Annotation of imach/src/imach.c, revision 1.185
1.185 ! brouard 1: /* $Id: imach.c,v 1.184 2015/03/11 11:52:39 brouard Exp $
1.126 brouard 2: $State: Exp $
1.163 brouard 3: $Log: imach.c,v $
1.185 ! brouard 4: Revision 1.184 2015/03/11 11:52:39 brouard
! 5: Summary: Back from Windows 8. Intel Compiler
! 6:
1.184 brouard 7: Revision 1.183 2015/03/10 20:34:32 brouard
8: Summary: 0.98q0, trying with directest, mnbrak fixed
9:
10: We use directest instead of original Powell test; probably no
11: incidence on the results, but better justifications;
12: We fixed Numerical Recipes mnbrak routine which was wrong and gave
13: wrong results.
14:
1.183 brouard 15: Revision 1.182 2015/02/12 08:19:57 brouard
16: Summary: Trying to keep directest which seems simpler and more general
17: Author: Nicolas Brouard
18:
1.182 brouard 19: Revision 1.181 2015/02/11 23:22:24 brouard
20: Summary: Comments on Powell added
21:
22: Author:
23:
1.181 brouard 24: Revision 1.180 2015/02/11 17:33:45 brouard
25: Summary: Finishing move from main to function (hpijx and prevalence_limit)
26:
1.180 brouard 27: Revision 1.179 2015/01/04 09:57:06 brouard
28: Summary: back to OS/X
29:
1.179 brouard 30: Revision 1.178 2015/01/04 09:35:48 brouard
31: *** empty log message ***
32:
1.178 brouard 33: Revision 1.177 2015/01/03 18:40:56 brouard
34: Summary: Still testing ilc32 on OSX
35:
1.177 brouard 36: Revision 1.176 2015/01/03 16:45:04 brouard
37: *** empty log message ***
38:
1.176 brouard 39: Revision 1.175 2015/01/03 16:33:42 brouard
40: *** empty log message ***
41:
1.175 brouard 42: Revision 1.174 2015/01/03 16:15:49 brouard
43: Summary: Still in cross-compilation
44:
1.174 brouard 45: Revision 1.173 2015/01/03 12:06:26 brouard
46: Summary: trying to detect cross-compilation
47:
1.173 brouard 48: Revision 1.172 2014/12/27 12:07:47 brouard
49: Summary: Back from Visual Studio and Intel, options for compiling for Windows XP
50:
1.172 brouard 51: Revision 1.171 2014/12/23 13:26:59 brouard
52: Summary: Back from Visual C
53:
54: Still problem with utsname.h on Windows
55:
1.171 brouard 56: Revision 1.170 2014/12/23 11:17:12 brouard
57: Summary: Cleaning some \%% back to %%
58:
59: The escape was mandatory for a specific compiler (which one?), but too many warnings.
60:
1.170 brouard 61: Revision 1.169 2014/12/22 23:08:31 brouard
62: Summary: 0.98p
63:
64: Outputs some informations on compiler used, OS etc. Testing on different platforms.
65:
1.169 brouard 66: Revision 1.168 2014/12/22 15:17:42 brouard
1.170 brouard 67: Summary: update
1.169 brouard 68:
1.168 brouard 69: Revision 1.167 2014/12/22 13:50:56 brouard
70: Summary: Testing uname and compiler version and if compiled 32 or 64
71:
72: Testing on Linux 64
73:
1.167 brouard 74: Revision 1.166 2014/12/22 11:40:47 brouard
75: *** empty log message ***
76:
1.166 brouard 77: Revision 1.165 2014/12/16 11:20:36 brouard
78: Summary: After compiling on Visual C
79:
80: * imach.c (Module): Merging 1.61 to 1.162
81:
1.165 brouard 82: Revision 1.164 2014/12/16 10:52:11 brouard
83: Summary: Merging with Visual C after suppressing some warnings for unused variables. Also fixing Saito's bug 0.98Xn
84:
85: * imach.c (Module): Merging 1.61 to 1.162
86:
1.164 brouard 87: Revision 1.163 2014/12/16 10:30:11 brouard
88: * imach.c (Module): Merging 1.61 to 1.162
89:
1.163 brouard 90: Revision 1.162 2014/09/25 11:43:39 brouard
91: Summary: temporary backup 0.99!
92:
1.162 brouard 93: Revision 1.1 2014/09/16 11:06:58 brouard
94: Summary: With some code (wrong) for nlopt
95:
96: Author:
97:
98: Revision 1.161 2014/09/15 20:41:41 brouard
99: Summary: Problem with macro SQR on Intel compiler
100:
1.161 brouard 101: Revision 1.160 2014/09/02 09:24:05 brouard
102: *** empty log message ***
103:
1.160 brouard 104: Revision 1.159 2014/09/01 10:34:10 brouard
105: Summary: WIN32
106: Author: Brouard
107:
1.159 brouard 108: Revision 1.158 2014/08/27 17:11:51 brouard
109: *** empty log message ***
110:
1.158 brouard 111: Revision 1.157 2014/08/27 16:26:55 brouard
112: Summary: Preparing windows Visual studio version
113: Author: Brouard
114:
115: In order to compile on Visual studio, time.h is now correct and time_t
116: and tm struct should be used. difftime should be used but sometimes I
117: just make the differences in raw time format (time(&now).
118: Trying to suppress #ifdef LINUX
119: Add xdg-open for __linux in order to open default browser.
120:
1.157 brouard 121: Revision 1.156 2014/08/25 20:10:10 brouard
122: *** empty log message ***
123:
1.156 brouard 124: Revision 1.155 2014/08/25 18:32:34 brouard
125: Summary: New compile, minor changes
126: Author: Brouard
127:
1.155 brouard 128: Revision 1.154 2014/06/20 17:32:08 brouard
129: Summary: Outputs now all graphs of convergence to period prevalence
130:
1.154 brouard 131: Revision 1.153 2014/06/20 16:45:46 brouard
132: Summary: If 3 live state, convergence to period prevalence on same graph
133: Author: Brouard
134:
1.153 brouard 135: Revision 1.152 2014/06/18 17:54:09 brouard
136: Summary: open browser, use gnuplot on same dir than imach if not found in the path
137:
1.152 brouard 138: Revision 1.151 2014/06/18 16:43:30 brouard
139: *** empty log message ***
140:
1.151 brouard 141: Revision 1.150 2014/06/18 16:42:35 brouard
142: Summary: If gnuplot is not in the path try on same directory than imach binary (OSX)
143: Author: brouard
144:
1.150 brouard 145: Revision 1.149 2014/06/18 15:51:14 brouard
146: Summary: Some fixes in parameter files errors
147: Author: Nicolas Brouard
148:
1.149 brouard 149: Revision 1.148 2014/06/17 17:38:48 brouard
150: Summary: Nothing new
151: Author: Brouard
152:
153: Just a new packaging for OS/X version 0.98nS
154:
1.148 brouard 155: Revision 1.147 2014/06/16 10:33:11 brouard
156: *** empty log message ***
157:
1.147 brouard 158: Revision 1.146 2014/06/16 10:20:28 brouard
159: Summary: Merge
160: Author: Brouard
161:
162: Merge, before building revised version.
163:
1.146 brouard 164: Revision 1.145 2014/06/10 21:23:15 brouard
165: Summary: Debugging with valgrind
166: Author: Nicolas Brouard
167:
168: Lot of changes in order to output the results with some covariates
169: After the Edimburgh REVES conference 2014, it seems mandatory to
170: improve the code.
171: No more memory valgrind error but a lot has to be done in order to
172: continue the work of splitting the code into subroutines.
173: Also, decodemodel has been improved. Tricode is still not
174: optimal. nbcode should be improved. Documentation has been added in
175: the source code.
176:
1.144 brouard 177: Revision 1.143 2014/01/26 09:45:38 brouard
178: Summary: Version 0.98nR (to be improved, but gives same optimization results as 0.98k. Nice, promising
179:
180: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
181: (Module): Version 0.98nR Running ok, but output format still only works for three covariates.
182:
1.143 brouard 183: Revision 1.142 2014/01/26 03:57:36 brouard
184: Summary: gnuplot changed plot w l 1 has to be changed to plot w l lt 2
185:
186: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
187:
1.142 brouard 188: Revision 1.141 2014/01/26 02:42:01 brouard
189: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
190:
1.141 brouard 191: Revision 1.140 2011/09/02 10:37:54 brouard
192: Summary: times.h is ok with mingw32 now.
193:
1.140 brouard 194: Revision 1.139 2010/06/14 07:50:17 brouard
195: After the theft of my laptop, I probably lost some lines of codes which were not uploaded to the CVS tree.
196: I remember having already fixed agemin agemax which are pointers now but not cvs saved.
197:
1.139 brouard 198: Revision 1.138 2010/04/30 18:19:40 brouard
199: *** empty log message ***
200:
1.138 brouard 201: Revision 1.137 2010/04/29 18:11:38 brouard
202: (Module): Checking covariates for more complex models
203: than V1+V2. A lot of change to be done. Unstable.
204:
1.137 brouard 205: Revision 1.136 2010/04/26 20:30:53 brouard
206: (Module): merging some libgsl code. Fixing computation
207: of likelione (using inter/intrapolation if mle = 0) in order to
208: get same likelihood as if mle=1.
209: Some cleaning of code and comments added.
210:
1.136 brouard 211: Revision 1.135 2009/10/29 15:33:14 brouard
212: (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
213:
1.135 brouard 214: Revision 1.134 2009/10/29 13:18:53 brouard
215: (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
216:
1.134 brouard 217: Revision 1.133 2009/07/06 10:21:25 brouard
218: just nforces
219:
1.133 brouard 220: Revision 1.132 2009/07/06 08:22:05 brouard
221: Many tings
222:
1.132 brouard 223: Revision 1.131 2009/06/20 16:22:47 brouard
224: Some dimensions resccaled
225:
1.131 brouard 226: Revision 1.130 2009/05/26 06:44:34 brouard
227: (Module): Max Covariate is now set to 20 instead of 8. A
228: lot of cleaning with variables initialized to 0. Trying to make
229: V2+V3*age+V1+V4 strb=V3*age+V1+V4 working better.
230:
1.130 brouard 231: Revision 1.129 2007/08/31 13:49:27 lievre
232: Modification of the way of exiting when the covariate is not binary in order to see on the window the error message before exiting
233:
1.129 lievre 234: Revision 1.128 2006/06/30 13:02:05 brouard
235: (Module): Clarifications on computing e.j
236:
1.128 brouard 237: Revision 1.127 2006/04/28 18:11:50 brouard
238: (Module): Yes the sum of survivors was wrong since
239: imach-114 because nhstepm was no more computed in the age
240: loop. Now we define nhstepma in the age loop.
241: (Module): In order to speed up (in case of numerous covariates) we
242: compute health expectancies (without variances) in a first step
243: and then all the health expectancies with variances or standard
244: deviation (needs data from the Hessian matrices) which slows the
245: computation.
246: In the future we should be able to stop the program is only health
247: expectancies and graph are needed without standard deviations.
248:
1.127 brouard 249: Revision 1.126 2006/04/28 17:23:28 brouard
250: (Module): Yes the sum of survivors was wrong since
251: imach-114 because nhstepm was no more computed in the age
252: loop. Now we define nhstepma in the age loop.
253: Version 0.98h
254:
1.126 brouard 255: Revision 1.125 2006/04/04 15:20:31 lievre
256: Errors in calculation of health expectancies. Age was not initialized.
257: Forecasting file added.
258:
259: Revision 1.124 2006/03/22 17:13:53 lievre
260: Parameters are printed with %lf instead of %f (more numbers after the comma).
261: The log-likelihood is printed in the log file
262:
263: Revision 1.123 2006/03/20 10:52:43 brouard
264: * imach.c (Module): <title> changed, corresponds to .htm file
265: name. <head> headers where missing.
266:
267: * imach.c (Module): Weights can have a decimal point as for
268: English (a comma might work with a correct LC_NUMERIC environment,
269: otherwise the weight is truncated).
270: Modification of warning when the covariates values are not 0 or
271: 1.
272: Version 0.98g
273:
274: Revision 1.122 2006/03/20 09:45:41 brouard
275: (Module): Weights can have a decimal point as for
276: English (a comma might work with a correct LC_NUMERIC environment,
277: otherwise the weight is truncated).
278: Modification of warning when the covariates values are not 0 or
279: 1.
280: Version 0.98g
281:
282: Revision 1.121 2006/03/16 17:45:01 lievre
283: * imach.c (Module): Comments concerning covariates added
284:
285: * imach.c (Module): refinements in the computation of lli if
286: status=-2 in order to have more reliable computation if stepm is
287: not 1 month. Version 0.98f
288:
289: Revision 1.120 2006/03/16 15:10:38 lievre
290: (Module): refinements in the computation of lli if
291: status=-2 in order to have more reliable computation if stepm is
292: not 1 month. Version 0.98f
293:
294: Revision 1.119 2006/03/15 17:42:26 brouard
295: (Module): Bug if status = -2, the loglikelihood was
296: computed as likelihood omitting the logarithm. Version O.98e
297:
298: Revision 1.118 2006/03/14 18:20:07 brouard
299: (Module): varevsij Comments added explaining the second
300: table of variances if popbased=1 .
301: (Module): Covariances of eij, ekl added, graphs fixed, new html link.
302: (Module): Function pstamp added
303: (Module): Version 0.98d
304:
305: Revision 1.117 2006/03/14 17:16:22 brouard
306: (Module): varevsij Comments added explaining the second
307: table of variances if popbased=1 .
308: (Module): Covariances of eij, ekl added, graphs fixed, new html link.
309: (Module): Function pstamp added
310: (Module): Version 0.98d
311:
312: Revision 1.116 2006/03/06 10:29:27 brouard
313: (Module): Variance-covariance wrong links and
314: varian-covariance of ej. is needed (Saito).
315:
316: Revision 1.115 2006/02/27 12:17:45 brouard
317: (Module): One freematrix added in mlikeli! 0.98c
318:
319: Revision 1.114 2006/02/26 12:57:58 brouard
320: (Module): Some improvements in processing parameter
321: filename with strsep.
322:
323: Revision 1.113 2006/02/24 14:20:24 brouard
324: (Module): Memory leaks checks with valgrind and:
325: datafile was not closed, some imatrix were not freed and on matrix
326: allocation too.
327:
328: Revision 1.112 2006/01/30 09:55:26 brouard
329: (Module): Back to gnuplot.exe instead of wgnuplot.exe
330:
331: Revision 1.111 2006/01/25 20:38:18 brouard
332: (Module): Lots of cleaning and bugs added (Gompertz)
333: (Module): Comments can be added in data file. Missing date values
334: can be a simple dot '.'.
335:
336: Revision 1.110 2006/01/25 00:51:50 brouard
337: (Module): Lots of cleaning and bugs added (Gompertz)
338:
339: Revision 1.109 2006/01/24 19:37:15 brouard
340: (Module): Comments (lines starting with a #) are allowed in data.
341:
342: Revision 1.108 2006/01/19 18:05:42 lievre
343: Gnuplot problem appeared...
344: To be fixed
345:
346: Revision 1.107 2006/01/19 16:20:37 brouard
347: Test existence of gnuplot in imach path
348:
349: Revision 1.106 2006/01/19 13:24:36 brouard
350: Some cleaning and links added in html output
351:
352: Revision 1.105 2006/01/05 20:23:19 lievre
353: *** empty log message ***
354:
355: Revision 1.104 2005/09/30 16:11:43 lievre
356: (Module): sump fixed, loop imx fixed, and simplifications.
357: (Module): If the status is missing at the last wave but we know
358: that the person is alive, then we can code his/her status as -2
359: (instead of missing=-1 in earlier versions) and his/her
360: contributions to the likelihood is 1 - Prob of dying from last
361: health status (= 1-p13= p11+p12 in the easiest case of somebody in
362: the healthy state at last known wave). Version is 0.98
363:
364: Revision 1.103 2005/09/30 15:54:49 lievre
365: (Module): sump fixed, loop imx fixed, and simplifications.
366:
367: Revision 1.102 2004/09/15 17:31:30 brouard
368: Add the possibility to read data file including tab characters.
369:
370: Revision 1.101 2004/09/15 10:38:38 brouard
371: Fix on curr_time
372:
373: Revision 1.100 2004/07/12 18:29:06 brouard
374: Add version for Mac OS X. Just define UNIX in Makefile
375:
376: Revision 1.99 2004/06/05 08:57:40 brouard
377: *** empty log message ***
378:
379: Revision 1.98 2004/05/16 15:05:56 brouard
380: New version 0.97 . First attempt to estimate force of mortality
381: directly from the data i.e. without the need of knowing the health
382: state at each age, but using a Gompertz model: log u =a + b*age .
383: This is the basic analysis of mortality and should be done before any
384: other analysis, in order to test if the mortality estimated from the
385: cross-longitudinal survey is different from the mortality estimated
386: from other sources like vital statistic data.
387:
388: The same imach parameter file can be used but the option for mle should be -3.
389:
1.133 brouard 390: Agnès, who wrote this part of the code, tried to keep most of the
1.126 brouard 391: former routines in order to include the new code within the former code.
392:
393: The output is very simple: only an estimate of the intercept and of
394: the slope with 95% confident intervals.
395:
396: Current limitations:
397: A) Even if you enter covariates, i.e. with the
398: model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
399: B) There is no computation of Life Expectancy nor Life Table.
400:
401: Revision 1.97 2004/02/20 13:25:42 lievre
402: Version 0.96d. Population forecasting command line is (temporarily)
403: suppressed.
404:
405: Revision 1.96 2003/07/15 15:38:55 brouard
406: * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
407: rewritten within the same printf. Workaround: many printfs.
408:
409: Revision 1.95 2003/07/08 07:54:34 brouard
410: * imach.c (Repository):
411: (Repository): Using imachwizard code to output a more meaningful covariance
412: matrix (cov(a12,c31) instead of numbers.
413:
414: Revision 1.94 2003/06/27 13:00:02 brouard
415: Just cleaning
416:
417: Revision 1.93 2003/06/25 16:33:55 brouard
418: (Module): On windows (cygwin) function asctime_r doesn't
419: exist so I changed back to asctime which exists.
420: (Module): Version 0.96b
421:
422: Revision 1.92 2003/06/25 16:30:45 brouard
423: (Module): On windows (cygwin) function asctime_r doesn't
424: exist so I changed back to asctime which exists.
425:
426: Revision 1.91 2003/06/25 15:30:29 brouard
427: * imach.c (Repository): Duplicated warning errors corrected.
428: (Repository): Elapsed time after each iteration is now output. It
429: helps to forecast when convergence will be reached. Elapsed time
430: is stamped in powell. We created a new html file for the graphs
431: concerning matrix of covariance. It has extension -cov.htm.
432:
433: Revision 1.90 2003/06/24 12:34:15 brouard
434: (Module): Some bugs corrected for windows. Also, when
435: mle=-1 a template is output in file "or"mypar.txt with the design
436: of the covariance matrix to be input.
437:
438: Revision 1.89 2003/06/24 12:30:52 brouard
439: (Module): Some bugs corrected for windows. Also, when
440: mle=-1 a template is output in file "or"mypar.txt with the design
441: of the covariance matrix to be input.
442:
443: Revision 1.88 2003/06/23 17:54:56 brouard
444: * 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.
445:
446: Revision 1.87 2003/06/18 12:26:01 brouard
447: Version 0.96
448:
449: Revision 1.86 2003/06/17 20:04:08 brouard
450: (Module): Change position of html and gnuplot routines and added
451: routine fileappend.
452:
453: Revision 1.85 2003/06/17 13:12:43 brouard
454: * imach.c (Repository): Check when date of death was earlier that
455: current date of interview. It may happen when the death was just
456: prior to the death. In this case, dh was negative and likelihood
457: was wrong (infinity). We still send an "Error" but patch by
458: assuming that the date of death was just one stepm after the
459: interview.
460: (Repository): Because some people have very long ID (first column)
461: we changed int to long in num[] and we added a new lvector for
462: memory allocation. But we also truncated to 8 characters (left
463: truncation)
464: (Repository): No more line truncation errors.
465:
466: Revision 1.84 2003/06/13 21:44:43 brouard
467: * imach.c (Repository): Replace "freqsummary" at a correct
468: place. It differs from routine "prevalence" which may be called
469: many times. Probs is memory consuming and must be used with
470: parcimony.
471: Version 0.95a3 (should output exactly the same maximization than 0.8a2)
472:
473: Revision 1.83 2003/06/10 13:39:11 lievre
474: *** empty log message ***
475:
476: Revision 1.82 2003/06/05 15:57:20 brouard
477: Add log in imach.c and fullversion number is now printed.
478:
479: */
480: /*
481: Interpolated Markov Chain
482:
483: Short summary of the programme:
484:
485: This program computes Healthy Life Expectancies from
486: cross-longitudinal data. Cross-longitudinal data consist in: -1- a
487: first survey ("cross") where individuals from different ages are
488: interviewed on their health status or degree of disability (in the
489: case of a health survey which is our main interest) -2- at least a
490: second wave of interviews ("longitudinal") which measure each change
491: (if any) in individual health status. Health expectancies are
492: computed from the time spent in each health state according to a
493: model. More health states you consider, more time is necessary to reach the
494: Maximum Likelihood of the parameters involved in the model. The
495: simplest model is the multinomial logistic model where pij is the
496: probability to be observed in state j at the second wave
497: conditional to be observed in state i at the first wave. Therefore
498: the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
499: 'age' is age and 'sex' is a covariate. If you want to have a more
500: complex model than "constant and age", you should modify the program
501: where the markup *Covariates have to be included here again* invites
502: you to do it. More covariates you add, slower the
503: convergence.
504:
505: The advantage of this computer programme, compared to a simple
506: multinomial logistic model, is clear when the delay between waves is not
507: identical for each individual. Also, if a individual missed an
508: intermediate interview, the information is lost, but taken into
509: account using an interpolation or extrapolation.
510:
511: hPijx is the probability to be observed in state i at age x+h
512: conditional to the observed state i at age x. The delay 'h' can be
513: split into an exact number (nh*stepm) of unobserved intermediate
514: states. This elementary transition (by month, quarter,
515: semester or year) is modelled as a multinomial logistic. The hPx
516: matrix is simply the matrix product of nh*stepm elementary matrices
517: and the contribution of each individual to the likelihood is simply
518: hPijx.
519:
520: Also this programme outputs the covariance matrix of the parameters but also
521: of the life expectancies. It also computes the period (stable) prevalence.
522:
1.133 brouard 523: Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
524: Institut national d'études démographiques, Paris.
1.126 brouard 525: This software have been partly granted by Euro-REVES, a concerted action
526: from the European Union.
527: It is copyrighted identically to a GNU software product, ie programme and
528: software can be distributed freely for non commercial use. Latest version
529: can be accessed at http://euroreves.ined.fr/imach .
530:
531: Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
532: or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
533:
534: **********************************************************************/
535: /*
536: main
537: read parameterfile
538: read datafile
539: concatwav
540: freqsummary
541: if (mle >= 1)
542: mlikeli
543: print results files
544: if mle==1
545: computes hessian
546: read end of parameter file: agemin, agemax, bage, fage, estepm
547: begin-prev-date,...
548: open gnuplot file
549: open html file
1.145 brouard 550: period (stable) prevalence | pl_nom 1-1 2-2 etc by covariate
551: for age prevalim() | #****** V1=0 V2=1 V3=1 V4=0 ******
552: | 65 1 0 2 1 3 1 4 0 0.96326 0.03674
553: freexexit2 possible for memory heap.
554:
555: h Pij x | pij_nom ficrestpij
556: # Cov Agex agex+h hpijx with i,j= 1-1 1-2 1-3 2-1 2-2 2-3
557: 1 85 85 1.00000 0.00000 0.00000 0.00000 1.00000 0.00000
558: 1 85 86 0.68299 0.22291 0.09410 0.71093 0.00000 0.28907
559:
560: 1 65 99 0.00364 0.00322 0.99314 0.00350 0.00310 0.99340
561: 1 65 100 0.00214 0.00204 0.99581 0.00206 0.00196 0.99597
562: variance of p one-step probabilities varprob | prob_nom ficresprob #One-step probabilities and stand. devi in ()
563: Standard deviation of one-step probabilities | probcor_nom ficresprobcor #One-step probabilities and correlation matrix
564: Matrix of variance covariance of one-step probabilities | probcov_nom ficresprobcov #One-step probabilities and covariance matrix
565:
1.126 brouard 566: forecasting if prevfcast==1 prevforecast call prevalence()
567: health expectancies
568: Variance-covariance of DFLE
569: prevalence()
570: movingaverage()
571: varevsij()
572: if popbased==1 varevsij(,popbased)
573: total life expectancies
574: Variance of period (stable) prevalence
575: end
576: */
577:
1.165 brouard 578: #define POWELL /* Instead of NLOPT */
1.183 brouard 579: /* #define POWELLORIGINAL */ /* Don't use Directest to decide new direction but original Powell test */
1.184 brouard 580: /* #define MNBRAKORIGINAL */ /* Don't use mnbrak fix */
1.126 brouard 581:
582: #include <math.h>
583: #include <stdio.h>
584: #include <stdlib.h>
585: #include <string.h>
1.159 brouard 586:
587: #ifdef _WIN32
588: #include <io.h>
1.172 brouard 589: #include <windows.h>
590: #include <tchar.h>
1.159 brouard 591: #else
1.126 brouard 592: #include <unistd.h>
1.159 brouard 593: #endif
1.126 brouard 594:
595: #include <limits.h>
596: #include <sys/types.h>
1.171 brouard 597:
598: #if defined(__GNUC__)
599: #include <sys/utsname.h> /* Doesn't work on Windows */
600: #endif
601:
1.126 brouard 602: #include <sys/stat.h>
603: #include <errno.h>
1.159 brouard 604: /* extern int errno; */
1.126 brouard 605:
1.157 brouard 606: /* #ifdef LINUX */
607: /* #include <time.h> */
608: /* #include "timeval.h" */
609: /* #else */
610: /* #include <sys/time.h> */
611: /* #endif */
612:
1.126 brouard 613: #include <time.h>
614:
1.136 brouard 615: #ifdef GSL
616: #include <gsl/gsl_errno.h>
617: #include <gsl/gsl_multimin.h>
618: #endif
619:
1.167 brouard 620:
1.162 brouard 621: #ifdef NLOPT
622: #include <nlopt.h>
623: typedef struct {
624: double (* function)(double [] );
625: } myfunc_data ;
626: #endif
627:
1.126 brouard 628: /* #include <libintl.h> */
629: /* #define _(String) gettext (String) */
630:
1.141 brouard 631: #define MAXLINE 1024 /* Was 256. Overflow with 312 with 2 states and 4 covariates. Should be ok */
1.126 brouard 632:
633: #define GNUPLOTPROGRAM "gnuplot"
634: /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
635: #define FILENAMELENGTH 132
636:
637: #define GLOCK_ERROR_NOPATH -1 /* empty path */
638: #define GLOCK_ERROR_GETCWD -2 /* cannot get cwd */
639:
1.144 brouard 640: #define MAXPARM 128 /**< Maximum number of parameters for the optimization */
641: #define NPARMAX 64 /**< (nlstate+ndeath-1)*nlstate*ncovmodel */
1.126 brouard 642:
643: #define NINTERVMAX 8
1.144 brouard 644: #define NLSTATEMAX 8 /**< Maximum number of live states (for func) */
645: #define NDEATHMAX 8 /**< Maximum number of dead states (for func) */
646: #define NCOVMAX 20 /**< Maximum number of covariates, including generated covariates V1*V2 */
1.145 brouard 647: #define codtabm(h,k) 1 & (h-1) >> (k-1) ;
1.126 brouard 648: #define MAXN 20000
1.144 brouard 649: #define YEARM 12. /**< Number of months per year */
1.126 brouard 650: #define AGESUP 130
651: #define AGEBASE 40
1.164 brouard 652: #define AGEGOMP 10 /**< Minimal age for Gompertz adjustment */
1.157 brouard 653: #ifdef _WIN32
654: #define DIRSEPARATOR '\\'
655: #define CHARSEPARATOR "\\"
656: #define ODIRSEPARATOR '/'
657: #else
1.126 brouard 658: #define DIRSEPARATOR '/'
659: #define CHARSEPARATOR "/"
660: #define ODIRSEPARATOR '\\'
661: #endif
662:
1.185 ! brouard 663: /* $Id: imach.c,v 1.184 2015/03/11 11:52:39 brouard Exp $ */
1.126 brouard 664: /* $State: Exp $ */
665:
1.183 brouard 666: char version[]="Imach version 0.98q0, March 2015,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121), Intel Software 2015";
1.185 ! brouard 667: char fullversion[]="$Revision: 1.184 $ $Date: 2015/03/11 11:52:39 $";
1.126 brouard 668: char strstart[80];
669: char optionfilext[10], optionfilefiname[FILENAMELENGTH];
1.130 brouard 670: int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings */
1.133 brouard 671: int nvar=0, nforce=0; /* Number of variables, number of forces */
1.145 brouard 672: /* Number of covariates model=V2+V1+ V3*age+V2*V4 */
673: int cptcovn=0; /**< cptcovn number of covariates added in the model (excepting constant and age and age*product) */
674: int cptcovt=0; /**< cptcovt number of covariates added in the model (excepting constant and age) */
675: int cptcovs=0; /**< cptcovs number of simple covariates V2+V1 =2 */
676: int cptcovage=0; /**< Number of covariates with age: V3*age only =1 */
677: int cptcovprodnoage=0; /**< Number of covariate products without age */
678: int cptcoveff=0; /* Total number of covariates to vary for printing results */
679: int cptcov=0; /* Working variable */
1.126 brouard 680: int npar=NPARMAX;
681: int nlstate=2; /* Number of live states */
682: int ndeath=1; /* Number of dead states */
1.130 brouard 683: int ncovmodel=0, ncovcol=0; /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
1.126 brouard 684: int popbased=0;
685:
686: int *wav; /* Number of waves for this individuual 0 is possible */
1.130 brouard 687: int maxwav=0; /* Maxim number of waves */
688: int jmin=0, jmax=0; /* min, max spacing between 2 waves */
689: int ijmin=0, ijmax=0; /* Individuals having jmin and jmax */
690: int gipmx=0, gsw=0; /* Global variables on the number of contributions
1.126 brouard 691: to the likelihood and the sum of weights (done by funcone)*/
1.130 brouard 692: int mle=1, weightopt=0;
1.126 brouard 693: int **mw; /* mw[mi][i] is number of the mi wave for this individual */
694: int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
695: int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
696: * wave mi and wave mi+1 is not an exact multiple of stepm. */
1.162 brouard 697: int countcallfunc=0; /* Count the number of calls to func */
1.130 brouard 698: double jmean=1; /* Mean space between 2 waves */
1.145 brouard 699: double **matprod2(); /* test */
1.126 brouard 700: double **oldm, **newm, **savm; /* Working pointers to matrices */
701: double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
1.136 brouard 702: /*FILE *fic ; */ /* Used in readdata only */
703: FILE *ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
1.126 brouard 704: FILE *ficlog, *ficrespow;
1.130 brouard 705: int globpr=0; /* Global variable for printing or not */
1.126 brouard 706: double fretone; /* Only one call to likelihood */
1.130 brouard 707: long ipmx=0; /* Number of contributions */
1.126 brouard 708: double sw; /* Sum of weights */
709: char filerespow[FILENAMELENGTH];
710: char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
711: FILE *ficresilk;
712: FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
713: FILE *ficresprobmorprev;
714: FILE *fichtm, *fichtmcov; /* Html File */
715: FILE *ficreseij;
716: char filerese[FILENAMELENGTH];
717: FILE *ficresstdeij;
718: char fileresstde[FILENAMELENGTH];
719: FILE *ficrescveij;
720: char filerescve[FILENAMELENGTH];
721: FILE *ficresvij;
722: char fileresv[FILENAMELENGTH];
723: FILE *ficresvpl;
724: char fileresvpl[FILENAMELENGTH];
725: char title[MAXLINE];
726: char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH], filerespl[FILENAMELENGTH];
727: char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
728: char tmpout[FILENAMELENGTH], tmpout2[FILENAMELENGTH];
729: char command[FILENAMELENGTH];
730: int outcmd=0;
731:
732: char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
733:
734: char filelog[FILENAMELENGTH]; /* Log file */
735: char filerest[FILENAMELENGTH];
736: char fileregp[FILENAMELENGTH];
737: char popfile[FILENAMELENGTH];
738:
739: char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
740:
1.157 brouard 741: /* struct timeval start_time, end_time, curr_time, last_time, forecast_time; */
742: /* struct timezone tzp; */
743: /* extern int gettimeofday(); */
744: struct tm tml, *gmtime(), *localtime();
745:
746: extern time_t time();
747:
748: struct tm start_time, end_time, curr_time, last_time, forecast_time;
749: time_t rstart_time, rend_time, rcurr_time, rlast_time, rforecast_time; /* raw time */
750: struct tm tm;
751:
1.126 brouard 752: char strcurr[80], strfor[80];
753:
754: char *endptr;
755: long lval;
756: double dval;
757:
758: #define NR_END 1
759: #define FREE_ARG char*
760: #define FTOL 1.0e-10
761:
762: #define NRANSI
763: #define ITMAX 200
764:
765: #define TOL 2.0e-4
766:
767: #define CGOLD 0.3819660
768: #define ZEPS 1.0e-10
769: #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);
770:
771: #define GOLD 1.618034
772: #define GLIMIT 100.0
773: #define TINY 1.0e-20
774:
775: static double maxarg1,maxarg2;
776: #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
777: #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
778:
779: #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
780: #define rint(a) floor(a+0.5)
1.166 brouard 781: /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/myutils_8h-source.html */
1.183 brouard 782: #define mytinydouble 1.0e-16
1.166 brouard 783: /* #define DEQUAL(a,b) (fabs((a)-(b))<mytinydouble) */
784: /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/mynrutils_8h-source.html */
785: /* static double dsqrarg; */
786: /* #define DSQR(a) (DEQUAL((dsqrarg=(a)),0.0) ? 0.0 : dsqrarg*dsqrarg) */
1.126 brouard 787: static double sqrarg;
788: #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
789: #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}
790: int agegomp= AGEGOMP;
791:
792: int imx;
793: int stepm=1;
794: /* Stepm, step in month: minimum step interpolation*/
795:
796: int estepm;
797: /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
798:
799: int m,nb;
800: long *num;
801: int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
802: double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
803: double **pmmij, ***probs;
804: double *ageexmed,*agecens;
805: double dateintmean=0;
806:
807: double *weight;
808: int **s; /* Status */
1.141 brouard 809: double *agedc;
1.145 brouard 810: double **covar; /**< covar[j,i], value of jth covariate for individual i,
1.141 brouard 811: * covar=matrix(0,NCOVMAX,1,n);
812: * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; */
813: double idx;
814: int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */
1.145 brouard 815: int *Ndum; /** Freq of modality (tricode */
1.141 brouard 816: int **codtab; /**< codtab=imatrix(1,100,1,10); */
817: int **Tvard, *Tprod, cptcovprod, *Tvaraff;
1.126 brouard 818: double *lsurv, *lpop, *tpop;
819:
1.143 brouard 820: double ftol=FTOL; /**< Tolerance for computing Max Likelihood */
821: double ftolhess; /**< Tolerance for computing hessian */
1.126 brouard 822:
823: /**************** split *************************/
824: static int split( char *path, char *dirc, char *name, char *ext, char *finame )
825: {
826: /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
827: the name of the file (name), its extension only (ext) and its first part of the name (finame)
828: */
829: char *ss; /* pointer */
830: int l1, l2; /* length counters */
831:
832: l1 = strlen(path ); /* length of path */
833: if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
834: ss= strrchr( path, DIRSEPARATOR ); /* find last / */
835: if ( ss == NULL ) { /* no directory, so determine current directory */
836: strcpy( name, path ); /* we got the fullname name because no directory */
837: /*if(strrchr(path, ODIRSEPARATOR )==NULL)
838: printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
839: /* get current working directory */
840: /* extern char* getcwd ( char *buf , int len);*/
1.184 brouard 841: #ifdef WIN32
842: if (_getcwd( dirc, FILENAME_MAX ) == NULL ) {
843: #else
844: if (getcwd(dirc, FILENAME_MAX) == NULL) {
845: #endif
1.126 brouard 846: return( GLOCK_ERROR_GETCWD );
847: }
848: /* got dirc from getcwd*/
849: printf(" DIRC = %s \n",dirc);
850: } else { /* strip direcotry from path */
851: ss++; /* after this, the filename */
852: l2 = strlen( ss ); /* length of filename */
853: if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
854: strcpy( name, ss ); /* save file name */
855: strncpy( dirc, path, l1 - l2 ); /* now the directory */
856: dirc[l1-l2] = 0; /* add zero */
857: printf(" DIRC2 = %s \n",dirc);
858: }
859: /* We add a separator at the end of dirc if not exists */
860: l1 = strlen( dirc ); /* length of directory */
861: if( dirc[l1-1] != DIRSEPARATOR ){
862: dirc[l1] = DIRSEPARATOR;
863: dirc[l1+1] = 0;
864: printf(" DIRC3 = %s \n",dirc);
865: }
866: ss = strrchr( name, '.' ); /* find last / */
867: if (ss >0){
868: ss++;
869: strcpy(ext,ss); /* save extension */
870: l1= strlen( name);
871: l2= strlen(ss)+1;
872: strncpy( finame, name, l1-l2);
873: finame[l1-l2]= 0;
874: }
875:
876: return( 0 ); /* we're done */
877: }
878:
879:
880: /******************************************/
881:
882: void replace_back_to_slash(char *s, char*t)
883: {
884: int i;
885: int lg=0;
886: i=0;
887: lg=strlen(t);
888: for(i=0; i<= lg; i++) {
889: (s[i] = t[i]);
890: if (t[i]== '\\') s[i]='/';
891: }
892: }
893:
1.132 brouard 894: char *trimbb(char *out, char *in)
1.137 brouard 895: { /* Trim multiple blanks in line but keeps first blanks if line starts with blanks */
1.132 brouard 896: char *s;
897: s=out;
898: while (*in != '\0'){
1.137 brouard 899: while( *in == ' ' && *(in+1) == ' '){ /* && *(in+1) != '\0'){*/
1.132 brouard 900: in++;
901: }
902: *out++ = *in++;
903: }
904: *out='\0';
905: return s;
906: }
907:
1.145 brouard 908: char *cutl(char *blocc, char *alocc, char *in, char occ)
909: {
910: /* cuts string in into blocc and alocc where blocc ends before first occurence of char 'occ'
911: and alocc starts after first occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
912: gives blocc="abcdef2ghi" and alocc="j".
913: If occ is not found blocc is null and alocc is equal to in. Returns blocc
914: */
1.160 brouard 915: char *s, *t;
1.145 brouard 916: t=in;s=in;
917: while ((*in != occ) && (*in != '\0')){
918: *alocc++ = *in++;
919: }
920: if( *in == occ){
921: *(alocc)='\0';
922: s=++in;
923: }
924:
925: if (s == t) {/* occ not found */
926: *(alocc-(in-s))='\0';
927: in=s;
928: }
929: while ( *in != '\0'){
930: *blocc++ = *in++;
931: }
932:
933: *blocc='\0';
934: return t;
935: }
1.137 brouard 936: char *cutv(char *blocc, char *alocc, char *in, char occ)
937: {
938: /* cuts string in into blocc and alocc where blocc ends before last occurence of char 'occ'
939: and alocc starts after last occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
940: gives blocc="abcdef2ghi" and alocc="j".
941: If occ is not found blocc is null and alocc is equal to in. Returns alocc
942: */
943: char *s, *t;
944: t=in;s=in;
945: while (*in != '\0'){
946: while( *in == occ){
947: *blocc++ = *in++;
948: s=in;
949: }
950: *blocc++ = *in++;
951: }
952: if (s == t) /* occ not found */
953: *(blocc-(in-s))='\0';
954: else
955: *(blocc-(in-s)-1)='\0';
956: in=s;
957: while ( *in != '\0'){
958: *alocc++ = *in++;
959: }
960:
961: *alocc='\0';
962: return s;
963: }
964:
1.126 brouard 965: int nbocc(char *s, char occ)
966: {
967: int i,j=0;
968: int lg=20;
969: i=0;
970: lg=strlen(s);
971: for(i=0; i<= lg; i++) {
972: if (s[i] == occ ) j++;
973: }
974: return j;
975: }
976:
1.137 brouard 977: /* void cutv(char *u,char *v, char*t, char occ) */
978: /* { */
979: /* /\* cuts string t into u and v where u ends before last occurence of char 'occ' */
980: /* and v starts after last occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2') */
981: /* gives u="abcdef2ghi" and v="j" *\/ */
982: /* int i,lg,j,p=0; */
983: /* i=0; */
984: /* lg=strlen(t); */
985: /* for(j=0; j<=lg-1; j++) { */
986: /* if((t[j]!= occ) && (t[j+1]== occ)) p=j+1; */
987: /* } */
1.126 brouard 988:
1.137 brouard 989: /* for(j=0; j<p; j++) { */
990: /* (u[j] = t[j]); */
991: /* } */
992: /* u[p]='\0'; */
1.126 brouard 993:
1.137 brouard 994: /* for(j=0; j<= lg; j++) { */
995: /* if (j>=(p+1))(v[j-p-1] = t[j]); */
996: /* } */
997: /* } */
1.126 brouard 998:
1.160 brouard 999: #ifdef _WIN32
1000: char * strsep(char **pp, const char *delim)
1001: {
1002: char *p, *q;
1003:
1004: if ((p = *pp) == NULL)
1005: return 0;
1006: if ((q = strpbrk (p, delim)) != NULL)
1007: {
1008: *pp = q + 1;
1009: *q = '\0';
1010: }
1011: else
1012: *pp = 0;
1013: return p;
1014: }
1015: #endif
1016:
1.126 brouard 1017: /********************** nrerror ********************/
1018:
1019: void nrerror(char error_text[])
1020: {
1021: fprintf(stderr,"ERREUR ...\n");
1022: fprintf(stderr,"%s\n",error_text);
1023: exit(EXIT_FAILURE);
1024: }
1025: /*********************** vector *******************/
1026: double *vector(int nl, int nh)
1027: {
1028: double *v;
1029: v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
1030: if (!v) nrerror("allocation failure in vector");
1031: return v-nl+NR_END;
1032: }
1033:
1034: /************************ free vector ******************/
1035: void free_vector(double*v, int nl, int nh)
1036: {
1037: free((FREE_ARG)(v+nl-NR_END));
1038: }
1039:
1040: /************************ivector *******************************/
1041: int *ivector(long nl,long nh)
1042: {
1043: int *v;
1044: v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
1045: if (!v) nrerror("allocation failure in ivector");
1046: return v-nl+NR_END;
1047: }
1048:
1049: /******************free ivector **************************/
1050: void free_ivector(int *v, long nl, long nh)
1051: {
1052: free((FREE_ARG)(v+nl-NR_END));
1053: }
1054:
1055: /************************lvector *******************************/
1056: long *lvector(long nl,long nh)
1057: {
1058: long *v;
1059: v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
1060: if (!v) nrerror("allocation failure in ivector");
1061: return v-nl+NR_END;
1062: }
1063:
1064: /******************free lvector **************************/
1065: void free_lvector(long *v, long nl, long nh)
1066: {
1067: free((FREE_ARG)(v+nl-NR_END));
1068: }
1069:
1070: /******************* imatrix *******************************/
1071: int **imatrix(long nrl, long nrh, long ncl, long nch)
1072: /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */
1073: {
1074: long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;
1075: int **m;
1076:
1077: /* allocate pointers to rows */
1078: m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));
1079: if (!m) nrerror("allocation failure 1 in matrix()");
1080: m += NR_END;
1081: m -= nrl;
1082:
1083:
1084: /* allocate rows and set pointers to them */
1085: m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));
1086: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
1087: m[nrl] += NR_END;
1088: m[nrl] -= ncl;
1089:
1090: for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;
1091:
1092: /* return pointer to array of pointers to rows */
1093: return m;
1094: }
1095:
1096: /****************** free_imatrix *************************/
1097: void free_imatrix(m,nrl,nrh,ncl,nch)
1098: int **m;
1099: long nch,ncl,nrh,nrl;
1100: /* free an int matrix allocated by imatrix() */
1101: {
1102: free((FREE_ARG) (m[nrl]+ncl-NR_END));
1103: free((FREE_ARG) (m+nrl-NR_END));
1104: }
1105:
1106: /******************* matrix *******************************/
1107: double **matrix(long nrl, long nrh, long ncl, long nch)
1108: {
1109: long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
1110: double **m;
1111:
1112: m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
1113: if (!m) nrerror("allocation failure 1 in matrix()");
1114: m += NR_END;
1115: m -= nrl;
1116:
1117: m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
1118: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
1119: m[nrl] += NR_END;
1120: m[nrl] -= ncl;
1121:
1122: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
1123: return m;
1.145 brouard 1124: /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) or &(m[1][0])
1125: m[i] = address of ith row of the table. &(m[i]) is its value which is another adress
1126: that of m[i][0]. In order to get the value p m[i][0] but it is unitialized.
1.126 brouard 1127: */
1128: }
1129:
1130: /*************************free matrix ************************/
1131: void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
1132: {
1133: free((FREE_ARG)(m[nrl]+ncl-NR_END));
1134: free((FREE_ARG)(m+nrl-NR_END));
1135: }
1136:
1137: /******************* ma3x *******************************/
1138: double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
1139: {
1140: long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
1141: double ***m;
1142:
1143: m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
1144: if (!m) nrerror("allocation failure 1 in matrix()");
1145: m += NR_END;
1146: m -= nrl;
1147:
1148: m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
1149: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
1150: m[nrl] += NR_END;
1151: m[nrl] -= ncl;
1152:
1153: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
1154:
1155: m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
1156: if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
1157: m[nrl][ncl] += NR_END;
1158: m[nrl][ncl] -= nll;
1159: for (j=ncl+1; j<=nch; j++)
1160: m[nrl][j]=m[nrl][j-1]+nlay;
1161:
1162: for (i=nrl+1; i<=nrh; i++) {
1163: m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
1164: for (j=ncl+1; j<=nch; j++)
1165: m[i][j]=m[i][j-1]+nlay;
1166: }
1167: return m;
1168: /* gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
1169: &(m[i][j][k]) <=> *((*(m+i) + j)+k)
1170: */
1171: }
1172:
1173: /*************************free ma3x ************************/
1174: void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
1175: {
1176: free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
1177: free((FREE_ARG)(m[nrl]+ncl-NR_END));
1178: free((FREE_ARG)(m+nrl-NR_END));
1179: }
1180:
1181: /*************** function subdirf ***********/
1182: char *subdirf(char fileres[])
1183: {
1184: /* Caution optionfilefiname is hidden */
1185: strcpy(tmpout,optionfilefiname);
1186: strcat(tmpout,"/"); /* Add to the right */
1187: strcat(tmpout,fileres);
1188: return tmpout;
1189: }
1190:
1191: /*************** function subdirf2 ***********/
1192: char *subdirf2(char fileres[], char *preop)
1193: {
1194:
1195: /* Caution optionfilefiname is hidden */
1196: strcpy(tmpout,optionfilefiname);
1197: strcat(tmpout,"/");
1198: strcat(tmpout,preop);
1199: strcat(tmpout,fileres);
1200: return tmpout;
1201: }
1202:
1203: /*************** function subdirf3 ***********/
1204: char *subdirf3(char fileres[], char *preop, char *preop2)
1205: {
1206:
1207: /* Caution optionfilefiname is hidden */
1208: strcpy(tmpout,optionfilefiname);
1209: strcat(tmpout,"/");
1210: strcat(tmpout,preop);
1211: strcat(tmpout,preop2);
1212: strcat(tmpout,fileres);
1213: return tmpout;
1214: }
1215:
1.162 brouard 1216: char *asc_diff_time(long time_sec, char ascdiff[])
1217: {
1218: long sec_left, days, hours, minutes;
1219: days = (time_sec) / (60*60*24);
1220: sec_left = (time_sec) % (60*60*24);
1221: hours = (sec_left) / (60*60) ;
1222: sec_left = (sec_left) %(60*60);
1223: minutes = (sec_left) /60;
1224: sec_left = (sec_left) % (60);
1225: sprintf(ascdiff,"%ld day(s) %ld hour(s) %ld minute(s) %ld second(s)",days, hours, minutes, sec_left);
1226: return ascdiff;
1227: }
1228:
1.126 brouard 1229: /***************** f1dim *************************/
1230: extern int ncom;
1231: extern double *pcom,*xicom;
1232: extern double (*nrfunc)(double []);
1233:
1234: double f1dim(double x)
1235: {
1236: int j;
1237: double f;
1238: double *xt;
1239:
1240: xt=vector(1,ncom);
1241: for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];
1242: f=(*nrfunc)(xt);
1243: free_vector(xt,1,ncom);
1244: return f;
1245: }
1246:
1247: /*****************brent *************************/
1248: double brent(double ax, double bx, double cx, double (*f)(double), double tol, double *xmin)
1249: {
1250: int iter;
1251: double a,b,d,etemp;
1.159 brouard 1252: double fu=0,fv,fw,fx;
1.164 brouard 1253: double ftemp=0.;
1.126 brouard 1254: double p,q,r,tol1,tol2,u,v,w,x,xm;
1255: double e=0.0;
1256:
1257: a=(ax < cx ? ax : cx);
1258: b=(ax > cx ? ax : cx);
1259: x=w=v=bx;
1260: fw=fv=fx=(*f)(x);
1261: for (iter=1;iter<=ITMAX;iter++) {
1262: xm=0.5*(a+b);
1263: tol2=2.0*(tol1=tol*fabs(x)+ZEPS);
1264: /* if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
1265: printf(".");fflush(stdout);
1266: fprintf(ficlog,".");fflush(ficlog);
1.162 brouard 1267: #ifdef DEBUGBRENT
1.126 brouard 1268: 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);
1269: 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);
1270: /* if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
1271: #endif
1272: if (fabs(x-xm) <= (tol2-0.5*(b-a))){
1273: *xmin=x;
1274: return fx;
1275: }
1276: ftemp=fu;
1277: if (fabs(e) > tol1) {
1278: r=(x-w)*(fx-fv);
1279: q=(x-v)*(fx-fw);
1280: p=(x-v)*q-(x-w)*r;
1281: q=2.0*(q-r);
1282: if (q > 0.0) p = -p;
1283: q=fabs(q);
1284: etemp=e;
1285: e=d;
1286: if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))
1287: d=CGOLD*(e=(x >= xm ? a-x : b-x));
1288: else {
1289: d=p/q;
1290: u=x+d;
1291: if (u-a < tol2 || b-u < tol2)
1292: d=SIGN(tol1,xm-x);
1293: }
1294: } else {
1295: d=CGOLD*(e=(x >= xm ? a-x : b-x));
1296: }
1297: u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));
1298: fu=(*f)(u);
1299: if (fu <= fx) {
1300: if (u >= x) a=x; else b=x;
1301: SHFT(v,w,x,u)
1.183 brouard 1302: SHFT(fv,fw,fx,fu)
1303: } else {
1304: if (u < x) a=u; else b=u;
1305: if (fu <= fw || w == x) {
1306: v=w;
1307: w=u;
1308: fv=fw;
1309: fw=fu;
1310: } else if (fu <= fv || v == x || v == w) {
1311: v=u;
1312: fv=fu;
1313: }
1314: }
1.126 brouard 1315: }
1316: nrerror("Too many iterations in brent");
1317: *xmin=x;
1318: return fx;
1319: }
1320:
1321: /****************** mnbrak ***********************/
1322:
1323: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,
1324: double (*func)(double))
1.183 brouard 1325: { /* Given a function func , and given distinct initial points ax and bx , this routine searches in
1326: the downhill direction (defined by the function as evaluated at the initial points) and returns
1327: new points ax , bx , cx that bracket a minimum of the function. Also returned are the function
1328: values at the three points, fa, fb , and fc such that fa > fb and fb < fc.
1329: */
1.126 brouard 1330: double ulim,u,r,q, dum;
1331: double fu;
1332:
1333: *fa=(*func)(*ax);
1334: *fb=(*func)(*bx);
1335: if (*fb > *fa) {
1336: SHFT(dum,*ax,*bx,dum)
1.183 brouard 1337: SHFT(dum,*fb,*fa,dum)
1338: }
1.126 brouard 1339: *cx=(*bx)+GOLD*(*bx-*ax);
1340: *fc=(*func)(*cx);
1.183 brouard 1341: #ifdef DEBUG
1342: printf("mnbrak0 *fb=%.12e *fc=%.12e\n",*fb,*fc);
1343: fprintf(ficlog,"mnbrak0 *fb=%.12e *fc=%.12e\n",*fb,*fc);
1344: #endif
1345: while (*fb > *fc) { /* Declining a,b,c with fa> fb > fc */
1.126 brouard 1346: r=(*bx-*ax)*(*fb-*fc);
1347: q=(*bx-*cx)*(*fb-*fa);
1348: u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/
1.183 brouard 1349: (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); /* Minimum abscissa of a parabolic estimated from (a,fa), (b,fb) and (c,fc). */
1350: ulim=(*bx)+GLIMIT*(*cx-*bx); /* Maximum abscissa where function should be evaluated */
1351: if ((*bx-u)*(u-*cx) > 0.0) { /* if u_p is between b and c */
1.126 brouard 1352: fu=(*func)(u);
1.163 brouard 1353: #ifdef DEBUG
1354: /* f(x)=A(x-u)**2+f(u) */
1355: double A, fparabu;
1356: A= (*fb - *fa)/(*bx-*ax)/(*bx+*ax-2*u);
1357: fparabu= *fa - A*(*ax-u)*(*ax-u);
1358: 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);
1359: 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 1360: /* And thus,it can be that fu > *fc even if fparabu < *fc */
1361: /* mnbrak (*ax=7.666299858533, *fa=299039.693133272231), (*bx=8.595447774979, *fb=298976.598289369489),
1362: (*cx=10.098840694817, *fc=298946.631474258087), (*u=9.852501168332, fu=298948.773013752128, fparabu=298945.434711494134) */
1363: /* In that case, there is no bracket in the output! Routine is wrong with many consequences.*/
1.163 brouard 1364: #endif
1.184 brouard 1365: #ifdef MNBRAKORIGINAL
1.183 brouard 1366: #else
1367: if (fu > *fc) {
1368: #ifdef DEBUG
1369: printf("mnbrak4 fu > fc \n");
1370: fprintf(ficlog, "mnbrak4 fu > fc\n");
1371: #endif
1372: /* 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 *\/ */
1373: /* SHFT(*fa,*fc,fu,*fc) /\* (b, u, c) is a bracket while test fb > fc will be fu > fc will exit *\/ */
1374: dum=u; /* Shifting c and u */
1375: u = *cx;
1376: *cx = dum;
1377: dum = fu;
1378: fu = *fc;
1379: *fc =dum;
1380: } else { /* end */
1381: #ifdef DEBUG
1382: printf("mnbrak3 fu < fc \n");
1383: fprintf(ficlog, "mnbrak3 fu < fc\n");
1384: #endif
1385: dum=u; /* Shifting c and u */
1386: u = *cx;
1387: *cx = dum;
1388: dum = fu;
1389: fu = *fc;
1390: *fc =dum;
1391: }
1392: #endif
1.162 brouard 1393: } else if ((*cx-u)*(u-ulim) > 0.0) { /* u is after c but before ulim */
1.183 brouard 1394: #ifdef DEBUG
1395: printf("mnbrak2 u after c but before ulim\n");
1396: fprintf(ficlog, "mnbrak2 u after c but before ulim\n");
1397: #endif
1.126 brouard 1398: fu=(*func)(u);
1399: if (fu < *fc) {
1.183 brouard 1400: #ifdef DEBUG
1401: printf("mnbrak2 u after c but before ulim AND fu < fc\n");
1402: fprintf(ficlog, "mnbrak2 u after c but before ulim AND fu <fc \n");
1403: #endif
1.126 brouard 1404: SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))
1.183 brouard 1405: SHFT(*fb,*fc,fu,(*func)(u))
1406: }
1.162 brouard 1407: } else if ((u-ulim)*(ulim-*cx) >= 0.0) { /* u outside ulim (verifying that ulim is beyond c) */
1.183 brouard 1408: #ifdef DEBUG
1409: printf("mnbrak2 u outside ulim (verifying that ulim is beyond c)\n");
1410: fprintf(ficlog, "mnbrak2 u outside ulim (verifying that ulim is beyond c)\n");
1411: #endif
1.126 brouard 1412: u=ulim;
1413: fu=(*func)(u);
1.183 brouard 1414: } else { /* u could be left to b (if r > q parabola has a maximum) */
1415: #ifdef DEBUG
1416: printf("mnbrak2 u could be left to b (if r > q parabola has a maximum)\n");
1417: fprintf(ficlog, "mnbrak2 u could be left to b (if r > q parabola has a maximum)\n");
1418: #endif
1.126 brouard 1419: u=(*cx)+GOLD*(*cx-*bx);
1420: fu=(*func)(u);
1.183 brouard 1421: } /* end tests */
1.126 brouard 1422: SHFT(*ax,*bx,*cx,u)
1.183 brouard 1423: SHFT(*fa,*fb,*fc,fu)
1424: #ifdef DEBUG
1425: 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);
1426: 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);
1427: #endif
1428: } /* 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 1429: }
1430:
1431: /*************** linmin ************************/
1.162 brouard 1432: /* Given an n -dimensional point p[1..n] and an n -dimensional direction xi[1..n] , moves and
1433: resets p to where the function func(p) takes on a minimum along the direction xi from p ,
1434: and replaces xi by the actual vector displacement that p was moved. Also returns as fret
1435: the value of func at the returned location p . This is actually all accomplished by calling the
1436: routines mnbrak and brent .*/
1.126 brouard 1437: int ncom;
1438: double *pcom,*xicom;
1439: double (*nrfunc)(double []);
1440:
1441: void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))
1442: {
1443: double brent(double ax, double bx, double cx,
1444: double (*f)(double), double tol, double *xmin);
1445: double f1dim(double x);
1446: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,
1447: double *fc, double (*func)(double));
1448: int j;
1449: double xx,xmin,bx,ax;
1450: double fx,fb,fa;
1451:
1452: ncom=n;
1453: pcom=vector(1,n);
1454: xicom=vector(1,n);
1455: nrfunc=func;
1456: for (j=1;j<=n;j++) {
1457: pcom[j]=p[j];
1458: xicom[j]=xi[j];
1459: }
1460: ax=0.0;
1461: xx=1.0;
1.162 brouard 1462: mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); /* Find a bracket a,x,b in direction n=xi ie xicom */
1463: *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); /* Find a minimum P+lambda n in that direction (lambdamin), with TOL between abscisses */
1.126 brouard 1464: #ifdef DEBUG
1465: printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
1466: fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
1467: #endif
1468: for (j=1;j<=n;j++) {
1469: xi[j] *= xmin;
1470: p[j] += xi[j];
1471: }
1472: free_vector(xicom,1,n);
1473: free_vector(pcom,1,n);
1474: }
1475:
1476:
1477: /*************** powell ************************/
1.162 brouard 1478: /*
1479: Minimization of a function func of n variables. Input consists of an initial starting point
1480: p[1..n] ; an initial matrix xi[1..n][1..n] , whose columns contain the initial set of di-
1481: rections (usually the n unit vectors); and ftol , the fractional tolerance in the function value
1482: such that failure to decrease by more than this amount on one iteration signals doneness. On
1483: output, p is set to the best point found, xi is the then-current direction set, fret is the returned
1484: function value at p , and iter is the number of iterations taken. The routine linmin is used.
1485: */
1.126 brouard 1486: void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,
1487: double (*func)(double []))
1488: {
1489: void linmin(double p[], double xi[], int n, double *fret,
1490: double (*func)(double []));
1491: int i,ibig,j;
1492: double del,t,*pt,*ptt,*xit;
1.181 brouard 1493: double directest;
1.126 brouard 1494: double fp,fptt;
1495: double *xits;
1496: int niterf, itmp;
1497:
1498: pt=vector(1,n);
1499: ptt=vector(1,n);
1500: xit=vector(1,n);
1501: xits=vector(1,n);
1502: *fret=(*func)(p);
1503: for (j=1;j<=n;j++) pt[j]=p[j];
1.157 brouard 1504: rcurr_time = time(NULL);
1.126 brouard 1505: for (*iter=1;;++(*iter)) {
1506: fp=(*fret);
1507: ibig=0;
1508: del=0.0;
1.157 brouard 1509: rlast_time=rcurr_time;
1510: /* (void) gettimeofday(&curr_time,&tzp); */
1511: rcurr_time = time(NULL);
1512: curr_time = *localtime(&rcurr_time);
1513: printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, rcurr_time-rlast_time, rcurr_time-rstart_time);fflush(stdout);
1514: fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret,rcurr_time-rlast_time, rcurr_time-rstart_time); fflush(ficlog);
1515: /* fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tm_sec-start_time.tm_sec); */
1.126 brouard 1516: for (i=1;i<=n;i++) {
1517: printf(" %d %.12f",i, p[i]);
1518: fprintf(ficlog," %d %.12lf",i, p[i]);
1519: fprintf(ficrespow," %.12lf", p[i]);
1520: }
1521: printf("\n");
1522: fprintf(ficlog,"\n");
1523: fprintf(ficrespow,"\n");fflush(ficrespow);
1524: if(*iter <=3){
1.157 brouard 1525: tml = *localtime(&rcurr_time);
1526: strcpy(strcurr,asctime(&tml));
1527: rforecast_time=rcurr_time;
1.126 brouard 1528: itmp = strlen(strcurr);
1529: if(strcurr[itmp-1]=='\n') /* Windows outputs with a new line */
1530: strcurr[itmp-1]='\0';
1.162 brouard 1531: printf("\nConsidering the time needed for the last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
1.157 brouard 1532: fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
1.126 brouard 1533: for(niterf=10;niterf<=30;niterf+=10){
1.157 brouard 1534: rforecast_time=rcurr_time+(niterf-*iter)*(rcurr_time-rlast_time);
1535: forecast_time = *localtime(&rforecast_time);
1536: strcpy(strfor,asctime(&forecast_time));
1.126 brouard 1537: itmp = strlen(strfor);
1538: if(strfor[itmp-1]=='\n')
1539: strfor[itmp-1]='\0';
1.157 brouard 1540: 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);
1541: 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 1542: }
1543: }
1544: for (i=1;i<=n;i++) {
1545: for (j=1;j<=n;j++) xit[j]=xi[j][i];
1546: fptt=(*fret);
1547: #ifdef DEBUG
1.164 brouard 1548: printf("fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
1549: fprintf(ficlog, "fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
1.126 brouard 1550: #endif
1551: printf("%d",i);fflush(stdout);
1552: fprintf(ficlog,"%d",i);fflush(ficlog);
1.183 brouard 1553: linmin(p,xit,n,fret,func); /* xit[n] has been loaded for direction i */
1.181 brouard 1554: if (fabs(fptt-(*fret)) > del) { /* We are keeping the max gain on each of the n directions
1555: because that direction will be replaced unless the gain del is small
1556: in comparison with the 'probable' gain, mu^2, with the last average direction.
1557: Unless the n directions are conjugate some gain in the determinant may be obtained
1558: with the new direction.
1559: */
1.126 brouard 1560: del=fabs(fptt-(*fret));
1561: ibig=i;
1562: }
1563: #ifdef DEBUG
1564: printf("%d %.12e",i,(*fret));
1565: fprintf(ficlog,"%d %.12e",i,(*fret));
1566: for (j=1;j<=n;j++) {
1567: xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
1568: printf(" x(%d)=%.12e",j,xit[j]);
1569: fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
1570: }
1571: for(j=1;j<=n;j++) {
1.162 brouard 1572: printf(" p(%d)=%.12e",j,p[j]);
1573: fprintf(ficlog," p(%d)=%.12e",j,p[j]);
1.126 brouard 1574: }
1575: printf("\n");
1576: fprintf(ficlog,"\n");
1577: #endif
1.162 brouard 1578: } /* end i */
1.182 brouard 1579: if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) { /* Did we reach enough precision? */
1.126 brouard 1580: #ifdef DEBUG
1581: int k[2],l;
1582: k[0]=1;
1583: k[1]=-1;
1584: printf("Max: %.12e",(*func)(p));
1585: fprintf(ficlog,"Max: %.12e",(*func)(p));
1586: for (j=1;j<=n;j++) {
1587: printf(" %.12e",p[j]);
1588: fprintf(ficlog," %.12e",p[j]);
1589: }
1590: printf("\n");
1591: fprintf(ficlog,"\n");
1592: for(l=0;l<=1;l++) {
1593: for (j=1;j<=n;j++) {
1594: ptt[j]=p[j]+(p[j]-pt[j])*k[l];
1595: printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
1596: fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
1597: }
1598: printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
1599: fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
1600: }
1601: #endif
1602:
1603:
1604: free_vector(xit,1,n);
1605: free_vector(xits,1,n);
1606: free_vector(ptt,1,n);
1607: free_vector(pt,1,n);
1608: return;
1609: }
1610: if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");
1.181 brouard 1611: for (j=1;j<=n;j++) { /* Computes the extrapolated point P_0 + 2 (P_n-P_0) */
1.126 brouard 1612: ptt[j]=2.0*p[j]-pt[j];
1613: xit[j]=p[j]-pt[j];
1614: pt[j]=p[j];
1615: }
1.181 brouard 1616: fptt=(*func)(ptt); /* f_3 */
1.161 brouard 1617: if (fptt < fp) { /* If extrapolated point is better, decide if we keep that new direction or not */
1.162 brouard 1618: /* (x1 f1=fp), (x2 f2=*fret), (x3 f3=fptt), (xm fm) */
1.161 brouard 1619: /* From x1 (P0) distance of x2 is at h and x3 is 2h */
1.162 brouard 1620: /* Let f"(x2) be the 2nd derivative equal everywhere. */
1621: /* Then the parabolic through (x1,f1), (x2,f2) and (x3,f3) */
1622: /* will reach at f3 = fm + h^2/2 f"m ; f" = (f1 -2f2 +f3 ) / h**2 */
1.181 brouard 1623: /* Conditional for using this new direction is that mu^2 = (f1-2f2+f3)^2 /2 < del */
1.161 brouard 1624: /* t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); */
1.183 brouard 1625: #ifdef NRCORIGINAL
1626: t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)- del*SQR(fp-fptt); /* Original Numerical Recipes in C*/
1627: #else
1628: 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 1629: t= t- del*SQR(fp-fptt);
1.183 brouard 1630: #endif
1.182 brouard 1631: directest = fp-2.0*(*fret)+fptt - 2.0 * del; /* If del was big enough we change it for a new direction */
1.161 brouard 1632: #ifdef DEBUG
1.181 brouard 1633: 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);
1634: 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 1635: printf("t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
1636: (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
1637: fprintf(ficlog,"t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
1638: (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
1639: 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);
1640: 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);
1641: #endif
1.183 brouard 1642: #ifdef POWELLORIGINAL
1643: if (t < 0.0) { /* Then we use it for new direction */
1644: #else
1.182 brouard 1645: if (directest*t < 0.0) { /* Contradiction between both tests */
1.184 brouard 1646: printf("directest= %.12lf, t= %.12lf, f1= %.12lf,f2= %.12lf,f3= %.12lf, del= %.12lf\n",directest, t, fp,(*fret),fptt,del);
1.182 brouard 1647: printf("f1-2f2+f3= %.12lf, f1-f2-del= %.12lf, f1-f3= %.12lf\n",fp-2.0*(*fret)+fptt, fp -(*fret) -del, fp-fptt);
1.184 brouard 1648: fprintf(ficlog,"directest= %.12lf, t= %.12lf, f1= %.12lf,f2= %.12lf,f3= %.12lf, del= %.12lf\n",directest, t, fp,(*fret),fptt, del);
1.182 brouard 1649: fprintf(ficlog,"f1-2f2+f3= %.12lf, f1-f2-del= %.12lf, f1-f3= %.12lf\n",fp-2.0*(*fret)+fptt, fp -(*fret) -del, fp-fptt);
1650: }
1.181 brouard 1651: if (directest < 0.0) { /* Then we use it for new direction */
1652: #endif
1653: linmin(p,xit,n,fret,func); /* computes minimum on the extrapolated direction.*/
1.126 brouard 1654: for (j=1;j<=n;j++) {
1.181 brouard 1655: xi[j][ibig]=xi[j][n]; /* Replace direction with biggest decrease by last direction n */
1656: xi[j][n]=xit[j]; /* and this nth direction by the by the average p_0 p_n */
1.126 brouard 1657: }
1.181 brouard 1658: printf("Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
1659: fprintf(ficlog,"Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
1.161 brouard 1660:
1.126 brouard 1661: #ifdef DEBUG
1.164 brouard 1662: printf("Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
1663: fprintf(ficlog,"Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
1.126 brouard 1664: for(j=1;j<=n;j++){
1665: printf(" %.12e",xit[j]);
1666: fprintf(ficlog," %.12e",xit[j]);
1667: }
1668: printf("\n");
1669: fprintf(ficlog,"\n");
1670: #endif
1.162 brouard 1671: } /* end of t negative */
1672: } /* end if (fptt < fp) */
1.126 brouard 1673: }
1674: }
1675:
1676: /**** Prevalence limit (stable or period prevalence) ****************/
1677:
1678: double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
1679: {
1680: /* Computes the prevalence limit in each live state at age x by left multiplying the unit
1681: matrix by transitions matrix until convergence is reached */
1.169 brouard 1682:
1.126 brouard 1683: int i, ii,j,k;
1684: double min, max, maxmin, maxmax,sumnew=0.;
1.145 brouard 1685: /* double **matprod2(); */ /* test */
1.131 brouard 1686: double **out, cov[NCOVMAX+1], **pmij();
1.126 brouard 1687: double **newm;
1688: double agefin, delaymax=50 ; /* Max number of years to converge */
1.169 brouard 1689:
1.126 brouard 1690: for (ii=1;ii<=nlstate+ndeath;ii++)
1691: for (j=1;j<=nlstate+ndeath;j++){
1692: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1693: }
1.169 brouard 1694:
1695: cov[1]=1.;
1696:
1697: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
1.126 brouard 1698: for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
1699: newm=savm;
1700: /* Covariates have to be included here again */
1.138 brouard 1701: cov[2]=agefin;
1702:
1703: for (k=1; k<=cptcovn;k++) {
1704: cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
1.145 brouard 1705: /*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 1706: }
1.145 brouard 1707: /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
1708: /* for (k=1; k<=cptcovprod;k++) /\* Useless *\/ */
1709: /* cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]] * nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]]; */
1.138 brouard 1710:
1711: /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
1712: /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
1713: /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
1.145 brouard 1714: /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
1715: /* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind *\/ */
1.142 brouard 1716: out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /* Bug Valgrind */
1.138 brouard 1717:
1.126 brouard 1718: savm=oldm;
1719: oldm=newm;
1720: maxmax=0.;
1721: for(j=1;j<=nlstate;j++){
1722: min=1.;
1723: max=0.;
1724: for(i=1; i<=nlstate; i++) {
1725: sumnew=0;
1726: for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
1727: prlim[i][j]= newm[i][j]/(1-sumnew);
1.145 brouard 1728: /*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 1729: max=FMAX(max,prlim[i][j]);
1730: min=FMIN(min,prlim[i][j]);
1731: }
1732: maxmin=max-min;
1733: maxmax=FMAX(maxmax,maxmin);
1.169 brouard 1734: } /* j loop */
1.126 brouard 1735: if(maxmax < ftolpl){
1736: return prlim;
1737: }
1.169 brouard 1738: } /* age loop */
1739: return prlim; /* should not reach here */
1.126 brouard 1740: }
1741:
1742: /*************** transition probabilities ***************/
1743:
1744: double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
1745: {
1.138 brouard 1746: /* According to parameters values stored in x and the covariate's values stored in cov,
1747: computes the probability to be observed in state j being in state i by appying the
1748: model to the ncovmodel covariates (including constant and age).
1749: lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc]
1750: and, according on how parameters are entered, the position of the coefficient xij(nc) of the
1751: ncth covariate in the global vector x is given by the formula:
1752: j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
1753: j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
1754: Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
1755: sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.
1756: Outputs ps[i][j] the probability to be observed in j being in j according to
1757: the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
1758: */
1759: double s1, lnpijopii;
1.126 brouard 1760: /*double t34;*/
1.164 brouard 1761: int i,j, nc, ii, jj;
1.126 brouard 1762:
1763: for(i=1; i<= nlstate; i++){
1764: for(j=1; j<i;j++){
1.138 brouard 1765: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
1766: /*lnpijopii += param[i][j][nc]*cov[nc];*/
1767: lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
1768: /* printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
1.126 brouard 1769: }
1.138 brouard 1770: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
1771: /* printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
1.126 brouard 1772: }
1773: for(j=i+1; j<=nlstate+ndeath;j++){
1.138 brouard 1774: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
1775: /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
1776: lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
1777: /* printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
1.126 brouard 1778: }
1.138 brouard 1779: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
1.126 brouard 1780: }
1781: }
1782:
1783: for(i=1; i<= nlstate; i++){
1784: s1=0;
1.131 brouard 1785: for(j=1; j<i; j++){
1.138 brouard 1786: s1+=exp(ps[i][j]); /* In fact sums pij/pii */
1.131 brouard 1787: /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
1788: }
1789: for(j=i+1; j<=nlstate+ndeath; j++){
1.138 brouard 1790: s1+=exp(ps[i][j]); /* In fact sums pij/pii */
1.131 brouard 1791: /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
1792: }
1.138 brouard 1793: /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
1.126 brouard 1794: ps[i][i]=1./(s1+1.);
1.138 brouard 1795: /* Computing other pijs */
1.126 brouard 1796: for(j=1; j<i; j++)
1797: ps[i][j]= exp(ps[i][j])*ps[i][i];
1798: for(j=i+1; j<=nlstate+ndeath; j++)
1799: ps[i][j]= exp(ps[i][j])*ps[i][i];
1800: /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
1801: } /* end i */
1802:
1803: for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
1804: for(jj=1; jj<= nlstate+ndeath; jj++){
1805: ps[ii][jj]=0;
1806: ps[ii][ii]=1;
1807: }
1808: }
1809:
1.145 brouard 1810:
1811: /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
1812: /* for(jj=1; jj<= nlstate+ndeath; jj++){ */
1813: /* printf(" pmij ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
1814: /* } */
1815: /* printf("\n "); */
1816: /* } */
1817: /* printf("\n ");printf("%lf ",cov[2]);*/
1818: /*
1.126 brouard 1819: for(i=1; i<= npar; i++) printf("%f ",x[i]);
1820: goto end;*/
1821: return ps;
1822: }
1823:
1824: /**************** Product of 2 matrices ******************/
1825:
1.145 brouard 1826: double **matprod2(double **out, double **in,int nrl, int nrh, int ncl, int nch, int ncolol, int ncoloh, double **b)
1.126 brouard 1827: {
1828: /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
1829: b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
1830: /* in, b, out are matrice of pointers which should have been initialized
1831: before: only the contents of out is modified. The function returns
1832: a pointer to pointers identical to out */
1.145 brouard 1833: int i, j, k;
1.126 brouard 1834: for(i=nrl; i<= nrh; i++)
1.145 brouard 1835: for(k=ncolol; k<=ncoloh; k++){
1836: out[i][k]=0.;
1837: for(j=ncl; j<=nch; j++)
1838: out[i][k] +=in[i][j]*b[j][k];
1839: }
1.126 brouard 1840: return out;
1841: }
1842:
1843:
1844: /************* Higher Matrix Product ***************/
1845:
1846: double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
1847: {
1848: /* Computes the transition matrix starting at age 'age' over
1849: 'nhstepm*hstepm*stepm' months (i.e. until
1850: age (in years) age+nhstepm*hstepm*stepm/12) by multiplying
1851: nhstepm*hstepm matrices.
1852: Output is stored in matrix po[i][j][h] for h every 'hstepm' step
1853: (typically every 2 years instead of every month which is too big
1854: for the memory).
1855: Model is determined by parameters x and covariates have to be
1856: included manually here.
1857:
1858: */
1859:
1860: int i, j, d, h, k;
1.131 brouard 1861: double **out, cov[NCOVMAX+1];
1.126 brouard 1862: double **newm;
1863:
1864: /* Hstepm could be zero and should return the unit matrix */
1865: for (i=1;i<=nlstate+ndeath;i++)
1866: for (j=1;j<=nlstate+ndeath;j++){
1867: oldm[i][j]=(i==j ? 1.0 : 0.0);
1868: po[i][j][0]=(i==j ? 1.0 : 0.0);
1869: }
1870: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
1871: for(h=1; h <=nhstepm; h++){
1872: for(d=1; d <=hstepm; d++){
1873: newm=savm;
1874: /* Covariates have to be included here again */
1875: cov[1]=1.;
1876: cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
1.131 brouard 1877: for (k=1; k<=cptcovn;k++)
1878: cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
1.126 brouard 1879: for (k=1; k<=cptcovage;k++)
1880: cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
1.145 brouard 1881: for (k=1; k<=cptcovprod;k++) /* Useless because included in cptcovn */
1.126 brouard 1882: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
1883:
1884:
1885: /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
1886: /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
1887: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
1888: pmij(pmmij,cov,ncovmodel,x,nlstate));
1889: savm=oldm;
1890: oldm=newm;
1891: }
1892: for(i=1; i<=nlstate+ndeath; i++)
1893: for(j=1;j<=nlstate+ndeath;j++) {
1894: po[i][j][h]=newm[i][j];
1.128 brouard 1895: /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
1.126 brouard 1896: }
1.128 brouard 1897: /*printf("h=%d ",h);*/
1.126 brouard 1898: } /* end h */
1.128 brouard 1899: /* printf("\n H=%d \n",h); */
1.126 brouard 1900: return po;
1901: }
1902:
1.162 brouard 1903: #ifdef NLOPT
1904: double myfunc(unsigned n, const double *p1, double *grad, void *pd){
1905: double fret;
1906: double *xt;
1907: int j;
1908: myfunc_data *d2 = (myfunc_data *) pd;
1909: /* xt = (p1-1); */
1910: xt=vector(1,n);
1911: for (j=1;j<=n;j++) xt[j]=p1[j-1]; /* xt[1]=p1[0] */
1912:
1913: fret=(d2->function)(xt); /* p xt[1]@8 is fine */
1914: /* fret=(*func)(xt); /\* p xt[1]@8 is fine *\/ */
1915: printf("Function = %.12lf ",fret);
1916: for (j=1;j<=n;j++) printf(" %d %.8lf", j, xt[j]);
1917: printf("\n");
1918: free_vector(xt,1,n);
1919: return fret;
1920: }
1921: #endif
1.126 brouard 1922:
1923: /*************** log-likelihood *************/
1924: double func( double *x)
1925: {
1926: int i, ii, j, k, mi, d, kk;
1.131 brouard 1927: double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
1.126 brouard 1928: double **out;
1929: double sw; /* Sum of weights */
1930: double lli; /* Individual log likelihood */
1931: int s1, s2;
1932: double bbh, survp;
1933: long ipmx;
1934: /*extern weight */
1935: /* We are differentiating ll according to initial status */
1936: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
1937: /*for(i=1;i<imx;i++)
1938: printf(" %d\n",s[4][i]);
1939: */
1.162 brouard 1940:
1941: ++countcallfunc;
1942:
1.126 brouard 1943: cov[1]=1.;
1944:
1945: for(k=1; k<=nlstate; k++) ll[k]=0.;
1946:
1947: if(mle==1){
1948: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1.138 brouard 1949: /* Computes the values of the ncovmodel covariates of the model
1950: depending if the covariates are fixed or variying (age dependent) and stores them in cov[]
1951: Then computes with function pmij which return a matrix p[i][j] giving the elementary probability
1952: to be observed in j being in i according to the model.
1953: */
1.145 brouard 1954: for (k=1; k<=cptcovn;k++){ /* Simple and product covariates without age* products */
1955: cov[2+k]=covar[Tvar[k]][i];
1956: }
1.137 brouard 1957: /* In model V2+V1*V4+age*V3+V3*V2 Tvar[1] is V2, Tvar[2=V1*V4]
1.138 brouard 1958: is 6, Tvar[3=age*V3] should not be computed because of age Tvar[4=V3*V2]
1.137 brouard 1959: has been calculated etc */
1.126 brouard 1960: for(mi=1; mi<= wav[i]-1; mi++){
1961: for (ii=1;ii<=nlstate+ndeath;ii++)
1962: for (j=1;j<=nlstate+ndeath;j++){
1963: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1964: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1965: }
1966: for(d=0; d<dh[mi][i]; d++){
1967: newm=savm;
1968: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1969: for (kk=1; kk<=cptcovage;kk++) {
1.137 brouard 1970: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; /* Tage[kk] gives the data-covariate associated with age */
1.126 brouard 1971: }
1972: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1973: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1974: savm=oldm;
1975: oldm=newm;
1976: } /* end mult */
1977:
1978: /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
1979: /* But now since version 0.9 we anticipate for bias at large stepm.
1980: * If stepm is larger than one month (smallest stepm) and if the exact delay
1981: * (in months) between two waves is not a multiple of stepm, we rounded to
1982: * the nearest (and in case of equal distance, to the lowest) interval but now
1983: * we keep into memory the bias bh[mi][i] and also the previous matrix product
1984: * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
1985: * probability in order to take into account the bias as a fraction of the way
1986: * from savm to out if bh is negative or even beyond if bh is positive. bh varies
1987: * -stepm/2 to stepm/2 .
1988: * For stepm=1 the results are the same as for previous versions of Imach.
1989: * For stepm > 1 the results are less biased than in previous versions.
1990: */
1991: s1=s[mw[mi][i]][i];
1992: s2=s[mw[mi+1][i]][i];
1993: bbh=(double)bh[mi][i]/(double)stepm;
1994: /* bias bh is positive if real duration
1995: * is higher than the multiple of stepm and negative otherwise.
1996: */
1997: /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
1998: if( s2 > nlstate){
1999: /* i.e. if s2 is a death state and if the date of death is known
2000: then the contribution to the likelihood is the probability to
2001: die between last step unit time and current step unit time,
2002: which is also equal to probability to die before dh
2003: minus probability to die before dh-stepm .
2004: In version up to 0.92 likelihood was computed
2005: as if date of death was unknown. Death was treated as any other
2006: health state: the date of the interview describes the actual state
2007: and not the date of a change in health state. The former idea was
2008: to consider that at each interview the state was recorded
2009: (healthy, disable or death) and IMaCh was corrected; but when we
2010: introduced the exact date of death then we should have modified
2011: the contribution of an exact death to the likelihood. This new
2012: contribution is smaller and very dependent of the step unit
2013: stepm. It is no more the probability to die between last interview
2014: and month of death but the probability to survive from last
2015: interview up to one month before death multiplied by the
2016: probability to die within a month. Thanks to Chris
2017: Jackson for correcting this bug. Former versions increased
2018: mortality artificially. The bad side is that we add another loop
2019: which slows down the processing. The difference can be up to 10%
2020: lower mortality.
2021: */
1.183 brouard 2022: /* If, at the beginning of the maximization mostly, the
2023: cumulative probability or probability to be dead is
2024: constant (ie = 1) over time d, the difference is equal to
2025: 0. out[s1][3] = savm[s1][3]: probability, being at state
2026: s1 at precedent wave, to be dead a month before current
2027: wave is equal to probability, being at state s1 at
2028: precedent wave, to be dead at mont of the current
2029: wave. Then the observed probability (that this person died)
2030: is null according to current estimated parameter. In fact,
2031: it should be very low but not zero otherwise the log go to
2032: infinity.
2033: */
2034: /* #ifdef INFINITYORIGINAL */
2035: /* lli=log(out[s1][s2] - savm[s1][s2]); */
2036: /* #else */
2037: /* if ((out[s1][s2] - savm[s1][s2]) < mytinydouble) */
2038: /* lli=log(mytinydouble); */
2039: /* else */
2040: /* lli=log(out[s1][s2] - savm[s1][s2]); */
2041: /* #endif */
2042: lli=log(out[s1][s2] - savm[s1][s2]);
1.126 brouard 2043:
2044: } else if (s2==-2) {
2045: for (j=1,survp=0. ; j<=nlstate; j++)
2046: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
2047: /*survp += out[s1][j]; */
2048: lli= log(survp);
2049: }
2050:
2051: else if (s2==-4) {
2052: for (j=3,survp=0. ; j<=nlstate; j++)
2053: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
2054: lli= log(survp);
2055: }
2056:
2057: else if (s2==-5) {
2058: for (j=1,survp=0. ; j<=2; j++)
2059: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
2060: lli= log(survp);
2061: }
2062:
2063: else{
2064: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
2065: /* 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 */
2066: }
2067: /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
2068: /*if(lli ==000.0)*/
2069: /*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); */
2070: ipmx +=1;
2071: sw += weight[i];
2072: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1.183 brouard 2073: /* if (lli < log(mytinydouble)){ */
2074: /* 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); */
2075: /* 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]); */
2076: /* } */
1.126 brouard 2077: } /* end of wave */
2078: } /* end of individual */
2079: } else if(mle==2){
2080: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
2081: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
2082: for(mi=1; mi<= wav[i]-1; mi++){
2083: for (ii=1;ii<=nlstate+ndeath;ii++)
2084: for (j=1;j<=nlstate+ndeath;j++){
2085: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2086: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2087: }
2088: for(d=0; d<=dh[mi][i]; d++){
2089: newm=savm;
2090: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
2091: for (kk=1; kk<=cptcovage;kk++) {
2092: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
2093: }
2094: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2095: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
2096: savm=oldm;
2097: oldm=newm;
2098: } /* end mult */
2099:
2100: s1=s[mw[mi][i]][i];
2101: s2=s[mw[mi+1][i]][i];
2102: bbh=(double)bh[mi][i]/(double)stepm;
2103: 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 */
2104: ipmx +=1;
2105: sw += weight[i];
2106: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
2107: } /* end of wave */
2108: } /* end of individual */
2109: } else if(mle==3){ /* exponential inter-extrapolation */
2110: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
2111: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
2112: for(mi=1; mi<= wav[i]-1; mi++){
2113: for (ii=1;ii<=nlstate+ndeath;ii++)
2114: for (j=1;j<=nlstate+ndeath;j++){
2115: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2116: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2117: }
2118: for(d=0; d<dh[mi][i]; d++){
2119: newm=savm;
2120: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
2121: for (kk=1; kk<=cptcovage;kk++) {
2122: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
2123: }
2124: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2125: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
2126: savm=oldm;
2127: oldm=newm;
2128: } /* end mult */
2129:
2130: s1=s[mw[mi][i]][i];
2131: s2=s[mw[mi+1][i]][i];
2132: bbh=(double)bh[mi][i]/(double)stepm;
2133: 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 */
2134: ipmx +=1;
2135: sw += weight[i];
2136: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
2137: } /* end of wave */
2138: } /* end of individual */
2139: }else if (mle==4){ /* ml=4 no inter-extrapolation */
2140: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
2141: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
2142: for(mi=1; mi<= wav[i]-1; mi++){
2143: for (ii=1;ii<=nlstate+ndeath;ii++)
2144: for (j=1;j<=nlstate+ndeath;j++){
2145: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2146: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2147: }
2148: for(d=0; d<dh[mi][i]; d++){
2149: newm=savm;
2150: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
2151: for (kk=1; kk<=cptcovage;kk++) {
2152: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
2153: }
2154:
2155: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2156: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
2157: savm=oldm;
2158: oldm=newm;
2159: } /* end mult */
2160:
2161: s1=s[mw[mi][i]][i];
2162: s2=s[mw[mi+1][i]][i];
2163: if( s2 > nlstate){
2164: lli=log(out[s1][s2] - savm[s1][s2]);
2165: }else{
2166: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
2167: }
2168: ipmx +=1;
2169: sw += weight[i];
2170: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
2171: /* 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]); */
2172: } /* end of wave */
2173: } /* end of individual */
2174: }else{ /* ml=5 no inter-extrapolation no jackson =0.8a */
2175: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
2176: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
2177: for(mi=1; mi<= wav[i]-1; mi++){
2178: for (ii=1;ii<=nlstate+ndeath;ii++)
2179: for (j=1;j<=nlstate+ndeath;j++){
2180: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2181: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2182: }
2183: for(d=0; d<dh[mi][i]; d++){
2184: newm=savm;
2185: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
2186: for (kk=1; kk<=cptcovage;kk++) {
2187: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
2188: }
2189:
2190: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2191: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
2192: savm=oldm;
2193: oldm=newm;
2194: } /* end mult */
2195:
2196: s1=s[mw[mi][i]][i];
2197: s2=s[mw[mi+1][i]][i];
2198: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
2199: ipmx +=1;
2200: sw += weight[i];
2201: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
2202: /*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]);*/
2203: } /* end of wave */
2204: } /* end of individual */
2205: } /* End of if */
2206: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
2207: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
2208: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
2209: return -l;
2210: }
2211:
2212: /*************** log-likelihood *************/
2213: double funcone( double *x)
2214: {
2215: /* Same as likeli but slower because of a lot of printf and if */
2216: int i, ii, j, k, mi, d, kk;
1.131 brouard 2217: double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
1.126 brouard 2218: double **out;
2219: double lli; /* Individual log likelihood */
2220: double llt;
2221: int s1, s2;
2222: double bbh, survp;
2223: /*extern weight */
2224: /* We are differentiating ll according to initial status */
2225: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
2226: /*for(i=1;i<imx;i++)
2227: printf(" %d\n",s[4][i]);
2228: */
2229: cov[1]=1.;
2230:
2231: for(k=1; k<=nlstate; k++) ll[k]=0.;
2232:
2233: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
2234: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
2235: for(mi=1; mi<= wav[i]-1; mi++){
2236: for (ii=1;ii<=nlstate+ndeath;ii++)
2237: for (j=1;j<=nlstate+ndeath;j++){
2238: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2239: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2240: }
2241: for(d=0; d<dh[mi][i]; d++){
2242: newm=savm;
2243: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
2244: for (kk=1; kk<=cptcovage;kk++) {
2245: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
2246: }
1.145 brouard 2247: /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
1.126 brouard 2248: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2249: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1.145 brouard 2250: /* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, */
2251: /* 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); */
1.126 brouard 2252: savm=oldm;
2253: oldm=newm;
2254: } /* end mult */
2255:
2256: s1=s[mw[mi][i]][i];
2257: s2=s[mw[mi+1][i]][i];
2258: bbh=(double)bh[mi][i]/(double)stepm;
2259: /* bias is positive if real duration
2260: * is higher than the multiple of stepm and negative otherwise.
2261: */
2262: if( s2 > nlstate && (mle <5) ){ /* Jackson */
2263: lli=log(out[s1][s2] - savm[s1][s2]);
2264: } else if (s2==-2) {
2265: for (j=1,survp=0. ; j<=nlstate; j++)
2266: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
2267: lli= log(survp);
2268: }else if (mle==1){
2269: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
2270: } else if(mle==2){
2271: 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 */
2272: } else if(mle==3){ /* exponential inter-extrapolation */
2273: 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 */
2274: } else if (mle==4){ /* mle=4 no inter-extrapolation */
2275: lli=log(out[s1][s2]); /* Original formula */
1.136 brouard 2276: } else{ /* mle=0 back to 1 */
2277: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
2278: /*lli=log(out[s1][s2]); */ /* Original formula */
1.126 brouard 2279: } /* End of if */
2280: ipmx +=1;
2281: sw += weight[i];
2282: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1.132 brouard 2283: /*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 2284: if(globpr){
1.141 brouard 2285: fprintf(ficresilk,"%9ld %6d %2d %2d %1d %1d %3d %11.6f %8.4f\
1.126 brouard 2286: %11.6f %11.6f %11.6f ", \
2287: num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
2288: 2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
2289: for(k=1,llt=0.,l=0.; k<=nlstate; k++){
2290: llt +=ll[k]*gipmx/gsw;
2291: fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
2292: }
2293: fprintf(ficresilk," %10.6f\n", -llt);
2294: }
2295: } /* end of wave */
2296: } /* end of individual */
2297: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
2298: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
2299: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
2300: if(globpr==0){ /* First time we count the contributions and weights */
2301: gipmx=ipmx;
2302: gsw=sw;
2303: }
2304: return -l;
2305: }
2306:
2307:
2308: /*************** function likelione ***********/
2309: void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
2310: {
2311: /* This routine should help understanding what is done with
2312: the selection of individuals/waves and
2313: to check the exact contribution to the likelihood.
2314: Plotting could be done.
2315: */
2316: int k;
2317:
2318: if(*globpri !=0){ /* Just counts and sums, no printings */
2319: strcpy(fileresilk,"ilk");
2320: strcat(fileresilk,fileres);
2321: if((ficresilk=fopen(fileresilk,"w"))==NULL) {
2322: printf("Problem with resultfile: %s\n", fileresilk);
2323: fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
2324: }
2325: 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");
2326: fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
2327: /* i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
2328: for(k=1; k<=nlstate; k++)
2329: fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
2330: fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
2331: }
2332:
2333: *fretone=(*funcone)(p);
2334: if(*globpri !=0){
2335: fclose(ficresilk);
2336: fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
2337: fflush(fichtm);
2338: }
2339: return;
2340: }
2341:
2342:
2343: /*********** Maximum Likelihood Estimation ***************/
2344:
2345: void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
2346: {
1.165 brouard 2347: int i,j, iter=0;
1.126 brouard 2348: double **xi;
2349: double fret;
2350: double fretone; /* Only one call to likelihood */
2351: /* char filerespow[FILENAMELENGTH];*/
1.162 brouard 2352:
2353: #ifdef NLOPT
2354: int creturn;
2355: nlopt_opt opt;
2356: /* double lb[9] = { -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL }; /\* lower bounds *\/ */
2357: double *lb;
2358: double minf; /* the minimum objective value, upon return */
2359: double * p1; /* Shifted parameters from 0 instead of 1 */
2360: myfunc_data dinst, *d = &dinst;
2361: #endif
2362:
2363:
1.126 brouard 2364: xi=matrix(1,npar,1,npar);
2365: for (i=1;i<=npar;i++)
2366: for (j=1;j<=npar;j++)
2367: xi[i][j]=(i==j ? 1.0 : 0.0);
2368: printf("Powell\n"); fprintf(ficlog,"Powell\n");
2369: strcpy(filerespow,"pow");
2370: strcat(filerespow,fileres);
2371: if((ficrespow=fopen(filerespow,"w"))==NULL) {
2372: printf("Problem with resultfile: %s\n", filerespow);
2373: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
2374: }
2375: fprintf(ficrespow,"# Powell\n# iter -2*LL");
2376: for (i=1;i<=nlstate;i++)
2377: for(j=1;j<=nlstate+ndeath;j++)
2378: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
2379: fprintf(ficrespow,"\n");
1.162 brouard 2380: #ifdef POWELL
1.126 brouard 2381: powell(p,xi,npar,ftol,&iter,&fret,func);
1.162 brouard 2382: #endif
1.126 brouard 2383:
1.162 brouard 2384: #ifdef NLOPT
2385: #ifdef NEWUOA
2386: opt = nlopt_create(NLOPT_LN_NEWUOA,npar);
2387: #else
2388: opt = nlopt_create(NLOPT_LN_BOBYQA,npar);
2389: #endif
2390: lb=vector(0,npar-1);
2391: for (i=0;i<npar;i++) lb[i]= -HUGE_VAL;
2392: nlopt_set_lower_bounds(opt, lb);
2393: nlopt_set_initial_step1(opt, 0.1);
2394:
2395: p1= (p+1); /* p *(p+1)@8 and p *(p1)@8 are equal p1[0]=p[1] */
2396: d->function = func;
2397: printf(" Func %.12lf \n",myfunc(npar,p1,NULL,d));
2398: nlopt_set_min_objective(opt, myfunc, d);
2399: nlopt_set_xtol_rel(opt, ftol);
2400: if ((creturn=nlopt_optimize(opt, p1, &minf)) < 0) {
2401: printf("nlopt failed! %d\n",creturn);
2402: }
2403: else {
2404: printf("found minimum after %d evaluations (NLOPT=%d)\n", countcallfunc ,NLOPT);
2405: printf("found minimum at f(%g,%g) = %0.10g\n", p[0], p[1], minf);
2406: iter=1; /* not equal */
2407: }
2408: nlopt_destroy(opt);
2409: #endif
1.126 brouard 2410: free_matrix(xi,1,npar,1,npar);
2411: fclose(ficrespow);
1.180 brouard 2412: printf("#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
2413: fprintf(ficlog,"#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
2414: fprintf(ficres,"#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
1.126 brouard 2415:
2416: }
2417:
2418: /**** Computes Hessian and covariance matrix ***/
2419: void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
2420: {
2421: double **a,**y,*x,pd;
2422: double **hess;
1.164 brouard 2423: int i, j;
1.126 brouard 2424: int *indx;
2425:
2426: double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
2427: double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
2428: void lubksb(double **a, int npar, int *indx, double b[]) ;
2429: void ludcmp(double **a, int npar, int *indx, double *d) ;
2430: double gompertz(double p[]);
2431: hess=matrix(1,npar,1,npar);
2432:
2433: printf("\nCalculation of the hessian matrix. Wait...\n");
2434: fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
2435: for (i=1;i<=npar;i++){
2436: printf("%d",i);fflush(stdout);
2437: fprintf(ficlog,"%d",i);fflush(ficlog);
2438:
2439: hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
2440:
2441: /* printf(" %f ",p[i]);
2442: printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
2443: }
2444:
2445: for (i=1;i<=npar;i++) {
2446: for (j=1;j<=npar;j++) {
2447: if (j>i) {
2448: printf(".%d%d",i,j);fflush(stdout);
2449: fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
2450: hess[i][j]=hessij(p,delti,i,j,func,npar);
2451:
2452: hess[j][i]=hess[i][j];
2453: /*printf(" %lf ",hess[i][j]);*/
2454: }
2455: }
2456: }
2457: printf("\n");
2458: fprintf(ficlog,"\n");
2459:
2460: printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
2461: fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
2462:
2463: a=matrix(1,npar,1,npar);
2464: y=matrix(1,npar,1,npar);
2465: x=vector(1,npar);
2466: indx=ivector(1,npar);
2467: for (i=1;i<=npar;i++)
2468: for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
2469: ludcmp(a,npar,indx,&pd);
2470:
2471: for (j=1;j<=npar;j++) {
2472: for (i=1;i<=npar;i++) x[i]=0;
2473: x[j]=1;
2474: lubksb(a,npar,indx,x);
2475: for (i=1;i<=npar;i++){
2476: matcov[i][j]=x[i];
2477: }
2478: }
2479:
2480: printf("\n#Hessian matrix#\n");
2481: fprintf(ficlog,"\n#Hessian matrix#\n");
2482: for (i=1;i<=npar;i++) {
2483: for (j=1;j<=npar;j++) {
2484: printf("%.3e ",hess[i][j]);
2485: fprintf(ficlog,"%.3e ",hess[i][j]);
2486: }
2487: printf("\n");
2488: fprintf(ficlog,"\n");
2489: }
2490:
2491: /* Recompute Inverse */
2492: for (i=1;i<=npar;i++)
2493: for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
2494: ludcmp(a,npar,indx,&pd);
2495:
2496: /* printf("\n#Hessian matrix recomputed#\n");
2497:
2498: for (j=1;j<=npar;j++) {
2499: for (i=1;i<=npar;i++) x[i]=0;
2500: x[j]=1;
2501: lubksb(a,npar,indx,x);
2502: for (i=1;i<=npar;i++){
2503: y[i][j]=x[i];
2504: printf("%.3e ",y[i][j]);
2505: fprintf(ficlog,"%.3e ",y[i][j]);
2506: }
2507: printf("\n");
2508: fprintf(ficlog,"\n");
2509: }
2510: */
2511:
2512: free_matrix(a,1,npar,1,npar);
2513: free_matrix(y,1,npar,1,npar);
2514: free_vector(x,1,npar);
2515: free_ivector(indx,1,npar);
2516: free_matrix(hess,1,npar,1,npar);
2517:
2518:
2519: }
2520:
2521: /*************** hessian matrix ****************/
2522: double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
2523: {
2524: int i;
2525: int l=1, lmax=20;
2526: double k1,k2;
1.132 brouard 2527: double p2[MAXPARM+1]; /* identical to x */
1.126 brouard 2528: double res;
2529: double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
2530: double fx;
2531: int k=0,kmax=10;
2532: double l1;
2533:
2534: fx=func(x);
2535: for (i=1;i<=npar;i++) p2[i]=x[i];
1.145 brouard 2536: for(l=0 ; l <=lmax; l++){ /* Enlarging the zone around the Maximum */
1.126 brouard 2537: l1=pow(10,l);
2538: delts=delt;
2539: for(k=1 ; k <kmax; k=k+1){
2540: delt = delta*(l1*k);
2541: p2[theta]=x[theta] +delt;
1.145 brouard 2542: k1=func(p2)-fx; /* Might be negative if too close to the theoretical maximum */
1.126 brouard 2543: p2[theta]=x[theta]-delt;
2544: k2=func(p2)-fx;
2545: /*res= (k1-2.0*fx+k2)/delt/delt; */
2546: res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
2547:
1.132 brouard 2548: #ifdef DEBUGHESS
1.126 brouard 2549: 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);
2550: 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);
2551: #endif
2552: /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
2553: if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
2554: k=kmax;
2555: }
2556: else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
1.164 brouard 2557: k=kmax; l=lmax*10;
1.126 brouard 2558: }
2559: else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){
2560: delts=delt;
2561: }
2562: }
2563: }
2564: delti[theta]=delts;
2565: return res;
2566:
2567: }
2568:
2569: double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
2570: {
2571: int i;
1.164 brouard 2572: int l=1, lmax=20;
1.126 brouard 2573: double k1,k2,k3,k4,res,fx;
1.132 brouard 2574: double p2[MAXPARM+1];
1.126 brouard 2575: int k;
2576:
2577: fx=func(x);
2578: for (k=1; k<=2; k++) {
2579: for (i=1;i<=npar;i++) p2[i]=x[i];
2580: p2[thetai]=x[thetai]+delti[thetai]/k;
2581: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
2582: k1=func(p2)-fx;
2583:
2584: p2[thetai]=x[thetai]+delti[thetai]/k;
2585: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
2586: k2=func(p2)-fx;
2587:
2588: p2[thetai]=x[thetai]-delti[thetai]/k;
2589: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
2590: k3=func(p2)-fx;
2591:
2592: p2[thetai]=x[thetai]-delti[thetai]/k;
2593: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
2594: k4=func(p2)-fx;
2595: res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
2596: #ifdef DEBUG
2597: 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);
2598: 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);
2599: #endif
2600: }
2601: return res;
2602: }
2603:
2604: /************** Inverse of matrix **************/
2605: void ludcmp(double **a, int n, int *indx, double *d)
2606: {
2607: int i,imax,j,k;
2608: double big,dum,sum,temp;
2609: double *vv;
2610:
2611: vv=vector(1,n);
2612: *d=1.0;
2613: for (i=1;i<=n;i++) {
2614: big=0.0;
2615: for (j=1;j<=n;j++)
2616: if ((temp=fabs(a[i][j])) > big) big=temp;
2617: if (big == 0.0) nrerror("Singular matrix in routine ludcmp");
2618: vv[i]=1.0/big;
2619: }
2620: for (j=1;j<=n;j++) {
2621: for (i=1;i<j;i++) {
2622: sum=a[i][j];
2623: for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];
2624: a[i][j]=sum;
2625: }
2626: big=0.0;
2627: for (i=j;i<=n;i++) {
2628: sum=a[i][j];
2629: for (k=1;k<j;k++)
2630: sum -= a[i][k]*a[k][j];
2631: a[i][j]=sum;
2632: if ( (dum=vv[i]*fabs(sum)) >= big) {
2633: big=dum;
2634: imax=i;
2635: }
2636: }
2637: if (j != imax) {
2638: for (k=1;k<=n;k++) {
2639: dum=a[imax][k];
2640: a[imax][k]=a[j][k];
2641: a[j][k]=dum;
2642: }
2643: *d = -(*d);
2644: vv[imax]=vv[j];
2645: }
2646: indx[j]=imax;
2647: if (a[j][j] == 0.0) a[j][j]=TINY;
2648: if (j != n) {
2649: dum=1.0/(a[j][j]);
2650: for (i=j+1;i<=n;i++) a[i][j] *= dum;
2651: }
2652: }
2653: free_vector(vv,1,n); /* Doesn't work */
2654: ;
2655: }
2656:
2657: void lubksb(double **a, int n, int *indx, double b[])
2658: {
2659: int i,ii=0,ip,j;
2660: double sum;
2661:
2662: for (i=1;i<=n;i++) {
2663: ip=indx[i];
2664: sum=b[ip];
2665: b[ip]=b[i];
2666: if (ii)
2667: for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];
2668: else if (sum) ii=i;
2669: b[i]=sum;
2670: }
2671: for (i=n;i>=1;i--) {
2672: sum=b[i];
2673: for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];
2674: b[i]=sum/a[i][i];
2675: }
2676: }
2677:
2678: void pstamp(FILE *fichier)
2679: {
2680: fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart);
2681: }
2682:
2683: /************ Frequencies ********************/
2684: 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[])
2685: { /* Some frequencies */
2686:
1.164 brouard 2687: int i, m, jk, j1, bool, z1,j;
1.126 brouard 2688: int first;
2689: double ***freq; /* Frequencies */
2690: double *pp, **prop;
2691: double pos,posprop, k2, dateintsum=0,k2cpt=0;
2692: char fileresp[FILENAMELENGTH];
2693:
2694: pp=vector(1,nlstate);
2695: prop=matrix(1,nlstate,iagemin,iagemax+3);
2696: strcpy(fileresp,"p");
2697: strcat(fileresp,fileres);
2698: if((ficresp=fopen(fileresp,"w"))==NULL) {
2699: printf("Problem with prevalence resultfile: %s\n", fileresp);
2700: fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
2701: exit(0);
2702: }
2703: freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
2704: j1=0;
2705:
2706: j=cptcoveff;
2707: if (cptcovn<1) {j=1;ncodemax[1]=1;}
2708:
2709: first=1;
2710:
1.169 brouard 2711: /* for(k1=1; k1<=j ; k1++){ */ /* Loop on covariates */
2712: /* for(i1=1; i1<=ncodemax[k1];i1++){ */ /* Now it is 2 */
2713: /* j1++; */
1.145 brouard 2714: for (j1 = 1; j1 <= (int) pow(2,cptcoveff); j1++){
1.126 brouard 2715: /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
2716: scanf("%d", i);*/
2717: for (i=-5; i<=nlstate+ndeath; i++)
2718: for (jk=-5; jk<=nlstate+ndeath; jk++)
2719: for(m=iagemin; m <= iagemax+3; m++)
2720: freq[i][jk][m]=0;
1.143 brouard 2721:
2722: for (i=1; i<=nlstate; i++)
2723: for(m=iagemin; m <= iagemax+3; m++)
2724: prop[i][m]=0;
1.126 brouard 2725:
2726: dateintsum=0;
2727: k2cpt=0;
2728: for (i=1; i<=imx; i++) {
2729: bool=1;
1.144 brouard 2730: if (cptcovn>0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
2731: for (z1=1; z1<=cptcoveff; z1++)
2732: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]){
1.145 brouard 2733: /* Tests if the value of each of the covariates of i is equal to filter j1 */
1.144 brouard 2734: bool=0;
1.145 brouard 2735: /* 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",
2736: bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtab[j1][z1],
2737: j1,z1,nbcode[Tvaraff[z1]][codtab[j1][z1]],j1);*/
1.144 brouard 2738: /* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtab[7][3]=1 and nbcde[3][?]=1*/
2739: }
1.126 brouard 2740: }
1.144 brouard 2741:
1.126 brouard 2742: if (bool==1){
2743: for(m=firstpass; m<=lastpass; m++){
2744: k2=anint[m][i]+(mint[m][i]/12.);
2745: /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
2746: if(agev[m][i]==0) agev[m][i]=iagemax+1;
2747: if(agev[m][i]==1) agev[m][i]=iagemax+2;
2748: if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
2749: if (m<lastpass) {
2750: freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
2751: freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
2752: }
2753:
2754: if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
2755: dateintsum=dateintsum+k2;
2756: k2cpt++;
2757: }
2758: /*}*/
2759: }
2760: }
1.145 brouard 2761: } /* end i */
1.126 brouard 2762:
2763: /* fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
2764: pstamp(ficresp);
2765: if (cptcovn>0) {
2766: fprintf(ficresp, "\n#********** Variable ");
2767: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
2768: fprintf(ficresp, "**********\n#");
1.143 brouard 2769: fprintf(ficlog, "\n#********** Variable ");
2770: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficlog, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
2771: fprintf(ficlog, "**********\n#");
1.126 brouard 2772: }
2773: for(i=1; i<=nlstate;i++)
2774: fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
2775: fprintf(ficresp, "\n");
2776:
2777: for(i=iagemin; i <= iagemax+3; i++){
2778: if(i==iagemax+3){
2779: fprintf(ficlog,"Total");
2780: }else{
2781: if(first==1){
2782: first=0;
2783: printf("See log file for details...\n");
2784: }
2785: fprintf(ficlog,"Age %d", i);
2786: }
2787: for(jk=1; jk <=nlstate ; jk++){
2788: for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
2789: pp[jk] += freq[jk][m][i];
2790: }
2791: for(jk=1; jk <=nlstate ; jk++){
2792: for(m=-1, pos=0; m <=0 ; m++)
2793: pos += freq[jk][m][i];
2794: if(pp[jk]>=1.e-10){
2795: if(first==1){
1.132 brouard 2796: printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
1.126 brouard 2797: }
2798: fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
2799: }else{
2800: if(first==1)
2801: printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
2802: fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
2803: }
2804: }
2805:
2806: for(jk=1; jk <=nlstate ; jk++){
2807: for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
2808: pp[jk] += freq[jk][m][i];
2809: }
2810: for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
2811: pos += pp[jk];
2812: posprop += prop[jk][i];
2813: }
2814: for(jk=1; jk <=nlstate ; jk++){
2815: if(pos>=1.e-5){
2816: if(first==1)
2817: printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
2818: fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
2819: }else{
2820: if(first==1)
2821: printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
2822: fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
2823: }
2824: if( i <= iagemax){
2825: if(pos>=1.e-5){
2826: fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
2827: /*probs[i][jk][j1]= pp[jk]/pos;*/
2828: /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
2829: }
2830: else
2831: fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
2832: }
2833: }
2834:
2835: for(jk=-1; jk <=nlstate+ndeath; jk++)
2836: for(m=-1; m <=nlstate+ndeath; m++)
2837: if(freq[jk][m][i] !=0 ) {
2838: if(first==1)
2839: printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
2840: fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
2841: }
2842: if(i <= iagemax)
2843: fprintf(ficresp,"\n");
2844: if(first==1)
2845: printf("Others in log...\n");
2846: fprintf(ficlog,"\n");
2847: }
1.145 brouard 2848: /*}*/
1.126 brouard 2849: }
2850: dateintmean=dateintsum/k2cpt;
2851:
2852: fclose(ficresp);
2853: free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
2854: free_vector(pp,1,nlstate);
2855: free_matrix(prop,1,nlstate,iagemin, iagemax+3);
2856: /* End of Freq */
2857: }
2858:
2859: /************ Prevalence ********************/
2860: 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)
2861: {
2862: /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
2863: in each health status at the date of interview (if between dateprev1 and dateprev2).
2864: We still use firstpass and lastpass as another selection.
2865: */
2866:
1.164 brouard 2867: int i, m, jk, j1, bool, z1,j;
2868:
2869: double **prop;
2870: double posprop;
1.126 brouard 2871: double y2; /* in fractional years */
2872: int iagemin, iagemax;
1.145 brouard 2873: int first; /** to stop verbosity which is redirected to log file */
1.126 brouard 2874:
2875: iagemin= (int) agemin;
2876: iagemax= (int) agemax;
2877: /*pp=vector(1,nlstate);*/
2878: prop=matrix(1,nlstate,iagemin,iagemax+3);
2879: /* freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
2880: j1=0;
2881:
1.145 brouard 2882: /*j=cptcoveff;*/
1.126 brouard 2883: if (cptcovn<1) {j=1;ncodemax[1]=1;}
2884:
1.145 brouard 2885: first=1;
2886: for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){
2887: /*for(i1=1; i1<=ncodemax[k1];i1++){
2888: j1++;*/
1.126 brouard 2889:
2890: for (i=1; i<=nlstate; i++)
2891: for(m=iagemin; m <= iagemax+3; m++)
2892: prop[i][m]=0.0;
2893:
2894: for (i=1; i<=imx; i++) { /* Each individual */
2895: bool=1;
2896: if (cptcovn>0) {
2897: for (z1=1; z1<=cptcoveff; z1++)
2898: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
2899: bool=0;
2900: }
2901: if (bool==1) {
2902: for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
2903: y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
2904: if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
2905: if(agev[m][i]==0) agev[m][i]=iagemax+1;
2906: if(agev[m][i]==1) agev[m][i]=iagemax+2;
2907: 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);
2908: if (s[m][i]>0 && s[m][i]<=nlstate) {
2909: /*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]]);*/
2910: prop[s[m][i]][(int)agev[m][i]] += weight[i];
2911: prop[s[m][i]][iagemax+3] += weight[i];
2912: }
2913: }
2914: } /* end selection of waves */
2915: }
2916: }
2917: for(i=iagemin; i <= iagemax+3; i++){
2918: for(jk=1,posprop=0; jk <=nlstate ; jk++) {
2919: posprop += prop[jk][i];
2920: }
1.145 brouard 2921:
1.126 brouard 2922: for(jk=1; jk <=nlstate ; jk++){
2923: if( i <= iagemax){
2924: if(posprop>=1.e-5){
2925: probs[i][jk][j1]= prop[jk][i]/posprop;
1.145 brouard 2926: } else{
2927: if(first==1){
2928: first=0;
2929: 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]);
2930: }
2931: }
1.126 brouard 2932: }
2933: }/* end jk */
2934: }/* end i */
1.145 brouard 2935: /*} *//* end i1 */
2936: } /* end j1 */
1.126 brouard 2937:
2938: /* free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
2939: /*free_vector(pp,1,nlstate);*/
2940: free_matrix(prop,1,nlstate, iagemin,iagemax+3);
2941: } /* End of prevalence */
2942:
2943: /************* Waves Concatenation ***************/
2944:
2945: 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)
2946: {
2947: /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
2948: Death is a valid wave (if date is known).
2949: mw[mi][i] is the mi (mi=1 to wav[i]) effective wave of individual i
2950: dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
2951: and mw[mi+1][i]. dh depends on stepm.
2952: */
2953:
2954: int i, mi, m;
2955: /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
2956: double sum=0., jmean=0.;*/
2957: int first;
2958: int j, k=0,jk, ju, jl;
2959: double sum=0.;
2960: first=0;
1.164 brouard 2961: jmin=100000;
1.126 brouard 2962: jmax=-1;
2963: jmean=0.;
2964: for(i=1; i<=imx; i++){
2965: mi=0;
2966: m=firstpass;
2967: while(s[m][i] <= nlstate){
2968: if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
2969: mw[++mi][i]=m;
2970: if(m >=lastpass)
2971: break;
2972: else
2973: m++;
2974: }/* end while */
2975: if (s[m][i] > nlstate){
2976: mi++; /* Death is another wave */
2977: /* if(mi==0) never been interviewed correctly before death */
2978: /* Only death is a correct wave */
2979: mw[mi][i]=m;
2980: }
2981:
2982: wav[i]=mi;
2983: if(mi==0){
2984: nbwarn++;
2985: if(first==0){
2986: printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
2987: first=1;
2988: }
2989: if(first==1){
2990: fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
2991: }
2992: } /* end mi==0 */
2993: } /* End individuals */
2994:
2995: for(i=1; i<=imx; i++){
2996: for(mi=1; mi<wav[i];mi++){
2997: if (stepm <=0)
2998: dh[mi][i]=1;
2999: else{
3000: if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
3001: if (agedc[i] < 2*AGESUP) {
3002: j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);
3003: if(j==0) j=1; /* Survives at least one month after exam */
3004: else if(j<0){
3005: nberr++;
3006: 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]);
3007: j=1; /* Temporary Dangerous patch */
3008: 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);
3009: 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]);
3010: 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);
3011: }
3012: k=k+1;
3013: if (j >= jmax){
3014: jmax=j;
3015: ijmax=i;
3016: }
3017: if (j <= jmin){
3018: jmin=j;
3019: ijmin=i;
3020: }
3021: sum=sum+j;
3022: /*if (j<0) printf("j=%d num=%d \n",j,i);*/
3023: /* printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
3024: }
3025: }
3026: else{
3027: j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
3028: /* 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]); */
3029:
3030: k=k+1;
3031: if (j >= jmax) {
3032: jmax=j;
3033: ijmax=i;
3034: }
3035: else if (j <= jmin){
3036: jmin=j;
3037: ijmin=i;
3038: }
3039: /* if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
3040: /*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]);*/
3041: if(j<0){
3042: nberr++;
3043: 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]);
3044: 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]);
3045: }
3046: sum=sum+j;
3047: }
3048: jk= j/stepm;
3049: jl= j -jk*stepm;
3050: ju= j -(jk+1)*stepm;
3051: if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
3052: if(jl==0){
3053: dh[mi][i]=jk;
3054: bh[mi][i]=0;
3055: }else{ /* We want a negative bias in order to only have interpolation ie
1.136 brouard 3056: * to avoid the price of an extra matrix product in likelihood */
1.126 brouard 3057: dh[mi][i]=jk+1;
3058: bh[mi][i]=ju;
3059: }
3060: }else{
3061: if(jl <= -ju){
3062: dh[mi][i]=jk;
3063: bh[mi][i]=jl; /* bias is positive if real duration
3064: * is higher than the multiple of stepm and negative otherwise.
3065: */
3066: }
3067: else{
3068: dh[mi][i]=jk+1;
3069: bh[mi][i]=ju;
3070: }
3071: if(dh[mi][i]==0){
3072: dh[mi][i]=1; /* At least one step */
3073: bh[mi][i]=ju; /* At least one step */
3074: /* 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);*/
3075: }
3076: } /* end if mle */
3077: }
3078: } /* end wave */
3079: }
3080: jmean=sum/k;
3081: 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 3082: 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 3083: }
3084:
3085: /*********** Tricode ****************************/
1.145 brouard 3086: void tricode(int *Tvar, int **nbcode, int imx, int *Ndum)
1.126 brouard 3087: {
1.144 brouard 3088: /**< Uses cptcovn+2*cptcovprod as the number of covariates */
3089: /* 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 3090: * Boring subroutine which should only output nbcode[Tvar[j]][k]
1.145 brouard 3091: * Tvar[5] in V2+V1+V3*age+V2*V4 is 2 (V2)
1.169 brouard 3092: * nbcode[Tvar[j]][1]=
1.144 brouard 3093: */
1.130 brouard 3094:
1.145 brouard 3095: int ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
1.136 brouard 3096: int modmaxcovj=0; /* Modality max of covariates j */
1.145 brouard 3097: int cptcode=0; /* Modality max of covariates j */
3098: int modmincovj=0; /* Modality min of covariates j */
3099:
3100:
1.126 brouard 3101: cptcoveff=0;
3102:
1.145 brouard 3103: for (k=-1; k < maxncov; k++) Ndum[k]=0;
1.144 brouard 3104: for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */
1.126 brouard 3105:
1.145 brouard 3106: /* Loop on covariates without age and products */
3107: for (j=1; j<=(cptcovs); j++) { /* model V1 + V2*age+ V3 + V3*V4 : V1 + V3 = 2 only */
3108: for (i=1; i<=imx; i++) { /* Lopp on individuals: reads the data file to get the maximum value of the
1.136 brouard 3109: modality of this covariate Vj*/
1.145 brouard 3110: ij=(int)(covar[Tvar[j]][i]); /* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i
3111: * If product of Vn*Vm, still boolean *:
3112: * If it was coded 1, 2, 3, 4 should be splitted into 3 boolean variables
3113: * 1 => 0 0 0, 2 => 0 0 1, 3 => 0 1 1, 4=1 0 0 */
3114: /* Finds for covariate j, n=Tvar[j] of Vn . ij is the
1.136 brouard 3115: modality of the nth covariate of individual i. */
1.145 brouard 3116: if (ij > modmaxcovj)
3117: modmaxcovj=ij;
3118: else if (ij < modmincovj)
3119: modmincovj=ij;
3120: if ((ij < -1) && (ij > NCOVMAX)){
3121: printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX );
3122: exit(1);
3123: }else
1.136 brouard 3124: Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/
1.145 brouard 3125: /* If coded 1, 2, 3 , counts the number of 1 Ndum[1], number of 2, Ndum[2], etc */
1.126 brouard 3126: /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
1.136 brouard 3127: /* getting the maximum value of the modality of the covariate
3128: (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and
3129: female is 1, then modmaxcovj=1.*/
1.126 brouard 3130: }
1.145 brouard 3131: printf(" Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", j, Tvar[j], modmincovj, modmaxcovj);
3132: cptcode=modmaxcovj;
1.137 brouard 3133: /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */
1.145 brouard 3134: /*for (i=0; i<=cptcode; i++) {*/
3135: for (i=modmincovj; i<=modmaxcovj; i++) { /* i=-1 ? 0 and 1*//* For each value of the modality of model-cov j */
3136: printf("Frequencies of covariates %d V%d %d\n", j, Tvar[j], Ndum[i]);
3137: if( Ndum[i] != 0 ){ /* Counts if nobody answered, empty modality */
3138: ncodemax[j]++; /* ncodemax[j]= Number of non-null modalities of the j th covariate. */
3139: }
3140: /* In fact ncodemax[j]=2 (dichotom. variables only) but it could be more for
3141: historical reasons: 3 if coded 1, 2, 3 and 4 and Ndum[2]=0 */
1.131 brouard 3142: } /* Ndum[-1] number of undefined modalities */
1.126 brouard 3143:
1.136 brouard 3144: /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */
1.145 brouard 3145: /* For covariate j, modalities could be 1, 2, 3, 4. If Ndum[2]=0 ncodemax[j] is not 4 but 3 */
3146: /* If Ndum[3}= 635; Ndum[4]=0; Ndum[5]=0; Ndum[6]=27; Ndum[7]=125;
3147: modmincovj=3; modmaxcovj = 7;
3148: There are only 3 modalities non empty (or 2 if 27 is too few) : ncodemax[j]=3;
3149: which will be coded 0, 1, 2 which in binary on 3-1 digits are 0=00 1=01, 2=10; defining two dummy
3150: variables V1_1 and V1_2.
3151: nbcode[Tvar[j]][ij]=k;
3152: nbcode[Tvar[j]][1]=0;
3153: nbcode[Tvar[j]][2]=1;
3154: nbcode[Tvar[j]][3]=2;
3155: */
3156: ij=1; /* ij is similar to i but can jumps over null modalities */
3157: for (i=modmincovj; i<=modmaxcovj; i++) { /* i= 1 to 2 for dichotomous, or from 1 to 3 */
3158: for (k=0; k<= cptcode; k++) { /* k=-1 ? k=0 to 1 *//* Could be 1 to 4 */
3159: /*recode from 0 */
1.131 brouard 3160: if (Ndum[k] != 0) { /* If at least one individual responded to this modality k */
3161: nbcode[Tvar[j]][ij]=k; /* stores the modality in an array nbcode.
3162: k is a modality. If we have model=V1+V1*sex
3163: then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
1.126 brouard 3164: ij++;
3165: }
3166: if (ij > ncodemax[j]) break;
1.137 brouard 3167: } /* end of loop on */
3168: } /* end of loop on modality */
3169: } /* end of loop on model-covariate j. nbcode[Tvarj][1]=0 and nbcode[Tvarj][2]=1 sets the value of covariate j*/
3170:
1.145 brouard 3171: for (k=-1; k< maxncov; k++) Ndum[k]=0;
1.137 brouard 3172:
1.145 brouard 3173: for (i=1; i<=ncovmodel-2; i++) { /* -2, cste and age */
3174: /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
3175: ij=Tvar[i]; /* Tvar might be -1 if status was unknown */
3176: Ndum[ij]++;
3177: }
1.126 brouard 3178:
3179: ij=1;
1.145 brouard 3180: for (i=0; i<= maxncov-1; i++) { /* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) */
3181: /*printf("Ndum[%d]=%d\n",i, Ndum[i]);*/
1.126 brouard 3182: if((Ndum[i]!=0) && (i<=ncovcol)){
1.145 brouard 3183: /*printf("diff Ndum[%d]=%d\n",i, Ndum[i]);*/
3184: Tvaraff[ij]=i; /*For printing (unclear) */
1.126 brouard 3185: ij++;
1.145 brouard 3186: }else
3187: Tvaraff[ij]=0;
1.126 brouard 3188: }
1.131 brouard 3189: ij--;
1.144 brouard 3190: cptcoveff=ij; /*Number of total covariates*/
1.145 brouard 3191:
1.126 brouard 3192: }
3193:
1.145 brouard 3194:
1.126 brouard 3195: /*********** Health Expectancies ****************/
3196:
1.127 brouard 3197: 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 3198:
3199: {
3200: /* Health expectancies, no variances */
1.164 brouard 3201: int i, j, nhstepm, hstepm, h, nstepm;
1.126 brouard 3202: int nhstepma, nstepma; /* Decreasing with age */
3203: double age, agelim, hf;
3204: double ***p3mat;
3205: double eip;
3206:
3207: pstamp(ficreseij);
3208: fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
3209: fprintf(ficreseij,"# Age");
3210: for(i=1; i<=nlstate;i++){
3211: for(j=1; j<=nlstate;j++){
3212: fprintf(ficreseij," e%1d%1d ",i,j);
3213: }
3214: fprintf(ficreseij," e%1d. ",i);
3215: }
3216: fprintf(ficreseij,"\n");
3217:
3218:
3219: if(estepm < stepm){
3220: printf ("Problem %d lower than %d\n",estepm, stepm);
3221: }
3222: else hstepm=estepm;
3223: /* We compute the life expectancy from trapezoids spaced every estepm months
3224: * This is mainly to measure the difference between two models: for example
3225: * if stepm=24 months pijx are given only every 2 years and by summing them
3226: * we are calculating an estimate of the Life Expectancy assuming a linear
3227: * progression in between and thus overestimating or underestimating according
3228: * to the curvature of the survival function. If, for the same date, we
3229: * estimate the model with stepm=1 month, we can keep estepm to 24 months
3230: * to compare the new estimate of Life expectancy with the same linear
3231: * hypothesis. A more precise result, taking into account a more precise
3232: * curvature will be obtained if estepm is as small as stepm. */
3233:
3234: /* For example we decided to compute the life expectancy with the smallest unit */
3235: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
3236: nhstepm is the number of hstepm from age to agelim
3237: nstepm is the number of stepm from age to agelin.
3238: Look at hpijx to understand the reason of that which relies in memory size
3239: and note for a fixed period like estepm months */
3240: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
3241: survival function given by stepm (the optimization length). Unfortunately it
3242: means that if the survival funtion is printed only each two years of age and if
3243: you sum them up and add 1 year (area under the trapezoids) you won't get the same
3244: results. So we changed our mind and took the option of the best precision.
3245: */
3246: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
3247:
3248: agelim=AGESUP;
3249: /* If stepm=6 months */
3250: /* Computed by stepm unit matrices, product of hstepm matrices, stored
3251: in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
3252:
3253: /* nhstepm age range expressed in number of stepm */
3254: nstepm=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
3255: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
3256: /* if (stepm >= YEARM) hstepm=1;*/
3257: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
3258: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3259:
3260: for (age=bage; age<=fage; age ++){
3261: nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
3262: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
3263: /* if (stepm >= YEARM) hstepm=1;*/
3264: nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
3265:
3266: /* If stepm=6 months */
3267: /* Computed by stepm unit matrices, product of hstepma matrices, stored
3268: in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
3269:
3270: hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
3271:
3272: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
3273:
3274: printf("%d|",(int)age);fflush(stdout);
3275: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
3276:
3277: /* Computing expectancies */
3278: for(i=1; i<=nlstate;i++)
3279: for(j=1; j<=nlstate;j++)
3280: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
3281: eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
3282:
3283: /* 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]);*/
3284:
3285: }
3286:
3287: fprintf(ficreseij,"%3.0f",age );
3288: for(i=1; i<=nlstate;i++){
3289: eip=0;
3290: for(j=1; j<=nlstate;j++){
3291: eip +=eij[i][j][(int)age];
3292: fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
3293: }
3294: fprintf(ficreseij,"%9.4f", eip );
3295: }
3296: fprintf(ficreseij,"\n");
3297:
3298: }
3299: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3300: printf("\n");
3301: fprintf(ficlog,"\n");
3302:
3303: }
3304:
1.127 brouard 3305: 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 3306:
3307: {
3308: /* Covariances of health expectancies eij and of total life expectancies according
3309: to initial status i, ei. .
3310: */
3311: int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
3312: int nhstepma, nstepma; /* Decreasing with age */
3313: double age, agelim, hf;
3314: double ***p3matp, ***p3matm, ***varhe;
3315: double **dnewm,**doldm;
3316: double *xp, *xm;
3317: double **gp, **gm;
3318: double ***gradg, ***trgradg;
3319: int theta;
3320:
3321: double eip, vip;
3322:
3323: varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
3324: xp=vector(1,npar);
3325: xm=vector(1,npar);
3326: dnewm=matrix(1,nlstate*nlstate,1,npar);
3327: doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
3328:
3329: pstamp(ficresstdeij);
3330: fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
3331: fprintf(ficresstdeij,"# Age");
3332: for(i=1; i<=nlstate;i++){
3333: for(j=1; j<=nlstate;j++)
3334: fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
3335: fprintf(ficresstdeij," e%1d. ",i);
3336: }
3337: fprintf(ficresstdeij,"\n");
3338:
3339: pstamp(ficrescveij);
3340: fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
3341: fprintf(ficrescveij,"# Age");
3342: for(i=1; i<=nlstate;i++)
3343: for(j=1; j<=nlstate;j++){
3344: cptj= (j-1)*nlstate+i;
3345: for(i2=1; i2<=nlstate;i2++)
3346: for(j2=1; j2<=nlstate;j2++){
3347: cptj2= (j2-1)*nlstate+i2;
3348: if(cptj2 <= cptj)
3349: fprintf(ficrescveij," %1d%1d,%1d%1d",i,j,i2,j2);
3350: }
3351: }
3352: fprintf(ficrescveij,"\n");
3353:
3354: if(estepm < stepm){
3355: printf ("Problem %d lower than %d\n",estepm, stepm);
3356: }
3357: else hstepm=estepm;
3358: /* We compute the life expectancy from trapezoids spaced every estepm months
3359: * This is mainly to measure the difference between two models: for example
3360: * if stepm=24 months pijx are given only every 2 years and by summing them
3361: * we are calculating an estimate of the Life Expectancy assuming a linear
3362: * progression in between and thus overestimating or underestimating according
3363: * to the curvature of the survival function. If, for the same date, we
3364: * estimate the model with stepm=1 month, we can keep estepm to 24 months
3365: * to compare the new estimate of Life expectancy with the same linear
3366: * hypothesis. A more precise result, taking into account a more precise
3367: * curvature will be obtained if estepm is as small as stepm. */
3368:
3369: /* For example we decided to compute the life expectancy with the smallest unit */
3370: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
3371: nhstepm is the number of hstepm from age to agelim
3372: nstepm is the number of stepm from age to agelin.
3373: Look at hpijx to understand the reason of that which relies in memory size
3374: and note for a fixed period like estepm months */
3375: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
3376: survival function given by stepm (the optimization length). Unfortunately it
3377: means that if the survival funtion is printed only each two years of age and if
3378: you sum them up and add 1 year (area under the trapezoids) you won't get the same
3379: results. So we changed our mind and took the option of the best precision.
3380: */
3381: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
3382:
3383: /* If stepm=6 months */
3384: /* nhstepm age range expressed in number of stepm */
3385: agelim=AGESUP;
3386: nstepm=(int) rint((agelim-bage)*YEARM/stepm);
3387: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
3388: /* if (stepm >= YEARM) hstepm=1;*/
3389: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
3390:
3391: p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3392: p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3393: gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
3394: trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
3395: gp=matrix(0,nhstepm,1,nlstate*nlstate);
3396: gm=matrix(0,nhstepm,1,nlstate*nlstate);
3397:
3398: for (age=bage; age<=fage; age ++){
3399: nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
3400: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
3401: /* if (stepm >= YEARM) hstepm=1;*/
3402: nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
3403:
3404: /* If stepm=6 months */
3405: /* Computed by stepm unit matrices, product of hstepma matrices, stored
3406: in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
3407:
3408: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
3409:
3410: /* Computing Variances of health expectancies */
3411: /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
3412: decrease memory allocation */
3413: for(theta=1; theta <=npar; theta++){
3414: for(i=1; i<=npar; i++){
3415: xp[i] = x[i] + (i==theta ?delti[theta]:0);
3416: xm[i] = x[i] - (i==theta ?delti[theta]:0);
3417: }
3418: hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);
3419: hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);
3420:
3421: for(j=1; j<= nlstate; j++){
3422: for(i=1; i<=nlstate; i++){
3423: for(h=0; h<=nhstepm-1; h++){
3424: gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
3425: gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
3426: }
3427: }
3428: }
3429:
3430: for(ij=1; ij<= nlstate*nlstate; ij++)
3431: for(h=0; h<=nhstepm-1; h++){
3432: gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
3433: }
3434: }/* End theta */
3435:
3436:
3437: for(h=0; h<=nhstepm-1; h++)
3438: for(j=1; j<=nlstate*nlstate;j++)
3439: for(theta=1; theta <=npar; theta++)
3440: trgradg[h][j][theta]=gradg[h][theta][j];
3441:
3442:
3443: for(ij=1;ij<=nlstate*nlstate;ij++)
3444: for(ji=1;ji<=nlstate*nlstate;ji++)
3445: varhe[ij][ji][(int)age] =0.;
3446:
3447: printf("%d|",(int)age);fflush(stdout);
3448: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
3449: for(h=0;h<=nhstepm-1;h++){
3450: for(k=0;k<=nhstepm-1;k++){
3451: matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
3452: matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
3453: for(ij=1;ij<=nlstate*nlstate;ij++)
3454: for(ji=1;ji<=nlstate*nlstate;ji++)
3455: varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
3456: }
3457: }
3458:
3459: /* Computing expectancies */
3460: hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
3461: for(i=1; i<=nlstate;i++)
3462: for(j=1; j<=nlstate;j++)
3463: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
3464: eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
3465:
3466: /* 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]);*/
3467:
3468: }
3469:
3470: fprintf(ficresstdeij,"%3.0f",age );
3471: for(i=1; i<=nlstate;i++){
3472: eip=0.;
3473: vip=0.;
3474: for(j=1; j<=nlstate;j++){
3475: eip += eij[i][j][(int)age];
3476: for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
3477: vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
3478: fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
3479: }
3480: fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
3481: }
3482: fprintf(ficresstdeij,"\n");
3483:
3484: fprintf(ficrescveij,"%3.0f",age );
3485: for(i=1; i<=nlstate;i++)
3486: for(j=1; j<=nlstate;j++){
3487: cptj= (j-1)*nlstate+i;
3488: for(i2=1; i2<=nlstate;i2++)
3489: for(j2=1; j2<=nlstate;j2++){
3490: cptj2= (j2-1)*nlstate+i2;
3491: if(cptj2 <= cptj)
3492: fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
3493: }
3494: }
3495: fprintf(ficrescveij,"\n");
3496:
3497: }
3498: free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
3499: free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
3500: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
3501: free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
3502: free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3503: free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3504: printf("\n");
3505: fprintf(ficlog,"\n");
3506:
3507: free_vector(xm,1,npar);
3508: free_vector(xp,1,npar);
3509: free_matrix(dnewm,1,nlstate*nlstate,1,npar);
3510: free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
3511: free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
3512: }
3513:
3514: /************ Variance ******************/
3515: 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[])
3516: {
3517: /* Variance of health expectancies */
3518: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
3519: /* double **newm;*/
1.169 brouard 3520: /* int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav)*/
3521:
3522: int movingaverage();
1.126 brouard 3523: double **dnewm,**doldm;
3524: double **dnewmp,**doldmp;
3525: int i, j, nhstepm, hstepm, h, nstepm ;
1.164 brouard 3526: int k;
1.126 brouard 3527: double *xp;
3528: double **gp, **gm; /* for var eij */
3529: double ***gradg, ***trgradg; /*for var eij */
3530: double **gradgp, **trgradgp; /* for var p point j */
3531: double *gpp, *gmp; /* for var p point j */
3532: double **varppt; /* for var p point j nlstate to nlstate+ndeath */
3533: double ***p3mat;
3534: double age,agelim, hf;
3535: double ***mobaverage;
3536: int theta;
3537: char digit[4];
3538: char digitp[25];
3539:
3540: char fileresprobmorprev[FILENAMELENGTH];
3541:
3542: if(popbased==1){
3543: if(mobilav!=0)
3544: strcpy(digitp,"-populbased-mobilav-");
3545: else strcpy(digitp,"-populbased-nomobil-");
3546: }
3547: else
3548: strcpy(digitp,"-stablbased-");
3549:
3550: if (mobilav!=0) {
3551: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3552: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
3553: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
3554: printf(" Error in movingaverage mobilav=%d\n",mobilav);
3555: }
3556: }
3557:
3558: strcpy(fileresprobmorprev,"prmorprev");
3559: sprintf(digit,"%-d",ij);
3560: /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
3561: strcat(fileresprobmorprev,digit); /* Tvar to be done */
3562: strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
3563: strcat(fileresprobmorprev,fileres);
3564: if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
3565: printf("Problem with resultfile: %s\n", fileresprobmorprev);
3566: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
3567: }
3568: printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
3569:
3570: fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
3571: pstamp(ficresprobmorprev);
3572: 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);
3573: fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
3574: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
3575: fprintf(ficresprobmorprev," p.%-d SE",j);
3576: for(i=1; i<=nlstate;i++)
3577: fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
3578: }
3579: fprintf(ficresprobmorprev,"\n");
3580: fprintf(ficgp,"\n# Routine varevsij");
3581: /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
3582: 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");
3583: fprintf(fichtm,"\n<br>%s <br>\n",digitp);
3584: /* } */
3585: varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
3586: pstamp(ficresvij);
3587: fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n# (weighted average of eij where weights are ");
3588: if(popbased==1)
1.128 brouard 3589: 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 3590: else
3591: fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
3592: fprintf(ficresvij,"# Age");
3593: for(i=1; i<=nlstate;i++)
3594: for(j=1; j<=nlstate;j++)
3595: fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
3596: fprintf(ficresvij,"\n");
3597:
3598: xp=vector(1,npar);
3599: dnewm=matrix(1,nlstate,1,npar);
3600: doldm=matrix(1,nlstate,1,nlstate);
3601: dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
3602: doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
3603:
3604: gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
3605: gpp=vector(nlstate+1,nlstate+ndeath);
3606: gmp=vector(nlstate+1,nlstate+ndeath);
3607: trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
3608:
3609: if(estepm < stepm){
3610: printf ("Problem %d lower than %d\n",estepm, stepm);
3611: }
3612: else hstepm=estepm;
3613: /* For example we decided to compute the life expectancy with the smallest unit */
3614: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
3615: nhstepm is the number of hstepm from age to agelim
3616: nstepm is the number of stepm from age to agelin.
1.128 brouard 3617: Look at function hpijx to understand why (it is linked to memory size questions) */
1.126 brouard 3618: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
3619: survival function given by stepm (the optimization length). Unfortunately it
3620: means that if the survival funtion is printed every two years of age and if
3621: you sum them up and add 1 year (area under the trapezoids) you won't get the same
3622: results. So we changed our mind and took the option of the best precision.
3623: */
3624: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
3625: agelim = AGESUP;
3626: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
3627: nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
3628: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
3629: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3630: gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
3631: gp=matrix(0,nhstepm,1,nlstate);
3632: gm=matrix(0,nhstepm,1,nlstate);
3633:
3634:
3635: for(theta=1; theta <=npar; theta++){
3636: for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
3637: xp[i] = x[i] + (i==theta ?delti[theta]:0);
3638: }
3639: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
3640: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
3641:
3642: if (popbased==1) {
3643: if(mobilav ==0){
3644: for(i=1; i<=nlstate;i++)
3645: prlim[i][i]=probs[(int)age][i][ij];
3646: }else{ /* mobilav */
3647: for(i=1; i<=nlstate;i++)
3648: prlim[i][i]=mobaverage[(int)age][i][ij];
3649: }
3650: }
3651:
3652: for(j=1; j<= nlstate; j++){
3653: for(h=0; h<=nhstepm; h++){
3654: for(i=1, gp[h][j]=0.;i<=nlstate;i++)
3655: gp[h][j] += prlim[i][i]*p3mat[i][j][h];
3656: }
3657: }
3658: /* This for computing probability of death (h=1 means
3659: computed over hstepm matrices product = hstepm*stepm months)
3660: as a weighted average of prlim.
3661: */
3662: for(j=nlstate+1;j<=nlstate+ndeath;j++){
3663: for(i=1,gpp[j]=0.; i<= nlstate; i++)
3664: gpp[j] += prlim[i][i]*p3mat[i][j][1];
3665: }
3666: /* end probability of death */
3667:
3668: for(i=1; i<=npar; i++) /* Computes gradient x - delta */
3669: xp[i] = x[i] - (i==theta ?delti[theta]:0);
3670: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
3671: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
3672:
3673: if (popbased==1) {
3674: if(mobilav ==0){
3675: for(i=1; i<=nlstate;i++)
3676: prlim[i][i]=probs[(int)age][i][ij];
3677: }else{ /* mobilav */
3678: for(i=1; i<=nlstate;i++)
3679: prlim[i][i]=mobaverage[(int)age][i][ij];
3680: }
3681: }
3682:
1.128 brouard 3683: for(j=1; j<= nlstate; j++){ /* Sum of wi * eij = e.j */
1.126 brouard 3684: for(h=0; h<=nhstepm; h++){
3685: for(i=1, gm[h][j]=0.;i<=nlstate;i++)
3686: gm[h][j] += prlim[i][i]*p3mat[i][j][h];
3687: }
3688: }
3689: /* This for computing probability of death (h=1 means
3690: computed over hstepm matrices product = hstepm*stepm months)
3691: as a weighted average of prlim.
3692: */
3693: for(j=nlstate+1;j<=nlstate+ndeath;j++){
3694: for(i=1,gmp[j]=0.; i<= nlstate; i++)
3695: gmp[j] += prlim[i][i]*p3mat[i][j][1];
3696: }
3697: /* end probability of death */
3698:
3699: for(j=1; j<= nlstate; j++) /* vareij */
3700: for(h=0; h<=nhstepm; h++){
3701: gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
3702: }
3703:
3704: for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
3705: gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
3706: }
3707:
3708: } /* End theta */
3709:
3710: trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
3711:
3712: for(h=0; h<=nhstepm; h++) /* veij */
3713: for(j=1; j<=nlstate;j++)
3714: for(theta=1; theta <=npar; theta++)
3715: trgradg[h][j][theta]=gradg[h][theta][j];
3716:
3717: for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
3718: for(theta=1; theta <=npar; theta++)
3719: trgradgp[j][theta]=gradgp[theta][j];
3720:
3721:
3722: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
3723: for(i=1;i<=nlstate;i++)
3724: for(j=1;j<=nlstate;j++)
3725: vareij[i][j][(int)age] =0.;
3726:
3727: for(h=0;h<=nhstepm;h++){
3728: for(k=0;k<=nhstepm;k++){
3729: matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
3730: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
3731: for(i=1;i<=nlstate;i++)
3732: for(j=1;j<=nlstate;j++)
3733: vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
3734: }
3735: }
3736:
3737: /* pptj */
3738: matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
3739: matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
3740: for(j=nlstate+1;j<=nlstate+ndeath;j++)
3741: for(i=nlstate+1;i<=nlstate+ndeath;i++)
3742: varppt[j][i]=doldmp[j][i];
3743: /* end ppptj */
3744: /* x centered again */
3745: hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);
3746: prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
3747:
3748: if (popbased==1) {
3749: if(mobilav ==0){
3750: for(i=1; i<=nlstate;i++)
3751: prlim[i][i]=probs[(int)age][i][ij];
3752: }else{ /* mobilav */
3753: for(i=1; i<=nlstate;i++)
3754: prlim[i][i]=mobaverage[(int)age][i][ij];
3755: }
3756: }
3757:
3758: /* This for computing probability of death (h=1 means
3759: computed over hstepm (estepm) matrices product = hstepm*stepm months)
3760: as a weighted average of prlim.
3761: */
3762: for(j=nlstate+1;j<=nlstate+ndeath;j++){
3763: for(i=1,gmp[j]=0.;i<= nlstate; i++)
3764: gmp[j] += prlim[i][i]*p3mat[i][j][1];
3765: }
3766: /* end probability of death */
3767:
3768: fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
3769: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
3770: fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
3771: for(i=1; i<=nlstate;i++){
3772: fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
3773: }
3774: }
3775: fprintf(ficresprobmorprev,"\n");
3776:
3777: fprintf(ficresvij,"%.0f ",age );
3778: for(i=1; i<=nlstate;i++)
3779: for(j=1; j<=nlstate;j++){
3780: fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
3781: }
3782: fprintf(ficresvij,"\n");
3783: free_matrix(gp,0,nhstepm,1,nlstate);
3784: free_matrix(gm,0,nhstepm,1,nlstate);
3785: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
3786: free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
3787: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3788: } /* End age */
3789: free_vector(gpp,nlstate+1,nlstate+ndeath);
3790: free_vector(gmp,nlstate+1,nlstate+ndeath);
3791: free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
3792: free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
1.145 brouard 3793: fprintf(ficgp,"\nunset parametric;unset label; set ter png small size 320, 240");
1.126 brouard 3794: /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
1.131 brouard 3795: fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
1.126 brouard 3796: /* fprintf(ficgp,"\n plot \"%s\" u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
3797: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
3798: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
1.145 brouard 3799: fprintf(ficgp,"\n plot \"%s\" u 1:($3) not w l lt 1 ",subdirf(fileresprobmorprev));
1.170 brouard 3800: fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)) t \"95%% interval\" w l lt 2 ",subdirf(fileresprobmorprev));
1.145 brouard 3801: fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)) not w l lt 2 ",subdirf(fileresprobmorprev));
1.126 brouard 3802: fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
3803: 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);
3804: /* 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);
3805: */
3806: /* fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
3807: fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
3808:
3809: free_vector(xp,1,npar);
3810: free_matrix(doldm,1,nlstate,1,nlstate);
3811: free_matrix(dnewm,1,nlstate,1,npar);
3812: free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
3813: free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
3814: free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
3815: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3816: fclose(ficresprobmorprev);
3817: fflush(ficgp);
3818: fflush(fichtm);
3819: } /* end varevsij */
3820:
3821: /************ Variance of prevlim ******************/
3822: 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[])
3823: {
3824: /* Variance of prevalence limit */
3825: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
1.164 brouard 3826:
1.126 brouard 3827: double **dnewm,**doldm;
3828: int i, j, nhstepm, hstepm;
3829: double *xp;
3830: double *gp, *gm;
3831: double **gradg, **trgradg;
3832: double age,agelim;
3833: int theta;
3834:
3835: pstamp(ficresvpl);
3836: fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
3837: fprintf(ficresvpl,"# Age");
3838: for(i=1; i<=nlstate;i++)
3839: fprintf(ficresvpl," %1d-%1d",i,i);
3840: fprintf(ficresvpl,"\n");
3841:
3842: xp=vector(1,npar);
3843: dnewm=matrix(1,nlstate,1,npar);
3844: doldm=matrix(1,nlstate,1,nlstate);
3845:
3846: hstepm=1*YEARM; /* Every year of age */
3847: hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
3848: agelim = AGESUP;
3849: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
3850: nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
3851: if (stepm >= YEARM) hstepm=1;
3852: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
3853: gradg=matrix(1,npar,1,nlstate);
3854: gp=vector(1,nlstate);
3855: gm=vector(1,nlstate);
3856:
3857: for(theta=1; theta <=npar; theta++){
3858: for(i=1; i<=npar; i++){ /* Computes gradient */
3859: xp[i] = x[i] + (i==theta ?delti[theta]:0);
3860: }
3861: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
3862: for(i=1;i<=nlstate;i++)
3863: gp[i] = prlim[i][i];
3864:
3865: for(i=1; i<=npar; i++) /* Computes gradient */
3866: xp[i] = x[i] - (i==theta ?delti[theta]:0);
3867: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
3868: for(i=1;i<=nlstate;i++)
3869: gm[i] = prlim[i][i];
3870:
3871: for(i=1;i<=nlstate;i++)
3872: gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
3873: } /* End theta */
3874:
3875: trgradg =matrix(1,nlstate,1,npar);
3876:
3877: for(j=1; j<=nlstate;j++)
3878: for(theta=1; theta <=npar; theta++)
3879: trgradg[j][theta]=gradg[theta][j];
3880:
3881: for(i=1;i<=nlstate;i++)
3882: varpl[i][(int)age] =0.;
3883: matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
3884: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
3885: for(i=1;i<=nlstate;i++)
3886: varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
3887:
3888: fprintf(ficresvpl,"%.0f ",age );
3889: for(i=1; i<=nlstate;i++)
3890: fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
3891: fprintf(ficresvpl,"\n");
3892: free_vector(gp,1,nlstate);
3893: free_vector(gm,1,nlstate);
3894: free_matrix(gradg,1,npar,1,nlstate);
3895: free_matrix(trgradg,1,nlstate,1,npar);
3896: } /* End age */
3897:
3898: free_vector(xp,1,npar);
3899: free_matrix(doldm,1,nlstate,1,npar);
3900: free_matrix(dnewm,1,nlstate,1,nlstate);
3901:
3902: }
3903:
3904: /************ Variance of one-step probabilities ******************/
3905: 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[])
3906: {
1.164 brouard 3907: int i, j=0, k1, l1, tj;
1.126 brouard 3908: int k2, l2, j1, z1;
1.164 brouard 3909: int k=0, l;
1.145 brouard 3910: int first=1, first1, first2;
1.126 brouard 3911: double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
3912: double **dnewm,**doldm;
3913: double *xp;
3914: double *gp, *gm;
3915: double **gradg, **trgradg;
3916: double **mu;
1.164 brouard 3917: double age, cov[NCOVMAX+1];
1.126 brouard 3918: double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
3919: int theta;
3920: char fileresprob[FILENAMELENGTH];
3921: char fileresprobcov[FILENAMELENGTH];
3922: char fileresprobcor[FILENAMELENGTH];
3923: double ***varpij;
3924:
3925: strcpy(fileresprob,"prob");
3926: strcat(fileresprob,fileres);
3927: if((ficresprob=fopen(fileresprob,"w"))==NULL) {
3928: printf("Problem with resultfile: %s\n", fileresprob);
3929: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
3930: }
3931: strcpy(fileresprobcov,"probcov");
3932: strcat(fileresprobcov,fileres);
3933: if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
3934: printf("Problem with resultfile: %s\n", fileresprobcov);
3935: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
3936: }
3937: strcpy(fileresprobcor,"probcor");
3938: strcat(fileresprobcor,fileres);
3939: if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
3940: printf("Problem with resultfile: %s\n", fileresprobcor);
3941: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
3942: }
3943: printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
3944: fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
3945: printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
3946: fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
3947: printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
3948: fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
3949: pstamp(ficresprob);
3950: fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
3951: fprintf(ficresprob,"# Age");
3952: pstamp(ficresprobcov);
3953: fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
3954: fprintf(ficresprobcov,"# Age");
3955: pstamp(ficresprobcor);
3956: fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
3957: fprintf(ficresprobcor,"# Age");
3958:
3959:
3960: for(i=1; i<=nlstate;i++)
3961: for(j=1; j<=(nlstate+ndeath);j++){
3962: fprintf(ficresprob," p%1d-%1d (SE)",i,j);
3963: fprintf(ficresprobcov," p%1d-%1d ",i,j);
3964: fprintf(ficresprobcor," p%1d-%1d ",i,j);
3965: }
3966: /* fprintf(ficresprob,"\n");
3967: fprintf(ficresprobcov,"\n");
3968: fprintf(ficresprobcor,"\n");
3969: */
1.131 brouard 3970: xp=vector(1,npar);
1.126 brouard 3971: dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
3972: doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
3973: mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
3974: varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
3975: first=1;
3976: fprintf(ficgp,"\n# Routine varprob");
3977: fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
3978: fprintf(fichtm,"\n");
3979:
3980: fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
3981: fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
3982: file %s<br>\n",optionfilehtmcov);
3983: fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
3984: and drawn. It helps understanding how is the covariance between two incidences.\
3985: They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
3986: 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. \
3987: It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
3988: would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
3989: standard deviations wide on each axis. <br>\
3990: Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
3991: and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
3992: To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
3993:
3994: cov[1]=1;
1.145 brouard 3995: /* tj=cptcoveff; */
3996: tj = (int) pow(2,cptcoveff);
1.126 brouard 3997: if (cptcovn<1) {tj=1;ncodemax[1]=1;}
3998: j1=0;
1.145 brouard 3999: for(j1=1; j1<=tj;j1++){
4000: /*for(i1=1; i1<=ncodemax[t];i1++){ */
4001: /*j1++;*/
1.126 brouard 4002: if (cptcovn>0) {
4003: fprintf(ficresprob, "\n#********** Variable ");
4004: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
4005: fprintf(ficresprob, "**********\n#\n");
4006: fprintf(ficresprobcov, "\n#********** Variable ");
4007: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
4008: fprintf(ficresprobcov, "**********\n#\n");
4009:
4010: fprintf(ficgp, "\n#********** Variable ");
4011: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
4012: fprintf(ficgp, "**********\n#\n");
4013:
4014:
4015: fprintf(fichtmcov, "\n<hr size=\"2\" color=\"#EC5E5E\">********** Variable ");
4016: for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
4017: fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
4018:
4019: fprintf(ficresprobcor, "\n#********** Variable ");
4020: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
4021: fprintf(ficresprobcor, "**********\n#");
4022: }
4023:
1.145 brouard 4024: gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
4025: trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
4026: gp=vector(1,(nlstate)*(nlstate+ndeath));
4027: gm=vector(1,(nlstate)*(nlstate+ndeath));
1.126 brouard 4028: for (age=bage; age<=fage; age ++){
4029: cov[2]=age;
4030: for (k=1; k<=cptcovn;k++) {
1.145 brouard 4031: cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];/* j1 1 2 3 4
4032: * 1 1 1 1 1
4033: * 2 2 1 1 1
4034: * 3 1 2 1 1
4035: */
4036: /* nbcode[1][1]=0 nbcode[1][2]=1;*/
1.126 brouard 4037: }
4038: for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
4039: for (k=1; k<=cptcovprod;k++)
4040: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
4041:
4042:
4043: for(theta=1; theta <=npar; theta++){
4044: for(i=1; i<=npar; i++)
4045: xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
4046:
4047: pmij(pmmij,cov,ncovmodel,xp,nlstate);
4048:
4049: k=0;
4050: for(i=1; i<= (nlstate); i++){
4051: for(j=1; j<=(nlstate+ndeath);j++){
4052: k=k+1;
4053: gp[k]=pmmij[i][j];
4054: }
4055: }
4056:
4057: for(i=1; i<=npar; i++)
4058: xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
4059:
4060: pmij(pmmij,cov,ncovmodel,xp,nlstate);
4061: k=0;
4062: for(i=1; i<=(nlstate); i++){
4063: for(j=1; j<=(nlstate+ndeath);j++){
4064: k=k+1;
4065: gm[k]=pmmij[i][j];
4066: }
4067: }
4068:
4069: for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)
4070: gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];
4071: }
4072:
4073: for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
4074: for(theta=1; theta <=npar; theta++)
4075: trgradg[j][theta]=gradg[theta][j];
4076:
4077: matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);
4078: matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
4079:
4080: pmij(pmmij,cov,ncovmodel,x,nlstate);
4081:
4082: k=0;
4083: for(i=1; i<=(nlstate); i++){
4084: for(j=1; j<=(nlstate+ndeath);j++){
4085: k=k+1;
4086: mu[k][(int) age]=pmmij[i][j];
4087: }
4088: }
4089: for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
4090: for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
4091: varpij[i][j][(int)age] = doldm[i][j];
4092:
4093: /*printf("\n%d ",(int)age);
4094: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
4095: printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
4096: fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
4097: }*/
4098:
4099: fprintf(ficresprob,"\n%d ",(int)age);
4100: fprintf(ficresprobcov,"\n%d ",(int)age);
4101: fprintf(ficresprobcor,"\n%d ",(int)age);
4102:
4103: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
4104: fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
4105: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
4106: fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
4107: fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
4108: }
4109: i=0;
4110: for (k=1; k<=(nlstate);k++){
4111: for (l=1; l<=(nlstate+ndeath);l++){
1.145 brouard 4112: i++;
1.126 brouard 4113: fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
4114: fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
4115: for (j=1; j<=i;j++){
1.145 brouard 4116: /* printf(" k=%d l=%d i=%d j=%d\n",k,l,i,j);fflush(stdout); */
1.126 brouard 4117: fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
4118: fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
4119: }
4120: }
4121: }/* end of loop for state */
4122: } /* end of loop for age */
1.145 brouard 4123: free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
4124: free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
4125: free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
4126: free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
4127:
1.126 brouard 4128: /* Confidence intervalle of pij */
4129: /*
1.131 brouard 4130: fprintf(ficgp,"\nunset parametric;unset label");
1.126 brouard 4131: fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
4132: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
4133: 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);
4134: fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
4135: fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
4136: fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
4137: */
4138:
4139: /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
1.145 brouard 4140: first1=1;first2=2;
1.126 brouard 4141: for (k2=1; k2<=(nlstate);k2++){
4142: for (l2=1; l2<=(nlstate+ndeath);l2++){
4143: if(l2==k2) continue;
4144: j=(k2-1)*(nlstate+ndeath)+l2;
4145: for (k1=1; k1<=(nlstate);k1++){
4146: for (l1=1; l1<=(nlstate+ndeath);l1++){
4147: if(l1==k1) continue;
4148: i=(k1-1)*(nlstate+ndeath)+l1;
4149: if(i<=j) continue;
4150: for (age=bage; age<=fage; age ++){
4151: if ((int)age %5==0){
4152: v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
4153: v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
4154: cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
4155: mu1=mu[i][(int) age]/stepm*YEARM ;
4156: mu2=mu[j][(int) age]/stepm*YEARM;
4157: c12=cv12/sqrt(v1*v2);
4158: /* Computing eigen value of matrix of covariance */
4159: lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
4160: lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
1.135 brouard 4161: if ((lc2 <0) || (lc1 <0) ){
1.145 brouard 4162: if(first2==1){
4163: first1=0;
4164: 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);
4165: }
4166: 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);
4167: /* lc1=fabs(lc1); */ /* If we want to have them positive */
4168: /* lc2=fabs(lc2); */
1.135 brouard 4169: }
4170:
1.126 brouard 4171: /* Eigen vectors */
4172: v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
4173: /*v21=sqrt(1.-v11*v11); *//* error */
4174: v21=(lc1-v1)/cv12*v11;
4175: v12=-v21;
4176: v22=v11;
4177: tnalp=v21/v11;
4178: if(first1==1){
4179: first1=0;
4180: 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);
4181: }
4182: 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);
4183: /*printf(fignu*/
4184: /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
4185: /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
4186: if(first==1){
4187: first=0;
4188: fprintf(ficgp,"\nset parametric;unset label");
4189: 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 4190: fprintf(ficgp,"\nset ter png small size 320, 240");
1.126 brouard 4191: fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
4192: :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
4193: %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
4194: subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
4195: subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
4196: fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
4197: fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
4198: fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
4199: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
4200: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
4201: 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",\
4202: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
4203: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
4204: }else{
4205: first=0;
4206: fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
4207: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
4208: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
4209: 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",\
4210: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
4211: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
4212: }/* if first */
4213: } /* age mod 5 */
4214: } /* end loop age */
4215: fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
4216: first=1;
4217: } /*l12 */
4218: } /* k12 */
4219: } /*l1 */
4220: }/* k1 */
1.169 brouard 4221: /* } */ /* loop covariates */
1.126 brouard 4222: }
4223: free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
4224: free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
4225: free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
4226: free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
4227: free_vector(xp,1,npar);
4228: fclose(ficresprob);
4229: fclose(ficresprobcov);
4230: fclose(ficresprobcor);
4231: fflush(ficgp);
4232: fflush(fichtmcov);
4233: }
4234:
4235:
4236: /******************* Printing html file ***********/
4237: void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
4238: int lastpass, int stepm, int weightopt, char model[],\
4239: int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
4240: int popforecast, int estepm ,\
4241: double jprev1, double mprev1,double anprev1, \
4242: double jprev2, double mprev2,double anprev2){
4243: int jj1, k1, i1, cpt;
4244:
4245: fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
4246: <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
4247: </ul>");
4248: fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \
4249: - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
4250: jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
4251: fprintf(fichtm,"\
4252: - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
4253: stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
4254: fprintf(fichtm,"\
4255: - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
4256: subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
4257: fprintf(fichtm,"\
1.128 brouard 4258: - (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 4259: <a href=\"%s\">%s</a> <br>\n",
4260: estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
4261: fprintf(fichtm,"\
4262: - Population projections by age and states: \
4263: <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileres,"f"),subdirf2(fileres,"f"));
4264:
4265: fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
4266:
1.145 brouard 4267: m=pow(2,cptcoveff);
1.126 brouard 4268: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
4269:
4270: jj1=0;
4271: for(k1=1; k1<=m;k1++){
4272: for(i1=1; i1<=ncodemax[k1];i1++){
4273: jj1++;
4274: if (cptcovn > 0) {
4275: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
4276: for (cpt=1; cpt<=cptcoveff;cpt++)
4277: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
4278: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
4279: }
4280: /* Pij */
1.145 brouard 4281: 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> \
4282: <img src=\"%s%d_1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
1.126 brouard 4283: /* Quasi-incidences */
4284: fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
1.145 brouard 4285: 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> \
4286: <img src=\"%s%d_2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
1.126 brouard 4287: /* Period (stable) prevalence in each health state */
1.154 brouard 4288: for(cpt=1; cpt<=nlstate;cpt++){
1.166 brouard 4289: 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> \
4290: <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 4291: }
4292: for(cpt=1; cpt<=nlstate;cpt++) {
1.154 brouard 4293: 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> \
4294: <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 4295: }
4296: } /* end i1 */
4297: }/* End k1 */
4298: fprintf(fichtm,"</ul>");
4299:
4300:
4301: fprintf(fichtm,"\
4302: \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
4303: - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);
4304:
4305: fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
4306: subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
4307: fprintf(fichtm,"\
4308: - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
4309: subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
4310:
4311: fprintf(fichtm,"\
4312: - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
4313: subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
4314: fprintf(fichtm,"\
4315: - 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): \
4316: <a href=\"%s\">%s</a> <br>\n</li>",
4317: estepm,subdirf2(fileres,"cve"),subdirf2(fileres,"cve"));
4318: fprintf(fichtm,"\
4319: - (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): \
4320: <a href=\"%s\">%s</a> <br>\n</li>",
4321: estepm,subdirf2(fileres,"stde"),subdirf2(fileres,"stde"));
4322: fprintf(fichtm,"\
1.128 brouard 4323: - 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 4324: estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
4325: fprintf(fichtm,"\
1.128 brouard 4326: - 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",
4327: estepm, subdirf2(fileres,"t"),subdirf2(fileres,"t"));
1.126 brouard 4328: fprintf(fichtm,"\
4329: - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
4330: subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
4331:
4332: /* if(popforecast==1) fprintf(fichtm,"\n */
4333: /* - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
4334: /* - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
4335: /* <br>",fileres,fileres,fileres,fileres); */
4336: /* else */
4337: /* 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); */
4338: fflush(fichtm);
4339: fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
4340:
1.145 brouard 4341: m=pow(2,cptcoveff);
1.126 brouard 4342: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
4343:
4344: jj1=0;
4345: for(k1=1; k1<=m;k1++){
4346: for(i1=1; i1<=ncodemax[k1];i1++){
4347: jj1++;
4348: if (cptcovn > 0) {
4349: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
4350: for (cpt=1; cpt<=cptcoveff;cpt++)
4351: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
4352: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
4353: }
4354: for(cpt=1; cpt<=nlstate;cpt++) {
4355: fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
1.145 brouard 4356: prevalence (with 95%% confidence interval) in state (%d): %s%d_%d.png <br>\
4357: <img src=\"%s%d_%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);
1.126 brouard 4358: }
4359: fprintf(fichtm,"\n<br>- Total life expectancy by age and \
1.128 brouard 4360: health expectancies in states (1) and (2). If popbased=1 the smooth (due to the model) \
4361: true period expectancies (those weighted with period prevalences are also\
4362: drawn in addition to the population based expectancies computed using\
4363: observed and cahotic prevalences: %s%d.png<br>\
1.126 brouard 4364: <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
4365: } /* end i1 */
4366: }/* End k1 */
4367: fprintf(fichtm,"</ul>");
4368: fflush(fichtm);
4369: }
4370:
4371: /******************* Gnuplot file **************/
4372: void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
4373:
4374: char dirfileres[132],optfileres[132];
1.164 brouard 4375: int cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,ij=0,l=0;
1.130 brouard 4376: int ng=0;
1.126 brouard 4377: /* if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
4378: /* printf("Problem with file %s",optionfilegnuplot); */
4379: /* fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
4380: /* } */
4381:
4382: /*#ifdef windows */
4383: fprintf(ficgp,"cd \"%s\" \n",pathc);
4384: /*#endif */
4385: m=pow(2,cptcoveff);
4386:
4387: strcpy(dirfileres,optionfilefiname);
4388: strcpy(optfileres,"vpl");
4389: /* 1eme*/
1.153 brouard 4390: fprintf(ficgp,"\n# 1st: Period (stable) prevalence with CI: 'vpl' files\n");
1.126 brouard 4391: for (cpt=1; cpt<= nlstate ; cpt ++) {
1.145 brouard 4392: for (k1=1; k1<= m ; k1 ++) { /* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */
4393: fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
4394: fprintf(ficgp,"\n#set out \"v%s%d_%d.png\" \n",optionfilefiname,cpt,k1);
1.126 brouard 4395: fprintf(ficgp,"set xlabel \"Age\" \n\
4396: set ylabel \"Probability\" \n\
1.145 brouard 4397: set ter png small size 320, 240\n\
1.170 brouard 4398: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
1.126 brouard 4399:
4400: for (i=1; i<= nlstate ; i ++) {
1.170 brouard 4401: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
4402: else fprintf(ficgp," %%*lf (%%*lf)");
1.126 brouard 4403: }
1.170 brouard 4404: 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 4405: for (i=1; i<= nlstate ; i ++) {
1.170 brouard 4406: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
4407: else fprintf(ficgp," %%*lf (%%*lf)");
1.126 brouard 4408: }
1.170 brouard 4409: fprintf(ficgp,"\" t\"95%% CI\" w l lt 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
1.126 brouard 4410: for (i=1; i<= nlstate ; i ++) {
1.170 brouard 4411: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
4412: else fprintf(ficgp," %%*lf (%%*lf)");
1.126 brouard 4413: }
1.145 brouard 4414: fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l lt 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
1.126 brouard 4415: }
4416: }
4417: /*2 eme*/
1.153 brouard 4418: fprintf(ficgp,"\n# 2nd: Total life expectancy with CI: 't' files\n");
1.126 brouard 4419: for (k1=1; k1<= m ; k1 ++) {
4420: fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
1.145 brouard 4421: fprintf(ficgp,"set ylabel \"Years\" \nset ter png small size 320, 240\nplot [%.f:%.f] ",ageminpar,fage);
1.126 brouard 4422:
4423: for (i=1; i<= nlstate+1 ; i ++) {
4424: k=2*i;
1.170 brouard 4425: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
1.126 brouard 4426: for (j=1; j<= nlstate+1 ; j ++) {
1.170 brouard 4427: if (j==i) fprintf(ficgp," %%lf (%%lf)");
4428: else fprintf(ficgp," %%*lf (%%*lf)");
1.126 brouard 4429: }
4430: if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
4431: else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
1.170 brouard 4432: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
1.126 brouard 4433: for (j=1; j<= nlstate+1 ; j ++) {
1.170 brouard 4434: if (j==i) fprintf(ficgp," %%lf (%%lf)");
4435: else fprintf(ficgp," %%*lf (%%*lf)");
1.126 brouard 4436: }
1.145 brouard 4437: fprintf(ficgp,"\" t\"\" w l lt 0,");
1.170 brouard 4438: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
1.126 brouard 4439: for (j=1; j<= nlstate+1 ; j ++) {
1.170 brouard 4440: if (j==i) fprintf(ficgp," %%lf (%%lf)");
4441: else fprintf(ficgp," %%*lf (%%*lf)");
1.126 brouard 4442: }
1.145 brouard 4443: if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l lt 0");
4444: else fprintf(ficgp,"\" t\"\" w l lt 0,");
1.126 brouard 4445: }
4446: }
4447:
4448: /*3eme*/
4449:
4450: for (k1=1; k1<= m ; k1 ++) {
4451: for (cpt=1; cpt<= nlstate ; cpt ++) {
4452: /* k=2+nlstate*(2*cpt-2); */
4453: k=2+(nlstate+1)*(cpt-1);
4454: fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
1.145 brouard 4455: fprintf(ficgp,"set ter png small size 320, 240\n\
1.126 brouard 4456: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
4457: /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
4458: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
4459: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
4460: fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
4461: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
4462: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
4463:
4464: */
4465: for (i=1; i< nlstate ; i ++) {
4466: 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);
4467: /* 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);*/
4468:
4469: }
4470: fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+nlstate,cpt);
4471: }
4472: }
4473:
4474: /* CV preval stable (period) */
1.153 brouard 4475: for (k1=1; k1<= m ; k1 ++) { /* For each multivariate if any */
4476: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
1.126 brouard 4477: k=3;
1.153 brouard 4478: fprintf(ficgp,"\n#\n#\n#CV preval stable (period): 'pij' files, cov=%d state=%d",k1, cpt);
1.145 brouard 4479: fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
1.126 brouard 4480: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
1.145 brouard 4481: set ter png small size 320, 240\n\
1.126 brouard 4482: unset log y\n\
1.153 brouard 4483: plot [%.f:%.f] ", ageminpar, agemaxpar);
4484: for (i=1; i<= nlstate ; i ++){
4485: if(i==1)
4486: fprintf(ficgp,"\"%s\"",subdirf2(fileres,"pij"));
4487: else
4488: fprintf(ficgp,", '' ");
1.154 brouard 4489: l=(nlstate+ndeath)*(i-1)+1;
4490: fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
1.153 brouard 4491: for (j=1; j<= (nlstate-1) ; j ++)
4492: fprintf(ficgp,"+$%d",k+l+j);
4493: fprintf(ficgp,")) t \"prev(%d,%d)\" w l",i,cpt);
4494: } /* nlstate */
4495: fprintf(ficgp,"\n");
4496: } /* end cpt state*/
4497: } /* end covariate */
1.126 brouard 4498:
4499: /* proba elementaires */
4500: for(i=1,jk=1; i <=nlstate; i++){
4501: for(k=1; k <=(nlstate+ndeath); k++){
4502: if (k != i) {
4503: for(j=1; j <=ncovmodel; j++){
4504: fprintf(ficgp,"p%d=%f ",jk,p[jk]);
4505: jk++;
4506: fprintf(ficgp,"\n");
4507: }
4508: }
4509: }
4510: }
1.145 brouard 4511: /*goto avoid;*/
1.126 brouard 4512: for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
4513: for(jk=1; jk <=m; jk++) {
1.145 brouard 4514: fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng);
1.126 brouard 4515: if (ng==2)
4516: fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
4517: else
4518: fprintf(ficgp,"\nset title \"Probability\"\n");
1.145 brouard 4519: fprintf(ficgp,"\nset ter png small size 320, 240\nset log y\nplot [%.f:%.f] ",ageminpar,agemaxpar);
1.126 brouard 4520: i=1;
4521: for(k2=1; k2<=nlstate; k2++) {
4522: k3=i;
4523: for(k=1; k<=(nlstate+ndeath); k++) {
4524: if (k != k2){
4525: if(ng==2)
4526: fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
4527: else
4528: fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
1.141 brouard 4529: ij=1;/* To be checked else nbcode[0][0] wrong */
1.126 brouard 4530: for(j=3; j <=ncovmodel; j++) {
1.145 brouard 4531: /* if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) { /\* Bug valgrind *\/ */
4532: /* /\*fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);*\/ */
4533: /* ij++; */
4534: /* } */
4535: /* else */
1.126 brouard 4536: fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
4537: }
4538: fprintf(ficgp,")/(1");
4539:
4540: for(k1=1; k1 <=nlstate; k1++){
4541: fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
4542: ij=1;
4543: for(j=3; j <=ncovmodel; j++){
1.145 brouard 4544: /* if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) { */
4545: /* fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]); */
4546: /* ij++; */
4547: /* } */
4548: /* else */
1.126 brouard 4549: fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
4550: }
4551: fprintf(ficgp,")");
4552: }
4553: fprintf(ficgp,") t \"p%d%d\" ", k2,k);
4554: if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
4555: i=i+ncovmodel;
4556: }
4557: } /* end k */
4558: } /* end k2 */
4559: } /* end jk */
4560: } /* end ng */
1.164 brouard 4561: /* avoid: */
1.126 brouard 4562: fflush(ficgp);
4563: } /* end gnuplot */
4564:
4565:
4566: /*************** Moving average **************/
4567: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
4568:
4569: int i, cpt, cptcod;
4570: int modcovmax =1;
4571: int mobilavrange, mob;
4572: double age;
4573:
4574: modcovmax=2*cptcoveff;/* Max number of modalities. We suppose
4575: a covariate has 2 modalities */
4576: if (cptcovn<1) modcovmax=1; /* At least 1 pass */
4577:
4578: if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
4579: if(mobilav==1) mobilavrange=5; /* default */
4580: else mobilavrange=mobilav;
4581: for (age=bage; age<=fage; age++)
4582: for (i=1; i<=nlstate;i++)
4583: for (cptcod=1;cptcod<=modcovmax;cptcod++)
4584: mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
4585: /* We keep the original values on the extreme ages bage, fage and for
4586: fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
4587: we use a 5 terms etc. until the borders are no more concerned.
4588: */
4589: for (mob=3;mob <=mobilavrange;mob=mob+2){
4590: for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
4591: for (i=1; i<=nlstate;i++){
4592: for (cptcod=1;cptcod<=modcovmax;cptcod++){
4593: mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
4594: for (cpt=1;cpt<=(mob-1)/2;cpt++){
4595: mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
4596: mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
4597: }
4598: mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
4599: }
4600: }
4601: }/* end age */
4602: }/* end mob */
4603: }else return -1;
4604: return 0;
4605: }/* End movingaverage */
4606:
4607:
4608: /************** Forecasting ******************/
1.169 brouard 4609: 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 4610: /* proj1, year, month, day of starting projection
4611: agemin, agemax range of age
4612: dateprev1 dateprev2 range of dates during which prevalence is computed
4613: anproj2 year of en of projection (same day and month as proj1).
4614: */
1.164 brouard 4615: int yearp, stepsize, hstepm, nhstepm, j, k, cptcod, i, h, i1;
1.126 brouard 4616: double agec; /* generic age */
4617: double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
4618: double *popeffectif,*popcount;
4619: double ***p3mat;
4620: double ***mobaverage;
4621: char fileresf[FILENAMELENGTH];
4622:
4623: agelim=AGESUP;
4624: prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
4625:
4626: strcpy(fileresf,"f");
4627: strcat(fileresf,fileres);
4628: if((ficresf=fopen(fileresf,"w"))==NULL) {
4629: printf("Problem with forecast resultfile: %s\n", fileresf);
4630: fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
4631: }
4632: printf("Computing forecasting: result on file '%s' \n", fileresf);
4633: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
4634:
4635: if (cptcoveff==0) ncodemax[cptcoveff]=1;
4636:
4637: if (mobilav!=0) {
4638: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4639: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
4640: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
4641: printf(" Error in movingaverage mobilav=%d\n",mobilav);
4642: }
4643: }
4644:
4645: stepsize=(int) (stepm+YEARM-1)/YEARM;
4646: if (stepm<=12) stepsize=1;
4647: if(estepm < stepm){
4648: printf ("Problem %d lower than %d\n",estepm, stepm);
4649: }
4650: else hstepm=estepm;
4651:
4652: hstepm=hstepm/stepm;
4653: yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp and
4654: fractional in yp1 */
4655: anprojmean=yp;
4656: yp2=modf((yp1*12),&yp);
4657: mprojmean=yp;
4658: yp1=modf((yp2*30.5),&yp);
4659: jprojmean=yp;
4660: if(jprojmean==0) jprojmean=1;
4661: if(mprojmean==0) jprojmean=1;
4662:
4663: i1=cptcoveff;
4664: if (cptcovn < 1){i1=1;}
4665:
4666: fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);
4667:
4668: fprintf(ficresf,"#****** Routine prevforecast **\n");
4669:
4670: /* if (h==(int)(YEARM*yearp)){ */
4671: for(cptcov=1, k=0;cptcov<=i1;cptcov++){
4672: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
4673: k=k+1;
4674: fprintf(ficresf,"\n#******");
4675: for(j=1;j<=cptcoveff;j++) {
4676: 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]]);
4677: }
4678: fprintf(ficresf,"******\n");
4679: fprintf(ficresf,"# Covariate valuofcovar yearproj age");
4680: for(j=1; j<=nlstate+ndeath;j++){
4681: for(i=1; i<=nlstate;i++)
4682: fprintf(ficresf," p%d%d",i,j);
4683: fprintf(ficresf," p.%d",j);
4684: }
4685: for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {
4686: fprintf(ficresf,"\n");
4687: fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);
4688:
4689: for (agec=fage; agec>=(ageminpar-1); agec--){
4690: nhstepm=(int) rint((agelim-agec)*YEARM/stepm);
4691: nhstepm = nhstepm/hstepm;
4692: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4693: oldm=oldms;savm=savms;
4694: hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);
4695:
4696: for (h=0; h<=nhstepm; h++){
4697: if (h*hstepm/YEARM*stepm ==yearp) {
4698: fprintf(ficresf,"\n");
4699: for(j=1;j<=cptcoveff;j++)
4700: fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4701: fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
4702: }
4703: for(j=1; j<=nlstate+ndeath;j++) {
4704: ppij=0.;
4705: for(i=1; i<=nlstate;i++) {
4706: if (mobilav==1)
4707: ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
4708: else {
4709: ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
4710: }
4711: if (h*hstepm/YEARM*stepm== yearp) {
4712: fprintf(ficresf," %.3f", p3mat[i][j][h]);
4713: }
4714: } /* end i */
4715: if (h*hstepm/YEARM*stepm==yearp) {
4716: fprintf(ficresf," %.3f", ppij);
4717: }
4718: }/* end j */
4719: } /* end h */
4720: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4721: } /* end agec */
4722: } /* end yearp */
4723: } /* end cptcod */
4724: } /* end cptcov */
4725:
4726: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4727:
4728: fclose(ficresf);
4729: }
4730:
4731: /************** Forecasting *****not tested NB*************/
1.169 brouard 4732: 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 4733:
4734: int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
4735: int *popage;
4736: double calagedatem, agelim, kk1, kk2;
4737: double *popeffectif,*popcount;
4738: double ***p3mat,***tabpop,***tabpopprev;
4739: double ***mobaverage;
4740: char filerespop[FILENAMELENGTH];
4741:
4742: tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4743: tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4744: agelim=AGESUP;
4745: calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
4746:
4747: prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
4748:
4749:
4750: strcpy(filerespop,"pop");
4751: strcat(filerespop,fileres);
4752: if((ficrespop=fopen(filerespop,"w"))==NULL) {
4753: printf("Problem with forecast resultfile: %s\n", filerespop);
4754: fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
4755: }
4756: printf("Computing forecasting: result on file '%s' \n", filerespop);
4757: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
4758:
4759: if (cptcoveff==0) ncodemax[cptcoveff]=1;
4760:
4761: if (mobilav!=0) {
4762: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4763: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
4764: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
4765: printf(" Error in movingaverage mobilav=%d\n",mobilav);
4766: }
4767: }
4768:
4769: stepsize=(int) (stepm+YEARM-1)/YEARM;
4770: if (stepm<=12) stepsize=1;
4771:
4772: agelim=AGESUP;
4773:
4774: hstepm=1;
4775: hstepm=hstepm/stepm;
4776:
4777: if (popforecast==1) {
4778: if((ficpop=fopen(popfile,"r"))==NULL) {
4779: printf("Problem with population file : %s\n",popfile);exit(0);
4780: fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
4781: }
4782: popage=ivector(0,AGESUP);
4783: popeffectif=vector(0,AGESUP);
4784: popcount=vector(0,AGESUP);
4785:
4786: i=1;
4787: while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
4788:
4789: imx=i;
4790: for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
4791: }
4792:
4793: for(cptcov=1,k=0;cptcov<=i2;cptcov++){
4794: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
4795: k=k+1;
4796: fprintf(ficrespop,"\n#******");
4797: for(j=1;j<=cptcoveff;j++) {
4798: fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4799: }
4800: fprintf(ficrespop,"******\n");
4801: fprintf(ficrespop,"# Age");
4802: for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
4803: if (popforecast==1) fprintf(ficrespop," [Population]");
4804:
4805: for (cpt=0; cpt<=0;cpt++) {
4806: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
4807:
4808: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
4809: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
4810: nhstepm = nhstepm/hstepm;
4811:
4812: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4813: oldm=oldms;savm=savms;
4814: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
4815:
4816: for (h=0; h<=nhstepm; h++){
4817: if (h==(int) (calagedatem+YEARM*cpt)) {
4818: fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
4819: }
4820: for(j=1; j<=nlstate+ndeath;j++) {
4821: kk1=0.;kk2=0;
4822: for(i=1; i<=nlstate;i++) {
4823: if (mobilav==1)
4824: kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
4825: else {
4826: kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
4827: }
4828: }
4829: if (h==(int)(calagedatem+12*cpt)){
4830: tabpop[(int)(agedeb)][j][cptcod]=kk1;
4831: /*fprintf(ficrespop," %.3f", kk1);
4832: if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
4833: }
4834: }
4835: for(i=1; i<=nlstate;i++){
4836: kk1=0.;
4837: for(j=1; j<=nlstate;j++){
4838: kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];
4839: }
4840: tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
4841: }
4842:
4843: if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++)
4844: fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
4845: }
4846: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4847: }
4848: }
4849:
4850: /******/
4851:
4852: for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {
4853: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
4854: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
4855: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
4856: nhstepm = nhstepm/hstepm;
4857:
4858: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4859: oldm=oldms;savm=savms;
4860: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
4861: for (h=0; h<=nhstepm; h++){
4862: if (h==(int) (calagedatem+YEARM*cpt)) {
4863: fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
4864: }
4865: for(j=1; j<=nlstate+ndeath;j++) {
4866: kk1=0.;kk2=0;
4867: for(i=1; i<=nlstate;i++) {
4868: kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];
4869: }
4870: if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);
4871: }
4872: }
4873: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4874: }
4875: }
4876: }
4877: }
4878:
4879: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4880:
4881: if (popforecast==1) {
4882: free_ivector(popage,0,AGESUP);
4883: free_vector(popeffectif,0,AGESUP);
4884: free_vector(popcount,0,AGESUP);
4885: }
4886: free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4887: free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4888: fclose(ficrespop);
4889: } /* End of popforecast */
4890:
4891: int fileappend(FILE *fichier, char *optionfich)
4892: {
4893: if((fichier=fopen(optionfich,"a"))==NULL) {
4894: printf("Problem with file: %s\n", optionfich);
4895: fprintf(ficlog,"Problem with file: %s\n", optionfich);
4896: return (0);
4897: }
4898: fflush(fichier);
4899: return (1);
4900: }
4901:
4902:
4903: /**************** function prwizard **********************/
4904: void prwizard(int ncovmodel, int nlstate, int ndeath, char model[], FILE *ficparo)
4905: {
4906:
4907: /* Wizard to print covariance matrix template */
4908:
1.164 brouard 4909: char ca[32], cb[32];
4910: int i,j, k, li, lj, lk, ll, jj, npar, itimes;
1.126 brouard 4911: int numlinepar;
4912:
4913: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
4914: fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
4915: for(i=1; i <=nlstate; i++){
4916: jj=0;
4917: for(j=1; j <=nlstate+ndeath; j++){
4918: if(j==i) continue;
4919: jj++;
4920: /*ca[0]= k+'a'-1;ca[1]='\0';*/
4921: printf("%1d%1d",i,j);
4922: fprintf(ficparo,"%1d%1d",i,j);
4923: for(k=1; k<=ncovmodel;k++){
4924: /* printf(" %lf",param[i][j][k]); */
4925: /* fprintf(ficparo," %lf",param[i][j][k]); */
4926: printf(" 0.");
4927: fprintf(ficparo," 0.");
4928: }
4929: printf("\n");
4930: fprintf(ficparo,"\n");
4931: }
4932: }
4933: printf("# Scales (for hessian or gradient estimation)\n");
4934: fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
4935: npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
4936: for(i=1; i <=nlstate; i++){
4937: jj=0;
4938: for(j=1; j <=nlstate+ndeath; j++){
4939: if(j==i) continue;
4940: jj++;
4941: fprintf(ficparo,"%1d%1d",i,j);
4942: printf("%1d%1d",i,j);
4943: fflush(stdout);
4944: for(k=1; k<=ncovmodel;k++){
4945: /* printf(" %le",delti3[i][j][k]); */
4946: /* fprintf(ficparo," %le",delti3[i][j][k]); */
4947: printf(" 0.");
4948: fprintf(ficparo," 0.");
4949: }
4950: numlinepar++;
4951: printf("\n");
4952: fprintf(ficparo,"\n");
4953: }
4954: }
4955: printf("# Covariance matrix\n");
4956: /* # 121 Var(a12)\n\ */
4957: /* # 122 Cov(b12,a12) Var(b12)\n\ */
4958: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
4959: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
4960: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
4961: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
4962: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
4963: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
4964: fflush(stdout);
4965: fprintf(ficparo,"# Covariance matrix\n");
4966: /* # 121 Var(a12)\n\ */
4967: /* # 122 Cov(b12,a12) Var(b12)\n\ */
4968: /* # ...\n\ */
4969: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
4970:
4971: for(itimes=1;itimes<=2;itimes++){
4972: jj=0;
4973: for(i=1; i <=nlstate; i++){
4974: for(j=1; j <=nlstate+ndeath; j++){
4975: if(j==i) continue;
4976: for(k=1; k<=ncovmodel;k++){
4977: jj++;
4978: ca[0]= k+'a'-1;ca[1]='\0';
4979: if(itimes==1){
4980: printf("#%1d%1d%d",i,j,k);
4981: fprintf(ficparo,"#%1d%1d%d",i,j,k);
4982: }else{
4983: printf("%1d%1d%d",i,j,k);
4984: fprintf(ficparo,"%1d%1d%d",i,j,k);
4985: /* printf(" %.5le",matcov[i][j]); */
4986: }
4987: ll=0;
4988: for(li=1;li <=nlstate; li++){
4989: for(lj=1;lj <=nlstate+ndeath; lj++){
4990: if(lj==li) continue;
4991: for(lk=1;lk<=ncovmodel;lk++){
4992: ll++;
4993: if(ll<=jj){
4994: cb[0]= lk +'a'-1;cb[1]='\0';
4995: if(ll<jj){
4996: if(itimes==1){
4997: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
4998: fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
4999: }else{
5000: printf(" 0.");
5001: fprintf(ficparo," 0.");
5002: }
5003: }else{
5004: if(itimes==1){
5005: printf(" Var(%s%1d%1d)",ca,i,j);
5006: fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
5007: }else{
5008: printf(" 0.");
5009: fprintf(ficparo," 0.");
5010: }
5011: }
5012: }
5013: } /* end lk */
5014: } /* end lj */
5015: } /* end li */
5016: printf("\n");
5017: fprintf(ficparo,"\n");
5018: numlinepar++;
5019: } /* end k*/
5020: } /*end j */
5021: } /* end i */
5022: } /* end itimes */
5023:
5024: } /* end of prwizard */
5025: /******************* Gompertz Likelihood ******************************/
5026: double gompertz(double x[])
5027: {
5028: double A,B,L=0.0,sump=0.,num=0.;
5029: int i,n=0; /* n is the size of the sample */
5030:
5031: for (i=0;i<=imx-1 ; i++) {
5032: sump=sump+weight[i];
5033: /* sump=sump+1;*/
5034: num=num+1;
5035: }
5036:
5037:
5038: /* for (i=0; i<=imx; i++)
5039: 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]);*/
5040:
5041: for (i=1;i<=imx ; i++)
5042: {
5043: if (cens[i] == 1 && wav[i]>1)
5044: A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
5045:
5046: if (cens[i] == 0 && wav[i]>1)
5047: A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
5048: +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);
5049:
5050: /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
5051: if (wav[i] > 1 ) { /* ??? */
5052: L=L+A*weight[i];
5053: /* 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]);*/
5054: }
5055: }
5056:
5057: /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
5058:
5059: return -2*L*num/sump;
5060: }
5061:
1.136 brouard 5062: #ifdef GSL
5063: /******************* Gompertz_f Likelihood ******************************/
5064: double gompertz_f(const gsl_vector *v, void *params)
5065: {
5066: double A,B,LL=0.0,sump=0.,num=0.;
5067: double *x= (double *) v->data;
5068: int i,n=0; /* n is the size of the sample */
5069:
5070: for (i=0;i<=imx-1 ; i++) {
5071: sump=sump+weight[i];
5072: /* sump=sump+1;*/
5073: num=num+1;
5074: }
5075:
5076:
5077: /* for (i=0; i<=imx; i++)
5078: 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]);*/
5079: printf("x[0]=%lf x[1]=%lf\n",x[0],x[1]);
5080: for (i=1;i<=imx ; i++)
5081: {
5082: if (cens[i] == 1 && wav[i]>1)
5083: A=-x[0]/(x[1])*(exp(x[1]*(agecens[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)));
5084:
5085: if (cens[i] == 0 && wav[i]>1)
5086: A=-x[0]/(x[1])*(exp(x[1]*(agedc[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)))
5087: +log(x[0]/YEARM)+x[1]*(agedc[i]-agegomp)+log(YEARM);
5088:
5089: /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
5090: if (wav[i] > 1 ) { /* ??? */
5091: LL=LL+A*weight[i];
5092: /* 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]);*/
5093: }
5094: }
5095:
5096: /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
5097: printf("x[0]=%lf x[1]=%lf -2*LL*num/sump=%lf\n",x[0],x[1],-2*LL*num/sump);
5098:
5099: return -2*LL*num/sump;
5100: }
5101: #endif
5102:
1.126 brouard 5103: /******************* Printing html file ***********/
5104: void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \
5105: int lastpass, int stepm, int weightopt, char model[],\
5106: int imx, double p[],double **matcov,double agemortsup){
5107: int i,k;
5108:
5109: fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
5110: fprintf(fichtm," mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
5111: for (i=1;i<=2;i++)
5112: 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]));
5113: fprintf(fichtm,"<br><br><img src=\"graphmort.png\">");
5114: fprintf(fichtm,"</ul>");
5115:
5116: fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
5117:
5118: 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>");
5119:
5120: for (k=agegomp;k<(agemortsup-2);k++)
5121: 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]);
5122:
5123:
5124: fflush(fichtm);
5125: }
5126:
5127: /******************* Gnuplot file **************/
5128: void printinggnuplotmort(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
5129:
5130: char dirfileres[132],optfileres[132];
1.164 brouard 5131:
1.126 brouard 5132: int ng;
5133:
5134:
5135: /*#ifdef windows */
5136: fprintf(ficgp,"cd \"%s\" \n",pathc);
5137: /*#endif */
5138:
5139:
5140: strcpy(dirfileres,optionfilefiname);
5141: strcpy(optfileres,"vpl");
5142: fprintf(ficgp,"set out \"graphmort.png\"\n ");
5143: fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n ");
1.145 brouard 5144: fprintf(ficgp, "set ter png small size 320, 240\n set log y\n");
5145: /* fprintf(ficgp, "set size 0.65,0.65\n"); */
1.126 brouard 5146: fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
5147:
5148: }
5149:
1.136 brouard 5150: int readdata(char datafile[], int firstobs, int lastobs, int *imax)
5151: {
1.126 brouard 5152:
1.136 brouard 5153: /*-------- data file ----------*/
5154: FILE *fic;
5155: char dummy[]=" ";
1.164 brouard 5156: int i=0, j=0, n=0;
1.136 brouard 5157: int linei, month, year,iout;
5158: char line[MAXLINE], linetmp[MAXLINE];
1.164 brouard 5159: char stra[MAXLINE], strb[MAXLINE];
1.136 brouard 5160: char *stratrunc;
5161: int lstra;
1.126 brouard 5162:
5163:
1.136 brouard 5164: if((fic=fopen(datafile,"r"))==NULL) {
5165: printf("Problem while opening datafile: %s\n", datafile);return 1;
5166: fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);return 1;
5167: }
1.126 brouard 5168:
1.136 brouard 5169: i=1;
5170: linei=0;
5171: while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
5172: linei=linei+1;
5173: for(j=strlen(line); j>=0;j--){ /* Untabifies line */
5174: if(line[j] == '\t')
5175: line[j] = ' ';
5176: }
5177: for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){
5178: ;
5179: };
5180: line[j+1]=0; /* Trims blanks at end of line */
5181: if(line[0]=='#'){
5182: fprintf(ficlog,"Comment line\n%s\n",line);
5183: printf("Comment line\n%s\n",line);
5184: continue;
5185: }
5186: trimbb(linetmp,line); /* Trims multiple blanks in line */
1.164 brouard 5187: strcpy(line, linetmp);
1.136 brouard 5188:
1.126 brouard 5189:
1.136 brouard 5190: for (j=maxwav;j>=1;j--){
1.137 brouard 5191: cutv(stra, strb, line, ' ');
1.136 brouard 5192: if(strb[0]=='.') { /* Missing status */
5193: lval=-1;
5194: }else{
5195: errno=0;
5196: lval=strtol(strb,&endptr,10);
5197: /* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
5198: if( strb[0]=='\0' || (*endptr != '\0')){
1.141 brouard 5199: 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);
5200: 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 5201: return 1;
5202: }
5203: }
5204: s[j][i]=lval;
5205:
5206: strcpy(line,stra);
5207: cutv(stra, strb,line,' ');
1.169 brouard 5208: if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
1.136 brouard 5209: }
1.169 brouard 5210: else if( (iout=sscanf(strb,"%s.",dummy)) != 0){
1.136 brouard 5211: month=99;
5212: year=9999;
5213: }else{
1.141 brouard 5214: 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);
5215: 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 5216: return 1;
5217: }
5218: anint[j][i]= (double) year;
5219: mint[j][i]= (double)month;
5220: strcpy(line,stra);
5221: } /* ENd Waves */
5222:
5223: cutv(stra, strb,line,' ');
1.169 brouard 5224: if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
1.136 brouard 5225: }
1.169 brouard 5226: else if( (iout=sscanf(strb,"%s.",dummy)) != 0){
1.136 brouard 5227: month=99;
5228: year=9999;
5229: }else{
1.141 brouard 5230: 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);
5231: 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 5232: return 1;
5233: }
5234: andc[i]=(double) year;
5235: moisdc[i]=(double) month;
5236: strcpy(line,stra);
5237:
5238: cutv(stra, strb,line,' ');
1.169 brouard 5239: if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
1.136 brouard 5240: }
1.169 brouard 5241: else if( (iout=sscanf(strb,"%s.", dummy)) != 0){
1.136 brouard 5242: month=99;
5243: year=9999;
5244: }else{
1.141 brouard 5245: 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);
5246: 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 5247: return 1;
5248: }
5249: if (year==9999) {
1.141 brouard 5250: 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);
5251: 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 5252: return 1;
1.126 brouard 5253:
1.136 brouard 5254: }
5255: annais[i]=(double)(year);
5256: moisnais[i]=(double)(month);
5257: strcpy(line,stra);
5258:
5259: cutv(stra, strb,line,' ');
5260: errno=0;
5261: dval=strtod(strb,&endptr);
5262: if( strb[0]=='\0' || (*endptr != '\0')){
1.141 brouard 5263: printf("Error reading data around '%f' at line number %d, \"%s\" for individual %d\nShould be a weight. Exiting.\n",dval, i,line,linei);
5264: 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 5265: fflush(ficlog);
5266: return 1;
5267: }
5268: weight[i]=dval;
5269: strcpy(line,stra);
5270:
5271: for (j=ncovcol;j>=1;j--){
5272: cutv(stra, strb,line,' ');
5273: if(strb[0]=='.') { /* Missing status */
5274: lval=-1;
5275: }else{
5276: errno=0;
5277: lval=strtol(strb,&endptr,10);
5278: if( strb[0]=='\0' || (*endptr != '\0')){
1.141 brouard 5279: 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);
5280: 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 5281: return 1;
5282: }
5283: }
5284: if(lval <-1 || lval >1){
1.141 brouard 5285: printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
1.136 brouard 5286: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
5287: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
5288: For example, for multinomial values like 1, 2 and 3,\n \
5289: build V1=0 V2=0 for the reference value (1),\n \
5290: V1=1 V2=0 for (2) \n \
5291: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
5292: output of IMaCh is often meaningless.\n \
5293: Exiting.\n",lval,linei, i,line,j);
1.141 brouard 5294: fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
1.136 brouard 5295: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
5296: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
5297: For example, for multinomial values like 1, 2 and 3,\n \
5298: build V1=0 V2=0 for the reference value (1),\n \
5299: V1=1 V2=0 for (2) \n \
5300: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
5301: output of IMaCh is often meaningless.\n \
5302: Exiting.\n",lval,linei, i,line,j);fflush(ficlog);
5303: return 1;
5304: }
5305: covar[j][i]=(double)(lval);
5306: strcpy(line,stra);
5307: }
5308: lstra=strlen(stra);
5309:
5310: if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
5311: stratrunc = &(stra[lstra-9]);
5312: num[i]=atol(stratrunc);
5313: }
5314: else
5315: num[i]=atol(stra);
5316: /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
5317: 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;}*/
5318:
5319: i=i+1;
5320: } /* End loop reading data */
1.126 brouard 5321:
1.136 brouard 5322: *imax=i-1; /* Number of individuals */
5323: fclose(fic);
5324:
5325: return (0);
1.164 brouard 5326: /* endread: */
1.136 brouard 5327: printf("Exiting readdata: ");
5328: fclose(fic);
5329: return (1);
1.126 brouard 5330:
5331:
5332:
1.136 brouard 5333: }
1.145 brouard 5334: void removespace(char *str) {
5335: char *p1 = str, *p2 = str;
5336: do
5337: while (*p2 == ' ')
5338: p2++;
1.169 brouard 5339: while (*p1++ == *p2++);
1.145 brouard 5340: }
5341:
5342: int decodemodel ( char model[], int lastobs) /**< This routine decode the model and returns:
5343: * Model V1+V2+V3+V8+V7*V8+V5*V6+V8*age+V3*age
5344: * - cptcovt total number of covariates of the model nbocc(+)+1 = 8
5345: * - cptcovn or number of covariates k of the models excluding age*products =6
5346: * - cptcovage number of covariates with age*products =2
5347: * - cptcovs number of simple covariates
5348: * - 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
5349: * which is a new column after the 9 (ncovcol) variables.
5350: * - if k is a product Vn*Vm covar[k][i] is filled with correct values for each individual
5351: * - Tprod[l] gives the kth covariates of the product Vn*Vm l=1 to cptcovprod-cptcovage
5352: * Tprod[1]@2 {5, 6}: position of first product V7*V8 is 5, and second V5*V6 is 6.
5353: * - Tvard[k] p Tvard[1][1]@4 {7, 8, 5, 6} for V7*V8 and V5*V6 .
5354: */
1.136 brouard 5355: {
1.145 brouard 5356: int i, j, k, ks;
1.164 brouard 5357: int j1, k1, k2;
1.136 brouard 5358: char modelsav[80];
1.145 brouard 5359: char stra[80], strb[80], strc[80], strd[80],stre[80];
1.136 brouard 5360:
1.145 brouard 5361: /*removespace(model);*/
1.136 brouard 5362: if (strlen(model) >1){ /* If there is at least 1 covariate */
1.145 brouard 5363: j=0, j1=0, k1=0, k2=-1, ks=0, cptcovn=0;
5364: j=nbocc(model,'+'); /**< j=Number of '+' */
5365: j1=nbocc(model,'*'); /**< j1=Number of '*' */
5366: cptcovs=j+1-j1; /**< Number of simple covariates V1+V2*age+V3 +V3*V4=> V1 + V3 =2 */
5367: cptcovt= j+1; /* Number of total covariates in the model V1 + V2*age+ V3 + V3*V4=> 4*/
5368: /* including age products which are counted in cptcovage.
1.169 brouard 5369: * but the covariates which are products must be treated separately: ncovn=4- 2=2 (V1+V3). */
1.145 brouard 5370: cptcovprod=j1; /**< Number of products V1*V2 +v3*age = 2 */
5371: cptcovprodnoage=0; /**< Number of covariate products without age: V3*V4 =1 */
1.136 brouard 5372: strcpy(modelsav,model);
1.137 brouard 5373: if (strstr(model,"AGE") !=0){
5374: printf("Error. AGE must be in lower case 'age' model=%s ",model);
5375: fprintf(ficlog,"Error. AGE must be in lower case model=%s ",model);fflush(ficlog);
1.136 brouard 5376: return 1;
5377: }
1.141 brouard 5378: if (strstr(model,"v") !=0){
5379: printf("Error. 'v' must be in upper case 'V' model=%s ",model);
5380: fprintf(ficlog,"Error. 'v' must be in upper case model=%s ",model);fflush(ficlog);
5381: return 1;
5382: }
1.136 brouard 5383:
1.145 brouard 5384: /* Design
5385: * V1 V2 V3 V4 V5 V6 V7 V8 V9 Weight
5386: * < ncovcol=8 >
5387: * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8
5388: * k= 1 2 3 4 5 6 7 8
5389: * cptcovn number of covariates (not including constant and age ) = # of + plus 1 = 7+1=8
5390: * covar[k,i], value of kth covariate if not including age for individual i:
5391: * covar[1][i]= (V2), covar[4][i]=(V3), covar[8][i]=(V8)
5392: * Tvar[k] # of the kth covariate: Tvar[1]=2 Tvar[4]=3 Tvar[8]=8
5393: * if multiplied by age: V3*age Tvar[3=V3*age]=3 (V3) Tvar[7]=8 and
5394: * Tage[++cptcovage]=k
5395: * if products, new covar are created after ncovcol with k1
5396: * Tvar[k]=ncovcol+k1; # of the kth covariate product: Tvar[5]=ncovcol+1=10 Tvar[6]=ncovcol+1=11
5397: * Tprod[k1]=k; Tprod[1]=5 Tprod[2]= 6; gives the position of the k1th product
5398: * 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
5399: * Tvar[cptcovn+k2]=Tvard[k1][1];Tvar[cptcovn+k2+1]=Tvard[k1][2];
5400: * Tvar[8+1]=5;Tvar[8+2]=6;Tvar[8+3]=7;Tvar[8+4]=8 inverted
5401: * V1 V2 V3 V4 V5 V6 V7 V8 V9 V10 V11
5402: * < ncovcol=8 >
5403: * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8 d1 d1 d2 d2
5404: * k= 1 2 3 4 5 6 7 8 9 10 11 12
5405: * Tvar[k]= 2 1 3 3 10 11 8 8 5 6 7 8
5406: * p Tvar[1]@12={2, 1, 3, 3, 11, 10, 8, 8, 7, 8, 5, 6}
5407: * p Tprod[1]@2={ 6, 5}
5408: *p Tvard[1][1]@4= {7, 8, 5, 6}
5409: * covar[k][i]= V2 V1 ? V3 V5*V6? V7*V8? ? V8
5410: * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
5411: *How to reorganize?
5412: * Model V1 + V2 + V3 + V8 + V5*V6 + V7*V8 + V3*age + V8*age
5413: * Tvars {2, 1, 3, 3, 11, 10, 8, 8, 7, 8, 5, 6}
5414: * {2, 1, 4, 8, 5, 6, 3, 7}
5415: * Struct []
5416: */
5417:
1.136 brouard 5418: /* This loop fills the array Tvar from the string 'model'.*/
5419: /* j is the number of + signs in the model V1+V2+V3 j=2 i=3 to 1 */
1.137 brouard 5420: /* modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4 */
5421: /* k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tage[cptcovage=1]=4 */
5422: /* k=3 V4 Tvar[k=3]= 4 (from V4) */
5423: /* k=2 V1 Tvar[k=2]= 1 (from V1) */
5424: /* k=1 Tvar[1]=2 (from V2) */
5425: /* k=5 Tvar[5] */
5426: /* for (k=1; k<=cptcovn;k++) { */
5427: /* cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]]; */
5428: /* } */
5429: /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
1.145 brouard 5430: /*
5431: * Treating invertedly V2+V1+V3*age+V2*V4 is as if written V2*V4 +V3*age + V1 + V2 */
5432: for(k=cptcovt; k>=1;k--) /**< Number of covariates */
5433: Tvar[k]=0;
5434: cptcovage=0;
5435: for(k=1; k<=cptcovt;k++){ /* Loop on total covariates of the model */
5436: cutl(stra,strb,modelsav,'+'); /* keeps in strb after the first '+'
5437: modelsav==V2+V1+V4+V3*age strb=V3*age stra=V2+V1+V4 */
1.137 brouard 5438: if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
1.136 brouard 5439: /* printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
5440: /*scanf("%d",i);*/
1.145 brouard 5441: if (strchr(strb,'*')) { /**< Model includes a product V2+V1+V4+V3*age strb=V3*age */
5442: cutl(strc,strd,strb,'*'); /**< strd*strc Vm*Vn: strb=V3*age(input) strc=age strd=V3 ; V3*V2 strc=V2, strd=V3 */
5443: if (strcmp(strc,"age")==0) { /**< Model includes age: Vn*age */
5444: /* covar is not filled and then is empty */
1.136 brouard 5445: cptcovprod--;
1.145 brouard 5446: cutl(stre,strb,strd,'V'); /* strd=V3(input): stre="3" */
5447: Tvar[k]=atoi(stre); /* V2+V1+V4+V3*age Tvar[4]=3 ; V1+V2*age Tvar[2]=2 */
1.136 brouard 5448: cptcovage++; /* Sums the number of covariates which include age as a product */
1.137 brouard 5449: Tage[cptcovage]=k; /* Tage[1] = 4 */
1.136 brouard 5450: /*printf("stre=%s ", stre);*/
1.137 brouard 5451: } else if (strcmp(strd,"age")==0) { /* or age*Vn */
1.136 brouard 5452: cptcovprod--;
1.145 brouard 5453: cutl(stre,strb,strc,'V');
1.136 brouard 5454: Tvar[k]=atoi(stre);
5455: cptcovage++;
5456: Tage[cptcovage]=k;
1.137 brouard 5457: } else { /* Age is not in the model product V2+V1+V1*V4+V3*age+V3*V2 strb=V3*V2*/
5458: /* loops on k1=1 (V3*V2) and k1=2 V4*V3 */
1.145 brouard 5459: cptcovn++;
5460: cptcovprodnoage++;k1++;
5461: cutl(stre,strb,strc,'V'); /* strc= Vn, stre is n; strb=V3*V2 stre=3 strc=*/
5462: Tvar[k]=ncovcol+k1; /* For model-covariate k tells which data-covariate to use but
1.137 brouard 5463: because this model-covariate is a construction we invent a new column
5464: ncovcol + k1
5465: If already ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2
5466: Tvar[3=V1*V4]=4+1 Tvar[5=V3*V2]=4 + 2= 6, etc */
1.145 brouard 5467: cutl(strc,strb,strd,'V'); /* strd was Vm, strc is m */
1.137 brouard 5468: Tprod[k1]=k; /* Tprod[1]=3(=V1*V4) for V2+V1+V1*V4+age*V3+V3*V2 */
1.145 brouard 5469: Tvard[k1][1] =atoi(strc); /* m 1 for V1*/
5470: Tvard[k1][2] =atoi(stre); /* n 4 for V4*/
5471: k2=k2+2;
5472: Tvar[cptcovt+k2]=Tvard[k1][1]; /* Tvar[(cptcovt=4+k2=1)=5]= 1 (V1) */
5473: Tvar[cptcovt+k2+1]=Tvard[k1][2]; /* Tvar[(cptcovt=4+(k2=1)+1)=6]= 4 (V4) */
1.137 brouard 5474: for (i=1; i<=lastobs;i++){
5475: /* Computes the new covariate which is a product of
1.145 brouard 5476: covar[n][i]* covar[m][i] and stores it at ncovol+k1 May not be defined */
1.136 brouard 5477: covar[ncovcol+k1][i]=covar[atoi(stre)][i]*covar[atoi(strc)][i];
1.137 brouard 5478: }
5479: } /* End age is not in the model */
5480: } /* End if model includes a product */
1.136 brouard 5481: else { /* no more sum */
5482: /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
5483: /* scanf("%d",i);*/
1.145 brouard 5484: cutl(strd,strc,strb,'V');
5485: ks++; /**< Number of simple covariates */
5486: cptcovn++;
5487: Tvar[k]=atoi(strd);
1.136 brouard 5488: }
1.137 brouard 5489: strcpy(modelsav,stra); /* modelsav=V2+V1+V4 stra=V2+V1+V4 */
1.136 brouard 5490: /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
5491: scanf("%d",i);*/
5492: } /* end of loop + */
5493: } /* end model */
5494:
5495: /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
5496: If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
5497:
5498: /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
5499: printf("cptcovprod=%d ", cptcovprod);
5500: fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
5501:
5502: scanf("%d ",i);*/
5503:
5504:
1.137 brouard 5505: return (0); /* with covar[new additional covariate if product] and Tage if age */
1.164 brouard 5506: /*endread:*/
1.136 brouard 5507: printf("Exiting decodemodel: ");
5508: return (1);
5509: }
5510:
1.169 brouard 5511: int calandcheckages(int imx, int maxwav, double *agemin, double *agemax, int *nberr, int *nbwarn )
1.136 brouard 5512: {
5513: int i, m;
5514:
5515: for (i=1; i<=imx; i++) {
5516: for(m=2; (m<= maxwav); m++) {
5517: if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
5518: anint[m][i]=9999;
5519: s[m][i]=-1;
5520: }
5521: if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
1.169 brouard 5522: *nberr = *nberr + 1;
5523: 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);
5524: 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 5525: s[m][i]=-1;
5526: }
5527: if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
1.169 brouard 5528: (*nberr)++;
1.136 brouard 5529: 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]);
5530: 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]);
5531: s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
5532: }
5533: }
5534: }
5535:
5536: for (i=1; i<=imx; i++) {
5537: agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
5538: for(m=firstpass; (m<= lastpass); m++){
5539: if(s[m][i] >0 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){
5540: if (s[m][i] >= nlstate+1) {
1.169 brouard 5541: if(agedc[i]>0){
5542: if((int)moisdc[i]!=99 && (int)andc[i]!=9999){
1.136 brouard 5543: agev[m][i]=agedc[i];
5544: /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
1.169 brouard 5545: }else {
1.136 brouard 5546: if ((int)andc[i]!=9999){
5547: nbwarn++;
5548: printf("Warning negative age at death: %ld line:%d\n",num[i],i);
5549: fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
5550: agev[m][i]=-1;
5551: }
5552: }
1.169 brouard 5553: } /* agedc > 0 */
1.136 brouard 5554: }
5555: else if(s[m][i] !=9){ /* Standard case, age in fractional
5556: years but with the precision of a month */
5557: agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
5558: if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
5559: agev[m][i]=1;
5560: else if(agev[m][i] < *agemin){
5561: *agemin=agev[m][i];
5562: printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], *agemin);
5563: }
5564: else if(agev[m][i] >*agemax){
5565: *agemax=agev[m][i];
1.156 brouard 5566: /* printf(" Max anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.2f\n",m,i,anint[m][i], i,annais[i], *agemax);*/
1.136 brouard 5567: }
5568: /*agev[m][i]=anint[m][i]-annais[i];*/
5569: /* agev[m][i] = age[i]+2*m;*/
5570: }
5571: else { /* =9 */
5572: agev[m][i]=1;
5573: s[m][i]=-1;
5574: }
5575: }
5576: else /*= 0 Unknown */
5577: agev[m][i]=1;
5578: }
5579:
5580: }
5581: for (i=1; i<=imx; i++) {
5582: for(m=firstpass; (m<=lastpass); m++){
5583: if (s[m][i] > (nlstate+ndeath)) {
1.169 brouard 5584: (*nberr)++;
1.136 brouard 5585: 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);
5586: 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);
5587: return 1;
5588: }
5589: }
5590: }
5591:
5592: /*for (i=1; i<=imx; i++){
5593: for (m=firstpass; (m<lastpass); m++){
5594: printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
5595: }
5596:
5597: }*/
5598:
5599:
1.139 brouard 5600: printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
5601: fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
1.136 brouard 5602:
5603: return (0);
1.164 brouard 5604: /* endread:*/
1.136 brouard 5605: printf("Exiting calandcheckages: ");
5606: return (1);
5607: }
5608:
1.172 brouard 5609: #if defined(_MSC_VER)
5610: /*printf("Visual C++ compiler: %s \n;", _MSC_FULL_VER);*/
5611: /*fprintf(ficlog, "Visual C++ compiler: %s \n;", _MSC_FULL_VER);*/
5612: //#include "stdafx.h"
5613: //#include <stdio.h>
5614: //#include <tchar.h>
5615: //#include <windows.h>
5616: //#include <iostream>
5617: typedef BOOL(WINAPI *LPFN_ISWOW64PROCESS) (HANDLE, PBOOL);
5618:
5619: LPFN_ISWOW64PROCESS fnIsWow64Process;
5620:
5621: BOOL IsWow64()
5622: {
5623: BOOL bIsWow64 = FALSE;
5624:
5625: //typedef BOOL (APIENTRY *LPFN_ISWOW64PROCESS)
5626: // (HANDLE, PBOOL);
5627:
5628: //LPFN_ISWOW64PROCESS fnIsWow64Process;
5629:
5630: HMODULE module = GetModuleHandle(_T("kernel32"));
5631: const char funcName[] = "IsWow64Process";
5632: fnIsWow64Process = (LPFN_ISWOW64PROCESS)
5633: GetProcAddress(module, funcName);
5634:
5635: if (NULL != fnIsWow64Process)
5636: {
5637: if (!fnIsWow64Process(GetCurrentProcess(),
5638: &bIsWow64))
5639: //throw std::exception("Unknown error");
5640: printf("Unknown error\n");
5641: }
5642: return bIsWow64 != FALSE;
5643: }
5644: #endif
1.177 brouard 5645:
1.169 brouard 5646: void syscompilerinfo()
1.167 brouard 5647: {
5648: /* #include "syscompilerinfo.h"*/
1.185 ! brouard 5649: /* command line Intel compiler 32bit windows, XP compatible:*/
! 5650: /* /GS /W3 /Gy
! 5651: /Zc:wchar_t /Zi /O2 /Fd"Release\vc120.pdb" /D "WIN32" /D "NDEBUG" /D
! 5652: "_CONSOLE" /D "_LIB" /D "_USING_V110_SDK71_" /D "_UNICODE" /D
! 5653: "UNICODE" /Qipo /Zc:forScope /Gd /Oi /MT /Fa"Release\" /EHsc /nologo
! 5654: /Fo"Release\" /Qprof-dir "Release\" /Fp"Release\IMaCh.pch"
! 5655: /* 64 bits */
! 5656: /*
! 5657: /GS /W3 /Gy
! 5658: /Zc:wchar_t /Zi /O2 /Fd"x64\Release\vc120.pdb" /D "WIN32" /D "NDEBUG"
! 5659: /D "_CONSOLE" /D "_LIB" /D "_UNICODE" /D "UNICODE" /Qipo /Zc:forScope
! 5660: /Oi /MD /Fa"x64\Release\" /EHsc /nologo /Fo"x64\Release\" /Qprof-dir
! 5661: "x64\Release\" /Fp"x64\Release\IMaCh.pch" */
! 5662: /* Optimization are useless and O3 is slower than O2 */
! 5663: /*
! 5664: /GS /W3 /Gy /Zc:wchar_t /Zi /O3 /Fd"x64\Release\vc120.pdb" /D "WIN32"
! 5665: /D "NDEBUG" /D "_CONSOLE" /D "_LIB" /D "_UNICODE" /D "UNICODE" /Qipo
! 5666: /Zc:forScope /Oi /MD /Fa"x64\Release\" /EHsc /nologo /Qparallel
! 5667: /Fo"x64\Release\" /Qprof-dir "x64\Release\" /Fp"x64\Release\IMaCh.pch"
! 5668: */
! 5669: /* Link is $/ /* /OUT:"visual studio
! 5670: 2013\Projects\IMaCh\Release\IMaCh.exe" /MANIFEST /NXCOMPAT
! 5671: /PDB:"visual studio
! 5672: 2013\Projects\IMaCh\Release\IMaCh.pdb" /DYNAMICBASE
! 5673: "kernel32.lib" "user32.lib" "gdi32.lib" "winspool.lib"
! 5674: "comdlg32.lib" "advapi32.lib" "shell32.lib" "ole32.lib"
! 5675: "oleaut32.lib" "uuid.lib" "odbc32.lib" "odbccp32.lib"
! 5676: /MACHINE:X86 /OPT:REF /SAFESEH /INCREMENTAL:NO
! 5677: /SUBSYSTEM:CONSOLE",5.01" /MANIFESTUAC:"level='asInvoker'
! 5678: uiAccess='false'"
! 5679: /ManifestFile:"Release\IMaCh.exe.intermediate.manifest" /OPT:ICF
! 5680: /NOLOGO /TLBID:1
! 5681: */
1.177 brouard 5682: #if defined __INTEL_COMPILER
1.178 brouard 5683: #if defined(__GNUC__)
5684: struct utsname sysInfo; /* For Intel on Linux and OS/X */
5685: #endif
1.177 brouard 5686: #elif defined(__GNUC__)
1.179 brouard 5687: #ifndef __APPLE__
1.174 brouard 5688: #include <gnu/libc-version.h> /* Only on gnu */
1.179 brouard 5689: #endif
1.177 brouard 5690: struct utsname sysInfo;
1.178 brouard 5691: int cross = CROSS;
5692: if (cross){
5693: printf("Cross-");
5694: fprintf(ficlog, "Cross-");
5695: }
1.174 brouard 5696: #endif
5697:
1.171 brouard 5698: #include <stdint.h>
1.178 brouard 5699:
1.169 brouard 5700: printf("Compiled with:");fprintf(ficlog,"Compiled with:");
5701: #if defined(__clang__)
5702: printf(" Clang/LLVM");fprintf(ficlog," Clang/LLVM"); /* Clang/LLVM. ---------------------------------------------- */
5703: #endif
5704: #if defined(__ICC) || defined(__INTEL_COMPILER)
5705: printf(" Intel ICC/ICPC");fprintf(ficlog," Intel ICC/ICPC");/* Intel ICC/ICPC. ------------------------------------------ */
5706: #endif
5707: #if defined(__GNUC__) || defined(__GNUG__)
5708: printf(" GNU GCC/G++");fprintf(ficlog," GNU GCC/G++");/* GNU GCC/G++. --------------------------------------------- */
5709: #endif
5710: #if defined(__HP_cc) || defined(__HP_aCC)
5711: printf(" Hewlett-Packard C/aC++");fprintf(fcilog," Hewlett-Packard C/aC++"); /* Hewlett-Packard C/aC++. ---------------------------------- */
5712: #endif
5713: #if defined(__IBMC__) || defined(__IBMCPP__)
5714: printf(" IBM XL C/C++"); fprintf(ficlog," IBM XL C/C++");/* IBM XL C/C++. -------------------------------------------- */
5715: #endif
5716: #if defined(_MSC_VER)
5717: printf(" Microsoft Visual Studio");fprintf(ficlog," Microsoft Visual Studio");/* Microsoft Visual Studio. --------------------------------- */
5718: #endif
5719: #if defined(__PGI)
5720: printf(" Portland Group PGCC/PGCPP");fprintf(ficlog," Portland Group PGCC/PGCPP");/* Portland Group PGCC/PGCPP. ------------------------------- */
5721: #endif
5722: #if defined(__SUNPRO_C) || defined(__SUNPRO_CC)
5723: printf(" Oracle Solaris Studio");fprintf(ficlog," Oracle Solaris Studio\n");/* Oracle Solaris Studio. ----------------------------------- */
1.167 brouard 5724: #endif
1.174 brouard 5725: printf(" for ");fprintf(ficlog," for ");
1.169 brouard 5726:
1.167 brouard 5727: // http://stackoverflow.com/questions/4605842/how-to-identify-platform-compiler-from-preprocessor-macros
5728: #ifdef _WIN32 // note the underscore: without it, it's not msdn official!
5729: // Windows (x64 and x86)
1.174 brouard 5730: printf("Windows (x64 and x86) ");fprintf(ficlog,"Windows (x64 and x86) ");
1.167 brouard 5731: #elif __unix__ // all unices, not all compilers
5732: // Unix
1.174 brouard 5733: printf("Unix ");fprintf(ficlog,"Unix ");
1.167 brouard 5734: #elif __linux__
5735: // linux
1.174 brouard 5736: printf("linux ");fprintf(ficlog,"linux ");
1.167 brouard 5737: #elif __APPLE__
1.174 brouard 5738: // Mac OS, not sure if this is covered by __posix__ and/or __unix__ though..
5739: printf("Mac OS ");fprintf(ficlog,"Mac OS ");
1.167 brouard 5740: #endif
5741:
5742: /* __MINGW32__ */
5743: /* __CYGWIN__ */
5744: /* __MINGW64__ */
5745: // http://msdn.microsoft.com/en-us/library/b0084kay.aspx
5746: /* _MSC_VER //the Visual C++ compiler is 17.00.51106.1, the _MSC_VER macro evaluates to 1700. Type cl /? */
5747: /* _MSC_FULL_VER //the Visual C++ compiler is 15.00.20706.01, the _MSC_FULL_VER macro evaluates to 150020706 */
5748: /* _WIN64 // Defined for applications for Win64. */
5749: /* _M_X64 // Defined for compilations that target x64 processors. */
5750: /* _DEBUG // Defined when you compile with /LDd, /MDd, and /MTd. */
1.171 brouard 5751:
1.167 brouard 5752: #if UINTPTR_MAX == 0xffffffff
1.174 brouard 5753: printf(" 32-bit"); fprintf(ficlog," 32-bit");/* 32-bit */
1.167 brouard 5754: #elif UINTPTR_MAX == 0xffffffffffffffff
1.174 brouard 5755: printf(" 64-bit"); fprintf(ficlog," 64-bit");/* 64-bit */
1.167 brouard 5756: #else
1.174 brouard 5757: printf(" wtf-bit"); fprintf(ficlog," wtf-bit");/* wtf */
1.167 brouard 5758: #endif
5759:
1.169 brouard 5760: #if defined(__GNUC__)
5761: # if defined(__GNUC_PATCHLEVEL__)
5762: # define __GNUC_VERSION__ (__GNUC__ * 10000 \
5763: + __GNUC_MINOR__ * 100 \
5764: + __GNUC_PATCHLEVEL__)
5765: # else
5766: # define __GNUC_VERSION__ (__GNUC__ * 10000 \
5767: + __GNUC_MINOR__ * 100)
5768: # endif
1.174 brouard 5769: printf(" using GNU C version %d.\n", __GNUC_VERSION__);
5770: fprintf(ficlog, " using GNU C version %d.\n", __GNUC_VERSION__);
1.176 brouard 5771:
5772: if (uname(&sysInfo) != -1) {
5773: printf("Running on: %s %s %s %s %s\n",sysInfo.sysname, sysInfo.nodename, sysInfo.release, sysInfo.version, sysInfo.machine);
5774: fprintf(ficlog,"Running on: %s %s %s %s %s\n ",sysInfo.sysname, sysInfo.nodename, sysInfo.release, sysInfo.version, sysInfo.machine);
5775: }
5776: else
5777: perror("uname() error");
1.179 brouard 5778: //#ifndef __INTEL_COMPILER
5779: #if !defined (__INTEL_COMPILER) && !defined(__APPLE__)
1.174 brouard 5780: printf("GNU libc version: %s\n", gnu_get_libc_version());
1.179 brouard 5781: fprintf(ficlog,"GNU libc version: %s\n", gnu_get_libc_version());
1.177 brouard 5782: #endif
1.169 brouard 5783: #endif
1.172 brouard 5784:
5785: // void main()
5786: // {
1.169 brouard 5787: #if defined(_MSC_VER)
1.174 brouard 5788: if (IsWow64()){
1.176 brouard 5789: printf("The program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n");
5790: fprintf(ficlog, "The program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n");
1.174 brouard 5791: }
5792: else{
1.176 brouard 5793: printf("The process is not running under WOW64 (i.e probably on a 64bit Windows).\n");
1.178 brouard 5794: fprintf(ficlog,"The programm is not running under WOW64 (i.e probably on a 64bit Windows).\n");
1.174 brouard 5795: }
1.172 brouard 5796: // printf("\nPress Enter to continue...");
5797: // getchar();
5798: // }
5799:
1.169 brouard 5800: #endif
5801:
1.167 brouard 5802:
5803: }
1.136 brouard 5804:
1.180 brouard 5805: int prevalence_limit(double *p, double **prlim, double ageminpar, double agemaxpar){
5806: /*--------------- Prevalence limit (period or stable prevalence) --------------*/
5807: int i, j, k, i1 ;
5808: double ftolpl = 1.e-10;
5809: double age, agebase, agelim;
5810:
5811: strcpy(filerespl,"pl");
5812: strcat(filerespl,fileres);
5813: if((ficrespl=fopen(filerespl,"w"))==NULL) {
5814: printf("Problem with period (stable) prevalence resultfile: %s\n", filerespl);return 1;
5815: fprintf(ficlog,"Problem with period (stable) prevalence resultfile: %s\n", filerespl);return 1;
5816: }
5817: printf("Computing period (stable) prevalence: result on file '%s' \n", filerespl);
5818: fprintf(ficlog,"Computing period (stable) prevalence: result on file '%s' \n", filerespl);
5819: pstamp(ficrespl);
5820: fprintf(ficrespl,"# Period (stable) prevalence \n");
5821: fprintf(ficrespl,"#Age ");
5822: for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
5823: fprintf(ficrespl,"\n");
5824:
5825: /* prlim=matrix(1,nlstate,1,nlstate);*/ /* back in main */
5826:
5827: agebase=ageminpar;
5828: agelim=agemaxpar;
5829:
5830: i1=pow(2,cptcoveff);
5831: if (cptcovn < 1){i1=1;}
5832:
5833: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
5834: /* for(cptcov=1,k=0;cptcov<=1;cptcov++){ */
5835: //for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
5836: k=k+1;
5837: /* to clean */
5838: //printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtab[cptcod][cptcov]);
5839: fprintf(ficrespl,"\n#******");
5840: printf("\n#******");
5841: fprintf(ficlog,"\n#******");
5842: for(j=1;j<=cptcoveff;j++) {
5843: fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5844: printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5845: fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5846: }
5847: fprintf(ficrespl,"******\n");
5848: printf("******\n");
5849: fprintf(ficlog,"******\n");
5850:
5851: fprintf(ficrespl,"#Age ");
5852: for(j=1;j<=cptcoveff;j++) {
5853: fprintf(ficrespl,"V%d %d",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5854: }
5855: for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
5856: fprintf(ficrespl,"\n");
5857:
5858: for (age=agebase; age<=agelim; age++){
5859: /* for (age=agebase; age<=agebase; age++){ */
5860: prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
5861: fprintf(ficrespl,"%.0f ",age );
5862: for(j=1;j<=cptcoveff;j++)
5863: fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5864: for(i=1; i<=nlstate;i++)
5865: fprintf(ficrespl," %.5f", prlim[i][i]);
5866: fprintf(ficrespl,"\n");
5867: } /* Age */
5868: /* was end of cptcod */
5869: } /* cptcov */
1.184 brouard 5870: return 0;
1.180 brouard 5871: }
5872:
5873: int hPijx(double *p, int bage, int fage){
5874: /*------------- h Pij x at various ages ------------*/
5875:
5876: int stepsize;
5877: int agelim;
5878: int hstepm;
5879: int nhstepm;
5880: int h, i, i1, j, k;
5881:
5882: double agedeb;
5883: double ***p3mat;
5884:
5885: strcpy(filerespij,"pij"); strcat(filerespij,fileres);
5886: if((ficrespij=fopen(filerespij,"w"))==NULL) {
5887: printf("Problem with Pij resultfile: %s\n", filerespij); return 1;
5888: fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij); return 1;
5889: }
5890: printf("Computing pij: result on file '%s' \n", filerespij);
5891: fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
5892:
5893: stepsize=(int) (stepm+YEARM-1)/YEARM;
5894: /*if (stepm<=24) stepsize=2;*/
5895:
5896: agelim=AGESUP;
5897: hstepm=stepsize*YEARM; /* Every year of age */
5898: hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
5899:
5900: /* hstepm=1; aff par mois*/
5901: pstamp(ficrespij);
5902: fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
5903: i1= pow(2,cptcoveff);
1.183 brouard 5904: /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */
5905: /* /\*for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*\/ */
5906: /* k=k+1; */
5907: for (k=1; k <= (int) pow(2,cptcoveff); k++){
5908: fprintf(ficrespij,"\n#****** ");
5909: for(j=1;j<=cptcoveff;j++)
5910: fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5911: fprintf(ficrespij,"******\n");
5912:
5913: for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
5914: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
5915: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
5916:
5917: /* nhstepm=nhstepm*YEARM; aff par mois*/
1.180 brouard 5918:
1.183 brouard 5919: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5920: oldm=oldms;savm=savms;
5921: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
5922: fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
5923: for(i=1; i<=nlstate;i++)
5924: for(j=1; j<=nlstate+ndeath;j++)
5925: fprintf(ficrespij," %1d-%1d",i,j);
5926: fprintf(ficrespij,"\n");
5927: for (h=0; h<=nhstepm; h++){
5928: /*agedebphstep = agedeb + h*hstepm/YEARM*stepm;*/
5929: fprintf(ficrespij,"%d %3.f %3.f",k, agedeb, agedeb + h*hstepm/YEARM*stepm );
1.180 brouard 5930: for(i=1; i<=nlstate;i++)
5931: for(j=1; j<=nlstate+ndeath;j++)
1.183 brouard 5932: fprintf(ficrespij," %.5f", p3mat[i][j][h]);
1.180 brouard 5933: fprintf(ficrespij,"\n");
5934: }
1.183 brouard 5935: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5936: fprintf(ficrespij,"\n");
5937: }
1.180 brouard 5938: /*}*/
5939: }
1.184 brouard 5940: return 0;
1.180 brouard 5941: }
5942:
5943:
1.136 brouard 5944: /***********************************************/
5945: /**************** Main Program *****************/
5946: /***********************************************/
5947:
5948: int main(int argc, char *argv[])
5949: {
5950: #ifdef GSL
5951: const gsl_multimin_fminimizer_type *T;
5952: size_t iteri = 0, it;
5953: int rval = GSL_CONTINUE;
5954: int status = GSL_SUCCESS;
5955: double ssval;
5956: #endif
5957: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
1.164 brouard 5958: int i,j, k, n=MAXN,iter=0,m,size=100, cptcod;
5959:
5960: int jj, ll, li, lj, lk;
1.136 brouard 5961: int numlinepar=0; /* Current linenumber of parameter file */
5962: int itimes;
5963: int NDIM=2;
5964: int vpopbased=0;
5965:
1.164 brouard 5966: char ca[32], cb[32];
1.136 brouard 5967: /* FILE *fichtm; *//* Html File */
5968: /* FILE *ficgp;*/ /*Gnuplot File */
5969: struct stat info;
1.164 brouard 5970: double agedeb;
1.136 brouard 5971: double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
5972:
1.165 brouard 5973: double fret;
1.136 brouard 5974: double dum; /* Dummy variable */
5975: double ***p3mat;
5976: double ***mobaverage;
1.164 brouard 5977:
5978: char line[MAXLINE];
1.136 brouard 5979: char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
5980: char pathr[MAXLINE], pathimach[MAXLINE];
1.164 brouard 5981: char *tok, *val; /* pathtot */
1.136 brouard 5982: int firstobs=1, lastobs=10;
1.164 brouard 5983: int c, h , cpt;
5984: int jl;
5985: int i1, j1, jk, stepsize;
5986: int *tab;
1.136 brouard 5987: int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
5988: int mobilav=0,popforecast=0;
5989: int hstepm, nhstepm;
5990: int agemortsup;
5991: float sumlpop=0.;
5992: double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
5993: double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
5994:
1.164 brouard 5995: double bage=0, fage=110, age, agelim, agebase;
1.136 brouard 5996: double ftolpl=FTOL;
5997: double **prlim;
5998: double ***param; /* Matrix of parameters */
5999: double *p;
6000: double **matcov; /* Matrix of covariance */
6001: double ***delti3; /* Scale */
6002: double *delti; /* Scale */
6003: double ***eij, ***vareij;
6004: double **varpl; /* Variances of prevalence limits by age */
6005: double *epj, vepp;
1.164 brouard 6006:
1.136 brouard 6007: double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
6008: double **ximort;
1.145 brouard 6009: char *alph[]={"a","a","b","c","d","e"}, str[4]="1234";
1.136 brouard 6010: int *dcwave;
6011:
1.164 brouard 6012: char z[1]="c";
1.136 brouard 6013:
6014: /*char *strt;*/
6015: char strtend[80];
1.126 brouard 6016:
1.164 brouard 6017:
1.126 brouard 6018: /* setlocale (LC_ALL, ""); */
6019: /* bindtextdomain (PACKAGE, LOCALEDIR); */
6020: /* textdomain (PACKAGE); */
6021: /* setlocale (LC_CTYPE, ""); */
6022: /* setlocale (LC_MESSAGES, ""); */
6023:
6024: /* gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
1.157 brouard 6025: rstart_time = time(NULL);
6026: /* (void) gettimeofday(&start_time,&tzp);*/
6027: start_time = *localtime(&rstart_time);
1.126 brouard 6028: curr_time=start_time;
1.157 brouard 6029: /*tml = *localtime(&start_time.tm_sec);*/
6030: /* strcpy(strstart,asctime(&tml)); */
6031: strcpy(strstart,asctime(&start_time));
1.126 brouard 6032:
6033: /* printf("Localtime (at start)=%s",strstart); */
1.157 brouard 6034: /* tp.tm_sec = tp.tm_sec +86400; */
6035: /* tm = *localtime(&start_time.tm_sec); */
1.126 brouard 6036: /* tmg.tm_year=tmg.tm_year +dsign*dyear; */
6037: /* tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
6038: /* tmg.tm_hour=tmg.tm_hour + 1; */
1.157 brouard 6039: /* tp.tm_sec = mktime(&tmg); */
1.126 brouard 6040: /* strt=asctime(&tmg); */
6041: /* printf("Time(after) =%s",strstart); */
6042: /* (void) time (&time_value);
6043: * printf("time=%d,t-=%d\n",time_value,time_value-86400);
6044: * tm = *localtime(&time_value);
6045: * strstart=asctime(&tm);
6046: * printf("tim_value=%d,asctime=%s\n",time_value,strstart);
6047: */
6048:
6049: nberr=0; /* Number of errors and warnings */
6050: nbwarn=0;
1.184 brouard 6051: #ifdef WIN32
6052: _getcwd(pathcd, size);
6053: #else
1.126 brouard 6054: getcwd(pathcd, size);
1.184 brouard 6055: #endif
1.126 brouard 6056:
6057: printf("\n%s\n%s",version,fullversion);
6058: if(argc <=1){
6059: printf("\nEnter the parameter file name: ");
6060: fgets(pathr,FILENAMELENGTH,stdin);
6061: i=strlen(pathr);
6062: if(pathr[i-1]=='\n')
6063: pathr[i-1]='\0';
1.156 brouard 6064: i=strlen(pathr);
6065: if(pathr[i-1]==' ') /* This may happen when dragging on oS/X! */
6066: pathr[i-1]='\0';
1.126 brouard 6067: for (tok = pathr; tok != NULL; ){
6068: printf("Pathr |%s|\n",pathr);
6069: while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
6070: printf("val= |%s| pathr=%s\n",val,pathr);
6071: strcpy (pathtot, val);
6072: if(pathr[0] == '\0') break; /* Dirty */
6073: }
6074: }
6075: else{
6076: strcpy(pathtot,argv[1]);
6077: }
6078: /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
6079: /*cygwin_split_path(pathtot,path,optionfile);
6080: printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
6081: /* cutv(path,optionfile,pathtot,'\\');*/
6082:
6083: /* Split argv[0], imach program to get pathimach */
6084: printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
6085: split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
6086: printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
6087: /* strcpy(pathimach,argv[0]); */
6088: /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
6089: split(pathtot,path,optionfile,optionfilext,optionfilefiname);
6090: printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
1.184 brouard 6091: #ifdef WIN32
6092: _chdir(path); /* Can be a relative path */
6093: if(_getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */
6094: #else
1.126 brouard 6095: chdir(path); /* Can be a relative path */
1.184 brouard 6096: if (getcwd(pathcd, MAXLINE) > 0) /* So pathcd is the full path */
6097: #endif
6098: printf("Current directory %s!\n",pathcd);
1.126 brouard 6099: strcpy(command,"mkdir ");
6100: strcat(command,optionfilefiname);
6101: if((outcmd=system(command)) != 0){
1.169 brouard 6102: printf("Directory already exists (or can't create it) %s%s, err=%d\n",path,optionfilefiname,outcmd);
1.126 brouard 6103: /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
6104: /* fclose(ficlog); */
6105: /* exit(1); */
6106: }
6107: /* if((imk=mkdir(optionfilefiname))<0){ */
6108: /* perror("mkdir"); */
6109: /* } */
6110:
6111: /*-------- arguments in the command line --------*/
6112:
6113: /* Log file */
6114: strcat(filelog, optionfilefiname);
6115: strcat(filelog,".log"); /* */
6116: if((ficlog=fopen(filelog,"w"))==NULL) {
6117: printf("Problem with logfile %s\n",filelog);
6118: goto end;
6119: }
6120: fprintf(ficlog,"Log filename:%s\n",filelog);
6121: fprintf(ficlog,"\n%s\n%s",version,fullversion);
6122: fprintf(ficlog,"\nEnter the parameter file name: \n");
6123: fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
6124: path=%s \n\
6125: optionfile=%s\n\
6126: optionfilext=%s\n\
1.156 brouard 6127: optionfilefiname='%s'\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
1.126 brouard 6128:
1.167 brouard 6129: syscompilerinfo();
6130:
1.126 brouard 6131: printf("Local time (at start):%s",strstart);
6132: fprintf(ficlog,"Local time (at start): %s",strstart);
6133: fflush(ficlog);
6134: /* (void) gettimeofday(&curr_time,&tzp); */
1.157 brouard 6135: /* printf("Elapsed time %d\n", asc_diff_time(curr_time.tm_sec-start_time.tm_sec,tmpout)); */
1.126 brouard 6136:
6137: /* */
6138: strcpy(fileres,"r");
6139: strcat(fileres, optionfilefiname);
6140: strcat(fileres,".txt"); /* Other files have txt extension */
6141:
6142: /*---------arguments file --------*/
6143:
6144: if((ficpar=fopen(optionfile,"r"))==NULL) {
1.155 brouard 6145: printf("Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
6146: fprintf(ficlog,"Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
1.126 brouard 6147: fflush(ficlog);
1.149 brouard 6148: /* goto end; */
6149: exit(70);
1.126 brouard 6150: }
6151:
6152:
6153:
6154: strcpy(filereso,"o");
6155: strcat(filereso,fileres);
6156: if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
6157: printf("Problem with Output resultfile: %s\n", filereso);
6158: fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
6159: fflush(ficlog);
6160: goto end;
6161: }
6162:
6163: /* Reads comments: lines beginning with '#' */
6164: numlinepar=0;
6165: while((c=getc(ficpar))=='#' && c!= EOF){
6166: ungetc(c,ficpar);
6167: fgets(line, MAXLINE, ficpar);
6168: numlinepar++;
1.141 brouard 6169: fputs(line,stdout);
1.126 brouard 6170: fputs(line,ficparo);
6171: fputs(line,ficlog);
6172: }
6173: ungetc(c,ficpar);
6174:
6175: 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=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);
6176: numlinepar++;
6177: 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=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model);
6178: 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=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
6179: 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=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
6180: fflush(ficlog);
6181: while((c=getc(ficpar))=='#' && c!= EOF){
6182: ungetc(c,ficpar);
6183: fgets(line, MAXLINE, ficpar);
6184: numlinepar++;
1.141 brouard 6185: fputs(line, stdout);
6186: //puts(line);
1.126 brouard 6187: fputs(line,ficparo);
6188: fputs(line,ficlog);
6189: }
6190: ungetc(c,ficpar);
6191:
6192:
1.145 brouard 6193: covar=matrix(0,NCOVMAX,1,n); /**< used in readdata */
1.136 brouard 6194: cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement plus one, indepently of n in Vn*/
6195: /* v1+v2+v3+v2*v4+v5*age makes cptcovn = 5
6196: v1+v2*age+v2*v3 makes cptcovn = 3
6197: */
6198: if (strlen(model)>1)
1.145 brouard 6199: 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*/
6200: else
6201: ncovmodel=2;
1.126 brouard 6202: nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
1.133 brouard 6203: nforce= (nlstate+ndeath-1)*nlstate; /* Number of forces ij from state i to j */
6204: npar= nforce*ncovmodel; /* Number of parameters like aij*/
1.131 brouard 6205: if(npar >MAXPARM || nlstate >NLSTATEMAX || ndeath >NDEATHMAX || ncovmodel>NCOVMAX){
6206: 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);
6207: 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);
6208: fflush(stdout);
6209: fclose (ficlog);
6210: goto end;
6211: }
1.126 brouard 6212: delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
6213: delti=delti3[1][1];
6214: /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
6215: if(mle==-1){ /* Print a wizard for help writing covariance matrix */
6216: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
6217: printf(" You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
6218: fprintf(ficlog," You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
6219: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
6220: fclose (ficparo);
6221: fclose (ficlog);
6222: goto end;
6223: exit(0);
6224: }
6225: else if(mle==-3) {
6226: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
6227: printf(" You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
6228: fprintf(ficlog," You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
6229: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
6230: matcov=matrix(1,npar,1,npar);
6231: }
6232: else{
1.145 brouard 6233: /* Read guessed parameters */
1.126 brouard 6234: /* Reads comments: lines beginning with '#' */
6235: while((c=getc(ficpar))=='#' && c!= EOF){
6236: ungetc(c,ficpar);
6237: fgets(line, MAXLINE, ficpar);
6238: numlinepar++;
1.141 brouard 6239: fputs(line,stdout);
1.126 brouard 6240: fputs(line,ficparo);
6241: fputs(line,ficlog);
6242: }
6243: ungetc(c,ficpar);
6244:
6245: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
6246: for(i=1; i <=nlstate; i++){
6247: j=0;
6248: for(jj=1; jj <=nlstate+ndeath; jj++){
6249: if(jj==i) continue;
6250: j++;
6251: fscanf(ficpar,"%1d%1d",&i1,&j1);
6252: if ((i1 != i) && (j1 != j)){
6253: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \
6254: It might be a problem of design; if ncovcol and the model are correct\n \
6255: run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1);
6256: exit(1);
6257: }
6258: fprintf(ficparo,"%1d%1d",i1,j1);
6259: if(mle==1)
6260: printf("%1d%1d",i,j);
6261: fprintf(ficlog,"%1d%1d",i,j);
6262: for(k=1; k<=ncovmodel;k++){
6263: fscanf(ficpar," %lf",¶m[i][j][k]);
6264: if(mle==1){
6265: printf(" %lf",param[i][j][k]);
6266: fprintf(ficlog," %lf",param[i][j][k]);
6267: }
6268: else
6269: fprintf(ficlog," %lf",param[i][j][k]);
6270: fprintf(ficparo," %lf",param[i][j][k]);
6271: }
6272: fscanf(ficpar,"\n");
6273: numlinepar++;
6274: if(mle==1)
6275: printf("\n");
6276: fprintf(ficlog,"\n");
6277: fprintf(ficparo,"\n");
6278: }
6279: }
6280: fflush(ficlog);
6281:
1.145 brouard 6282: /* Reads scales values */
1.126 brouard 6283: p=param[1][1];
6284:
6285: /* Reads comments: lines beginning with '#' */
6286: while((c=getc(ficpar))=='#' && c!= EOF){
6287: ungetc(c,ficpar);
6288: fgets(line, MAXLINE, ficpar);
6289: numlinepar++;
1.141 brouard 6290: fputs(line,stdout);
1.126 brouard 6291: fputs(line,ficparo);
6292: fputs(line,ficlog);
6293: }
6294: ungetc(c,ficpar);
6295:
6296: for(i=1; i <=nlstate; i++){
6297: for(j=1; j <=nlstate+ndeath-1; j++){
6298: fscanf(ficpar,"%1d%1d",&i1,&j1);
1.164 brouard 6299: if ( (i1-i) * (j1-j) != 0){
1.126 brouard 6300: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
6301: exit(1);
6302: }
6303: printf("%1d%1d",i,j);
6304: fprintf(ficparo,"%1d%1d",i1,j1);
6305: fprintf(ficlog,"%1d%1d",i1,j1);
6306: for(k=1; k<=ncovmodel;k++){
6307: fscanf(ficpar,"%le",&delti3[i][j][k]);
6308: printf(" %le",delti3[i][j][k]);
6309: fprintf(ficparo," %le",delti3[i][j][k]);
6310: fprintf(ficlog," %le",delti3[i][j][k]);
6311: }
6312: fscanf(ficpar,"\n");
6313: numlinepar++;
6314: printf("\n");
6315: fprintf(ficparo,"\n");
6316: fprintf(ficlog,"\n");
6317: }
6318: }
6319: fflush(ficlog);
6320:
1.145 brouard 6321: /* Reads covariance matrix */
1.126 brouard 6322: delti=delti3[1][1];
6323:
6324:
6325: /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
6326:
6327: /* Reads comments: lines beginning with '#' */
6328: while((c=getc(ficpar))=='#' && c!= EOF){
6329: ungetc(c,ficpar);
6330: fgets(line, MAXLINE, ficpar);
6331: numlinepar++;
1.141 brouard 6332: fputs(line,stdout);
1.126 brouard 6333: fputs(line,ficparo);
6334: fputs(line,ficlog);
6335: }
6336: ungetc(c,ficpar);
6337:
6338: matcov=matrix(1,npar,1,npar);
1.131 brouard 6339: for(i=1; i <=npar; i++)
6340: for(j=1; j <=npar; j++) matcov[i][j]=0.;
6341:
1.126 brouard 6342: for(i=1; i <=npar; i++){
1.145 brouard 6343: fscanf(ficpar,"%s",str);
1.126 brouard 6344: if(mle==1)
6345: printf("%s",str);
6346: fprintf(ficlog,"%s",str);
6347: fprintf(ficparo,"%s",str);
6348: for(j=1; j <=i; j++){
6349: fscanf(ficpar," %le",&matcov[i][j]);
6350: if(mle==1){
6351: printf(" %.5le",matcov[i][j]);
6352: }
6353: fprintf(ficlog," %.5le",matcov[i][j]);
6354: fprintf(ficparo," %.5le",matcov[i][j]);
6355: }
6356: fscanf(ficpar,"\n");
6357: numlinepar++;
6358: if(mle==1)
6359: printf("\n");
6360: fprintf(ficlog,"\n");
6361: fprintf(ficparo,"\n");
6362: }
6363: for(i=1; i <=npar; i++)
6364: for(j=i+1;j<=npar;j++)
6365: matcov[i][j]=matcov[j][i];
6366:
6367: if(mle==1)
6368: printf("\n");
6369: fprintf(ficlog,"\n");
6370:
6371: fflush(ficlog);
6372:
6373: /*-------- Rewriting parameter file ----------*/
6374: strcpy(rfileres,"r"); /* "Rparameterfile */
6375: strcat(rfileres,optionfilefiname); /* Parameter file first name*/
6376: strcat(rfileres,"."); /* */
6377: strcat(rfileres,optionfilext); /* Other files have txt extension */
6378: if((ficres =fopen(rfileres,"w"))==NULL) {
6379: printf("Problem writing new parameter file: %s\n", fileres);goto end;
6380: fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
6381: }
6382: fprintf(ficres,"#%s\n",version);
6383: } /* End of mle != -3 */
6384:
6385:
6386: n= lastobs;
6387: num=lvector(1,n);
6388: moisnais=vector(1,n);
6389: annais=vector(1,n);
6390: moisdc=vector(1,n);
6391: andc=vector(1,n);
6392: agedc=vector(1,n);
6393: cod=ivector(1,n);
6394: weight=vector(1,n);
6395: for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
6396: mint=matrix(1,maxwav,1,n);
6397: anint=matrix(1,maxwav,1,n);
1.131 brouard 6398: s=imatrix(1,maxwav+1,1,n); /* s[i][j] health state for wave i and individual j */
1.126 brouard 6399: tab=ivector(1,NCOVMAX);
1.144 brouard 6400: ncodemax=ivector(1,NCOVMAX); /* Number of code per covariate; if O and 1 only, 2**ncov; V1+V2+V3+V4=>16 */
1.126 brouard 6401:
1.136 brouard 6402: /* Reads data from file datafile */
6403: if (readdata(datafile, firstobs, lastobs, &imx)==1)
6404: goto end;
6405:
6406: /* Calculation of the number of parameters from char model */
1.137 brouard 6407: /* modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4
6408: k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tag[cptcovage=1]=4
6409: k=3 V4 Tvar[k=3]= 4 (from V4)
6410: k=2 V1 Tvar[k=2]= 1 (from V1)
6411: k=1 Tvar[1]=2 (from V2)
6412: */
6413: Tvar=ivector(1,NCOVMAX); /* Was 15 changed to NCOVMAX. */
6414: /* V2+V1+V4+age*V3 is a model with 4 covariates (3 plus signs).
6415: For each model-covariate stores the data-covariate id. Tvar[1]=2, Tvar[2]=1, Tvar[3]=4,
6416: Tvar[4=age*V3] is 3 and 'age' is recorded in Tage.
6417: */
6418: /* For model-covariate k tells which data-covariate to use but
6419: because this model-covariate is a construction we invent a new column
6420: ncovcol + k1
6421: If already ncovcol=4 and model=V2+V1+V1*V4+age*V3
6422: Tvar[3=V1*V4]=4+1 etc */
1.145 brouard 6423: Tprod=ivector(1,NCOVMAX); /* Gives the position of a product */
1.137 brouard 6424: /* Tprod[k1=1]=3(=V1*V4) for V2+V1+V1*V4+age*V3
6425: if V2+V1+V1*V4+age*V3+V3*V2 TProd[k1=2]=5 (V3*V2)
6426: */
1.145 brouard 6427: Tvaraff=ivector(1,NCOVMAX); /* Unclear */
6428: 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 6429: * For V3*V2 (in V2+V1+V1*V4+age*V3+V3*V2), V3*V2 position is 2nd.
6430: * Tvard[k1=2][1]=3 (V3) Tvard[k1=2][2]=2(V2) */
1.145 brouard 6431: Tage=ivector(1,NCOVMAX); /* Gives the covariate id of covariates associated with age: V2 + V1 + age*V4 + V3*age
1.137 brouard 6432: 4 covariates (3 plus signs)
6433: Tage[1=V3*age]= 4; Tage[2=age*V4] = 3
6434: */
1.136 brouard 6435:
6436: if(decodemodel(model, lastobs) == 1)
6437: goto end;
6438:
1.137 brouard 6439: if((double)(lastobs-imx)/(double)imx > 1.10){
6440: nbwarn++;
6441: 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);
6442: 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);
6443: }
1.136 brouard 6444: /* if(mle==1){*/
1.137 brouard 6445: if (weightopt != 1) { /* Maximisation without weights. We can have weights different from 1 but want no weight*/
6446: for(i=1;i<=imx;i++) weight[i]=1.0; /* changed to imx */
1.136 brouard 6447: }
6448:
6449: /*-calculation of age at interview from date of interview and age at death -*/
6450: agev=matrix(1,maxwav,1,imx);
6451:
6452: if(calandcheckages(imx, maxwav, &agemin, &agemax, &nberr, &nbwarn) == 1)
6453: goto end;
6454:
1.126 brouard 6455:
1.136 brouard 6456: agegomp=(int)agemin;
6457: free_vector(moisnais,1,n);
6458: free_vector(annais,1,n);
1.126 brouard 6459: /* free_matrix(mint,1,maxwav,1,n);
6460: free_matrix(anint,1,maxwav,1,n);*/
6461: free_vector(moisdc,1,n);
6462: free_vector(andc,1,n);
1.145 brouard 6463: /* */
6464:
1.126 brouard 6465: wav=ivector(1,imx);
6466: dh=imatrix(1,lastpass-firstpass+1,1,imx);
6467: bh=imatrix(1,lastpass-firstpass+1,1,imx);
6468: mw=imatrix(1,lastpass-firstpass+1,1,imx);
6469:
6470: /* Concatenates waves */
6471: concatwav(wav, dh, bh, mw, s, agedc, agev, firstpass, lastpass, imx, nlstate, stepm);
1.145 brouard 6472: /* */
6473:
1.126 brouard 6474: /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
6475:
6476: nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
6477: ncodemax[1]=1;
1.145 brouard 6478: Ndum =ivector(-1,NCOVMAX);
6479: if (ncovmodel > 2)
6480: tricode(Tvar,nbcode,imx, Ndum); /**< Fills nbcode[Tvar[j]][l]; */
6481:
6482: codtab=imatrix(1,100,1,10); /* codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) */
6483: /*printf(" codtab[1,1],codtab[100,10]=%d,%d\n", codtab[1][1],codtab[100][10]);*/
6484: h=0;
6485:
6486:
6487: /*if (cptcovn > 0) */
1.126 brouard 6488:
1.145 brouard 6489:
1.126 brouard 6490: m=pow(2,cptcoveff);
6491:
1.131 brouard 6492: for(k=1;k<=cptcoveff; k++){ /* scans any effective covariate */
1.143 brouard 6493: 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 */
6494: for(j=1; j <= ncodemax[k]; j++){ /* For each modality of this covariate ncodemax=2*/
6495: 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 6496: h++;
1.141 brouard 6497: if (h>m)
1.136 brouard 6498: h=1;
1.144 brouard 6499: /**< codtab(h,k) k = codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) + 1
1.143 brouard 6500: * h 1 2 3 4
6501: *______________________________
6502: * 1 i=1 1 i=1 1 i=1 1 i=1 1
6503: * 2 2 1 1 1
6504: * 3 i=2 1 2 1 1
6505: * 4 2 2 1 1
6506: * 5 i=3 1 i=2 1 2 1
6507: * 6 2 1 2 1
6508: * 7 i=4 1 2 2 1
6509: * 8 2 2 2 1
6510: * 9 i=5 1 i=3 1 i=2 1 1
6511: * 10 2 1 1 1
6512: * 11 i=6 1 2 1 1
6513: * 12 2 2 1 1
6514: * 13 i=7 1 i=4 1 2 1
6515: * 14 2 1 2 1
6516: * 15 i=8 1 2 2 1
6517: * 16 2 2 2 1
6518: */
1.141 brouard 6519: codtab[h][k]=j;
1.145 brouard 6520: /*codtab[h][Tvar[k]]=j;*/
1.130 brouard 6521: 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 6522: }
6523: }
6524: }
6525: }
6526: /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);
6527: codtab[1][2]=1;codtab[2][2]=2; */
6528: /* for(i=1; i <=m ;i++){
6529: for(k=1; k <=cptcovn; k++){
1.131 brouard 6530: printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
1.126 brouard 6531: }
6532: printf("\n");
6533: }
6534: scanf("%d",i);*/
1.145 brouard 6535:
6536: free_ivector(Ndum,-1,NCOVMAX);
6537:
6538:
1.126 brouard 6539:
6540: /*------------ gnuplot -------------*/
6541: strcpy(optionfilegnuplot,optionfilefiname);
6542: if(mle==-3)
6543: strcat(optionfilegnuplot,"-mort");
6544: strcat(optionfilegnuplot,".gp");
6545:
6546: if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
6547: printf("Problem with file %s",optionfilegnuplot);
6548: }
6549: else{
6550: fprintf(ficgp,"\n# %s\n", version);
6551: fprintf(ficgp,"# %s\n", optionfilegnuplot);
1.141 brouard 6552: //fprintf(ficgp,"set missing 'NaNq'\n");
6553: fprintf(ficgp,"set datafile missing 'NaNq'\n");
1.126 brouard 6554: }
6555: /* fclose(ficgp);*/
6556: /*--------- index.htm --------*/
6557:
6558: strcpy(optionfilehtm,optionfilefiname); /* Main html file */
6559: if(mle==-3)
6560: strcat(optionfilehtm,"-mort");
6561: strcat(optionfilehtm,".htm");
6562: if((fichtm=fopen(optionfilehtm,"w"))==NULL) {
1.131 brouard 6563: printf("Problem with %s \n",optionfilehtm);
6564: exit(0);
1.126 brouard 6565: }
6566:
6567: strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
6568: strcat(optionfilehtmcov,"-cov.htm");
6569: if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL) {
6570: printf("Problem with %s \n",optionfilehtmcov), exit(0);
6571: }
6572: else{
6573: fprintf(fichtmcov,"<html><head>\n<title>IMaCh Cov %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
6574: <hr size=\"2\" color=\"#EC5E5E\"> \n\
6575: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n",\
6576: optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
6577: }
6578:
6579: fprintf(fichtm,"<html><head>\n<title>IMaCh %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
6580: <hr size=\"2\" color=\"#EC5E5E\"> \n\
6581: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
6582: \n\
6583: <hr size=\"2\" color=\"#EC5E5E\">\
6584: <ul><li><h4>Parameter files</h4>\n\
6585: - Parameter file: <a href=\"%s.%s\">%s.%s</a><br>\n\
6586: - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
6587: - Log file of the run: <a href=\"%s\">%s</a><br>\n\
6588: - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
6589: - Date and time at start: %s</ul>\n",\
6590: optionfilehtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
6591: optionfilefiname,optionfilext,optionfilefiname,optionfilext,\
6592: fileres,fileres,\
6593: filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
6594: fflush(fichtm);
6595:
6596: strcpy(pathr,path);
6597: strcat(pathr,optionfilefiname);
1.184 brouard 6598: #ifdef WIN32
6599: _chdir(optionfilefiname); /* Move to directory named optionfile */
6600: #else
1.126 brouard 6601: chdir(optionfilefiname); /* Move to directory named optionfile */
1.184 brouard 6602: #endif
6603:
1.126 brouard 6604:
6605: /* Calculates basic frequencies. Computes observed prevalence at single age
6606: and prints on file fileres'p'. */
6607: freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart);
6608:
6609: fprintf(fichtm,"\n");
6610: fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
6611: Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
6612: Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
6613: imx,agemin,agemax,jmin,jmax,jmean);
6614: pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
6615: oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
6616: newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
6617: savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
6618: oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
6619:
6620:
6621: /* For Powell, parameters are in a vector p[] starting at p[1]
6622: so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
6623: p=param[1][1]; /* *(*(*(param +1)+1)+0) */
6624:
6625: globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
6626:
6627: if (mle==-3){
1.136 brouard 6628: ximort=matrix(1,NDIM,1,NDIM);
6629: /* ximort=gsl_matrix_alloc(1,NDIM,1,NDIM); */
1.126 brouard 6630: cens=ivector(1,n);
6631: ageexmed=vector(1,n);
6632: agecens=vector(1,n);
6633: dcwave=ivector(1,n);
6634:
6635: for (i=1; i<=imx; i++){
6636: dcwave[i]=-1;
6637: for (m=firstpass; m<=lastpass; m++)
6638: if (s[m][i]>nlstate) {
6639: dcwave[i]=m;
6640: /* printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
6641: break;
6642: }
6643: }
6644:
6645: for (i=1; i<=imx; i++) {
6646: if (wav[i]>0){
6647: ageexmed[i]=agev[mw[1][i]][i];
6648: j=wav[i];
6649: agecens[i]=1.;
6650:
6651: if (ageexmed[i]> 1 && wav[i] > 0){
6652: agecens[i]=agev[mw[j][i]][i];
6653: cens[i]= 1;
6654: }else if (ageexmed[i]< 1)
6655: cens[i]= -1;
6656: if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
6657: cens[i]=0 ;
6658: }
6659: else cens[i]=-1;
6660: }
6661:
6662: for (i=1;i<=NDIM;i++) {
6663: for (j=1;j<=NDIM;j++)
6664: ximort[i][j]=(i == j ? 1.0 : 0.0);
6665: }
6666:
1.145 brouard 6667: /*p[1]=0.0268; p[NDIM]=0.083;*/
1.126 brouard 6668: /*printf("%lf %lf", p[1], p[2]);*/
6669:
6670:
1.136 brouard 6671: #ifdef GSL
6672: printf("GSL optimization\n"); fprintf(ficlog,"Powell\n");
1.162 brouard 6673: #else
1.126 brouard 6674: printf("Powell\n"); fprintf(ficlog,"Powell\n");
1.136 brouard 6675: #endif
1.126 brouard 6676: strcpy(filerespow,"pow-mort");
6677: strcat(filerespow,fileres);
6678: if((ficrespow=fopen(filerespow,"w"))==NULL) {
6679: printf("Problem with resultfile: %s\n", filerespow);
6680: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
6681: }
1.136 brouard 6682: #ifdef GSL
6683: fprintf(ficrespow,"# GSL optimization\n# iter -2*LL");
1.162 brouard 6684: #else
1.126 brouard 6685: fprintf(ficrespow,"# Powell\n# iter -2*LL");
1.136 brouard 6686: #endif
1.126 brouard 6687: /* for (i=1;i<=nlstate;i++)
6688: for(j=1;j<=nlstate+ndeath;j++)
6689: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
6690: */
6691: fprintf(ficrespow,"\n");
1.136 brouard 6692: #ifdef GSL
6693: /* gsl starts here */
6694: T = gsl_multimin_fminimizer_nmsimplex;
6695: gsl_multimin_fminimizer *sfm = NULL;
6696: gsl_vector *ss, *x;
6697: gsl_multimin_function minex_func;
6698:
6699: /* Initial vertex size vector */
6700: ss = gsl_vector_alloc (NDIM);
6701:
6702: if (ss == NULL){
6703: GSL_ERROR_VAL ("failed to allocate space for ss", GSL_ENOMEM, 0);
6704: }
6705: /* Set all step sizes to 1 */
6706: gsl_vector_set_all (ss, 0.001);
6707:
6708: /* Starting point */
1.126 brouard 6709:
1.136 brouard 6710: x = gsl_vector_alloc (NDIM);
6711:
6712: if (x == NULL){
6713: gsl_vector_free(ss);
6714: GSL_ERROR_VAL ("failed to allocate space for x", GSL_ENOMEM, 0);
6715: }
6716:
6717: /* Initialize method and iterate */
6718: /* p[1]=0.0268; p[NDIM]=0.083; */
6719: /* gsl_vector_set(x, 0, 0.0268); */
6720: /* gsl_vector_set(x, 1, 0.083); */
6721: gsl_vector_set(x, 0, p[1]);
6722: gsl_vector_set(x, 1, p[2]);
6723:
6724: minex_func.f = &gompertz_f;
6725: minex_func.n = NDIM;
6726: minex_func.params = (void *)&p; /* ??? */
6727:
6728: sfm = gsl_multimin_fminimizer_alloc (T, NDIM);
6729: gsl_multimin_fminimizer_set (sfm, &minex_func, x, ss);
6730:
6731: printf("Iterations beginning .....\n\n");
6732: printf("Iter. # Intercept Slope -Log Likelihood Simplex size\n");
6733:
6734: iteri=0;
6735: while (rval == GSL_CONTINUE){
6736: iteri++;
6737: status = gsl_multimin_fminimizer_iterate(sfm);
6738:
6739: if (status) printf("error: %s\n", gsl_strerror (status));
6740: fflush(0);
6741:
6742: if (status)
6743: break;
6744:
6745: rval = gsl_multimin_test_size (gsl_multimin_fminimizer_size (sfm), 1e-6);
6746: ssval = gsl_multimin_fminimizer_size (sfm);
6747:
6748: if (rval == GSL_SUCCESS)
6749: printf ("converged to a local maximum at\n");
6750:
6751: printf("%5d ", iteri);
6752: for (it = 0; it < NDIM; it++){
6753: printf ("%10.5f ", gsl_vector_get (sfm->x, it));
6754: }
6755: printf("f() = %-10.5f ssize = %.7f\n", sfm->fval, ssval);
6756: }
6757:
6758: printf("\n\n Please note: Program should be run many times with varying starting points to detemine global maximum\n\n");
6759:
6760: gsl_vector_free(x); /* initial values */
6761: gsl_vector_free(ss); /* inital step size */
6762: for (it=0; it<NDIM; it++){
6763: p[it+1]=gsl_vector_get(sfm->x,it);
6764: fprintf(ficrespow," %.12lf", p[it]);
6765: }
6766: gsl_multimin_fminimizer_free (sfm); /* p *(sfm.x.data) et p *(sfm.x.data+1) */
6767: #endif
6768: #ifdef POWELL
6769: powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
6770: #endif
1.126 brouard 6771: fclose(ficrespow);
6772:
6773: hesscov(matcov, p, NDIM, delti, 1e-4, gompertz);
6774:
6775: for(i=1; i <=NDIM; i++)
6776: for(j=i+1;j<=NDIM;j++)
6777: matcov[i][j]=matcov[j][i];
6778:
6779: printf("\nCovariance matrix\n ");
6780: for(i=1; i <=NDIM; i++) {
6781: for(j=1;j<=NDIM;j++){
6782: printf("%f ",matcov[i][j]);
6783: }
6784: printf("\n ");
6785: }
6786:
6787: printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
6788: for (i=1;i<=NDIM;i++)
6789: printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
6790:
6791: lsurv=vector(1,AGESUP);
6792: lpop=vector(1,AGESUP);
6793: tpop=vector(1,AGESUP);
6794: lsurv[agegomp]=100000;
6795:
6796: for (k=agegomp;k<=AGESUP;k++) {
6797: agemortsup=k;
6798: if (p[1]*exp(p[2]*(k-agegomp))>1) break;
6799: }
6800:
6801: for (k=agegomp;k<agemortsup;k++)
6802: lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
6803:
6804: for (k=agegomp;k<agemortsup;k++){
6805: lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
6806: sumlpop=sumlpop+lpop[k];
6807: }
6808:
6809: tpop[agegomp]=sumlpop;
6810: for (k=agegomp;k<(agemortsup-3);k++){
6811: /* tpop[k+1]=2;*/
6812: tpop[k+1]=tpop[k]-lpop[k];
6813: }
6814:
6815:
6816: printf("\nAge lx qx dx Lx Tx e(x)\n");
6817: for (k=agegomp;k<(agemortsup-2);k++)
6818: 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]);
6819:
6820:
6821: replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
6822: printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
6823:
6824: printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \
6825: stepm, weightopt,\
6826: model,imx,p,matcov,agemortsup);
6827:
6828: free_vector(lsurv,1,AGESUP);
6829: free_vector(lpop,1,AGESUP);
6830: free_vector(tpop,1,AGESUP);
1.136 brouard 6831: #ifdef GSL
6832: free_ivector(cens,1,n);
6833: free_vector(agecens,1,n);
6834: free_ivector(dcwave,1,n);
6835: free_matrix(ximort,1,NDIM,1,NDIM);
6836: #endif
1.126 brouard 6837: } /* Endof if mle==-3 */
6838:
6839: else{ /* For mle >=1 */
1.132 brouard 6840: globpr=0;/* debug */
6841: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
1.126 brouard 6842: printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
6843: for (k=1; k<=npar;k++)
6844: printf(" %d %8.5f",k,p[k]);
6845: printf("\n");
6846: globpr=1; /* to print the contributions */
6847: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
6848: printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
6849: for (k=1; k<=npar;k++)
6850: printf(" %d %8.5f",k,p[k]);
6851: printf("\n");
6852: if(mle>=1){ /* Could be 1 or 2 */
6853: mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
6854: }
6855:
6856: /*--------- results files --------------*/
6857: 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=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate, ndeath, maxwav, weightopt,model);
6858:
6859:
6860: fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
6861: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
6862: fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
6863: for(i=1,jk=1; i <=nlstate; i++){
6864: for(k=1; k <=(nlstate+ndeath); k++){
6865: if (k != i) {
6866: printf("%d%d ",i,k);
6867: fprintf(ficlog,"%d%d ",i,k);
6868: fprintf(ficres,"%1d%1d ",i,k);
6869: for(j=1; j <=ncovmodel; j++){
6870: printf("%lf ",p[jk]);
6871: fprintf(ficlog,"%lf ",p[jk]);
6872: fprintf(ficres,"%lf ",p[jk]);
6873: jk++;
6874: }
6875: printf("\n");
6876: fprintf(ficlog,"\n");
6877: fprintf(ficres,"\n");
6878: }
6879: }
6880: }
6881: if(mle!=0){
6882: /* Computing hessian and covariance matrix */
6883: ftolhess=ftol; /* Usually correct */
6884: hesscov(matcov, p, npar, delti, ftolhess, func);
6885: }
6886: fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
6887: printf("# Scales (for hessian or gradient estimation)\n");
6888: fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
6889: for(i=1,jk=1; i <=nlstate; i++){
6890: for(j=1; j <=nlstate+ndeath; j++){
6891: if (j!=i) {
6892: fprintf(ficres,"%1d%1d",i,j);
6893: printf("%1d%1d",i,j);
6894: fprintf(ficlog,"%1d%1d",i,j);
6895: for(k=1; k<=ncovmodel;k++){
6896: printf(" %.5e",delti[jk]);
6897: fprintf(ficlog," %.5e",delti[jk]);
6898: fprintf(ficres," %.5e",delti[jk]);
6899: jk++;
6900: }
6901: printf("\n");
6902: fprintf(ficlog,"\n");
6903: fprintf(ficres,"\n");
6904: }
6905: }
6906: }
6907:
6908: 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");
6909: if(mle>=1)
6910: 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");
6911: 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");
6912: /* # 121 Var(a12)\n\ */
6913: /* # 122 Cov(b12,a12) Var(b12)\n\ */
6914: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
6915: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
6916: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
6917: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
6918: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
6919: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
6920:
6921:
6922: /* Just to have a covariance matrix which will be more understandable
6923: even is we still don't want to manage dictionary of variables
6924: */
6925: for(itimes=1;itimes<=2;itimes++){
6926: jj=0;
6927: for(i=1; i <=nlstate; i++){
6928: for(j=1; j <=nlstate+ndeath; j++){
6929: if(j==i) continue;
6930: for(k=1; k<=ncovmodel;k++){
6931: jj++;
6932: ca[0]= k+'a'-1;ca[1]='\0';
6933: if(itimes==1){
6934: if(mle>=1)
6935: printf("#%1d%1d%d",i,j,k);
6936: fprintf(ficlog,"#%1d%1d%d",i,j,k);
6937: fprintf(ficres,"#%1d%1d%d",i,j,k);
6938: }else{
6939: if(mle>=1)
6940: printf("%1d%1d%d",i,j,k);
6941: fprintf(ficlog,"%1d%1d%d",i,j,k);
6942: fprintf(ficres,"%1d%1d%d",i,j,k);
6943: }
6944: ll=0;
6945: for(li=1;li <=nlstate; li++){
6946: for(lj=1;lj <=nlstate+ndeath; lj++){
6947: if(lj==li) continue;
6948: for(lk=1;lk<=ncovmodel;lk++){
6949: ll++;
6950: if(ll<=jj){
6951: cb[0]= lk +'a'-1;cb[1]='\0';
6952: if(ll<jj){
6953: if(itimes==1){
6954: if(mle>=1)
6955: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
6956: fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
6957: fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
6958: }else{
6959: if(mle>=1)
6960: printf(" %.5e",matcov[jj][ll]);
6961: fprintf(ficlog," %.5e",matcov[jj][ll]);
6962: fprintf(ficres," %.5e",matcov[jj][ll]);
6963: }
6964: }else{
6965: if(itimes==1){
6966: if(mle>=1)
6967: printf(" Var(%s%1d%1d)",ca,i,j);
6968: fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
6969: fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
6970: }else{
6971: if(mle>=1)
6972: printf(" %.5e",matcov[jj][ll]);
6973: fprintf(ficlog," %.5e",matcov[jj][ll]);
6974: fprintf(ficres," %.5e",matcov[jj][ll]);
6975: }
6976: }
6977: }
6978: } /* end lk */
6979: } /* end lj */
6980: } /* end li */
6981: if(mle>=1)
6982: printf("\n");
6983: fprintf(ficlog,"\n");
6984: fprintf(ficres,"\n");
6985: numlinepar++;
6986: } /* end k*/
6987: } /*end j */
6988: } /* end i */
6989: } /* end itimes */
6990:
6991: fflush(ficlog);
6992: fflush(ficres);
6993:
6994: while((c=getc(ficpar))=='#' && c!= EOF){
6995: ungetc(c,ficpar);
6996: fgets(line, MAXLINE, ficpar);
1.141 brouard 6997: fputs(line,stdout);
1.126 brouard 6998: fputs(line,ficparo);
6999: }
7000: ungetc(c,ficpar);
7001:
7002: estepm=0;
7003: fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
7004: if (estepm==0 || estepm < stepm) estepm=stepm;
7005: if (fage <= 2) {
7006: bage = ageminpar;
7007: fage = agemaxpar;
7008: }
7009:
7010: fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
7011: fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
7012: fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
7013:
7014: while((c=getc(ficpar))=='#' && c!= EOF){
7015: ungetc(c,ficpar);
7016: fgets(line, MAXLINE, ficpar);
1.141 brouard 7017: fputs(line,stdout);
1.126 brouard 7018: fputs(line,ficparo);
7019: }
7020: ungetc(c,ficpar);
7021:
7022: 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);
7023: 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);
7024: 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);
7025: printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
7026: 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);
7027:
7028: while((c=getc(ficpar))=='#' && c!= EOF){
7029: ungetc(c,ficpar);
7030: fgets(line, MAXLINE, ficpar);
1.141 brouard 7031: fputs(line,stdout);
1.126 brouard 7032: fputs(line,ficparo);
7033: }
7034: ungetc(c,ficpar);
7035:
7036:
7037: dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
7038: dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
7039:
7040: fscanf(ficpar,"pop_based=%d\n",&popbased);
7041: fprintf(ficparo,"pop_based=%d\n",popbased);
7042: fprintf(ficres,"pop_based=%d\n",popbased);
7043:
7044: while((c=getc(ficpar))=='#' && c!= EOF){
7045: ungetc(c,ficpar);
7046: fgets(line, MAXLINE, ficpar);
1.141 brouard 7047: fputs(line,stdout);
1.126 brouard 7048: fputs(line,ficparo);
7049: }
7050: ungetc(c,ficpar);
7051:
7052: 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);
7053: 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);
7054: 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);
7055: 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);
7056: 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);
7057: /* day and month of proj2 are not used but only year anproj2.*/
7058:
7059:
7060:
1.145 brouard 7061: /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint); */
7062: /* ,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2); */
1.126 brouard 7063:
7064: replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
7065: printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
7066:
7067: printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
7068: model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
7069: jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
7070:
7071: /*------------ free_vector -------------*/
7072: /* chdir(path); */
7073:
7074: free_ivector(wav,1,imx);
7075: free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
7076: free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
7077: free_imatrix(mw,1,lastpass-firstpass+1,1,imx);
7078: free_lvector(num,1,n);
7079: free_vector(agedc,1,n);
7080: /*free_matrix(covar,0,NCOVMAX,1,n);*/
7081: /*free_matrix(covar,1,NCOVMAX,1,n);*/
7082: fclose(ficparo);
7083: fclose(ficres);
7084:
7085:
7086: /*--------------- Prevalence limit (period or stable prevalence) --------------*/
1.180 brouard 7087: /*#include "prevlim.h"*/ /* Use ficrespl, ficlog */
7088: prlim=matrix(1,nlstate,1,nlstate);
7089: prevalence_limit(p, prlim, ageminpar, agemaxpar);
1.126 brouard 7090: fclose(ficrespl);
7091:
1.145 brouard 7092: #ifdef FREEEXIT2
7093: #include "freeexit2.h"
7094: #endif
7095:
1.126 brouard 7096: /*------------- h Pij x at various ages ------------*/
1.180 brouard 7097: /*#include "hpijx.h"*/
7098: hPijx(p, bage, fage);
1.145 brouard 7099: fclose(ficrespij);
1.126 brouard 7100:
1.145 brouard 7101: /*-------------- Variance of one-step probabilities---*/
7102: k=1;
1.126 brouard 7103: varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
7104:
7105:
7106: probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
7107: for(i=1;i<=AGESUP;i++)
7108: for(j=1;j<=NCOVMAX;j++)
7109: for(k=1;k<=NCOVMAX;k++)
7110: probs[i][j][k]=0.;
7111:
7112: /*---------- Forecasting ------------------*/
7113: /*if((stepm == 1) && (strcmp(model,".")==0)){*/
7114: if(prevfcast==1){
7115: /* if(stepm ==1){*/
7116: prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
7117: /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
7118: /* } */
7119: /* else{ */
7120: /* erreur=108; */
7121: /* 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); */
7122: /* 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); */
7123: /* } */
7124: }
7125:
7126:
1.127 brouard 7127: /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
7128:
7129: prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
7130: /* 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",\
7131: ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
7132: */
1.126 brouard 7133:
1.127 brouard 7134: if (mobilav!=0) {
7135: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
7136: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
7137: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
7138: printf(" Error in movingaverage mobilav=%d\n",mobilav);
7139: }
1.126 brouard 7140: }
7141:
7142:
1.127 brouard 7143: /*---------- Health expectancies, no variances ------------*/
7144:
1.126 brouard 7145: strcpy(filerese,"e");
7146: strcat(filerese,fileres);
7147: if((ficreseij=fopen(filerese,"w"))==NULL) {
7148: printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
7149: fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
7150: }
7151: printf("Computing Health Expectancies: result on file '%s' \n", filerese);
7152: fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
1.145 brouard 7153: /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
7154: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
7155:
7156: for (k=1; k <= (int) pow(2,cptcoveff); k++){
1.127 brouard 7157: fprintf(ficreseij,"\n#****** ");
7158: for(j=1;j<=cptcoveff;j++) {
7159: fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
7160: }
7161: fprintf(ficreseij,"******\n");
7162:
7163: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
7164: oldm=oldms;savm=savms;
7165: evsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart);
7166:
7167: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
1.145 brouard 7168: /*}*/
1.127 brouard 7169: }
7170: fclose(ficreseij);
7171:
7172:
7173: /*---------- Health expectancies and variances ------------*/
7174:
7175:
7176: strcpy(filerest,"t");
7177: strcat(filerest,fileres);
7178: if((ficrest=fopen(filerest,"w"))==NULL) {
7179: printf("Problem with total LE resultfile: %s\n", filerest);goto end;
7180: fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
7181: }
7182: printf("Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);
7183: fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);
7184:
1.126 brouard 7185:
7186: strcpy(fileresstde,"stde");
7187: strcat(fileresstde,fileres);
7188: if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {
7189: printf("Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
7190: fprintf(ficlog,"Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
7191: }
7192: printf("Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
7193: fprintf(ficlog,"Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
7194:
7195: strcpy(filerescve,"cve");
7196: strcat(filerescve,fileres);
7197: if((ficrescveij=fopen(filerescve,"w"))==NULL) {
7198: printf("Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
7199: fprintf(ficlog,"Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
7200: }
7201: printf("Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
7202: fprintf(ficlog,"Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
7203:
7204: strcpy(fileresv,"v");
7205: strcat(fileresv,fileres);
7206: if((ficresvij=fopen(fileresv,"w"))==NULL) {
7207: printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
7208: fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
7209: }
7210: printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
7211: fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
7212:
1.145 brouard 7213: /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
7214: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
7215:
7216: for (k=1; k <= (int) pow(2,cptcoveff); k++){
7217: fprintf(ficrest,"\n#****** ");
1.126 brouard 7218: for(j=1;j<=cptcoveff;j++)
7219: fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
7220: fprintf(ficrest,"******\n");
7221:
7222: fprintf(ficresstdeij,"\n#****** ");
7223: fprintf(ficrescveij,"\n#****** ");
7224: for(j=1;j<=cptcoveff;j++) {
7225: fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
7226: fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
7227: }
7228: fprintf(ficresstdeij,"******\n");
7229: fprintf(ficrescveij,"******\n");
7230:
7231: fprintf(ficresvij,"\n#****** ");
7232: for(j=1;j<=cptcoveff;j++)
7233: fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
7234: fprintf(ficresvij,"******\n");
7235:
7236: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
7237: oldm=oldms;savm=savms;
1.127 brouard 7238: cvevsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);
1.145 brouard 7239: /*
7240: */
7241: /* goto endfree; */
1.126 brouard 7242:
7243: vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
7244: pstamp(ficrest);
1.145 brouard 7245:
7246:
1.128 brouard 7247: for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
1.145 brouard 7248: oldm=oldms;savm=savms; /* Segmentation fault */
1.161 brouard 7249: cptcod= 0; /* To be deleted */
7250: 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 7251: 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 7252: if(vpopbased==1)
7253: 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);
7254: else
7255: fprintf(ficrest,"the age specific period (stable) prevalences in each health state \n");
7256: fprintf(ficrest,"# Age e.. (std) ");
7257: for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
7258: fprintf(ficrest,"\n");
1.126 brouard 7259:
1.128 brouard 7260: epj=vector(1,nlstate+1);
7261: for(age=bage; age <=fage ;age++){
7262: prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
7263: if (vpopbased==1) {
7264: if(mobilav ==0){
7265: for(i=1; i<=nlstate;i++)
7266: prlim[i][i]=probs[(int)age][i][k];
7267: }else{ /* mobilav */
7268: for(i=1; i<=nlstate;i++)
7269: prlim[i][i]=mobaverage[(int)age][i][k];
7270: }
1.126 brouard 7271: }
7272:
1.128 brouard 7273: fprintf(ficrest," %4.0f",age);
7274: for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
7275: for(i=1, epj[j]=0.;i <=nlstate;i++) {
7276: epj[j] += prlim[i][i]*eij[i][j][(int)age];
7277: /* printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
7278: }
7279: epj[nlstate+1] +=epj[j];
1.126 brouard 7280: }
7281:
1.128 brouard 7282: for(i=1, vepp=0.;i <=nlstate;i++)
7283: for(j=1;j <=nlstate;j++)
7284: vepp += vareij[i][j][(int)age];
7285: fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
7286: for(j=1;j <=nlstate;j++){
7287: fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
7288: }
7289: fprintf(ficrest,"\n");
1.126 brouard 7290: }
7291: }
7292: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
7293: free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
7294: free_vector(epj,1,nlstate+1);
1.145 brouard 7295: /*}*/
1.126 brouard 7296: }
7297: free_vector(weight,1,n);
1.145 brouard 7298: free_imatrix(Tvard,1,NCOVMAX,1,2);
1.126 brouard 7299: free_imatrix(s,1,maxwav+1,1,n);
7300: free_matrix(anint,1,maxwav,1,n);
7301: free_matrix(mint,1,maxwav,1,n);
7302: free_ivector(cod,1,n);
7303: free_ivector(tab,1,NCOVMAX);
7304: fclose(ficresstdeij);
7305: fclose(ficrescveij);
7306: fclose(ficresvij);
7307: fclose(ficrest);
7308: fclose(ficpar);
7309:
7310: /*------- Variance of period (stable) prevalence------*/
7311:
7312: strcpy(fileresvpl,"vpl");
7313: strcat(fileresvpl,fileres);
7314: if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
7315: printf("Problem with variance of period (stable) prevalence resultfile: %s\n", fileresvpl);
7316: exit(0);
7317: }
7318: printf("Computing Variance-covariance of period (stable) prevalence: file '%s' \n", fileresvpl);
7319:
1.145 brouard 7320: /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
7321: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
7322:
7323: for (k=1; k <= (int) pow(2,cptcoveff); k++){
7324: fprintf(ficresvpl,"\n#****** ");
1.126 brouard 7325: for(j=1;j<=cptcoveff;j++)
7326: fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
7327: fprintf(ficresvpl,"******\n");
7328:
7329: varpl=matrix(1,nlstate,(int) bage, (int) fage);
7330: oldm=oldms;savm=savms;
7331: varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k,strstart);
7332: free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
1.145 brouard 7333: /*}*/
1.126 brouard 7334: }
7335:
7336: fclose(ficresvpl);
7337:
7338: /*---------- End : free ----------------*/
7339: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
7340: free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
7341: } /* mle==-3 arrives here for freeing */
1.164 brouard 7342: /* endfree:*/
1.141 brouard 7343: free_matrix(prlim,1,nlstate,1,nlstate); /*here or after loop ? */
1.126 brouard 7344: free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
7345: free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
7346: free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
7347: free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
7348: free_matrix(covar,0,NCOVMAX,1,n);
7349: free_matrix(matcov,1,npar,1,npar);
7350: /*free_vector(delti,1,npar);*/
7351: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
7352: free_matrix(agev,1,maxwav,1,imx);
7353: free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
7354:
1.145 brouard 7355: free_ivector(ncodemax,1,NCOVMAX);
7356: free_ivector(Tvar,1,NCOVMAX);
7357: free_ivector(Tprod,1,NCOVMAX);
7358: free_ivector(Tvaraff,1,NCOVMAX);
7359: free_ivector(Tage,1,NCOVMAX);
1.126 brouard 7360:
7361: free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
7362: free_imatrix(codtab,1,100,1,10);
7363: fflush(fichtm);
7364: fflush(ficgp);
7365:
7366:
7367: if((nberr >0) || (nbwarn>0)){
7368: printf("End of Imach with %d errors and/or %d warnings\n",nberr,nbwarn);
7369: fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
7370: }else{
7371: printf("End of Imach\n");
7372: fprintf(ficlog,"End of Imach\n");
7373: }
7374: printf("See log file on %s\n",filelog);
7375: /* gettimeofday(&end_time, (struct timezone*)0);*/ /* after time */
1.157 brouard 7376: /*(void) gettimeofday(&end_time,&tzp);*/
7377: rend_time = time(NULL);
7378: end_time = *localtime(&rend_time);
7379: /* tml = *localtime(&end_time.tm_sec); */
7380: strcpy(strtend,asctime(&end_time));
1.126 brouard 7381: printf("Local time at start %s\nLocal time at end %s",strstart, strtend);
7382: fprintf(ficlog,"Local time at start %s\nLocal time at end %s\n",strstart, strtend);
1.157 brouard 7383: printf("Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
1.126 brouard 7384:
1.157 brouard 7385: printf("Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
7386: fprintf(ficlog,"Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
7387: fprintf(ficlog,"Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
1.126 brouard 7388: /* printf("Total time was %d uSec.\n", total_usecs);*/
7389: /* if(fileappend(fichtm,optionfilehtm)){ */
7390: fprintf(fichtm,"<br>Local time at start %s<br>Local time at end %s<br>\n</body></html>",strstart, strtend);
7391: fclose(fichtm);
7392: fprintf(fichtmcov,"<br>Local time at start %s<br>Local time at end %s<br>\n</body></html>",strstart, strtend);
7393: fclose(fichtmcov);
7394: fclose(ficgp);
7395: fclose(ficlog);
7396: /*------ End -----------*/
7397:
7398:
7399: printf("Before Current directory %s!\n",pathcd);
1.184 brouard 7400: #ifdef WIN32
7401: if (_chdir(pathcd) != 0)
7402: printf("Can't move to directory %s!\n",path);
7403: if(_getcwd(pathcd,MAXLINE) > 0)
7404: #else
1.126 brouard 7405: if(chdir(pathcd) != 0)
1.184 brouard 7406: printf("Can't move to directory %s!\n", path);
7407: if (getcwd(pathcd, MAXLINE) > 0)
7408: #endif
1.126 brouard 7409: printf("Current directory %s!\n",pathcd);
7410: /*strcat(plotcmd,CHARSEPARATOR);*/
7411: sprintf(plotcmd,"gnuplot");
1.157 brouard 7412: #ifdef _WIN32
1.126 brouard 7413: sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
7414: #endif
7415: if(!stat(plotcmd,&info)){
1.158 brouard 7416: printf("Error or gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
1.126 brouard 7417: if(!stat(getenv("GNUPLOTBIN"),&info)){
1.158 brouard 7418: printf("Error or gnuplot program not found: '%s' Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);
1.126 brouard 7419: }else
7420: strcpy(pplotcmd,plotcmd);
1.157 brouard 7421: #ifdef __unix
1.126 brouard 7422: strcpy(plotcmd,GNUPLOTPROGRAM);
7423: if(!stat(plotcmd,&info)){
1.158 brouard 7424: printf("Error gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
1.126 brouard 7425: }else
7426: strcpy(pplotcmd,plotcmd);
7427: #endif
7428: }else
7429: strcpy(pplotcmd,plotcmd);
7430:
7431: sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
1.158 brouard 7432: printf("Starting graphs with: '%s'\n",plotcmd);fflush(stdout);
1.126 brouard 7433:
7434: if((outcmd=system(plotcmd)) != 0){
1.158 brouard 7435: printf("gnuplot command might not be in your path: '%s', err=%d\n", plotcmd, outcmd);
1.154 brouard 7436: printf("\n Trying if gnuplot resides on the same directory that IMaCh\n");
1.152 brouard 7437: sprintf(plotcmd,"%sgnuplot %s", pathimach, optionfilegnuplot);
1.150 brouard 7438: if((outcmd=system(plotcmd)) != 0)
1.153 brouard 7439: printf("\n Still a problem with gnuplot command %s, err=%d\n", plotcmd, outcmd);
1.126 brouard 7440: }
1.158 brouard 7441: printf(" Successful, please wait...");
1.126 brouard 7442: while (z[0] != 'q') {
7443: /* chdir(path); */
1.154 brouard 7444: printf("\nType e to edit results with your browser, g to graph again and q for exit: ");
1.126 brouard 7445: scanf("%s",z);
7446: /* if (z[0] == 'c') system("./imach"); */
7447: if (z[0] == 'e') {
1.158 brouard 7448: #ifdef __APPLE__
1.152 brouard 7449: sprintf(pplotcmd, "open %s", optionfilehtm);
1.157 brouard 7450: #elif __linux
7451: sprintf(pplotcmd, "xdg-open %s", optionfilehtm);
1.153 brouard 7452: #else
1.152 brouard 7453: sprintf(pplotcmd, "%s", optionfilehtm);
1.153 brouard 7454: #endif
7455: printf("Starting browser with: %s",pplotcmd);fflush(stdout);
7456: system(pplotcmd);
1.126 brouard 7457: }
7458: else if (z[0] == 'g') system(plotcmd);
7459: else if (z[0] == 'q') exit(0);
7460: }
7461: end:
7462: while (z[0] != 'q') {
7463: printf("\nType q for exiting: ");
7464: scanf("%s",z);
7465: }
7466: }
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