for(i=1; i<=nlstate;i++)
4029: for(j=1; j<=nlstate;j++){
4030: fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
4031: }
4032: fprintf(ficresvij,"\n");
4033: free_matrix(gp,0,nhstepm,1,nlstate);
4034: free_matrix(gm,0,nhstepm,1,nlstate);
4035: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
4036: free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
4037: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4038: } /* End age */
4039: free_vector(gpp,nlstate+1,nlstate+ndeath);
4040: free_vector(gmp,nlstate+1,nlstate+ndeath);
4041: free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
4042: free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
1.145 brouard 4043: fprintf(ficgp,"\nunset parametric;unset label; set ter png small size 320, 240");
1.126 brouard 4044: /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
1.131 brouard 4045: fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
1.126 brouard 4046: /* fprintf(ficgp,"\n plot \"%s\" u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
4047: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
4048: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
1.145 brouard 4049: fprintf(ficgp,"\n plot \"%s\" u 1:($3) not w l lt 1 ",subdirf(fileresprobmorprev));
1.170 brouard 4050: fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)) t \"95%% interval\" w l lt 2 ",subdirf(fileresprobmorprev));
1.145 brouard 4051: fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)) not w l lt 2 ",subdirf(fileresprobmorprev));
1.126 brouard 4052: fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
4053: fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"%s%s.png\"> <br>\n", estepm,subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
4054: /* 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.png\"> <br>\n", stepm,YEARM,digitp,digit);
4055: */
4056: /* fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
4057: fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
4058:
4059: free_vector(xp,1,npar);
4060: free_matrix(doldm,1,nlstate,1,nlstate);
4061: free_matrix(dnewm,1,nlstate,1,npar);
4062: free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
4063: free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
4064: free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
4065: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4066: fclose(ficresprobmorprev);
4067: fflush(ficgp);
4068: fflush(fichtm);
4069: } /* end varevsij */
4070:
4071: /************ Variance of prevlim ******************/
4072: 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 ij, char strstart[])
4073: {
4074: /* Variance of prevalence limit */
4075: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
1.164 brouard 4076:
1.126 brouard 4077: double **dnewm,**doldm;
4078: int i, j, nhstepm, hstepm;
4079: double *xp;
4080: double *gp, *gm;
4081: double **gradg, **trgradg;
4082: double age,agelim;
4083: int theta;
4084:
4085: pstamp(ficresvpl);
4086: fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
4087: fprintf(ficresvpl,"# Age");
4088: for(i=1; i<=nlstate;i++)
4089: fprintf(ficresvpl," %1d-%1d",i,i);
4090: fprintf(ficresvpl,"\n");
4091:
4092: xp=vector(1,npar);
4093: dnewm=matrix(1,nlstate,1,npar);
4094: doldm=matrix(1,nlstate,1,nlstate);
4095:
4096: hstepm=1*YEARM; /* Every year of age */
4097: hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
4098: agelim = AGESUP;
4099: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
4100: nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
4101: if (stepm >= YEARM) hstepm=1;
4102: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
4103: gradg=matrix(1,npar,1,nlstate);
4104: gp=vector(1,nlstate);
4105: gm=vector(1,nlstate);
4106:
4107: for(theta=1; theta <=npar; theta++){
4108: for(i=1; i<=npar; i++){ /* Computes gradient */
4109: xp[i] = x[i] + (i==theta ?delti[theta]:0);
4110: }
4111: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
4112: for(i=1;i<=nlstate;i++)
4113: gp[i] = prlim[i][i];
4114:
4115: for(i=1; i<=npar; i++) /* Computes gradient */
4116: xp[i] = x[i] - (i==theta ?delti[theta]:0);
4117: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
4118: for(i=1;i<=nlstate;i++)
4119: gm[i] = prlim[i][i];
4120:
4121: for(i=1;i<=nlstate;i++)
4122: gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
4123: } /* End theta */
4124:
4125: trgradg =matrix(1,nlstate,1,npar);
4126:
4127: for(j=1; j<=nlstate;j++)
4128: for(theta=1; theta <=npar; theta++)
4129: trgradg[j][theta]=gradg[theta][j];
4130:
4131: for(i=1;i<=nlstate;i++)
4132: varpl[i][(int)age] =0.;
4133: matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
4134: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
4135: for(i=1;i<=nlstate;i++)
4136: varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
4137:
4138: fprintf(ficresvpl,"%.0f ",age );
4139: for(i=1; i<=nlstate;i++)
4140: fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
4141: fprintf(ficresvpl,"\n");
4142: free_vector(gp,1,nlstate);
4143: free_vector(gm,1,nlstate);
4144: free_matrix(gradg,1,npar,1,nlstate);
4145: free_matrix(trgradg,1,nlstate,1,npar);
4146: } /* End age */
4147:
4148: free_vector(xp,1,npar);
4149: free_matrix(doldm,1,nlstate,1,npar);
4150: free_matrix(dnewm,1,nlstate,1,nlstate);
4151:
4152: }
4153:
4154: /************ Variance of one-step probabilities ******************/
4155: 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[])
4156: {
1.164 brouard 4157: int i, j=0, k1, l1, tj;
1.126 brouard 4158: int k2, l2, j1, z1;
1.164 brouard 4159: int k=0, l;
1.145 brouard 4160: int first=1, first1, first2;
1.126 brouard 4161: double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
4162: double **dnewm,**doldm;
4163: double *xp;
4164: double *gp, *gm;
4165: double **gradg, **trgradg;
4166: double **mu;
1.164 brouard 4167: double age, cov[NCOVMAX+1];
1.126 brouard 4168: double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
4169: int theta;
4170: char fileresprob[FILENAMELENGTH];
4171: char fileresprobcov[FILENAMELENGTH];
4172: char fileresprobcor[FILENAMELENGTH];
4173: double ***varpij;
4174:
4175: strcpy(fileresprob,"prob");
4176: strcat(fileresprob,fileres);
4177: if((ficresprob=fopen(fileresprob,"w"))==NULL) {
4178: printf("Problem with resultfile: %s\n", fileresprob);
4179: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
4180: }
4181: strcpy(fileresprobcov,"probcov");
4182: strcat(fileresprobcov,fileres);
4183: if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
4184: printf("Problem with resultfile: %s\n", fileresprobcov);
4185: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
4186: }
4187: strcpy(fileresprobcor,"probcor");
4188: strcat(fileresprobcor,fileres);
4189: if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
4190: printf("Problem with resultfile: %s\n", fileresprobcor);
4191: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
4192: }
4193: printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
4194: fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
4195: printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
4196: fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
4197: printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
4198: fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
4199: pstamp(ficresprob);
4200: fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
4201: fprintf(ficresprob,"# Age");
4202: pstamp(ficresprobcov);
4203: fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
4204: fprintf(ficresprobcov,"# Age");
4205: pstamp(ficresprobcor);
4206: fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
4207: fprintf(ficresprobcor,"# Age");
4208:
4209:
4210: for(i=1; i<=nlstate;i++)
4211: for(j=1; j<=(nlstate+ndeath);j++){
4212: fprintf(ficresprob," p%1d-%1d (SE)",i,j);
4213: fprintf(ficresprobcov," p%1d-%1d ",i,j);
4214: fprintf(ficresprobcor," p%1d-%1d ",i,j);
4215: }
4216: /* fprintf(ficresprob,"\n");
4217: fprintf(ficresprobcov,"\n");
4218: fprintf(ficresprobcor,"\n");
4219: */
1.131 brouard 4220: xp=vector(1,npar);
1.126 brouard 4221: dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
4222: doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
4223: mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
4224: varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
4225: first=1;
4226: fprintf(ficgp,"\n# Routine varprob");
4227: fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
4228: fprintf(fichtm,"\n");
4229:
4230: fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
4231: fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
4232: file %s<br>\n",optionfilehtmcov);
4233: fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
4234: and drawn. It helps understanding how is the covariance between two incidences.\
4235: They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
4236: 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. \
4237: It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
4238: would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
4239: standard deviations wide on each axis. <br>\
4240: Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
4241: and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
4242: To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
4243:
4244: cov[1]=1;
1.145 brouard 4245: /* tj=cptcoveff; */
4246: tj = (int) pow(2,cptcoveff);
1.126 brouard 4247: if (cptcovn<1) {tj=1;ncodemax[1]=1;}
4248: j1=0;
1.145 brouard 4249: for(j1=1; j1<=tj;j1++){
4250: /*for(i1=1; i1<=ncodemax[t];i1++){ */
4251: /*j1++;*/
1.126 brouard 4252: if (cptcovn>0) {
4253: fprintf(ficresprob, "\n#********** Variable ");
4254: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
4255: fprintf(ficresprob, "**********\n#\n");
4256: fprintf(ficresprobcov, "\n#********** Variable ");
4257: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
4258: fprintf(ficresprobcov, "**********\n#\n");
4259:
4260: fprintf(ficgp, "\n#********** Variable ");
4261: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
4262: fprintf(ficgp, "**********\n#\n");
4263:
4264:
4265: fprintf(fichtmcov, "\n<hr size=\"2\" color=\"#EC5E5E\">********** Variable ");
4266: for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
4267: fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
4268:
4269: fprintf(ficresprobcor, "\n#********** Variable ");
4270: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
4271: fprintf(ficresprobcor, "**********\n#");
4272: }
4273:
1.145 brouard 4274: gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
4275: trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
4276: gp=vector(1,(nlstate)*(nlstate+ndeath));
4277: gm=vector(1,(nlstate)*(nlstate+ndeath));
1.126 brouard 4278: for (age=bage; age<=fage; age ++){
4279: cov[2]=age;
1.187 brouard 4280: if(nagesqr==1)
4281: cov[3]= age*age;
1.126 brouard 4282: for (k=1; k<=cptcovn;k++) {
1.187 brouard 4283: cov[2+nagesqr+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];/* j1 1 2 3 4
1.145 brouard 4284: * 1 1 1 1 1
4285: * 2 2 1 1 1
4286: * 3 1 2 1 1
4287: */
4288: /* nbcode[1][1]=0 nbcode[1][2]=1;*/
1.126 brouard 4289: }
1.186 brouard 4290: /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
4291: for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtab[ij][Tvar[Tage[k]]]]*cov[2];
1.126 brouard 4292: for (k=1; k<=cptcovprod;k++)
1.187 brouard 4293: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
1.126 brouard 4294:
4295:
4296: for(theta=1; theta <=npar; theta++){
4297: for(i=1; i<=npar; i++)
4298: xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
4299:
4300: pmij(pmmij,cov,ncovmodel,xp,nlstate);
4301:
4302: k=0;
4303: for(i=1; i<= (nlstate); i++){
4304: for(j=1; j<=(nlstate+ndeath);j++){
4305: k=k+1;
4306: gp[k]=pmmij[i][j];
4307: }
4308: }
4309:
4310: for(i=1; i<=npar; i++)
4311: xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
4312:
4313: pmij(pmmij,cov,ncovmodel,xp,nlstate);
4314: k=0;
4315: for(i=1; i<=(nlstate); i++){
4316: for(j=1; j<=(nlstate+ndeath);j++){
4317: k=k+1;
4318: gm[k]=pmmij[i][j];
4319: }
4320: }
4321:
4322: for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)
4323: gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];
4324: }
4325:
4326: for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
4327: for(theta=1; theta <=npar; theta++)
4328: trgradg[j][theta]=gradg[theta][j];
4329:
4330: matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);
4331: matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
4332:
4333: pmij(pmmij,cov,ncovmodel,x,nlstate);
4334:
4335: k=0;
4336: for(i=1; i<=(nlstate); i++){
4337: for(j=1; j<=(nlstate+ndeath);j++){
4338: k=k+1;
4339: mu[k][(int) age]=pmmij[i][j];
4340: }
4341: }
4342: for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
4343: for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
4344: varpij[i][j][(int)age] = doldm[i][j];
4345:
4346: /*printf("\n%d ",(int)age);
4347: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
4348: printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
4349: fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
4350: }*/
4351:
4352: fprintf(ficresprob,"\n%d ",(int)age);
4353: fprintf(ficresprobcov,"\n%d ",(int)age);
4354: fprintf(ficresprobcor,"\n%d ",(int)age);
4355:
4356: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
4357: fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
4358: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
4359: fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
4360: fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
4361: }
4362: i=0;
4363: for (k=1; k<=(nlstate);k++){
4364: for (l=1; l<=(nlstate+ndeath);l++){
1.145 brouard 4365: i++;
1.126 brouard 4366: fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
4367: fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
4368: for (j=1; j<=i;j++){
1.145 brouard 4369: /* printf(" k=%d l=%d i=%d j=%d\n",k,l,i,j);fflush(stdout); */
1.126 brouard 4370: fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
4371: fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
4372: }
4373: }
4374: }/* end of loop for state */
4375: } /* end of loop for age */
1.145 brouard 4376: free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
4377: free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
4378: free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
4379: free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
4380:
1.126 brouard 4381: /* Confidence intervalle of pij */
4382: /*
1.131 brouard 4383: fprintf(ficgp,"\nunset parametric;unset label");
1.126 brouard 4384: fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
4385: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
4386: 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);
4387: fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
4388: fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
4389: fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
4390: */
4391:
4392: /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
1.145 brouard 4393: first1=1;first2=2;
1.126 brouard 4394: for (k2=1; k2<=(nlstate);k2++){
4395: for (l2=1; l2<=(nlstate+ndeath);l2++){
4396: if(l2==k2) continue;
4397: j=(k2-1)*(nlstate+ndeath)+l2;
4398: for (k1=1; k1<=(nlstate);k1++){
4399: for (l1=1; l1<=(nlstate+ndeath);l1++){
4400: if(l1==k1) continue;
4401: i=(k1-1)*(nlstate+ndeath)+l1;
4402: if(i<=j) continue;
4403: for (age=bage; age<=fage; age ++){
4404: if ((int)age %5==0){
4405: v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
4406: v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
4407: cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
4408: mu1=mu[i][(int) age]/stepm*YEARM ;
4409: mu2=mu[j][(int) age]/stepm*YEARM;
4410: c12=cv12/sqrt(v1*v2);
4411: /* Computing eigen value of matrix of covariance */
4412: lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
4413: lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
1.135 brouard 4414: if ((lc2 <0) || (lc1 <0) ){
1.145 brouard 4415: if(first2==1){
4416: first1=0;
4417: 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);
4418: }
4419: 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);
4420: /* lc1=fabs(lc1); */ /* If we want to have them positive */
4421: /* lc2=fabs(lc2); */
1.135 brouard 4422: }
4423:
1.126 brouard 4424: /* Eigen vectors */
4425: v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
4426: /*v21=sqrt(1.-v11*v11); *//* error */
4427: v21=(lc1-v1)/cv12*v11;
4428: v12=-v21;
4429: v22=v11;
4430: tnalp=v21/v11;
4431: if(first1==1){
4432: first1=0;
4433: 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);
4434: }
4435: 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);
4436: /*printf(fignu*/
4437: /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
4438: /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
4439: if(first==1){
4440: first=0;
4441: fprintf(ficgp,"\nset parametric;unset label");
4442: fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k1,l1,k2,l2);
1.145 brouard 4443: fprintf(ficgp,"\nset ter png small size 320, 240");
1.126 brouard 4444: fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
4445: :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
4446: %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
4447: subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
4448: subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
4449: fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
4450: fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
4451: fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
4452: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
4453: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
4454: 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",\
4455: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
4456: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
4457: }else{
4458: first=0;
4459: fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
4460: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
4461: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
4462: 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",\
4463: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
4464: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
4465: }/* if first */
4466: } /* age mod 5 */
4467: } /* end loop age */
4468: fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
4469: first=1;
4470: } /*l12 */
4471: } /* k12 */
4472: } /*l1 */
4473: }/* k1 */
1.169 brouard 4474: /* } */ /* loop covariates */
1.126 brouard 4475: }
4476: free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
4477: free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
4478: free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
4479: free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
4480: free_vector(xp,1,npar);
4481: fclose(ficresprob);
4482: fclose(ficresprobcov);
4483: fclose(ficresprobcor);
4484: fflush(ficgp);
4485: fflush(fichtmcov);
4486: }
4487:
4488:
4489: /******************* Printing html file ***********/
4490: void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
4491: int lastpass, int stepm, int weightopt, char model[],\
4492: int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
4493: int popforecast, int estepm ,\
4494: double jprev1, double mprev1,double anprev1, \
4495: double jprev2, double mprev2,double anprev2){
4496: int jj1, k1, i1, cpt;
4497:
4498: fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
4499: <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
4500: </ul>");
4501: fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \
4502: - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
4503: jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
4504: fprintf(fichtm,"\
4505: - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
4506: stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
4507: fprintf(fichtm,"\
4508: - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
4509: subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
4510: fprintf(fichtm,"\
1.128 brouard 4511: - (a) Life expectancies by health status at initial age, ei. (b) health expectancies by health status at initial age, eij . If one or more covariates are included, specific tables for each value of the covariate are output in sequences within the same file (estepm=%2d months): \
1.126 brouard 4512: <a href=\"%s\">%s</a> <br>\n",
4513: estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
4514: fprintf(fichtm,"\
4515: - Population projections by age and states: \
4516: <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileres,"f"),subdirf2(fileres,"f"));
4517:
4518: fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
4519:
1.145 brouard 4520: m=pow(2,cptcoveff);
1.126 brouard 4521: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
4522:
4523: jj1=0;
4524: for(k1=1; k1<=m;k1++){
1.192 brouard 4525: /* for(i1=1; i1<=ncodemax[k1];i1++){ */
1.126 brouard 4526: jj1++;
4527: if (cptcovn > 0) {
4528: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
1.192 brouard 4529: for (cpt=1; cpt<=cptcoveff;cpt++){
1.126 brouard 4530: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
1.192 brouard 4531: printf(" V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);fflush(stdout);
4532: }
1.126 brouard 4533: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
4534: }
4535: /* Pij */
1.145 brouard 4536: fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i, %d (stepm) months before: <a href=\"%s%d_1.png\">%s%d_1.png</a><br> \
4537: <img src=\"%s%d_1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
1.126 brouard 4538: /* Quasi-incidences */
4539: fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
1.145 brouard 4540: before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: <a href=\"%s%d_2.png\">%s%d_2.png</a><br> \
4541: <img src=\"%s%d_2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
1.126 brouard 4542: /* Period (stable) prevalence in each health state */
1.154 brouard 4543: for(cpt=1; cpt<=nlstate;cpt++){
1.166 brouard 4544: fprintf(fichtm,"<br>- 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.png\">%s%d_%d.png</a><br> \
4545: <img src=\"%s%d_%d.png\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
1.126 brouard 4546: }
4547: for(cpt=1; cpt<=nlstate;cpt++) {
1.154 brouard 4548: 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) : <a href=\"%s%d%d.png\">%s%d%d.png</a> <br> \
4549: <img src=\"%s%d%d.png\">",cpt,nlstate,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
1.126 brouard 4550: }
1.192 brouard 4551: /* } /\* end i1 *\/ */
1.126 brouard 4552: }/* End k1 */
4553: fprintf(fichtm,"</ul>");
4554:
4555: fprintf(fichtm,"\
4556: \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
1.193 brouard 4557: - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br> \
4558: - 95%% confidence intervals and T statistics are in the log file.<br>\n", rfileres,rfileres);
1.126 brouard 4559:
1.193 brouard 4560: fprintf(fichtm," - Standard deviation of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
1.126 brouard 4561: subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
4562: fprintf(fichtm,"\
4563: - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
4564: subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
4565:
4566: fprintf(fichtm,"\
4567: - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
4568: subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
4569: fprintf(fichtm,"\
4570: - 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): \
4571: <a href=\"%s\">%s</a> <br>\n</li>",
4572: estepm,subdirf2(fileres,"cve"),subdirf2(fileres,"cve"));
4573: fprintf(fichtm,"\
4574: - (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): \
4575: <a href=\"%s\">%s</a> <br>\n</li>",
4576: estepm,subdirf2(fileres,"stde"),subdirf2(fileres,"stde"));
4577: fprintf(fichtm,"\
1.128 brouard 4578: - 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",
1.126 brouard 4579: estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
4580: fprintf(fichtm,"\
1.128 brouard 4581: - 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",
4582: estepm, subdirf2(fileres,"t"),subdirf2(fileres,"t"));
1.126 brouard 4583: fprintf(fichtm,"\
4584: - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
4585: subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
4586:
4587: /* if(popforecast==1) fprintf(fichtm,"\n */
4588: /* - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
4589: /* - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
4590: /* <br>",fileres,fileres,fileres,fileres); */
4591: /* else */
4592: /* 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); */
4593: fflush(fichtm);
4594: fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
4595:
1.145 brouard 4596: m=pow(2,cptcoveff);
1.126 brouard 4597: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
4598:
4599: jj1=0;
4600: for(k1=1; k1<=m;k1++){
1.192 brouard 4601: /* for(i1=1; i1<=ncodemax[k1];i1++){ */
1.126 brouard 4602: jj1++;
4603: if (cptcovn > 0) {
4604: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
4605: for (cpt=1; cpt<=cptcoveff;cpt++)
4606: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
4607: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
4608: }
4609: for(cpt=1; cpt<=nlstate;cpt++) {
4610: fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
1.145 brouard 4611: prevalence (with 95%% confidence interval) in state (%d): %s%d_%d.png <br>\
4612: <img src=\"%s%d_%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);
1.126 brouard 4613: }
4614: fprintf(fichtm,"\n<br>- Total life expectancy by age and \
1.128 brouard 4615: health expectancies in states (1) and (2). If popbased=1 the smooth (due to the model) \
4616: true period expectancies (those weighted with period prevalences are also\
4617: drawn in addition to the population based expectancies computed using\
4618: observed and cahotic prevalences: %s%d.png<br>\
1.126 brouard 4619: <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
1.192 brouard 4620: /* } /\* end i1 *\/ */
1.126 brouard 4621: }/* End k1 */
4622: fprintf(fichtm,"</ul>");
4623: fflush(fichtm);
4624: }
4625:
4626: /******************* Gnuplot file **************/
4627: void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
4628:
4629: char dirfileres[132],optfileres[132];
1.164 brouard 4630: int cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,ij=0,l=0;
1.130 brouard 4631: int ng=0;
1.126 brouard 4632: /* if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
4633: /* printf("Problem with file %s",optionfilegnuplot); */
4634: /* fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
4635: /* } */
4636:
4637: /*#ifdef windows */
4638: fprintf(ficgp,"cd \"%s\" \n",pathc);
4639: /*#endif */
4640: m=pow(2,cptcoveff);
4641:
4642: strcpy(dirfileres,optionfilefiname);
4643: strcpy(optfileres,"vpl");
4644: /* 1eme*/
1.153 brouard 4645: fprintf(ficgp,"\n# 1st: Period (stable) prevalence with CI: 'vpl' files\n");
1.126 brouard 4646: for (cpt=1; cpt<= nlstate ; cpt ++) {
1.145 brouard 4647: for (k1=1; k1<= m ; k1 ++) { /* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */
4648: fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
4649: fprintf(ficgp,"\n#set out \"v%s%d_%d.png\" \n",optionfilefiname,cpt,k1);
1.126 brouard 4650: fprintf(ficgp,"set xlabel \"Age\" \n\
4651: set ylabel \"Probability\" \n\
1.145 brouard 4652: set ter png small size 320, 240\n\
1.170 brouard 4653: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
1.126 brouard 4654:
4655: for (i=1; i<= nlstate ; i ++) {
1.170 brouard 4656: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
4657: else fprintf(ficgp," %%*lf (%%*lf)");
1.126 brouard 4658: }
1.170 brouard 4659: fprintf(ficgp,"\" t\"Period (stable) prevalence\" w l lt 0,\"%s\" every :::%d::%d u 1:($2+1.96*$3) \"%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
1.126 brouard 4660: for (i=1; i<= nlstate ; i ++) {
1.170 brouard 4661: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
4662: else fprintf(ficgp," %%*lf (%%*lf)");
1.126 brouard 4663: }
1.170 brouard 4664: fprintf(ficgp,"\" t\"95%% CI\" w l lt 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
1.126 brouard 4665: for (i=1; i<= nlstate ; i ++) {
1.170 brouard 4666: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
4667: else fprintf(ficgp," %%*lf (%%*lf)");
1.126 brouard 4668: }
1.145 brouard 4669: fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l lt 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
1.126 brouard 4670: }
4671: }
4672: /*2 eme*/
1.153 brouard 4673: fprintf(ficgp,"\n# 2nd: Total life expectancy with CI: 't' files\n");
1.126 brouard 4674: for (k1=1; k1<= m ; k1 ++) {
4675: fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
1.145 brouard 4676: fprintf(ficgp,"set ylabel \"Years\" \nset ter png small size 320, 240\nplot [%.f:%.f] ",ageminpar,fage);
1.126 brouard 4677:
4678: for (i=1; i<= nlstate+1 ; i ++) {
4679: k=2*i;
1.170 brouard 4680: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
1.126 brouard 4681: for (j=1; j<= nlstate+1 ; j ++) {
1.170 brouard 4682: if (j==i) fprintf(ficgp," %%lf (%%lf)");
4683: else fprintf(ficgp," %%*lf (%%*lf)");
1.126 brouard 4684: }
4685: if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
4686: else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
1.170 brouard 4687: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
1.126 brouard 4688: for (j=1; j<= nlstate+1 ; j ++) {
1.170 brouard 4689: if (j==i) fprintf(ficgp," %%lf (%%lf)");
4690: else fprintf(ficgp," %%*lf (%%*lf)");
1.126 brouard 4691: }
1.145 brouard 4692: fprintf(ficgp,"\" t\"\" w l lt 0,");
1.170 brouard 4693: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
1.126 brouard 4694: for (j=1; j<= nlstate+1 ; j ++) {
1.170 brouard 4695: if (j==i) fprintf(ficgp," %%lf (%%lf)");
4696: else fprintf(ficgp," %%*lf (%%*lf)");
1.126 brouard 4697: }
1.145 brouard 4698: if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l lt 0");
4699: else fprintf(ficgp,"\" t\"\" w l lt 0,");
1.126 brouard 4700: }
4701: }
4702:
4703: /*3eme*/
4704:
4705: for (k1=1; k1<= m ; k1 ++) {
4706: for (cpt=1; cpt<= nlstate ; cpt ++) {
4707: /* k=2+nlstate*(2*cpt-2); */
4708: k=2+(nlstate+1)*(cpt-1);
4709: fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
1.145 brouard 4710: fprintf(ficgp,"set ter png small size 320, 240\n\
1.126 brouard 4711: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
4712: /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
4713: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
4714: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
4715: fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
4716: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
4717: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
4718:
4719: */
4720: for (i=1; i< nlstate ; i ++) {
4721: fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+i,cpt,i+1);
4722: /* 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);*/
4723:
4724: }
4725: fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+nlstate,cpt);
4726: }
4727: }
4728:
4729: /* CV preval stable (period) */
1.153 brouard 4730: for (k1=1; k1<= m ; k1 ++) { /* For each multivariate if any */
4731: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
1.126 brouard 4732: k=3;
1.153 brouard 4733: fprintf(ficgp,"\n#\n#\n#CV preval stable (period): 'pij' files, cov=%d state=%d",k1, cpt);
1.145 brouard 4734: fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
1.126 brouard 4735: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
1.145 brouard 4736: set ter png small size 320, 240\n\
1.126 brouard 4737: unset log y\n\
1.153 brouard 4738: plot [%.f:%.f] ", ageminpar, agemaxpar);
4739: for (i=1; i<= nlstate ; i ++){
4740: if(i==1)
4741: fprintf(ficgp,"\"%s\"",subdirf2(fileres,"pij"));
4742: else
4743: fprintf(ficgp,", '' ");
1.154 brouard 4744: l=(nlstate+ndeath)*(i-1)+1;
4745: fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
1.153 brouard 4746: for (j=1; j<= (nlstate-1) ; j ++)
4747: fprintf(ficgp,"+$%d",k+l+j);
4748: fprintf(ficgp,")) t \"prev(%d,%d)\" w l",i,cpt);
4749: } /* nlstate */
4750: fprintf(ficgp,"\n");
4751: } /* end cpt state*/
4752: } /* end covariate */
1.126 brouard 4753:
4754: /* proba elementaires */
1.187 brouard 4755: fprintf(ficgp,"\n##############\n#MLE estimated parameters\n#############\n");
1.126 brouard 4756: for(i=1,jk=1; i <=nlstate; i++){
1.187 brouard 4757: fprintf(ficgp,"# initial state %d\n",i);
1.126 brouard 4758: for(k=1; k <=(nlstate+ndeath); k++){
4759: if (k != i) {
1.187 brouard 4760: fprintf(ficgp,"# current state %d\n",k);
1.126 brouard 4761: for(j=1; j <=ncovmodel; j++){
1.187 brouard 4762: fprintf(ficgp,"p%d=%f; ",jk,p[jk]);
1.126 brouard 4763: jk++;
4764: }
1.187 brouard 4765: fprintf(ficgp,"\n");
1.126 brouard 4766: }
4767: }
4768: }
1.187 brouard 4769: fprintf(ficgp,"##############\n#\n");
4770:
1.145 brouard 4771: /*goto avoid;*/
1.187 brouard 4772: fprintf(ficgp,"\n##############\n#Graphics of of probabilities or incidences\n#############\n");
4773: fprintf(ficgp,"# logi(p12/p11)=a12+b12*age+c12age*age+d12*V1+e12*V1*age\n");
4774: fprintf(ficgp,"# logi(p12/p11)=p1 +p2*age +p3*age*age+ p4*V1+ p5*V1*age\n");
4775: fprintf(ficgp,"# logi(p13/p11)=a13+b13*age+c13age*age+d13*V1+e13*V1*age\n");
4776: fprintf(ficgp,"# logi(p13/p11)=p6 +p7*age +p8*age*age+ p9*V1+ p10*V1*age\n");
4777: fprintf(ficgp,"# p12+p13+p14+p11=1=p11(1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n");
4778: fprintf(ficgp,"# +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age)+...)\n");
4779: fprintf(ficgp,"# p11=1/(1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n");
4780: fprintf(ficgp,"# +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age)+...)\n");
4781: fprintf(ficgp,"# p12=exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)/\n");
4782: fprintf(ficgp,"# (1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n");
4783: fprintf(ficgp,"# +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age))\n");
4784: fprintf(ficgp,"# +exp(a14+b14*age+c14age*age+d14*V1+e14*V1*age)+...)\n");
4785: fprintf(ficgp,"#\n");
1.126 brouard 4786: for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
1.187 brouard 4787: fprintf(ficgp,"# ng=%d\n",ng);
4788: fprintf(ficgp,"# jk=1 to 2^%d=%d\n",cptcoveff,m);
1.126 brouard 4789: for(jk=1; jk <=m; jk++) {
1.187 brouard 4790: fprintf(ficgp,"# jk=%d\n",jk);
1.145 brouard 4791: fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng);
1.126 brouard 4792: if (ng==2)
4793: fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
4794: else
4795: fprintf(ficgp,"\nset title \"Probability\"\n");
1.145 brouard 4796: fprintf(ficgp,"\nset ter png small size 320, 240\nset log y\nplot [%.f:%.f] ",ageminpar,agemaxpar);
1.126 brouard 4797: i=1;
4798: for(k2=1; k2<=nlstate; k2++) {
4799: k3=i;
4800: for(k=1; k<=(nlstate+ndeath); k++) {
4801: if (k != k2){
4802: if(ng==2)
1.187 brouard 4803: if(nagesqr==0)
4804: fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
4805: else /* nagesqr =1 */
4806: fprintf(ficgp," %f*exp(p%d+p%d*x+p%d*x*x",YEARM/stepm,i,i+1,i+1+nagesqr);
1.126 brouard 4807: else
1.187 brouard 4808: if(nagesqr==0)
4809: fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
4810: else /* nagesqr =1 */
4811: fprintf(ficgp," exp(p%d+p%d*x+p%d*x*x",i,i+1,i+1+nagesqr);
1.141 brouard 4812: ij=1;/* To be checked else nbcode[0][0] wrong */
1.187 brouard 4813: for(j=3; j <=ncovmodel-nagesqr; j++) {
1.186 brouard 4814: if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) { /* Bug valgrind */
1.187 brouard 4815: fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
1.186 brouard 4816: ij++;
4817: }
4818: else
1.187 brouard 4819: fprintf(ficgp,"+p%d*%d",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
1.126 brouard 4820: }
4821: fprintf(ficgp,")/(1");
4822:
1.187 brouard 4823: for(k1=1; k1 <=nlstate; k1++){
4824: if(nagesqr==0)
4825: fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
4826: else /* nagesqr =1 */
4827: 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);
4828:
1.126 brouard 4829: ij=1;
1.187 brouard 4830: for(j=3; j <=ncovmodel-nagesqr; j++){
1.186 brouard 4831: if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
1.187 brouard 4832: fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
1.186 brouard 4833: ij++;
4834: }
4835: else
1.187 brouard 4836: fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
1.126 brouard 4837: }
4838: fprintf(ficgp,")");
4839: }
4840: fprintf(ficgp,") t \"p%d%d\" ", k2,k);
4841: if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
4842: i=i+ncovmodel;
4843: }
4844: } /* end k */
4845: } /* end k2 */
4846: } /* end jk */
4847: } /* end ng */
1.164 brouard 4848: /* avoid: */
1.126 brouard 4849: fflush(ficgp);
4850: } /* end gnuplot */
4851:
4852:
4853: /*************** Moving average **************/
4854: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
4855:
4856: int i, cpt, cptcod;
4857: int modcovmax =1;
4858: int mobilavrange, mob;
4859: double age;
4860:
4861: modcovmax=2*cptcoveff;/* Max number of modalities. We suppose
4862: a covariate has 2 modalities */
4863: if (cptcovn<1) modcovmax=1; /* At least 1 pass */
4864:
4865: if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
4866: if(mobilav==1) mobilavrange=5; /* default */
4867: else mobilavrange=mobilav;
4868: for (age=bage; age<=fage; age++)
4869: for (i=1; i<=nlstate;i++)
4870: for (cptcod=1;cptcod<=modcovmax;cptcod++)
4871: mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
4872: /* We keep the original values on the extreme ages bage, fage and for
4873: fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
4874: we use a 5 terms etc. until the borders are no more concerned.
4875: */
4876: for (mob=3;mob <=mobilavrange;mob=mob+2){
4877: for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
4878: for (i=1; i<=nlstate;i++){
4879: for (cptcod=1;cptcod<=modcovmax;cptcod++){
4880: mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
4881: for (cpt=1;cpt<=(mob-1)/2;cpt++){
4882: mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
4883: mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
4884: }
4885: mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
4886: }
4887: }
4888: }/* end age */
4889: }/* end mob */
4890: }else return -1;
4891: return 0;
4892: }/* End movingaverage */
4893:
4894:
4895: /************** Forecasting ******************/
1.169 brouard 4896: 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 4897: /* proj1, year, month, day of starting projection
4898: agemin, agemax range of age
4899: dateprev1 dateprev2 range of dates during which prevalence is computed
4900: anproj2 year of en of projection (same day and month as proj1).
4901: */
1.164 brouard 4902: int yearp, stepsize, hstepm, nhstepm, j, k, cptcod, i, h, i1;
1.126 brouard 4903: double agec; /* generic age */
4904: double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
4905: double *popeffectif,*popcount;
4906: double ***p3mat;
4907: double ***mobaverage;
4908: char fileresf[FILENAMELENGTH];
4909:
4910: agelim=AGESUP;
4911: prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
4912:
4913: strcpy(fileresf,"f");
4914: strcat(fileresf,fileres);
4915: if((ficresf=fopen(fileresf,"w"))==NULL) {
4916: printf("Problem with forecast resultfile: %s\n", fileresf);
4917: fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
4918: }
4919: printf("Computing forecasting: result on file '%s' \n", fileresf);
4920: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
4921:
4922: if (cptcoveff==0) ncodemax[cptcoveff]=1;
4923:
4924: if (mobilav!=0) {
4925: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4926: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
4927: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
4928: printf(" Error in movingaverage mobilav=%d\n",mobilav);
4929: }
4930: }
4931:
4932: stepsize=(int) (stepm+YEARM-1)/YEARM;
4933: if (stepm<=12) stepsize=1;
4934: if(estepm < stepm){
4935: printf ("Problem %d lower than %d\n",estepm, stepm);
4936: }
4937: else hstepm=estepm;
4938:
4939: hstepm=hstepm/stepm;
4940: yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp and
4941: fractional in yp1 */
4942: anprojmean=yp;
4943: yp2=modf((yp1*12),&yp);
4944: mprojmean=yp;
4945: yp1=modf((yp2*30.5),&yp);
4946: jprojmean=yp;
4947: if(jprojmean==0) jprojmean=1;
4948: if(mprojmean==0) jprojmean=1;
4949:
4950: i1=cptcoveff;
4951: if (cptcovn < 1){i1=1;}
4952:
4953: fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);
4954:
4955: fprintf(ficresf,"#****** Routine prevforecast **\n");
4956:
4957: /* if (h==(int)(YEARM*yearp)){ */
4958: for(cptcov=1, k=0;cptcov<=i1;cptcov++){
4959: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
4960: k=k+1;
4961: fprintf(ficresf,"\n#******");
4962: for(j=1;j<=cptcoveff;j++) {
4963: fprintf(ficresf," V%d=%d, hpijx=probability over h years, hp.jx is weighted by observed prev ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4964: }
4965: fprintf(ficresf,"******\n");
4966: fprintf(ficresf,"# Covariate valuofcovar yearproj age");
4967: for(j=1; j<=nlstate+ndeath;j++){
4968: for(i=1; i<=nlstate;i++)
4969: fprintf(ficresf," p%d%d",i,j);
4970: fprintf(ficresf," p.%d",j);
4971: }
4972: for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {
4973: fprintf(ficresf,"\n");
4974: fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);
4975:
4976: for (agec=fage; agec>=(ageminpar-1); agec--){
4977: nhstepm=(int) rint((agelim-agec)*YEARM/stepm);
4978: nhstepm = nhstepm/hstepm;
4979: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4980: oldm=oldms;savm=savms;
4981: hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);
4982:
4983: for (h=0; h<=nhstepm; h++){
4984: if (h*hstepm/YEARM*stepm ==yearp) {
4985: fprintf(ficresf,"\n");
4986: for(j=1;j<=cptcoveff;j++)
4987: fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4988: fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
4989: }
4990: for(j=1; j<=nlstate+ndeath;j++) {
4991: ppij=0.;
4992: for(i=1; i<=nlstate;i++) {
4993: if (mobilav==1)
4994: ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
4995: else {
4996: ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
4997: }
4998: if (h*hstepm/YEARM*stepm== yearp) {
4999: fprintf(ficresf," %.3f", p3mat[i][j][h]);
5000: }
5001: } /* end i */
5002: if (h*hstepm/YEARM*stepm==yearp) {
5003: fprintf(ficresf," %.3f", ppij);
5004: }
5005: }/* end j */
5006: } /* end h */
5007: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5008: } /* end agec */
5009: } /* end yearp */
5010: } /* end cptcod */
5011: } /* end cptcov */
5012:
5013: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
5014:
5015: fclose(ficresf);
5016: }
5017:
5018: /************** Forecasting *****not tested NB*************/
1.169 brouard 5019: void populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){
1.126 brouard 5020:
5021: int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
5022: int *popage;
5023: double calagedatem, agelim, kk1, kk2;
5024: double *popeffectif,*popcount;
5025: double ***p3mat,***tabpop,***tabpopprev;
5026: double ***mobaverage;
5027: char filerespop[FILENAMELENGTH];
5028:
5029: tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
5030: tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
5031: agelim=AGESUP;
5032: calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
5033:
5034: prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
5035:
5036:
5037: strcpy(filerespop,"pop");
5038: strcat(filerespop,fileres);
5039: if((ficrespop=fopen(filerespop,"w"))==NULL) {
5040: printf("Problem with forecast resultfile: %s\n", filerespop);
5041: fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
5042: }
5043: printf("Computing forecasting: result on file '%s' \n", filerespop);
5044: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
5045:
5046: if (cptcoveff==0) ncodemax[cptcoveff]=1;
5047:
5048: if (mobilav!=0) {
5049: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
5050: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
5051: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
5052: printf(" Error in movingaverage mobilav=%d\n",mobilav);
5053: }
5054: }
5055:
5056: stepsize=(int) (stepm+YEARM-1)/YEARM;
5057: if (stepm<=12) stepsize=1;
5058:
5059: agelim=AGESUP;
5060:
5061: hstepm=1;
5062: hstepm=hstepm/stepm;
5063:
5064: if (popforecast==1) {
5065: if((ficpop=fopen(popfile,"r"))==NULL) {
5066: printf("Problem with population file : %s\n",popfile);exit(0);
5067: fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
5068: }
5069: popage=ivector(0,AGESUP);
5070: popeffectif=vector(0,AGESUP);
5071: popcount=vector(0,AGESUP);
5072:
5073: i=1;
5074: while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
5075:
5076: imx=i;
5077: for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
5078: }
5079:
5080: for(cptcov=1,k=0;cptcov<=i2;cptcov++){
5081: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
5082: k=k+1;
5083: fprintf(ficrespop,"\n#******");
5084: for(j=1;j<=cptcoveff;j++) {
5085: fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5086: }
5087: fprintf(ficrespop,"******\n");
5088: fprintf(ficrespop,"# Age");
5089: for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
5090: if (popforecast==1) fprintf(ficrespop," [Population]");
5091:
5092: for (cpt=0; cpt<=0;cpt++) {
5093: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
5094:
5095: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
5096: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
5097: nhstepm = nhstepm/hstepm;
5098:
5099: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5100: oldm=oldms;savm=savms;
5101: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
5102:
5103: for (h=0; h<=nhstepm; h++){
5104: if (h==(int) (calagedatem+YEARM*cpt)) {
5105: fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
5106: }
5107: for(j=1; j<=nlstate+ndeath;j++) {
5108: kk1=0.;kk2=0;
5109: for(i=1; i<=nlstate;i++) {
5110: if (mobilav==1)
5111: kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
5112: else {
5113: kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
5114: }
5115: }
5116: if (h==(int)(calagedatem+12*cpt)){
5117: tabpop[(int)(agedeb)][j][cptcod]=kk1;
5118: /*fprintf(ficrespop," %.3f", kk1);
5119: if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
5120: }
5121: }
5122: for(i=1; i<=nlstate;i++){
5123: kk1=0.;
5124: for(j=1; j<=nlstate;j++){
5125: kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];
5126: }
5127: tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
5128: }
5129:
5130: if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++)
5131: fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
5132: }
5133: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5134: }
5135: }
5136:
5137: /******/
5138:
5139: for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {
5140: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
5141: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
5142: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
5143: nhstepm = nhstepm/hstepm;
5144:
5145: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5146: oldm=oldms;savm=savms;
5147: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
5148: for (h=0; h<=nhstepm; h++){
5149: if (h==(int) (calagedatem+YEARM*cpt)) {
5150: fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
5151: }
5152: for(j=1; j<=nlstate+ndeath;j++) {
5153: kk1=0.;kk2=0;
5154: for(i=1; i<=nlstate;i++) {
5155: kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];
5156: }
5157: if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);
5158: }
5159: }
5160: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5161: }
5162: }
5163: }
5164: }
5165:
5166: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
5167:
5168: if (popforecast==1) {
5169: free_ivector(popage,0,AGESUP);
5170: free_vector(popeffectif,0,AGESUP);
5171: free_vector(popcount,0,AGESUP);
5172: }
5173: free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
5174: free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
5175: fclose(ficrespop);
5176: } /* End of popforecast */
5177:
5178: int fileappend(FILE *fichier, char *optionfich)
5179: {
5180: if((fichier=fopen(optionfich,"a"))==NULL) {
5181: printf("Problem with file: %s\n", optionfich);
5182: fprintf(ficlog,"Problem with file: %s\n", optionfich);
5183: return (0);
5184: }
5185: fflush(fichier);
5186: return (1);
5187: }
5188:
5189:
5190: /**************** function prwizard **********************/
5191: void prwizard(int ncovmodel, int nlstate, int ndeath, char model[], FILE *ficparo)
5192: {
5193:
5194: /* Wizard to print covariance matrix template */
5195:
1.164 brouard 5196: char ca[32], cb[32];
5197: int i,j, k, li, lj, lk, ll, jj, npar, itimes;
1.126 brouard 5198: int numlinepar;
5199:
5200: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
5201: fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
5202: for(i=1; i <=nlstate; i++){
5203: jj=0;
5204: for(j=1; j <=nlstate+ndeath; j++){
5205: if(j==i) continue;
5206: jj++;
5207: /*ca[0]= k+'a'-1;ca[1]='\0';*/
5208: printf("%1d%1d",i,j);
5209: fprintf(ficparo,"%1d%1d",i,j);
5210: for(k=1; k<=ncovmodel;k++){
5211: /* printf(" %lf",param[i][j][k]); */
5212: /* fprintf(ficparo," %lf",param[i][j][k]); */
5213: printf(" 0.");
5214: fprintf(ficparo," 0.");
5215: }
5216: printf("\n");
5217: fprintf(ficparo,"\n");
5218: }
5219: }
5220: printf("# Scales (for hessian or gradient estimation)\n");
5221: fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
5222: npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
5223: for(i=1; i <=nlstate; i++){
5224: jj=0;
5225: for(j=1; j <=nlstate+ndeath; j++){
5226: if(j==i) continue;
5227: jj++;
5228: fprintf(ficparo,"%1d%1d",i,j);
5229: printf("%1d%1d",i,j);
5230: fflush(stdout);
5231: for(k=1; k<=ncovmodel;k++){
5232: /* printf(" %le",delti3[i][j][k]); */
5233: /* fprintf(ficparo," %le",delti3[i][j][k]); */
5234: printf(" 0.");
5235: fprintf(ficparo," 0.");
5236: }
5237: numlinepar++;
5238: printf("\n");
5239: fprintf(ficparo,"\n");
5240: }
5241: }
5242: printf("# Covariance matrix\n");
5243: /* # 121 Var(a12)\n\ */
5244: /* # 122 Cov(b12,a12) Var(b12)\n\ */
5245: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
5246: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
5247: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
5248: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
5249: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
5250: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
5251: fflush(stdout);
5252: fprintf(ficparo,"# Covariance matrix\n");
5253: /* # 121 Var(a12)\n\ */
5254: /* # 122 Cov(b12,a12) Var(b12)\n\ */
5255: /* # ...\n\ */
5256: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
5257:
5258: for(itimes=1;itimes<=2;itimes++){
5259: jj=0;
5260: for(i=1; i <=nlstate; i++){
5261: for(j=1; j <=nlstate+ndeath; j++){
5262: if(j==i) continue;
5263: for(k=1; k<=ncovmodel;k++){
5264: jj++;
5265: ca[0]= k+'a'-1;ca[1]='\0';
5266: if(itimes==1){
5267: printf("#%1d%1d%d",i,j,k);
5268: fprintf(ficparo,"#%1d%1d%d",i,j,k);
5269: }else{
5270: printf("%1d%1d%d",i,j,k);
5271: fprintf(ficparo,"%1d%1d%d",i,j,k);
5272: /* printf(" %.5le",matcov[i][j]); */
5273: }
5274: ll=0;
5275: for(li=1;li <=nlstate; li++){
5276: for(lj=1;lj <=nlstate+ndeath; lj++){
5277: if(lj==li) continue;
5278: for(lk=1;lk<=ncovmodel;lk++){
5279: ll++;
5280: if(ll<=jj){
5281: cb[0]= lk +'a'-1;cb[1]='\0';
5282: if(ll<jj){
5283: if(itimes==1){
5284: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
5285: fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
5286: }else{
5287: printf(" 0.");
5288: fprintf(ficparo," 0.");
5289: }
5290: }else{
5291: if(itimes==1){
5292: printf(" Var(%s%1d%1d)",ca,i,j);
5293: fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
5294: }else{
5295: printf(" 0.");
5296: fprintf(ficparo," 0.");
5297: }
5298: }
5299: }
5300: } /* end lk */
5301: } /* end lj */
5302: } /* end li */
5303: printf("\n");
5304: fprintf(ficparo,"\n");
5305: numlinepar++;
5306: } /* end k*/
5307: } /*end j */
5308: } /* end i */
5309: } /* end itimes */
5310:
5311: } /* end of prwizard */
5312: /******************* Gompertz Likelihood ******************************/
5313: double gompertz(double x[])
5314: {
5315: double A,B,L=0.0,sump=0.,num=0.;
5316: int i,n=0; /* n is the size of the sample */
5317:
5318: for (i=0;i<=imx-1 ; i++) {
5319: sump=sump+weight[i];
5320: /* sump=sump+1;*/
5321: num=num+1;
5322: }
5323:
5324:
5325: /* for (i=0; i<=imx; i++)
5326: 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]);*/
5327:
5328: for (i=1;i<=imx ; i++)
5329: {
5330: if (cens[i] == 1 && wav[i]>1)
5331: A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
5332:
5333: if (cens[i] == 0 && wav[i]>1)
5334: A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
5335: +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);
5336:
5337: /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
5338: if (wav[i] > 1 ) { /* ??? */
5339: L=L+A*weight[i];
5340: /* 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]);*/
5341: }
5342: }
5343:
5344: /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
5345:
5346: return -2*L*num/sump;
5347: }
5348:
1.136 brouard 5349: #ifdef GSL
5350: /******************* Gompertz_f Likelihood ******************************/
5351: double gompertz_f(const gsl_vector *v, void *params)
5352: {
5353: double A,B,LL=0.0,sump=0.,num=0.;
5354: double *x= (double *) v->data;
5355: int i,n=0; /* n is the size of the sample */
5356:
5357: for (i=0;i<=imx-1 ; i++) {
5358: sump=sump+weight[i];
5359: /* sump=sump+1;*/
5360: num=num+1;
5361: }
5362:
5363:
5364: /* for (i=0; i<=imx; i++)
5365: 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]);*/
5366: printf("x[0]=%lf x[1]=%lf\n",x[0],x[1]);
5367: for (i=1;i<=imx ; i++)
5368: {
5369: if (cens[i] == 1 && wav[i]>1)
5370: A=-x[0]/(x[1])*(exp(x[1]*(agecens[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)));
5371:
5372: if (cens[i] == 0 && wav[i]>1)
5373: A=-x[0]/(x[1])*(exp(x[1]*(agedc[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)))
5374: +log(x[0]/YEARM)+x[1]*(agedc[i]-agegomp)+log(YEARM);
5375:
5376: /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
5377: if (wav[i] > 1 ) { /* ??? */
5378: LL=LL+A*weight[i];
5379: /* 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]);*/
5380: }
5381: }
5382:
5383: /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
5384: printf("x[0]=%lf x[1]=%lf -2*LL*num/sump=%lf\n",x[0],x[1],-2*LL*num/sump);
5385:
5386: return -2*LL*num/sump;
5387: }
5388: #endif
5389:
1.126 brouard 5390: /******************* Printing html file ***********/
5391: void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \
5392: int lastpass, int stepm, int weightopt, char model[],\
5393: int imx, double p[],double **matcov,double agemortsup){
5394: int i,k;
5395:
5396: fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
5397: fprintf(fichtm," mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
5398: for (i=1;i<=2;i++)
5399: 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]));
5400: fprintf(fichtm,"<br><br><img src=\"graphmort.png\">");
5401: fprintf(fichtm,"</ul>");
5402:
5403: fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
5404:
5405: 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>");
5406:
5407: for (k=agegomp;k<(agemortsup-2);k++)
5408: 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]);
5409:
5410:
5411: fflush(fichtm);
5412: }
5413:
5414: /******************* Gnuplot file **************/
5415: void printinggnuplotmort(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
5416:
5417: char dirfileres[132],optfileres[132];
1.164 brouard 5418:
1.126 brouard 5419: int ng;
5420:
5421:
5422: /*#ifdef windows */
5423: fprintf(ficgp,"cd \"%s\" \n",pathc);
5424: /*#endif */
5425:
5426:
5427: strcpy(dirfileres,optionfilefiname);
5428: strcpy(optfileres,"vpl");
5429: fprintf(ficgp,"set out \"graphmort.png\"\n ");
5430: fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n ");
1.145 brouard 5431: fprintf(ficgp, "set ter png small size 320, 240\n set log y\n");
5432: /* fprintf(ficgp, "set size 0.65,0.65\n"); */
1.126 brouard 5433: fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
5434:
5435: }
5436:
1.136 brouard 5437: int readdata(char datafile[], int firstobs, int lastobs, int *imax)
5438: {
1.126 brouard 5439:
1.136 brouard 5440: /*-------- data file ----------*/
5441: FILE *fic;
5442: char dummy[]=" ";
1.164 brouard 5443: int i=0, j=0, n=0;
1.136 brouard 5444: int linei, month, year,iout;
5445: char line[MAXLINE], linetmp[MAXLINE];
1.164 brouard 5446: char stra[MAXLINE], strb[MAXLINE];
1.136 brouard 5447: char *stratrunc;
5448: int lstra;
1.126 brouard 5449:
5450:
1.136 brouard 5451: if((fic=fopen(datafile,"r"))==NULL) {
1.195 brouard 5452: printf("Problem while opening datafile: %s\n", datafile);fflush(stdout);
5453: fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);fflush(ficlog);return 1;
1.136 brouard 5454: }
1.126 brouard 5455:
1.136 brouard 5456: i=1;
5457: linei=0;
5458: while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
5459: linei=linei+1;
5460: for(j=strlen(line); j>=0;j--){ /* Untabifies line */
5461: if(line[j] == '\t')
5462: line[j] = ' ';
5463: }
5464: for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){
5465: ;
5466: };
5467: line[j+1]=0; /* Trims blanks at end of line */
5468: if(line[0]=='#'){
5469: fprintf(ficlog,"Comment line\n%s\n",line);
5470: printf("Comment line\n%s\n",line);
5471: continue;
5472: }
5473: trimbb(linetmp,line); /* Trims multiple blanks in line */
1.164 brouard 5474: strcpy(line, linetmp);
1.136 brouard 5475:
1.126 brouard 5476:
1.136 brouard 5477: for (j=maxwav;j>=1;j--){
1.137 brouard 5478: cutv(stra, strb, line, ' ');
1.136 brouard 5479: if(strb[0]=='.') { /* Missing status */
5480: lval=-1;
5481: }else{
5482: errno=0;
5483: lval=strtol(strb,&endptr,10);
5484: /* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
5485: if( strb[0]=='\0' || (*endptr != '\0')){
1.141 brouard 5486: 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);
5487: fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong. Exiting.\n", strb, linei,i,line,j,maxwav);fflush(ficlog);
1.136 brouard 5488: return 1;
5489: }
5490: }
5491: s[j][i]=lval;
5492:
5493: strcpy(line,stra);
5494: cutv(stra, strb,line,' ');
1.169 brouard 5495: if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
1.136 brouard 5496: }
1.169 brouard 5497: else if( (iout=sscanf(strb,"%s.",dummy)) != 0){
1.136 brouard 5498: month=99;
5499: year=9999;
5500: }else{
1.141 brouard 5501: 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);
5502: fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of interview (mm/yyyy or .) at wave %d. Exiting.\n",strb, linei,i, line,j);fflush(ficlog);
1.136 brouard 5503: return 1;
5504: }
5505: anint[j][i]= (double) year;
5506: mint[j][i]= (double)month;
5507: strcpy(line,stra);
5508: } /* ENd Waves */
5509:
5510: cutv(stra, strb,line,' ');
1.169 brouard 5511: if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
1.136 brouard 5512: }
1.169 brouard 5513: else if( (iout=sscanf(strb,"%s.",dummy)) != 0){
1.136 brouard 5514: month=99;
5515: year=9999;
5516: }else{
1.141 brouard 5517: 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);
5518: fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of death (mm/yyyy or .). Exiting.\n",strb, linei,i,line);fflush(ficlog);
1.136 brouard 5519: return 1;
5520: }
5521: andc[i]=(double) year;
5522: moisdc[i]=(double) month;
5523: strcpy(line,stra);
5524:
5525: cutv(stra, strb,line,' ');
1.169 brouard 5526: if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
1.136 brouard 5527: }
1.169 brouard 5528: else if( (iout=sscanf(strb,"%s.", dummy)) != 0){
1.136 brouard 5529: month=99;
5530: year=9999;
5531: }else{
1.141 brouard 5532: 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);
5533: fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .). Exiting.\n",strb, linei,i,line);fflush(ficlog);
1.136 brouard 5534: return 1;
5535: }
5536: if (year==9999) {
1.141 brouard 5537: 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);
5538: fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy) but at least the year of birth should be given. Exiting.\n",strb, linei,i,line);fflush(ficlog);
1.136 brouard 5539: return 1;
1.126 brouard 5540:
1.136 brouard 5541: }
5542: annais[i]=(double)(year);
5543: moisnais[i]=(double)(month);
5544: strcpy(line,stra);
5545:
5546: cutv(stra, strb,line,' ');
5547: errno=0;
5548: dval=strtod(strb,&endptr);
5549: if( strb[0]=='\0' || (*endptr != '\0')){
1.141 brouard 5550: printf("Error reading data around '%f' at line number %d, \"%s\" for individual %d\nShould be a weight. Exiting.\n",dval, i,line,linei);
5551: 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 5552: fflush(ficlog);
5553: return 1;
5554: }
5555: weight[i]=dval;
5556: strcpy(line,stra);
5557:
5558: for (j=ncovcol;j>=1;j--){
5559: cutv(stra, strb,line,' ');
5560: if(strb[0]=='.') { /* Missing status */
5561: lval=-1;
5562: }else{
5563: errno=0;
5564: lval=strtol(strb,&endptr,10);
5565: if( strb[0]=='\0' || (*endptr != '\0')){
1.141 brouard 5566: 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);
5567: fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\nShould be a covariate value (=0 for the reference or 1 for alternative). Exiting.\n",lval, linei,i, line);fflush(ficlog);
1.136 brouard 5568: return 1;
5569: }
5570: }
5571: if(lval <-1 || lval >1){
1.141 brouard 5572: printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
1.136 brouard 5573: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
5574: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
5575: For example, for multinomial values like 1, 2 and 3,\n \
5576: build V1=0 V2=0 for the reference value (1),\n \
5577: V1=1 V2=0 for (2) \n \
5578: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
5579: output of IMaCh is often meaningless.\n \
5580: Exiting.\n",lval,linei, i,line,j);
1.141 brouard 5581: fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
1.136 brouard 5582: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
5583: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
5584: For example, for multinomial values like 1, 2 and 3,\n \
5585: build V1=0 V2=0 for the reference value (1),\n \
5586: V1=1 V2=0 for (2) \n \
5587: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
5588: output of IMaCh is often meaningless.\n \
5589: Exiting.\n",lval,linei, i,line,j);fflush(ficlog);
5590: return 1;
5591: }
5592: covar[j][i]=(double)(lval);
5593: strcpy(line,stra);
5594: }
5595: lstra=strlen(stra);
5596:
5597: if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
5598: stratrunc = &(stra[lstra-9]);
5599: num[i]=atol(stratrunc);
5600: }
5601: else
5602: num[i]=atol(stra);
5603: /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
5604: 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;}*/
5605:
5606: i=i+1;
5607: } /* End loop reading data */
1.126 brouard 5608:
1.136 brouard 5609: *imax=i-1; /* Number of individuals */
5610: fclose(fic);
5611:
5612: return (0);
1.164 brouard 5613: /* endread: */
1.136 brouard 5614: printf("Exiting readdata: ");
5615: fclose(fic);
5616: return (1);
1.126 brouard 5617:
5618:
5619:
1.136 brouard 5620: }
1.145 brouard 5621: void removespace(char *str) {
5622: char *p1 = str, *p2 = str;
5623: do
5624: while (*p2 == ' ')
5625: p2++;
1.169 brouard 5626: while (*p1++ == *p2++);
1.145 brouard 5627: }
5628:
5629: int decodemodel ( char model[], int lastobs) /**< This routine decode the model and returns:
1.187 brouard 5630: * Model V1+V2+V3+V8+V7*V8+V5*V6+V8*age+V3*age+age*age
5631: * - nagesqr = 1 if age*age in the model, otherwise 0.
5632: * - cptcovt total number of covariates of the model nbocc(+)+1 = 8 excepting constant and age and age*age
5633: * - cptcovn or number of covariates k of the models excluding age*products =6 and age*age
1.145 brouard 5634: * - cptcovage number of covariates with age*products =2
5635: * - cptcovs number of simple covariates
5636: * - 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
5637: * which is a new column after the 9 (ncovcol) variables.
5638: * - if k is a product Vn*Vm covar[k][i] is filled with correct values for each individual
5639: * - Tprod[l] gives the kth covariates of the product Vn*Vm l=1 to cptcovprod-cptcovage
5640: * Tprod[1]@2 {5, 6}: position of first product V7*V8 is 5, and second V5*V6 is 6.
5641: * - Tvard[k] p Tvard[1][1]@4 {7, 8, 5, 6} for V7*V8 and V5*V6 .
5642: */
1.136 brouard 5643: {
1.145 brouard 5644: int i, j, k, ks;
1.164 brouard 5645: int j1, k1, k2;
1.136 brouard 5646: char modelsav[80];
1.145 brouard 5647: char stra[80], strb[80], strc[80], strd[80],stre[80];
1.187 brouard 5648: char *strpt;
1.136 brouard 5649:
1.145 brouard 5650: /*removespace(model);*/
1.136 brouard 5651: if (strlen(model) >1){ /* If there is at least 1 covariate */
1.145 brouard 5652: j=0, j1=0, k1=0, k2=-1, ks=0, cptcovn=0;
1.137 brouard 5653: if (strstr(model,"AGE") !=0){
1.192 brouard 5654: printf("Error. AGE must be in lower case 'age' model=1+age+%s. ",model);
5655: fprintf(ficlog,"Error. AGE must be in lower case model=1+age+%s. ",model);fflush(ficlog);
1.136 brouard 5656: return 1;
5657: }
1.141 brouard 5658: if (strstr(model,"v") !=0){
5659: printf("Error. 'v' must be in upper case 'V' model=%s ",model);
5660: fprintf(ficlog,"Error. 'v' must be in upper case model=%s ",model);fflush(ficlog);
5661: return 1;
5662: }
1.187 brouard 5663: strcpy(modelsav,model);
5664: if ((strpt=strstr(model,"age*age")) !=0){
5665: printf(" strpt=%s, model=%s\n",strpt, model);
5666: if(strpt != model){
5667: printf("Error in model: 'model=%s'; 'age*age' should in first place before other covariates\n \
1.192 brouard 5668: 'model=1+age+age*age+V1.' or 'model=1+age+age*age+V1+V1*age.', please swap as well as \n \
1.187 brouard 5669: corresponding column of parameters.\n",model);
5670: fprintf(ficlog,"Error in model: 'model=%s'; 'age*age' should in first place before other covariates\n \
1.192 brouard 5671: 'model=1+age+age*age+V1.' or 'model=1+age+age*age+V1+V1*age.', please swap as well as \n \
1.187 brouard 5672: corresponding column of parameters.\n",model); fflush(ficlog);
5673: return 1;
5674: }
5675:
5676: nagesqr=1;
5677: if (strstr(model,"+age*age") !=0)
5678: substrchaine(modelsav, model, "+age*age");
5679: else if (strstr(model,"age*age+") !=0)
5680: substrchaine(modelsav, model, "age*age+");
5681: else
5682: substrchaine(modelsav, model, "age*age");
5683: }else
5684: nagesqr=0;
5685: if (strlen(modelsav) >1){
5686: j=nbocc(modelsav,'+'); /**< j=Number of '+' */
5687: j1=nbocc(modelsav,'*'); /**< j1=Number of '*' */
5688: cptcovs=j+1-j1; /**< Number of simple covariates V1+V1*age+V3 +V3*V4+age*age=> V1 + V3 =2 */
5689: cptcovt= j+1; /* Number of total covariates in the model, not including
5690: * cst, age and age*age
5691: * V1+V1*age+ V3 + V3*V4+age*age=> 4*/
5692: /* including age products which are counted in cptcovage.
5693: * but the covariates which are products must be treated
5694: * separately: ncovn=4- 2=2 (V1+V3). */
5695: cptcovprod=j1; /**< Number of products V1*V2 +v3*age = 2 */
5696: cptcovprodnoage=0; /**< Number of covariate products without age: V3*V4 =1 */
5697:
5698:
5699: /* Design
5700: * V1 V2 V3 V4 V5 V6 V7 V8 V9 Weight
5701: * < ncovcol=8 >
5702: * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8
5703: * k= 1 2 3 4 5 6 7 8
5704: * cptcovn number of covariates (not including constant and age ) = # of + plus 1 = 7+1=8
5705: * covar[k,i], value of kth covariate if not including age for individual i:
5706: * covar[1][i]= (V2), covar[4][i]=(V3), covar[8][i]=(V8)
5707: * Tvar[k] # of the kth covariate: Tvar[1]=2 Tvar[4]=3 Tvar[8]=8
5708: * if multiplied by age: V3*age Tvar[3=V3*age]=3 (V3) Tvar[7]=8 and
5709: * Tage[++cptcovage]=k
5710: * if products, new covar are created after ncovcol with k1
5711: * Tvar[k]=ncovcol+k1; # of the kth covariate product: Tvar[5]=ncovcol+1=10 Tvar[6]=ncovcol+1=11
5712: * Tprod[k1]=k; Tprod[1]=5 Tprod[2]= 6; gives the position of the k1th product
5713: * 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
5714: * Tvar[cptcovn+k2]=Tvard[k1][1];Tvar[cptcovn+k2+1]=Tvard[k1][2];
5715: * Tvar[8+1]=5;Tvar[8+2]=6;Tvar[8+3]=7;Tvar[8+4]=8 inverted
5716: * V1 V2 V3 V4 V5 V6 V7 V8 V9 V10 V11
5717: * < ncovcol=8 >
5718: * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8 d1 d1 d2 d2
5719: * k= 1 2 3 4 5 6 7 8 9 10 11 12
5720: * Tvar[k]= 2 1 3 3 10 11 8 8 5 6 7 8
5721: * p Tvar[1]@12={2, 1, 3, 3, 11, 10, 8, 8, 7, 8, 5, 6}
5722: * p Tprod[1]@2={ 6, 5}
5723: *p Tvard[1][1]@4= {7, 8, 5, 6}
5724: * covar[k][i]= V2 V1 ? V3 V5*V6? V7*V8? ? V8
5725: * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
5726: *How to reorganize?
5727: * Model V1 + V2 + V3 + V8 + V5*V6 + V7*V8 + V3*age + V8*age
5728: * Tvars {2, 1, 3, 3, 11, 10, 8, 8, 7, 8, 5, 6}
5729: * {2, 1, 4, 8, 5, 6, 3, 7}
5730: * Struct []
5731: */
1.145 brouard 5732:
1.187 brouard 5733: /* This loop fills the array Tvar from the string 'model'.*/
5734: /* j is the number of + signs in the model V1+V2+V3 j=2 i=3 to 1 */
5735: /* modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4 */
5736: /* k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tage[cptcovage=1]=4 */
5737: /* k=3 V4 Tvar[k=3]= 4 (from V4) */
5738: /* k=2 V1 Tvar[k=2]= 1 (from V1) */
5739: /* k=1 Tvar[1]=2 (from V2) */
5740: /* k=5 Tvar[5] */
5741: /* for (k=1; k<=cptcovn;k++) { */
5742: /* cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]]; */
5743: /* } */
5744: /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtab[ij][Tvar[Tage[k]]]]*cov[2]; */
5745: /*
5746: * Treating invertedly V2+V1+V3*age+V2*V4 is as if written V2*V4 +V3*age + V1 + V2 */
5747: for(k=cptcovt; k>=1;k--) /**< Number of covariates */
1.145 brouard 5748: Tvar[k]=0;
1.187 brouard 5749: cptcovage=0;
5750: for(k=1; k<=cptcovt;k++){ /* Loop on total covariates of the model */
5751: cutl(stra,strb,modelsav,'+'); /* keeps in strb after the first '+'
5752: modelsav==V2+V1+V4+V3*age strb=V3*age stra=V2+V1+V4 */
5753: if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
5754: /* printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
5755: /*scanf("%d",i);*/
5756: if (strchr(strb,'*')) { /**< Model includes a product V2+V1+V4+V3*age strb=V3*age */
5757: cutl(strc,strd,strb,'*'); /**< strd*strc Vm*Vn: strb=V3*age(input) strc=age strd=V3 ; V3*V2 strc=V2, strd=V3 */
5758: if (strcmp(strc,"age")==0) { /**< Model includes age: Vn*age */
5759: /* covar is not filled and then is empty */
5760: cptcovprod--;
5761: cutl(stre,strb,strd,'V'); /* strd=V3(input): stre="3" */
5762: Tvar[k]=atoi(stre); /* V2+V1+V4+V3*age Tvar[4]=3 ; V1+V2*age Tvar[2]=2; V1+V1*age Tvar[2]=1 */
5763: cptcovage++; /* Sums the number of covariates which include age as a product */
5764: Tage[cptcovage]=k; /* Tvar[4]=3, Tage[1] = 4 or V1+V1*age Tvar[2]=1, Tage[1]=2 */
5765: /*printf("stre=%s ", stre);*/
5766: } else if (strcmp(strd,"age")==0) { /* or age*Vn */
5767: cptcovprod--;
5768: cutl(stre,strb,strc,'V');
5769: Tvar[k]=atoi(stre);
5770: cptcovage++;
5771: Tage[cptcovage]=k;
5772: } else { /* Age is not in the model product V2+V1+V1*V4+V3*age+V3*V2 strb=V3*V2*/
5773: /* loops on k1=1 (V3*V2) and k1=2 V4*V3 */
5774: cptcovn++;
5775: cptcovprodnoage++;k1++;
5776: cutl(stre,strb,strc,'V'); /* strc= Vn, stre is n; strb=V3*V2 stre=3 strc=*/
5777: Tvar[k]=ncovcol+k1; /* For model-covariate k tells which data-covariate to use but
5778: because this model-covariate is a construction we invent a new column
5779: ncovcol + k1
5780: If already ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2
5781: Tvar[3=V1*V4]=4+1 Tvar[5=V3*V2]=4 + 2= 6, etc */
5782: cutl(strc,strb,strd,'V'); /* strd was Vm, strc is m */
5783: Tprod[k1]=k; /* Tprod[1]=3(=V1*V4) for V2+V1+V1*V4+age*V3+V3*V2 */
5784: Tvard[k1][1] =atoi(strc); /* m 1 for V1*/
5785: Tvard[k1][2] =atoi(stre); /* n 4 for V4*/
5786: k2=k2+2;
5787: Tvar[cptcovt+k2]=Tvard[k1][1]; /* Tvar[(cptcovt=4+k2=1)=5]= 1 (V1) */
5788: Tvar[cptcovt+k2+1]=Tvard[k1][2]; /* Tvar[(cptcovt=4+(k2=1)+1)=6]= 4 (V4) */
5789: for (i=1; i<=lastobs;i++){
5790: /* Computes the new covariate which is a product of
5791: covar[n][i]* covar[m][i] and stores it at ncovol+k1 May not be defined */
5792: covar[ncovcol+k1][i]=covar[atoi(stre)][i]*covar[atoi(strc)][i];
5793: }
5794: } /* End age is not in the model */
5795: } /* End if model includes a product */
5796: else { /* no more sum */
5797: /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
5798: /* scanf("%d",i);*/
5799: cutl(strd,strc,strb,'V');
5800: ks++; /**< Number of simple covariates */
1.145 brouard 5801: cptcovn++;
1.187 brouard 5802: Tvar[k]=atoi(strd);
5803: }
5804: strcpy(modelsav,stra); /* modelsav=V2+V1+V4 stra=V2+V1+V4 */
5805: /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
5806: scanf("%d",i);*/
5807: } /* end of loop + on total covariates */
5808: } /* end if strlen(modelsave == 0) age*age might exist */
5809: } /* end if strlen(model == 0) */
1.136 brouard 5810:
5811: /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
5812: If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
5813:
5814: /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
5815: printf("cptcovprod=%d ", cptcovprod);
5816: fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
5817:
5818: scanf("%d ",i);*/
5819:
5820:
1.137 brouard 5821: return (0); /* with covar[new additional covariate if product] and Tage if age */
1.164 brouard 5822: /*endread:*/
1.136 brouard 5823: printf("Exiting decodemodel: ");
5824: return (1);
5825: }
5826:
1.169 brouard 5827: int calandcheckages(int imx, int maxwav, double *agemin, double *agemax, int *nberr, int *nbwarn )
1.136 brouard 5828: {
5829: int i, m;
5830:
5831: for (i=1; i<=imx; i++) {
5832: for(m=2; (m<= maxwav); m++) {
5833: if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
5834: anint[m][i]=9999;
5835: s[m][i]=-1;
5836: }
5837: if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
1.169 brouard 5838: *nberr = *nberr + 1;
5839: printf("Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased (%d)\n",(int)moisdc[i],(int)andc[i],num[i],i, *nberr);
5840: fprintf(ficlog,"Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased (%d)\n",(int)moisdc[i],(int)andc[i],num[i],i, *nberr);
1.136 brouard 5841: s[m][i]=-1;
5842: }
5843: if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
1.169 brouard 5844: (*nberr)++;
1.136 brouard 5845: 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]);
5846: 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]);
5847: s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
5848: }
5849: }
5850: }
5851:
5852: for (i=1; i<=imx; i++) {
5853: agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
5854: for(m=firstpass; (m<= lastpass); m++){
5855: if(s[m][i] >0 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){
5856: if (s[m][i] >= nlstate+1) {
1.169 brouard 5857: if(agedc[i]>0){
5858: if((int)moisdc[i]!=99 && (int)andc[i]!=9999){
1.136 brouard 5859: agev[m][i]=agedc[i];
5860: /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
1.169 brouard 5861: }else {
1.136 brouard 5862: if ((int)andc[i]!=9999){
5863: nbwarn++;
5864: printf("Warning negative age at death: %ld line:%d\n",num[i],i);
5865: fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
5866: agev[m][i]=-1;
5867: }
5868: }
1.169 brouard 5869: } /* agedc > 0 */
1.136 brouard 5870: }
5871: else if(s[m][i] !=9){ /* Standard case, age in fractional
5872: years but with the precision of a month */
5873: agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
5874: if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
5875: agev[m][i]=1;
5876: else if(agev[m][i] < *agemin){
5877: *agemin=agev[m][i];
5878: printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], *agemin);
5879: }
5880: else if(agev[m][i] >*agemax){
5881: *agemax=agev[m][i];
1.156 brouard 5882: /* printf(" Max anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.2f\n",m,i,anint[m][i], i,annais[i], *agemax);*/
1.136 brouard 5883: }
5884: /*agev[m][i]=anint[m][i]-annais[i];*/
5885: /* agev[m][i] = age[i]+2*m;*/
5886: }
5887: else { /* =9 */
5888: agev[m][i]=1;
5889: s[m][i]=-1;
5890: }
5891: }
5892: else /*= 0 Unknown */
5893: agev[m][i]=1;
5894: }
5895:
5896: }
5897: for (i=1; i<=imx; i++) {
5898: for(m=firstpass; (m<=lastpass); m++){
5899: if (s[m][i] > (nlstate+ndeath)) {
1.169 brouard 5900: (*nberr)++;
1.136 brouard 5901: 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);
5902: 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);
5903: return 1;
5904: }
5905: }
5906: }
5907:
5908: /*for (i=1; i<=imx; i++){
5909: for (m=firstpass; (m<lastpass); m++){
5910: printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
5911: }
5912:
5913: }*/
5914:
5915:
1.139 brouard 5916: printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
5917: fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
1.136 brouard 5918:
5919: return (0);
1.164 brouard 5920: /* endread:*/
1.136 brouard 5921: printf("Exiting calandcheckages: ");
5922: return (1);
5923: }
5924:
1.172 brouard 5925: #if defined(_MSC_VER)
5926: /*printf("Visual C++ compiler: %s \n;", _MSC_FULL_VER);*/
5927: /*fprintf(ficlog, "Visual C++ compiler: %s \n;", _MSC_FULL_VER);*/
5928: //#include "stdafx.h"
5929: //#include <stdio.h>
5930: //#include <tchar.h>
5931: //#include <windows.h>
5932: //#include <iostream>
5933: typedef BOOL(WINAPI *LPFN_ISWOW64PROCESS) (HANDLE, PBOOL);
5934:
5935: LPFN_ISWOW64PROCESS fnIsWow64Process;
5936:
5937: BOOL IsWow64()
5938: {
5939: BOOL bIsWow64 = FALSE;
5940:
5941: //typedef BOOL (APIENTRY *LPFN_ISWOW64PROCESS)
5942: // (HANDLE, PBOOL);
5943:
5944: //LPFN_ISWOW64PROCESS fnIsWow64Process;
5945:
5946: HMODULE module = GetModuleHandle(_T("kernel32"));
5947: const char funcName[] = "IsWow64Process";
5948: fnIsWow64Process = (LPFN_ISWOW64PROCESS)
5949: GetProcAddress(module, funcName);
5950:
5951: if (NULL != fnIsWow64Process)
5952: {
5953: if (!fnIsWow64Process(GetCurrentProcess(),
5954: &bIsWow64))
5955: //throw std::exception("Unknown error");
5956: printf("Unknown error\n");
5957: }
5958: return bIsWow64 != FALSE;
5959: }
5960: #endif
1.177 brouard 5961:
1.191 brouard 5962: void syscompilerinfo(int logged)
1.167 brouard 5963: {
5964: /* #include "syscompilerinfo.h"*/
1.185 brouard 5965: /* command line Intel compiler 32bit windows, XP compatible:*/
5966: /* /GS /W3 /Gy
5967: /Zc:wchar_t /Zi /O2 /Fd"Release\vc120.pdb" /D "WIN32" /D "NDEBUG" /D
5968: "_CONSOLE" /D "_LIB" /D "_USING_V110_SDK71_" /D "_UNICODE" /D
5969: "UNICODE" /Qipo /Zc:forScope /Gd /Oi /MT /Fa"Release\" /EHsc /nologo
1.186 brouard 5970: /Fo"Release\" /Qprof-dir "Release\" /Fp"Release\IMaCh.pch"
5971: */
5972: /* 64 bits */
1.185 brouard 5973: /*
5974: /GS /W3 /Gy
5975: /Zc:wchar_t /Zi /O2 /Fd"x64\Release\vc120.pdb" /D "WIN32" /D "NDEBUG"
5976: /D "_CONSOLE" /D "_LIB" /D "_UNICODE" /D "UNICODE" /Qipo /Zc:forScope
5977: /Oi /MD /Fa"x64\Release\" /EHsc /nologo /Fo"x64\Release\" /Qprof-dir
5978: "x64\Release\" /Fp"x64\Release\IMaCh.pch" */
5979: /* Optimization are useless and O3 is slower than O2 */
5980: /*
5981: /GS /W3 /Gy /Zc:wchar_t /Zi /O3 /Fd"x64\Release\vc120.pdb" /D "WIN32"
5982: /D "NDEBUG" /D "_CONSOLE" /D "_LIB" /D "_UNICODE" /D "UNICODE" /Qipo
5983: /Zc:forScope /Oi /MD /Fa"x64\Release\" /EHsc /nologo /Qparallel
5984: /Fo"x64\Release\" /Qprof-dir "x64\Release\" /Fp"x64\Release\IMaCh.pch"
5985: */
1.186 brouard 5986: /* Link is */ /* /OUT:"visual studio
1.185 brouard 5987: 2013\Projects\IMaCh\Release\IMaCh.exe" /MANIFEST /NXCOMPAT
5988: /PDB:"visual studio
5989: 2013\Projects\IMaCh\Release\IMaCh.pdb" /DYNAMICBASE
5990: "kernel32.lib" "user32.lib" "gdi32.lib" "winspool.lib"
5991: "comdlg32.lib" "advapi32.lib" "shell32.lib" "ole32.lib"
5992: "oleaut32.lib" "uuid.lib" "odbc32.lib" "odbccp32.lib"
5993: /MACHINE:X86 /OPT:REF /SAFESEH /INCREMENTAL:NO
5994: /SUBSYSTEM:CONSOLE",5.01" /MANIFESTUAC:"level='asInvoker'
5995: uiAccess='false'"
5996: /ManifestFile:"Release\IMaCh.exe.intermediate.manifest" /OPT:ICF
5997: /NOLOGO /TLBID:1
5998: */
1.177 brouard 5999: #if defined __INTEL_COMPILER
1.178 brouard 6000: #if defined(__GNUC__)
6001: struct utsname sysInfo; /* For Intel on Linux and OS/X */
6002: #endif
1.177 brouard 6003: #elif defined(__GNUC__)
1.179 brouard 6004: #ifndef __APPLE__
1.174 brouard 6005: #include <gnu/libc-version.h> /* Only on gnu */
1.179 brouard 6006: #endif
1.177 brouard 6007: struct utsname sysInfo;
1.178 brouard 6008: int cross = CROSS;
6009: if (cross){
6010: printf("Cross-");
1.191 brouard 6011: if(logged) fprintf(ficlog, "Cross-");
1.178 brouard 6012: }
1.174 brouard 6013: #endif
6014:
1.171 brouard 6015: #include <stdint.h>
1.178 brouard 6016:
1.191 brouard 6017: printf("Compiled with:");if(logged)fprintf(ficlog,"Compiled with:");
1.169 brouard 6018: #if defined(__clang__)
1.191 brouard 6019: printf(" Clang/LLVM");if(logged)fprintf(ficlog," Clang/LLVM"); /* Clang/LLVM. ---------------------------------------------- */
1.169 brouard 6020: #endif
6021: #if defined(__ICC) || defined(__INTEL_COMPILER)
1.191 brouard 6022: printf(" Intel ICC/ICPC");if(logged)fprintf(ficlog," Intel ICC/ICPC");/* Intel ICC/ICPC. ------------------------------------------ */
1.169 brouard 6023: #endif
6024: #if defined(__GNUC__) || defined(__GNUG__)
1.191 brouard 6025: printf(" GNU GCC/G++");if(logged)fprintf(ficlog," GNU GCC/G++");/* GNU GCC/G++. --------------------------------------------- */
1.169 brouard 6026: #endif
6027: #if defined(__HP_cc) || defined(__HP_aCC)
1.191 brouard 6028: printf(" Hewlett-Packard C/aC++");if(logged)fprintf(fcilog," Hewlett-Packard C/aC++"); /* Hewlett-Packard C/aC++. ---------------------------------- */
1.169 brouard 6029: #endif
6030: #if defined(__IBMC__) || defined(__IBMCPP__)
1.191 brouard 6031: printf(" IBM XL C/C++"); if(logged) fprintf(ficlog," IBM XL C/C++");/* IBM XL C/C++. -------------------------------------------- */
1.169 brouard 6032: #endif
6033: #if defined(_MSC_VER)
1.191 brouard 6034: printf(" Microsoft Visual Studio");if(logged)fprintf(ficlog," Microsoft Visual Studio");/* Microsoft Visual Studio. --------------------------------- */
1.169 brouard 6035: #endif
6036: #if defined(__PGI)
1.191 brouard 6037: printf(" Portland Group PGCC/PGCPP");if(logged) fprintf(ficlog," Portland Group PGCC/PGCPP");/* Portland Group PGCC/PGCPP. ------------------------------- */
1.169 brouard 6038: #endif
6039: #if defined(__SUNPRO_C) || defined(__SUNPRO_CC)
1.191 brouard 6040: printf(" Oracle Solaris Studio");if(logged)fprintf(ficlog," Oracle Solaris Studio\n");/* Oracle Solaris Studio. ----------------------------------- */
1.167 brouard 6041: #endif
1.191 brouard 6042: printf(" for "); if (logged) fprintf(ficlog, " for ");
1.169 brouard 6043:
1.167 brouard 6044: // http://stackoverflow.com/questions/4605842/how-to-identify-platform-compiler-from-preprocessor-macros
6045: #ifdef _WIN32 // note the underscore: without it, it's not msdn official!
6046: // Windows (x64 and x86)
1.191 brouard 6047: printf("Windows (x64 and x86) ");if(logged) fprintf(ficlog,"Windows (x64 and x86) ");
1.167 brouard 6048: #elif __unix__ // all unices, not all compilers
6049: // Unix
1.191 brouard 6050: printf("Unix ");if(logged) fprintf(ficlog,"Unix ");
1.167 brouard 6051: #elif __linux__
6052: // linux
1.191 brouard 6053: printf("linux ");if(logged) fprintf(ficlog,"linux ");
1.167 brouard 6054: #elif __APPLE__
1.174 brouard 6055: // Mac OS, not sure if this is covered by __posix__ and/or __unix__ though..
1.191 brouard 6056: printf("Mac OS ");if(logged) fprintf(ficlog,"Mac OS ");
1.167 brouard 6057: #endif
6058:
6059: /* __MINGW32__ */
6060: /* __CYGWIN__ */
6061: /* __MINGW64__ */
6062: // http://msdn.microsoft.com/en-us/library/b0084kay.aspx
6063: /* _MSC_VER //the Visual C++ compiler is 17.00.51106.1, the _MSC_VER macro evaluates to 1700. Type cl /? */
6064: /* _MSC_FULL_VER //the Visual C++ compiler is 15.00.20706.01, the _MSC_FULL_VER macro evaluates to 150020706 */
6065: /* _WIN64 // Defined for applications for Win64. */
6066: /* _M_X64 // Defined for compilations that target x64 processors. */
6067: /* _DEBUG // Defined when you compile with /LDd, /MDd, and /MTd. */
1.171 brouard 6068:
1.167 brouard 6069: #if UINTPTR_MAX == 0xffffffff
1.191 brouard 6070: printf(" 32-bit"); if(logged) fprintf(ficlog," 32-bit");/* 32-bit */
1.167 brouard 6071: #elif UINTPTR_MAX == 0xffffffffffffffff
1.191 brouard 6072: printf(" 64-bit"); if(logged) fprintf(ficlog," 64-bit");/* 64-bit */
1.167 brouard 6073: #else
1.191 brouard 6074: printf(" wtf-bit"); if(logged) fprintf(ficlog," wtf-bit");/* wtf */
1.167 brouard 6075: #endif
6076:
1.169 brouard 6077: #if defined(__GNUC__)
6078: # if defined(__GNUC_PATCHLEVEL__)
6079: # define __GNUC_VERSION__ (__GNUC__ * 10000 \
6080: + __GNUC_MINOR__ * 100 \
6081: + __GNUC_PATCHLEVEL__)
6082: # else
6083: # define __GNUC_VERSION__ (__GNUC__ * 10000 \
6084: + __GNUC_MINOR__ * 100)
6085: # endif
1.174 brouard 6086: printf(" using GNU C version %d.\n", __GNUC_VERSION__);
1.191 brouard 6087: if(logged) fprintf(ficlog, " using GNU C version %d.\n", __GNUC_VERSION__);
1.176 brouard 6088:
6089: if (uname(&sysInfo) != -1) {
6090: printf("Running on: %s %s %s %s %s\n",sysInfo.sysname, sysInfo.nodename, sysInfo.release, sysInfo.version, sysInfo.machine);
1.191 brouard 6091: 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 6092: }
6093: else
6094: perror("uname() error");
1.179 brouard 6095: //#ifndef __INTEL_COMPILER
6096: #if !defined (__INTEL_COMPILER) && !defined(__APPLE__)
1.174 brouard 6097: printf("GNU libc version: %s\n", gnu_get_libc_version());
1.191 brouard 6098: if(logged) fprintf(ficlog,"GNU libc version: %s\n", gnu_get_libc_version());
1.177 brouard 6099: #endif
1.169 brouard 6100: #endif
1.172 brouard 6101:
6102: // void main()
6103: // {
1.169 brouard 6104: #if defined(_MSC_VER)
1.174 brouard 6105: if (IsWow64()){
1.191 brouard 6106: printf("\nThe program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n");
6107: if (logged) fprintf(ficlog, "\nThe program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n");
1.174 brouard 6108: }
6109: else{
1.191 brouard 6110: printf("\nThe program is not running under WOW64 (i.e probably on a 64bit Windows).\n");
6111: if (logged) fprintf(ficlog, "\nThe programm is not running under WOW64 (i.e probably on a 64bit Windows).\n");
1.174 brouard 6112: }
1.172 brouard 6113: // printf("\nPress Enter to continue...");
6114: // getchar();
6115: // }
6116:
1.169 brouard 6117: #endif
6118:
1.167 brouard 6119:
6120: }
1.136 brouard 6121:
1.180 brouard 6122: int prevalence_limit(double *p, double **prlim, double ageminpar, double agemaxpar){
6123: /*--------------- Prevalence limit (period or stable prevalence) --------------*/
6124: int i, j, k, i1 ;
6125: double ftolpl = 1.e-10;
6126: double age, agebase, agelim;
6127:
6128: strcpy(filerespl,"pl");
6129: strcat(filerespl,fileres);
6130: if((ficrespl=fopen(filerespl,"w"))==NULL) {
6131: printf("Problem with period (stable) prevalence resultfile: %s\n", filerespl);return 1;
6132: fprintf(ficlog,"Problem with period (stable) prevalence resultfile: %s\n", filerespl);return 1;
6133: }
6134: printf("Computing period (stable) prevalence: result on file '%s' \n", filerespl);
6135: fprintf(ficlog,"Computing period (stable) prevalence: result on file '%s' \n", filerespl);
6136: pstamp(ficrespl);
6137: fprintf(ficrespl,"# Period (stable) prevalence \n");
6138: fprintf(ficrespl,"#Age ");
6139: for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
6140: fprintf(ficrespl,"\n");
6141:
6142: /* prlim=matrix(1,nlstate,1,nlstate);*/ /* back in main */
6143:
6144: agebase=ageminpar;
6145: agelim=agemaxpar;
6146:
6147: i1=pow(2,cptcoveff);
6148: if (cptcovn < 1){i1=1;}
6149:
6150: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
6151: /* for(cptcov=1,k=0;cptcov<=1;cptcov++){ */
6152: //for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
6153: k=k+1;
6154: /* to clean */
6155: //printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtab[cptcod][cptcov]);
6156: fprintf(ficrespl,"\n#******");
6157: printf("\n#******");
6158: fprintf(ficlog,"\n#******");
6159: for(j=1;j<=cptcoveff;j++) {
6160: fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6161: printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6162: fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6163: }
6164: fprintf(ficrespl,"******\n");
6165: printf("******\n");
6166: fprintf(ficlog,"******\n");
6167:
6168: fprintf(ficrespl,"#Age ");
6169: for(j=1;j<=cptcoveff;j++) {
6170: fprintf(ficrespl,"V%d %d",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6171: }
6172: for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
6173: fprintf(ficrespl,"\n");
6174:
6175: for (age=agebase; age<=agelim; age++){
6176: /* for (age=agebase; age<=agebase; age++){ */
6177: prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
6178: fprintf(ficrespl,"%.0f ",age );
6179: for(j=1;j<=cptcoveff;j++)
6180: fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6181: for(i=1; i<=nlstate;i++)
6182: fprintf(ficrespl," %.5f", prlim[i][i]);
6183: fprintf(ficrespl,"\n");
6184: } /* Age */
6185: /* was end of cptcod */
6186: } /* cptcov */
1.184 brouard 6187: return 0;
1.180 brouard 6188: }
6189:
6190: int hPijx(double *p, int bage, int fage){
6191: /*------------- h Pij x at various ages ------------*/
6192:
6193: int stepsize;
6194: int agelim;
6195: int hstepm;
6196: int nhstepm;
6197: int h, i, i1, j, k;
6198:
6199: double agedeb;
6200: double ***p3mat;
6201:
6202: strcpy(filerespij,"pij"); strcat(filerespij,fileres);
6203: if((ficrespij=fopen(filerespij,"w"))==NULL) {
6204: printf("Problem with Pij resultfile: %s\n", filerespij); return 1;
6205: fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij); return 1;
6206: }
6207: printf("Computing pij: result on file '%s' \n", filerespij);
6208: fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
6209:
6210: stepsize=(int) (stepm+YEARM-1)/YEARM;
6211: /*if (stepm<=24) stepsize=2;*/
6212:
6213: agelim=AGESUP;
6214: hstepm=stepsize*YEARM; /* Every year of age */
6215: hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
6216:
6217: /* hstepm=1; aff par mois*/
6218: pstamp(ficrespij);
6219: fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
6220: i1= pow(2,cptcoveff);
1.183 brouard 6221: /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */
6222: /* /\*for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*\/ */
6223: /* k=k+1; */
6224: for (k=1; k <= (int) pow(2,cptcoveff); k++){
6225: fprintf(ficrespij,"\n#****** ");
6226: for(j=1;j<=cptcoveff;j++)
6227: fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6228: fprintf(ficrespij,"******\n");
6229:
6230: for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
6231: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
6232: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
6233:
6234: /* nhstepm=nhstepm*YEARM; aff par mois*/
1.180 brouard 6235:
1.183 brouard 6236: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
6237: oldm=oldms;savm=savms;
6238: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
6239: fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
6240: for(i=1; i<=nlstate;i++)
6241: for(j=1; j<=nlstate+ndeath;j++)
6242: fprintf(ficrespij," %1d-%1d",i,j);
6243: fprintf(ficrespij,"\n");
6244: for (h=0; h<=nhstepm; h++){
6245: /*agedebphstep = agedeb + h*hstepm/YEARM*stepm;*/
6246: fprintf(ficrespij,"%d %3.f %3.f",k, agedeb, agedeb + h*hstepm/YEARM*stepm );
1.180 brouard 6247: for(i=1; i<=nlstate;i++)
6248: for(j=1; j<=nlstate+ndeath;j++)
1.183 brouard 6249: fprintf(ficrespij," %.5f", p3mat[i][j][h]);
1.180 brouard 6250: fprintf(ficrespij,"\n");
6251: }
1.183 brouard 6252: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
6253: fprintf(ficrespij,"\n");
6254: }
1.180 brouard 6255: /*}*/
6256: }
1.184 brouard 6257: return 0;
1.180 brouard 6258: }
6259:
6260:
1.136 brouard 6261: /***********************************************/
6262: /**************** Main Program *****************/
6263: /***********************************************/
6264:
6265: int main(int argc, char *argv[])
6266: {
6267: #ifdef GSL
6268: const gsl_multimin_fminimizer_type *T;
6269: size_t iteri = 0, it;
6270: int rval = GSL_CONTINUE;
6271: int status = GSL_SUCCESS;
6272: double ssval;
6273: #endif
6274: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
1.164 brouard 6275: int i,j, k, n=MAXN,iter=0,m,size=100, cptcod;
6276:
6277: int jj, ll, li, lj, lk;
1.136 brouard 6278: int numlinepar=0; /* Current linenumber of parameter file */
6279: int itimes;
6280: int NDIM=2;
6281: int vpopbased=0;
6282:
1.164 brouard 6283: char ca[32], cb[32];
1.136 brouard 6284: /* FILE *fichtm; *//* Html File */
6285: /* FILE *ficgp;*/ /*Gnuplot File */
6286: struct stat info;
1.191 brouard 6287: double agedeb=0.;
1.194 brouard 6288:
6289: double ageminpar=AGEOVERFLOW,agemin=AGEOVERFLOW, agemaxpar=-AGEOVERFLOW, agemax=-AGEOVERFLOW;
1.136 brouard 6290:
1.165 brouard 6291: double fret;
1.191 brouard 6292: double dum=0.; /* Dummy variable */
1.136 brouard 6293: double ***p3mat;
6294: double ***mobaverage;
1.164 brouard 6295:
6296: char line[MAXLINE];
1.136 brouard 6297: char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
6298: char pathr[MAXLINE], pathimach[MAXLINE];
1.164 brouard 6299: char *tok, *val; /* pathtot */
1.136 brouard 6300: int firstobs=1, lastobs=10;
1.195 brouard 6301: int c, h , cpt, c2;
1.191 brouard 6302: int jl=0;
6303: int i1, j1, jk, stepsize=0;
1.194 brouard 6304: int count=0;
6305:
1.164 brouard 6306: int *tab;
1.136 brouard 6307: int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
6308: int mobilav=0,popforecast=0;
1.191 brouard 6309: int hstepm=0, nhstepm=0;
1.136 brouard 6310: int agemortsup;
6311: float sumlpop=0.;
6312: double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
6313: double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
6314:
1.191 brouard 6315: double bage=0, fage=110., age, agelim=0., agebase=0.;
1.136 brouard 6316: double ftolpl=FTOL;
6317: double **prlim;
6318: double ***param; /* Matrix of parameters */
6319: double *p;
6320: double **matcov; /* Matrix of covariance */
6321: double ***delti3; /* Scale */
6322: double *delti; /* Scale */
6323: double ***eij, ***vareij;
6324: double **varpl; /* Variances of prevalence limits by age */
6325: double *epj, vepp;
1.164 brouard 6326:
1.136 brouard 6327: double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
6328: double **ximort;
1.145 brouard 6329: char *alph[]={"a","a","b","c","d","e"}, str[4]="1234";
1.136 brouard 6330: int *dcwave;
6331:
1.164 brouard 6332: char z[1]="c";
1.136 brouard 6333:
6334: /*char *strt;*/
6335: char strtend[80];
1.126 brouard 6336:
1.164 brouard 6337:
1.126 brouard 6338: /* setlocale (LC_ALL, ""); */
6339: /* bindtextdomain (PACKAGE, LOCALEDIR); */
6340: /* textdomain (PACKAGE); */
6341: /* setlocale (LC_CTYPE, ""); */
6342: /* setlocale (LC_MESSAGES, ""); */
6343:
6344: /* gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
1.157 brouard 6345: rstart_time = time(NULL);
6346: /* (void) gettimeofday(&start_time,&tzp);*/
6347: start_time = *localtime(&rstart_time);
1.126 brouard 6348: curr_time=start_time;
1.157 brouard 6349: /*tml = *localtime(&start_time.tm_sec);*/
6350: /* strcpy(strstart,asctime(&tml)); */
6351: strcpy(strstart,asctime(&start_time));
1.126 brouard 6352:
6353: /* printf("Localtime (at start)=%s",strstart); */
1.157 brouard 6354: /* tp.tm_sec = tp.tm_sec +86400; */
6355: /* tm = *localtime(&start_time.tm_sec); */
1.126 brouard 6356: /* tmg.tm_year=tmg.tm_year +dsign*dyear; */
6357: /* tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
6358: /* tmg.tm_hour=tmg.tm_hour + 1; */
1.157 brouard 6359: /* tp.tm_sec = mktime(&tmg); */
1.126 brouard 6360: /* strt=asctime(&tmg); */
6361: /* printf("Time(after) =%s",strstart); */
6362: /* (void) time (&time_value);
6363: * printf("time=%d,t-=%d\n",time_value,time_value-86400);
6364: * tm = *localtime(&time_value);
6365: * strstart=asctime(&tm);
6366: * printf("tim_value=%d,asctime=%s\n",time_value,strstart);
6367: */
6368:
6369: nberr=0; /* Number of errors and warnings */
6370: nbwarn=0;
1.184 brouard 6371: #ifdef WIN32
6372: _getcwd(pathcd, size);
6373: #else
1.126 brouard 6374: getcwd(pathcd, size);
1.184 brouard 6375: #endif
1.191 brouard 6376: syscompilerinfo(0);
1.196 ! brouard 6377: printf("\nIMaCh version %s, %s\n%s",version, copyright, fullversion);
1.126 brouard 6378: if(argc <=1){
6379: printf("\nEnter the parameter file name: ");
6380: fgets(pathr,FILENAMELENGTH,stdin);
6381: i=strlen(pathr);
6382: if(pathr[i-1]=='\n')
6383: pathr[i-1]='\0';
1.156 brouard 6384: i=strlen(pathr);
6385: if(pathr[i-1]==' ') /* This may happen when dragging on oS/X! */
6386: pathr[i-1]='\0';
1.126 brouard 6387: for (tok = pathr; tok != NULL; ){
6388: printf("Pathr |%s|\n",pathr);
6389: while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
6390: printf("val= |%s| pathr=%s\n",val,pathr);
6391: strcpy (pathtot, val);
6392: if(pathr[0] == '\0') break; /* Dirty */
6393: }
6394: }
6395: else{
6396: strcpy(pathtot,argv[1]);
6397: }
6398: /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
6399: /*cygwin_split_path(pathtot,path,optionfile);
6400: printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
6401: /* cutv(path,optionfile,pathtot,'\\');*/
6402:
6403: /* Split argv[0], imach program to get pathimach */
6404: printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
6405: split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
6406: printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
6407: /* strcpy(pathimach,argv[0]); */
6408: /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
6409: split(pathtot,path,optionfile,optionfilext,optionfilefiname);
6410: printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
1.184 brouard 6411: #ifdef WIN32
6412: _chdir(path); /* Can be a relative path */
6413: if(_getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */
6414: #else
1.126 brouard 6415: chdir(path); /* Can be a relative path */
1.184 brouard 6416: if (getcwd(pathcd, MAXLINE) > 0) /* So pathcd is the full path */
6417: #endif
6418: printf("Current directory %s!\n",pathcd);
1.126 brouard 6419: strcpy(command,"mkdir ");
6420: strcat(command,optionfilefiname);
6421: if((outcmd=system(command)) != 0){
1.169 brouard 6422: printf("Directory already exists (or can't create it) %s%s, err=%d\n",path,optionfilefiname,outcmd);
1.126 brouard 6423: /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
6424: /* fclose(ficlog); */
6425: /* exit(1); */
6426: }
6427: /* if((imk=mkdir(optionfilefiname))<0){ */
6428: /* perror("mkdir"); */
6429: /* } */
6430:
6431: /*-------- arguments in the command line --------*/
6432:
1.186 brouard 6433: /* Main Log file */
1.126 brouard 6434: strcat(filelog, optionfilefiname);
6435: strcat(filelog,".log"); /* */
6436: if((ficlog=fopen(filelog,"w"))==NULL) {
6437: printf("Problem with logfile %s\n",filelog);
6438: goto end;
6439: }
6440: fprintf(ficlog,"Log filename:%s\n",filelog);
6441: fprintf(ficlog,"\n%s\n%s",version,fullversion);
6442: fprintf(ficlog,"\nEnter the parameter file name: \n");
6443: fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
6444: path=%s \n\
6445: optionfile=%s\n\
6446: optionfilext=%s\n\
1.156 brouard 6447: optionfilefiname='%s'\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
1.126 brouard 6448:
1.191 brouard 6449: syscompilerinfo(0);
1.167 brouard 6450:
1.126 brouard 6451: printf("Local time (at start):%s",strstart);
6452: fprintf(ficlog,"Local time (at start): %s",strstart);
6453: fflush(ficlog);
6454: /* (void) gettimeofday(&curr_time,&tzp); */
1.157 brouard 6455: /* printf("Elapsed time %d\n", asc_diff_time(curr_time.tm_sec-start_time.tm_sec,tmpout)); */
1.126 brouard 6456:
6457: /* */
6458: strcpy(fileres,"r");
6459: strcat(fileres, optionfilefiname);
6460: strcat(fileres,".txt"); /* Other files have txt extension */
6461:
1.186 brouard 6462: /* Main ---------arguments file --------*/
1.126 brouard 6463:
6464: if((ficpar=fopen(optionfile,"r"))==NULL) {
1.155 brouard 6465: printf("Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
6466: fprintf(ficlog,"Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
1.126 brouard 6467: fflush(ficlog);
1.149 brouard 6468: /* goto end; */
6469: exit(70);
1.126 brouard 6470: }
6471:
6472:
6473:
6474: strcpy(filereso,"o");
6475: strcat(filereso,fileres);
6476: if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
6477: printf("Problem with Output resultfile: %s\n", filereso);
6478: fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
6479: fflush(ficlog);
6480: goto end;
6481: }
6482:
6483: /* Reads comments: lines beginning with '#' */
6484: numlinepar=0;
6485: while((c=getc(ficpar))=='#' && c!= EOF){
6486: ungetc(c,ficpar);
6487: fgets(line, MAXLINE, ficpar);
6488: numlinepar++;
1.141 brouard 6489: fputs(line,stdout);
1.126 brouard 6490: fputs(line,ficparo);
6491: fputs(line,ficlog);
6492: }
6493: ungetc(c,ficpar);
6494:
1.187 brouard 6495: 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);
1.194 brouard 6496: numlinepar=numlinepar+3; /* In general */
1.187 brouard 6497: 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);
6498: if(model[strlen(model)-1]=='.') /* Suppressing leading dot in the model */
6499: model[strlen(model)-1]='\0';
6500: fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=1+age+%s.\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
6501: fprintf(ficlog,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=1+age+%s.\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
1.126 brouard 6502: fflush(ficlog);
1.190 brouard 6503: /* if(model[0]=='#'|| model[0]== '\0'){ */
6504: if(model[0]=='#'){
1.187 brouard 6505: printf("Error in 'model' line: model should start with 'model=1+age+' and end with '.' \n \
6506: 'model=1+age+.' or 'model=1+age+V1.' or 'model=1+age+age*age+V1+V1*age.' or \n \
6507: 'model=1+age+V1+V2.' or 'model=1+age+V1+V2+V1*V2.' etc. \n"); \
6508: if(mle != -1){
6509: printf("Fix the model line and run imach with mle=-1 to get a correct template of the parameter file.\n");
6510: exit(1);
6511: }
6512: }
1.126 brouard 6513: while((c=getc(ficpar))=='#' && c!= EOF){
6514: ungetc(c,ficpar);
6515: fgets(line, MAXLINE, ficpar);
6516: numlinepar++;
1.195 brouard 6517: if(line[1]=='q'){ /* This #q will quit imach (the answer is q) */
6518: z[0]=line[1];
6519: }
6520: /* printf("****line [1] = %c \n",line[1]); */
1.141 brouard 6521: fputs(line, stdout);
6522: //puts(line);
1.126 brouard 6523: fputs(line,ficparo);
6524: fputs(line,ficlog);
6525: }
6526: ungetc(c,ficpar);
6527:
6528:
1.145 brouard 6529: covar=matrix(0,NCOVMAX,1,n); /**< used in readdata */
1.136 brouard 6530: cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement plus one, indepently of n in Vn*/
6531: /* v1+v2+v3+v2*v4+v5*age makes cptcovn = 5
6532: v1+v2*age+v2*v3 makes cptcovn = 3
6533: */
6534: if (strlen(model)>1)
1.187 brouard 6535: 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 6536: else
1.187 brouard 6537: ncovmodel=2; /* Constant and age */
1.133 brouard 6538: nforce= (nlstate+ndeath-1)*nlstate; /* Number of forces ij from state i to j */
6539: npar= nforce*ncovmodel; /* Number of parameters like aij*/
1.131 brouard 6540: if(npar >MAXPARM || nlstate >NLSTATEMAX || ndeath >NDEATHMAX || ncovmodel>NCOVMAX){
6541: 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);
6542: 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);
6543: fflush(stdout);
6544: fclose (ficlog);
6545: goto end;
6546: }
1.126 brouard 6547: delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
6548: delti=delti3[1][1];
6549: /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
6550: if(mle==-1){ /* Print a wizard for help writing covariance matrix */
6551: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
1.191 brouard 6552: printf(" You chose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
6553: fprintf(ficlog," You chose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
1.126 brouard 6554: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
6555: fclose (ficparo);
6556: fclose (ficlog);
6557: goto end;
6558: exit(0);
6559: }
1.186 brouard 6560: else if(mle==-3) { /* Main Wizard */
1.126 brouard 6561: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
1.192 brouard 6562: printf(" You chose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
6563: fprintf(ficlog," You chose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
1.126 brouard 6564: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
6565: matcov=matrix(1,npar,1,npar);
6566: }
6567: else{
1.145 brouard 6568: /* Read guessed parameters */
1.126 brouard 6569: /* Reads comments: lines beginning with '#' */
6570: while((c=getc(ficpar))=='#' && c!= EOF){
6571: ungetc(c,ficpar);
6572: fgets(line, MAXLINE, ficpar);
6573: numlinepar++;
1.141 brouard 6574: fputs(line,stdout);
1.126 brouard 6575: fputs(line,ficparo);
6576: fputs(line,ficlog);
6577: }
6578: ungetc(c,ficpar);
6579:
6580: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
6581: for(i=1; i <=nlstate; i++){
6582: j=0;
6583: for(jj=1; jj <=nlstate+ndeath; jj++){
6584: if(jj==i) continue;
6585: j++;
6586: fscanf(ficpar,"%1d%1d",&i1,&j1);
1.193 brouard 6587: if ((i1 != i) || (j1 != jj)){
1.126 brouard 6588: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \
6589: It might be a problem of design; if ncovcol and the model are correct\n \
6590: run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1);
6591: exit(1);
6592: }
6593: fprintf(ficparo,"%1d%1d",i1,j1);
6594: if(mle==1)
1.193 brouard 6595: printf("%1d%1d",i,jj);
6596: fprintf(ficlog,"%1d%1d",i,jj);
1.126 brouard 6597: for(k=1; k<=ncovmodel;k++){
6598: fscanf(ficpar," %lf",¶m[i][j][k]);
6599: if(mle==1){
6600: printf(" %lf",param[i][j][k]);
6601: fprintf(ficlog," %lf",param[i][j][k]);
6602: }
6603: else
6604: fprintf(ficlog," %lf",param[i][j][k]);
6605: fprintf(ficparo," %lf",param[i][j][k]);
6606: }
6607: fscanf(ficpar,"\n");
6608: numlinepar++;
6609: if(mle==1)
6610: printf("\n");
6611: fprintf(ficlog,"\n");
6612: fprintf(ficparo,"\n");
6613: }
6614: }
6615: fflush(ficlog);
6616:
1.145 brouard 6617: /* Reads scales values */
1.126 brouard 6618: p=param[1][1];
6619:
6620: /* Reads comments: lines beginning with '#' */
6621: while((c=getc(ficpar))=='#' && c!= EOF){
6622: ungetc(c,ficpar);
6623: fgets(line, MAXLINE, ficpar);
6624: numlinepar++;
1.141 brouard 6625: fputs(line,stdout);
1.126 brouard 6626: fputs(line,ficparo);
6627: fputs(line,ficlog);
6628: }
6629: ungetc(c,ficpar);
6630:
6631: for(i=1; i <=nlstate; i++){
6632: for(j=1; j <=nlstate+ndeath-1; j++){
6633: fscanf(ficpar,"%1d%1d",&i1,&j1);
1.164 brouard 6634: if ( (i1-i) * (j1-j) != 0){
1.126 brouard 6635: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
6636: exit(1);
6637: }
6638: printf("%1d%1d",i,j);
6639: fprintf(ficparo,"%1d%1d",i1,j1);
6640: fprintf(ficlog,"%1d%1d",i1,j1);
6641: for(k=1; k<=ncovmodel;k++){
6642: fscanf(ficpar,"%le",&delti3[i][j][k]);
6643: printf(" %le",delti3[i][j][k]);
6644: fprintf(ficparo," %le",delti3[i][j][k]);
6645: fprintf(ficlog," %le",delti3[i][j][k]);
6646: }
6647: fscanf(ficpar,"\n");
6648: numlinepar++;
6649: printf("\n");
6650: fprintf(ficparo,"\n");
6651: fprintf(ficlog,"\n");
6652: }
6653: }
6654: fflush(ficlog);
6655:
1.145 brouard 6656: /* Reads covariance matrix */
1.126 brouard 6657: delti=delti3[1][1];
6658:
6659:
6660: /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
6661:
6662: /* Reads comments: lines beginning with '#' */
6663: while((c=getc(ficpar))=='#' && c!= EOF){
6664: ungetc(c,ficpar);
6665: fgets(line, MAXLINE, ficpar);
6666: numlinepar++;
1.141 brouard 6667: fputs(line,stdout);
1.126 brouard 6668: fputs(line,ficparo);
6669: fputs(line,ficlog);
6670: }
6671: ungetc(c,ficpar);
6672:
6673: matcov=matrix(1,npar,1,npar);
1.131 brouard 6674: for(i=1; i <=npar; i++)
6675: for(j=1; j <=npar; j++) matcov[i][j]=0.;
6676:
1.194 brouard 6677: /* Scans npar lines */
1.126 brouard 6678: for(i=1; i <=npar; i++){
1.194 brouard 6679: count=fscanf(ficpar,"%1d%1d%1d",&i1,&j1,&jk);
6680: if(count != 3){
6681: printf("Error! Error in parameter file %s at line %d after line starting with %1d%1d%1d\n\
6682: This is probably because your covariance matrix doesn't \n contain exactly %d lines corresponding to your model line '1+age+%s'.\n\
6683: Please run with mle=-1 to get a correct covariance matrix.\n",optionfile,numlinepar, i1,j1,jk, npar, model);
6684: fprintf(ficlog,"Error! Error in parameter file %s at line %d after line starting with %1d%1d%1d\n\
6685: This is probably because your covariance matrix doesn't \n contain exactly %d lines corresponding to your model line '1+age+%s'.\n\
6686: Please run with mle=-1 to get a correct covariance matrix.\n",optionfile,numlinepar, i1,j1,jk, npar, model);
6687: exit(1);
6688: }else
1.126 brouard 6689: if(mle==1)
1.194 brouard 6690: printf("%1d%1d%1d",i1,j1,jk);
6691: fprintf(ficlog,"%1d%1d%1d",i1,j1,jk);
6692: fprintf(ficparo,"%1d%1d%1d",i1,j1,jk);
1.126 brouard 6693: for(j=1; j <=i; j++){
6694: fscanf(ficpar," %le",&matcov[i][j]);
6695: if(mle==1){
6696: printf(" %.5le",matcov[i][j]);
6697: }
6698: fprintf(ficlog," %.5le",matcov[i][j]);
6699: fprintf(ficparo," %.5le",matcov[i][j]);
6700: }
6701: fscanf(ficpar,"\n");
6702: numlinepar++;
6703: if(mle==1)
6704: printf("\n");
6705: fprintf(ficlog,"\n");
6706: fprintf(ficparo,"\n");
6707: }
1.194 brouard 6708: /* End of read covariance matrix npar lines */
1.126 brouard 6709: for(i=1; i <=npar; i++)
6710: for(j=i+1;j<=npar;j++)
6711: matcov[i][j]=matcov[j][i];
6712:
6713: if(mle==1)
6714: printf("\n");
6715: fprintf(ficlog,"\n");
6716:
6717: fflush(ficlog);
6718:
6719: /*-------- Rewriting parameter file ----------*/
6720: strcpy(rfileres,"r"); /* "Rparameterfile */
6721: strcat(rfileres,optionfilefiname); /* Parameter file first name*/
6722: strcat(rfileres,"."); /* */
6723: strcat(rfileres,optionfilext); /* Other files have txt extension */
6724: if((ficres =fopen(rfileres,"w"))==NULL) {
6725: printf("Problem writing new parameter file: %s\n", fileres);goto end;
6726: fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
6727: }
6728: fprintf(ficres,"#%s\n",version);
6729: } /* End of mle != -3 */
6730:
1.186 brouard 6731: /* Main data
6732: */
1.126 brouard 6733: n= lastobs;
6734: num=lvector(1,n);
6735: moisnais=vector(1,n);
6736: annais=vector(1,n);
6737: moisdc=vector(1,n);
6738: andc=vector(1,n);
6739: agedc=vector(1,n);
6740: cod=ivector(1,n);
6741: weight=vector(1,n);
6742: for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
6743: mint=matrix(1,maxwav,1,n);
6744: anint=matrix(1,maxwav,1,n);
1.131 brouard 6745: s=imatrix(1,maxwav+1,1,n); /* s[i][j] health state for wave i and individual j */
1.126 brouard 6746: tab=ivector(1,NCOVMAX);
1.144 brouard 6747: ncodemax=ivector(1,NCOVMAX); /* Number of code per covariate; if O and 1 only, 2**ncov; V1+V2+V3+V4=>16 */
1.192 brouard 6748: 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 6749:
1.136 brouard 6750: /* Reads data from file datafile */
6751: if (readdata(datafile, firstobs, lastobs, &imx)==1)
6752: goto end;
6753:
6754: /* Calculation of the number of parameters from char model */
1.137 brouard 6755: /* modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4
6756: k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tag[cptcovage=1]=4
6757: k=3 V4 Tvar[k=3]= 4 (from V4)
6758: k=2 V1 Tvar[k=2]= 1 (from V1)
6759: k=1 Tvar[1]=2 (from V2)
6760: */
6761: Tvar=ivector(1,NCOVMAX); /* Was 15 changed to NCOVMAX. */
6762: /* V2+V1+V4+age*V3 is a model with 4 covariates (3 plus signs).
6763: For each model-covariate stores the data-covariate id. Tvar[1]=2, Tvar[2]=1, Tvar[3]=4,
6764: Tvar[4=age*V3] is 3 and 'age' is recorded in Tage.
6765: */
6766: /* For model-covariate k tells which data-covariate to use but
6767: because this model-covariate is a construction we invent a new column
6768: ncovcol + k1
6769: If already ncovcol=4 and model=V2+V1+V1*V4+age*V3
6770: Tvar[3=V1*V4]=4+1 etc */
1.145 brouard 6771: Tprod=ivector(1,NCOVMAX); /* Gives the position of a product */
1.137 brouard 6772: /* Tprod[k1=1]=3(=V1*V4) for V2+V1+V1*V4+age*V3
6773: if V2+V1+V1*V4+age*V3+V3*V2 TProd[k1=2]=5 (V3*V2)
6774: */
1.145 brouard 6775: Tvaraff=ivector(1,NCOVMAX); /* Unclear */
6776: 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 6777: * For V3*V2 (in V2+V1+V1*V4+age*V3+V3*V2), V3*V2 position is 2nd.
6778: * Tvard[k1=2][1]=3 (V3) Tvard[k1=2][2]=2(V2) */
1.145 brouard 6779: Tage=ivector(1,NCOVMAX); /* Gives the covariate id of covariates associated with age: V2 + V1 + age*V4 + V3*age
1.137 brouard 6780: 4 covariates (3 plus signs)
6781: Tage[1=V3*age]= 4; Tage[2=age*V4] = 3
6782: */
1.136 brouard 6783:
1.186 brouard 6784: /* Main decodemodel */
6785:
1.187 brouard 6786:
1.136 brouard 6787: if(decodemodel(model, lastobs) == 1)
6788: goto end;
6789:
1.137 brouard 6790: if((double)(lastobs-imx)/(double)imx > 1.10){
6791: nbwarn++;
6792: 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);
6793: 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);
6794: }
1.136 brouard 6795: /* if(mle==1){*/
1.137 brouard 6796: if (weightopt != 1) { /* Maximisation without weights. We can have weights different from 1 but want no weight*/
6797: for(i=1;i<=imx;i++) weight[i]=1.0; /* changed to imx */
1.136 brouard 6798: }
6799:
6800: /*-calculation of age at interview from date of interview and age at death -*/
6801: agev=matrix(1,maxwav,1,imx);
6802:
6803: if(calandcheckages(imx, maxwav, &agemin, &agemax, &nberr, &nbwarn) == 1)
6804: goto end;
6805:
1.126 brouard 6806:
1.136 brouard 6807: agegomp=(int)agemin;
6808: free_vector(moisnais,1,n);
6809: free_vector(annais,1,n);
1.126 brouard 6810: /* free_matrix(mint,1,maxwav,1,n);
6811: free_matrix(anint,1,maxwav,1,n);*/
6812: free_vector(moisdc,1,n);
6813: free_vector(andc,1,n);
1.145 brouard 6814: /* */
6815:
1.126 brouard 6816: wav=ivector(1,imx);
6817: dh=imatrix(1,lastpass-firstpass+1,1,imx);
6818: bh=imatrix(1,lastpass-firstpass+1,1,imx);
6819: mw=imatrix(1,lastpass-firstpass+1,1,imx);
6820:
6821: /* Concatenates waves */
6822: concatwav(wav, dh, bh, mw, s, agedc, agev, firstpass, lastpass, imx, nlstate, stepm);
1.145 brouard 6823: /* */
6824:
1.126 brouard 6825: /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
6826:
6827: nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
6828: ncodemax[1]=1;
1.145 brouard 6829: Ndum =ivector(-1,NCOVMAX);
1.187 brouard 6830: if (ncovmodel-nagesqr > 2 ) /* That is if covariate other than cst, age and age*age */
1.145 brouard 6831: tricode(Tvar,nbcode,imx, Ndum); /**< Fills nbcode[Tvar[j]][l]; */
1.186 brouard 6832: /* Nbcode gives the value of the lth modality of jth covariate, in
6833: V2+V1*age, there are 3 covariates Tvar[2]=1 (V1).*/
6834: /* 1 to ncodemax[j] is the maximum value of this jth covariate */
1.145 brouard 6835:
6836: codtab=imatrix(1,100,1,10); /* codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) */
6837: /*printf(" codtab[1,1],codtab[100,10]=%d,%d\n", codtab[1][1],codtab[100][10]);*/
1.186 brouard 6838: /* codtab gives the value 1 or 2 of the hth combination of k covariates (1 or 2).*/
1.145 brouard 6839: h=0;
6840:
6841:
6842: /*if (cptcovn > 0) */
1.126 brouard 6843:
1.145 brouard 6844:
1.126 brouard 6845: m=pow(2,cptcoveff);
6846:
1.131 brouard 6847: for(k=1;k<=cptcoveff; k++){ /* scans any effective covariate */
1.143 brouard 6848: for(i=1; i <=pow(2,cptcoveff-k);i++){ /* i=1 to 8/1=8; i=1 to 8/2=4; i=1 to 8/8=1 */
6849: for(j=1; j <= ncodemax[k]; j++){ /* For each modality of this covariate ncodemax=2*/
6850: for(cpt=1; cpt <=pow(2,k-1); cpt++){ /* cpt=1 to 8/2**(3+1-1 or 3+1-3) =1 or 4 */
1.126 brouard 6851: h++;
1.141 brouard 6852: if (h>m)
1.136 brouard 6853: h=1;
1.144 brouard 6854: /**< codtab(h,k) k = codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) + 1
1.186 brouard 6855: * For k=4 covariates, h goes from 1 to 2**k
6856: * codtabm(h,k)= 1 & (h-1) >> (k-1) ;
6857: * h\k 1 2 3 4
1.143 brouard 6858: *______________________________
6859: * 1 i=1 1 i=1 1 i=1 1 i=1 1
6860: * 2 2 1 1 1
6861: * 3 i=2 1 2 1 1
6862: * 4 2 2 1 1
6863: * 5 i=3 1 i=2 1 2 1
6864: * 6 2 1 2 1
6865: * 7 i=4 1 2 2 1
6866: * 8 2 2 2 1
6867: * 9 i=5 1 i=3 1 i=2 1 1
6868: * 10 2 1 1 1
6869: * 11 i=6 1 2 1 1
6870: * 12 2 2 1 1
6871: * 13 i=7 1 i=4 1 2 1
6872: * 14 2 1 2 1
6873: * 15 i=8 1 2 2 1
6874: * 16 2 2 2 1
6875: */
1.141 brouard 6876: codtab[h][k]=j;
1.186 brouard 6877: /* codtab[12][3]=1; */
1.145 brouard 6878: /*codtab[h][Tvar[k]]=j;*/
1.130 brouard 6879: printf("h=%d k=%d j=%d codtab[h][k]=%d Tvar[k]=%d codtab[h][Tvar[k]]=%d \n",h, k,j,codtab[h][k],Tvar[k],codtab[h][Tvar[k]]);
1.126 brouard 6880: }
6881: }
6882: }
6883: }
6884: /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);
6885: codtab[1][2]=1;codtab[2][2]=2; */
6886: /* for(i=1; i <=m ;i++){
6887: for(k=1; k <=cptcovn; k++){
1.131 brouard 6888: printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
1.126 brouard 6889: }
6890: printf("\n");
6891: }
6892: scanf("%d",i);*/
1.145 brouard 6893:
6894: free_ivector(Ndum,-1,NCOVMAX);
6895:
6896:
1.126 brouard 6897:
1.186 brouard 6898: /* Initialisation of ----------- gnuplot -------------*/
1.126 brouard 6899: strcpy(optionfilegnuplot,optionfilefiname);
6900: if(mle==-3)
6901: strcat(optionfilegnuplot,"-mort");
6902: strcat(optionfilegnuplot,".gp");
6903:
6904: if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
6905: printf("Problem with file %s",optionfilegnuplot);
6906: }
6907: else{
6908: fprintf(ficgp,"\n# %s\n", version);
6909: fprintf(ficgp,"# %s\n", optionfilegnuplot);
1.141 brouard 6910: //fprintf(ficgp,"set missing 'NaNq'\n");
6911: fprintf(ficgp,"set datafile missing 'NaNq'\n");
1.126 brouard 6912: }
6913: /* fclose(ficgp);*/
1.186 brouard 6914:
6915:
6916: /* Initialisation of --------- index.htm --------*/
1.126 brouard 6917:
6918: strcpy(optionfilehtm,optionfilefiname); /* Main html file */
6919: if(mle==-3)
6920: strcat(optionfilehtm,"-mort");
6921: strcat(optionfilehtm,".htm");
6922: if((fichtm=fopen(optionfilehtm,"w"))==NULL) {
1.131 brouard 6923: printf("Problem with %s \n",optionfilehtm);
6924: exit(0);
1.126 brouard 6925: }
6926:
6927: strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
6928: strcat(optionfilehtmcov,"-cov.htm");
6929: if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL) {
6930: printf("Problem with %s \n",optionfilehtmcov), exit(0);
6931: }
6932: else{
6933: fprintf(fichtmcov,"<html><head>\n<title>IMaCh Cov %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
6934: <hr size=\"2\" color=\"#EC5E5E\"> \n\
6935: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n",\
6936: optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
6937: }
6938:
6939: fprintf(fichtm,"<html><head>\n<title>IMaCh %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
6940: <hr size=\"2\" color=\"#EC5E5E\"> \n\
6941: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
6942: \n\
6943: <hr size=\"2\" color=\"#EC5E5E\">\
6944: <ul><li><h4>Parameter files</h4>\n\
6945: - Parameter file: <a href=\"%s.%s\">%s.%s</a><br>\n\
6946: - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
6947: - Log file of the run: <a href=\"%s\">%s</a><br>\n\
6948: - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
6949: - Date and time at start: %s</ul>\n",\
6950: optionfilehtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
6951: optionfilefiname,optionfilext,optionfilefiname,optionfilext,\
6952: fileres,fileres,\
6953: filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
6954: fflush(fichtm);
6955:
6956: strcpy(pathr,path);
6957: strcat(pathr,optionfilefiname);
1.184 brouard 6958: #ifdef WIN32
6959: _chdir(optionfilefiname); /* Move to directory named optionfile */
6960: #else
1.126 brouard 6961: chdir(optionfilefiname); /* Move to directory named optionfile */
1.184 brouard 6962: #endif
6963:
1.126 brouard 6964:
6965: /* Calculates basic frequencies. Computes observed prevalence at single age
6966: and prints on file fileres'p'. */
6967: freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart);
6968:
6969: fprintf(fichtm,"\n");
6970: fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
6971: Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
6972: Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
6973: imx,agemin,agemax,jmin,jmax,jmean);
6974: pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
6975: oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
6976: newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
6977: savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
6978: oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
6979:
6980:
6981: /* For Powell, parameters are in a vector p[] starting at p[1]
6982: so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
6983: p=param[1][1]; /* *(*(*(param +1)+1)+0) */
6984:
6985: globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
1.186 brouard 6986: /* For mortality only */
1.126 brouard 6987: if (mle==-3){
1.136 brouard 6988: ximort=matrix(1,NDIM,1,NDIM);
1.186 brouard 6989: /* ximort=gsl_matrix_alloc(1,NDIM,1,NDIM); */
1.126 brouard 6990: cens=ivector(1,n);
6991: ageexmed=vector(1,n);
6992: agecens=vector(1,n);
6993: dcwave=ivector(1,n);
6994:
6995: for (i=1; i<=imx; i++){
6996: dcwave[i]=-1;
6997: for (m=firstpass; m<=lastpass; m++)
6998: if (s[m][i]>nlstate) {
6999: dcwave[i]=m;
7000: /* printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
7001: break;
7002: }
7003: }
7004:
7005: for (i=1; i<=imx; i++) {
7006: if (wav[i]>0){
7007: ageexmed[i]=agev[mw[1][i]][i];
7008: j=wav[i];
7009: agecens[i]=1.;
7010:
7011: if (ageexmed[i]> 1 && wav[i] > 0){
7012: agecens[i]=agev[mw[j][i]][i];
7013: cens[i]= 1;
7014: }else if (ageexmed[i]< 1)
7015: cens[i]= -1;
7016: if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
7017: cens[i]=0 ;
7018: }
7019: else cens[i]=-1;
7020: }
7021:
7022: for (i=1;i<=NDIM;i++) {
7023: for (j=1;j<=NDIM;j++)
7024: ximort[i][j]=(i == j ? 1.0 : 0.0);
7025: }
7026:
1.145 brouard 7027: /*p[1]=0.0268; p[NDIM]=0.083;*/
1.126 brouard 7028: /*printf("%lf %lf", p[1], p[2]);*/
7029:
7030:
1.136 brouard 7031: #ifdef GSL
7032: printf("GSL optimization\n"); fprintf(ficlog,"Powell\n");
1.162 brouard 7033: #else
1.126 brouard 7034: printf("Powell\n"); fprintf(ficlog,"Powell\n");
1.136 brouard 7035: #endif
1.126 brouard 7036: strcpy(filerespow,"pow-mort");
7037: strcat(filerespow,fileres);
7038: if((ficrespow=fopen(filerespow,"w"))==NULL) {
7039: printf("Problem with resultfile: %s\n", filerespow);
7040: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
7041: }
1.136 brouard 7042: #ifdef GSL
7043: fprintf(ficrespow,"# GSL optimization\n# iter -2*LL");
1.162 brouard 7044: #else
1.126 brouard 7045: fprintf(ficrespow,"# Powell\n# iter -2*LL");
1.136 brouard 7046: #endif
1.126 brouard 7047: /* for (i=1;i<=nlstate;i++)
7048: for(j=1;j<=nlstate+ndeath;j++)
7049: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
7050: */
7051: fprintf(ficrespow,"\n");
1.136 brouard 7052: #ifdef GSL
7053: /* gsl starts here */
7054: T = gsl_multimin_fminimizer_nmsimplex;
7055: gsl_multimin_fminimizer *sfm = NULL;
7056: gsl_vector *ss, *x;
7057: gsl_multimin_function minex_func;
7058:
7059: /* Initial vertex size vector */
7060: ss = gsl_vector_alloc (NDIM);
7061:
7062: if (ss == NULL){
7063: GSL_ERROR_VAL ("failed to allocate space for ss", GSL_ENOMEM, 0);
7064: }
7065: /* Set all step sizes to 1 */
7066: gsl_vector_set_all (ss, 0.001);
7067:
7068: /* Starting point */
1.126 brouard 7069:
1.136 brouard 7070: x = gsl_vector_alloc (NDIM);
7071:
7072: if (x == NULL){
7073: gsl_vector_free(ss);
7074: GSL_ERROR_VAL ("failed to allocate space for x", GSL_ENOMEM, 0);
7075: }
7076:
7077: /* Initialize method and iterate */
7078: /* p[1]=0.0268; p[NDIM]=0.083; */
1.186 brouard 7079: /* gsl_vector_set(x, 0, 0.0268); */
7080: /* gsl_vector_set(x, 1, 0.083); */
1.136 brouard 7081: gsl_vector_set(x, 0, p[1]);
7082: gsl_vector_set(x, 1, p[2]);
7083:
7084: minex_func.f = &gompertz_f;
7085: minex_func.n = NDIM;
7086: minex_func.params = (void *)&p; /* ??? */
7087:
7088: sfm = gsl_multimin_fminimizer_alloc (T, NDIM);
7089: gsl_multimin_fminimizer_set (sfm, &minex_func, x, ss);
7090:
7091: printf("Iterations beginning .....\n\n");
7092: printf("Iter. # Intercept Slope -Log Likelihood Simplex size\n");
7093:
7094: iteri=0;
7095: while (rval == GSL_CONTINUE){
7096: iteri++;
7097: status = gsl_multimin_fminimizer_iterate(sfm);
7098:
7099: if (status) printf("error: %s\n", gsl_strerror (status));
7100: fflush(0);
7101:
7102: if (status)
7103: break;
7104:
7105: rval = gsl_multimin_test_size (gsl_multimin_fminimizer_size (sfm), 1e-6);
7106: ssval = gsl_multimin_fminimizer_size (sfm);
7107:
7108: if (rval == GSL_SUCCESS)
7109: printf ("converged to a local maximum at\n");
7110:
7111: printf("%5d ", iteri);
7112: for (it = 0; it < NDIM; it++){
7113: printf ("%10.5f ", gsl_vector_get (sfm->x, it));
7114: }
7115: printf("f() = %-10.5f ssize = %.7f\n", sfm->fval, ssval);
7116: }
7117:
7118: printf("\n\n Please note: Program should be run many times with varying starting points to detemine global maximum\n\n");
7119:
7120: gsl_vector_free(x); /* initial values */
7121: gsl_vector_free(ss); /* inital step size */
7122: for (it=0; it<NDIM; it++){
7123: p[it+1]=gsl_vector_get(sfm->x,it);
7124: fprintf(ficrespow," %.12lf", p[it]);
7125: }
7126: gsl_multimin_fminimizer_free (sfm); /* p *(sfm.x.data) et p *(sfm.x.data+1) */
7127: #endif
7128: #ifdef POWELL
7129: powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
7130: #endif
1.126 brouard 7131: fclose(ficrespow);
7132:
7133: hesscov(matcov, p, NDIM, delti, 1e-4, gompertz);
7134:
7135: for(i=1; i <=NDIM; i++)
7136: for(j=i+1;j<=NDIM;j++)
7137: matcov[i][j]=matcov[j][i];
7138:
7139: printf("\nCovariance matrix\n ");
7140: for(i=1; i <=NDIM; i++) {
7141: for(j=1;j<=NDIM;j++){
7142: printf("%f ",matcov[i][j]);
7143: }
7144: printf("\n ");
7145: }
7146:
7147: printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
1.193 brouard 7148: for (i=1;i<=NDIM;i++) {
1.126 brouard 7149: printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
1.193 brouard 7150: fprintf(ficlog,"%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
7151: }
1.126 brouard 7152: lsurv=vector(1,AGESUP);
7153: lpop=vector(1,AGESUP);
7154: tpop=vector(1,AGESUP);
7155: lsurv[agegomp]=100000;
7156:
7157: for (k=agegomp;k<=AGESUP;k++) {
7158: agemortsup=k;
7159: if (p[1]*exp(p[2]*(k-agegomp))>1) break;
7160: }
7161:
7162: for (k=agegomp;k<agemortsup;k++)
7163: lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
7164:
7165: for (k=agegomp;k<agemortsup;k++){
7166: lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
7167: sumlpop=sumlpop+lpop[k];
7168: }
7169:
7170: tpop[agegomp]=sumlpop;
7171: for (k=agegomp;k<(agemortsup-3);k++){
7172: /* tpop[k+1]=2;*/
7173: tpop[k+1]=tpop[k]-lpop[k];
7174: }
7175:
7176:
7177: printf("\nAge lx qx dx Lx Tx e(x)\n");
7178: for (k=agegomp;k<(agemortsup-2);k++)
7179: 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]);
7180:
7181:
7182: replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
1.194 brouard 7183: if(ageminpar == AGEOVERFLOW ||agemaxpar == AGEOVERFLOW){
7184: printf("Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
7185: This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\
7186: Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
7187: fprintf(ficlog,"Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
7188: This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\
7189: Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
7190: }else
7191: printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
1.126 brouard 7192: printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \
7193: stepm, weightopt,\
7194: model,imx,p,matcov,agemortsup);
7195:
7196: free_vector(lsurv,1,AGESUP);
7197: free_vector(lpop,1,AGESUP);
7198: free_vector(tpop,1,AGESUP);
1.136 brouard 7199: #ifdef GSL
7200: free_ivector(cens,1,n);
7201: free_vector(agecens,1,n);
7202: free_ivector(dcwave,1,n);
7203: free_matrix(ximort,1,NDIM,1,NDIM);
7204: #endif
1.186 brouard 7205: } /* Endof if mle==-3 mortality only */
7206: /* Standard maximisation */
1.126 brouard 7207: else{ /* For mle >=1 */
1.132 brouard 7208: globpr=0;/* debug */
1.186 brouard 7209: /* Computes likelihood for initial parameters */
1.132 brouard 7210: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
1.126 brouard 7211: printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
7212: for (k=1; k<=npar;k++)
7213: printf(" %d %8.5f",k,p[k]);
7214: printf("\n");
1.186 brouard 7215: globpr=1; /* again, to print the contributions */
1.126 brouard 7216: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
7217: printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
7218: for (k=1; k<=npar;k++)
7219: printf(" %d %8.5f",k,p[k]);
7220: printf("\n");
1.186 brouard 7221: if(mle>=1){ /* Could be 1 or 2, Real Maximisation */
1.126 brouard 7222: mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
7223: }
7224:
7225: /*--------- results files --------------*/
1.192 brouard 7226: fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=1+age+%s.\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate, ndeath, maxwav, weightopt,model);
1.126 brouard 7227:
7228:
7229: fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
7230: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
7231: fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
7232: for(i=1,jk=1; i <=nlstate; i++){
7233: for(k=1; k <=(nlstate+ndeath); k++){
7234: if (k != i) {
7235: printf("%d%d ",i,k);
7236: fprintf(ficlog,"%d%d ",i,k);
7237: fprintf(ficres,"%1d%1d ",i,k);
7238: for(j=1; j <=ncovmodel; j++){
1.190 brouard 7239: printf("%12.7f ",p[jk]);
7240: fprintf(ficlog,"%12.7f ",p[jk]);
7241: fprintf(ficres,"%12.7f ",p[jk]);
1.126 brouard 7242: jk++;
7243: }
7244: printf("\n");
7245: fprintf(ficlog,"\n");
7246: fprintf(ficres,"\n");
7247: }
7248: }
7249: }
7250: if(mle!=0){
7251: /* Computing hessian and covariance matrix */
7252: ftolhess=ftol; /* Usually correct */
7253: hesscov(matcov, p, npar, delti, ftolhess, func);
7254: }
1.193 brouard 7255: printf("Parameters and 95%% confidence intervals\n");
7256: fprintf(ficlog, "Parameters, T and confidence intervals\n");
7257: for(i=1,jk=1; i <=nlstate; i++){
7258: for(k=1; k <=(nlstate+ndeath); k++){
7259: if (k != i) {
7260: printf("%d%d ",i,k);
7261: fprintf(ficlog,"%d%d ",i,k);
7262: for(j=1; j <=ncovmodel; j++){
7263: printf("%12.7f T=%8.3f CI=[%12.7f ; %12.7f] ",p[jk], p[jk]/sqrt(matcov[jk][jk]), p[jk]-2*sqrt(matcov[jk][jk]),p[jk]+2*sqrt(matcov[jk][jk]));
7264: fprintf(ficlog,"%12.7f T=%8.3f CI=[%12.7f ; %12.7f] ",p[jk], p[jk]/sqrt(matcov[jk][jk]), p[jk]-2*sqrt(matcov[jk][jk]),p[jk]+2*sqrt(matcov[jk][jk]));
7265: jk++;
7266: }
7267: printf("\n");
7268: fprintf(ficlog,"\n");
7269: }
7270: }
7271: }
7272:
1.126 brouard 7273: fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
7274: printf("# Scales (for hessian or gradient estimation)\n");
7275: fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
7276: for(i=1,jk=1; i <=nlstate; i++){
7277: for(j=1; j <=nlstate+ndeath; j++){
7278: if (j!=i) {
7279: fprintf(ficres,"%1d%1d",i,j);
7280: printf("%1d%1d",i,j);
7281: fprintf(ficlog,"%1d%1d",i,j);
7282: for(k=1; k<=ncovmodel;k++){
7283: printf(" %.5e",delti[jk]);
7284: fprintf(ficlog," %.5e",delti[jk]);
7285: fprintf(ficres," %.5e",delti[jk]);
7286: jk++;
7287: }
7288: printf("\n");
7289: fprintf(ficlog,"\n");
7290: fprintf(ficres,"\n");
7291: }
7292: }
7293: }
7294:
7295: 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");
7296: if(mle>=1)
7297: 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");
7298: 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");
7299: /* # 121 Var(a12)\n\ */
7300: /* # 122 Cov(b12,a12) Var(b12)\n\ */
7301: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
7302: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
7303: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
7304: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
7305: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
7306: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
7307:
7308:
7309: /* Just to have a covariance matrix which will be more understandable
7310: even is we still don't want to manage dictionary of variables
7311: */
7312: for(itimes=1;itimes<=2;itimes++){
7313: jj=0;
7314: for(i=1; i <=nlstate; i++){
7315: for(j=1; j <=nlstate+ndeath; j++){
7316: if(j==i) continue;
7317: for(k=1; k<=ncovmodel;k++){
7318: jj++;
7319: ca[0]= k+'a'-1;ca[1]='\0';
7320: if(itimes==1){
7321: if(mle>=1)
7322: printf("#%1d%1d%d",i,j,k);
7323: fprintf(ficlog,"#%1d%1d%d",i,j,k);
7324: fprintf(ficres,"#%1d%1d%d",i,j,k);
7325: }else{
7326: if(mle>=1)
7327: printf("%1d%1d%d",i,j,k);
7328: fprintf(ficlog,"%1d%1d%d",i,j,k);
7329: fprintf(ficres,"%1d%1d%d",i,j,k);
7330: }
7331: ll=0;
7332: for(li=1;li <=nlstate; li++){
7333: for(lj=1;lj <=nlstate+ndeath; lj++){
7334: if(lj==li) continue;
7335: for(lk=1;lk<=ncovmodel;lk++){
7336: ll++;
7337: if(ll<=jj){
7338: cb[0]= lk +'a'-1;cb[1]='\0';
7339: if(ll<jj){
7340: if(itimes==1){
7341: if(mle>=1)
7342: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
7343: fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
7344: fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
7345: }else{
7346: if(mle>=1)
7347: printf(" %.5e",matcov[jj][ll]);
7348: fprintf(ficlog," %.5e",matcov[jj][ll]);
7349: fprintf(ficres," %.5e",matcov[jj][ll]);
7350: }
7351: }else{
7352: if(itimes==1){
7353: if(mle>=1)
7354: printf(" Var(%s%1d%1d)",ca,i,j);
7355: fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
7356: fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
7357: }else{
7358: if(mle>=1)
7359: printf(" %.5e",matcov[jj][ll]);
7360: fprintf(ficlog," %.5e",matcov[jj][ll]);
7361: fprintf(ficres," %.5e",matcov[jj][ll]);
7362: }
7363: }
7364: }
7365: } /* end lk */
7366: } /* end lj */
7367: } /* end li */
7368: if(mle>=1)
7369: printf("\n");
7370: fprintf(ficlog,"\n");
7371: fprintf(ficres,"\n");
7372: numlinepar++;
7373: } /* end k*/
7374: } /*end j */
7375: } /* end i */
7376: } /* end itimes */
7377:
7378: fflush(ficlog);
7379: fflush(ficres);
7380:
7381: while((c=getc(ficpar))=='#' && c!= EOF){
7382: ungetc(c,ficpar);
7383: fgets(line, MAXLINE, ficpar);
1.141 brouard 7384: fputs(line,stdout);
1.126 brouard 7385: fputs(line,ficparo);
7386: }
7387: ungetc(c,ficpar);
7388:
7389: estepm=0;
7390: fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
7391: if (estepm==0 || estepm < stepm) estepm=stepm;
7392: if (fage <= 2) {
7393: bage = ageminpar;
7394: fage = agemaxpar;
7395: }
7396:
7397: fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
7398: fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
7399: fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
1.186 brouard 7400:
7401: /* Other stuffs, more or less useful */
1.126 brouard 7402: while((c=getc(ficpar))=='#' && c!= EOF){
7403: ungetc(c,ficpar);
7404: fgets(line, MAXLINE, ficpar);
1.141 brouard 7405: fputs(line,stdout);
1.126 brouard 7406: fputs(line,ficparo);
7407: }
7408: ungetc(c,ficpar);
7409:
7410: 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);
7411: 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);
7412: 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);
7413: printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
7414: 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);
7415:
7416: while((c=getc(ficpar))=='#' && c!= EOF){
7417: ungetc(c,ficpar);
7418: fgets(line, MAXLINE, ficpar);
1.141 brouard 7419: fputs(line,stdout);
1.126 brouard 7420: fputs(line,ficparo);
7421: }
7422: ungetc(c,ficpar);
7423:
7424:
7425: dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
7426: dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
7427:
7428: fscanf(ficpar,"pop_based=%d\n",&popbased);
1.193 brouard 7429: fprintf(ficlog,"pop_based=%d\n",popbased);
1.126 brouard 7430: fprintf(ficparo,"pop_based=%d\n",popbased);
7431: fprintf(ficres,"pop_based=%d\n",popbased);
7432:
7433: while((c=getc(ficpar))=='#' && c!= EOF){
7434: ungetc(c,ficpar);
7435: fgets(line, MAXLINE, ficpar);
1.141 brouard 7436: fputs(line,stdout);
1.126 brouard 7437: fputs(line,ficparo);
7438: }
7439: ungetc(c,ficpar);
7440:
7441: 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);
7442: 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);
7443: 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);
7444: 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);
7445: 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);
7446: /* day and month of proj2 are not used but only year anproj2.*/
7447:
7448:
7449:
1.145 brouard 7450: /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint); */
7451: /* ,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2); */
1.126 brouard 7452:
7453: replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
1.194 brouard 7454: if(ageminpar == AGEOVERFLOW ||agemaxpar == -AGEOVERFLOW){
7455: printf("Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
7456: This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\
7457: Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
7458: fprintf(ficlog,"Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
7459: This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\
7460: Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
7461: }else
7462: printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
1.126 brouard 7463:
7464: printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
7465: model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
7466: jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
7467:
7468: /*------------ free_vector -------------*/
7469: /* chdir(path); */
7470:
7471: free_ivector(wav,1,imx);
7472: free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
7473: free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
7474: free_imatrix(mw,1,lastpass-firstpass+1,1,imx);
7475: free_lvector(num,1,n);
7476: free_vector(agedc,1,n);
7477: /*free_matrix(covar,0,NCOVMAX,1,n);*/
7478: /*free_matrix(covar,1,NCOVMAX,1,n);*/
7479: fclose(ficparo);
7480: fclose(ficres);
7481:
7482:
1.186 brouard 7483: /* Other results (useful)*/
7484:
7485:
1.126 brouard 7486: /*--------------- Prevalence limit (period or stable prevalence) --------------*/
1.180 brouard 7487: /*#include "prevlim.h"*/ /* Use ficrespl, ficlog */
7488: prlim=matrix(1,nlstate,1,nlstate);
7489: prevalence_limit(p, prlim, ageminpar, agemaxpar);
1.126 brouard 7490: fclose(ficrespl);
7491:
1.145 brouard 7492: #ifdef FREEEXIT2
7493: #include "freeexit2.h"
7494: #endif
7495:
1.126 brouard 7496: /*------------- h Pij x at various ages ------------*/
1.180 brouard 7497: /*#include "hpijx.h"*/
7498: hPijx(p, bage, fage);
1.145 brouard 7499: fclose(ficrespij);
1.126 brouard 7500:
1.145 brouard 7501: /*-------------- Variance of one-step probabilities---*/
7502: k=1;
1.126 brouard 7503: varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
7504:
7505:
7506: probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
7507: for(i=1;i<=AGESUP;i++)
7508: for(j=1;j<=NCOVMAX;j++)
7509: for(k=1;k<=NCOVMAX;k++)
7510: probs[i][j][k]=0.;
7511:
7512: /*---------- Forecasting ------------------*/
7513: /*if((stepm == 1) && (strcmp(model,".")==0)){*/
7514: if(prevfcast==1){
7515: /* if(stepm ==1){*/
7516: prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
7517: /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
7518: /* } */
7519: /* else{ */
7520: /* erreur=108; */
7521: /* printf("Warning %d!! You can only forecast the prevalences if the optimization\n has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
7522: /* fprintf(ficlog,"Warning %d!! You can only forecast the prevalences if the optimization\n has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
7523: /* } */
7524: }
1.186 brouard 7525:
7526: /* ------ Other prevalence ratios------------ */
1.126 brouard 7527:
1.127 brouard 7528: /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
7529:
7530: prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
7531: /* printf("ageminpar=%f, agemax=%f, s[lastpass][imx]=%d, agev[lastpass][imx]=%f, nlstate=%d, imx=%d, mint[lastpass][imx]=%f, anint[lastpass][imx]=%f,dateprev1=%f, dateprev2=%f, firstpass=%d, lastpass=%d\n",\
7532: ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
7533: */
1.126 brouard 7534:
1.127 brouard 7535: if (mobilav!=0) {
7536: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
7537: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
7538: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
7539: printf(" Error in movingaverage mobilav=%d\n",mobilav);
7540: }
1.126 brouard 7541: }
7542:
7543:
1.127 brouard 7544: /*---------- Health expectancies, no variances ------------*/
7545:
1.126 brouard 7546: strcpy(filerese,"e");
7547: strcat(filerese,fileres);
7548: if((ficreseij=fopen(filerese,"w"))==NULL) {
7549: printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
7550: fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
7551: }
7552: printf("Computing Health Expectancies: result on file '%s' \n", filerese);
7553: fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
1.145 brouard 7554: /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
7555: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
7556:
7557: for (k=1; k <= (int) pow(2,cptcoveff); k++){
1.127 brouard 7558: fprintf(ficreseij,"\n#****** ");
7559: for(j=1;j<=cptcoveff;j++) {
7560: fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
7561: }
7562: fprintf(ficreseij,"******\n");
7563:
7564: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
7565: oldm=oldms;savm=savms;
7566: evsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart);
7567:
7568: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
1.145 brouard 7569: /*}*/
1.127 brouard 7570: }
7571: fclose(ficreseij);
7572:
7573:
7574: /*---------- Health expectancies and variances ------------*/
7575:
7576:
7577: strcpy(filerest,"t");
7578: strcat(filerest,fileres);
7579: if((ficrest=fopen(filerest,"w"))==NULL) {
7580: printf("Problem with total LE resultfile: %s\n", filerest);goto end;
7581: fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
7582: }
7583: printf("Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);
7584: fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);
7585:
1.126 brouard 7586:
7587: strcpy(fileresstde,"stde");
7588: strcat(fileresstde,fileres);
7589: if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {
7590: printf("Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
7591: fprintf(ficlog,"Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
7592: }
7593: printf("Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
7594: fprintf(ficlog,"Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
7595:
7596: strcpy(filerescve,"cve");
7597: strcat(filerescve,fileres);
7598: if((ficrescveij=fopen(filerescve,"w"))==NULL) {
7599: printf("Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
7600: fprintf(ficlog,"Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
7601: }
7602: printf("Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
7603: fprintf(ficlog,"Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
7604:
7605: strcpy(fileresv,"v");
7606: strcat(fileresv,fileres);
7607: if((ficresvij=fopen(fileresv,"w"))==NULL) {
7608: printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
7609: fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
7610: }
7611: printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
7612: fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
7613:
1.145 brouard 7614: /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
7615: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
7616:
7617: for (k=1; k <= (int) pow(2,cptcoveff); k++){
7618: fprintf(ficrest,"\n#****** ");
1.126 brouard 7619: for(j=1;j<=cptcoveff;j++)
7620: fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
7621: fprintf(ficrest,"******\n");
7622:
7623: fprintf(ficresstdeij,"\n#****** ");
7624: fprintf(ficrescveij,"\n#****** ");
7625: for(j=1;j<=cptcoveff;j++) {
7626: fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
7627: fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
7628: }
7629: fprintf(ficresstdeij,"******\n");
7630: fprintf(ficrescveij,"******\n");
7631:
7632: fprintf(ficresvij,"\n#****** ");
7633: for(j=1;j<=cptcoveff;j++)
7634: fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
7635: fprintf(ficresvij,"******\n");
7636:
7637: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
7638: oldm=oldms;savm=savms;
1.127 brouard 7639: cvevsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);
1.145 brouard 7640: /*
7641: */
7642: /* goto endfree; */
1.126 brouard 7643:
7644: vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
7645: pstamp(ficrest);
1.145 brouard 7646:
7647:
1.128 brouard 7648: for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
1.145 brouard 7649: oldm=oldms;savm=savms; /* Segmentation fault */
1.161 brouard 7650: cptcod= 0; /* To be deleted */
7651: varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,vpopbased,mobilav, strstart); /* cptcod not initialized Intel */
1.145 brouard 7652: fprintf(ficrest,"# Total life expectancy with std error and decomposition into time to be expected in each health state\n# (weighted average of eij where weights are ");
1.128 brouard 7653: if(vpopbased==1)
7654: 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);
7655: else
7656: fprintf(ficrest,"the age specific period (stable) prevalences in each health state \n");
7657: fprintf(ficrest,"# Age e.. (std) ");
7658: for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
7659: fprintf(ficrest,"\n");
1.126 brouard 7660:
1.128 brouard 7661: epj=vector(1,nlstate+1);
7662: for(age=bage; age <=fage ;age++){
7663: prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
7664: if (vpopbased==1) {
7665: if(mobilav ==0){
7666: for(i=1; i<=nlstate;i++)
7667: prlim[i][i]=probs[(int)age][i][k];
7668: }else{ /* mobilav */
7669: for(i=1; i<=nlstate;i++)
7670: prlim[i][i]=mobaverage[(int)age][i][k];
7671: }
1.126 brouard 7672: }
7673:
1.128 brouard 7674: fprintf(ficrest," %4.0f",age);
7675: for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
7676: for(i=1, epj[j]=0.;i <=nlstate;i++) {
7677: epj[j] += prlim[i][i]*eij[i][j][(int)age];
7678: /* printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
7679: }
7680: epj[nlstate+1] +=epj[j];
1.126 brouard 7681: }
7682:
1.128 brouard 7683: for(i=1, vepp=0.;i <=nlstate;i++)
7684: for(j=1;j <=nlstate;j++)
7685: vepp += vareij[i][j][(int)age];
7686: fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
7687: for(j=1;j <=nlstate;j++){
7688: fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
7689: }
7690: fprintf(ficrest,"\n");
1.126 brouard 7691: }
7692: }
7693: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
7694: free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
7695: free_vector(epj,1,nlstate+1);
1.145 brouard 7696: /*}*/
1.126 brouard 7697: }
7698: free_vector(weight,1,n);
1.145 brouard 7699: free_imatrix(Tvard,1,NCOVMAX,1,2);
1.126 brouard 7700: free_imatrix(s,1,maxwav+1,1,n);
7701: free_matrix(anint,1,maxwav,1,n);
7702: free_matrix(mint,1,maxwav,1,n);
7703: free_ivector(cod,1,n);
7704: free_ivector(tab,1,NCOVMAX);
7705: fclose(ficresstdeij);
7706: fclose(ficrescveij);
7707: fclose(ficresvij);
7708: fclose(ficrest);
7709: fclose(ficpar);
7710:
7711: /*------- Variance of period (stable) prevalence------*/
7712:
7713: strcpy(fileresvpl,"vpl");
7714: strcat(fileresvpl,fileres);
7715: if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
7716: printf("Problem with variance of period (stable) prevalence resultfile: %s\n", fileresvpl);
7717: exit(0);
7718: }
7719: printf("Computing Variance-covariance of period (stable) prevalence: file '%s' \n", fileresvpl);
7720:
1.145 brouard 7721: /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
7722: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
7723:
7724: for (k=1; k <= (int) pow(2,cptcoveff); k++){
7725: fprintf(ficresvpl,"\n#****** ");
1.126 brouard 7726: for(j=1;j<=cptcoveff;j++)
7727: fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
7728: fprintf(ficresvpl,"******\n");
7729:
7730: varpl=matrix(1,nlstate,(int) bage, (int) fage);
7731: oldm=oldms;savm=savms;
7732: varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k,strstart);
7733: free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
1.145 brouard 7734: /*}*/
1.126 brouard 7735: }
7736:
7737: fclose(ficresvpl);
7738:
7739: /*---------- End : free ----------------*/
7740: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
7741: free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
7742: } /* mle==-3 arrives here for freeing */
1.164 brouard 7743: /* endfree:*/
1.141 brouard 7744: free_matrix(prlim,1,nlstate,1,nlstate); /*here or after loop ? */
1.126 brouard 7745: free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
7746: free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
7747: free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
7748: free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
7749: free_matrix(covar,0,NCOVMAX,1,n);
7750: free_matrix(matcov,1,npar,1,npar);
7751: /*free_vector(delti,1,npar);*/
7752: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
7753: free_matrix(agev,1,maxwav,1,imx);
7754: free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
7755:
1.145 brouard 7756: free_ivector(ncodemax,1,NCOVMAX);
1.192 brouard 7757: free_ivector(ncodemaxwundef,1,NCOVMAX);
1.145 brouard 7758: free_ivector(Tvar,1,NCOVMAX);
7759: free_ivector(Tprod,1,NCOVMAX);
7760: free_ivector(Tvaraff,1,NCOVMAX);
7761: free_ivector(Tage,1,NCOVMAX);
1.126 brouard 7762:
7763: free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
7764: free_imatrix(codtab,1,100,1,10);
7765: fflush(fichtm);
7766: fflush(ficgp);
7767:
7768:
7769: if((nberr >0) || (nbwarn>0)){
7770: printf("End of Imach with %d errors and/or %d warnings\n",nberr,nbwarn);
7771: fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
7772: }else{
7773: printf("End of Imach\n");
7774: fprintf(ficlog,"End of Imach\n");
7775: }
7776: printf("See log file on %s\n",filelog);
7777: /* gettimeofday(&end_time, (struct timezone*)0);*/ /* after time */
1.157 brouard 7778: /*(void) gettimeofday(&end_time,&tzp);*/
7779: rend_time = time(NULL);
7780: end_time = *localtime(&rend_time);
7781: /* tml = *localtime(&end_time.tm_sec); */
7782: strcpy(strtend,asctime(&end_time));
1.126 brouard 7783: printf("Local time at start %s\nLocal time at end %s",strstart, strtend);
7784: fprintf(ficlog,"Local time at start %s\nLocal time at end %s\n",strstart, strtend);
1.157 brouard 7785: printf("Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
1.126 brouard 7786:
1.157 brouard 7787: printf("Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
7788: fprintf(ficlog,"Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
7789: fprintf(ficlog,"Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
1.126 brouard 7790: /* printf("Total time was %d uSec.\n", total_usecs);*/
7791: /* if(fileappend(fichtm,optionfilehtm)){ */
7792: fprintf(fichtm,"<br>Local time at start %s<br>Local time at end %s<br>\n</body></html>",strstart, strtend);
7793: fclose(fichtm);
7794: fprintf(fichtmcov,"<br>Local time at start %s<br>Local time at end %s<br>\n</body></html>",strstart, strtend);
7795: fclose(fichtmcov);
7796: fclose(ficgp);
7797: fclose(ficlog);
7798: /*------ End -----------*/
7799:
7800:
7801: printf("Before Current directory %s!\n",pathcd);
1.184 brouard 7802: #ifdef WIN32
7803: if (_chdir(pathcd) != 0)
7804: printf("Can't move to directory %s!\n",path);
7805: if(_getcwd(pathcd,MAXLINE) > 0)
7806: #else
1.126 brouard 7807: if(chdir(pathcd) != 0)
1.184 brouard 7808: printf("Can't move to directory %s!\n", path);
7809: if (getcwd(pathcd, MAXLINE) > 0)
7810: #endif
1.126 brouard 7811: printf("Current directory %s!\n",pathcd);
7812: /*strcat(plotcmd,CHARSEPARATOR);*/
7813: sprintf(plotcmd,"gnuplot");
1.157 brouard 7814: #ifdef _WIN32
1.126 brouard 7815: sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
7816: #endif
7817: if(!stat(plotcmd,&info)){
1.158 brouard 7818: printf("Error or gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
1.126 brouard 7819: if(!stat(getenv("GNUPLOTBIN"),&info)){
1.158 brouard 7820: printf("Error or gnuplot program not found: '%s' Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);
1.126 brouard 7821: }else
7822: strcpy(pplotcmd,plotcmd);
1.157 brouard 7823: #ifdef __unix
1.126 brouard 7824: strcpy(plotcmd,GNUPLOTPROGRAM);
7825: if(!stat(plotcmd,&info)){
1.158 brouard 7826: printf("Error gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
1.126 brouard 7827: }else
7828: strcpy(pplotcmd,plotcmd);
7829: #endif
7830: }else
7831: strcpy(pplotcmd,plotcmd);
7832:
7833: sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
1.158 brouard 7834: printf("Starting graphs with: '%s'\n",plotcmd);fflush(stdout);
1.126 brouard 7835:
7836: if((outcmd=system(plotcmd)) != 0){
1.158 brouard 7837: printf("gnuplot command might not be in your path: '%s', err=%d\n", plotcmd, outcmd);
1.154 brouard 7838: printf("\n Trying if gnuplot resides on the same directory that IMaCh\n");
1.152 brouard 7839: sprintf(plotcmd,"%sgnuplot %s", pathimach, optionfilegnuplot);
1.150 brouard 7840: if((outcmd=system(plotcmd)) != 0)
1.153 brouard 7841: printf("\n Still a problem with gnuplot command %s, err=%d\n", plotcmd, outcmd);
1.126 brouard 7842: }
1.158 brouard 7843: printf(" Successful, please wait...");
1.126 brouard 7844: while (z[0] != 'q') {
7845: /* chdir(path); */
1.154 brouard 7846: printf("\nType e to edit results with your browser, g to graph again and q for exit: ");
1.126 brouard 7847: scanf("%s",z);
7848: /* if (z[0] == 'c') system("./imach"); */
7849: if (z[0] == 'e') {
1.158 brouard 7850: #ifdef __APPLE__
1.152 brouard 7851: sprintf(pplotcmd, "open %s", optionfilehtm);
1.157 brouard 7852: #elif __linux
7853: sprintf(pplotcmd, "xdg-open %s", optionfilehtm);
1.153 brouard 7854: #else
1.152 brouard 7855: sprintf(pplotcmd, "%s", optionfilehtm);
1.153 brouard 7856: #endif
7857: printf("Starting browser with: %s",pplotcmd);fflush(stdout);
7858: system(pplotcmd);
1.126 brouard 7859: }
7860: else if (z[0] == 'g') system(plotcmd);
7861: else if (z[0] == 'q') exit(0);
7862: }
7863: end:
7864: while (z[0] != 'q') {
1.195 brouard 7865: printf("\nType q for exiting: "); fflush(stdout);
1.126 brouard 7866: scanf("%s",z);
7867: }
7868: }
FreeBSD-CVSweb <freebsd-cvsweb@FreeBSD.org>
![[BACK]](/icons/small/back.gif){kind=icon}
Return to imach.c CVS log ![[TXT]](/icons/small/text.gif){kind=icon}
![[DIR]](/icons/small/dir.gif){kind=icon}
Up to [Local Repository] / imach / src