Annotation of imach/src/imach.c, revision 1.176
1.176 ! brouard 1: /* $Id: imach.c,v 1.175 2015/01/03 16:33:42 brouard Exp $
1.126 brouard 2: $State: Exp $
1.163 brouard 3: $Log: imach.c,v $
1.176 ! brouard 4: Revision 1.175 2015/01/03 16:33:42 brouard
! 5: *** empty log message ***
! 6:
1.175 brouard 7: Revision 1.174 2015/01/03 16:15:49 brouard
8: Summary: Still in cross-compilation
9:
1.174 brouard 10: Revision 1.173 2015/01/03 12:06:26 brouard
11: Summary: trying to detect cross-compilation
12:
1.173 brouard 13: Revision 1.172 2014/12/27 12:07:47 brouard
14: Summary: Back from Visual Studio and Intel, options for compiling for Windows XP
15:
1.172 brouard 16: Revision 1.171 2014/12/23 13:26:59 brouard
17: Summary: Back from Visual C
18:
19: Still problem with utsname.h on Windows
20:
1.171 brouard 21: Revision 1.170 2014/12/23 11:17:12 brouard
22: Summary: Cleaning some \%% back to %%
23:
24: The escape was mandatory for a specific compiler (which one?), but too many warnings.
25:
1.170 brouard 26: Revision 1.169 2014/12/22 23:08:31 brouard
27: Summary: 0.98p
28:
29: Outputs some informations on compiler used, OS etc. Testing on different platforms.
30:
1.169 brouard 31: Revision 1.168 2014/12/22 15:17:42 brouard
1.170 brouard 32: Summary: update
1.169 brouard 33:
1.168 brouard 34: Revision 1.167 2014/12/22 13:50:56 brouard
35: Summary: Testing uname and compiler version and if compiled 32 or 64
36:
37: Testing on Linux 64
38:
1.167 brouard 39: Revision 1.166 2014/12/22 11:40:47 brouard
40: *** empty log message ***
41:
1.166 brouard 42: Revision 1.165 2014/12/16 11:20:36 brouard
43: Summary: After compiling on Visual C
44:
45: * imach.c (Module): Merging 1.61 to 1.162
46:
1.165 brouard 47: Revision 1.164 2014/12/16 10:52:11 brouard
48: Summary: Merging with Visual C after suppressing some warnings for unused variables. Also fixing Saito's bug 0.98Xn
49:
50: * imach.c (Module): Merging 1.61 to 1.162
51:
1.164 brouard 52: Revision 1.163 2014/12/16 10:30:11 brouard
53: * imach.c (Module): Merging 1.61 to 1.162
54:
1.163 brouard 55: Revision 1.162 2014/09/25 11:43:39 brouard
56: Summary: temporary backup 0.99!
57:
1.162 brouard 58: Revision 1.1 2014/09/16 11:06:58 brouard
59: Summary: With some code (wrong) for nlopt
60:
61: Author:
62:
63: Revision 1.161 2014/09/15 20:41:41 brouard
64: Summary: Problem with macro SQR on Intel compiler
65:
1.161 brouard 66: Revision 1.160 2014/09/02 09:24:05 brouard
67: *** empty log message ***
68:
1.160 brouard 69: Revision 1.159 2014/09/01 10:34:10 brouard
70: Summary: WIN32
71: Author: Brouard
72:
1.159 brouard 73: Revision 1.158 2014/08/27 17:11:51 brouard
74: *** empty log message ***
75:
1.158 brouard 76: Revision 1.157 2014/08/27 16:26:55 brouard
77: Summary: Preparing windows Visual studio version
78: Author: Brouard
79:
80: In order to compile on Visual studio, time.h is now correct and time_t
81: and tm struct should be used. difftime should be used but sometimes I
82: just make the differences in raw time format (time(&now).
83: Trying to suppress #ifdef LINUX
84: Add xdg-open for __linux in order to open default browser.
85:
1.157 brouard 86: Revision 1.156 2014/08/25 20:10:10 brouard
87: *** empty log message ***
88:
1.156 brouard 89: Revision 1.155 2014/08/25 18:32:34 brouard
90: Summary: New compile, minor changes
91: Author: Brouard
92:
1.155 brouard 93: Revision 1.154 2014/06/20 17:32:08 brouard
94: Summary: Outputs now all graphs of convergence to period prevalence
95:
1.154 brouard 96: Revision 1.153 2014/06/20 16:45:46 brouard
97: Summary: If 3 live state, convergence to period prevalence on same graph
98: Author: Brouard
99:
1.153 brouard 100: Revision 1.152 2014/06/18 17:54:09 brouard
101: Summary: open browser, use gnuplot on same dir than imach if not found in the path
102:
1.152 brouard 103: Revision 1.151 2014/06/18 16:43:30 brouard
104: *** empty log message ***
105:
1.151 brouard 106: Revision 1.150 2014/06/18 16:42:35 brouard
107: Summary: If gnuplot is not in the path try on same directory than imach binary (OSX)
108: Author: brouard
109:
1.150 brouard 110: Revision 1.149 2014/06/18 15:51:14 brouard
111: Summary: Some fixes in parameter files errors
112: Author: Nicolas Brouard
113:
1.149 brouard 114: Revision 1.148 2014/06/17 17:38:48 brouard
115: Summary: Nothing new
116: Author: Brouard
117:
118: Just a new packaging for OS/X version 0.98nS
119:
1.148 brouard 120: Revision 1.147 2014/06/16 10:33:11 brouard
121: *** empty log message ***
122:
1.147 brouard 123: Revision 1.146 2014/06/16 10:20:28 brouard
124: Summary: Merge
125: Author: Brouard
126:
127: Merge, before building revised version.
128:
1.146 brouard 129: Revision 1.145 2014/06/10 21:23:15 brouard
130: Summary: Debugging with valgrind
131: Author: Nicolas Brouard
132:
133: Lot of changes in order to output the results with some covariates
134: After the Edimburgh REVES conference 2014, it seems mandatory to
135: improve the code.
136: No more memory valgrind error but a lot has to be done in order to
137: continue the work of splitting the code into subroutines.
138: Also, decodemodel has been improved. Tricode is still not
139: optimal. nbcode should be improved. Documentation has been added in
140: the source code.
141:
1.144 brouard 142: Revision 1.143 2014/01/26 09:45:38 brouard
143: Summary: Version 0.98nR (to be improved, but gives same optimization results as 0.98k. Nice, promising
144:
145: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
146: (Module): Version 0.98nR Running ok, but output format still only works for three covariates.
147:
1.143 brouard 148: Revision 1.142 2014/01/26 03:57:36 brouard
149: Summary: gnuplot changed plot w l 1 has to be changed to plot w l lt 2
150:
151: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
152:
1.142 brouard 153: Revision 1.141 2014/01/26 02:42:01 brouard
154: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
155:
1.141 brouard 156: Revision 1.140 2011/09/02 10:37:54 brouard
157: Summary: times.h is ok with mingw32 now.
158:
1.140 brouard 159: Revision 1.139 2010/06/14 07:50:17 brouard
160: After the theft of my laptop, I probably lost some lines of codes which were not uploaded to the CVS tree.
161: I remember having already fixed agemin agemax which are pointers now but not cvs saved.
162:
1.139 brouard 163: Revision 1.138 2010/04/30 18:19:40 brouard
164: *** empty log message ***
165:
1.138 brouard 166: Revision 1.137 2010/04/29 18:11:38 brouard
167: (Module): Checking covariates for more complex models
168: than V1+V2. A lot of change to be done. Unstable.
169:
1.137 brouard 170: Revision 1.136 2010/04/26 20:30:53 brouard
171: (Module): merging some libgsl code. Fixing computation
172: of likelione (using inter/intrapolation if mle = 0) in order to
173: get same likelihood as if mle=1.
174: Some cleaning of code and comments added.
175:
1.136 brouard 176: Revision 1.135 2009/10/29 15:33:14 brouard
177: (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
178:
1.135 brouard 179: Revision 1.134 2009/10/29 13:18:53 brouard
180: (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
181:
1.134 brouard 182: Revision 1.133 2009/07/06 10:21:25 brouard
183: just nforces
184:
1.133 brouard 185: Revision 1.132 2009/07/06 08:22:05 brouard
186: Many tings
187:
1.132 brouard 188: Revision 1.131 2009/06/20 16:22:47 brouard
189: Some dimensions resccaled
190:
1.131 brouard 191: Revision 1.130 2009/05/26 06:44:34 brouard
192: (Module): Max Covariate is now set to 20 instead of 8. A
193: lot of cleaning with variables initialized to 0. Trying to make
194: V2+V3*age+V1+V4 strb=V3*age+V1+V4 working better.
195:
1.130 brouard 196: Revision 1.129 2007/08/31 13:49:27 lievre
197: Modification of the way of exiting when the covariate is not binary in order to see on the window the error message before exiting
198:
1.129 lievre 199: Revision 1.128 2006/06/30 13:02:05 brouard
200: (Module): Clarifications on computing e.j
201:
1.128 brouard 202: Revision 1.127 2006/04/28 18:11:50 brouard
203: (Module): Yes the sum of survivors was wrong since
204: imach-114 because nhstepm was no more computed in the age
205: loop. Now we define nhstepma in the age loop.
206: (Module): In order to speed up (in case of numerous covariates) we
207: compute health expectancies (without variances) in a first step
208: and then all the health expectancies with variances or standard
209: deviation (needs data from the Hessian matrices) which slows the
210: computation.
211: In the future we should be able to stop the program is only health
212: expectancies and graph are needed without standard deviations.
213:
1.127 brouard 214: Revision 1.126 2006/04/28 17:23:28 brouard
215: (Module): Yes the sum of survivors was wrong since
216: imach-114 because nhstepm was no more computed in the age
217: loop. Now we define nhstepma in the age loop.
218: Version 0.98h
219:
1.126 brouard 220: Revision 1.125 2006/04/04 15:20:31 lievre
221: Errors in calculation of health expectancies. Age was not initialized.
222: Forecasting file added.
223:
224: Revision 1.124 2006/03/22 17:13:53 lievre
225: Parameters are printed with %lf instead of %f (more numbers after the comma).
226: The log-likelihood is printed in the log file
227:
228: Revision 1.123 2006/03/20 10:52:43 brouard
229: * imach.c (Module): <title> changed, corresponds to .htm file
230: name. <head> headers where missing.
231:
232: * imach.c (Module): Weights can have a decimal point as for
233: English (a comma might work with a correct LC_NUMERIC environment,
234: otherwise the weight is truncated).
235: Modification of warning when the covariates values are not 0 or
236: 1.
237: Version 0.98g
238:
239: Revision 1.122 2006/03/20 09:45:41 brouard
240: (Module): Weights can have a decimal point as for
241: English (a comma might work with a correct LC_NUMERIC environment,
242: otherwise the weight is truncated).
243: Modification of warning when the covariates values are not 0 or
244: 1.
245: Version 0.98g
246:
247: Revision 1.121 2006/03/16 17:45:01 lievre
248: * imach.c (Module): Comments concerning covariates added
249:
250: * imach.c (Module): refinements in the computation of lli if
251: status=-2 in order to have more reliable computation if stepm is
252: not 1 month. Version 0.98f
253:
254: Revision 1.120 2006/03/16 15:10:38 lievre
255: (Module): refinements in the computation of lli if
256: status=-2 in order to have more reliable computation if stepm is
257: not 1 month. Version 0.98f
258:
259: Revision 1.119 2006/03/15 17:42:26 brouard
260: (Module): Bug if status = -2, the loglikelihood was
261: computed as likelihood omitting the logarithm. Version O.98e
262:
263: Revision 1.118 2006/03/14 18:20:07 brouard
264: (Module): varevsij Comments added explaining the second
265: table of variances if popbased=1 .
266: (Module): Covariances of eij, ekl added, graphs fixed, new html link.
267: (Module): Function pstamp added
268: (Module): Version 0.98d
269:
270: Revision 1.117 2006/03/14 17:16:22 brouard
271: (Module): varevsij Comments added explaining the second
272: table of variances if popbased=1 .
273: (Module): Covariances of eij, ekl added, graphs fixed, new html link.
274: (Module): Function pstamp added
275: (Module): Version 0.98d
276:
277: Revision 1.116 2006/03/06 10:29:27 brouard
278: (Module): Variance-covariance wrong links and
279: varian-covariance of ej. is needed (Saito).
280:
281: Revision 1.115 2006/02/27 12:17:45 brouard
282: (Module): One freematrix added in mlikeli! 0.98c
283:
284: Revision 1.114 2006/02/26 12:57:58 brouard
285: (Module): Some improvements in processing parameter
286: filename with strsep.
287:
288: Revision 1.113 2006/02/24 14:20:24 brouard
289: (Module): Memory leaks checks with valgrind and:
290: datafile was not closed, some imatrix were not freed and on matrix
291: allocation too.
292:
293: Revision 1.112 2006/01/30 09:55:26 brouard
294: (Module): Back to gnuplot.exe instead of wgnuplot.exe
295:
296: Revision 1.111 2006/01/25 20:38:18 brouard
297: (Module): Lots of cleaning and bugs added (Gompertz)
298: (Module): Comments can be added in data file. Missing date values
299: can be a simple dot '.'.
300:
301: Revision 1.110 2006/01/25 00:51:50 brouard
302: (Module): Lots of cleaning and bugs added (Gompertz)
303:
304: Revision 1.109 2006/01/24 19:37:15 brouard
305: (Module): Comments (lines starting with a #) are allowed in data.
306:
307: Revision 1.108 2006/01/19 18:05:42 lievre
308: Gnuplot problem appeared...
309: To be fixed
310:
311: Revision 1.107 2006/01/19 16:20:37 brouard
312: Test existence of gnuplot in imach path
313:
314: Revision 1.106 2006/01/19 13:24:36 brouard
315: Some cleaning and links added in html output
316:
317: Revision 1.105 2006/01/05 20:23:19 lievre
318: *** empty log message ***
319:
320: Revision 1.104 2005/09/30 16:11:43 lievre
321: (Module): sump fixed, loop imx fixed, and simplifications.
322: (Module): If the status is missing at the last wave but we know
323: that the person is alive, then we can code his/her status as -2
324: (instead of missing=-1 in earlier versions) and his/her
325: contributions to the likelihood is 1 - Prob of dying from last
326: health status (= 1-p13= p11+p12 in the easiest case of somebody in
327: the healthy state at last known wave). Version is 0.98
328:
329: Revision 1.103 2005/09/30 15:54:49 lievre
330: (Module): sump fixed, loop imx fixed, and simplifications.
331:
332: Revision 1.102 2004/09/15 17:31:30 brouard
333: Add the possibility to read data file including tab characters.
334:
335: Revision 1.101 2004/09/15 10:38:38 brouard
336: Fix on curr_time
337:
338: Revision 1.100 2004/07/12 18:29:06 brouard
339: Add version for Mac OS X. Just define UNIX in Makefile
340:
341: Revision 1.99 2004/06/05 08:57:40 brouard
342: *** empty log message ***
343:
344: Revision 1.98 2004/05/16 15:05:56 brouard
345: New version 0.97 . First attempt to estimate force of mortality
346: directly from the data i.e. without the need of knowing the health
347: state at each age, but using a Gompertz model: log u =a + b*age .
348: This is the basic analysis of mortality and should be done before any
349: other analysis, in order to test if the mortality estimated from the
350: cross-longitudinal survey is different from the mortality estimated
351: from other sources like vital statistic data.
352:
353: The same imach parameter file can be used but the option for mle should be -3.
354:
1.133 brouard 355: Agnès, who wrote this part of the code, tried to keep most of the
1.126 brouard 356: former routines in order to include the new code within the former code.
357:
358: The output is very simple: only an estimate of the intercept and of
359: the slope with 95% confident intervals.
360:
361: Current limitations:
362: A) Even if you enter covariates, i.e. with the
363: model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
364: B) There is no computation of Life Expectancy nor Life Table.
365:
366: Revision 1.97 2004/02/20 13:25:42 lievre
367: Version 0.96d. Population forecasting command line is (temporarily)
368: suppressed.
369:
370: Revision 1.96 2003/07/15 15:38:55 brouard
371: * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
372: rewritten within the same printf. Workaround: many printfs.
373:
374: Revision 1.95 2003/07/08 07:54:34 brouard
375: * imach.c (Repository):
376: (Repository): Using imachwizard code to output a more meaningful covariance
377: matrix (cov(a12,c31) instead of numbers.
378:
379: Revision 1.94 2003/06/27 13:00:02 brouard
380: Just cleaning
381:
382: Revision 1.93 2003/06/25 16:33:55 brouard
383: (Module): On windows (cygwin) function asctime_r doesn't
384: exist so I changed back to asctime which exists.
385: (Module): Version 0.96b
386:
387: Revision 1.92 2003/06/25 16:30:45 brouard
388: (Module): On windows (cygwin) function asctime_r doesn't
389: exist so I changed back to asctime which exists.
390:
391: Revision 1.91 2003/06/25 15:30:29 brouard
392: * imach.c (Repository): Duplicated warning errors corrected.
393: (Repository): Elapsed time after each iteration is now output. It
394: helps to forecast when convergence will be reached. Elapsed time
395: is stamped in powell. We created a new html file for the graphs
396: concerning matrix of covariance. It has extension -cov.htm.
397:
398: Revision 1.90 2003/06/24 12:34:15 brouard
399: (Module): Some bugs corrected for windows. Also, when
400: mle=-1 a template is output in file "or"mypar.txt with the design
401: of the covariance matrix to be input.
402:
403: Revision 1.89 2003/06/24 12:30:52 brouard
404: (Module): Some bugs corrected for windows. Also, when
405: mle=-1 a template is output in file "or"mypar.txt with the design
406: of the covariance matrix to be input.
407:
408: Revision 1.88 2003/06/23 17:54:56 brouard
409: * 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.
410:
411: Revision 1.87 2003/06/18 12:26:01 brouard
412: Version 0.96
413:
414: Revision 1.86 2003/06/17 20:04:08 brouard
415: (Module): Change position of html and gnuplot routines and added
416: routine fileappend.
417:
418: Revision 1.85 2003/06/17 13:12:43 brouard
419: * imach.c (Repository): Check when date of death was earlier that
420: current date of interview. It may happen when the death was just
421: prior to the death. In this case, dh was negative and likelihood
422: was wrong (infinity). We still send an "Error" but patch by
423: assuming that the date of death was just one stepm after the
424: interview.
425: (Repository): Because some people have very long ID (first column)
426: we changed int to long in num[] and we added a new lvector for
427: memory allocation. But we also truncated to 8 characters (left
428: truncation)
429: (Repository): No more line truncation errors.
430:
431: Revision 1.84 2003/06/13 21:44:43 brouard
432: * imach.c (Repository): Replace "freqsummary" at a correct
433: place. It differs from routine "prevalence" which may be called
434: many times. Probs is memory consuming and must be used with
435: parcimony.
436: Version 0.95a3 (should output exactly the same maximization than 0.8a2)
437:
438: Revision 1.83 2003/06/10 13:39:11 lievre
439: *** empty log message ***
440:
441: Revision 1.82 2003/06/05 15:57:20 brouard
442: Add log in imach.c and fullversion number is now printed.
443:
444: */
445: /*
446: Interpolated Markov Chain
447:
448: Short summary of the programme:
449:
450: This program computes Healthy Life Expectancies from
451: cross-longitudinal data. Cross-longitudinal data consist in: -1- a
452: first survey ("cross") where individuals from different ages are
453: interviewed on their health status or degree of disability (in the
454: case of a health survey which is our main interest) -2- at least a
455: second wave of interviews ("longitudinal") which measure each change
456: (if any) in individual health status. Health expectancies are
457: computed from the time spent in each health state according to a
458: model. More health states you consider, more time is necessary to reach the
459: Maximum Likelihood of the parameters involved in the model. The
460: simplest model is the multinomial logistic model where pij is the
461: probability to be observed in state j at the second wave
462: conditional to be observed in state i at the first wave. Therefore
463: the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
464: 'age' is age and 'sex' is a covariate. If you want to have a more
465: complex model than "constant and age", you should modify the program
466: where the markup *Covariates have to be included here again* invites
467: you to do it. More covariates you add, slower the
468: convergence.
469:
470: The advantage of this computer programme, compared to a simple
471: multinomial logistic model, is clear when the delay between waves is not
472: identical for each individual. Also, if a individual missed an
473: intermediate interview, the information is lost, but taken into
474: account using an interpolation or extrapolation.
475:
476: hPijx is the probability to be observed in state i at age x+h
477: conditional to the observed state i at age x. The delay 'h' can be
478: split into an exact number (nh*stepm) of unobserved intermediate
479: states. This elementary transition (by month, quarter,
480: semester or year) is modelled as a multinomial logistic. The hPx
481: matrix is simply the matrix product of nh*stepm elementary matrices
482: and the contribution of each individual to the likelihood is simply
483: hPijx.
484:
485: Also this programme outputs the covariance matrix of the parameters but also
486: of the life expectancies. It also computes the period (stable) prevalence.
487:
1.133 brouard 488: Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
489: Institut national d'études démographiques, Paris.
1.126 brouard 490: This software have been partly granted by Euro-REVES, a concerted action
491: from the European Union.
492: It is copyrighted identically to a GNU software product, ie programme and
493: software can be distributed freely for non commercial use. Latest version
494: can be accessed at http://euroreves.ined.fr/imach .
495:
496: Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
497: or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
498:
499: **********************************************************************/
500: /*
501: main
502: read parameterfile
503: read datafile
504: concatwav
505: freqsummary
506: if (mle >= 1)
507: mlikeli
508: print results files
509: if mle==1
510: computes hessian
511: read end of parameter file: agemin, agemax, bage, fage, estepm
512: begin-prev-date,...
513: open gnuplot file
514: open html file
1.145 brouard 515: period (stable) prevalence | pl_nom 1-1 2-2 etc by covariate
516: for age prevalim() | #****** V1=0 V2=1 V3=1 V4=0 ******
517: | 65 1 0 2 1 3 1 4 0 0.96326 0.03674
518: freexexit2 possible for memory heap.
519:
520: h Pij x | pij_nom ficrestpij
521: # Cov Agex agex+h hpijx with i,j= 1-1 1-2 1-3 2-1 2-2 2-3
522: 1 85 85 1.00000 0.00000 0.00000 0.00000 1.00000 0.00000
523: 1 85 86 0.68299 0.22291 0.09410 0.71093 0.00000 0.28907
524:
525: 1 65 99 0.00364 0.00322 0.99314 0.00350 0.00310 0.99340
526: 1 65 100 0.00214 0.00204 0.99581 0.00206 0.00196 0.99597
527: variance of p one-step probabilities varprob | prob_nom ficresprob #One-step probabilities and stand. devi in ()
528: Standard deviation of one-step probabilities | probcor_nom ficresprobcor #One-step probabilities and correlation matrix
529: Matrix of variance covariance of one-step probabilities | probcov_nom ficresprobcov #One-step probabilities and covariance matrix
530:
1.126 brouard 531: forecasting if prevfcast==1 prevforecast call prevalence()
532: health expectancies
533: Variance-covariance of DFLE
534: prevalence()
535: movingaverage()
536: varevsij()
537: if popbased==1 varevsij(,popbased)
538: total life expectancies
539: Variance of period (stable) prevalence
540: end
541: */
542:
1.165 brouard 543: #define POWELL /* Instead of NLOPT */
1.126 brouard 544:
545: #include <math.h>
546: #include <stdio.h>
547: #include <stdlib.h>
548: #include <string.h>
1.159 brouard 549:
550: #ifdef _WIN32
551: #include <io.h>
1.172 brouard 552: #include <windows.h>
553: #include <tchar.h>
1.159 brouard 554: #else
1.126 brouard 555: #include <unistd.h>
1.159 brouard 556: #endif
1.126 brouard 557:
558: #include <limits.h>
559: #include <sys/types.h>
1.171 brouard 560:
561: #if defined(__GNUC__)
562: #include <sys/utsname.h> /* Doesn't work on Windows */
563: #endif
564:
1.126 brouard 565: #include <sys/stat.h>
566: #include <errno.h>
1.159 brouard 567: /* extern int errno; */
1.126 brouard 568:
1.157 brouard 569: /* #ifdef LINUX */
570: /* #include <time.h> */
571: /* #include "timeval.h" */
572: /* #else */
573: /* #include <sys/time.h> */
574: /* #endif */
575:
1.126 brouard 576: #include <time.h>
577:
1.136 brouard 578: #ifdef GSL
579: #include <gsl/gsl_errno.h>
580: #include <gsl/gsl_multimin.h>
581: #endif
582:
1.167 brouard 583:
1.162 brouard 584: #ifdef NLOPT
585: #include <nlopt.h>
586: typedef struct {
587: double (* function)(double [] );
588: } myfunc_data ;
589: #endif
590:
1.126 brouard 591: /* #include <libintl.h> */
592: /* #define _(String) gettext (String) */
593:
1.141 brouard 594: #define MAXLINE 1024 /* Was 256. Overflow with 312 with 2 states and 4 covariates. Should be ok */
1.126 brouard 595:
596: #define GNUPLOTPROGRAM "gnuplot"
597: /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
598: #define FILENAMELENGTH 132
599:
600: #define GLOCK_ERROR_NOPATH -1 /* empty path */
601: #define GLOCK_ERROR_GETCWD -2 /* cannot get cwd */
602:
1.144 brouard 603: #define MAXPARM 128 /**< Maximum number of parameters for the optimization */
604: #define NPARMAX 64 /**< (nlstate+ndeath-1)*nlstate*ncovmodel */
1.126 brouard 605:
606: #define NINTERVMAX 8
1.144 brouard 607: #define NLSTATEMAX 8 /**< Maximum number of live states (for func) */
608: #define NDEATHMAX 8 /**< Maximum number of dead states (for func) */
609: #define NCOVMAX 20 /**< Maximum number of covariates, including generated covariates V1*V2 */
1.145 brouard 610: #define codtabm(h,k) 1 & (h-1) >> (k-1) ;
1.126 brouard 611: #define MAXN 20000
1.144 brouard 612: #define YEARM 12. /**< Number of months per year */
1.126 brouard 613: #define AGESUP 130
614: #define AGEBASE 40
1.164 brouard 615: #define AGEGOMP 10 /**< Minimal age for Gompertz adjustment */
1.157 brouard 616: #ifdef _WIN32
617: #define DIRSEPARATOR '\\'
618: #define CHARSEPARATOR "\\"
619: #define ODIRSEPARATOR '/'
620: #else
1.126 brouard 621: #define DIRSEPARATOR '/'
622: #define CHARSEPARATOR "/"
623: #define ODIRSEPARATOR '\\'
624: #endif
625:
1.176 ! brouard 626: /* $Id: imach.c,v 1.175 2015/01/03 16:33:42 brouard Exp $ */
1.126 brouard 627: /* $State: Exp $ */
628:
1.169 brouard 629: char version[]="Imach version 0.98p, December 2014,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121), Intel Software 2015";
1.176 ! brouard 630: char fullversion[]="$Revision: 1.175 $ $Date: 2015/01/03 16:33:42 $";
1.126 brouard 631: char strstart[80];
632: char optionfilext[10], optionfilefiname[FILENAMELENGTH];
1.130 brouard 633: int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings */
1.133 brouard 634: int nvar=0, nforce=0; /* Number of variables, number of forces */
1.145 brouard 635: /* Number of covariates model=V2+V1+ V3*age+V2*V4 */
636: int cptcovn=0; /**< cptcovn number of covariates added in the model (excepting constant and age and age*product) */
637: int cptcovt=0; /**< cptcovt number of covariates added in the model (excepting constant and age) */
638: int cptcovs=0; /**< cptcovs number of simple covariates V2+V1 =2 */
639: int cptcovage=0; /**< Number of covariates with age: V3*age only =1 */
640: int cptcovprodnoage=0; /**< Number of covariate products without age */
641: int cptcoveff=0; /* Total number of covariates to vary for printing results */
642: int cptcov=0; /* Working variable */
1.126 brouard 643: int npar=NPARMAX;
644: int nlstate=2; /* Number of live states */
645: int ndeath=1; /* Number of dead states */
1.130 brouard 646: int ncovmodel=0, ncovcol=0; /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
1.126 brouard 647: int popbased=0;
648:
649: int *wav; /* Number of waves for this individuual 0 is possible */
1.130 brouard 650: int maxwav=0; /* Maxim number of waves */
651: int jmin=0, jmax=0; /* min, max spacing between 2 waves */
652: int ijmin=0, ijmax=0; /* Individuals having jmin and jmax */
653: int gipmx=0, gsw=0; /* Global variables on the number of contributions
1.126 brouard 654: to the likelihood and the sum of weights (done by funcone)*/
1.130 brouard 655: int mle=1, weightopt=0;
1.126 brouard 656: int **mw; /* mw[mi][i] is number of the mi wave for this individual */
657: int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
658: int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
659: * wave mi and wave mi+1 is not an exact multiple of stepm. */
1.162 brouard 660: int countcallfunc=0; /* Count the number of calls to func */
1.130 brouard 661: double jmean=1; /* Mean space between 2 waves */
1.145 brouard 662: double **matprod2(); /* test */
1.126 brouard 663: double **oldm, **newm, **savm; /* Working pointers to matrices */
664: double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
1.136 brouard 665: /*FILE *fic ; */ /* Used in readdata only */
666: FILE *ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
1.126 brouard 667: FILE *ficlog, *ficrespow;
1.130 brouard 668: int globpr=0; /* Global variable for printing or not */
1.126 brouard 669: double fretone; /* Only one call to likelihood */
1.130 brouard 670: long ipmx=0; /* Number of contributions */
1.126 brouard 671: double sw; /* Sum of weights */
672: char filerespow[FILENAMELENGTH];
673: char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
674: FILE *ficresilk;
675: FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
676: FILE *ficresprobmorprev;
677: FILE *fichtm, *fichtmcov; /* Html File */
678: FILE *ficreseij;
679: char filerese[FILENAMELENGTH];
680: FILE *ficresstdeij;
681: char fileresstde[FILENAMELENGTH];
682: FILE *ficrescveij;
683: char filerescve[FILENAMELENGTH];
684: FILE *ficresvij;
685: char fileresv[FILENAMELENGTH];
686: FILE *ficresvpl;
687: char fileresvpl[FILENAMELENGTH];
688: char title[MAXLINE];
689: char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH], filerespl[FILENAMELENGTH];
690: char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
691: char tmpout[FILENAMELENGTH], tmpout2[FILENAMELENGTH];
692: char command[FILENAMELENGTH];
693: int outcmd=0;
694:
695: char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
696:
697: char filelog[FILENAMELENGTH]; /* Log file */
698: char filerest[FILENAMELENGTH];
699: char fileregp[FILENAMELENGTH];
700: char popfile[FILENAMELENGTH];
701:
702: char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
703:
1.157 brouard 704: /* struct timeval start_time, end_time, curr_time, last_time, forecast_time; */
705: /* struct timezone tzp; */
706: /* extern int gettimeofday(); */
707: struct tm tml, *gmtime(), *localtime();
708:
709: extern time_t time();
710:
711: struct tm start_time, end_time, curr_time, last_time, forecast_time;
712: time_t rstart_time, rend_time, rcurr_time, rlast_time, rforecast_time; /* raw time */
713: struct tm tm;
714:
1.126 brouard 715: char strcurr[80], strfor[80];
716:
717: char *endptr;
718: long lval;
719: double dval;
720:
721: #define NR_END 1
722: #define FREE_ARG char*
723: #define FTOL 1.0e-10
724:
725: #define NRANSI
726: #define ITMAX 200
727:
728: #define TOL 2.0e-4
729:
730: #define CGOLD 0.3819660
731: #define ZEPS 1.0e-10
732: #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);
733:
734: #define GOLD 1.618034
735: #define GLIMIT 100.0
736: #define TINY 1.0e-20
737:
738: static double maxarg1,maxarg2;
739: #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
740: #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
741:
742: #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
743: #define rint(a) floor(a+0.5)
1.166 brouard 744: /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/myutils_8h-source.html */
745: /* #define mytinydouble 1.0e-16 */
746: /* #define DEQUAL(a,b) (fabs((a)-(b))<mytinydouble) */
747: /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/mynrutils_8h-source.html */
748: /* static double dsqrarg; */
749: /* #define DSQR(a) (DEQUAL((dsqrarg=(a)),0.0) ? 0.0 : dsqrarg*dsqrarg) */
1.126 brouard 750: static double sqrarg;
751: #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
752: #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}
753: int agegomp= AGEGOMP;
754:
755: int imx;
756: int stepm=1;
757: /* Stepm, step in month: minimum step interpolation*/
758:
759: int estepm;
760: /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
761:
762: int m,nb;
763: long *num;
764: int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
765: double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
766: double **pmmij, ***probs;
767: double *ageexmed,*agecens;
768: double dateintmean=0;
769:
770: double *weight;
771: int **s; /* Status */
1.141 brouard 772: double *agedc;
1.145 brouard 773: double **covar; /**< covar[j,i], value of jth covariate for individual i,
1.141 brouard 774: * covar=matrix(0,NCOVMAX,1,n);
775: * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; */
776: double idx;
777: int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */
1.145 brouard 778: int *Ndum; /** Freq of modality (tricode */
1.141 brouard 779: int **codtab; /**< codtab=imatrix(1,100,1,10); */
780: int **Tvard, *Tprod, cptcovprod, *Tvaraff;
1.126 brouard 781: double *lsurv, *lpop, *tpop;
782:
1.143 brouard 783: double ftol=FTOL; /**< Tolerance for computing Max Likelihood */
784: double ftolhess; /**< Tolerance for computing hessian */
1.126 brouard 785:
786: /**************** split *************************/
787: static int split( char *path, char *dirc, char *name, char *ext, char *finame )
788: {
789: /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
790: the name of the file (name), its extension only (ext) and its first part of the name (finame)
791: */
792: char *ss; /* pointer */
793: int l1, l2; /* length counters */
794:
795: l1 = strlen(path ); /* length of path */
796: if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
797: ss= strrchr( path, DIRSEPARATOR ); /* find last / */
798: if ( ss == NULL ) { /* no directory, so determine current directory */
799: strcpy( name, path ); /* we got the fullname name because no directory */
800: /*if(strrchr(path, ODIRSEPARATOR )==NULL)
801: printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
802: /* get current working directory */
803: /* extern char* getcwd ( char *buf , int len);*/
804: if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
805: return( GLOCK_ERROR_GETCWD );
806: }
807: /* got dirc from getcwd*/
808: printf(" DIRC = %s \n",dirc);
809: } else { /* strip direcotry from path */
810: ss++; /* after this, the filename */
811: l2 = strlen( ss ); /* length of filename */
812: if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
813: strcpy( name, ss ); /* save file name */
814: strncpy( dirc, path, l1 - l2 ); /* now the directory */
815: dirc[l1-l2] = 0; /* add zero */
816: printf(" DIRC2 = %s \n",dirc);
817: }
818: /* We add a separator at the end of dirc if not exists */
819: l1 = strlen( dirc ); /* length of directory */
820: if( dirc[l1-1] != DIRSEPARATOR ){
821: dirc[l1] = DIRSEPARATOR;
822: dirc[l1+1] = 0;
823: printf(" DIRC3 = %s \n",dirc);
824: }
825: ss = strrchr( name, '.' ); /* find last / */
826: if (ss >0){
827: ss++;
828: strcpy(ext,ss); /* save extension */
829: l1= strlen( name);
830: l2= strlen(ss)+1;
831: strncpy( finame, name, l1-l2);
832: finame[l1-l2]= 0;
833: }
834:
835: return( 0 ); /* we're done */
836: }
837:
838:
839: /******************************************/
840:
841: void replace_back_to_slash(char *s, char*t)
842: {
843: int i;
844: int lg=0;
845: i=0;
846: lg=strlen(t);
847: for(i=0; i<= lg; i++) {
848: (s[i] = t[i]);
849: if (t[i]== '\\') s[i]='/';
850: }
851: }
852:
1.132 brouard 853: char *trimbb(char *out, char *in)
1.137 brouard 854: { /* Trim multiple blanks in line but keeps first blanks if line starts with blanks */
1.132 brouard 855: char *s;
856: s=out;
857: while (*in != '\0'){
1.137 brouard 858: while( *in == ' ' && *(in+1) == ' '){ /* && *(in+1) != '\0'){*/
1.132 brouard 859: in++;
860: }
861: *out++ = *in++;
862: }
863: *out='\0';
864: return s;
865: }
866:
1.145 brouard 867: char *cutl(char *blocc, char *alocc, char *in, char occ)
868: {
869: /* cuts string in into blocc and alocc where blocc ends before first occurence of char 'occ'
870: and alocc starts after first occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
871: gives blocc="abcdef2ghi" and alocc="j".
872: If occ is not found blocc is null and alocc is equal to in. Returns blocc
873: */
1.160 brouard 874: char *s, *t;
1.145 brouard 875: t=in;s=in;
876: while ((*in != occ) && (*in != '\0')){
877: *alocc++ = *in++;
878: }
879: if( *in == occ){
880: *(alocc)='\0';
881: s=++in;
882: }
883:
884: if (s == t) {/* occ not found */
885: *(alocc-(in-s))='\0';
886: in=s;
887: }
888: while ( *in != '\0'){
889: *blocc++ = *in++;
890: }
891:
892: *blocc='\0';
893: return t;
894: }
1.137 brouard 895: char *cutv(char *blocc, char *alocc, char *in, char occ)
896: {
897: /* cuts string in into blocc and alocc where blocc ends before last occurence of char 'occ'
898: and alocc starts after last occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
899: gives blocc="abcdef2ghi" and alocc="j".
900: If occ is not found blocc is null and alocc is equal to in. Returns alocc
901: */
902: char *s, *t;
903: t=in;s=in;
904: while (*in != '\0'){
905: while( *in == occ){
906: *blocc++ = *in++;
907: s=in;
908: }
909: *blocc++ = *in++;
910: }
911: if (s == t) /* occ not found */
912: *(blocc-(in-s))='\0';
913: else
914: *(blocc-(in-s)-1)='\0';
915: in=s;
916: while ( *in != '\0'){
917: *alocc++ = *in++;
918: }
919:
920: *alocc='\0';
921: return s;
922: }
923:
1.126 brouard 924: int nbocc(char *s, char occ)
925: {
926: int i,j=0;
927: int lg=20;
928: i=0;
929: lg=strlen(s);
930: for(i=0; i<= lg; i++) {
931: if (s[i] == occ ) j++;
932: }
933: return j;
934: }
935:
1.137 brouard 936: /* void cutv(char *u,char *v, char*t, char occ) */
937: /* { */
938: /* /\* cuts string t into u and v where u ends before last occurence of char 'occ' */
939: /* and v starts after last occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2') */
940: /* gives u="abcdef2ghi" and v="j" *\/ */
941: /* int i,lg,j,p=0; */
942: /* i=0; */
943: /* lg=strlen(t); */
944: /* for(j=0; j<=lg-1; j++) { */
945: /* if((t[j]!= occ) && (t[j+1]== occ)) p=j+1; */
946: /* } */
1.126 brouard 947:
1.137 brouard 948: /* for(j=0; j<p; j++) { */
949: /* (u[j] = t[j]); */
950: /* } */
951: /* u[p]='\0'; */
1.126 brouard 952:
1.137 brouard 953: /* for(j=0; j<= lg; j++) { */
954: /* if (j>=(p+1))(v[j-p-1] = t[j]); */
955: /* } */
956: /* } */
1.126 brouard 957:
1.160 brouard 958: #ifdef _WIN32
959: char * strsep(char **pp, const char *delim)
960: {
961: char *p, *q;
962:
963: if ((p = *pp) == NULL)
964: return 0;
965: if ((q = strpbrk (p, delim)) != NULL)
966: {
967: *pp = q + 1;
968: *q = '\0';
969: }
970: else
971: *pp = 0;
972: return p;
973: }
974: #endif
975:
1.126 brouard 976: /********************** nrerror ********************/
977:
978: void nrerror(char error_text[])
979: {
980: fprintf(stderr,"ERREUR ...\n");
981: fprintf(stderr,"%s\n",error_text);
982: exit(EXIT_FAILURE);
983: }
984: /*********************** vector *******************/
985: double *vector(int nl, int nh)
986: {
987: double *v;
988: v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
989: if (!v) nrerror("allocation failure in vector");
990: return v-nl+NR_END;
991: }
992:
993: /************************ free vector ******************/
994: void free_vector(double*v, int nl, int nh)
995: {
996: free((FREE_ARG)(v+nl-NR_END));
997: }
998:
999: /************************ivector *******************************/
1000: int *ivector(long nl,long nh)
1001: {
1002: int *v;
1003: v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
1004: if (!v) nrerror("allocation failure in ivector");
1005: return v-nl+NR_END;
1006: }
1007:
1008: /******************free ivector **************************/
1009: void free_ivector(int *v, long nl, long nh)
1010: {
1011: free((FREE_ARG)(v+nl-NR_END));
1012: }
1013:
1014: /************************lvector *******************************/
1015: long *lvector(long nl,long nh)
1016: {
1017: long *v;
1018: v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
1019: if (!v) nrerror("allocation failure in ivector");
1020: return v-nl+NR_END;
1021: }
1022:
1023: /******************free lvector **************************/
1024: void free_lvector(long *v, long nl, long nh)
1025: {
1026: free((FREE_ARG)(v+nl-NR_END));
1027: }
1028:
1029: /******************* imatrix *******************************/
1030: int **imatrix(long nrl, long nrh, long ncl, long nch)
1031: /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */
1032: {
1033: long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;
1034: int **m;
1035:
1036: /* allocate pointers to rows */
1037: m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));
1038: if (!m) nrerror("allocation failure 1 in matrix()");
1039: m += NR_END;
1040: m -= nrl;
1041:
1042:
1043: /* allocate rows and set pointers to them */
1044: m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));
1045: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
1046: m[nrl] += NR_END;
1047: m[nrl] -= ncl;
1048:
1049: for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;
1050:
1051: /* return pointer to array of pointers to rows */
1052: return m;
1053: }
1054:
1055: /****************** free_imatrix *************************/
1056: void free_imatrix(m,nrl,nrh,ncl,nch)
1057: int **m;
1058: long nch,ncl,nrh,nrl;
1059: /* free an int matrix allocated by imatrix() */
1060: {
1061: free((FREE_ARG) (m[nrl]+ncl-NR_END));
1062: free((FREE_ARG) (m+nrl-NR_END));
1063: }
1064:
1065: /******************* matrix *******************************/
1066: double **matrix(long nrl, long nrh, long ncl, long nch)
1067: {
1068: long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
1069: double **m;
1070:
1071: m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
1072: if (!m) nrerror("allocation failure 1 in matrix()");
1073: m += NR_END;
1074: m -= nrl;
1075:
1076: m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
1077: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
1078: m[nrl] += NR_END;
1079: m[nrl] -= ncl;
1080:
1081: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
1082: return m;
1.145 brouard 1083: /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) or &(m[1][0])
1084: m[i] = address of ith row of the table. &(m[i]) is its value which is another adress
1085: that of m[i][0]. In order to get the value p m[i][0] but it is unitialized.
1.126 brouard 1086: */
1087: }
1088:
1089: /*************************free matrix ************************/
1090: void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
1091: {
1092: free((FREE_ARG)(m[nrl]+ncl-NR_END));
1093: free((FREE_ARG)(m+nrl-NR_END));
1094: }
1095:
1096: /******************* ma3x *******************************/
1097: double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
1098: {
1099: long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
1100: double ***m;
1101:
1102: m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
1103: if (!m) nrerror("allocation failure 1 in matrix()");
1104: m += NR_END;
1105: m -= nrl;
1106:
1107: m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
1108: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
1109: m[nrl] += NR_END;
1110: m[nrl] -= ncl;
1111:
1112: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
1113:
1114: m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
1115: if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
1116: m[nrl][ncl] += NR_END;
1117: m[nrl][ncl] -= nll;
1118: for (j=ncl+1; j<=nch; j++)
1119: m[nrl][j]=m[nrl][j-1]+nlay;
1120:
1121: for (i=nrl+1; i<=nrh; i++) {
1122: m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
1123: for (j=ncl+1; j<=nch; j++)
1124: m[i][j]=m[i][j-1]+nlay;
1125: }
1126: return m;
1127: /* gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
1128: &(m[i][j][k]) <=> *((*(m+i) + j)+k)
1129: */
1130: }
1131:
1132: /*************************free ma3x ************************/
1133: void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
1134: {
1135: free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
1136: free((FREE_ARG)(m[nrl]+ncl-NR_END));
1137: free((FREE_ARG)(m+nrl-NR_END));
1138: }
1139:
1140: /*************** function subdirf ***********/
1141: char *subdirf(char fileres[])
1142: {
1143: /* Caution optionfilefiname is hidden */
1144: strcpy(tmpout,optionfilefiname);
1145: strcat(tmpout,"/"); /* Add to the right */
1146: strcat(tmpout,fileres);
1147: return tmpout;
1148: }
1149:
1150: /*************** function subdirf2 ***********/
1151: char *subdirf2(char fileres[], char *preop)
1152: {
1153:
1154: /* Caution optionfilefiname is hidden */
1155: strcpy(tmpout,optionfilefiname);
1156: strcat(tmpout,"/");
1157: strcat(tmpout,preop);
1158: strcat(tmpout,fileres);
1159: return tmpout;
1160: }
1161:
1162: /*************** function subdirf3 ***********/
1163: char *subdirf3(char fileres[], char *preop, char *preop2)
1164: {
1165:
1166: /* Caution optionfilefiname is hidden */
1167: strcpy(tmpout,optionfilefiname);
1168: strcat(tmpout,"/");
1169: strcat(tmpout,preop);
1170: strcat(tmpout,preop2);
1171: strcat(tmpout,fileres);
1172: return tmpout;
1173: }
1174:
1.162 brouard 1175: char *asc_diff_time(long time_sec, char ascdiff[])
1176: {
1177: long sec_left, days, hours, minutes;
1178: days = (time_sec) / (60*60*24);
1179: sec_left = (time_sec) % (60*60*24);
1180: hours = (sec_left) / (60*60) ;
1181: sec_left = (sec_left) %(60*60);
1182: minutes = (sec_left) /60;
1183: sec_left = (sec_left) % (60);
1184: sprintf(ascdiff,"%ld day(s) %ld hour(s) %ld minute(s) %ld second(s)",days, hours, minutes, sec_left);
1185: return ascdiff;
1186: }
1187:
1.126 brouard 1188: /***************** f1dim *************************/
1189: extern int ncom;
1190: extern double *pcom,*xicom;
1191: extern double (*nrfunc)(double []);
1192:
1193: double f1dim(double x)
1194: {
1195: int j;
1196: double f;
1197: double *xt;
1198:
1199: xt=vector(1,ncom);
1200: for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];
1201: f=(*nrfunc)(xt);
1202: free_vector(xt,1,ncom);
1203: return f;
1204: }
1205:
1206: /*****************brent *************************/
1207: double brent(double ax, double bx, double cx, double (*f)(double), double tol, double *xmin)
1208: {
1209: int iter;
1210: double a,b,d,etemp;
1.159 brouard 1211: double fu=0,fv,fw,fx;
1.164 brouard 1212: double ftemp=0.;
1.126 brouard 1213: double p,q,r,tol1,tol2,u,v,w,x,xm;
1214: double e=0.0;
1215:
1216: a=(ax < cx ? ax : cx);
1217: b=(ax > cx ? ax : cx);
1218: x=w=v=bx;
1219: fw=fv=fx=(*f)(x);
1220: for (iter=1;iter<=ITMAX;iter++) {
1221: xm=0.5*(a+b);
1222: tol2=2.0*(tol1=tol*fabs(x)+ZEPS);
1223: /* if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
1224: printf(".");fflush(stdout);
1225: fprintf(ficlog,".");fflush(ficlog);
1.162 brouard 1226: #ifdef DEBUGBRENT
1.126 brouard 1227: 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);
1228: 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);
1229: /* if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
1230: #endif
1231: if (fabs(x-xm) <= (tol2-0.5*(b-a))){
1232: *xmin=x;
1233: return fx;
1234: }
1235: ftemp=fu;
1236: if (fabs(e) > tol1) {
1237: r=(x-w)*(fx-fv);
1238: q=(x-v)*(fx-fw);
1239: p=(x-v)*q-(x-w)*r;
1240: q=2.0*(q-r);
1241: if (q > 0.0) p = -p;
1242: q=fabs(q);
1243: etemp=e;
1244: e=d;
1245: if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))
1246: d=CGOLD*(e=(x >= xm ? a-x : b-x));
1247: else {
1248: d=p/q;
1249: u=x+d;
1250: if (u-a < tol2 || b-u < tol2)
1251: d=SIGN(tol1,xm-x);
1252: }
1253: } else {
1254: d=CGOLD*(e=(x >= xm ? a-x : b-x));
1255: }
1256: u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));
1257: fu=(*f)(u);
1258: if (fu <= fx) {
1259: if (u >= x) a=x; else b=x;
1260: SHFT(v,w,x,u)
1261: SHFT(fv,fw,fx,fu)
1262: } else {
1263: if (u < x) a=u; else b=u;
1264: if (fu <= fw || w == x) {
1265: v=w;
1266: w=u;
1267: fv=fw;
1268: fw=fu;
1269: } else if (fu <= fv || v == x || v == w) {
1270: v=u;
1271: fv=fu;
1272: }
1273: }
1274: }
1275: nrerror("Too many iterations in brent");
1276: *xmin=x;
1277: return fx;
1278: }
1279:
1280: /****************** mnbrak ***********************/
1281:
1282: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,
1283: double (*func)(double))
1284: {
1285: double ulim,u,r,q, dum;
1286: double fu;
1287:
1288: *fa=(*func)(*ax);
1289: *fb=(*func)(*bx);
1290: if (*fb > *fa) {
1291: SHFT(dum,*ax,*bx,dum)
1292: SHFT(dum,*fb,*fa,dum)
1293: }
1294: *cx=(*bx)+GOLD*(*bx-*ax);
1295: *fc=(*func)(*cx);
1.162 brouard 1296: while (*fb > *fc) { /* Declining fa, fb, fc */
1.126 brouard 1297: r=(*bx-*ax)*(*fb-*fc);
1298: q=(*bx-*cx)*(*fb-*fa);
1299: u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/
1.162 brouard 1300: (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); /* Minimum abscisse of a parabolic estimated from (a,fa), (b,fb) and (c,fc). */
1301: ulim=(*bx)+GLIMIT*(*cx-*bx); /* Maximum abscisse where function can be evaluated */
1302: if ((*bx-u)*(u-*cx) > 0.0) { /* if u between b and c */
1.126 brouard 1303: fu=(*func)(u);
1.163 brouard 1304: #ifdef DEBUG
1305: /* f(x)=A(x-u)**2+f(u) */
1306: double A, fparabu;
1307: A= (*fb - *fa)/(*bx-*ax)/(*bx+*ax-2*u);
1308: fparabu= *fa - A*(*ax-u)*(*ax-u);
1309: 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);
1310: 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);
1311: #endif
1.162 brouard 1312: } else if ((*cx-u)*(u-ulim) > 0.0) { /* u is after c but before ulim */
1.126 brouard 1313: fu=(*func)(u);
1314: if (fu < *fc) {
1315: SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))
1316: SHFT(*fb,*fc,fu,(*func)(u))
1317: }
1.162 brouard 1318: } else if ((u-ulim)*(ulim-*cx) >= 0.0) { /* u outside ulim (verifying that ulim is beyond c) */
1.126 brouard 1319: u=ulim;
1320: fu=(*func)(u);
1321: } else {
1322: u=(*cx)+GOLD*(*cx-*bx);
1323: fu=(*func)(u);
1324: }
1325: SHFT(*ax,*bx,*cx,u)
1326: SHFT(*fa,*fb,*fc,fu)
1327: }
1328: }
1329:
1330: /*************** linmin ************************/
1.162 brouard 1331: /* Given an n -dimensional point p[1..n] and an n -dimensional direction xi[1..n] , moves and
1332: resets p to where the function func(p) takes on a minimum along the direction xi from p ,
1333: and replaces xi by the actual vector displacement that p was moved. Also returns as fret
1334: the value of func at the returned location p . This is actually all accomplished by calling the
1335: routines mnbrak and brent .*/
1.126 brouard 1336: int ncom;
1337: double *pcom,*xicom;
1338: double (*nrfunc)(double []);
1339:
1340: void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))
1341: {
1342: double brent(double ax, double bx, double cx,
1343: double (*f)(double), double tol, double *xmin);
1344: double f1dim(double x);
1345: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,
1346: double *fc, double (*func)(double));
1347: int j;
1348: double xx,xmin,bx,ax;
1349: double fx,fb,fa;
1350:
1351: ncom=n;
1352: pcom=vector(1,n);
1353: xicom=vector(1,n);
1354: nrfunc=func;
1355: for (j=1;j<=n;j++) {
1356: pcom[j]=p[j];
1357: xicom[j]=xi[j];
1358: }
1359: ax=0.0;
1360: xx=1.0;
1.162 brouard 1361: mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); /* Find a bracket a,x,b in direction n=xi ie xicom */
1362: *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 1363: #ifdef DEBUG
1364: printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
1365: fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
1366: #endif
1367: for (j=1;j<=n;j++) {
1368: xi[j] *= xmin;
1369: p[j] += xi[j];
1370: }
1371: free_vector(xicom,1,n);
1372: free_vector(pcom,1,n);
1373: }
1374:
1375:
1376: /*************** powell ************************/
1.162 brouard 1377: /*
1378: Minimization of a function func of n variables. Input consists of an initial starting point
1379: p[1..n] ; an initial matrix xi[1..n][1..n] , whose columns contain the initial set of di-
1380: rections (usually the n unit vectors); and ftol , the fractional tolerance in the function value
1381: such that failure to decrease by more than this amount on one iteration signals doneness. On
1382: output, p is set to the best point found, xi is the then-current direction set, fret is the returned
1383: function value at p , and iter is the number of iterations taken. The routine linmin is used.
1384: */
1.126 brouard 1385: void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,
1386: double (*func)(double []))
1387: {
1388: void linmin(double p[], double xi[], int n, double *fret,
1389: double (*func)(double []));
1390: int i,ibig,j;
1391: double del,t,*pt,*ptt,*xit;
1392: double fp,fptt;
1393: double *xits;
1394: int niterf, itmp;
1395:
1396: pt=vector(1,n);
1397: ptt=vector(1,n);
1398: xit=vector(1,n);
1399: xits=vector(1,n);
1400: *fret=(*func)(p);
1401: for (j=1;j<=n;j++) pt[j]=p[j];
1.157 brouard 1402: rcurr_time = time(NULL);
1.126 brouard 1403: for (*iter=1;;++(*iter)) {
1404: fp=(*fret);
1405: ibig=0;
1406: del=0.0;
1.157 brouard 1407: rlast_time=rcurr_time;
1408: /* (void) gettimeofday(&curr_time,&tzp); */
1409: rcurr_time = time(NULL);
1410: curr_time = *localtime(&rcurr_time);
1411: printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, rcurr_time-rlast_time, rcurr_time-rstart_time);fflush(stdout);
1412: fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret,rcurr_time-rlast_time, rcurr_time-rstart_time); fflush(ficlog);
1413: /* fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tm_sec-start_time.tm_sec); */
1.126 brouard 1414: for (i=1;i<=n;i++) {
1415: printf(" %d %.12f",i, p[i]);
1416: fprintf(ficlog," %d %.12lf",i, p[i]);
1417: fprintf(ficrespow," %.12lf", p[i]);
1418: }
1419: printf("\n");
1420: fprintf(ficlog,"\n");
1421: fprintf(ficrespow,"\n");fflush(ficrespow);
1422: if(*iter <=3){
1.157 brouard 1423: tml = *localtime(&rcurr_time);
1424: strcpy(strcurr,asctime(&tml));
1425: rforecast_time=rcurr_time;
1.126 brouard 1426: itmp = strlen(strcurr);
1427: if(strcurr[itmp-1]=='\n') /* Windows outputs with a new line */
1428: strcurr[itmp-1]='\0';
1.162 brouard 1429: printf("\nConsidering the time needed for the last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
1.157 brouard 1430: fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
1.126 brouard 1431: for(niterf=10;niterf<=30;niterf+=10){
1.157 brouard 1432: rforecast_time=rcurr_time+(niterf-*iter)*(rcurr_time-rlast_time);
1433: forecast_time = *localtime(&rforecast_time);
1434: strcpy(strfor,asctime(&forecast_time));
1.126 brouard 1435: itmp = strlen(strfor);
1436: if(strfor[itmp-1]=='\n')
1437: strfor[itmp-1]='\0';
1.157 brouard 1438: 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);
1439: 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 1440: }
1441: }
1442: for (i=1;i<=n;i++) {
1443: for (j=1;j<=n;j++) xit[j]=xi[j][i];
1444: fptt=(*fret);
1445: #ifdef DEBUG
1.164 brouard 1446: printf("fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
1447: fprintf(ficlog, "fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
1.126 brouard 1448: #endif
1449: printf("%d",i);fflush(stdout);
1450: fprintf(ficlog,"%d",i);fflush(ficlog);
1451: linmin(p,xit,n,fret,func);
1452: if (fabs(fptt-(*fret)) > del) {
1453: del=fabs(fptt-(*fret));
1454: ibig=i;
1455: }
1456: #ifdef DEBUG
1457: printf("%d %.12e",i,(*fret));
1458: fprintf(ficlog,"%d %.12e",i,(*fret));
1459: for (j=1;j<=n;j++) {
1460: xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
1461: printf(" x(%d)=%.12e",j,xit[j]);
1462: fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
1463: }
1464: for(j=1;j<=n;j++) {
1.162 brouard 1465: printf(" p(%d)=%.12e",j,p[j]);
1466: fprintf(ficlog," p(%d)=%.12e",j,p[j]);
1.126 brouard 1467: }
1468: printf("\n");
1469: fprintf(ficlog,"\n");
1470: #endif
1.162 brouard 1471: } /* end i */
1.126 brouard 1472: if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
1473: #ifdef DEBUG
1474: int k[2],l;
1475: k[0]=1;
1476: k[1]=-1;
1477: printf("Max: %.12e",(*func)(p));
1478: fprintf(ficlog,"Max: %.12e",(*func)(p));
1479: for (j=1;j<=n;j++) {
1480: printf(" %.12e",p[j]);
1481: fprintf(ficlog," %.12e",p[j]);
1482: }
1483: printf("\n");
1484: fprintf(ficlog,"\n");
1485: for(l=0;l<=1;l++) {
1486: for (j=1;j<=n;j++) {
1487: ptt[j]=p[j]+(p[j]-pt[j])*k[l];
1488: printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
1489: fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
1490: }
1491: printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
1492: fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
1493: }
1494: #endif
1495:
1496:
1497: free_vector(xit,1,n);
1498: free_vector(xits,1,n);
1499: free_vector(ptt,1,n);
1500: free_vector(pt,1,n);
1501: return;
1502: }
1503: if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");
1.161 brouard 1504: for (j=1;j<=n;j++) { /* Computes an extrapolated point */
1.126 brouard 1505: ptt[j]=2.0*p[j]-pt[j];
1506: xit[j]=p[j]-pt[j];
1507: pt[j]=p[j];
1508: }
1509: fptt=(*func)(ptt);
1.161 brouard 1510: if (fptt < fp) { /* If extrapolated point is better, decide if we keep that new direction or not */
1.162 brouard 1511: /* (x1 f1=fp), (x2 f2=*fret), (x3 f3=fptt), (xm fm) */
1.161 brouard 1512: /* From x1 (P0) distance of x2 is at h and x3 is 2h */
1.162 brouard 1513: /* Let f"(x2) be the 2nd derivative equal everywhere. */
1514: /* Then the parabolic through (x1,f1), (x2,f2) and (x3,f3) */
1515: /* will reach at f3 = fm + h^2/2 f"m ; f" = (f1 -2f2 +f3 ) / h**2 */
1.161 brouard 1516: /* f1-f3 = delta(2h) = 2 h**2 f'' = 2(f1- 2f2 +f3) */
1517: /* Thus we compare delta(2h) with observed f1-f3 */
1.162 brouard 1518: /* or best gain on one ancient line 'del' with total */
1519: /* gain f1-f2 = f1 - f2 - 'del' with del */
1.161 brouard 1520: /* t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); */
1.162 brouard 1521:
1.161 brouard 1522: t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del);
1523: t= t- del*SQR(fp-fptt);
1524: printf("t1= %.12lf, t2= %.12lf, t=%.12lf\n", 2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del),del*SQR(fp-fptt),t);
1525: fprintf(ficlog,"t1= %.12lf, t2= %.12lf, t=%.12lf\n", 2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del),del*SQR(fp-fptt),t);
1526: #ifdef DEBUG
1527: printf("t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
1528: (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
1529: fprintf(ficlog,"t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
1530: (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
1531: 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);
1532: 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);
1533: #endif
1534: if (t < 0.0) { /* Then we use it for last direction */
1535: linmin(p,xit,n,fret,func); /* computes mean on the extrapolated direction.*/
1.126 brouard 1536: for (j=1;j<=n;j++) {
1.161 brouard 1537: xi[j][ibig]=xi[j][n]; /* Replace the direction with biggest decrease by n */
1538: xi[j][n]=xit[j]; /* and nth direction by the extrapolated */
1.126 brouard 1539: }
1.161 brouard 1540: printf("Gaining to use average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
1.169 brouard 1541: fprintf(ficlog,"Gaining to use average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
1.161 brouard 1542:
1.126 brouard 1543: #ifdef DEBUG
1.164 brouard 1544: printf("Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
1545: fprintf(ficlog,"Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
1.126 brouard 1546: for(j=1;j<=n;j++){
1547: printf(" %.12e",xit[j]);
1548: fprintf(ficlog," %.12e",xit[j]);
1549: }
1550: printf("\n");
1551: fprintf(ficlog,"\n");
1552: #endif
1.162 brouard 1553: } /* end of t negative */
1554: } /* end if (fptt < fp) */
1.126 brouard 1555: }
1556: }
1557:
1558: /**** Prevalence limit (stable or period prevalence) ****************/
1559:
1560: double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
1561: {
1562: /* Computes the prevalence limit in each live state at age x by left multiplying the unit
1563: matrix by transitions matrix until convergence is reached */
1.169 brouard 1564:
1.126 brouard 1565: int i, ii,j,k;
1566: double min, max, maxmin, maxmax,sumnew=0.;
1.145 brouard 1567: /* double **matprod2(); */ /* test */
1.131 brouard 1568: double **out, cov[NCOVMAX+1], **pmij();
1.126 brouard 1569: double **newm;
1570: double agefin, delaymax=50 ; /* Max number of years to converge */
1.169 brouard 1571:
1.126 brouard 1572: for (ii=1;ii<=nlstate+ndeath;ii++)
1573: for (j=1;j<=nlstate+ndeath;j++){
1574: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1575: }
1.169 brouard 1576:
1577: cov[1]=1.;
1578:
1579: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
1.126 brouard 1580: for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
1581: newm=savm;
1582: /* Covariates have to be included here again */
1.138 brouard 1583: cov[2]=agefin;
1584:
1585: for (k=1; k<=cptcovn;k++) {
1586: cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
1.145 brouard 1587: /*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 1588: }
1.145 brouard 1589: /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
1590: /* for (k=1; k<=cptcovprod;k++) /\* Useless *\/ */
1591: /* 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 1592:
1593: /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
1594: /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
1595: /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
1.145 brouard 1596: /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
1597: /* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind *\/ */
1.142 brouard 1598: out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /* Bug Valgrind */
1.138 brouard 1599:
1.126 brouard 1600: savm=oldm;
1601: oldm=newm;
1602: maxmax=0.;
1603: for(j=1;j<=nlstate;j++){
1604: min=1.;
1605: max=0.;
1606: for(i=1; i<=nlstate; i++) {
1607: sumnew=0;
1608: for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
1609: prlim[i][j]= newm[i][j]/(1-sumnew);
1.145 brouard 1610: /*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 1611: max=FMAX(max,prlim[i][j]);
1612: min=FMIN(min,prlim[i][j]);
1613: }
1614: maxmin=max-min;
1615: maxmax=FMAX(maxmax,maxmin);
1.169 brouard 1616: } /* j loop */
1.126 brouard 1617: if(maxmax < ftolpl){
1618: return prlim;
1619: }
1.169 brouard 1620: } /* age loop */
1621: return prlim; /* should not reach here */
1.126 brouard 1622: }
1623:
1624: /*************** transition probabilities ***************/
1625:
1626: double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
1627: {
1.138 brouard 1628: /* According to parameters values stored in x and the covariate's values stored in cov,
1629: computes the probability to be observed in state j being in state i by appying the
1630: model to the ncovmodel covariates (including constant and age).
1631: lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc]
1632: and, according on how parameters are entered, the position of the coefficient xij(nc) of the
1633: ncth covariate in the global vector x is given by the formula:
1634: j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
1635: j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
1636: Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
1637: sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.
1638: Outputs ps[i][j] the probability to be observed in j being in j according to
1639: the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
1640: */
1641: double s1, lnpijopii;
1.126 brouard 1642: /*double t34;*/
1.164 brouard 1643: int i,j, nc, ii, jj;
1.126 brouard 1644:
1645: for(i=1; i<= nlstate; i++){
1646: for(j=1; j<i;j++){
1.138 brouard 1647: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
1648: /*lnpijopii += param[i][j][nc]*cov[nc];*/
1649: lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
1650: /* printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
1.126 brouard 1651: }
1.138 brouard 1652: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
1653: /* printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
1.126 brouard 1654: }
1655: for(j=i+1; j<=nlstate+ndeath;j++){
1.138 brouard 1656: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
1657: /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
1658: lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
1659: /* printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
1.126 brouard 1660: }
1.138 brouard 1661: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
1.126 brouard 1662: }
1663: }
1664:
1665: for(i=1; i<= nlstate; i++){
1666: s1=0;
1.131 brouard 1667: for(j=1; j<i; j++){
1.138 brouard 1668: s1+=exp(ps[i][j]); /* In fact sums pij/pii */
1.131 brouard 1669: /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
1670: }
1671: for(j=i+1; j<=nlstate+ndeath; j++){
1.138 brouard 1672: s1+=exp(ps[i][j]); /* In fact sums pij/pii */
1.131 brouard 1673: /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
1674: }
1.138 brouard 1675: /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
1.126 brouard 1676: ps[i][i]=1./(s1+1.);
1.138 brouard 1677: /* Computing other pijs */
1.126 brouard 1678: for(j=1; j<i; j++)
1679: ps[i][j]= exp(ps[i][j])*ps[i][i];
1680: for(j=i+1; j<=nlstate+ndeath; j++)
1681: ps[i][j]= exp(ps[i][j])*ps[i][i];
1682: /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
1683: } /* end i */
1684:
1685: for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
1686: for(jj=1; jj<= nlstate+ndeath; jj++){
1687: ps[ii][jj]=0;
1688: ps[ii][ii]=1;
1689: }
1690: }
1691:
1.145 brouard 1692:
1693: /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
1694: /* for(jj=1; jj<= nlstate+ndeath; jj++){ */
1695: /* printf(" pmij ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
1696: /* } */
1697: /* printf("\n "); */
1698: /* } */
1699: /* printf("\n ");printf("%lf ",cov[2]);*/
1700: /*
1.126 brouard 1701: for(i=1; i<= npar; i++) printf("%f ",x[i]);
1702: goto end;*/
1703: return ps;
1704: }
1705:
1706: /**************** Product of 2 matrices ******************/
1707:
1.145 brouard 1708: double **matprod2(double **out, double **in,int nrl, int nrh, int ncl, int nch, int ncolol, int ncoloh, double **b)
1.126 brouard 1709: {
1710: /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
1711: b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
1712: /* in, b, out are matrice of pointers which should have been initialized
1713: before: only the contents of out is modified. The function returns
1714: a pointer to pointers identical to out */
1.145 brouard 1715: int i, j, k;
1.126 brouard 1716: for(i=nrl; i<= nrh; i++)
1.145 brouard 1717: for(k=ncolol; k<=ncoloh; k++){
1718: out[i][k]=0.;
1719: for(j=ncl; j<=nch; j++)
1720: out[i][k] +=in[i][j]*b[j][k];
1721: }
1.126 brouard 1722: return out;
1723: }
1724:
1725:
1726: /************* Higher Matrix Product ***************/
1727:
1728: double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
1729: {
1730: /* Computes the transition matrix starting at age 'age' over
1731: 'nhstepm*hstepm*stepm' months (i.e. until
1732: age (in years) age+nhstepm*hstepm*stepm/12) by multiplying
1733: nhstepm*hstepm matrices.
1734: Output is stored in matrix po[i][j][h] for h every 'hstepm' step
1735: (typically every 2 years instead of every month which is too big
1736: for the memory).
1737: Model is determined by parameters x and covariates have to be
1738: included manually here.
1739:
1740: */
1741:
1742: int i, j, d, h, k;
1.131 brouard 1743: double **out, cov[NCOVMAX+1];
1.126 brouard 1744: double **newm;
1745:
1746: /* Hstepm could be zero and should return the unit matrix */
1747: for (i=1;i<=nlstate+ndeath;i++)
1748: for (j=1;j<=nlstate+ndeath;j++){
1749: oldm[i][j]=(i==j ? 1.0 : 0.0);
1750: po[i][j][0]=(i==j ? 1.0 : 0.0);
1751: }
1752: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
1753: for(h=1; h <=nhstepm; h++){
1754: for(d=1; d <=hstepm; d++){
1755: newm=savm;
1756: /* Covariates have to be included here again */
1757: cov[1]=1.;
1758: cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
1.131 brouard 1759: for (k=1; k<=cptcovn;k++)
1760: cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
1.126 brouard 1761: for (k=1; k<=cptcovage;k++)
1762: cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
1.145 brouard 1763: for (k=1; k<=cptcovprod;k++) /* Useless because included in cptcovn */
1.126 brouard 1764: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
1765:
1766:
1767: /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
1768: /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
1769: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
1770: pmij(pmmij,cov,ncovmodel,x,nlstate));
1771: savm=oldm;
1772: oldm=newm;
1773: }
1774: for(i=1; i<=nlstate+ndeath; i++)
1775: for(j=1;j<=nlstate+ndeath;j++) {
1776: po[i][j][h]=newm[i][j];
1.128 brouard 1777: /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
1.126 brouard 1778: }
1.128 brouard 1779: /*printf("h=%d ",h);*/
1.126 brouard 1780: } /* end h */
1.128 brouard 1781: /* printf("\n H=%d \n",h); */
1.126 brouard 1782: return po;
1783: }
1784:
1.162 brouard 1785: #ifdef NLOPT
1786: double myfunc(unsigned n, const double *p1, double *grad, void *pd){
1787: double fret;
1788: double *xt;
1789: int j;
1790: myfunc_data *d2 = (myfunc_data *) pd;
1791: /* xt = (p1-1); */
1792: xt=vector(1,n);
1793: for (j=1;j<=n;j++) xt[j]=p1[j-1]; /* xt[1]=p1[0] */
1794:
1795: fret=(d2->function)(xt); /* p xt[1]@8 is fine */
1796: /* fret=(*func)(xt); /\* p xt[1]@8 is fine *\/ */
1797: printf("Function = %.12lf ",fret);
1798: for (j=1;j<=n;j++) printf(" %d %.8lf", j, xt[j]);
1799: printf("\n");
1800: free_vector(xt,1,n);
1801: return fret;
1802: }
1803: #endif
1.126 brouard 1804:
1805: /*************** log-likelihood *************/
1806: double func( double *x)
1807: {
1808: int i, ii, j, k, mi, d, kk;
1.131 brouard 1809: double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
1.126 brouard 1810: double **out;
1811: double sw; /* Sum of weights */
1812: double lli; /* Individual log likelihood */
1813: int s1, s2;
1814: double bbh, survp;
1815: long ipmx;
1816: /*extern weight */
1817: /* We are differentiating ll according to initial status */
1818: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
1819: /*for(i=1;i<imx;i++)
1820: printf(" %d\n",s[4][i]);
1821: */
1.162 brouard 1822:
1823: ++countcallfunc;
1824:
1.126 brouard 1825: cov[1]=1.;
1826:
1827: for(k=1; k<=nlstate; k++) ll[k]=0.;
1828:
1829: if(mle==1){
1830: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1.138 brouard 1831: /* Computes the values of the ncovmodel covariates of the model
1832: depending if the covariates are fixed or variying (age dependent) and stores them in cov[]
1833: Then computes with function pmij which return a matrix p[i][j] giving the elementary probability
1834: to be observed in j being in i according to the model.
1835: */
1.145 brouard 1836: for (k=1; k<=cptcovn;k++){ /* Simple and product covariates without age* products */
1837: cov[2+k]=covar[Tvar[k]][i];
1838: }
1.137 brouard 1839: /* In model V2+V1*V4+age*V3+V3*V2 Tvar[1] is V2, Tvar[2=V1*V4]
1.138 brouard 1840: is 6, Tvar[3=age*V3] should not be computed because of age Tvar[4=V3*V2]
1.137 brouard 1841: has been calculated etc */
1.126 brouard 1842: for(mi=1; mi<= wav[i]-1; mi++){
1843: for (ii=1;ii<=nlstate+ndeath;ii++)
1844: for (j=1;j<=nlstate+ndeath;j++){
1845: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1846: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1847: }
1848: for(d=0; d<dh[mi][i]; d++){
1849: newm=savm;
1850: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1851: for (kk=1; kk<=cptcovage;kk++) {
1.137 brouard 1852: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; /* Tage[kk] gives the data-covariate associated with age */
1.126 brouard 1853: }
1854: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1855: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1856: savm=oldm;
1857: oldm=newm;
1858: } /* end mult */
1859:
1860: /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
1861: /* But now since version 0.9 we anticipate for bias at large stepm.
1862: * If stepm is larger than one month (smallest stepm) and if the exact delay
1863: * (in months) between two waves is not a multiple of stepm, we rounded to
1864: * the nearest (and in case of equal distance, to the lowest) interval but now
1865: * we keep into memory the bias bh[mi][i] and also the previous matrix product
1866: * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
1867: * probability in order to take into account the bias as a fraction of the way
1868: * from savm to out if bh is negative or even beyond if bh is positive. bh varies
1869: * -stepm/2 to stepm/2 .
1870: * For stepm=1 the results are the same as for previous versions of Imach.
1871: * For stepm > 1 the results are less biased than in previous versions.
1872: */
1873: s1=s[mw[mi][i]][i];
1874: s2=s[mw[mi+1][i]][i];
1875: bbh=(double)bh[mi][i]/(double)stepm;
1876: /* bias bh is positive if real duration
1877: * is higher than the multiple of stepm and negative otherwise.
1878: */
1879: /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
1880: if( s2 > nlstate){
1881: /* i.e. if s2 is a death state and if the date of death is known
1882: then the contribution to the likelihood is the probability to
1883: die between last step unit time and current step unit time,
1884: which is also equal to probability to die before dh
1885: minus probability to die before dh-stepm .
1886: In version up to 0.92 likelihood was computed
1887: as if date of death was unknown. Death was treated as any other
1888: health state: the date of the interview describes the actual state
1889: and not the date of a change in health state. The former idea was
1890: to consider that at each interview the state was recorded
1891: (healthy, disable or death) and IMaCh was corrected; but when we
1892: introduced the exact date of death then we should have modified
1893: the contribution of an exact death to the likelihood. This new
1894: contribution is smaller and very dependent of the step unit
1895: stepm. It is no more the probability to die between last interview
1896: and month of death but the probability to survive from last
1897: interview up to one month before death multiplied by the
1898: probability to die within a month. Thanks to Chris
1899: Jackson for correcting this bug. Former versions increased
1900: mortality artificially. The bad side is that we add another loop
1901: which slows down the processing. The difference can be up to 10%
1902: lower mortality.
1903: */
1904: lli=log(out[s1][s2] - savm[s1][s2]);
1905:
1906:
1907: } else if (s2==-2) {
1908: for (j=1,survp=0. ; j<=nlstate; j++)
1909: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
1910: /*survp += out[s1][j]; */
1911: lli= log(survp);
1912: }
1913:
1914: else if (s2==-4) {
1915: for (j=3,survp=0. ; j<=nlstate; j++)
1916: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
1917: lli= log(survp);
1918: }
1919:
1920: else if (s2==-5) {
1921: for (j=1,survp=0. ; j<=2; j++)
1922: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
1923: lli= log(survp);
1924: }
1925:
1926: else{
1927: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
1928: /* 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 */
1929: }
1930: /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
1931: /*if(lli ==000.0)*/
1932: /*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); */
1933: ipmx +=1;
1934: sw += weight[i];
1935: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1936: } /* end of wave */
1937: } /* end of individual */
1938: } else if(mle==2){
1939: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1940: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1941: for(mi=1; mi<= wav[i]-1; mi++){
1942: for (ii=1;ii<=nlstate+ndeath;ii++)
1943: for (j=1;j<=nlstate+ndeath;j++){
1944: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1945: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1946: }
1947: for(d=0; d<=dh[mi][i]; d++){
1948: newm=savm;
1949: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1950: for (kk=1; kk<=cptcovage;kk++) {
1951: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1952: }
1953: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1954: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1955: savm=oldm;
1956: oldm=newm;
1957: } /* end mult */
1958:
1959: s1=s[mw[mi][i]][i];
1960: s2=s[mw[mi+1][i]][i];
1961: bbh=(double)bh[mi][i]/(double)stepm;
1962: 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 */
1963: ipmx +=1;
1964: sw += weight[i];
1965: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1966: } /* end of wave */
1967: } /* end of individual */
1968: } else if(mle==3){ /* exponential inter-extrapolation */
1969: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1970: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1971: for(mi=1; mi<= wav[i]-1; mi++){
1972: for (ii=1;ii<=nlstate+ndeath;ii++)
1973: for (j=1;j<=nlstate+ndeath;j++){
1974: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1975: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1976: }
1977: for(d=0; d<dh[mi][i]; d++){
1978: newm=savm;
1979: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1980: for (kk=1; kk<=cptcovage;kk++) {
1981: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1982: }
1983: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1984: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1985: savm=oldm;
1986: oldm=newm;
1987: } /* end mult */
1988:
1989: s1=s[mw[mi][i]][i];
1990: s2=s[mw[mi+1][i]][i];
1991: bbh=(double)bh[mi][i]/(double)stepm;
1992: 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 */
1993: ipmx +=1;
1994: sw += weight[i];
1995: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1996: } /* end of wave */
1997: } /* end of individual */
1998: }else if (mle==4){ /* ml=4 no inter-extrapolation */
1999: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
2000: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
2001: for(mi=1; mi<= wav[i]-1; mi++){
2002: for (ii=1;ii<=nlstate+ndeath;ii++)
2003: for (j=1;j<=nlstate+ndeath;j++){
2004: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2005: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2006: }
2007: for(d=0; d<dh[mi][i]; d++){
2008: newm=savm;
2009: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
2010: for (kk=1; kk<=cptcovage;kk++) {
2011: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
2012: }
2013:
2014: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2015: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
2016: savm=oldm;
2017: oldm=newm;
2018: } /* end mult */
2019:
2020: s1=s[mw[mi][i]][i];
2021: s2=s[mw[mi+1][i]][i];
2022: if( s2 > nlstate){
2023: lli=log(out[s1][s2] - savm[s1][s2]);
2024: }else{
2025: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
2026: }
2027: ipmx +=1;
2028: sw += weight[i];
2029: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
2030: /* 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]); */
2031: } /* end of wave */
2032: } /* end of individual */
2033: }else{ /* ml=5 no inter-extrapolation no jackson =0.8a */
2034: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
2035: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
2036: for(mi=1; mi<= wav[i]-1; mi++){
2037: for (ii=1;ii<=nlstate+ndeath;ii++)
2038: for (j=1;j<=nlstate+ndeath;j++){
2039: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2040: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2041: }
2042: for(d=0; d<dh[mi][i]; d++){
2043: newm=savm;
2044: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
2045: for (kk=1; kk<=cptcovage;kk++) {
2046: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
2047: }
2048:
2049: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2050: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
2051: savm=oldm;
2052: oldm=newm;
2053: } /* end mult */
2054:
2055: s1=s[mw[mi][i]][i];
2056: s2=s[mw[mi+1][i]][i];
2057: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
2058: ipmx +=1;
2059: sw += weight[i];
2060: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
2061: /*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]);*/
2062: } /* end of wave */
2063: } /* end of individual */
2064: } /* End of if */
2065: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
2066: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
2067: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
2068: return -l;
2069: }
2070:
2071: /*************** log-likelihood *************/
2072: double funcone( double *x)
2073: {
2074: /* Same as likeli but slower because of a lot of printf and if */
2075: int i, ii, j, k, mi, d, kk;
1.131 brouard 2076: double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
1.126 brouard 2077: double **out;
2078: double lli; /* Individual log likelihood */
2079: double llt;
2080: int s1, s2;
2081: double bbh, survp;
2082: /*extern weight */
2083: /* We are differentiating ll according to initial status */
2084: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
2085: /*for(i=1;i<imx;i++)
2086: printf(" %d\n",s[4][i]);
2087: */
2088: cov[1]=1.;
2089:
2090: for(k=1; k<=nlstate; k++) ll[k]=0.;
2091:
2092: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
2093: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
2094: for(mi=1; mi<= wav[i]-1; mi++){
2095: for (ii=1;ii<=nlstate+ndeath;ii++)
2096: for (j=1;j<=nlstate+ndeath;j++){
2097: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2098: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2099: }
2100: for(d=0; d<dh[mi][i]; d++){
2101: newm=savm;
2102: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
2103: for (kk=1; kk<=cptcovage;kk++) {
2104: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
2105: }
1.145 brouard 2106: /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
1.126 brouard 2107: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2108: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1.145 brouard 2109: /* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, */
2110: /* 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); */
1.126 brouard 2111: savm=oldm;
2112: oldm=newm;
2113: } /* end mult */
2114:
2115: s1=s[mw[mi][i]][i];
2116: s2=s[mw[mi+1][i]][i];
2117: bbh=(double)bh[mi][i]/(double)stepm;
2118: /* bias is positive if real duration
2119: * is higher than the multiple of stepm and negative otherwise.
2120: */
2121: if( s2 > nlstate && (mle <5) ){ /* Jackson */
2122: lli=log(out[s1][s2] - savm[s1][s2]);
2123: } else if (s2==-2) {
2124: for (j=1,survp=0. ; j<=nlstate; j++)
2125: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
2126: lli= log(survp);
2127: }else if (mle==1){
2128: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
2129: } else if(mle==2){
2130: 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 */
2131: } else if(mle==3){ /* exponential inter-extrapolation */
2132: 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 */
2133: } else if (mle==4){ /* mle=4 no inter-extrapolation */
2134: lli=log(out[s1][s2]); /* Original formula */
1.136 brouard 2135: } else{ /* mle=0 back to 1 */
2136: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
2137: /*lli=log(out[s1][s2]); */ /* Original formula */
1.126 brouard 2138: } /* End of if */
2139: ipmx +=1;
2140: sw += weight[i];
2141: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1.132 brouard 2142: /*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 2143: if(globpr){
1.141 brouard 2144: fprintf(ficresilk,"%9ld %6d %2d %2d %1d %1d %3d %11.6f %8.4f\
1.126 brouard 2145: %11.6f %11.6f %11.6f ", \
2146: num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
2147: 2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
2148: for(k=1,llt=0.,l=0.; k<=nlstate; k++){
2149: llt +=ll[k]*gipmx/gsw;
2150: fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
2151: }
2152: fprintf(ficresilk," %10.6f\n", -llt);
2153: }
2154: } /* end of wave */
2155: } /* end of individual */
2156: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
2157: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
2158: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
2159: if(globpr==0){ /* First time we count the contributions and weights */
2160: gipmx=ipmx;
2161: gsw=sw;
2162: }
2163: return -l;
2164: }
2165:
2166:
2167: /*************** function likelione ***********/
2168: void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
2169: {
2170: /* This routine should help understanding what is done with
2171: the selection of individuals/waves and
2172: to check the exact contribution to the likelihood.
2173: Plotting could be done.
2174: */
2175: int k;
2176:
2177: if(*globpri !=0){ /* Just counts and sums, no printings */
2178: strcpy(fileresilk,"ilk");
2179: strcat(fileresilk,fileres);
2180: if((ficresilk=fopen(fileresilk,"w"))==NULL) {
2181: printf("Problem with resultfile: %s\n", fileresilk);
2182: fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
2183: }
2184: 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");
2185: fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
2186: /* i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
2187: for(k=1; k<=nlstate; k++)
2188: fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
2189: fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
2190: }
2191:
2192: *fretone=(*funcone)(p);
2193: if(*globpri !=0){
2194: fclose(ficresilk);
2195: fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
2196: fflush(fichtm);
2197: }
2198: return;
2199: }
2200:
2201:
2202: /*********** Maximum Likelihood Estimation ***************/
2203:
2204: void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
2205: {
1.165 brouard 2206: int i,j, iter=0;
1.126 brouard 2207: double **xi;
2208: double fret;
2209: double fretone; /* Only one call to likelihood */
2210: /* char filerespow[FILENAMELENGTH];*/
1.162 brouard 2211:
2212: #ifdef NLOPT
2213: int creturn;
2214: nlopt_opt opt;
2215: /* double lb[9] = { -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL }; /\* lower bounds *\/ */
2216: double *lb;
2217: double minf; /* the minimum objective value, upon return */
2218: double * p1; /* Shifted parameters from 0 instead of 1 */
2219: myfunc_data dinst, *d = &dinst;
2220: #endif
2221:
2222:
1.126 brouard 2223: xi=matrix(1,npar,1,npar);
2224: for (i=1;i<=npar;i++)
2225: for (j=1;j<=npar;j++)
2226: xi[i][j]=(i==j ? 1.0 : 0.0);
2227: printf("Powell\n"); fprintf(ficlog,"Powell\n");
2228: strcpy(filerespow,"pow");
2229: strcat(filerespow,fileres);
2230: if((ficrespow=fopen(filerespow,"w"))==NULL) {
2231: printf("Problem with resultfile: %s\n", filerespow);
2232: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
2233: }
2234: fprintf(ficrespow,"# Powell\n# iter -2*LL");
2235: for (i=1;i<=nlstate;i++)
2236: for(j=1;j<=nlstate+ndeath;j++)
2237: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
2238: fprintf(ficrespow,"\n");
1.162 brouard 2239: #ifdef POWELL
1.126 brouard 2240: powell(p,xi,npar,ftol,&iter,&fret,func);
1.162 brouard 2241: #endif
1.126 brouard 2242:
1.162 brouard 2243: #ifdef NLOPT
2244: #ifdef NEWUOA
2245: opt = nlopt_create(NLOPT_LN_NEWUOA,npar);
2246: #else
2247: opt = nlopt_create(NLOPT_LN_BOBYQA,npar);
2248: #endif
2249: lb=vector(0,npar-1);
2250: for (i=0;i<npar;i++) lb[i]= -HUGE_VAL;
2251: nlopt_set_lower_bounds(opt, lb);
2252: nlopt_set_initial_step1(opt, 0.1);
2253:
2254: p1= (p+1); /* p *(p+1)@8 and p *(p1)@8 are equal p1[0]=p[1] */
2255: d->function = func;
2256: printf(" Func %.12lf \n",myfunc(npar,p1,NULL,d));
2257: nlopt_set_min_objective(opt, myfunc, d);
2258: nlopt_set_xtol_rel(opt, ftol);
2259: if ((creturn=nlopt_optimize(opt, p1, &minf)) < 0) {
2260: printf("nlopt failed! %d\n",creturn);
2261: }
2262: else {
2263: printf("found minimum after %d evaluations (NLOPT=%d)\n", countcallfunc ,NLOPT);
2264: printf("found minimum at f(%g,%g) = %0.10g\n", p[0], p[1], minf);
2265: iter=1; /* not equal */
2266: }
2267: nlopt_destroy(opt);
2268: #endif
1.126 brouard 2269: free_matrix(xi,1,npar,1,npar);
2270: fclose(ficrespow);
1.162 brouard 2271: printf("\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
2272: fprintf(ficlog,"\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
2273: fprintf(ficres,"\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
1.126 brouard 2274:
2275: }
2276:
2277: /**** Computes Hessian and covariance matrix ***/
2278: void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
2279: {
2280: double **a,**y,*x,pd;
2281: double **hess;
1.164 brouard 2282: int i, j;
1.126 brouard 2283: int *indx;
2284:
2285: double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
2286: double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
2287: void lubksb(double **a, int npar, int *indx, double b[]) ;
2288: void ludcmp(double **a, int npar, int *indx, double *d) ;
2289: double gompertz(double p[]);
2290: hess=matrix(1,npar,1,npar);
2291:
2292: printf("\nCalculation of the hessian matrix. Wait...\n");
2293: fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
2294: for (i=1;i<=npar;i++){
2295: printf("%d",i);fflush(stdout);
2296: fprintf(ficlog,"%d",i);fflush(ficlog);
2297:
2298: hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
2299:
2300: /* printf(" %f ",p[i]);
2301: printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
2302: }
2303:
2304: for (i=1;i<=npar;i++) {
2305: for (j=1;j<=npar;j++) {
2306: if (j>i) {
2307: printf(".%d%d",i,j);fflush(stdout);
2308: fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
2309: hess[i][j]=hessij(p,delti,i,j,func,npar);
2310:
2311: hess[j][i]=hess[i][j];
2312: /*printf(" %lf ",hess[i][j]);*/
2313: }
2314: }
2315: }
2316: printf("\n");
2317: fprintf(ficlog,"\n");
2318:
2319: printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
2320: fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
2321:
2322: a=matrix(1,npar,1,npar);
2323: y=matrix(1,npar,1,npar);
2324: x=vector(1,npar);
2325: indx=ivector(1,npar);
2326: for (i=1;i<=npar;i++)
2327: for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
2328: ludcmp(a,npar,indx,&pd);
2329:
2330: for (j=1;j<=npar;j++) {
2331: for (i=1;i<=npar;i++) x[i]=0;
2332: x[j]=1;
2333: lubksb(a,npar,indx,x);
2334: for (i=1;i<=npar;i++){
2335: matcov[i][j]=x[i];
2336: }
2337: }
2338:
2339: printf("\n#Hessian matrix#\n");
2340: fprintf(ficlog,"\n#Hessian matrix#\n");
2341: for (i=1;i<=npar;i++) {
2342: for (j=1;j<=npar;j++) {
2343: printf("%.3e ",hess[i][j]);
2344: fprintf(ficlog,"%.3e ",hess[i][j]);
2345: }
2346: printf("\n");
2347: fprintf(ficlog,"\n");
2348: }
2349:
2350: /* Recompute Inverse */
2351: for (i=1;i<=npar;i++)
2352: for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
2353: ludcmp(a,npar,indx,&pd);
2354:
2355: /* printf("\n#Hessian matrix recomputed#\n");
2356:
2357: for (j=1;j<=npar;j++) {
2358: for (i=1;i<=npar;i++) x[i]=0;
2359: x[j]=1;
2360: lubksb(a,npar,indx,x);
2361: for (i=1;i<=npar;i++){
2362: y[i][j]=x[i];
2363: printf("%.3e ",y[i][j]);
2364: fprintf(ficlog,"%.3e ",y[i][j]);
2365: }
2366: printf("\n");
2367: fprintf(ficlog,"\n");
2368: }
2369: */
2370:
2371: free_matrix(a,1,npar,1,npar);
2372: free_matrix(y,1,npar,1,npar);
2373: free_vector(x,1,npar);
2374: free_ivector(indx,1,npar);
2375: free_matrix(hess,1,npar,1,npar);
2376:
2377:
2378: }
2379:
2380: /*************** hessian matrix ****************/
2381: double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
2382: {
2383: int i;
2384: int l=1, lmax=20;
2385: double k1,k2;
1.132 brouard 2386: double p2[MAXPARM+1]; /* identical to x */
1.126 brouard 2387: double res;
2388: double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
2389: double fx;
2390: int k=0,kmax=10;
2391: double l1;
2392:
2393: fx=func(x);
2394: for (i=1;i<=npar;i++) p2[i]=x[i];
1.145 brouard 2395: for(l=0 ; l <=lmax; l++){ /* Enlarging the zone around the Maximum */
1.126 brouard 2396: l1=pow(10,l);
2397: delts=delt;
2398: for(k=1 ; k <kmax; k=k+1){
2399: delt = delta*(l1*k);
2400: p2[theta]=x[theta] +delt;
1.145 brouard 2401: k1=func(p2)-fx; /* Might be negative if too close to the theoretical maximum */
1.126 brouard 2402: p2[theta]=x[theta]-delt;
2403: k2=func(p2)-fx;
2404: /*res= (k1-2.0*fx+k2)/delt/delt; */
2405: res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
2406:
1.132 brouard 2407: #ifdef DEBUGHESS
1.126 brouard 2408: 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);
2409: 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);
2410: #endif
2411: /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
2412: if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
2413: k=kmax;
2414: }
2415: else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
1.164 brouard 2416: k=kmax; l=lmax*10;
1.126 brouard 2417: }
2418: else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){
2419: delts=delt;
2420: }
2421: }
2422: }
2423: delti[theta]=delts;
2424: return res;
2425:
2426: }
2427:
2428: double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
2429: {
2430: int i;
1.164 brouard 2431: int l=1, lmax=20;
1.126 brouard 2432: double k1,k2,k3,k4,res,fx;
1.132 brouard 2433: double p2[MAXPARM+1];
1.126 brouard 2434: int k;
2435:
2436: fx=func(x);
2437: for (k=1; k<=2; k++) {
2438: for (i=1;i<=npar;i++) p2[i]=x[i];
2439: p2[thetai]=x[thetai]+delti[thetai]/k;
2440: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
2441: k1=func(p2)-fx;
2442:
2443: p2[thetai]=x[thetai]+delti[thetai]/k;
2444: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
2445: k2=func(p2)-fx;
2446:
2447: p2[thetai]=x[thetai]-delti[thetai]/k;
2448: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
2449: k3=func(p2)-fx;
2450:
2451: p2[thetai]=x[thetai]-delti[thetai]/k;
2452: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
2453: k4=func(p2)-fx;
2454: res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
2455: #ifdef DEBUG
2456: 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);
2457: 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);
2458: #endif
2459: }
2460: return res;
2461: }
2462:
2463: /************** Inverse of matrix **************/
2464: void ludcmp(double **a, int n, int *indx, double *d)
2465: {
2466: int i,imax,j,k;
2467: double big,dum,sum,temp;
2468: double *vv;
2469:
2470: vv=vector(1,n);
2471: *d=1.0;
2472: for (i=1;i<=n;i++) {
2473: big=0.0;
2474: for (j=1;j<=n;j++)
2475: if ((temp=fabs(a[i][j])) > big) big=temp;
2476: if (big == 0.0) nrerror("Singular matrix in routine ludcmp");
2477: vv[i]=1.0/big;
2478: }
2479: for (j=1;j<=n;j++) {
2480: for (i=1;i<j;i++) {
2481: sum=a[i][j];
2482: for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];
2483: a[i][j]=sum;
2484: }
2485: big=0.0;
2486: for (i=j;i<=n;i++) {
2487: sum=a[i][j];
2488: for (k=1;k<j;k++)
2489: sum -= a[i][k]*a[k][j];
2490: a[i][j]=sum;
2491: if ( (dum=vv[i]*fabs(sum)) >= big) {
2492: big=dum;
2493: imax=i;
2494: }
2495: }
2496: if (j != imax) {
2497: for (k=1;k<=n;k++) {
2498: dum=a[imax][k];
2499: a[imax][k]=a[j][k];
2500: a[j][k]=dum;
2501: }
2502: *d = -(*d);
2503: vv[imax]=vv[j];
2504: }
2505: indx[j]=imax;
2506: if (a[j][j] == 0.0) a[j][j]=TINY;
2507: if (j != n) {
2508: dum=1.0/(a[j][j]);
2509: for (i=j+1;i<=n;i++) a[i][j] *= dum;
2510: }
2511: }
2512: free_vector(vv,1,n); /* Doesn't work */
2513: ;
2514: }
2515:
2516: void lubksb(double **a, int n, int *indx, double b[])
2517: {
2518: int i,ii=0,ip,j;
2519: double sum;
2520:
2521: for (i=1;i<=n;i++) {
2522: ip=indx[i];
2523: sum=b[ip];
2524: b[ip]=b[i];
2525: if (ii)
2526: for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];
2527: else if (sum) ii=i;
2528: b[i]=sum;
2529: }
2530: for (i=n;i>=1;i--) {
2531: sum=b[i];
2532: for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];
2533: b[i]=sum/a[i][i];
2534: }
2535: }
2536:
2537: void pstamp(FILE *fichier)
2538: {
2539: fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart);
2540: }
2541:
2542: /************ Frequencies ********************/
2543: 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[])
2544: { /* Some frequencies */
2545:
1.164 brouard 2546: int i, m, jk, j1, bool, z1,j;
1.126 brouard 2547: int first;
2548: double ***freq; /* Frequencies */
2549: double *pp, **prop;
2550: double pos,posprop, k2, dateintsum=0,k2cpt=0;
2551: char fileresp[FILENAMELENGTH];
2552:
2553: pp=vector(1,nlstate);
2554: prop=matrix(1,nlstate,iagemin,iagemax+3);
2555: strcpy(fileresp,"p");
2556: strcat(fileresp,fileres);
2557: if((ficresp=fopen(fileresp,"w"))==NULL) {
2558: printf("Problem with prevalence resultfile: %s\n", fileresp);
2559: fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
2560: exit(0);
2561: }
2562: freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
2563: j1=0;
2564:
2565: j=cptcoveff;
2566: if (cptcovn<1) {j=1;ncodemax[1]=1;}
2567:
2568: first=1;
2569:
1.169 brouard 2570: /* for(k1=1; k1<=j ; k1++){ */ /* Loop on covariates */
2571: /* for(i1=1; i1<=ncodemax[k1];i1++){ */ /* Now it is 2 */
2572: /* j1++; */
1.145 brouard 2573: for (j1 = 1; j1 <= (int) pow(2,cptcoveff); j1++){
1.126 brouard 2574: /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
2575: scanf("%d", i);*/
2576: for (i=-5; i<=nlstate+ndeath; i++)
2577: for (jk=-5; jk<=nlstate+ndeath; jk++)
2578: for(m=iagemin; m <= iagemax+3; m++)
2579: freq[i][jk][m]=0;
1.143 brouard 2580:
2581: for (i=1; i<=nlstate; i++)
2582: for(m=iagemin; m <= iagemax+3; m++)
2583: prop[i][m]=0;
1.126 brouard 2584:
2585: dateintsum=0;
2586: k2cpt=0;
2587: for (i=1; i<=imx; i++) {
2588: bool=1;
1.144 brouard 2589: if (cptcovn>0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
2590: for (z1=1; z1<=cptcoveff; z1++)
2591: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]){
1.145 brouard 2592: /* Tests if the value of each of the covariates of i is equal to filter j1 */
1.144 brouard 2593: bool=0;
1.145 brouard 2594: /* 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",
2595: bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtab[j1][z1],
2596: j1,z1,nbcode[Tvaraff[z1]][codtab[j1][z1]],j1);*/
1.144 brouard 2597: /* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtab[7][3]=1 and nbcde[3][?]=1*/
2598: }
1.126 brouard 2599: }
1.144 brouard 2600:
1.126 brouard 2601: if (bool==1){
2602: for(m=firstpass; m<=lastpass; m++){
2603: k2=anint[m][i]+(mint[m][i]/12.);
2604: /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
2605: if(agev[m][i]==0) agev[m][i]=iagemax+1;
2606: if(agev[m][i]==1) agev[m][i]=iagemax+2;
2607: if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
2608: if (m<lastpass) {
2609: freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
2610: freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
2611: }
2612:
2613: if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
2614: dateintsum=dateintsum+k2;
2615: k2cpt++;
2616: }
2617: /*}*/
2618: }
2619: }
1.145 brouard 2620: } /* end i */
1.126 brouard 2621:
2622: /* fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
2623: pstamp(ficresp);
2624: if (cptcovn>0) {
2625: fprintf(ficresp, "\n#********** Variable ");
2626: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
2627: fprintf(ficresp, "**********\n#");
1.143 brouard 2628: fprintf(ficlog, "\n#********** Variable ");
2629: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficlog, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
2630: fprintf(ficlog, "**********\n#");
1.126 brouard 2631: }
2632: for(i=1; i<=nlstate;i++)
2633: fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
2634: fprintf(ficresp, "\n");
2635:
2636: for(i=iagemin; i <= iagemax+3; i++){
2637: if(i==iagemax+3){
2638: fprintf(ficlog,"Total");
2639: }else{
2640: if(first==1){
2641: first=0;
2642: printf("See log file for details...\n");
2643: }
2644: fprintf(ficlog,"Age %d", i);
2645: }
2646: for(jk=1; jk <=nlstate ; jk++){
2647: for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
2648: pp[jk] += freq[jk][m][i];
2649: }
2650: for(jk=1; jk <=nlstate ; jk++){
2651: for(m=-1, pos=0; m <=0 ; m++)
2652: pos += freq[jk][m][i];
2653: if(pp[jk]>=1.e-10){
2654: if(first==1){
1.132 brouard 2655: printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
1.126 brouard 2656: }
2657: fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
2658: }else{
2659: if(first==1)
2660: printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
2661: fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
2662: }
2663: }
2664:
2665: for(jk=1; jk <=nlstate ; jk++){
2666: for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
2667: pp[jk] += freq[jk][m][i];
2668: }
2669: for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
2670: pos += pp[jk];
2671: posprop += prop[jk][i];
2672: }
2673: for(jk=1; jk <=nlstate ; jk++){
2674: if(pos>=1.e-5){
2675: if(first==1)
2676: printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
2677: fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
2678: }else{
2679: if(first==1)
2680: printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
2681: fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
2682: }
2683: if( i <= iagemax){
2684: if(pos>=1.e-5){
2685: fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
2686: /*probs[i][jk][j1]= pp[jk]/pos;*/
2687: /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
2688: }
2689: else
2690: fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
2691: }
2692: }
2693:
2694: for(jk=-1; jk <=nlstate+ndeath; jk++)
2695: for(m=-1; m <=nlstate+ndeath; m++)
2696: if(freq[jk][m][i] !=0 ) {
2697: if(first==1)
2698: printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
2699: fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
2700: }
2701: if(i <= iagemax)
2702: fprintf(ficresp,"\n");
2703: if(first==1)
2704: printf("Others in log...\n");
2705: fprintf(ficlog,"\n");
2706: }
1.145 brouard 2707: /*}*/
1.126 brouard 2708: }
2709: dateintmean=dateintsum/k2cpt;
2710:
2711: fclose(ficresp);
2712: free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
2713: free_vector(pp,1,nlstate);
2714: free_matrix(prop,1,nlstate,iagemin, iagemax+3);
2715: /* End of Freq */
2716: }
2717:
2718: /************ Prevalence ********************/
2719: 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)
2720: {
2721: /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
2722: in each health status at the date of interview (if between dateprev1 and dateprev2).
2723: We still use firstpass and lastpass as another selection.
2724: */
2725:
1.164 brouard 2726: int i, m, jk, j1, bool, z1,j;
2727:
2728: double **prop;
2729: double posprop;
1.126 brouard 2730: double y2; /* in fractional years */
2731: int iagemin, iagemax;
1.145 brouard 2732: int first; /** to stop verbosity which is redirected to log file */
1.126 brouard 2733:
2734: iagemin= (int) agemin;
2735: iagemax= (int) agemax;
2736: /*pp=vector(1,nlstate);*/
2737: prop=matrix(1,nlstate,iagemin,iagemax+3);
2738: /* freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
2739: j1=0;
2740:
1.145 brouard 2741: /*j=cptcoveff;*/
1.126 brouard 2742: if (cptcovn<1) {j=1;ncodemax[1]=1;}
2743:
1.145 brouard 2744: first=1;
2745: for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){
2746: /*for(i1=1; i1<=ncodemax[k1];i1++){
2747: j1++;*/
1.126 brouard 2748:
2749: for (i=1; i<=nlstate; i++)
2750: for(m=iagemin; m <= iagemax+3; m++)
2751: prop[i][m]=0.0;
2752:
2753: for (i=1; i<=imx; i++) { /* Each individual */
2754: bool=1;
2755: if (cptcovn>0) {
2756: for (z1=1; z1<=cptcoveff; z1++)
2757: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
2758: bool=0;
2759: }
2760: if (bool==1) {
2761: for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
2762: y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
2763: if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
2764: if(agev[m][i]==0) agev[m][i]=iagemax+1;
2765: if(agev[m][i]==1) agev[m][i]=iagemax+2;
2766: 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);
2767: if (s[m][i]>0 && s[m][i]<=nlstate) {
2768: /*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]]);*/
2769: prop[s[m][i]][(int)agev[m][i]] += weight[i];
2770: prop[s[m][i]][iagemax+3] += weight[i];
2771: }
2772: }
2773: } /* end selection of waves */
2774: }
2775: }
2776: for(i=iagemin; i <= iagemax+3; i++){
2777: for(jk=1,posprop=0; jk <=nlstate ; jk++) {
2778: posprop += prop[jk][i];
2779: }
1.145 brouard 2780:
1.126 brouard 2781: for(jk=1; jk <=nlstate ; jk++){
2782: if( i <= iagemax){
2783: if(posprop>=1.e-5){
2784: probs[i][jk][j1]= prop[jk][i]/posprop;
1.145 brouard 2785: } else{
2786: if(first==1){
2787: first=0;
2788: 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]);
2789: }
2790: }
1.126 brouard 2791: }
2792: }/* end jk */
2793: }/* end i */
1.145 brouard 2794: /*} *//* end i1 */
2795: } /* end j1 */
1.126 brouard 2796:
2797: /* free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
2798: /*free_vector(pp,1,nlstate);*/
2799: free_matrix(prop,1,nlstate, iagemin,iagemax+3);
2800: } /* End of prevalence */
2801:
2802: /************* Waves Concatenation ***************/
2803:
2804: 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)
2805: {
2806: /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
2807: Death is a valid wave (if date is known).
2808: mw[mi][i] is the mi (mi=1 to wav[i]) effective wave of individual i
2809: dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
2810: and mw[mi+1][i]. dh depends on stepm.
2811: */
2812:
2813: int i, mi, m;
2814: /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
2815: double sum=0., jmean=0.;*/
2816: int first;
2817: int j, k=0,jk, ju, jl;
2818: double sum=0.;
2819: first=0;
1.164 brouard 2820: jmin=100000;
1.126 brouard 2821: jmax=-1;
2822: jmean=0.;
2823: for(i=1; i<=imx; i++){
2824: mi=0;
2825: m=firstpass;
2826: while(s[m][i] <= nlstate){
2827: if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
2828: mw[++mi][i]=m;
2829: if(m >=lastpass)
2830: break;
2831: else
2832: m++;
2833: }/* end while */
2834: if (s[m][i] > nlstate){
2835: mi++; /* Death is another wave */
2836: /* if(mi==0) never been interviewed correctly before death */
2837: /* Only death is a correct wave */
2838: mw[mi][i]=m;
2839: }
2840:
2841: wav[i]=mi;
2842: if(mi==0){
2843: nbwarn++;
2844: if(first==0){
2845: printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
2846: first=1;
2847: }
2848: if(first==1){
2849: fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
2850: }
2851: } /* end mi==0 */
2852: } /* End individuals */
2853:
2854: for(i=1; i<=imx; i++){
2855: for(mi=1; mi<wav[i];mi++){
2856: if (stepm <=0)
2857: dh[mi][i]=1;
2858: else{
2859: if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
2860: if (agedc[i] < 2*AGESUP) {
2861: j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);
2862: if(j==0) j=1; /* Survives at least one month after exam */
2863: else if(j<0){
2864: nberr++;
2865: 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]);
2866: j=1; /* Temporary Dangerous patch */
2867: 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);
2868: 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]);
2869: 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);
2870: }
2871: k=k+1;
2872: if (j >= jmax){
2873: jmax=j;
2874: ijmax=i;
2875: }
2876: if (j <= jmin){
2877: jmin=j;
2878: ijmin=i;
2879: }
2880: sum=sum+j;
2881: /*if (j<0) printf("j=%d num=%d \n",j,i);*/
2882: /* printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
2883: }
2884: }
2885: else{
2886: j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
2887: /* 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]); */
2888:
2889: k=k+1;
2890: if (j >= jmax) {
2891: jmax=j;
2892: ijmax=i;
2893: }
2894: else if (j <= jmin){
2895: jmin=j;
2896: ijmin=i;
2897: }
2898: /* if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
2899: /*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]);*/
2900: if(j<0){
2901: nberr++;
2902: 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]);
2903: 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]);
2904: }
2905: sum=sum+j;
2906: }
2907: jk= j/stepm;
2908: jl= j -jk*stepm;
2909: ju= j -(jk+1)*stepm;
2910: if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
2911: if(jl==0){
2912: dh[mi][i]=jk;
2913: bh[mi][i]=0;
2914: }else{ /* We want a negative bias in order to only have interpolation ie
1.136 brouard 2915: * to avoid the price of an extra matrix product in likelihood */
1.126 brouard 2916: dh[mi][i]=jk+1;
2917: bh[mi][i]=ju;
2918: }
2919: }else{
2920: if(jl <= -ju){
2921: dh[mi][i]=jk;
2922: bh[mi][i]=jl; /* bias is positive if real duration
2923: * is higher than the multiple of stepm and negative otherwise.
2924: */
2925: }
2926: else{
2927: dh[mi][i]=jk+1;
2928: bh[mi][i]=ju;
2929: }
2930: if(dh[mi][i]==0){
2931: dh[mi][i]=1; /* At least one step */
2932: bh[mi][i]=ju; /* At least one step */
2933: /* 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);*/
2934: }
2935: } /* end if mle */
2936: }
2937: } /* end wave */
2938: }
2939: jmean=sum/k;
2940: 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 2941: 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 2942: }
2943:
2944: /*********** Tricode ****************************/
1.145 brouard 2945: void tricode(int *Tvar, int **nbcode, int imx, int *Ndum)
1.126 brouard 2946: {
1.144 brouard 2947: /**< Uses cptcovn+2*cptcovprod as the number of covariates */
2948: /* 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 2949: * Boring subroutine which should only output nbcode[Tvar[j]][k]
1.145 brouard 2950: * Tvar[5] in V2+V1+V3*age+V2*V4 is 2 (V2)
1.169 brouard 2951: * nbcode[Tvar[j]][1]=
1.144 brouard 2952: */
1.130 brouard 2953:
1.145 brouard 2954: int ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
1.136 brouard 2955: int modmaxcovj=0; /* Modality max of covariates j */
1.145 brouard 2956: int cptcode=0; /* Modality max of covariates j */
2957: int modmincovj=0; /* Modality min of covariates j */
2958:
2959:
1.126 brouard 2960: cptcoveff=0;
2961:
1.145 brouard 2962: for (k=-1; k < maxncov; k++) Ndum[k]=0;
1.144 brouard 2963: for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */
1.126 brouard 2964:
1.145 brouard 2965: /* Loop on covariates without age and products */
2966: for (j=1; j<=(cptcovs); j++) { /* model V1 + V2*age+ V3 + V3*V4 : V1 + V3 = 2 only */
2967: for (i=1; i<=imx; i++) { /* Lopp on individuals: reads the data file to get the maximum value of the
1.136 brouard 2968: modality of this covariate Vj*/
1.145 brouard 2969: ij=(int)(covar[Tvar[j]][i]); /* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i
2970: * If product of Vn*Vm, still boolean *:
2971: * If it was coded 1, 2, 3, 4 should be splitted into 3 boolean variables
2972: * 1 => 0 0 0, 2 => 0 0 1, 3 => 0 1 1, 4=1 0 0 */
2973: /* Finds for covariate j, n=Tvar[j] of Vn . ij is the
1.136 brouard 2974: modality of the nth covariate of individual i. */
1.145 brouard 2975: if (ij > modmaxcovj)
2976: modmaxcovj=ij;
2977: else if (ij < modmincovj)
2978: modmincovj=ij;
2979: if ((ij < -1) && (ij > NCOVMAX)){
2980: printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX );
2981: exit(1);
2982: }else
1.136 brouard 2983: Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/
1.145 brouard 2984: /* If coded 1, 2, 3 , counts the number of 1 Ndum[1], number of 2, Ndum[2], etc */
1.126 brouard 2985: /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
1.136 brouard 2986: /* getting the maximum value of the modality of the covariate
2987: (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and
2988: female is 1, then modmaxcovj=1.*/
1.126 brouard 2989: }
1.145 brouard 2990: printf(" Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", j, Tvar[j], modmincovj, modmaxcovj);
2991: cptcode=modmaxcovj;
1.137 brouard 2992: /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */
1.145 brouard 2993: /*for (i=0; i<=cptcode; i++) {*/
2994: for (i=modmincovj; i<=modmaxcovj; i++) { /* i=-1 ? 0 and 1*//* For each value of the modality of model-cov j */
2995: printf("Frequencies of covariates %d V%d %d\n", j, Tvar[j], Ndum[i]);
2996: if( Ndum[i] != 0 ){ /* Counts if nobody answered, empty modality */
2997: ncodemax[j]++; /* ncodemax[j]= Number of non-null modalities of the j th covariate. */
2998: }
2999: /* In fact ncodemax[j]=2 (dichotom. variables only) but it could be more for
3000: historical reasons: 3 if coded 1, 2, 3 and 4 and Ndum[2]=0 */
1.131 brouard 3001: } /* Ndum[-1] number of undefined modalities */
1.126 brouard 3002:
1.136 brouard 3003: /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */
1.145 brouard 3004: /* For covariate j, modalities could be 1, 2, 3, 4. If Ndum[2]=0 ncodemax[j] is not 4 but 3 */
3005: /* If Ndum[3}= 635; Ndum[4]=0; Ndum[5]=0; Ndum[6]=27; Ndum[7]=125;
3006: modmincovj=3; modmaxcovj = 7;
3007: There are only 3 modalities non empty (or 2 if 27 is too few) : ncodemax[j]=3;
3008: which will be coded 0, 1, 2 which in binary on 3-1 digits are 0=00 1=01, 2=10; defining two dummy
3009: variables V1_1 and V1_2.
3010: nbcode[Tvar[j]][ij]=k;
3011: nbcode[Tvar[j]][1]=0;
3012: nbcode[Tvar[j]][2]=1;
3013: nbcode[Tvar[j]][3]=2;
3014: */
3015: ij=1; /* ij is similar to i but can jumps over null modalities */
3016: for (i=modmincovj; i<=modmaxcovj; i++) { /* i= 1 to 2 for dichotomous, or from 1 to 3 */
3017: for (k=0; k<= cptcode; k++) { /* k=-1 ? k=0 to 1 *//* Could be 1 to 4 */
3018: /*recode from 0 */
1.131 brouard 3019: if (Ndum[k] != 0) { /* If at least one individual responded to this modality k */
3020: nbcode[Tvar[j]][ij]=k; /* stores the modality in an array nbcode.
3021: k is a modality. If we have model=V1+V1*sex
3022: then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
1.126 brouard 3023: ij++;
3024: }
3025: if (ij > ncodemax[j]) break;
1.137 brouard 3026: } /* end of loop on */
3027: } /* end of loop on modality */
3028: } /* end of loop on model-covariate j. nbcode[Tvarj][1]=0 and nbcode[Tvarj][2]=1 sets the value of covariate j*/
3029:
1.145 brouard 3030: for (k=-1; k< maxncov; k++) Ndum[k]=0;
1.137 brouard 3031:
1.145 brouard 3032: for (i=1; i<=ncovmodel-2; i++) { /* -2, cste and age */
3033: /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
3034: ij=Tvar[i]; /* Tvar might be -1 if status was unknown */
3035: Ndum[ij]++;
3036: }
1.126 brouard 3037:
3038: ij=1;
1.145 brouard 3039: for (i=0; i<= maxncov-1; i++) { /* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) */
3040: /*printf("Ndum[%d]=%d\n",i, Ndum[i]);*/
1.126 brouard 3041: if((Ndum[i]!=0) && (i<=ncovcol)){
1.145 brouard 3042: /*printf("diff Ndum[%d]=%d\n",i, Ndum[i]);*/
3043: Tvaraff[ij]=i; /*For printing (unclear) */
1.126 brouard 3044: ij++;
1.145 brouard 3045: }else
3046: Tvaraff[ij]=0;
1.126 brouard 3047: }
1.131 brouard 3048: ij--;
1.144 brouard 3049: cptcoveff=ij; /*Number of total covariates*/
1.145 brouard 3050:
1.126 brouard 3051: }
3052:
1.145 brouard 3053:
1.126 brouard 3054: /*********** Health Expectancies ****************/
3055:
1.127 brouard 3056: 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 3057:
3058: {
3059: /* Health expectancies, no variances */
1.164 brouard 3060: int i, j, nhstepm, hstepm, h, nstepm;
1.126 brouard 3061: int nhstepma, nstepma; /* Decreasing with age */
3062: double age, agelim, hf;
3063: double ***p3mat;
3064: double eip;
3065:
3066: pstamp(ficreseij);
3067: fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
3068: fprintf(ficreseij,"# Age");
3069: for(i=1; i<=nlstate;i++){
3070: for(j=1; j<=nlstate;j++){
3071: fprintf(ficreseij," e%1d%1d ",i,j);
3072: }
3073: fprintf(ficreseij," e%1d. ",i);
3074: }
3075: fprintf(ficreseij,"\n");
3076:
3077:
3078: if(estepm < stepm){
3079: printf ("Problem %d lower than %d\n",estepm, stepm);
3080: }
3081: else hstepm=estepm;
3082: /* We compute the life expectancy from trapezoids spaced every estepm months
3083: * This is mainly to measure the difference between two models: for example
3084: * if stepm=24 months pijx are given only every 2 years and by summing them
3085: * we are calculating an estimate of the Life Expectancy assuming a linear
3086: * progression in between and thus overestimating or underestimating according
3087: * to the curvature of the survival function. If, for the same date, we
3088: * estimate the model with stepm=1 month, we can keep estepm to 24 months
3089: * to compare the new estimate of Life expectancy with the same linear
3090: * hypothesis. A more precise result, taking into account a more precise
3091: * curvature will be obtained if estepm is as small as stepm. */
3092:
3093: /* For example we decided to compute the life expectancy with the smallest unit */
3094: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
3095: nhstepm is the number of hstepm from age to agelim
3096: nstepm is the number of stepm from age to agelin.
3097: Look at hpijx to understand the reason of that which relies in memory size
3098: and note for a fixed period like estepm months */
3099: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
3100: survival function given by stepm (the optimization length). Unfortunately it
3101: means that if the survival funtion is printed only each two years of age and if
3102: you sum them up and add 1 year (area under the trapezoids) you won't get the same
3103: results. So we changed our mind and took the option of the best precision.
3104: */
3105: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
3106:
3107: agelim=AGESUP;
3108: /* If stepm=6 months */
3109: /* Computed by stepm unit matrices, product of hstepm matrices, stored
3110: in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
3111:
3112: /* nhstepm age range expressed in number of stepm */
3113: nstepm=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
3114: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
3115: /* if (stepm >= YEARM) hstepm=1;*/
3116: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
3117: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3118:
3119: for (age=bage; age<=fage; age ++){
3120: nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
3121: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
3122: /* if (stepm >= YEARM) hstepm=1;*/
3123: nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
3124:
3125: /* If stepm=6 months */
3126: /* Computed by stepm unit matrices, product of hstepma matrices, stored
3127: in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
3128:
3129: hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
3130:
3131: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
3132:
3133: printf("%d|",(int)age);fflush(stdout);
3134: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
3135:
3136: /* Computing expectancies */
3137: for(i=1; i<=nlstate;i++)
3138: for(j=1; j<=nlstate;j++)
3139: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
3140: eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
3141:
3142: /* 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]);*/
3143:
3144: }
3145:
3146: fprintf(ficreseij,"%3.0f",age );
3147: for(i=1; i<=nlstate;i++){
3148: eip=0;
3149: for(j=1; j<=nlstate;j++){
3150: eip +=eij[i][j][(int)age];
3151: fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
3152: }
3153: fprintf(ficreseij,"%9.4f", eip );
3154: }
3155: fprintf(ficreseij,"\n");
3156:
3157: }
3158: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3159: printf("\n");
3160: fprintf(ficlog,"\n");
3161:
3162: }
3163:
1.127 brouard 3164: 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 3165:
3166: {
3167: /* Covariances of health expectancies eij and of total life expectancies according
3168: to initial status i, ei. .
3169: */
3170: int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
3171: int nhstepma, nstepma; /* Decreasing with age */
3172: double age, agelim, hf;
3173: double ***p3matp, ***p3matm, ***varhe;
3174: double **dnewm,**doldm;
3175: double *xp, *xm;
3176: double **gp, **gm;
3177: double ***gradg, ***trgradg;
3178: int theta;
3179:
3180: double eip, vip;
3181:
3182: varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
3183: xp=vector(1,npar);
3184: xm=vector(1,npar);
3185: dnewm=matrix(1,nlstate*nlstate,1,npar);
3186: doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
3187:
3188: pstamp(ficresstdeij);
3189: fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
3190: fprintf(ficresstdeij,"# Age");
3191: for(i=1; i<=nlstate;i++){
3192: for(j=1; j<=nlstate;j++)
3193: fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
3194: fprintf(ficresstdeij," e%1d. ",i);
3195: }
3196: fprintf(ficresstdeij,"\n");
3197:
3198: pstamp(ficrescveij);
3199: fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
3200: fprintf(ficrescveij,"# Age");
3201: for(i=1; i<=nlstate;i++)
3202: for(j=1; j<=nlstate;j++){
3203: cptj= (j-1)*nlstate+i;
3204: for(i2=1; i2<=nlstate;i2++)
3205: for(j2=1; j2<=nlstate;j2++){
3206: cptj2= (j2-1)*nlstate+i2;
3207: if(cptj2 <= cptj)
3208: fprintf(ficrescveij," %1d%1d,%1d%1d",i,j,i2,j2);
3209: }
3210: }
3211: fprintf(ficrescveij,"\n");
3212:
3213: if(estepm < stepm){
3214: printf ("Problem %d lower than %d\n",estepm, stepm);
3215: }
3216: else hstepm=estepm;
3217: /* We compute the life expectancy from trapezoids spaced every estepm months
3218: * This is mainly to measure the difference between two models: for example
3219: * if stepm=24 months pijx are given only every 2 years and by summing them
3220: * we are calculating an estimate of the Life Expectancy assuming a linear
3221: * progression in between and thus overestimating or underestimating according
3222: * to the curvature of the survival function. If, for the same date, we
3223: * estimate the model with stepm=1 month, we can keep estepm to 24 months
3224: * to compare the new estimate of Life expectancy with the same linear
3225: * hypothesis. A more precise result, taking into account a more precise
3226: * curvature will be obtained if estepm is as small as stepm. */
3227:
3228: /* For example we decided to compute the life expectancy with the smallest unit */
3229: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
3230: nhstepm is the number of hstepm from age to agelim
3231: nstepm is the number of stepm from age to agelin.
3232: Look at hpijx to understand the reason of that which relies in memory size
3233: and note for a fixed period like estepm months */
3234: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
3235: survival function given by stepm (the optimization length). Unfortunately it
3236: means that if the survival funtion is printed only each two years of age and if
3237: you sum them up and add 1 year (area under the trapezoids) you won't get the same
3238: results. So we changed our mind and took the option of the best precision.
3239: */
3240: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
3241:
3242: /* If stepm=6 months */
3243: /* nhstepm age range expressed in number of stepm */
3244: agelim=AGESUP;
3245: nstepm=(int) rint((agelim-bage)*YEARM/stepm);
3246: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
3247: /* if (stepm >= YEARM) hstepm=1;*/
3248: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
3249:
3250: p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3251: p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3252: gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
3253: trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
3254: gp=matrix(0,nhstepm,1,nlstate*nlstate);
3255: gm=matrix(0,nhstepm,1,nlstate*nlstate);
3256:
3257: for (age=bage; age<=fage; age ++){
3258: nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
3259: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
3260: /* if (stepm >= YEARM) hstepm=1;*/
3261: nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
3262:
3263: /* If stepm=6 months */
3264: /* Computed by stepm unit matrices, product of hstepma matrices, stored
3265: in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
3266:
3267: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
3268:
3269: /* Computing Variances of health expectancies */
3270: /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
3271: decrease memory allocation */
3272: for(theta=1; theta <=npar; theta++){
3273: for(i=1; i<=npar; i++){
3274: xp[i] = x[i] + (i==theta ?delti[theta]:0);
3275: xm[i] = x[i] - (i==theta ?delti[theta]:0);
3276: }
3277: hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);
3278: hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);
3279:
3280: for(j=1; j<= nlstate; j++){
3281: for(i=1; i<=nlstate; i++){
3282: for(h=0; h<=nhstepm-1; h++){
3283: gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
3284: gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
3285: }
3286: }
3287: }
3288:
3289: for(ij=1; ij<= nlstate*nlstate; ij++)
3290: for(h=0; h<=nhstepm-1; h++){
3291: gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
3292: }
3293: }/* End theta */
3294:
3295:
3296: for(h=0; h<=nhstepm-1; h++)
3297: for(j=1; j<=nlstate*nlstate;j++)
3298: for(theta=1; theta <=npar; theta++)
3299: trgradg[h][j][theta]=gradg[h][theta][j];
3300:
3301:
3302: for(ij=1;ij<=nlstate*nlstate;ij++)
3303: for(ji=1;ji<=nlstate*nlstate;ji++)
3304: varhe[ij][ji][(int)age] =0.;
3305:
3306: printf("%d|",(int)age);fflush(stdout);
3307: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
3308: for(h=0;h<=nhstepm-1;h++){
3309: for(k=0;k<=nhstepm-1;k++){
3310: matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
3311: matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
3312: for(ij=1;ij<=nlstate*nlstate;ij++)
3313: for(ji=1;ji<=nlstate*nlstate;ji++)
3314: varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
3315: }
3316: }
3317:
3318: /* Computing expectancies */
3319: hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
3320: for(i=1; i<=nlstate;i++)
3321: for(j=1; j<=nlstate;j++)
3322: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
3323: eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
3324:
3325: /* 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]);*/
3326:
3327: }
3328:
3329: fprintf(ficresstdeij,"%3.0f",age );
3330: for(i=1; i<=nlstate;i++){
3331: eip=0.;
3332: vip=0.;
3333: for(j=1; j<=nlstate;j++){
3334: eip += eij[i][j][(int)age];
3335: for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
3336: vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
3337: fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
3338: }
3339: fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
3340: }
3341: fprintf(ficresstdeij,"\n");
3342:
3343: fprintf(ficrescveij,"%3.0f",age );
3344: for(i=1; i<=nlstate;i++)
3345: for(j=1; j<=nlstate;j++){
3346: cptj= (j-1)*nlstate+i;
3347: for(i2=1; i2<=nlstate;i2++)
3348: for(j2=1; j2<=nlstate;j2++){
3349: cptj2= (j2-1)*nlstate+i2;
3350: if(cptj2 <= cptj)
3351: fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
3352: }
3353: }
3354: fprintf(ficrescveij,"\n");
3355:
3356: }
3357: free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
3358: free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
3359: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
3360: free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
3361: free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3362: free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3363: printf("\n");
3364: fprintf(ficlog,"\n");
3365:
3366: free_vector(xm,1,npar);
3367: free_vector(xp,1,npar);
3368: free_matrix(dnewm,1,nlstate*nlstate,1,npar);
3369: free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
3370: free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
3371: }
3372:
3373: /************ Variance ******************/
3374: 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[])
3375: {
3376: /* Variance of health expectancies */
3377: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
3378: /* double **newm;*/
1.169 brouard 3379: /* int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav)*/
3380:
3381: int movingaverage();
1.126 brouard 3382: double **dnewm,**doldm;
3383: double **dnewmp,**doldmp;
3384: int i, j, nhstepm, hstepm, h, nstepm ;
1.164 brouard 3385: int k;
1.126 brouard 3386: double *xp;
3387: double **gp, **gm; /* for var eij */
3388: double ***gradg, ***trgradg; /*for var eij */
3389: double **gradgp, **trgradgp; /* for var p point j */
3390: double *gpp, *gmp; /* for var p point j */
3391: double **varppt; /* for var p point j nlstate to nlstate+ndeath */
3392: double ***p3mat;
3393: double age,agelim, hf;
3394: double ***mobaverage;
3395: int theta;
3396: char digit[4];
3397: char digitp[25];
3398:
3399: char fileresprobmorprev[FILENAMELENGTH];
3400:
3401: if(popbased==1){
3402: if(mobilav!=0)
3403: strcpy(digitp,"-populbased-mobilav-");
3404: else strcpy(digitp,"-populbased-nomobil-");
3405: }
3406: else
3407: strcpy(digitp,"-stablbased-");
3408:
3409: if (mobilav!=0) {
3410: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3411: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
3412: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
3413: printf(" Error in movingaverage mobilav=%d\n",mobilav);
3414: }
3415: }
3416:
3417: strcpy(fileresprobmorprev,"prmorprev");
3418: sprintf(digit,"%-d",ij);
3419: /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
3420: strcat(fileresprobmorprev,digit); /* Tvar to be done */
3421: strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
3422: strcat(fileresprobmorprev,fileres);
3423: if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
3424: printf("Problem with resultfile: %s\n", fileresprobmorprev);
3425: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
3426: }
3427: printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
3428:
3429: fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
3430: pstamp(ficresprobmorprev);
3431: 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);
3432: fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
3433: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
3434: fprintf(ficresprobmorprev," p.%-d SE",j);
3435: for(i=1; i<=nlstate;i++)
3436: fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
3437: }
3438: fprintf(ficresprobmorprev,"\n");
3439: fprintf(ficgp,"\n# Routine varevsij");
3440: /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
3441: 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");
3442: fprintf(fichtm,"\n<br>%s <br>\n",digitp);
3443: /* } */
3444: varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
3445: pstamp(ficresvij);
3446: fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n# (weighted average of eij where weights are ");
3447: if(popbased==1)
1.128 brouard 3448: 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 3449: else
3450: fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
3451: fprintf(ficresvij,"# Age");
3452: for(i=1; i<=nlstate;i++)
3453: for(j=1; j<=nlstate;j++)
3454: fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
3455: fprintf(ficresvij,"\n");
3456:
3457: xp=vector(1,npar);
3458: dnewm=matrix(1,nlstate,1,npar);
3459: doldm=matrix(1,nlstate,1,nlstate);
3460: dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
3461: doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
3462:
3463: gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
3464: gpp=vector(nlstate+1,nlstate+ndeath);
3465: gmp=vector(nlstate+1,nlstate+ndeath);
3466: trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
3467:
3468: if(estepm < stepm){
3469: printf ("Problem %d lower than %d\n",estepm, stepm);
3470: }
3471: else hstepm=estepm;
3472: /* For example we decided to compute the life expectancy with the smallest unit */
3473: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
3474: nhstepm is the number of hstepm from age to agelim
3475: nstepm is the number of stepm from age to agelin.
1.128 brouard 3476: Look at function hpijx to understand why (it is linked to memory size questions) */
1.126 brouard 3477: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
3478: survival function given by stepm (the optimization length). Unfortunately it
3479: means that if the survival funtion is printed every two years of age and if
3480: you sum them up and add 1 year (area under the trapezoids) you won't get the same
3481: results. So we changed our mind and took the option of the best precision.
3482: */
3483: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
3484: agelim = AGESUP;
3485: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
3486: nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
3487: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
3488: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3489: gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
3490: gp=matrix(0,nhstepm,1,nlstate);
3491: gm=matrix(0,nhstepm,1,nlstate);
3492:
3493:
3494: for(theta=1; theta <=npar; theta++){
3495: for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
3496: xp[i] = x[i] + (i==theta ?delti[theta]:0);
3497: }
3498: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
3499: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
3500:
3501: if (popbased==1) {
3502: if(mobilav ==0){
3503: for(i=1; i<=nlstate;i++)
3504: prlim[i][i]=probs[(int)age][i][ij];
3505: }else{ /* mobilav */
3506: for(i=1; i<=nlstate;i++)
3507: prlim[i][i]=mobaverage[(int)age][i][ij];
3508: }
3509: }
3510:
3511: for(j=1; j<= nlstate; j++){
3512: for(h=0; h<=nhstepm; h++){
3513: for(i=1, gp[h][j]=0.;i<=nlstate;i++)
3514: gp[h][j] += prlim[i][i]*p3mat[i][j][h];
3515: }
3516: }
3517: /* This for computing probability of death (h=1 means
3518: computed over hstepm matrices product = hstepm*stepm months)
3519: as a weighted average of prlim.
3520: */
3521: for(j=nlstate+1;j<=nlstate+ndeath;j++){
3522: for(i=1,gpp[j]=0.; i<= nlstate; i++)
3523: gpp[j] += prlim[i][i]*p3mat[i][j][1];
3524: }
3525: /* end probability of death */
3526:
3527: for(i=1; i<=npar; i++) /* Computes gradient x - delta */
3528: xp[i] = x[i] - (i==theta ?delti[theta]:0);
3529: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
3530: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
3531:
3532: if (popbased==1) {
3533: if(mobilav ==0){
3534: for(i=1; i<=nlstate;i++)
3535: prlim[i][i]=probs[(int)age][i][ij];
3536: }else{ /* mobilav */
3537: for(i=1; i<=nlstate;i++)
3538: prlim[i][i]=mobaverage[(int)age][i][ij];
3539: }
3540: }
3541:
1.128 brouard 3542: for(j=1; j<= nlstate; j++){ /* Sum of wi * eij = e.j */
1.126 brouard 3543: for(h=0; h<=nhstepm; h++){
3544: for(i=1, gm[h][j]=0.;i<=nlstate;i++)
3545: gm[h][j] += prlim[i][i]*p3mat[i][j][h];
3546: }
3547: }
3548: /* This for computing probability of death (h=1 means
3549: computed over hstepm matrices product = hstepm*stepm months)
3550: as a weighted average of prlim.
3551: */
3552: for(j=nlstate+1;j<=nlstate+ndeath;j++){
3553: for(i=1,gmp[j]=0.; i<= nlstate; i++)
3554: gmp[j] += prlim[i][i]*p3mat[i][j][1];
3555: }
3556: /* end probability of death */
3557:
3558: for(j=1; j<= nlstate; j++) /* vareij */
3559: for(h=0; h<=nhstepm; h++){
3560: gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
3561: }
3562:
3563: for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
3564: gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
3565: }
3566:
3567: } /* End theta */
3568:
3569: trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
3570:
3571: for(h=0; h<=nhstepm; h++) /* veij */
3572: for(j=1; j<=nlstate;j++)
3573: for(theta=1; theta <=npar; theta++)
3574: trgradg[h][j][theta]=gradg[h][theta][j];
3575:
3576: for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
3577: for(theta=1; theta <=npar; theta++)
3578: trgradgp[j][theta]=gradgp[theta][j];
3579:
3580:
3581: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
3582: for(i=1;i<=nlstate;i++)
3583: for(j=1;j<=nlstate;j++)
3584: vareij[i][j][(int)age] =0.;
3585:
3586: for(h=0;h<=nhstepm;h++){
3587: for(k=0;k<=nhstepm;k++){
3588: matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
3589: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
3590: for(i=1;i<=nlstate;i++)
3591: for(j=1;j<=nlstate;j++)
3592: vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
3593: }
3594: }
3595:
3596: /* pptj */
3597: matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
3598: matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
3599: for(j=nlstate+1;j<=nlstate+ndeath;j++)
3600: for(i=nlstate+1;i<=nlstate+ndeath;i++)
3601: varppt[j][i]=doldmp[j][i];
3602: /* end ppptj */
3603: /* x centered again */
3604: hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);
3605: prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
3606:
3607: if (popbased==1) {
3608: if(mobilav ==0){
3609: for(i=1; i<=nlstate;i++)
3610: prlim[i][i]=probs[(int)age][i][ij];
3611: }else{ /* mobilav */
3612: for(i=1; i<=nlstate;i++)
3613: prlim[i][i]=mobaverage[(int)age][i][ij];
3614: }
3615: }
3616:
3617: /* This for computing probability of death (h=1 means
3618: computed over hstepm (estepm) matrices product = hstepm*stepm months)
3619: as a weighted average of prlim.
3620: */
3621: for(j=nlstate+1;j<=nlstate+ndeath;j++){
3622: for(i=1,gmp[j]=0.;i<= nlstate; i++)
3623: gmp[j] += prlim[i][i]*p3mat[i][j][1];
3624: }
3625: /* end probability of death */
3626:
3627: fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
3628: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
3629: fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
3630: for(i=1; i<=nlstate;i++){
3631: fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
3632: }
3633: }
3634: fprintf(ficresprobmorprev,"\n");
3635:
3636: fprintf(ficresvij,"%.0f ",age );
3637: for(i=1; i<=nlstate;i++)
3638: for(j=1; j<=nlstate;j++){
3639: fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
3640: }
3641: fprintf(ficresvij,"\n");
3642: free_matrix(gp,0,nhstepm,1,nlstate);
3643: free_matrix(gm,0,nhstepm,1,nlstate);
3644: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
3645: free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
3646: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3647: } /* End age */
3648: free_vector(gpp,nlstate+1,nlstate+ndeath);
3649: free_vector(gmp,nlstate+1,nlstate+ndeath);
3650: free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
3651: free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
1.145 brouard 3652: fprintf(ficgp,"\nunset parametric;unset label; set ter png small size 320, 240");
1.126 brouard 3653: /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
1.131 brouard 3654: fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
1.126 brouard 3655: /* fprintf(ficgp,"\n plot \"%s\" u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
3656: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
3657: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
1.145 brouard 3658: fprintf(ficgp,"\n plot \"%s\" u 1:($3) not w l lt 1 ",subdirf(fileresprobmorprev));
1.170 brouard 3659: fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)) t \"95%% interval\" w l lt 2 ",subdirf(fileresprobmorprev));
1.145 brouard 3660: fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)) not w l lt 2 ",subdirf(fileresprobmorprev));
1.126 brouard 3661: fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
3662: 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);
3663: /* 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);
3664: */
3665: /* fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
3666: fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
3667:
3668: free_vector(xp,1,npar);
3669: free_matrix(doldm,1,nlstate,1,nlstate);
3670: free_matrix(dnewm,1,nlstate,1,npar);
3671: free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
3672: free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
3673: free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
3674: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3675: fclose(ficresprobmorprev);
3676: fflush(ficgp);
3677: fflush(fichtm);
3678: } /* end varevsij */
3679:
3680: /************ Variance of prevlim ******************/
3681: 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[])
3682: {
3683: /* Variance of prevalence limit */
3684: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
1.164 brouard 3685:
1.126 brouard 3686: double **dnewm,**doldm;
3687: int i, j, nhstepm, hstepm;
3688: double *xp;
3689: double *gp, *gm;
3690: double **gradg, **trgradg;
3691: double age,agelim;
3692: int theta;
3693:
3694: pstamp(ficresvpl);
3695: fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
3696: fprintf(ficresvpl,"# Age");
3697: for(i=1; i<=nlstate;i++)
3698: fprintf(ficresvpl," %1d-%1d",i,i);
3699: fprintf(ficresvpl,"\n");
3700:
3701: xp=vector(1,npar);
3702: dnewm=matrix(1,nlstate,1,npar);
3703: doldm=matrix(1,nlstate,1,nlstate);
3704:
3705: hstepm=1*YEARM; /* Every year of age */
3706: hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
3707: agelim = AGESUP;
3708: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
3709: nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
3710: if (stepm >= YEARM) hstepm=1;
3711: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
3712: gradg=matrix(1,npar,1,nlstate);
3713: gp=vector(1,nlstate);
3714: gm=vector(1,nlstate);
3715:
3716: for(theta=1; theta <=npar; theta++){
3717: for(i=1; i<=npar; i++){ /* Computes gradient */
3718: xp[i] = x[i] + (i==theta ?delti[theta]:0);
3719: }
3720: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
3721: for(i=1;i<=nlstate;i++)
3722: gp[i] = prlim[i][i];
3723:
3724: for(i=1; i<=npar; i++) /* Computes gradient */
3725: xp[i] = x[i] - (i==theta ?delti[theta]:0);
3726: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
3727: for(i=1;i<=nlstate;i++)
3728: gm[i] = prlim[i][i];
3729:
3730: for(i=1;i<=nlstate;i++)
3731: gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
3732: } /* End theta */
3733:
3734: trgradg =matrix(1,nlstate,1,npar);
3735:
3736: for(j=1; j<=nlstate;j++)
3737: for(theta=1; theta <=npar; theta++)
3738: trgradg[j][theta]=gradg[theta][j];
3739:
3740: for(i=1;i<=nlstate;i++)
3741: varpl[i][(int)age] =0.;
3742: matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
3743: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
3744: for(i=1;i<=nlstate;i++)
3745: varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
3746:
3747: fprintf(ficresvpl,"%.0f ",age );
3748: for(i=1; i<=nlstate;i++)
3749: fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
3750: fprintf(ficresvpl,"\n");
3751: free_vector(gp,1,nlstate);
3752: free_vector(gm,1,nlstate);
3753: free_matrix(gradg,1,npar,1,nlstate);
3754: free_matrix(trgradg,1,nlstate,1,npar);
3755: } /* End age */
3756:
3757: free_vector(xp,1,npar);
3758: free_matrix(doldm,1,nlstate,1,npar);
3759: free_matrix(dnewm,1,nlstate,1,nlstate);
3760:
3761: }
3762:
3763: /************ Variance of one-step probabilities ******************/
3764: 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[])
3765: {
1.164 brouard 3766: int i, j=0, k1, l1, tj;
1.126 brouard 3767: int k2, l2, j1, z1;
1.164 brouard 3768: int k=0, l;
1.145 brouard 3769: int first=1, first1, first2;
1.126 brouard 3770: double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
3771: double **dnewm,**doldm;
3772: double *xp;
3773: double *gp, *gm;
3774: double **gradg, **trgradg;
3775: double **mu;
1.164 brouard 3776: double age, cov[NCOVMAX+1];
1.126 brouard 3777: double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
3778: int theta;
3779: char fileresprob[FILENAMELENGTH];
3780: char fileresprobcov[FILENAMELENGTH];
3781: char fileresprobcor[FILENAMELENGTH];
3782: double ***varpij;
3783:
3784: strcpy(fileresprob,"prob");
3785: strcat(fileresprob,fileres);
3786: if((ficresprob=fopen(fileresprob,"w"))==NULL) {
3787: printf("Problem with resultfile: %s\n", fileresprob);
3788: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
3789: }
3790: strcpy(fileresprobcov,"probcov");
3791: strcat(fileresprobcov,fileres);
3792: if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
3793: printf("Problem with resultfile: %s\n", fileresprobcov);
3794: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
3795: }
3796: strcpy(fileresprobcor,"probcor");
3797: strcat(fileresprobcor,fileres);
3798: if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
3799: printf("Problem with resultfile: %s\n", fileresprobcor);
3800: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
3801: }
3802: printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
3803: fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
3804: printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
3805: fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
3806: printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
3807: fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
3808: pstamp(ficresprob);
3809: fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
3810: fprintf(ficresprob,"# Age");
3811: pstamp(ficresprobcov);
3812: fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
3813: fprintf(ficresprobcov,"# Age");
3814: pstamp(ficresprobcor);
3815: fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
3816: fprintf(ficresprobcor,"# Age");
3817:
3818:
3819: for(i=1; i<=nlstate;i++)
3820: for(j=1; j<=(nlstate+ndeath);j++){
3821: fprintf(ficresprob," p%1d-%1d (SE)",i,j);
3822: fprintf(ficresprobcov," p%1d-%1d ",i,j);
3823: fprintf(ficresprobcor," p%1d-%1d ",i,j);
3824: }
3825: /* fprintf(ficresprob,"\n");
3826: fprintf(ficresprobcov,"\n");
3827: fprintf(ficresprobcor,"\n");
3828: */
1.131 brouard 3829: xp=vector(1,npar);
1.126 brouard 3830: dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
3831: doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
3832: mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
3833: varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
3834: first=1;
3835: fprintf(ficgp,"\n# Routine varprob");
3836: fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
3837: fprintf(fichtm,"\n");
3838:
3839: fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
3840: fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
3841: file %s<br>\n",optionfilehtmcov);
3842: fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
3843: and drawn. It helps understanding how is the covariance between two incidences.\
3844: They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
3845: 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. \
3846: It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
3847: would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
3848: standard deviations wide on each axis. <br>\
3849: Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
3850: and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
3851: To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
3852:
3853: cov[1]=1;
1.145 brouard 3854: /* tj=cptcoveff; */
3855: tj = (int) pow(2,cptcoveff);
1.126 brouard 3856: if (cptcovn<1) {tj=1;ncodemax[1]=1;}
3857: j1=0;
1.145 brouard 3858: for(j1=1; j1<=tj;j1++){
3859: /*for(i1=1; i1<=ncodemax[t];i1++){ */
3860: /*j1++;*/
1.126 brouard 3861: if (cptcovn>0) {
3862: fprintf(ficresprob, "\n#********** Variable ");
3863: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3864: fprintf(ficresprob, "**********\n#\n");
3865: fprintf(ficresprobcov, "\n#********** Variable ");
3866: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3867: fprintf(ficresprobcov, "**********\n#\n");
3868:
3869: fprintf(ficgp, "\n#********** Variable ");
3870: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3871: fprintf(ficgp, "**********\n#\n");
3872:
3873:
3874: fprintf(fichtmcov, "\n<hr size=\"2\" color=\"#EC5E5E\">********** Variable ");
3875: for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3876: fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
3877:
3878: fprintf(ficresprobcor, "\n#********** Variable ");
3879: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3880: fprintf(ficresprobcor, "**********\n#");
3881: }
3882:
1.145 brouard 3883: gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
3884: trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
3885: gp=vector(1,(nlstate)*(nlstate+ndeath));
3886: gm=vector(1,(nlstate)*(nlstate+ndeath));
1.126 brouard 3887: for (age=bage; age<=fage; age ++){
3888: cov[2]=age;
3889: for (k=1; k<=cptcovn;k++) {
1.145 brouard 3890: cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];/* j1 1 2 3 4
3891: * 1 1 1 1 1
3892: * 2 2 1 1 1
3893: * 3 1 2 1 1
3894: */
3895: /* nbcode[1][1]=0 nbcode[1][2]=1;*/
1.126 brouard 3896: }
3897: for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
3898: for (k=1; k<=cptcovprod;k++)
3899: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
3900:
3901:
3902: for(theta=1; theta <=npar; theta++){
3903: for(i=1; i<=npar; i++)
3904: xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
3905:
3906: pmij(pmmij,cov,ncovmodel,xp,nlstate);
3907:
3908: k=0;
3909: for(i=1; i<= (nlstate); i++){
3910: for(j=1; j<=(nlstate+ndeath);j++){
3911: k=k+1;
3912: gp[k]=pmmij[i][j];
3913: }
3914: }
3915:
3916: for(i=1; i<=npar; i++)
3917: xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
3918:
3919: pmij(pmmij,cov,ncovmodel,xp,nlstate);
3920: k=0;
3921: for(i=1; i<=(nlstate); i++){
3922: for(j=1; j<=(nlstate+ndeath);j++){
3923: k=k+1;
3924: gm[k]=pmmij[i][j];
3925: }
3926: }
3927:
3928: for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)
3929: gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];
3930: }
3931:
3932: for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
3933: for(theta=1; theta <=npar; theta++)
3934: trgradg[j][theta]=gradg[theta][j];
3935:
3936: matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);
3937: matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
3938:
3939: pmij(pmmij,cov,ncovmodel,x,nlstate);
3940:
3941: k=0;
3942: for(i=1; i<=(nlstate); i++){
3943: for(j=1; j<=(nlstate+ndeath);j++){
3944: k=k+1;
3945: mu[k][(int) age]=pmmij[i][j];
3946: }
3947: }
3948: for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
3949: for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
3950: varpij[i][j][(int)age] = doldm[i][j];
3951:
3952: /*printf("\n%d ",(int)age);
3953: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
3954: printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
3955: fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
3956: }*/
3957:
3958: fprintf(ficresprob,"\n%d ",(int)age);
3959: fprintf(ficresprobcov,"\n%d ",(int)age);
3960: fprintf(ficresprobcor,"\n%d ",(int)age);
3961:
3962: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
3963: fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
3964: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
3965: fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
3966: fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
3967: }
3968: i=0;
3969: for (k=1; k<=(nlstate);k++){
3970: for (l=1; l<=(nlstate+ndeath);l++){
1.145 brouard 3971: i++;
1.126 brouard 3972: fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
3973: fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
3974: for (j=1; j<=i;j++){
1.145 brouard 3975: /* printf(" k=%d l=%d i=%d j=%d\n",k,l,i,j);fflush(stdout); */
1.126 brouard 3976: fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
3977: fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
3978: }
3979: }
3980: }/* end of loop for state */
3981: } /* end of loop for age */
1.145 brouard 3982: free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
3983: free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
3984: free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
3985: free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
3986:
1.126 brouard 3987: /* Confidence intervalle of pij */
3988: /*
1.131 brouard 3989: fprintf(ficgp,"\nunset parametric;unset label");
1.126 brouard 3990: fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
3991: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
3992: 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);
3993: fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
3994: fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
3995: fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
3996: */
3997:
3998: /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
1.145 brouard 3999: first1=1;first2=2;
1.126 brouard 4000: for (k2=1; k2<=(nlstate);k2++){
4001: for (l2=1; l2<=(nlstate+ndeath);l2++){
4002: if(l2==k2) continue;
4003: j=(k2-1)*(nlstate+ndeath)+l2;
4004: for (k1=1; k1<=(nlstate);k1++){
4005: for (l1=1; l1<=(nlstate+ndeath);l1++){
4006: if(l1==k1) continue;
4007: i=(k1-1)*(nlstate+ndeath)+l1;
4008: if(i<=j) continue;
4009: for (age=bage; age<=fage; age ++){
4010: if ((int)age %5==0){
4011: v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
4012: v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
4013: cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
4014: mu1=mu[i][(int) age]/stepm*YEARM ;
4015: mu2=mu[j][(int) age]/stepm*YEARM;
4016: c12=cv12/sqrt(v1*v2);
4017: /* Computing eigen value of matrix of covariance */
4018: lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
4019: lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
1.135 brouard 4020: if ((lc2 <0) || (lc1 <0) ){
1.145 brouard 4021: if(first2==1){
4022: first1=0;
4023: 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);
4024: }
4025: 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);
4026: /* lc1=fabs(lc1); */ /* If we want to have them positive */
4027: /* lc2=fabs(lc2); */
1.135 brouard 4028: }
4029:
1.126 brouard 4030: /* Eigen vectors */
4031: v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
4032: /*v21=sqrt(1.-v11*v11); *//* error */
4033: v21=(lc1-v1)/cv12*v11;
4034: v12=-v21;
4035: v22=v11;
4036: tnalp=v21/v11;
4037: if(first1==1){
4038: first1=0;
4039: 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);
4040: }
4041: 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);
4042: /*printf(fignu*/
4043: /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
4044: /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
4045: if(first==1){
4046: first=0;
4047: fprintf(ficgp,"\nset parametric;unset label");
4048: 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 4049: fprintf(ficgp,"\nset ter png small size 320, 240");
1.126 brouard 4050: fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
4051: :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
4052: %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
4053: subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
4054: subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
4055: fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
4056: fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
4057: fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
4058: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
4059: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
4060: 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",\
4061: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
4062: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
4063: }else{
4064: first=0;
4065: fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
4066: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
4067: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
4068: 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",\
4069: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
4070: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
4071: }/* if first */
4072: } /* age mod 5 */
4073: } /* end loop age */
4074: fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
4075: first=1;
4076: } /*l12 */
4077: } /* k12 */
4078: } /*l1 */
4079: }/* k1 */
1.169 brouard 4080: /* } */ /* loop covariates */
1.126 brouard 4081: }
4082: free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
4083: free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
4084: free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
4085: free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
4086: free_vector(xp,1,npar);
4087: fclose(ficresprob);
4088: fclose(ficresprobcov);
4089: fclose(ficresprobcor);
4090: fflush(ficgp);
4091: fflush(fichtmcov);
4092: }
4093:
4094:
4095: /******************* Printing html file ***********/
4096: void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
4097: int lastpass, int stepm, int weightopt, char model[],\
4098: int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
4099: int popforecast, int estepm ,\
4100: double jprev1, double mprev1,double anprev1, \
4101: double jprev2, double mprev2,double anprev2){
4102: int jj1, k1, i1, cpt;
4103:
4104: fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
4105: <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
4106: </ul>");
4107: fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \
4108: - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
4109: jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
4110: fprintf(fichtm,"\
4111: - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
4112: stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
4113: fprintf(fichtm,"\
4114: - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
4115: subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
4116: fprintf(fichtm,"\
1.128 brouard 4117: - (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 4118: <a href=\"%s\">%s</a> <br>\n",
4119: estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
4120: fprintf(fichtm,"\
4121: - Population projections by age and states: \
4122: <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileres,"f"),subdirf2(fileres,"f"));
4123:
4124: fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
4125:
1.145 brouard 4126: m=pow(2,cptcoveff);
1.126 brouard 4127: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
4128:
4129: jj1=0;
4130: for(k1=1; k1<=m;k1++){
4131: for(i1=1; i1<=ncodemax[k1];i1++){
4132: jj1++;
4133: if (cptcovn > 0) {
4134: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
4135: for (cpt=1; cpt<=cptcoveff;cpt++)
4136: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
4137: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
4138: }
4139: /* Pij */
1.145 brouard 4140: 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> \
4141: <img src=\"%s%d_1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
1.126 brouard 4142: /* Quasi-incidences */
4143: fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
1.145 brouard 4144: 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> \
4145: <img src=\"%s%d_2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
1.126 brouard 4146: /* Period (stable) prevalence in each health state */
1.154 brouard 4147: for(cpt=1; cpt<=nlstate;cpt++){
1.166 brouard 4148: 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> \
4149: <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 4150: }
4151: for(cpt=1; cpt<=nlstate;cpt++) {
1.154 brouard 4152: 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> \
4153: <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 4154: }
4155: } /* end i1 */
4156: }/* End k1 */
4157: fprintf(fichtm,"</ul>");
4158:
4159:
4160: fprintf(fichtm,"\
4161: \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
4162: - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);
4163:
4164: fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
4165: subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
4166: fprintf(fichtm,"\
4167: - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
4168: subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
4169:
4170: fprintf(fichtm,"\
4171: - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
4172: subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
4173: fprintf(fichtm,"\
4174: - 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): \
4175: <a href=\"%s\">%s</a> <br>\n</li>",
4176: estepm,subdirf2(fileres,"cve"),subdirf2(fileres,"cve"));
4177: fprintf(fichtm,"\
4178: - (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): \
4179: <a href=\"%s\">%s</a> <br>\n</li>",
4180: estepm,subdirf2(fileres,"stde"),subdirf2(fileres,"stde"));
4181: fprintf(fichtm,"\
1.128 brouard 4182: - 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 4183: estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
4184: fprintf(fichtm,"\
1.128 brouard 4185: - 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",
4186: estepm, subdirf2(fileres,"t"),subdirf2(fileres,"t"));
1.126 brouard 4187: fprintf(fichtm,"\
4188: - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
4189: subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
4190:
4191: /* if(popforecast==1) fprintf(fichtm,"\n */
4192: /* - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
4193: /* - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
4194: /* <br>",fileres,fileres,fileres,fileres); */
4195: /* else */
4196: /* 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); */
4197: fflush(fichtm);
4198: fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
4199:
1.145 brouard 4200: m=pow(2,cptcoveff);
1.126 brouard 4201: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
4202:
4203: jj1=0;
4204: for(k1=1; k1<=m;k1++){
4205: for(i1=1; i1<=ncodemax[k1];i1++){
4206: jj1++;
4207: if (cptcovn > 0) {
4208: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
4209: for (cpt=1; cpt<=cptcoveff;cpt++)
4210: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
4211: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
4212: }
4213: for(cpt=1; cpt<=nlstate;cpt++) {
4214: fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
1.145 brouard 4215: prevalence (with 95%% confidence interval) in state (%d): %s%d_%d.png <br>\
4216: <img src=\"%s%d_%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);
1.126 brouard 4217: }
4218: fprintf(fichtm,"\n<br>- Total life expectancy by age and \
1.128 brouard 4219: health expectancies in states (1) and (2). If popbased=1 the smooth (due to the model) \
4220: true period expectancies (those weighted with period prevalences are also\
4221: drawn in addition to the population based expectancies computed using\
4222: observed and cahotic prevalences: %s%d.png<br>\
1.126 brouard 4223: <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
4224: } /* end i1 */
4225: }/* End k1 */
4226: fprintf(fichtm,"</ul>");
4227: fflush(fichtm);
4228: }
4229:
4230: /******************* Gnuplot file **************/
4231: void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
4232:
4233: char dirfileres[132],optfileres[132];
1.164 brouard 4234: int cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,ij=0,l=0;
1.130 brouard 4235: int ng=0;
1.126 brouard 4236: /* if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
4237: /* printf("Problem with file %s",optionfilegnuplot); */
4238: /* fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
4239: /* } */
4240:
4241: /*#ifdef windows */
4242: fprintf(ficgp,"cd \"%s\" \n",pathc);
4243: /*#endif */
4244: m=pow(2,cptcoveff);
4245:
4246: strcpy(dirfileres,optionfilefiname);
4247: strcpy(optfileres,"vpl");
4248: /* 1eme*/
1.153 brouard 4249: fprintf(ficgp,"\n# 1st: Period (stable) prevalence with CI: 'vpl' files\n");
1.126 brouard 4250: for (cpt=1; cpt<= nlstate ; cpt ++) {
1.145 brouard 4251: for (k1=1; k1<= m ; k1 ++) { /* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */
4252: fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
4253: fprintf(ficgp,"\n#set out \"v%s%d_%d.png\" \n",optionfilefiname,cpt,k1);
1.126 brouard 4254: fprintf(ficgp,"set xlabel \"Age\" \n\
4255: set ylabel \"Probability\" \n\
1.145 brouard 4256: set ter png small size 320, 240\n\
1.170 brouard 4257: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
1.126 brouard 4258:
4259: for (i=1; i<= nlstate ; i ++) {
1.170 brouard 4260: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
4261: else fprintf(ficgp," %%*lf (%%*lf)");
1.126 brouard 4262: }
1.170 brouard 4263: 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 4264: for (i=1; i<= nlstate ; i ++) {
1.170 brouard 4265: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
4266: else fprintf(ficgp," %%*lf (%%*lf)");
1.126 brouard 4267: }
1.170 brouard 4268: fprintf(ficgp,"\" t\"95%% CI\" w l lt 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
1.126 brouard 4269: for (i=1; i<= nlstate ; i ++) {
1.170 brouard 4270: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
4271: else fprintf(ficgp," %%*lf (%%*lf)");
1.126 brouard 4272: }
1.145 brouard 4273: fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l lt 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
1.126 brouard 4274: }
4275: }
4276: /*2 eme*/
1.153 brouard 4277: fprintf(ficgp,"\n# 2nd: Total life expectancy with CI: 't' files\n");
1.126 brouard 4278: for (k1=1; k1<= m ; k1 ++) {
4279: fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
1.145 brouard 4280: fprintf(ficgp,"set ylabel \"Years\" \nset ter png small size 320, 240\nplot [%.f:%.f] ",ageminpar,fage);
1.126 brouard 4281:
4282: for (i=1; i<= nlstate+1 ; i ++) {
4283: k=2*i;
1.170 brouard 4284: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
1.126 brouard 4285: for (j=1; j<= nlstate+1 ; j ++) {
1.170 brouard 4286: if (j==i) fprintf(ficgp," %%lf (%%lf)");
4287: else fprintf(ficgp," %%*lf (%%*lf)");
1.126 brouard 4288: }
4289: if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
4290: else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
1.170 brouard 4291: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
1.126 brouard 4292: for (j=1; j<= nlstate+1 ; j ++) {
1.170 brouard 4293: if (j==i) fprintf(ficgp," %%lf (%%lf)");
4294: else fprintf(ficgp," %%*lf (%%*lf)");
1.126 brouard 4295: }
1.145 brouard 4296: fprintf(ficgp,"\" t\"\" w l lt 0,");
1.170 brouard 4297: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
1.126 brouard 4298: for (j=1; j<= nlstate+1 ; j ++) {
1.170 brouard 4299: if (j==i) fprintf(ficgp," %%lf (%%lf)");
4300: else fprintf(ficgp," %%*lf (%%*lf)");
1.126 brouard 4301: }
1.145 brouard 4302: if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l lt 0");
4303: else fprintf(ficgp,"\" t\"\" w l lt 0,");
1.126 brouard 4304: }
4305: }
4306:
4307: /*3eme*/
4308:
4309: for (k1=1; k1<= m ; k1 ++) {
4310: for (cpt=1; cpt<= nlstate ; cpt ++) {
4311: /* k=2+nlstate*(2*cpt-2); */
4312: k=2+(nlstate+1)*(cpt-1);
4313: fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
1.145 brouard 4314: fprintf(ficgp,"set ter png small size 320, 240\n\
1.126 brouard 4315: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
4316: /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
4317: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
4318: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
4319: fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
4320: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
4321: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
4322:
4323: */
4324: for (i=1; i< nlstate ; i ++) {
4325: 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);
4326: /* 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);*/
4327:
4328: }
4329: fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+nlstate,cpt);
4330: }
4331: }
4332:
4333: /* CV preval stable (period) */
1.153 brouard 4334: for (k1=1; k1<= m ; k1 ++) { /* For each multivariate if any */
4335: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
1.126 brouard 4336: k=3;
1.153 brouard 4337: fprintf(ficgp,"\n#\n#\n#CV preval stable (period): 'pij' files, cov=%d state=%d",k1, cpt);
1.145 brouard 4338: fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
1.126 brouard 4339: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
1.145 brouard 4340: set ter png small size 320, 240\n\
1.126 brouard 4341: unset log y\n\
1.153 brouard 4342: plot [%.f:%.f] ", ageminpar, agemaxpar);
4343: for (i=1; i<= nlstate ; i ++){
4344: if(i==1)
4345: fprintf(ficgp,"\"%s\"",subdirf2(fileres,"pij"));
4346: else
4347: fprintf(ficgp,", '' ");
1.154 brouard 4348: l=(nlstate+ndeath)*(i-1)+1;
4349: fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
1.153 brouard 4350: for (j=1; j<= (nlstate-1) ; j ++)
4351: fprintf(ficgp,"+$%d",k+l+j);
4352: fprintf(ficgp,")) t \"prev(%d,%d)\" w l",i,cpt);
4353: } /* nlstate */
4354: fprintf(ficgp,"\n");
4355: } /* end cpt state*/
4356: } /* end covariate */
1.126 brouard 4357:
4358: /* proba elementaires */
4359: for(i=1,jk=1; i <=nlstate; i++){
4360: for(k=1; k <=(nlstate+ndeath); k++){
4361: if (k != i) {
4362: for(j=1; j <=ncovmodel; j++){
4363: fprintf(ficgp,"p%d=%f ",jk,p[jk]);
4364: jk++;
4365: fprintf(ficgp,"\n");
4366: }
4367: }
4368: }
4369: }
1.145 brouard 4370: /*goto avoid;*/
1.126 brouard 4371: for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
4372: for(jk=1; jk <=m; jk++) {
1.145 brouard 4373: fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng);
1.126 brouard 4374: if (ng==2)
4375: fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
4376: else
4377: fprintf(ficgp,"\nset title \"Probability\"\n");
1.145 brouard 4378: fprintf(ficgp,"\nset ter png small size 320, 240\nset log y\nplot [%.f:%.f] ",ageminpar,agemaxpar);
1.126 brouard 4379: i=1;
4380: for(k2=1; k2<=nlstate; k2++) {
4381: k3=i;
4382: for(k=1; k<=(nlstate+ndeath); k++) {
4383: if (k != k2){
4384: if(ng==2)
4385: fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
4386: else
4387: fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
1.141 brouard 4388: ij=1;/* To be checked else nbcode[0][0] wrong */
1.126 brouard 4389: for(j=3; j <=ncovmodel; j++) {
1.145 brouard 4390: /* if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) { /\* Bug valgrind *\/ */
4391: /* /\*fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);*\/ */
4392: /* ij++; */
4393: /* } */
4394: /* else */
1.126 brouard 4395: fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
4396: }
4397: fprintf(ficgp,")/(1");
4398:
4399: for(k1=1; k1 <=nlstate; k1++){
4400: fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
4401: ij=1;
4402: for(j=3; j <=ncovmodel; j++){
1.145 brouard 4403: /* if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) { */
4404: /* fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]); */
4405: /* ij++; */
4406: /* } */
4407: /* else */
1.126 brouard 4408: fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
4409: }
4410: fprintf(ficgp,")");
4411: }
4412: fprintf(ficgp,") t \"p%d%d\" ", k2,k);
4413: if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
4414: i=i+ncovmodel;
4415: }
4416: } /* end k */
4417: } /* end k2 */
4418: } /* end jk */
4419: } /* end ng */
1.164 brouard 4420: /* avoid: */
1.126 brouard 4421: fflush(ficgp);
4422: } /* end gnuplot */
4423:
4424:
4425: /*************** Moving average **************/
4426: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
4427:
4428: int i, cpt, cptcod;
4429: int modcovmax =1;
4430: int mobilavrange, mob;
4431: double age;
4432:
4433: modcovmax=2*cptcoveff;/* Max number of modalities. We suppose
4434: a covariate has 2 modalities */
4435: if (cptcovn<1) modcovmax=1; /* At least 1 pass */
4436:
4437: if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
4438: if(mobilav==1) mobilavrange=5; /* default */
4439: else mobilavrange=mobilav;
4440: for (age=bage; age<=fage; age++)
4441: for (i=1; i<=nlstate;i++)
4442: for (cptcod=1;cptcod<=modcovmax;cptcod++)
4443: mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
4444: /* We keep the original values on the extreme ages bage, fage and for
4445: fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
4446: we use a 5 terms etc. until the borders are no more concerned.
4447: */
4448: for (mob=3;mob <=mobilavrange;mob=mob+2){
4449: for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
4450: for (i=1; i<=nlstate;i++){
4451: for (cptcod=1;cptcod<=modcovmax;cptcod++){
4452: mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
4453: for (cpt=1;cpt<=(mob-1)/2;cpt++){
4454: mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
4455: mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
4456: }
4457: mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
4458: }
4459: }
4460: }/* end age */
4461: }/* end mob */
4462: }else return -1;
4463: return 0;
4464: }/* End movingaverage */
4465:
4466:
4467: /************** Forecasting ******************/
1.169 brouard 4468: 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 4469: /* proj1, year, month, day of starting projection
4470: agemin, agemax range of age
4471: dateprev1 dateprev2 range of dates during which prevalence is computed
4472: anproj2 year of en of projection (same day and month as proj1).
4473: */
1.164 brouard 4474: int yearp, stepsize, hstepm, nhstepm, j, k, cptcod, i, h, i1;
1.126 brouard 4475: double agec; /* generic age */
4476: double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
4477: double *popeffectif,*popcount;
4478: double ***p3mat;
4479: double ***mobaverage;
4480: char fileresf[FILENAMELENGTH];
4481:
4482: agelim=AGESUP;
4483: prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
4484:
4485: strcpy(fileresf,"f");
4486: strcat(fileresf,fileres);
4487: if((ficresf=fopen(fileresf,"w"))==NULL) {
4488: printf("Problem with forecast resultfile: %s\n", fileresf);
4489: fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
4490: }
4491: printf("Computing forecasting: result on file '%s' \n", fileresf);
4492: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
4493:
4494: if (cptcoveff==0) ncodemax[cptcoveff]=1;
4495:
4496: if (mobilav!=0) {
4497: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4498: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
4499: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
4500: printf(" Error in movingaverage mobilav=%d\n",mobilav);
4501: }
4502: }
4503:
4504: stepsize=(int) (stepm+YEARM-1)/YEARM;
4505: if (stepm<=12) stepsize=1;
4506: if(estepm < stepm){
4507: printf ("Problem %d lower than %d\n",estepm, stepm);
4508: }
4509: else hstepm=estepm;
4510:
4511: hstepm=hstepm/stepm;
4512: yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp and
4513: fractional in yp1 */
4514: anprojmean=yp;
4515: yp2=modf((yp1*12),&yp);
4516: mprojmean=yp;
4517: yp1=modf((yp2*30.5),&yp);
4518: jprojmean=yp;
4519: if(jprojmean==0) jprojmean=1;
4520: if(mprojmean==0) jprojmean=1;
4521:
4522: i1=cptcoveff;
4523: if (cptcovn < 1){i1=1;}
4524:
4525: fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);
4526:
4527: fprintf(ficresf,"#****** Routine prevforecast **\n");
4528:
4529: /* if (h==(int)(YEARM*yearp)){ */
4530: for(cptcov=1, k=0;cptcov<=i1;cptcov++){
4531: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
4532: k=k+1;
4533: fprintf(ficresf,"\n#******");
4534: for(j=1;j<=cptcoveff;j++) {
4535: 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]]);
4536: }
4537: fprintf(ficresf,"******\n");
4538: fprintf(ficresf,"# Covariate valuofcovar yearproj age");
4539: for(j=1; j<=nlstate+ndeath;j++){
4540: for(i=1; i<=nlstate;i++)
4541: fprintf(ficresf," p%d%d",i,j);
4542: fprintf(ficresf," p.%d",j);
4543: }
4544: for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {
4545: fprintf(ficresf,"\n");
4546: fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);
4547:
4548: for (agec=fage; agec>=(ageminpar-1); agec--){
4549: nhstepm=(int) rint((agelim-agec)*YEARM/stepm);
4550: nhstepm = nhstepm/hstepm;
4551: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4552: oldm=oldms;savm=savms;
4553: hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);
4554:
4555: for (h=0; h<=nhstepm; h++){
4556: if (h*hstepm/YEARM*stepm ==yearp) {
4557: fprintf(ficresf,"\n");
4558: for(j=1;j<=cptcoveff;j++)
4559: fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4560: fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
4561: }
4562: for(j=1; j<=nlstate+ndeath;j++) {
4563: ppij=0.;
4564: for(i=1; i<=nlstate;i++) {
4565: if (mobilav==1)
4566: ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
4567: else {
4568: ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
4569: }
4570: if (h*hstepm/YEARM*stepm== yearp) {
4571: fprintf(ficresf," %.3f", p3mat[i][j][h]);
4572: }
4573: } /* end i */
4574: if (h*hstepm/YEARM*stepm==yearp) {
4575: fprintf(ficresf," %.3f", ppij);
4576: }
4577: }/* end j */
4578: } /* end h */
4579: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4580: } /* end agec */
4581: } /* end yearp */
4582: } /* end cptcod */
4583: } /* end cptcov */
4584:
4585: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4586:
4587: fclose(ficresf);
4588: }
4589:
4590: /************** Forecasting *****not tested NB*************/
1.169 brouard 4591: 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 4592:
4593: int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
4594: int *popage;
4595: double calagedatem, agelim, kk1, kk2;
4596: double *popeffectif,*popcount;
4597: double ***p3mat,***tabpop,***tabpopprev;
4598: double ***mobaverage;
4599: char filerespop[FILENAMELENGTH];
4600:
4601: tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4602: tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4603: agelim=AGESUP;
4604: calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
4605:
4606: prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
4607:
4608:
4609: strcpy(filerespop,"pop");
4610: strcat(filerespop,fileres);
4611: if((ficrespop=fopen(filerespop,"w"))==NULL) {
4612: printf("Problem with forecast resultfile: %s\n", filerespop);
4613: fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
4614: }
4615: printf("Computing forecasting: result on file '%s' \n", filerespop);
4616: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
4617:
4618: if (cptcoveff==0) ncodemax[cptcoveff]=1;
4619:
4620: if (mobilav!=0) {
4621: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4622: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
4623: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
4624: printf(" Error in movingaverage mobilav=%d\n",mobilav);
4625: }
4626: }
4627:
4628: stepsize=(int) (stepm+YEARM-1)/YEARM;
4629: if (stepm<=12) stepsize=1;
4630:
4631: agelim=AGESUP;
4632:
4633: hstepm=1;
4634: hstepm=hstepm/stepm;
4635:
4636: if (popforecast==1) {
4637: if((ficpop=fopen(popfile,"r"))==NULL) {
4638: printf("Problem with population file : %s\n",popfile);exit(0);
4639: fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
4640: }
4641: popage=ivector(0,AGESUP);
4642: popeffectif=vector(0,AGESUP);
4643: popcount=vector(0,AGESUP);
4644:
4645: i=1;
4646: while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
4647:
4648: imx=i;
4649: for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
4650: }
4651:
4652: for(cptcov=1,k=0;cptcov<=i2;cptcov++){
4653: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
4654: k=k+1;
4655: fprintf(ficrespop,"\n#******");
4656: for(j=1;j<=cptcoveff;j++) {
4657: fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4658: }
4659: fprintf(ficrespop,"******\n");
4660: fprintf(ficrespop,"# Age");
4661: for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
4662: if (popforecast==1) fprintf(ficrespop," [Population]");
4663:
4664: for (cpt=0; cpt<=0;cpt++) {
4665: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
4666:
4667: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
4668: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
4669: nhstepm = nhstepm/hstepm;
4670:
4671: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4672: oldm=oldms;savm=savms;
4673: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
4674:
4675: for (h=0; h<=nhstepm; h++){
4676: if (h==(int) (calagedatem+YEARM*cpt)) {
4677: fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
4678: }
4679: for(j=1; j<=nlstate+ndeath;j++) {
4680: kk1=0.;kk2=0;
4681: for(i=1; i<=nlstate;i++) {
4682: if (mobilav==1)
4683: kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
4684: else {
4685: kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
4686: }
4687: }
4688: if (h==(int)(calagedatem+12*cpt)){
4689: tabpop[(int)(agedeb)][j][cptcod]=kk1;
4690: /*fprintf(ficrespop," %.3f", kk1);
4691: if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
4692: }
4693: }
4694: for(i=1; i<=nlstate;i++){
4695: kk1=0.;
4696: for(j=1; j<=nlstate;j++){
4697: kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];
4698: }
4699: tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
4700: }
4701:
4702: if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++)
4703: fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
4704: }
4705: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4706: }
4707: }
4708:
4709: /******/
4710:
4711: for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {
4712: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
4713: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
4714: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
4715: nhstepm = nhstepm/hstepm;
4716:
4717: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4718: oldm=oldms;savm=savms;
4719: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
4720: for (h=0; h<=nhstepm; h++){
4721: if (h==(int) (calagedatem+YEARM*cpt)) {
4722: fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
4723: }
4724: for(j=1; j<=nlstate+ndeath;j++) {
4725: kk1=0.;kk2=0;
4726: for(i=1; i<=nlstate;i++) {
4727: kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];
4728: }
4729: if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);
4730: }
4731: }
4732: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4733: }
4734: }
4735: }
4736: }
4737:
4738: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4739:
4740: if (popforecast==1) {
4741: free_ivector(popage,0,AGESUP);
4742: free_vector(popeffectif,0,AGESUP);
4743: free_vector(popcount,0,AGESUP);
4744: }
4745: free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4746: free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4747: fclose(ficrespop);
4748: } /* End of popforecast */
4749:
4750: int fileappend(FILE *fichier, char *optionfich)
4751: {
4752: if((fichier=fopen(optionfich,"a"))==NULL) {
4753: printf("Problem with file: %s\n", optionfich);
4754: fprintf(ficlog,"Problem with file: %s\n", optionfich);
4755: return (0);
4756: }
4757: fflush(fichier);
4758: return (1);
4759: }
4760:
4761:
4762: /**************** function prwizard **********************/
4763: void prwizard(int ncovmodel, int nlstate, int ndeath, char model[], FILE *ficparo)
4764: {
4765:
4766: /* Wizard to print covariance matrix template */
4767:
1.164 brouard 4768: char ca[32], cb[32];
4769: int i,j, k, li, lj, lk, ll, jj, npar, itimes;
1.126 brouard 4770: int numlinepar;
4771:
4772: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
4773: fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
4774: for(i=1; i <=nlstate; i++){
4775: jj=0;
4776: for(j=1; j <=nlstate+ndeath; j++){
4777: if(j==i) continue;
4778: jj++;
4779: /*ca[0]= k+'a'-1;ca[1]='\0';*/
4780: printf("%1d%1d",i,j);
4781: fprintf(ficparo,"%1d%1d",i,j);
4782: for(k=1; k<=ncovmodel;k++){
4783: /* printf(" %lf",param[i][j][k]); */
4784: /* fprintf(ficparo," %lf",param[i][j][k]); */
4785: printf(" 0.");
4786: fprintf(ficparo," 0.");
4787: }
4788: printf("\n");
4789: fprintf(ficparo,"\n");
4790: }
4791: }
4792: printf("# Scales (for hessian or gradient estimation)\n");
4793: fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
4794: npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
4795: for(i=1; i <=nlstate; i++){
4796: jj=0;
4797: for(j=1; j <=nlstate+ndeath; j++){
4798: if(j==i) continue;
4799: jj++;
4800: fprintf(ficparo,"%1d%1d",i,j);
4801: printf("%1d%1d",i,j);
4802: fflush(stdout);
4803: for(k=1; k<=ncovmodel;k++){
4804: /* printf(" %le",delti3[i][j][k]); */
4805: /* fprintf(ficparo," %le",delti3[i][j][k]); */
4806: printf(" 0.");
4807: fprintf(ficparo," 0.");
4808: }
4809: numlinepar++;
4810: printf("\n");
4811: fprintf(ficparo,"\n");
4812: }
4813: }
4814: printf("# Covariance matrix\n");
4815: /* # 121 Var(a12)\n\ */
4816: /* # 122 Cov(b12,a12) Var(b12)\n\ */
4817: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
4818: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
4819: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
4820: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
4821: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
4822: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
4823: fflush(stdout);
4824: fprintf(ficparo,"# Covariance matrix\n");
4825: /* # 121 Var(a12)\n\ */
4826: /* # 122 Cov(b12,a12) Var(b12)\n\ */
4827: /* # ...\n\ */
4828: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
4829:
4830: for(itimes=1;itimes<=2;itimes++){
4831: jj=0;
4832: for(i=1; i <=nlstate; i++){
4833: for(j=1; j <=nlstate+ndeath; j++){
4834: if(j==i) continue;
4835: for(k=1; k<=ncovmodel;k++){
4836: jj++;
4837: ca[0]= k+'a'-1;ca[1]='\0';
4838: if(itimes==1){
4839: printf("#%1d%1d%d",i,j,k);
4840: fprintf(ficparo,"#%1d%1d%d",i,j,k);
4841: }else{
4842: printf("%1d%1d%d",i,j,k);
4843: fprintf(ficparo,"%1d%1d%d",i,j,k);
4844: /* printf(" %.5le",matcov[i][j]); */
4845: }
4846: ll=0;
4847: for(li=1;li <=nlstate; li++){
4848: for(lj=1;lj <=nlstate+ndeath; lj++){
4849: if(lj==li) continue;
4850: for(lk=1;lk<=ncovmodel;lk++){
4851: ll++;
4852: if(ll<=jj){
4853: cb[0]= lk +'a'-1;cb[1]='\0';
4854: if(ll<jj){
4855: if(itimes==1){
4856: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
4857: fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
4858: }else{
4859: printf(" 0.");
4860: fprintf(ficparo," 0.");
4861: }
4862: }else{
4863: if(itimes==1){
4864: printf(" Var(%s%1d%1d)",ca,i,j);
4865: fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
4866: }else{
4867: printf(" 0.");
4868: fprintf(ficparo," 0.");
4869: }
4870: }
4871: }
4872: } /* end lk */
4873: } /* end lj */
4874: } /* end li */
4875: printf("\n");
4876: fprintf(ficparo,"\n");
4877: numlinepar++;
4878: } /* end k*/
4879: } /*end j */
4880: } /* end i */
4881: } /* end itimes */
4882:
4883: } /* end of prwizard */
4884: /******************* Gompertz Likelihood ******************************/
4885: double gompertz(double x[])
4886: {
4887: double A,B,L=0.0,sump=0.,num=0.;
4888: int i,n=0; /* n is the size of the sample */
4889:
4890: for (i=0;i<=imx-1 ; i++) {
4891: sump=sump+weight[i];
4892: /* sump=sump+1;*/
4893: num=num+1;
4894: }
4895:
4896:
4897: /* for (i=0; i<=imx; i++)
4898: 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]);*/
4899:
4900: for (i=1;i<=imx ; i++)
4901: {
4902: if (cens[i] == 1 && wav[i]>1)
4903: A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
4904:
4905: if (cens[i] == 0 && wav[i]>1)
4906: A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
4907: +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);
4908:
4909: /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
4910: if (wav[i] > 1 ) { /* ??? */
4911: L=L+A*weight[i];
4912: /* 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]);*/
4913: }
4914: }
4915:
4916: /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
4917:
4918: return -2*L*num/sump;
4919: }
4920:
1.136 brouard 4921: #ifdef GSL
4922: /******************* Gompertz_f Likelihood ******************************/
4923: double gompertz_f(const gsl_vector *v, void *params)
4924: {
4925: double A,B,LL=0.0,sump=0.,num=0.;
4926: double *x= (double *) v->data;
4927: int i,n=0; /* n is the size of the sample */
4928:
4929: for (i=0;i<=imx-1 ; i++) {
4930: sump=sump+weight[i];
4931: /* sump=sump+1;*/
4932: num=num+1;
4933: }
4934:
4935:
4936: /* for (i=0; i<=imx; i++)
4937: 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]);*/
4938: printf("x[0]=%lf x[1]=%lf\n",x[0],x[1]);
4939: for (i=1;i<=imx ; i++)
4940: {
4941: if (cens[i] == 1 && wav[i]>1)
4942: A=-x[0]/(x[1])*(exp(x[1]*(agecens[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)));
4943:
4944: if (cens[i] == 0 && wav[i]>1)
4945: A=-x[0]/(x[1])*(exp(x[1]*(agedc[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)))
4946: +log(x[0]/YEARM)+x[1]*(agedc[i]-agegomp)+log(YEARM);
4947:
4948: /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
4949: if (wav[i] > 1 ) { /* ??? */
4950: LL=LL+A*weight[i];
4951: /* 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]);*/
4952: }
4953: }
4954:
4955: /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
4956: printf("x[0]=%lf x[1]=%lf -2*LL*num/sump=%lf\n",x[0],x[1],-2*LL*num/sump);
4957:
4958: return -2*LL*num/sump;
4959: }
4960: #endif
4961:
1.126 brouard 4962: /******************* Printing html file ***********/
4963: void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \
4964: int lastpass, int stepm, int weightopt, char model[],\
4965: int imx, double p[],double **matcov,double agemortsup){
4966: int i,k;
4967:
4968: fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
4969: fprintf(fichtm," mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
4970: for (i=1;i<=2;i++)
4971: 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]));
4972: fprintf(fichtm,"<br><br><img src=\"graphmort.png\">");
4973: fprintf(fichtm,"</ul>");
4974:
4975: fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
4976:
4977: 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>");
4978:
4979: for (k=agegomp;k<(agemortsup-2);k++)
4980: 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]);
4981:
4982:
4983: fflush(fichtm);
4984: }
4985:
4986: /******************* Gnuplot file **************/
4987: void printinggnuplotmort(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
4988:
4989: char dirfileres[132],optfileres[132];
1.164 brouard 4990:
1.126 brouard 4991: int ng;
4992:
4993:
4994: /*#ifdef windows */
4995: fprintf(ficgp,"cd \"%s\" \n",pathc);
4996: /*#endif */
4997:
4998:
4999: strcpy(dirfileres,optionfilefiname);
5000: strcpy(optfileres,"vpl");
5001: fprintf(ficgp,"set out \"graphmort.png\"\n ");
5002: fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n ");
1.145 brouard 5003: fprintf(ficgp, "set ter png small size 320, 240\n set log y\n");
5004: /* fprintf(ficgp, "set size 0.65,0.65\n"); */
1.126 brouard 5005: fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
5006:
5007: }
5008:
1.136 brouard 5009: int readdata(char datafile[], int firstobs, int lastobs, int *imax)
5010: {
1.126 brouard 5011:
1.136 brouard 5012: /*-------- data file ----------*/
5013: FILE *fic;
5014: char dummy[]=" ";
1.164 brouard 5015: int i=0, j=0, n=0;
1.136 brouard 5016: int linei, month, year,iout;
5017: char line[MAXLINE], linetmp[MAXLINE];
1.164 brouard 5018: char stra[MAXLINE], strb[MAXLINE];
1.136 brouard 5019: char *stratrunc;
5020: int lstra;
1.126 brouard 5021:
5022:
1.136 brouard 5023: if((fic=fopen(datafile,"r"))==NULL) {
5024: printf("Problem while opening datafile: %s\n", datafile);return 1;
5025: fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);return 1;
5026: }
1.126 brouard 5027:
1.136 brouard 5028: i=1;
5029: linei=0;
5030: while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
5031: linei=linei+1;
5032: for(j=strlen(line); j>=0;j--){ /* Untabifies line */
5033: if(line[j] == '\t')
5034: line[j] = ' ';
5035: }
5036: for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){
5037: ;
5038: };
5039: line[j+1]=0; /* Trims blanks at end of line */
5040: if(line[0]=='#'){
5041: fprintf(ficlog,"Comment line\n%s\n",line);
5042: printf("Comment line\n%s\n",line);
5043: continue;
5044: }
5045: trimbb(linetmp,line); /* Trims multiple blanks in line */
1.164 brouard 5046: strcpy(line, linetmp);
1.136 brouard 5047:
1.126 brouard 5048:
1.136 brouard 5049: for (j=maxwav;j>=1;j--){
1.137 brouard 5050: cutv(stra, strb, line, ' ');
1.136 brouard 5051: if(strb[0]=='.') { /* Missing status */
5052: lval=-1;
5053: }else{
5054: errno=0;
5055: lval=strtol(strb,&endptr,10);
5056: /* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
5057: if( strb[0]=='\0' || (*endptr != '\0')){
1.141 brouard 5058: 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);
5059: 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 5060: return 1;
5061: }
5062: }
5063: s[j][i]=lval;
5064:
5065: strcpy(line,stra);
5066: cutv(stra, strb,line,' ');
1.169 brouard 5067: if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
1.136 brouard 5068: }
1.169 brouard 5069: else if( (iout=sscanf(strb,"%s.",dummy)) != 0){
1.136 brouard 5070: month=99;
5071: year=9999;
5072: }else{
1.141 brouard 5073: 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);
5074: 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 5075: return 1;
5076: }
5077: anint[j][i]= (double) year;
5078: mint[j][i]= (double)month;
5079: strcpy(line,stra);
5080: } /* ENd Waves */
5081:
5082: cutv(stra, strb,line,' ');
1.169 brouard 5083: if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
1.136 brouard 5084: }
1.169 brouard 5085: else if( (iout=sscanf(strb,"%s.",dummy)) != 0){
1.136 brouard 5086: month=99;
5087: year=9999;
5088: }else{
1.141 brouard 5089: 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);
5090: 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 5091: return 1;
5092: }
5093: andc[i]=(double) year;
5094: moisdc[i]=(double) month;
5095: strcpy(line,stra);
5096:
5097: cutv(stra, strb,line,' ');
1.169 brouard 5098: if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
1.136 brouard 5099: }
1.169 brouard 5100: else if( (iout=sscanf(strb,"%s.", dummy)) != 0){
1.136 brouard 5101: month=99;
5102: year=9999;
5103: }else{
1.141 brouard 5104: 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);
5105: 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 5106: return 1;
5107: }
5108: if (year==9999) {
1.141 brouard 5109: 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);
5110: 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 5111: return 1;
1.126 brouard 5112:
1.136 brouard 5113: }
5114: annais[i]=(double)(year);
5115: moisnais[i]=(double)(month);
5116: strcpy(line,stra);
5117:
5118: cutv(stra, strb,line,' ');
5119: errno=0;
5120: dval=strtod(strb,&endptr);
5121: if( strb[0]=='\0' || (*endptr != '\0')){
1.141 brouard 5122: printf("Error reading data around '%f' at line number %d, \"%s\" for individual %d\nShould be a weight. Exiting.\n",dval, i,line,linei);
5123: 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 5124: fflush(ficlog);
5125: return 1;
5126: }
5127: weight[i]=dval;
5128: strcpy(line,stra);
5129:
5130: for (j=ncovcol;j>=1;j--){
5131: cutv(stra, strb,line,' ');
5132: if(strb[0]=='.') { /* Missing status */
5133: lval=-1;
5134: }else{
5135: errno=0;
5136: lval=strtol(strb,&endptr,10);
5137: if( strb[0]=='\0' || (*endptr != '\0')){
1.141 brouard 5138: 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);
5139: 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 5140: return 1;
5141: }
5142: }
5143: if(lval <-1 || lval >1){
1.141 brouard 5144: printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
1.136 brouard 5145: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
5146: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
5147: For example, for multinomial values like 1, 2 and 3,\n \
5148: build V1=0 V2=0 for the reference value (1),\n \
5149: V1=1 V2=0 for (2) \n \
5150: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
5151: output of IMaCh is often meaningless.\n \
5152: Exiting.\n",lval,linei, i,line,j);
1.141 brouard 5153: fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
1.136 brouard 5154: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
5155: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
5156: For example, for multinomial values like 1, 2 and 3,\n \
5157: build V1=0 V2=0 for the reference value (1),\n \
5158: V1=1 V2=0 for (2) \n \
5159: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
5160: output of IMaCh is often meaningless.\n \
5161: Exiting.\n",lval,linei, i,line,j);fflush(ficlog);
5162: return 1;
5163: }
5164: covar[j][i]=(double)(lval);
5165: strcpy(line,stra);
5166: }
5167: lstra=strlen(stra);
5168:
5169: if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
5170: stratrunc = &(stra[lstra-9]);
5171: num[i]=atol(stratrunc);
5172: }
5173: else
5174: num[i]=atol(stra);
5175: /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
5176: 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;}*/
5177:
5178: i=i+1;
5179: } /* End loop reading data */
1.126 brouard 5180:
1.136 brouard 5181: *imax=i-1; /* Number of individuals */
5182: fclose(fic);
5183:
5184: return (0);
1.164 brouard 5185: /* endread: */
1.136 brouard 5186: printf("Exiting readdata: ");
5187: fclose(fic);
5188: return (1);
1.126 brouard 5189:
5190:
5191:
1.136 brouard 5192: }
1.145 brouard 5193: void removespace(char *str) {
5194: char *p1 = str, *p2 = str;
5195: do
5196: while (*p2 == ' ')
5197: p2++;
1.169 brouard 5198: while (*p1++ == *p2++);
1.145 brouard 5199: }
5200:
5201: int decodemodel ( char model[], int lastobs) /**< This routine decode the model and returns:
5202: * Model V1+V2+V3+V8+V7*V8+V5*V6+V8*age+V3*age
5203: * - cptcovt total number of covariates of the model nbocc(+)+1 = 8
5204: * - cptcovn or number of covariates k of the models excluding age*products =6
5205: * - cptcovage number of covariates with age*products =2
5206: * - cptcovs number of simple covariates
5207: * - 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
5208: * which is a new column after the 9 (ncovcol) variables.
5209: * - if k is a product Vn*Vm covar[k][i] is filled with correct values for each individual
5210: * - Tprod[l] gives the kth covariates of the product Vn*Vm l=1 to cptcovprod-cptcovage
5211: * Tprod[1]@2 {5, 6}: position of first product V7*V8 is 5, and second V5*V6 is 6.
5212: * - Tvard[k] p Tvard[1][1]@4 {7, 8, 5, 6} for V7*V8 and V5*V6 .
5213: */
1.136 brouard 5214: {
1.145 brouard 5215: int i, j, k, ks;
1.164 brouard 5216: int j1, k1, k2;
1.136 brouard 5217: char modelsav[80];
1.145 brouard 5218: char stra[80], strb[80], strc[80], strd[80],stre[80];
1.136 brouard 5219:
1.145 brouard 5220: /*removespace(model);*/
1.136 brouard 5221: if (strlen(model) >1){ /* If there is at least 1 covariate */
1.145 brouard 5222: j=0, j1=0, k1=0, k2=-1, ks=0, cptcovn=0;
5223: j=nbocc(model,'+'); /**< j=Number of '+' */
5224: j1=nbocc(model,'*'); /**< j1=Number of '*' */
5225: cptcovs=j+1-j1; /**< Number of simple covariates V1+V2*age+V3 +V3*V4=> V1 + V3 =2 */
5226: cptcovt= j+1; /* Number of total covariates in the model V1 + V2*age+ V3 + V3*V4=> 4*/
5227: /* including age products which are counted in cptcovage.
1.169 brouard 5228: * but the covariates which are products must be treated separately: ncovn=4- 2=2 (V1+V3). */
1.145 brouard 5229: cptcovprod=j1; /**< Number of products V1*V2 +v3*age = 2 */
5230: cptcovprodnoage=0; /**< Number of covariate products without age: V3*V4 =1 */
1.136 brouard 5231: strcpy(modelsav,model);
1.137 brouard 5232: if (strstr(model,"AGE") !=0){
5233: printf("Error. AGE must be in lower case 'age' model=%s ",model);
5234: fprintf(ficlog,"Error. AGE must be in lower case model=%s ",model);fflush(ficlog);
1.136 brouard 5235: return 1;
5236: }
1.141 brouard 5237: if (strstr(model,"v") !=0){
5238: printf("Error. 'v' must be in upper case 'V' model=%s ",model);
5239: fprintf(ficlog,"Error. 'v' must be in upper case model=%s ",model);fflush(ficlog);
5240: return 1;
5241: }
1.136 brouard 5242:
1.145 brouard 5243: /* Design
5244: * V1 V2 V3 V4 V5 V6 V7 V8 V9 Weight
5245: * < ncovcol=8 >
5246: * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8
5247: * k= 1 2 3 4 5 6 7 8
5248: * cptcovn number of covariates (not including constant and age ) = # of + plus 1 = 7+1=8
5249: * covar[k,i], value of kth covariate if not including age for individual i:
5250: * covar[1][i]= (V2), covar[4][i]=(V3), covar[8][i]=(V8)
5251: * Tvar[k] # of the kth covariate: Tvar[1]=2 Tvar[4]=3 Tvar[8]=8
5252: * if multiplied by age: V3*age Tvar[3=V3*age]=3 (V3) Tvar[7]=8 and
5253: * Tage[++cptcovage]=k
5254: * if products, new covar are created after ncovcol with k1
5255: * Tvar[k]=ncovcol+k1; # of the kth covariate product: Tvar[5]=ncovcol+1=10 Tvar[6]=ncovcol+1=11
5256: * Tprod[k1]=k; Tprod[1]=5 Tprod[2]= 6; gives the position of the k1th product
5257: * 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
5258: * Tvar[cptcovn+k2]=Tvard[k1][1];Tvar[cptcovn+k2+1]=Tvard[k1][2];
5259: * Tvar[8+1]=5;Tvar[8+2]=6;Tvar[8+3]=7;Tvar[8+4]=8 inverted
5260: * V1 V2 V3 V4 V5 V6 V7 V8 V9 V10 V11
5261: * < ncovcol=8 >
5262: * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8 d1 d1 d2 d2
5263: * k= 1 2 3 4 5 6 7 8 9 10 11 12
5264: * Tvar[k]= 2 1 3 3 10 11 8 8 5 6 7 8
5265: * p Tvar[1]@12={2, 1, 3, 3, 11, 10, 8, 8, 7, 8, 5, 6}
5266: * p Tprod[1]@2={ 6, 5}
5267: *p Tvard[1][1]@4= {7, 8, 5, 6}
5268: * covar[k][i]= V2 V1 ? V3 V5*V6? V7*V8? ? V8
5269: * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
5270: *How to reorganize?
5271: * Model V1 + V2 + V3 + V8 + V5*V6 + V7*V8 + V3*age + V8*age
5272: * Tvars {2, 1, 3, 3, 11, 10, 8, 8, 7, 8, 5, 6}
5273: * {2, 1, 4, 8, 5, 6, 3, 7}
5274: * Struct []
5275: */
5276:
1.136 brouard 5277: /* This loop fills the array Tvar from the string 'model'.*/
5278: /* j is the number of + signs in the model V1+V2+V3 j=2 i=3 to 1 */
1.137 brouard 5279: /* modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4 */
5280: /* k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tage[cptcovage=1]=4 */
5281: /* k=3 V4 Tvar[k=3]= 4 (from V4) */
5282: /* k=2 V1 Tvar[k=2]= 1 (from V1) */
5283: /* k=1 Tvar[1]=2 (from V2) */
5284: /* k=5 Tvar[5] */
5285: /* for (k=1; k<=cptcovn;k++) { */
5286: /* cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]]; */
5287: /* } */
5288: /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
1.145 brouard 5289: /*
5290: * Treating invertedly V2+V1+V3*age+V2*V4 is as if written V2*V4 +V3*age + V1 + V2 */
5291: for(k=cptcovt; k>=1;k--) /**< Number of covariates */
5292: Tvar[k]=0;
5293: cptcovage=0;
5294: for(k=1; k<=cptcovt;k++){ /* Loop on total covariates of the model */
5295: cutl(stra,strb,modelsav,'+'); /* keeps in strb after the first '+'
5296: modelsav==V2+V1+V4+V3*age strb=V3*age stra=V2+V1+V4 */
1.137 brouard 5297: if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
1.136 brouard 5298: /* printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
5299: /*scanf("%d",i);*/
1.145 brouard 5300: if (strchr(strb,'*')) { /**< Model includes a product V2+V1+V4+V3*age strb=V3*age */
5301: cutl(strc,strd,strb,'*'); /**< strd*strc Vm*Vn: strb=V3*age(input) strc=age strd=V3 ; V3*V2 strc=V2, strd=V3 */
5302: if (strcmp(strc,"age")==0) { /**< Model includes age: Vn*age */
5303: /* covar is not filled and then is empty */
1.136 brouard 5304: cptcovprod--;
1.145 brouard 5305: cutl(stre,strb,strd,'V'); /* strd=V3(input): stre="3" */
5306: Tvar[k]=atoi(stre); /* V2+V1+V4+V3*age Tvar[4]=3 ; V1+V2*age Tvar[2]=2 */
1.136 brouard 5307: cptcovage++; /* Sums the number of covariates which include age as a product */
1.137 brouard 5308: Tage[cptcovage]=k; /* Tage[1] = 4 */
1.136 brouard 5309: /*printf("stre=%s ", stre);*/
1.137 brouard 5310: } else if (strcmp(strd,"age")==0) { /* or age*Vn */
1.136 brouard 5311: cptcovprod--;
1.145 brouard 5312: cutl(stre,strb,strc,'V');
1.136 brouard 5313: Tvar[k]=atoi(stre);
5314: cptcovage++;
5315: Tage[cptcovage]=k;
1.137 brouard 5316: } else { /* Age is not in the model product V2+V1+V1*V4+V3*age+V3*V2 strb=V3*V2*/
5317: /* loops on k1=1 (V3*V2) and k1=2 V4*V3 */
1.145 brouard 5318: cptcovn++;
5319: cptcovprodnoage++;k1++;
5320: cutl(stre,strb,strc,'V'); /* strc= Vn, stre is n; strb=V3*V2 stre=3 strc=*/
5321: Tvar[k]=ncovcol+k1; /* For model-covariate k tells which data-covariate to use but
1.137 brouard 5322: because this model-covariate is a construction we invent a new column
5323: ncovcol + k1
5324: If already ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2
5325: Tvar[3=V1*V4]=4+1 Tvar[5=V3*V2]=4 + 2= 6, etc */
1.145 brouard 5326: cutl(strc,strb,strd,'V'); /* strd was Vm, strc is m */
1.137 brouard 5327: Tprod[k1]=k; /* Tprod[1]=3(=V1*V4) for V2+V1+V1*V4+age*V3+V3*V2 */
1.145 brouard 5328: Tvard[k1][1] =atoi(strc); /* m 1 for V1*/
5329: Tvard[k1][2] =atoi(stre); /* n 4 for V4*/
5330: k2=k2+2;
5331: Tvar[cptcovt+k2]=Tvard[k1][1]; /* Tvar[(cptcovt=4+k2=1)=5]= 1 (V1) */
5332: Tvar[cptcovt+k2+1]=Tvard[k1][2]; /* Tvar[(cptcovt=4+(k2=1)+1)=6]= 4 (V4) */
1.137 brouard 5333: for (i=1; i<=lastobs;i++){
5334: /* Computes the new covariate which is a product of
1.145 brouard 5335: covar[n][i]* covar[m][i] and stores it at ncovol+k1 May not be defined */
1.136 brouard 5336: covar[ncovcol+k1][i]=covar[atoi(stre)][i]*covar[atoi(strc)][i];
1.137 brouard 5337: }
5338: } /* End age is not in the model */
5339: } /* End if model includes a product */
1.136 brouard 5340: else { /* no more sum */
5341: /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
5342: /* scanf("%d",i);*/
1.145 brouard 5343: cutl(strd,strc,strb,'V');
5344: ks++; /**< Number of simple covariates */
5345: cptcovn++;
5346: Tvar[k]=atoi(strd);
1.136 brouard 5347: }
1.137 brouard 5348: strcpy(modelsav,stra); /* modelsav=V2+V1+V4 stra=V2+V1+V4 */
1.136 brouard 5349: /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
5350: scanf("%d",i);*/
5351: } /* end of loop + */
5352: } /* end model */
5353:
5354: /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
5355: If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
5356:
5357: /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
5358: printf("cptcovprod=%d ", cptcovprod);
5359: fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
5360:
5361: scanf("%d ",i);*/
5362:
5363:
1.137 brouard 5364: return (0); /* with covar[new additional covariate if product] and Tage if age */
1.164 brouard 5365: /*endread:*/
1.136 brouard 5366: printf("Exiting decodemodel: ");
5367: return (1);
5368: }
5369:
1.169 brouard 5370: int calandcheckages(int imx, int maxwav, double *agemin, double *agemax, int *nberr, int *nbwarn )
1.136 brouard 5371: {
5372: int i, m;
5373:
5374: for (i=1; i<=imx; i++) {
5375: for(m=2; (m<= maxwav); m++) {
5376: if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
5377: anint[m][i]=9999;
5378: s[m][i]=-1;
5379: }
5380: if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
1.169 brouard 5381: *nberr = *nberr + 1;
5382: 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);
5383: 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 5384: s[m][i]=-1;
5385: }
5386: if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
1.169 brouard 5387: (*nberr)++;
1.136 brouard 5388: 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]);
5389: 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]);
5390: s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
5391: }
5392: }
5393: }
5394:
5395: for (i=1; i<=imx; i++) {
5396: agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
5397: for(m=firstpass; (m<= lastpass); m++){
5398: if(s[m][i] >0 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){
5399: if (s[m][i] >= nlstate+1) {
1.169 brouard 5400: if(agedc[i]>0){
5401: if((int)moisdc[i]!=99 && (int)andc[i]!=9999){
1.136 brouard 5402: agev[m][i]=agedc[i];
5403: /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
1.169 brouard 5404: }else {
1.136 brouard 5405: if ((int)andc[i]!=9999){
5406: nbwarn++;
5407: printf("Warning negative age at death: %ld line:%d\n",num[i],i);
5408: fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
5409: agev[m][i]=-1;
5410: }
5411: }
1.169 brouard 5412: } /* agedc > 0 */
1.136 brouard 5413: }
5414: else if(s[m][i] !=9){ /* Standard case, age in fractional
5415: years but with the precision of a month */
5416: agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
5417: if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
5418: agev[m][i]=1;
5419: else if(agev[m][i] < *agemin){
5420: *agemin=agev[m][i];
5421: printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], *agemin);
5422: }
5423: else if(agev[m][i] >*agemax){
5424: *agemax=agev[m][i];
1.156 brouard 5425: /* printf(" Max anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.2f\n",m,i,anint[m][i], i,annais[i], *agemax);*/
1.136 brouard 5426: }
5427: /*agev[m][i]=anint[m][i]-annais[i];*/
5428: /* agev[m][i] = age[i]+2*m;*/
5429: }
5430: else { /* =9 */
5431: agev[m][i]=1;
5432: s[m][i]=-1;
5433: }
5434: }
5435: else /*= 0 Unknown */
5436: agev[m][i]=1;
5437: }
5438:
5439: }
5440: for (i=1; i<=imx; i++) {
5441: for(m=firstpass; (m<=lastpass); m++){
5442: if (s[m][i] > (nlstate+ndeath)) {
1.169 brouard 5443: (*nberr)++;
1.136 brouard 5444: 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);
5445: 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);
5446: return 1;
5447: }
5448: }
5449: }
5450:
5451: /*for (i=1; i<=imx; i++){
5452: for (m=firstpass; (m<lastpass); m++){
5453: printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
5454: }
5455:
5456: }*/
5457:
5458:
1.139 brouard 5459: printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
5460: fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
1.136 brouard 5461:
5462: return (0);
1.164 brouard 5463: /* endread:*/
1.136 brouard 5464: printf("Exiting calandcheckages: ");
5465: return (1);
5466: }
5467:
1.172 brouard 5468: #if defined(_MSC_VER)
5469: /*printf("Visual C++ compiler: %s \n;", _MSC_FULL_VER);*/
5470: /*fprintf(ficlog, "Visual C++ compiler: %s \n;", _MSC_FULL_VER);*/
5471: //#include "stdafx.h"
5472: //#include <stdio.h>
5473: //#include <tchar.h>
5474: //#include <windows.h>
5475: //#include <iostream>
5476: typedef BOOL(WINAPI *LPFN_ISWOW64PROCESS) (HANDLE, PBOOL);
5477:
5478: LPFN_ISWOW64PROCESS fnIsWow64Process;
5479:
5480: BOOL IsWow64()
5481: {
5482: BOOL bIsWow64 = FALSE;
5483:
5484: //typedef BOOL (APIENTRY *LPFN_ISWOW64PROCESS)
5485: // (HANDLE, PBOOL);
5486:
5487: //LPFN_ISWOW64PROCESS fnIsWow64Process;
5488:
5489: HMODULE module = GetModuleHandle(_T("kernel32"));
5490: const char funcName[] = "IsWow64Process";
5491: fnIsWow64Process = (LPFN_ISWOW64PROCESS)
5492: GetProcAddress(module, funcName);
5493:
5494: if (NULL != fnIsWow64Process)
5495: {
5496: if (!fnIsWow64Process(GetCurrentProcess(),
5497: &bIsWow64))
5498: //throw std::exception("Unknown error");
5499: printf("Unknown error\n");
5500: }
5501: return bIsWow64 != FALSE;
5502: }
5503: #endif
1.169 brouard 5504: void syscompilerinfo()
1.167 brouard 5505: {
5506: /* #include "syscompilerinfo.h"*/
1.174 brouard 5507: #if defined(__GNUC__)
5508: #include <gnu/libc-version.h> /* Only on gnu */
1.176 ! brouard 5509: struct utsname sysInfo;
1.174 brouard 5510: #endif
5511:
1.171 brouard 5512: #include <stdint.h>
1.175 brouard 5513: int cross = CROSS;
5514: if (cross){
5515: printf("Cross-");
5516: fprintf(ficlog,"Cross-");
5517: }
1.169 brouard 5518: printf("Compiled with:");fprintf(ficlog,"Compiled with:");
5519: #if defined(__clang__)
5520: printf(" Clang/LLVM");fprintf(ficlog," Clang/LLVM"); /* Clang/LLVM. ---------------------------------------------- */
5521: #endif
5522: #if defined(__ICC) || defined(__INTEL_COMPILER)
5523: printf(" Intel ICC/ICPC");fprintf(ficlog," Intel ICC/ICPC");/* Intel ICC/ICPC. ------------------------------------------ */
5524: #endif
5525: #if defined(__GNUC__) || defined(__GNUG__)
5526: printf(" GNU GCC/G++");fprintf(ficlog," GNU GCC/G++");/* GNU GCC/G++. --------------------------------------------- */
5527: #endif
5528: #if defined(__HP_cc) || defined(__HP_aCC)
5529: printf(" Hewlett-Packard C/aC++");fprintf(fcilog," Hewlett-Packard C/aC++"); /* Hewlett-Packard C/aC++. ---------------------------------- */
5530: #endif
5531: #if defined(__IBMC__) || defined(__IBMCPP__)
5532: printf(" IBM XL C/C++"); fprintf(ficlog," IBM XL C/C++");/* IBM XL C/C++. -------------------------------------------- */
5533: #endif
5534: #if defined(_MSC_VER)
5535: printf(" Microsoft Visual Studio");fprintf(ficlog," Microsoft Visual Studio");/* Microsoft Visual Studio. --------------------------------- */
5536: #endif
5537: #if defined(__PGI)
5538: printf(" Portland Group PGCC/PGCPP");fprintf(ficlog," Portland Group PGCC/PGCPP");/* Portland Group PGCC/PGCPP. ------------------------------- */
5539: #endif
5540: #if defined(__SUNPRO_C) || defined(__SUNPRO_CC)
5541: printf(" Oracle Solaris Studio");fprintf(ficlog," Oracle Solaris Studio\n");/* Oracle Solaris Studio. ----------------------------------- */
1.167 brouard 5542: #endif
1.174 brouard 5543: printf(" for ");fprintf(ficlog," for ");
1.169 brouard 5544:
1.167 brouard 5545: // http://stackoverflow.com/questions/4605842/how-to-identify-platform-compiler-from-preprocessor-macros
5546: #ifdef _WIN32 // note the underscore: without it, it's not msdn official!
5547: // Windows (x64 and x86)
1.174 brouard 5548: printf("Windows (x64 and x86) ");fprintf(ficlog,"Windows (x64 and x86) ");
1.167 brouard 5549: #elif __unix__ // all unices, not all compilers
5550: // Unix
1.174 brouard 5551: printf("Unix ");fprintf(ficlog,"Unix ");
1.167 brouard 5552: #elif __linux__
5553: // linux
1.174 brouard 5554: printf("linux ");fprintf(ficlog,"linux ");
1.167 brouard 5555: #elif __APPLE__
1.174 brouard 5556: // Mac OS, not sure if this is covered by __posix__ and/or __unix__ though..
5557: printf("Mac OS ");fprintf(ficlog,"Mac OS ");
1.167 brouard 5558: #endif
5559:
5560: /* __MINGW32__ */
5561: /* __CYGWIN__ */
5562: /* __MINGW64__ */
5563: // http://msdn.microsoft.com/en-us/library/b0084kay.aspx
5564: /* _MSC_VER //the Visual C++ compiler is 17.00.51106.1, the _MSC_VER macro evaluates to 1700. Type cl /? */
5565: /* _MSC_FULL_VER //the Visual C++ compiler is 15.00.20706.01, the _MSC_FULL_VER macro evaluates to 150020706 */
5566: /* _WIN64 // Defined for applications for Win64. */
5567: /* _M_X64 // Defined for compilations that target x64 processors. */
5568: /* _DEBUG // Defined when you compile with /LDd, /MDd, and /MTd. */
1.171 brouard 5569:
1.167 brouard 5570: #if UINTPTR_MAX == 0xffffffff
1.174 brouard 5571: printf(" 32-bit"); fprintf(ficlog," 32-bit");/* 32-bit */
1.167 brouard 5572: #elif UINTPTR_MAX == 0xffffffffffffffff
1.174 brouard 5573: printf(" 64-bit"); fprintf(ficlog," 64-bit");/* 64-bit */
1.167 brouard 5574: #else
1.174 brouard 5575: printf(" wtf-bit"); fprintf(ficlog," wtf-bit");/* wtf */
1.167 brouard 5576: #endif
5577:
1.169 brouard 5578: #if defined(__GNUC__)
5579: # if defined(__GNUC_PATCHLEVEL__)
5580: # define __GNUC_VERSION__ (__GNUC__ * 10000 \
5581: + __GNUC_MINOR__ * 100 \
5582: + __GNUC_PATCHLEVEL__)
5583: # else
5584: # define __GNUC_VERSION__ (__GNUC__ * 10000 \
5585: + __GNUC_MINOR__ * 100)
5586: # endif
1.174 brouard 5587: printf(" using GNU C version %d.\n", __GNUC_VERSION__);
5588: fprintf(ficlog, " using GNU C version %d.\n", __GNUC_VERSION__);
1.176 ! brouard 5589:
! 5590: if (uname(&sysInfo) != -1) {
! 5591: printf("Running on: %s %s %s %s %s\n",sysInfo.sysname, sysInfo.nodename, sysInfo.release, sysInfo.version, sysInfo.machine);
! 5592: fprintf(ficlog,"Running on: %s %s %s %s %s\n ",sysInfo.sysname, sysInfo.nodename, sysInfo.release, sysInfo.version, sysInfo.machine);
! 5593: }
! 5594: else
! 5595: perror("uname() error");
1.174 brouard 5596: printf("GNU libc version: %s\n", gnu_get_libc_version());
5597: fprintf(ficlog,"GNU libc version: %s\n", gnu_get_libc_version());
5598:
1.169 brouard 5599: #endif
1.172 brouard 5600:
5601: // void main()
5602: // {
1.169 brouard 5603: #if defined(_MSC_VER)
1.174 brouard 5604: if (IsWow64()){
1.176 ! brouard 5605: printf("The program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n");
! 5606: fprintf(ficlog, "The program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n");
1.174 brouard 5607: }
5608: else{
1.176 ! brouard 5609: printf("The process is not running under WOW64 (i.e probably on a 64bit Windows).\n");
! 5610: frintf(ficlog,"The programm is not running under WOW64 (i.e probably on a 64bit Windows).\n");
1.174 brouard 5611: }
1.172 brouard 5612: // printf("\nPress Enter to continue...");
5613: // getchar();
5614: // }
5615:
1.169 brouard 5616: #endif
5617:
1.167 brouard 5618:
5619: }
1.136 brouard 5620:
5621: /***********************************************/
5622: /**************** Main Program *****************/
5623: /***********************************************/
5624:
5625: int main(int argc, char *argv[])
5626: {
5627: #ifdef GSL
5628: const gsl_multimin_fminimizer_type *T;
5629: size_t iteri = 0, it;
5630: int rval = GSL_CONTINUE;
5631: int status = GSL_SUCCESS;
5632: double ssval;
5633: #endif
5634: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
1.164 brouard 5635: int i,j, k, n=MAXN,iter=0,m,size=100, cptcod;
5636:
5637: int jj, ll, li, lj, lk;
1.136 brouard 5638: int numlinepar=0; /* Current linenumber of parameter file */
5639: int itimes;
5640: int NDIM=2;
5641: int vpopbased=0;
5642:
1.164 brouard 5643: char ca[32], cb[32];
1.136 brouard 5644: /* FILE *fichtm; *//* Html File */
5645: /* FILE *ficgp;*/ /*Gnuplot File */
5646: struct stat info;
1.164 brouard 5647: double agedeb;
1.136 brouard 5648: double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
5649:
1.165 brouard 5650: double fret;
1.136 brouard 5651: double dum; /* Dummy variable */
5652: double ***p3mat;
5653: double ***mobaverage;
1.164 brouard 5654:
5655: char line[MAXLINE];
1.136 brouard 5656: char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
5657: char pathr[MAXLINE], pathimach[MAXLINE];
1.164 brouard 5658: char *tok, *val; /* pathtot */
1.136 brouard 5659: int firstobs=1, lastobs=10;
1.164 brouard 5660: int c, h , cpt;
5661: int jl;
5662: int i1, j1, jk, stepsize;
5663: int *tab;
1.136 brouard 5664: int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
5665: int mobilav=0,popforecast=0;
5666: int hstepm, nhstepm;
5667: int agemortsup;
5668: float sumlpop=0.;
5669: double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
5670: double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
5671:
1.164 brouard 5672: double bage=0, fage=110, age, agelim, agebase;
1.136 brouard 5673: double ftolpl=FTOL;
5674: double **prlim;
5675: double ***param; /* Matrix of parameters */
5676: double *p;
5677: double **matcov; /* Matrix of covariance */
5678: double ***delti3; /* Scale */
5679: double *delti; /* Scale */
5680: double ***eij, ***vareij;
5681: double **varpl; /* Variances of prevalence limits by age */
5682: double *epj, vepp;
1.164 brouard 5683:
1.136 brouard 5684: double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
5685: double **ximort;
1.145 brouard 5686: char *alph[]={"a","a","b","c","d","e"}, str[4]="1234";
1.136 brouard 5687: int *dcwave;
5688:
1.164 brouard 5689: char z[1]="c";
1.136 brouard 5690:
5691: /*char *strt;*/
5692: char strtend[80];
1.126 brouard 5693:
1.164 brouard 5694:
1.126 brouard 5695: /* setlocale (LC_ALL, ""); */
5696: /* bindtextdomain (PACKAGE, LOCALEDIR); */
5697: /* textdomain (PACKAGE); */
5698: /* setlocale (LC_CTYPE, ""); */
5699: /* setlocale (LC_MESSAGES, ""); */
5700:
5701: /* gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
1.157 brouard 5702: rstart_time = time(NULL);
5703: /* (void) gettimeofday(&start_time,&tzp);*/
5704: start_time = *localtime(&rstart_time);
1.126 brouard 5705: curr_time=start_time;
1.157 brouard 5706: /*tml = *localtime(&start_time.tm_sec);*/
5707: /* strcpy(strstart,asctime(&tml)); */
5708: strcpy(strstart,asctime(&start_time));
1.126 brouard 5709:
5710: /* printf("Localtime (at start)=%s",strstart); */
1.157 brouard 5711: /* tp.tm_sec = tp.tm_sec +86400; */
5712: /* tm = *localtime(&start_time.tm_sec); */
1.126 brouard 5713: /* tmg.tm_year=tmg.tm_year +dsign*dyear; */
5714: /* tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
5715: /* tmg.tm_hour=tmg.tm_hour + 1; */
1.157 brouard 5716: /* tp.tm_sec = mktime(&tmg); */
1.126 brouard 5717: /* strt=asctime(&tmg); */
5718: /* printf("Time(after) =%s",strstart); */
5719: /* (void) time (&time_value);
5720: * printf("time=%d,t-=%d\n",time_value,time_value-86400);
5721: * tm = *localtime(&time_value);
5722: * strstart=asctime(&tm);
5723: * printf("tim_value=%d,asctime=%s\n",time_value,strstart);
5724: */
5725:
5726: nberr=0; /* Number of errors and warnings */
5727: nbwarn=0;
5728: getcwd(pathcd, size);
5729:
5730: printf("\n%s\n%s",version,fullversion);
5731: if(argc <=1){
5732: printf("\nEnter the parameter file name: ");
5733: fgets(pathr,FILENAMELENGTH,stdin);
5734: i=strlen(pathr);
5735: if(pathr[i-1]=='\n')
5736: pathr[i-1]='\0';
1.156 brouard 5737: i=strlen(pathr);
5738: if(pathr[i-1]==' ') /* This may happen when dragging on oS/X! */
5739: pathr[i-1]='\0';
1.126 brouard 5740: for (tok = pathr; tok != NULL; ){
5741: printf("Pathr |%s|\n",pathr);
5742: while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
5743: printf("val= |%s| pathr=%s\n",val,pathr);
5744: strcpy (pathtot, val);
5745: if(pathr[0] == '\0') break; /* Dirty */
5746: }
5747: }
5748: else{
5749: strcpy(pathtot,argv[1]);
5750: }
5751: /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
5752: /*cygwin_split_path(pathtot,path,optionfile);
5753: printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
5754: /* cutv(path,optionfile,pathtot,'\\');*/
5755:
5756: /* Split argv[0], imach program to get pathimach */
5757: printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
5758: split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
5759: printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
5760: /* strcpy(pathimach,argv[0]); */
5761: /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
5762: split(pathtot,path,optionfile,optionfilext,optionfilefiname);
5763: printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
5764: chdir(path); /* Can be a relative path */
5765: if(getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */
5766: printf("Current directory %s!\n",pathcd);
5767: strcpy(command,"mkdir ");
5768: strcat(command,optionfilefiname);
5769: if((outcmd=system(command)) != 0){
1.169 brouard 5770: printf("Directory already exists (or can't create it) %s%s, err=%d\n",path,optionfilefiname,outcmd);
1.126 brouard 5771: /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
5772: /* fclose(ficlog); */
5773: /* exit(1); */
5774: }
5775: /* if((imk=mkdir(optionfilefiname))<0){ */
5776: /* perror("mkdir"); */
5777: /* } */
5778:
5779: /*-------- arguments in the command line --------*/
5780:
5781: /* Log file */
5782: strcat(filelog, optionfilefiname);
5783: strcat(filelog,".log"); /* */
5784: if((ficlog=fopen(filelog,"w"))==NULL) {
5785: printf("Problem with logfile %s\n",filelog);
5786: goto end;
5787: }
5788: fprintf(ficlog,"Log filename:%s\n",filelog);
5789: fprintf(ficlog,"\n%s\n%s",version,fullversion);
5790: fprintf(ficlog,"\nEnter the parameter file name: \n");
5791: fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
5792: path=%s \n\
5793: optionfile=%s\n\
5794: optionfilext=%s\n\
1.156 brouard 5795: optionfilefiname='%s'\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
1.126 brouard 5796:
1.167 brouard 5797: syscompilerinfo();
5798:
1.126 brouard 5799: printf("Local time (at start):%s",strstart);
5800: fprintf(ficlog,"Local time (at start): %s",strstart);
5801: fflush(ficlog);
5802: /* (void) gettimeofday(&curr_time,&tzp); */
1.157 brouard 5803: /* printf("Elapsed time %d\n", asc_diff_time(curr_time.tm_sec-start_time.tm_sec,tmpout)); */
1.126 brouard 5804:
5805: /* */
5806: strcpy(fileres,"r");
5807: strcat(fileres, optionfilefiname);
5808: strcat(fileres,".txt"); /* Other files have txt extension */
5809:
5810: /*---------arguments file --------*/
5811:
5812: if((ficpar=fopen(optionfile,"r"))==NULL) {
1.155 brouard 5813: printf("Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
5814: fprintf(ficlog,"Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
1.126 brouard 5815: fflush(ficlog);
1.149 brouard 5816: /* goto end; */
5817: exit(70);
1.126 brouard 5818: }
5819:
5820:
5821:
5822: strcpy(filereso,"o");
5823: strcat(filereso,fileres);
5824: if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
5825: printf("Problem with Output resultfile: %s\n", filereso);
5826: fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
5827: fflush(ficlog);
5828: goto end;
5829: }
5830:
5831: /* Reads comments: lines beginning with '#' */
5832: numlinepar=0;
5833: while((c=getc(ficpar))=='#' && c!= EOF){
5834: ungetc(c,ficpar);
5835: fgets(line, MAXLINE, ficpar);
5836: numlinepar++;
1.141 brouard 5837: fputs(line,stdout);
1.126 brouard 5838: fputs(line,ficparo);
5839: fputs(line,ficlog);
5840: }
5841: ungetc(c,ficpar);
5842:
5843: 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);
5844: numlinepar++;
5845: 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);
5846: 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);
5847: 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);
5848: fflush(ficlog);
5849: while((c=getc(ficpar))=='#' && c!= EOF){
5850: ungetc(c,ficpar);
5851: fgets(line, MAXLINE, ficpar);
5852: numlinepar++;
1.141 brouard 5853: fputs(line, stdout);
5854: //puts(line);
1.126 brouard 5855: fputs(line,ficparo);
5856: fputs(line,ficlog);
5857: }
5858: ungetc(c,ficpar);
5859:
5860:
1.145 brouard 5861: covar=matrix(0,NCOVMAX,1,n); /**< used in readdata */
1.136 brouard 5862: cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement plus one, indepently of n in Vn*/
5863: /* v1+v2+v3+v2*v4+v5*age makes cptcovn = 5
5864: v1+v2*age+v2*v3 makes cptcovn = 3
5865: */
5866: if (strlen(model)>1)
1.145 brouard 5867: 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*/
5868: else
5869: ncovmodel=2;
1.126 brouard 5870: nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
1.133 brouard 5871: nforce= (nlstate+ndeath-1)*nlstate; /* Number of forces ij from state i to j */
5872: npar= nforce*ncovmodel; /* Number of parameters like aij*/
1.131 brouard 5873: if(npar >MAXPARM || nlstate >NLSTATEMAX || ndeath >NDEATHMAX || ncovmodel>NCOVMAX){
5874: 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);
5875: 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);
5876: fflush(stdout);
5877: fclose (ficlog);
5878: goto end;
5879: }
1.126 brouard 5880: delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
5881: delti=delti3[1][1];
5882: /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
5883: if(mle==-1){ /* Print a wizard for help writing covariance matrix */
5884: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
5885: printf(" You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
5886: fprintf(ficlog," You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
5887: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
5888: fclose (ficparo);
5889: fclose (ficlog);
5890: goto end;
5891: exit(0);
5892: }
5893: else if(mle==-3) {
5894: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
5895: printf(" You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
5896: fprintf(ficlog," You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
5897: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
5898: matcov=matrix(1,npar,1,npar);
5899: }
5900: else{
1.145 brouard 5901: /* Read guessed parameters */
1.126 brouard 5902: /* Reads comments: lines beginning with '#' */
5903: while((c=getc(ficpar))=='#' && c!= EOF){
5904: ungetc(c,ficpar);
5905: fgets(line, MAXLINE, ficpar);
5906: numlinepar++;
1.141 brouard 5907: fputs(line,stdout);
1.126 brouard 5908: fputs(line,ficparo);
5909: fputs(line,ficlog);
5910: }
5911: ungetc(c,ficpar);
5912:
5913: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
5914: for(i=1; i <=nlstate; i++){
5915: j=0;
5916: for(jj=1; jj <=nlstate+ndeath; jj++){
5917: if(jj==i) continue;
5918: j++;
5919: fscanf(ficpar,"%1d%1d",&i1,&j1);
5920: if ((i1 != i) && (j1 != j)){
5921: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \
5922: It might be a problem of design; if ncovcol and the model are correct\n \
5923: run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1);
5924: exit(1);
5925: }
5926: fprintf(ficparo,"%1d%1d",i1,j1);
5927: if(mle==1)
5928: printf("%1d%1d",i,j);
5929: fprintf(ficlog,"%1d%1d",i,j);
5930: for(k=1; k<=ncovmodel;k++){
5931: fscanf(ficpar," %lf",¶m[i][j][k]);
5932: if(mle==1){
5933: printf(" %lf",param[i][j][k]);
5934: fprintf(ficlog," %lf",param[i][j][k]);
5935: }
5936: else
5937: fprintf(ficlog," %lf",param[i][j][k]);
5938: fprintf(ficparo," %lf",param[i][j][k]);
5939: }
5940: fscanf(ficpar,"\n");
5941: numlinepar++;
5942: if(mle==1)
5943: printf("\n");
5944: fprintf(ficlog,"\n");
5945: fprintf(ficparo,"\n");
5946: }
5947: }
5948: fflush(ficlog);
5949:
1.145 brouard 5950: /* Reads scales values */
1.126 brouard 5951: p=param[1][1];
5952:
5953: /* Reads comments: lines beginning with '#' */
5954: while((c=getc(ficpar))=='#' && c!= EOF){
5955: ungetc(c,ficpar);
5956: fgets(line, MAXLINE, ficpar);
5957: numlinepar++;
1.141 brouard 5958: fputs(line,stdout);
1.126 brouard 5959: fputs(line,ficparo);
5960: fputs(line,ficlog);
5961: }
5962: ungetc(c,ficpar);
5963:
5964: for(i=1; i <=nlstate; i++){
5965: for(j=1; j <=nlstate+ndeath-1; j++){
5966: fscanf(ficpar,"%1d%1d",&i1,&j1);
1.164 brouard 5967: if ( (i1-i) * (j1-j) != 0){
1.126 brouard 5968: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
5969: exit(1);
5970: }
5971: printf("%1d%1d",i,j);
5972: fprintf(ficparo,"%1d%1d",i1,j1);
5973: fprintf(ficlog,"%1d%1d",i1,j1);
5974: for(k=1; k<=ncovmodel;k++){
5975: fscanf(ficpar,"%le",&delti3[i][j][k]);
5976: printf(" %le",delti3[i][j][k]);
5977: fprintf(ficparo," %le",delti3[i][j][k]);
5978: fprintf(ficlog," %le",delti3[i][j][k]);
5979: }
5980: fscanf(ficpar,"\n");
5981: numlinepar++;
5982: printf("\n");
5983: fprintf(ficparo,"\n");
5984: fprintf(ficlog,"\n");
5985: }
5986: }
5987: fflush(ficlog);
5988:
1.145 brouard 5989: /* Reads covariance matrix */
1.126 brouard 5990: delti=delti3[1][1];
5991:
5992:
5993: /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
5994:
5995: /* Reads comments: lines beginning with '#' */
5996: while((c=getc(ficpar))=='#' && c!= EOF){
5997: ungetc(c,ficpar);
5998: fgets(line, MAXLINE, ficpar);
5999: numlinepar++;
1.141 brouard 6000: fputs(line,stdout);
1.126 brouard 6001: fputs(line,ficparo);
6002: fputs(line,ficlog);
6003: }
6004: ungetc(c,ficpar);
6005:
6006: matcov=matrix(1,npar,1,npar);
1.131 brouard 6007: for(i=1; i <=npar; i++)
6008: for(j=1; j <=npar; j++) matcov[i][j]=0.;
6009:
1.126 brouard 6010: for(i=1; i <=npar; i++){
1.145 brouard 6011: fscanf(ficpar,"%s",str);
1.126 brouard 6012: if(mle==1)
6013: printf("%s",str);
6014: fprintf(ficlog,"%s",str);
6015: fprintf(ficparo,"%s",str);
6016: for(j=1; j <=i; j++){
6017: fscanf(ficpar," %le",&matcov[i][j]);
6018: if(mle==1){
6019: printf(" %.5le",matcov[i][j]);
6020: }
6021: fprintf(ficlog," %.5le",matcov[i][j]);
6022: fprintf(ficparo," %.5le",matcov[i][j]);
6023: }
6024: fscanf(ficpar,"\n");
6025: numlinepar++;
6026: if(mle==1)
6027: printf("\n");
6028: fprintf(ficlog,"\n");
6029: fprintf(ficparo,"\n");
6030: }
6031: for(i=1; i <=npar; i++)
6032: for(j=i+1;j<=npar;j++)
6033: matcov[i][j]=matcov[j][i];
6034:
6035: if(mle==1)
6036: printf("\n");
6037: fprintf(ficlog,"\n");
6038:
6039: fflush(ficlog);
6040:
6041: /*-------- Rewriting parameter file ----------*/
6042: strcpy(rfileres,"r"); /* "Rparameterfile */
6043: strcat(rfileres,optionfilefiname); /* Parameter file first name*/
6044: strcat(rfileres,"."); /* */
6045: strcat(rfileres,optionfilext); /* Other files have txt extension */
6046: if((ficres =fopen(rfileres,"w"))==NULL) {
6047: printf("Problem writing new parameter file: %s\n", fileres);goto end;
6048: fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
6049: }
6050: fprintf(ficres,"#%s\n",version);
6051: } /* End of mle != -3 */
6052:
6053:
6054: n= lastobs;
6055: num=lvector(1,n);
6056: moisnais=vector(1,n);
6057: annais=vector(1,n);
6058: moisdc=vector(1,n);
6059: andc=vector(1,n);
6060: agedc=vector(1,n);
6061: cod=ivector(1,n);
6062: weight=vector(1,n);
6063: for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
6064: mint=matrix(1,maxwav,1,n);
6065: anint=matrix(1,maxwav,1,n);
1.131 brouard 6066: s=imatrix(1,maxwav+1,1,n); /* s[i][j] health state for wave i and individual j */
1.126 brouard 6067: tab=ivector(1,NCOVMAX);
1.144 brouard 6068: ncodemax=ivector(1,NCOVMAX); /* Number of code per covariate; if O and 1 only, 2**ncov; V1+V2+V3+V4=>16 */
1.126 brouard 6069:
1.136 brouard 6070: /* Reads data from file datafile */
6071: if (readdata(datafile, firstobs, lastobs, &imx)==1)
6072: goto end;
6073:
6074: /* Calculation of the number of parameters from char model */
1.137 brouard 6075: /* modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4
6076: k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tag[cptcovage=1]=4
6077: k=3 V4 Tvar[k=3]= 4 (from V4)
6078: k=2 V1 Tvar[k=2]= 1 (from V1)
6079: k=1 Tvar[1]=2 (from V2)
6080: */
6081: Tvar=ivector(1,NCOVMAX); /* Was 15 changed to NCOVMAX. */
6082: /* V2+V1+V4+age*V3 is a model with 4 covariates (3 plus signs).
6083: For each model-covariate stores the data-covariate id. Tvar[1]=2, Tvar[2]=1, Tvar[3]=4,
6084: Tvar[4=age*V3] is 3 and 'age' is recorded in Tage.
6085: */
6086: /* For model-covariate k tells which data-covariate to use but
6087: because this model-covariate is a construction we invent a new column
6088: ncovcol + k1
6089: If already ncovcol=4 and model=V2+V1+V1*V4+age*V3
6090: Tvar[3=V1*V4]=4+1 etc */
1.145 brouard 6091: Tprod=ivector(1,NCOVMAX); /* Gives the position of a product */
1.137 brouard 6092: /* Tprod[k1=1]=3(=V1*V4) for V2+V1+V1*V4+age*V3
6093: if V2+V1+V1*V4+age*V3+V3*V2 TProd[k1=2]=5 (V3*V2)
6094: */
1.145 brouard 6095: Tvaraff=ivector(1,NCOVMAX); /* Unclear */
6096: 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 6097: * For V3*V2 (in V2+V1+V1*V4+age*V3+V3*V2), V3*V2 position is 2nd.
6098: * Tvard[k1=2][1]=3 (V3) Tvard[k1=2][2]=2(V2) */
1.145 brouard 6099: Tage=ivector(1,NCOVMAX); /* Gives the covariate id of covariates associated with age: V2 + V1 + age*V4 + V3*age
1.137 brouard 6100: 4 covariates (3 plus signs)
6101: Tage[1=V3*age]= 4; Tage[2=age*V4] = 3
6102: */
1.136 brouard 6103:
6104: if(decodemodel(model, lastobs) == 1)
6105: goto end;
6106:
1.137 brouard 6107: if((double)(lastobs-imx)/(double)imx > 1.10){
6108: nbwarn++;
6109: 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);
6110: 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);
6111: }
1.136 brouard 6112: /* if(mle==1){*/
1.137 brouard 6113: if (weightopt != 1) { /* Maximisation without weights. We can have weights different from 1 but want no weight*/
6114: for(i=1;i<=imx;i++) weight[i]=1.0; /* changed to imx */
1.136 brouard 6115: }
6116:
6117: /*-calculation of age at interview from date of interview and age at death -*/
6118: agev=matrix(1,maxwav,1,imx);
6119:
6120: if(calandcheckages(imx, maxwav, &agemin, &agemax, &nberr, &nbwarn) == 1)
6121: goto end;
6122:
1.126 brouard 6123:
1.136 brouard 6124: agegomp=(int)agemin;
6125: free_vector(moisnais,1,n);
6126: free_vector(annais,1,n);
1.126 brouard 6127: /* free_matrix(mint,1,maxwav,1,n);
6128: free_matrix(anint,1,maxwav,1,n);*/
6129: free_vector(moisdc,1,n);
6130: free_vector(andc,1,n);
1.145 brouard 6131: /* */
6132:
1.126 brouard 6133: wav=ivector(1,imx);
6134: dh=imatrix(1,lastpass-firstpass+1,1,imx);
6135: bh=imatrix(1,lastpass-firstpass+1,1,imx);
6136: mw=imatrix(1,lastpass-firstpass+1,1,imx);
6137:
6138: /* Concatenates waves */
6139: concatwav(wav, dh, bh, mw, s, agedc, agev, firstpass, lastpass, imx, nlstate, stepm);
1.145 brouard 6140: /* */
6141:
1.126 brouard 6142: /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
6143:
6144: nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
6145: ncodemax[1]=1;
1.145 brouard 6146: Ndum =ivector(-1,NCOVMAX);
6147: if (ncovmodel > 2)
6148: tricode(Tvar,nbcode,imx, Ndum); /**< Fills nbcode[Tvar[j]][l]; */
6149:
6150: codtab=imatrix(1,100,1,10); /* codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) */
6151: /*printf(" codtab[1,1],codtab[100,10]=%d,%d\n", codtab[1][1],codtab[100][10]);*/
6152: h=0;
6153:
6154:
6155: /*if (cptcovn > 0) */
1.126 brouard 6156:
1.145 brouard 6157:
1.126 brouard 6158: m=pow(2,cptcoveff);
6159:
1.131 brouard 6160: for(k=1;k<=cptcoveff; k++){ /* scans any effective covariate */
1.143 brouard 6161: 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 */
6162: for(j=1; j <= ncodemax[k]; j++){ /* For each modality of this covariate ncodemax=2*/
6163: 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 6164: h++;
1.141 brouard 6165: if (h>m)
1.136 brouard 6166: h=1;
1.144 brouard 6167: /**< codtab(h,k) k = codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) + 1
1.143 brouard 6168: * h 1 2 3 4
6169: *______________________________
6170: * 1 i=1 1 i=1 1 i=1 1 i=1 1
6171: * 2 2 1 1 1
6172: * 3 i=2 1 2 1 1
6173: * 4 2 2 1 1
6174: * 5 i=3 1 i=2 1 2 1
6175: * 6 2 1 2 1
6176: * 7 i=4 1 2 2 1
6177: * 8 2 2 2 1
6178: * 9 i=5 1 i=3 1 i=2 1 1
6179: * 10 2 1 1 1
6180: * 11 i=6 1 2 1 1
6181: * 12 2 2 1 1
6182: * 13 i=7 1 i=4 1 2 1
6183: * 14 2 1 2 1
6184: * 15 i=8 1 2 2 1
6185: * 16 2 2 2 1
6186: */
1.141 brouard 6187: codtab[h][k]=j;
1.145 brouard 6188: /*codtab[h][Tvar[k]]=j;*/
1.130 brouard 6189: 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 6190: }
6191: }
6192: }
6193: }
6194: /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);
6195: codtab[1][2]=1;codtab[2][2]=2; */
6196: /* for(i=1; i <=m ;i++){
6197: for(k=1; k <=cptcovn; k++){
1.131 brouard 6198: printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
1.126 brouard 6199: }
6200: printf("\n");
6201: }
6202: scanf("%d",i);*/
1.145 brouard 6203:
6204: free_ivector(Ndum,-1,NCOVMAX);
6205:
6206:
1.126 brouard 6207:
6208: /*------------ gnuplot -------------*/
6209: strcpy(optionfilegnuplot,optionfilefiname);
6210: if(mle==-3)
6211: strcat(optionfilegnuplot,"-mort");
6212: strcat(optionfilegnuplot,".gp");
6213:
6214: if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
6215: printf("Problem with file %s",optionfilegnuplot);
6216: }
6217: else{
6218: fprintf(ficgp,"\n# %s\n", version);
6219: fprintf(ficgp,"# %s\n", optionfilegnuplot);
1.141 brouard 6220: //fprintf(ficgp,"set missing 'NaNq'\n");
6221: fprintf(ficgp,"set datafile missing 'NaNq'\n");
1.126 brouard 6222: }
6223: /* fclose(ficgp);*/
6224: /*--------- index.htm --------*/
6225:
6226: strcpy(optionfilehtm,optionfilefiname); /* Main html file */
6227: if(mle==-3)
6228: strcat(optionfilehtm,"-mort");
6229: strcat(optionfilehtm,".htm");
6230: if((fichtm=fopen(optionfilehtm,"w"))==NULL) {
1.131 brouard 6231: printf("Problem with %s \n",optionfilehtm);
6232: exit(0);
1.126 brouard 6233: }
6234:
6235: strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
6236: strcat(optionfilehtmcov,"-cov.htm");
6237: if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL) {
6238: printf("Problem with %s \n",optionfilehtmcov), exit(0);
6239: }
6240: else{
6241: fprintf(fichtmcov,"<html><head>\n<title>IMaCh Cov %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
6242: <hr size=\"2\" color=\"#EC5E5E\"> \n\
6243: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n",\
6244: optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
6245: }
6246:
6247: fprintf(fichtm,"<html><head>\n<title>IMaCh %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
6248: <hr size=\"2\" color=\"#EC5E5E\"> \n\
6249: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
6250: \n\
6251: <hr size=\"2\" color=\"#EC5E5E\">\
6252: <ul><li><h4>Parameter files</h4>\n\
6253: - Parameter file: <a href=\"%s.%s\">%s.%s</a><br>\n\
6254: - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
6255: - Log file of the run: <a href=\"%s\">%s</a><br>\n\
6256: - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
6257: - Date and time at start: %s</ul>\n",\
6258: optionfilehtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
6259: optionfilefiname,optionfilext,optionfilefiname,optionfilext,\
6260: fileres,fileres,\
6261: filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
6262: fflush(fichtm);
6263:
6264: strcpy(pathr,path);
6265: strcat(pathr,optionfilefiname);
6266: chdir(optionfilefiname); /* Move to directory named optionfile */
6267:
6268: /* Calculates basic frequencies. Computes observed prevalence at single age
6269: and prints on file fileres'p'. */
6270: freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart);
6271:
6272: fprintf(fichtm,"\n");
6273: fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
6274: Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
6275: Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
6276: imx,agemin,agemax,jmin,jmax,jmean);
6277: pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
6278: oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
6279: newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
6280: savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
6281: oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
6282:
6283:
6284: /* For Powell, parameters are in a vector p[] starting at p[1]
6285: so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
6286: p=param[1][1]; /* *(*(*(param +1)+1)+0) */
6287:
6288: globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
6289:
6290: if (mle==-3){
1.136 brouard 6291: ximort=matrix(1,NDIM,1,NDIM);
6292: /* ximort=gsl_matrix_alloc(1,NDIM,1,NDIM); */
1.126 brouard 6293: cens=ivector(1,n);
6294: ageexmed=vector(1,n);
6295: agecens=vector(1,n);
6296: dcwave=ivector(1,n);
6297:
6298: for (i=1; i<=imx; i++){
6299: dcwave[i]=-1;
6300: for (m=firstpass; m<=lastpass; m++)
6301: if (s[m][i]>nlstate) {
6302: dcwave[i]=m;
6303: /* printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
6304: break;
6305: }
6306: }
6307:
6308: for (i=1; i<=imx; i++) {
6309: if (wav[i]>0){
6310: ageexmed[i]=agev[mw[1][i]][i];
6311: j=wav[i];
6312: agecens[i]=1.;
6313:
6314: if (ageexmed[i]> 1 && wav[i] > 0){
6315: agecens[i]=agev[mw[j][i]][i];
6316: cens[i]= 1;
6317: }else if (ageexmed[i]< 1)
6318: cens[i]= -1;
6319: if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
6320: cens[i]=0 ;
6321: }
6322: else cens[i]=-1;
6323: }
6324:
6325: for (i=1;i<=NDIM;i++) {
6326: for (j=1;j<=NDIM;j++)
6327: ximort[i][j]=(i == j ? 1.0 : 0.0);
6328: }
6329:
1.145 brouard 6330: /*p[1]=0.0268; p[NDIM]=0.083;*/
1.126 brouard 6331: /*printf("%lf %lf", p[1], p[2]);*/
6332:
6333:
1.136 brouard 6334: #ifdef GSL
6335: printf("GSL optimization\n"); fprintf(ficlog,"Powell\n");
1.162 brouard 6336: #else
1.126 brouard 6337: printf("Powell\n"); fprintf(ficlog,"Powell\n");
1.136 brouard 6338: #endif
1.126 brouard 6339: strcpy(filerespow,"pow-mort");
6340: strcat(filerespow,fileres);
6341: if((ficrespow=fopen(filerespow,"w"))==NULL) {
6342: printf("Problem with resultfile: %s\n", filerespow);
6343: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
6344: }
1.136 brouard 6345: #ifdef GSL
6346: fprintf(ficrespow,"# GSL optimization\n# iter -2*LL");
1.162 brouard 6347: #else
1.126 brouard 6348: fprintf(ficrespow,"# Powell\n# iter -2*LL");
1.136 brouard 6349: #endif
1.126 brouard 6350: /* for (i=1;i<=nlstate;i++)
6351: for(j=1;j<=nlstate+ndeath;j++)
6352: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
6353: */
6354: fprintf(ficrespow,"\n");
1.136 brouard 6355: #ifdef GSL
6356: /* gsl starts here */
6357: T = gsl_multimin_fminimizer_nmsimplex;
6358: gsl_multimin_fminimizer *sfm = NULL;
6359: gsl_vector *ss, *x;
6360: gsl_multimin_function minex_func;
6361:
6362: /* Initial vertex size vector */
6363: ss = gsl_vector_alloc (NDIM);
6364:
6365: if (ss == NULL){
6366: GSL_ERROR_VAL ("failed to allocate space for ss", GSL_ENOMEM, 0);
6367: }
6368: /* Set all step sizes to 1 */
6369: gsl_vector_set_all (ss, 0.001);
6370:
6371: /* Starting point */
1.126 brouard 6372:
1.136 brouard 6373: x = gsl_vector_alloc (NDIM);
6374:
6375: if (x == NULL){
6376: gsl_vector_free(ss);
6377: GSL_ERROR_VAL ("failed to allocate space for x", GSL_ENOMEM, 0);
6378: }
6379:
6380: /* Initialize method and iterate */
6381: /* p[1]=0.0268; p[NDIM]=0.083; */
6382: /* gsl_vector_set(x, 0, 0.0268); */
6383: /* gsl_vector_set(x, 1, 0.083); */
6384: gsl_vector_set(x, 0, p[1]);
6385: gsl_vector_set(x, 1, p[2]);
6386:
6387: minex_func.f = &gompertz_f;
6388: minex_func.n = NDIM;
6389: minex_func.params = (void *)&p; /* ??? */
6390:
6391: sfm = gsl_multimin_fminimizer_alloc (T, NDIM);
6392: gsl_multimin_fminimizer_set (sfm, &minex_func, x, ss);
6393:
6394: printf("Iterations beginning .....\n\n");
6395: printf("Iter. # Intercept Slope -Log Likelihood Simplex size\n");
6396:
6397: iteri=0;
6398: while (rval == GSL_CONTINUE){
6399: iteri++;
6400: status = gsl_multimin_fminimizer_iterate(sfm);
6401:
6402: if (status) printf("error: %s\n", gsl_strerror (status));
6403: fflush(0);
6404:
6405: if (status)
6406: break;
6407:
6408: rval = gsl_multimin_test_size (gsl_multimin_fminimizer_size (sfm), 1e-6);
6409: ssval = gsl_multimin_fminimizer_size (sfm);
6410:
6411: if (rval == GSL_SUCCESS)
6412: printf ("converged to a local maximum at\n");
6413:
6414: printf("%5d ", iteri);
6415: for (it = 0; it < NDIM; it++){
6416: printf ("%10.5f ", gsl_vector_get (sfm->x, it));
6417: }
6418: printf("f() = %-10.5f ssize = %.7f\n", sfm->fval, ssval);
6419: }
6420:
6421: printf("\n\n Please note: Program should be run many times with varying starting points to detemine global maximum\n\n");
6422:
6423: gsl_vector_free(x); /* initial values */
6424: gsl_vector_free(ss); /* inital step size */
6425: for (it=0; it<NDIM; it++){
6426: p[it+1]=gsl_vector_get(sfm->x,it);
6427: fprintf(ficrespow," %.12lf", p[it]);
6428: }
6429: gsl_multimin_fminimizer_free (sfm); /* p *(sfm.x.data) et p *(sfm.x.data+1) */
6430: #endif
6431: #ifdef POWELL
6432: powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
6433: #endif
1.126 brouard 6434: fclose(ficrespow);
6435:
6436: hesscov(matcov, p, NDIM, delti, 1e-4, gompertz);
6437:
6438: for(i=1; i <=NDIM; i++)
6439: for(j=i+1;j<=NDIM;j++)
6440: matcov[i][j]=matcov[j][i];
6441:
6442: printf("\nCovariance matrix\n ");
6443: for(i=1; i <=NDIM; i++) {
6444: for(j=1;j<=NDIM;j++){
6445: printf("%f ",matcov[i][j]);
6446: }
6447: printf("\n ");
6448: }
6449:
6450: printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
6451: for (i=1;i<=NDIM;i++)
6452: printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
6453:
6454: lsurv=vector(1,AGESUP);
6455: lpop=vector(1,AGESUP);
6456: tpop=vector(1,AGESUP);
6457: lsurv[agegomp]=100000;
6458:
6459: for (k=agegomp;k<=AGESUP;k++) {
6460: agemortsup=k;
6461: if (p[1]*exp(p[2]*(k-agegomp))>1) break;
6462: }
6463:
6464: for (k=agegomp;k<agemortsup;k++)
6465: lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
6466:
6467: for (k=agegomp;k<agemortsup;k++){
6468: lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
6469: sumlpop=sumlpop+lpop[k];
6470: }
6471:
6472: tpop[agegomp]=sumlpop;
6473: for (k=agegomp;k<(agemortsup-3);k++){
6474: /* tpop[k+1]=2;*/
6475: tpop[k+1]=tpop[k]-lpop[k];
6476: }
6477:
6478:
6479: printf("\nAge lx qx dx Lx Tx e(x)\n");
6480: for (k=agegomp;k<(agemortsup-2);k++)
6481: 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]);
6482:
6483:
6484: replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
6485: printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
6486:
6487: printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \
6488: stepm, weightopt,\
6489: model,imx,p,matcov,agemortsup);
6490:
6491: free_vector(lsurv,1,AGESUP);
6492: free_vector(lpop,1,AGESUP);
6493: free_vector(tpop,1,AGESUP);
1.136 brouard 6494: #ifdef GSL
6495: free_ivector(cens,1,n);
6496: free_vector(agecens,1,n);
6497: free_ivector(dcwave,1,n);
6498: free_matrix(ximort,1,NDIM,1,NDIM);
6499: #endif
1.126 brouard 6500: } /* Endof if mle==-3 */
6501:
6502: else{ /* For mle >=1 */
1.132 brouard 6503: globpr=0;/* debug */
6504: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
1.126 brouard 6505: printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
6506: for (k=1; k<=npar;k++)
6507: printf(" %d %8.5f",k,p[k]);
6508: printf("\n");
6509: globpr=1; /* to print the contributions */
6510: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
6511: printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
6512: for (k=1; k<=npar;k++)
6513: printf(" %d %8.5f",k,p[k]);
6514: printf("\n");
6515: if(mle>=1){ /* Could be 1 or 2 */
6516: mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
6517: }
6518:
6519: /*--------- results files --------------*/
6520: 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);
6521:
6522:
6523: fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
6524: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
6525: fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
6526: for(i=1,jk=1; i <=nlstate; i++){
6527: for(k=1; k <=(nlstate+ndeath); k++){
6528: if (k != i) {
6529: printf("%d%d ",i,k);
6530: fprintf(ficlog,"%d%d ",i,k);
6531: fprintf(ficres,"%1d%1d ",i,k);
6532: for(j=1; j <=ncovmodel; j++){
6533: printf("%lf ",p[jk]);
6534: fprintf(ficlog,"%lf ",p[jk]);
6535: fprintf(ficres,"%lf ",p[jk]);
6536: jk++;
6537: }
6538: printf("\n");
6539: fprintf(ficlog,"\n");
6540: fprintf(ficres,"\n");
6541: }
6542: }
6543: }
6544: if(mle!=0){
6545: /* Computing hessian and covariance matrix */
6546: ftolhess=ftol; /* Usually correct */
6547: hesscov(matcov, p, npar, delti, ftolhess, func);
6548: }
6549: fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
6550: printf("# Scales (for hessian or gradient estimation)\n");
6551: fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
6552: for(i=1,jk=1; i <=nlstate; i++){
6553: for(j=1; j <=nlstate+ndeath; j++){
6554: if (j!=i) {
6555: fprintf(ficres,"%1d%1d",i,j);
6556: printf("%1d%1d",i,j);
6557: fprintf(ficlog,"%1d%1d",i,j);
6558: for(k=1; k<=ncovmodel;k++){
6559: printf(" %.5e",delti[jk]);
6560: fprintf(ficlog," %.5e",delti[jk]);
6561: fprintf(ficres," %.5e",delti[jk]);
6562: jk++;
6563: }
6564: printf("\n");
6565: fprintf(ficlog,"\n");
6566: fprintf(ficres,"\n");
6567: }
6568: }
6569: }
6570:
6571: 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");
6572: if(mle>=1)
6573: 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");
6574: 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");
6575: /* # 121 Var(a12)\n\ */
6576: /* # 122 Cov(b12,a12) Var(b12)\n\ */
6577: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
6578: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
6579: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
6580: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
6581: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
6582: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
6583:
6584:
6585: /* Just to have a covariance matrix which will be more understandable
6586: even is we still don't want to manage dictionary of variables
6587: */
6588: for(itimes=1;itimes<=2;itimes++){
6589: jj=0;
6590: for(i=1; i <=nlstate; i++){
6591: for(j=1; j <=nlstate+ndeath; j++){
6592: if(j==i) continue;
6593: for(k=1; k<=ncovmodel;k++){
6594: jj++;
6595: ca[0]= k+'a'-1;ca[1]='\0';
6596: if(itimes==1){
6597: if(mle>=1)
6598: printf("#%1d%1d%d",i,j,k);
6599: fprintf(ficlog,"#%1d%1d%d",i,j,k);
6600: fprintf(ficres,"#%1d%1d%d",i,j,k);
6601: }else{
6602: if(mle>=1)
6603: printf("%1d%1d%d",i,j,k);
6604: fprintf(ficlog,"%1d%1d%d",i,j,k);
6605: fprintf(ficres,"%1d%1d%d",i,j,k);
6606: }
6607: ll=0;
6608: for(li=1;li <=nlstate; li++){
6609: for(lj=1;lj <=nlstate+ndeath; lj++){
6610: if(lj==li) continue;
6611: for(lk=1;lk<=ncovmodel;lk++){
6612: ll++;
6613: if(ll<=jj){
6614: cb[0]= lk +'a'-1;cb[1]='\0';
6615: if(ll<jj){
6616: if(itimes==1){
6617: if(mle>=1)
6618: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
6619: fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
6620: fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
6621: }else{
6622: if(mle>=1)
6623: printf(" %.5e",matcov[jj][ll]);
6624: fprintf(ficlog," %.5e",matcov[jj][ll]);
6625: fprintf(ficres," %.5e",matcov[jj][ll]);
6626: }
6627: }else{
6628: if(itimes==1){
6629: if(mle>=1)
6630: printf(" Var(%s%1d%1d)",ca,i,j);
6631: fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
6632: fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
6633: }else{
6634: if(mle>=1)
6635: printf(" %.5e",matcov[jj][ll]);
6636: fprintf(ficlog," %.5e",matcov[jj][ll]);
6637: fprintf(ficres," %.5e",matcov[jj][ll]);
6638: }
6639: }
6640: }
6641: } /* end lk */
6642: } /* end lj */
6643: } /* end li */
6644: if(mle>=1)
6645: printf("\n");
6646: fprintf(ficlog,"\n");
6647: fprintf(ficres,"\n");
6648: numlinepar++;
6649: } /* end k*/
6650: } /*end j */
6651: } /* end i */
6652: } /* end itimes */
6653:
6654: fflush(ficlog);
6655: fflush(ficres);
6656:
6657: while((c=getc(ficpar))=='#' && c!= EOF){
6658: ungetc(c,ficpar);
6659: fgets(line, MAXLINE, ficpar);
1.141 brouard 6660: fputs(line,stdout);
1.126 brouard 6661: fputs(line,ficparo);
6662: }
6663: ungetc(c,ficpar);
6664:
6665: estepm=0;
6666: fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
6667: if (estepm==0 || estepm < stepm) estepm=stepm;
6668: if (fage <= 2) {
6669: bage = ageminpar;
6670: fage = agemaxpar;
6671: }
6672:
6673: fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
6674: fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
6675: fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
6676:
6677: while((c=getc(ficpar))=='#' && c!= EOF){
6678: ungetc(c,ficpar);
6679: fgets(line, MAXLINE, ficpar);
1.141 brouard 6680: fputs(line,stdout);
1.126 brouard 6681: fputs(line,ficparo);
6682: }
6683: ungetc(c,ficpar);
6684:
6685: 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);
6686: 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);
6687: 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);
6688: printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
6689: 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);
6690:
6691: while((c=getc(ficpar))=='#' && c!= EOF){
6692: ungetc(c,ficpar);
6693: fgets(line, MAXLINE, ficpar);
1.141 brouard 6694: fputs(line,stdout);
1.126 brouard 6695: fputs(line,ficparo);
6696: }
6697: ungetc(c,ficpar);
6698:
6699:
6700: dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
6701: dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
6702:
6703: fscanf(ficpar,"pop_based=%d\n",&popbased);
6704: fprintf(ficparo,"pop_based=%d\n",popbased);
6705: fprintf(ficres,"pop_based=%d\n",popbased);
6706:
6707: while((c=getc(ficpar))=='#' && c!= EOF){
6708: ungetc(c,ficpar);
6709: fgets(line, MAXLINE, ficpar);
1.141 brouard 6710: fputs(line,stdout);
1.126 brouard 6711: fputs(line,ficparo);
6712: }
6713: ungetc(c,ficpar);
6714:
6715: 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);
6716: 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);
6717: 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);
6718: 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);
6719: 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);
6720: /* day and month of proj2 are not used but only year anproj2.*/
6721:
6722:
6723:
1.145 brouard 6724: /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint); */
6725: /* ,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2); */
1.126 brouard 6726:
6727: replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
6728: printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
6729:
6730: printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
6731: model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
6732: jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
6733:
6734: /*------------ free_vector -------------*/
6735: /* chdir(path); */
6736:
6737: free_ivector(wav,1,imx);
6738: free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
6739: free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
6740: free_imatrix(mw,1,lastpass-firstpass+1,1,imx);
6741: free_lvector(num,1,n);
6742: free_vector(agedc,1,n);
6743: /*free_matrix(covar,0,NCOVMAX,1,n);*/
6744: /*free_matrix(covar,1,NCOVMAX,1,n);*/
6745: fclose(ficparo);
6746: fclose(ficres);
6747:
6748:
6749: /*--------------- Prevalence limit (period or stable prevalence) --------------*/
1.145 brouard 6750: #include "prevlim.h" /* Use ficrespl, ficlog */
1.126 brouard 6751: fclose(ficrespl);
6752:
1.145 brouard 6753: #ifdef FREEEXIT2
6754: #include "freeexit2.h"
6755: #endif
6756:
1.126 brouard 6757: /*------------- h Pij x at various ages ------------*/
1.145 brouard 6758: #include "hpijx.h"
6759: fclose(ficrespij);
1.126 brouard 6760:
1.145 brouard 6761: /*-------------- Variance of one-step probabilities---*/
6762: k=1;
1.126 brouard 6763: varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
6764:
6765:
6766: probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
6767: for(i=1;i<=AGESUP;i++)
6768: for(j=1;j<=NCOVMAX;j++)
6769: for(k=1;k<=NCOVMAX;k++)
6770: probs[i][j][k]=0.;
6771:
6772: /*---------- Forecasting ------------------*/
6773: /*if((stepm == 1) && (strcmp(model,".")==0)){*/
6774: if(prevfcast==1){
6775: /* if(stepm ==1){*/
6776: prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
6777: /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
6778: /* } */
6779: /* else{ */
6780: /* erreur=108; */
6781: /* 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); */
6782: /* 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); */
6783: /* } */
6784: }
6785:
6786:
1.127 brouard 6787: /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
6788:
6789: prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
6790: /* 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",\
6791: ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
6792: */
1.126 brouard 6793:
1.127 brouard 6794: if (mobilav!=0) {
6795: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
6796: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
6797: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
6798: printf(" Error in movingaverage mobilav=%d\n",mobilav);
6799: }
1.126 brouard 6800: }
6801:
6802:
1.127 brouard 6803: /*---------- Health expectancies, no variances ------------*/
6804:
1.126 brouard 6805: strcpy(filerese,"e");
6806: strcat(filerese,fileres);
6807: if((ficreseij=fopen(filerese,"w"))==NULL) {
6808: printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
6809: fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
6810: }
6811: printf("Computing Health Expectancies: result on file '%s' \n", filerese);
6812: fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
1.145 brouard 6813: /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
6814: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
6815:
6816: for (k=1; k <= (int) pow(2,cptcoveff); k++){
1.127 brouard 6817: fprintf(ficreseij,"\n#****** ");
6818: for(j=1;j<=cptcoveff;j++) {
6819: fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6820: }
6821: fprintf(ficreseij,"******\n");
6822:
6823: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
6824: oldm=oldms;savm=savms;
6825: evsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart);
6826:
6827: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
1.145 brouard 6828: /*}*/
1.127 brouard 6829: }
6830: fclose(ficreseij);
6831:
6832:
6833: /*---------- Health expectancies and variances ------------*/
6834:
6835:
6836: strcpy(filerest,"t");
6837: strcat(filerest,fileres);
6838: if((ficrest=fopen(filerest,"w"))==NULL) {
6839: printf("Problem with total LE resultfile: %s\n", filerest);goto end;
6840: fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
6841: }
6842: printf("Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);
6843: fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);
6844:
1.126 brouard 6845:
6846: strcpy(fileresstde,"stde");
6847: strcat(fileresstde,fileres);
6848: if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {
6849: printf("Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
6850: fprintf(ficlog,"Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
6851: }
6852: printf("Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
6853: fprintf(ficlog,"Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
6854:
6855: strcpy(filerescve,"cve");
6856: strcat(filerescve,fileres);
6857: if((ficrescveij=fopen(filerescve,"w"))==NULL) {
6858: printf("Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
6859: fprintf(ficlog,"Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
6860: }
6861: printf("Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
6862: fprintf(ficlog,"Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
6863:
6864: strcpy(fileresv,"v");
6865: strcat(fileresv,fileres);
6866: if((ficresvij=fopen(fileresv,"w"))==NULL) {
6867: printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
6868: fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
6869: }
6870: printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
6871: fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
6872:
1.145 brouard 6873: /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
6874: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
6875:
6876: for (k=1; k <= (int) pow(2,cptcoveff); k++){
6877: fprintf(ficrest,"\n#****** ");
1.126 brouard 6878: for(j=1;j<=cptcoveff;j++)
6879: fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6880: fprintf(ficrest,"******\n");
6881:
6882: fprintf(ficresstdeij,"\n#****** ");
6883: fprintf(ficrescveij,"\n#****** ");
6884: for(j=1;j<=cptcoveff;j++) {
6885: fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6886: fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6887: }
6888: fprintf(ficresstdeij,"******\n");
6889: fprintf(ficrescveij,"******\n");
6890:
6891: fprintf(ficresvij,"\n#****** ");
6892: for(j=1;j<=cptcoveff;j++)
6893: fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6894: fprintf(ficresvij,"******\n");
6895:
6896: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
6897: oldm=oldms;savm=savms;
1.127 brouard 6898: cvevsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);
1.145 brouard 6899: /*
6900: */
6901: /* goto endfree; */
1.126 brouard 6902:
6903: vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
6904: pstamp(ficrest);
1.145 brouard 6905:
6906:
1.128 brouard 6907: for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
1.145 brouard 6908: oldm=oldms;savm=savms; /* Segmentation fault */
1.161 brouard 6909: cptcod= 0; /* To be deleted */
6910: 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 6911: 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 6912: if(vpopbased==1)
6913: 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);
6914: else
6915: fprintf(ficrest,"the age specific period (stable) prevalences in each health state \n");
6916: fprintf(ficrest,"# Age e.. (std) ");
6917: for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
6918: fprintf(ficrest,"\n");
1.126 brouard 6919:
1.128 brouard 6920: epj=vector(1,nlstate+1);
6921: for(age=bage; age <=fage ;age++){
6922: prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
6923: if (vpopbased==1) {
6924: if(mobilav ==0){
6925: for(i=1; i<=nlstate;i++)
6926: prlim[i][i]=probs[(int)age][i][k];
6927: }else{ /* mobilav */
6928: for(i=1; i<=nlstate;i++)
6929: prlim[i][i]=mobaverage[(int)age][i][k];
6930: }
1.126 brouard 6931: }
6932:
1.128 brouard 6933: fprintf(ficrest," %4.0f",age);
6934: for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
6935: for(i=1, epj[j]=0.;i <=nlstate;i++) {
6936: epj[j] += prlim[i][i]*eij[i][j][(int)age];
6937: /* printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
6938: }
6939: epj[nlstate+1] +=epj[j];
1.126 brouard 6940: }
6941:
1.128 brouard 6942: for(i=1, vepp=0.;i <=nlstate;i++)
6943: for(j=1;j <=nlstate;j++)
6944: vepp += vareij[i][j][(int)age];
6945: fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
6946: for(j=1;j <=nlstate;j++){
6947: fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
6948: }
6949: fprintf(ficrest,"\n");
1.126 brouard 6950: }
6951: }
6952: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
6953: free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
6954: free_vector(epj,1,nlstate+1);
1.145 brouard 6955: /*}*/
1.126 brouard 6956: }
6957: free_vector(weight,1,n);
1.145 brouard 6958: free_imatrix(Tvard,1,NCOVMAX,1,2);
1.126 brouard 6959: free_imatrix(s,1,maxwav+1,1,n);
6960: free_matrix(anint,1,maxwav,1,n);
6961: free_matrix(mint,1,maxwav,1,n);
6962: free_ivector(cod,1,n);
6963: free_ivector(tab,1,NCOVMAX);
6964: fclose(ficresstdeij);
6965: fclose(ficrescveij);
6966: fclose(ficresvij);
6967: fclose(ficrest);
6968: fclose(ficpar);
6969:
6970: /*------- Variance of period (stable) prevalence------*/
6971:
6972: strcpy(fileresvpl,"vpl");
6973: strcat(fileresvpl,fileres);
6974: if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
6975: printf("Problem with variance of period (stable) prevalence resultfile: %s\n", fileresvpl);
6976: exit(0);
6977: }
6978: printf("Computing Variance-covariance of period (stable) prevalence: file '%s' \n", fileresvpl);
6979:
1.145 brouard 6980: /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
6981: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
6982:
6983: for (k=1; k <= (int) pow(2,cptcoveff); k++){
6984: fprintf(ficresvpl,"\n#****** ");
1.126 brouard 6985: for(j=1;j<=cptcoveff;j++)
6986: fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6987: fprintf(ficresvpl,"******\n");
6988:
6989: varpl=matrix(1,nlstate,(int) bage, (int) fage);
6990: oldm=oldms;savm=savms;
6991: varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k,strstart);
6992: free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
1.145 brouard 6993: /*}*/
1.126 brouard 6994: }
6995:
6996: fclose(ficresvpl);
6997:
6998: /*---------- End : free ----------------*/
6999: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
7000: free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
7001: } /* mle==-3 arrives here for freeing */
1.164 brouard 7002: /* endfree:*/
1.141 brouard 7003: free_matrix(prlim,1,nlstate,1,nlstate); /*here or after loop ? */
1.126 brouard 7004: free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
7005: free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
7006: free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
7007: free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
7008: free_matrix(covar,0,NCOVMAX,1,n);
7009: free_matrix(matcov,1,npar,1,npar);
7010: /*free_vector(delti,1,npar);*/
7011: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
7012: free_matrix(agev,1,maxwav,1,imx);
7013: free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
7014:
1.145 brouard 7015: free_ivector(ncodemax,1,NCOVMAX);
7016: free_ivector(Tvar,1,NCOVMAX);
7017: free_ivector(Tprod,1,NCOVMAX);
7018: free_ivector(Tvaraff,1,NCOVMAX);
7019: free_ivector(Tage,1,NCOVMAX);
1.126 brouard 7020:
7021: free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
7022: free_imatrix(codtab,1,100,1,10);
7023: fflush(fichtm);
7024: fflush(ficgp);
7025:
7026:
7027: if((nberr >0) || (nbwarn>0)){
7028: printf("End of Imach with %d errors and/or %d warnings\n",nberr,nbwarn);
7029: fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
7030: }else{
7031: printf("End of Imach\n");
7032: fprintf(ficlog,"End of Imach\n");
7033: }
7034: printf("See log file on %s\n",filelog);
7035: /* gettimeofday(&end_time, (struct timezone*)0);*/ /* after time */
1.157 brouard 7036: /*(void) gettimeofday(&end_time,&tzp);*/
7037: rend_time = time(NULL);
7038: end_time = *localtime(&rend_time);
7039: /* tml = *localtime(&end_time.tm_sec); */
7040: strcpy(strtend,asctime(&end_time));
1.126 brouard 7041: printf("Local time at start %s\nLocal time at end %s",strstart, strtend);
7042: fprintf(ficlog,"Local time at start %s\nLocal time at end %s\n",strstart, strtend);
1.157 brouard 7043: printf("Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
1.126 brouard 7044:
1.157 brouard 7045: printf("Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
7046: fprintf(ficlog,"Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
7047: fprintf(ficlog,"Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
1.126 brouard 7048: /* printf("Total time was %d uSec.\n", total_usecs);*/
7049: /* if(fileappend(fichtm,optionfilehtm)){ */
7050: fprintf(fichtm,"<br>Local time at start %s<br>Local time at end %s<br>\n</body></html>",strstart, strtend);
7051: fclose(fichtm);
7052: fprintf(fichtmcov,"<br>Local time at start %s<br>Local time at end %s<br>\n</body></html>",strstart, strtend);
7053: fclose(fichtmcov);
7054: fclose(ficgp);
7055: fclose(ficlog);
7056: /*------ End -----------*/
7057:
7058:
7059: printf("Before Current directory %s!\n",pathcd);
7060: if(chdir(pathcd) != 0)
7061: printf("Can't move to directory %s!\n",path);
7062: if(getcwd(pathcd,MAXLINE) > 0)
7063: printf("Current directory %s!\n",pathcd);
7064: /*strcat(plotcmd,CHARSEPARATOR);*/
7065: sprintf(plotcmd,"gnuplot");
1.157 brouard 7066: #ifdef _WIN32
1.126 brouard 7067: sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
7068: #endif
7069: if(!stat(plotcmd,&info)){
1.158 brouard 7070: printf("Error or gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
1.126 brouard 7071: if(!stat(getenv("GNUPLOTBIN"),&info)){
1.158 brouard 7072: printf("Error or gnuplot program not found: '%s' Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);
1.126 brouard 7073: }else
7074: strcpy(pplotcmd,plotcmd);
1.157 brouard 7075: #ifdef __unix
1.126 brouard 7076: strcpy(plotcmd,GNUPLOTPROGRAM);
7077: if(!stat(plotcmd,&info)){
1.158 brouard 7078: printf("Error gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
1.126 brouard 7079: }else
7080: strcpy(pplotcmd,plotcmd);
7081: #endif
7082: }else
7083: strcpy(pplotcmd,plotcmd);
7084:
7085: sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
1.158 brouard 7086: printf("Starting graphs with: '%s'\n",plotcmd);fflush(stdout);
1.126 brouard 7087:
7088: if((outcmd=system(plotcmd)) != 0){
1.158 brouard 7089: printf("gnuplot command might not be in your path: '%s', err=%d\n", plotcmd, outcmd);
1.154 brouard 7090: printf("\n Trying if gnuplot resides on the same directory that IMaCh\n");
1.152 brouard 7091: sprintf(plotcmd,"%sgnuplot %s", pathimach, optionfilegnuplot);
1.150 brouard 7092: if((outcmd=system(plotcmd)) != 0)
1.153 brouard 7093: printf("\n Still a problem with gnuplot command %s, err=%d\n", plotcmd, outcmd);
1.126 brouard 7094: }
1.158 brouard 7095: printf(" Successful, please wait...");
1.126 brouard 7096: while (z[0] != 'q') {
7097: /* chdir(path); */
1.154 brouard 7098: printf("\nType e to edit results with your browser, g to graph again and q for exit: ");
1.126 brouard 7099: scanf("%s",z);
7100: /* if (z[0] == 'c') system("./imach"); */
7101: if (z[0] == 'e') {
1.158 brouard 7102: #ifdef __APPLE__
1.152 brouard 7103: sprintf(pplotcmd, "open %s", optionfilehtm);
1.157 brouard 7104: #elif __linux
7105: sprintf(pplotcmd, "xdg-open %s", optionfilehtm);
1.153 brouard 7106: #else
1.152 brouard 7107: sprintf(pplotcmd, "%s", optionfilehtm);
1.153 brouard 7108: #endif
7109: printf("Starting browser with: %s",pplotcmd);fflush(stdout);
7110: system(pplotcmd);
1.126 brouard 7111: }
7112: else if (z[0] == 'g') system(plotcmd);
7113: else if (z[0] == 'q') exit(0);
7114: }
7115: end:
7116: while (z[0] != 'q') {
7117: printf("\nType q for exiting: ");
7118: scanf("%s",z);
7119: }
7120: }
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