1: /* $Id: imach.c,v 1.179 2015/01/04 09:57:06 brouard Exp $
2: $State: Exp $
3: $Log: imach.c,v $
4: Revision 1.179 2015/01/04 09:57:06 brouard
5: Summary: back to OS/X
6:
7: Revision 1.178 2015/01/04 09:35:48 brouard
8: *** empty log message ***
9:
10: Revision 1.177 2015/01/03 18:40:56 brouard
11: Summary: Still testing ilc32 on OSX
12:
13: Revision 1.176 2015/01/03 16:45:04 brouard
14: *** empty log message ***
15:
16: Revision 1.175 2015/01/03 16:33:42 brouard
17: *** empty log message ***
18:
19: Revision 1.174 2015/01/03 16:15:49 brouard
20: Summary: Still in cross-compilation
21:
22: Revision 1.173 2015/01/03 12:06:26 brouard
23: Summary: trying to detect cross-compilation
24:
25: Revision 1.172 2014/12/27 12:07:47 brouard
26: Summary: Back from Visual Studio and Intel, options for compiling for Windows XP
27:
28: Revision 1.171 2014/12/23 13:26:59 brouard
29: Summary: Back from Visual C
30:
31: Still problem with utsname.h on Windows
32:
33: Revision 1.170 2014/12/23 11:17:12 brouard
34: Summary: Cleaning some \%% back to %%
35:
36: The escape was mandatory for a specific compiler (which one?), but too many warnings.
37:
38: Revision 1.169 2014/12/22 23:08:31 brouard
39: Summary: 0.98p
40:
41: Outputs some informations on compiler used, OS etc. Testing on different platforms.
42:
43: Revision 1.168 2014/12/22 15:17:42 brouard
44: Summary: update
45:
46: Revision 1.167 2014/12/22 13:50:56 brouard
47: Summary: Testing uname and compiler version and if compiled 32 or 64
48:
49: Testing on Linux 64
50:
51: Revision 1.166 2014/12/22 11:40:47 brouard
52: *** empty log message ***
53:
54: Revision 1.165 2014/12/16 11:20:36 brouard
55: Summary: After compiling on Visual C
56:
57: * imach.c (Module): Merging 1.61 to 1.162
58:
59: Revision 1.164 2014/12/16 10:52:11 brouard
60: Summary: Merging with Visual C after suppressing some warnings for unused variables. Also fixing Saito's bug 0.98Xn
61:
62: * imach.c (Module): Merging 1.61 to 1.162
63:
64: Revision 1.163 2014/12/16 10:30:11 brouard
65: * imach.c (Module): Merging 1.61 to 1.162
66:
67: Revision 1.162 2014/09/25 11:43:39 brouard
68: Summary: temporary backup 0.99!
69:
70: Revision 1.1 2014/09/16 11:06:58 brouard
71: Summary: With some code (wrong) for nlopt
72:
73: Author:
74:
75: Revision 1.161 2014/09/15 20:41:41 brouard
76: Summary: Problem with macro SQR on Intel compiler
77:
78: Revision 1.160 2014/09/02 09:24:05 brouard
79: *** empty log message ***
80:
81: Revision 1.159 2014/09/01 10:34:10 brouard
82: Summary: WIN32
83: Author: Brouard
84:
85: Revision 1.158 2014/08/27 17:11:51 brouard
86: *** empty log message ***
87:
88: Revision 1.157 2014/08/27 16:26:55 brouard
89: Summary: Preparing windows Visual studio version
90: Author: Brouard
91:
92: In order to compile on Visual studio, time.h is now correct and time_t
93: and tm struct should be used. difftime should be used but sometimes I
94: just make the differences in raw time format (time(&now).
95: Trying to suppress #ifdef LINUX
96: Add xdg-open for __linux in order to open default browser.
97:
98: Revision 1.156 2014/08/25 20:10:10 brouard
99: *** empty log message ***
100:
101: Revision 1.155 2014/08/25 18:32:34 brouard
102: Summary: New compile, minor changes
103: Author: Brouard
104:
105: Revision 1.154 2014/06/20 17:32:08 brouard
106: Summary: Outputs now all graphs of convergence to period prevalence
107:
108: Revision 1.153 2014/06/20 16:45:46 brouard
109: Summary: If 3 live state, convergence to period prevalence on same graph
110: Author: Brouard
111:
112: Revision 1.152 2014/06/18 17:54:09 brouard
113: Summary: open browser, use gnuplot on same dir than imach if not found in the path
114:
115: Revision 1.151 2014/06/18 16:43:30 brouard
116: *** empty log message ***
117:
118: Revision 1.150 2014/06/18 16:42:35 brouard
119: Summary: If gnuplot is not in the path try on same directory than imach binary (OSX)
120: Author: brouard
121:
122: Revision 1.149 2014/06/18 15:51:14 brouard
123: Summary: Some fixes in parameter files errors
124: Author: Nicolas Brouard
125:
126: Revision 1.148 2014/06/17 17:38:48 brouard
127: Summary: Nothing new
128: Author: Brouard
129:
130: Just a new packaging for OS/X version 0.98nS
131:
132: Revision 1.147 2014/06/16 10:33:11 brouard
133: *** empty log message ***
134:
135: Revision 1.146 2014/06/16 10:20:28 brouard
136: Summary: Merge
137: Author: Brouard
138:
139: Merge, before building revised version.
140:
141: Revision 1.145 2014/06/10 21:23:15 brouard
142: Summary: Debugging with valgrind
143: Author: Nicolas Brouard
144:
145: Lot of changes in order to output the results with some covariates
146: After the Edimburgh REVES conference 2014, it seems mandatory to
147: improve the code.
148: No more memory valgrind error but a lot has to be done in order to
149: continue the work of splitting the code into subroutines.
150: Also, decodemodel has been improved. Tricode is still not
151: optimal. nbcode should be improved. Documentation has been added in
152: the source code.
153:
154: Revision 1.143 2014/01/26 09:45:38 brouard
155: Summary: Version 0.98nR (to be improved, but gives same optimization results as 0.98k. Nice, promising
156:
157: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
158: (Module): Version 0.98nR Running ok, but output format still only works for three covariates.
159:
160: Revision 1.142 2014/01/26 03:57:36 brouard
161: Summary: gnuplot changed plot w l 1 has to be changed to plot w l lt 2
162:
163: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
164:
165: Revision 1.141 2014/01/26 02:42:01 brouard
166: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
167:
168: Revision 1.140 2011/09/02 10:37:54 brouard
169: Summary: times.h is ok with mingw32 now.
170:
171: Revision 1.139 2010/06/14 07:50:17 brouard
172: After the theft of my laptop, I probably lost some lines of codes which were not uploaded to the CVS tree.
173: I remember having already fixed agemin agemax which are pointers now but not cvs saved.
174:
175: Revision 1.138 2010/04/30 18:19:40 brouard
176: *** empty log message ***
177:
178: Revision 1.137 2010/04/29 18:11:38 brouard
179: (Module): Checking covariates for more complex models
180: than V1+V2. A lot of change to be done. Unstable.
181:
182: Revision 1.136 2010/04/26 20:30:53 brouard
183: (Module): merging some libgsl code. Fixing computation
184: of likelione (using inter/intrapolation if mle = 0) in order to
185: get same likelihood as if mle=1.
186: Some cleaning of code and comments added.
187:
188: Revision 1.135 2009/10/29 15:33:14 brouard
189: (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
190:
191: Revision 1.134 2009/10/29 13:18:53 brouard
192: (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
193:
194: Revision 1.133 2009/07/06 10:21:25 brouard
195: just nforces
196:
197: Revision 1.132 2009/07/06 08:22:05 brouard
198: Many tings
199:
200: Revision 1.131 2009/06/20 16:22:47 brouard
201: Some dimensions resccaled
202:
203: Revision 1.130 2009/05/26 06:44:34 brouard
204: (Module): Max Covariate is now set to 20 instead of 8. A
205: lot of cleaning with variables initialized to 0. Trying to make
206: V2+V3*age+V1+V4 strb=V3*age+V1+V4 working better.
207:
208: Revision 1.129 2007/08/31 13:49:27 lievre
209: Modification of the way of exiting when the covariate is not binary in order to see on the window the error message before exiting
210:
211: Revision 1.128 2006/06/30 13:02:05 brouard
212: (Module): Clarifications on computing e.j
213:
214: Revision 1.127 2006/04/28 18:11:50 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: (Module): In order to speed up (in case of numerous covariates) we
219: compute health expectancies (without variances) in a first step
220: and then all the health expectancies with variances or standard
221: deviation (needs data from the Hessian matrices) which slows the
222: computation.
223: In the future we should be able to stop the program is only health
224: expectancies and graph are needed without standard deviations.
225:
226: Revision 1.126 2006/04/28 17:23:28 brouard
227: (Module): Yes the sum of survivors was wrong since
228: imach-114 because nhstepm was no more computed in the age
229: loop. Now we define nhstepma in the age loop.
230: Version 0.98h
231:
232: Revision 1.125 2006/04/04 15:20:31 lievre
233: Errors in calculation of health expectancies. Age was not initialized.
234: Forecasting file added.
235:
236: Revision 1.124 2006/03/22 17:13:53 lievre
237: Parameters are printed with %lf instead of %f (more numbers after the comma).
238: The log-likelihood is printed in the log file
239:
240: Revision 1.123 2006/03/20 10:52:43 brouard
241: * imach.c (Module): <title> changed, corresponds to .htm file
242: name. <head> headers where missing.
243:
244: * imach.c (Module): Weights can have a decimal point as for
245: English (a comma might work with a correct LC_NUMERIC environment,
246: otherwise the weight is truncated).
247: Modification of warning when the covariates values are not 0 or
248: 1.
249: Version 0.98g
250:
251: Revision 1.122 2006/03/20 09:45:41 brouard
252: (Module): Weights can have a decimal point as for
253: English (a comma might work with a correct LC_NUMERIC environment,
254: otherwise the weight is truncated).
255: Modification of warning when the covariates values are not 0 or
256: 1.
257: Version 0.98g
258:
259: Revision 1.121 2006/03/16 17:45:01 lievre
260: * imach.c (Module): Comments concerning covariates added
261:
262: * imach.c (Module): refinements in the computation of lli if
263: status=-2 in order to have more reliable computation if stepm is
264: not 1 month. Version 0.98f
265:
266: Revision 1.120 2006/03/16 15:10:38 lievre
267: (Module): refinements in the computation of lli if
268: status=-2 in order to have more reliable computation if stepm is
269: not 1 month. Version 0.98f
270:
271: Revision 1.119 2006/03/15 17:42:26 brouard
272: (Module): Bug if status = -2, the loglikelihood was
273: computed as likelihood omitting the logarithm. Version O.98e
274:
275: Revision 1.118 2006/03/14 18:20:07 brouard
276: (Module): varevsij Comments added explaining the second
277: table of variances if popbased=1 .
278: (Module): Covariances of eij, ekl added, graphs fixed, new html link.
279: (Module): Function pstamp added
280: (Module): Version 0.98d
281:
282: Revision 1.117 2006/03/14 17:16:22 brouard
283: (Module): varevsij Comments added explaining the second
284: table of variances if popbased=1 .
285: (Module): Covariances of eij, ekl added, graphs fixed, new html link.
286: (Module): Function pstamp added
287: (Module): Version 0.98d
288:
289: Revision 1.116 2006/03/06 10:29:27 brouard
290: (Module): Variance-covariance wrong links and
291: varian-covariance of ej. is needed (Saito).
292:
293: Revision 1.115 2006/02/27 12:17:45 brouard
294: (Module): One freematrix added in mlikeli! 0.98c
295:
296: Revision 1.114 2006/02/26 12:57:58 brouard
297: (Module): Some improvements in processing parameter
298: filename with strsep.
299:
300: Revision 1.113 2006/02/24 14:20:24 brouard
301: (Module): Memory leaks checks with valgrind and:
302: datafile was not closed, some imatrix were not freed and on matrix
303: allocation too.
304:
305: Revision 1.112 2006/01/30 09:55:26 brouard
306: (Module): Back to gnuplot.exe instead of wgnuplot.exe
307:
308: Revision 1.111 2006/01/25 20:38:18 brouard
309: (Module): Lots of cleaning and bugs added (Gompertz)
310: (Module): Comments can be added in data file. Missing date values
311: can be a simple dot '.'.
312:
313: Revision 1.110 2006/01/25 00:51:50 brouard
314: (Module): Lots of cleaning and bugs added (Gompertz)
315:
316: Revision 1.109 2006/01/24 19:37:15 brouard
317: (Module): Comments (lines starting with a #) are allowed in data.
318:
319: Revision 1.108 2006/01/19 18:05:42 lievre
320: Gnuplot problem appeared...
321: To be fixed
322:
323: Revision 1.107 2006/01/19 16:20:37 brouard
324: Test existence of gnuplot in imach path
325:
326: Revision 1.106 2006/01/19 13:24:36 brouard
327: Some cleaning and links added in html output
328:
329: Revision 1.105 2006/01/05 20:23:19 lievre
330: *** empty log message ***
331:
332: Revision 1.104 2005/09/30 16:11:43 lievre
333: (Module): sump fixed, loop imx fixed, and simplifications.
334: (Module): If the status is missing at the last wave but we know
335: that the person is alive, then we can code his/her status as -2
336: (instead of missing=-1 in earlier versions) and his/her
337: contributions to the likelihood is 1 - Prob of dying from last
338: health status (= 1-p13= p11+p12 in the easiest case of somebody in
339: the healthy state at last known wave). Version is 0.98
340:
341: Revision 1.103 2005/09/30 15:54:49 lievre
342: (Module): sump fixed, loop imx fixed, and simplifications.
343:
344: Revision 1.102 2004/09/15 17:31:30 brouard
345: Add the possibility to read data file including tab characters.
346:
347: Revision 1.101 2004/09/15 10:38:38 brouard
348: Fix on curr_time
349:
350: Revision 1.100 2004/07/12 18:29:06 brouard
351: Add version for Mac OS X. Just define UNIX in Makefile
352:
353: Revision 1.99 2004/06/05 08:57:40 brouard
354: *** empty log message ***
355:
356: Revision 1.98 2004/05/16 15:05:56 brouard
357: New version 0.97 . First attempt to estimate force of mortality
358: directly from the data i.e. without the need of knowing the health
359: state at each age, but using a Gompertz model: log u =a + b*age .
360: This is the basic analysis of mortality and should be done before any
361: other analysis, in order to test if the mortality estimated from the
362: cross-longitudinal survey is different from the mortality estimated
363: from other sources like vital statistic data.
364:
365: The same imach parameter file can be used but the option for mle should be -3.
366:
367: Agnès, who wrote this part of the code, tried to keep most of the
368: former routines in order to include the new code within the former code.
369:
370: The output is very simple: only an estimate of the intercept and of
371: the slope with 95% confident intervals.
372:
373: Current limitations:
374: A) Even if you enter covariates, i.e. with the
375: model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
376: B) There is no computation of Life Expectancy nor Life Table.
377:
378: Revision 1.97 2004/02/20 13:25:42 lievre
379: Version 0.96d. Population forecasting command line is (temporarily)
380: suppressed.
381:
382: Revision 1.96 2003/07/15 15:38:55 brouard
383: * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
384: rewritten within the same printf. Workaround: many printfs.
385:
386: Revision 1.95 2003/07/08 07:54:34 brouard
387: * imach.c (Repository):
388: (Repository): Using imachwizard code to output a more meaningful covariance
389: matrix (cov(a12,c31) instead of numbers.
390:
391: Revision 1.94 2003/06/27 13:00:02 brouard
392: Just cleaning
393:
394: Revision 1.93 2003/06/25 16:33:55 brouard
395: (Module): On windows (cygwin) function asctime_r doesn't
396: exist so I changed back to asctime which exists.
397: (Module): Version 0.96b
398:
399: Revision 1.92 2003/06/25 16:30:45 brouard
400: (Module): On windows (cygwin) function asctime_r doesn't
401: exist so I changed back to asctime which exists.
402:
403: Revision 1.91 2003/06/25 15:30:29 brouard
404: * imach.c (Repository): Duplicated warning errors corrected.
405: (Repository): Elapsed time after each iteration is now output. It
406: helps to forecast when convergence will be reached. Elapsed time
407: is stamped in powell. We created a new html file for the graphs
408: concerning matrix of covariance. It has extension -cov.htm.
409:
410: Revision 1.90 2003/06/24 12:34:15 brouard
411: (Module): Some bugs corrected for windows. Also, when
412: mle=-1 a template is output in file "or"mypar.txt with the design
413: of the covariance matrix to be input.
414:
415: Revision 1.89 2003/06/24 12:30:52 brouard
416: (Module): Some bugs corrected for windows. Also, when
417: mle=-1 a template is output in file "or"mypar.txt with the design
418: of the covariance matrix to be input.
419:
420: Revision 1.88 2003/06/23 17:54:56 brouard
421: * 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.
422:
423: Revision 1.87 2003/06/18 12:26:01 brouard
424: Version 0.96
425:
426: Revision 1.86 2003/06/17 20:04:08 brouard
427: (Module): Change position of html and gnuplot routines and added
428: routine fileappend.
429:
430: Revision 1.85 2003/06/17 13:12:43 brouard
431: * imach.c (Repository): Check when date of death was earlier that
432: current date of interview. It may happen when the death was just
433: prior to the death. In this case, dh was negative and likelihood
434: was wrong (infinity). We still send an "Error" but patch by
435: assuming that the date of death was just one stepm after the
436: interview.
437: (Repository): Because some people have very long ID (first column)
438: we changed int to long in num[] and we added a new lvector for
439: memory allocation. But we also truncated to 8 characters (left
440: truncation)
441: (Repository): No more line truncation errors.
442:
443: Revision 1.84 2003/06/13 21:44:43 brouard
444: * imach.c (Repository): Replace "freqsummary" at a correct
445: place. It differs from routine "prevalence" which may be called
446: many times. Probs is memory consuming and must be used with
447: parcimony.
448: Version 0.95a3 (should output exactly the same maximization than 0.8a2)
449:
450: Revision 1.83 2003/06/10 13:39:11 lievre
451: *** empty log message ***
452:
453: Revision 1.82 2003/06/05 15:57:20 brouard
454: Add log in imach.c and fullversion number is now printed.
455:
456: */
457: /*
458: Interpolated Markov Chain
459:
460: Short summary of the programme:
461:
462: This program computes Healthy Life Expectancies from
463: cross-longitudinal data. Cross-longitudinal data consist in: -1- a
464: first survey ("cross") where individuals from different ages are
465: interviewed on their health status or degree of disability (in the
466: case of a health survey which is our main interest) -2- at least a
467: second wave of interviews ("longitudinal") which measure each change
468: (if any) in individual health status. Health expectancies are
469: computed from the time spent in each health state according to a
470: model. More health states you consider, more time is necessary to reach the
471: Maximum Likelihood of the parameters involved in the model. The
472: simplest model is the multinomial logistic model where pij is the
473: probability to be observed in state j at the second wave
474: conditional to be observed in state i at the first wave. Therefore
475: the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
476: 'age' is age and 'sex' is a covariate. If you want to have a more
477: complex model than "constant and age", you should modify the program
478: where the markup *Covariates have to be included here again* invites
479: you to do it. More covariates you add, slower the
480: convergence.
481:
482: The advantage of this computer programme, compared to a simple
483: multinomial logistic model, is clear when the delay between waves is not
484: identical for each individual. Also, if a individual missed an
485: intermediate interview, the information is lost, but taken into
486: account using an interpolation or extrapolation.
487:
488: hPijx is the probability to be observed in state i at age x+h
489: conditional to the observed state i at age x. The delay 'h' can be
490: split into an exact number (nh*stepm) of unobserved intermediate
491: states. This elementary transition (by month, quarter,
492: semester or year) is modelled as a multinomial logistic. The hPx
493: matrix is simply the matrix product of nh*stepm elementary matrices
494: and the contribution of each individual to the likelihood is simply
495: hPijx.
496:
497: Also this programme outputs the covariance matrix of the parameters but also
498: of the life expectancies. It also computes the period (stable) prevalence.
499:
500: Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
501: Institut national d'études démographiques, Paris.
502: This software have been partly granted by Euro-REVES, a concerted action
503: from the European Union.
504: It is copyrighted identically to a GNU software product, ie programme and
505: software can be distributed freely for non commercial use. Latest version
506: can be accessed at http://euroreves.ined.fr/imach .
507:
508: Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
509: or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
510:
511: **********************************************************************/
512: /*
513: main
514: read parameterfile
515: read datafile
516: concatwav
517: freqsummary
518: if (mle >= 1)
519: mlikeli
520: print results files
521: if mle==1
522: computes hessian
523: read end of parameter file: agemin, agemax, bage, fage, estepm
524: begin-prev-date,...
525: open gnuplot file
526: open html file
527: period (stable) prevalence | pl_nom 1-1 2-2 etc by covariate
528: for age prevalim() | #****** V1=0 V2=1 V3=1 V4=0 ******
529: | 65 1 0 2 1 3 1 4 0 0.96326 0.03674
530: freexexit2 possible for memory heap.
531:
532: h Pij x | pij_nom ficrestpij
533: # Cov Agex agex+h hpijx with i,j= 1-1 1-2 1-3 2-1 2-2 2-3
534: 1 85 85 1.00000 0.00000 0.00000 0.00000 1.00000 0.00000
535: 1 85 86 0.68299 0.22291 0.09410 0.71093 0.00000 0.28907
536:
537: 1 65 99 0.00364 0.00322 0.99314 0.00350 0.00310 0.99340
538: 1 65 100 0.00214 0.00204 0.99581 0.00206 0.00196 0.99597
539: variance of p one-step probabilities varprob | prob_nom ficresprob #One-step probabilities and stand. devi in ()
540: Standard deviation of one-step probabilities | probcor_nom ficresprobcor #One-step probabilities and correlation matrix
541: Matrix of variance covariance of one-step probabilities | probcov_nom ficresprobcov #One-step probabilities and covariance matrix
542:
543: forecasting if prevfcast==1 prevforecast call prevalence()
544: health expectancies
545: Variance-covariance of DFLE
546: prevalence()
547: movingaverage()
548: varevsij()
549: if popbased==1 varevsij(,popbased)
550: total life expectancies
551: Variance of period (stable) prevalence
552: end
553: */
554:
555: #define POWELL /* Instead of NLOPT */
556:
557: #include <math.h>
558: #include <stdio.h>
559: #include <stdlib.h>
560: #include <string.h>
561:
562: #ifdef _WIN32
563: #include <io.h>
564: #include <windows.h>
565: #include <tchar.h>
566: #else
567: #include <unistd.h>
568: #endif
569:
570: #include <limits.h>
571: #include <sys/types.h>
572:
573: #if defined(__GNUC__)
574: #include <sys/utsname.h> /* Doesn't work on Windows */
575: #endif
576:
577: #include <sys/stat.h>
578: #include <errno.h>
579: /* extern int errno; */
580:
581: /* #ifdef LINUX */
582: /* #include <time.h> */
583: /* #include "timeval.h" */
584: /* #else */
585: /* #include <sys/time.h> */
586: /* #endif */
587:
588: #include <time.h>
589:
590: #ifdef GSL
591: #include <gsl/gsl_errno.h>
592: #include <gsl/gsl_multimin.h>
593: #endif
594:
595:
596: #ifdef NLOPT
597: #include <nlopt.h>
598: typedef struct {
599: double (* function)(double [] );
600: } myfunc_data ;
601: #endif
602:
603: /* #include <libintl.h> */
604: /* #define _(String) gettext (String) */
605:
606: #define MAXLINE 1024 /* Was 256. Overflow with 312 with 2 states and 4 covariates. Should be ok */
607:
608: #define GNUPLOTPROGRAM "gnuplot"
609: /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
610: #define FILENAMELENGTH 132
611:
612: #define GLOCK_ERROR_NOPATH -1 /* empty path */
613: #define GLOCK_ERROR_GETCWD -2 /* cannot get cwd */
614:
615: #define MAXPARM 128 /**< Maximum number of parameters for the optimization */
616: #define NPARMAX 64 /**< (nlstate+ndeath-1)*nlstate*ncovmodel */
617:
618: #define NINTERVMAX 8
619: #define NLSTATEMAX 8 /**< Maximum number of live states (for func) */
620: #define NDEATHMAX 8 /**< Maximum number of dead states (for func) */
621: #define NCOVMAX 20 /**< Maximum number of covariates, including generated covariates V1*V2 */
622: #define codtabm(h,k) 1 & (h-1) >> (k-1) ;
623: #define MAXN 20000
624: #define YEARM 12. /**< Number of months per year */
625: #define AGESUP 130
626: #define AGEBASE 40
627: #define AGEGOMP 10 /**< Minimal age for Gompertz adjustment */
628: #ifdef _WIN32
629: #define DIRSEPARATOR '\\'
630: #define CHARSEPARATOR "\\"
631: #define ODIRSEPARATOR '/'
632: #else
633: #define DIRSEPARATOR '/'
634: #define CHARSEPARATOR "/"
635: #define ODIRSEPARATOR '\\'
636: #endif
637:
638: /* $Id: imach.c,v 1.179 2015/01/04 09:57:06 brouard Exp $ */
639: /* $State: Exp $ */
640:
641: 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";
642: char fullversion[]="$Revision: 1.179 $ $Date: 2015/01/04 09:57:06 $";
643: char strstart[80];
644: char optionfilext[10], optionfilefiname[FILENAMELENGTH];
645: int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings */
646: int nvar=0, nforce=0; /* Number of variables, number of forces */
647: /* Number of covariates model=V2+V1+ V3*age+V2*V4 */
648: int cptcovn=0; /**< cptcovn number of covariates added in the model (excepting constant and age and age*product) */
649: int cptcovt=0; /**< cptcovt number of covariates added in the model (excepting constant and age) */
650: int cptcovs=0; /**< cptcovs number of simple covariates V2+V1 =2 */
651: int cptcovage=0; /**< Number of covariates with age: V3*age only =1 */
652: int cptcovprodnoage=0; /**< Number of covariate products without age */
653: int cptcoveff=0; /* Total number of covariates to vary for printing results */
654: int cptcov=0; /* Working variable */
655: int npar=NPARMAX;
656: int nlstate=2; /* Number of live states */
657: int ndeath=1; /* Number of dead states */
658: int ncovmodel=0, ncovcol=0; /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
659: int popbased=0;
660:
661: int *wav; /* Number of waves for this individuual 0 is possible */
662: int maxwav=0; /* Maxim number of waves */
663: int jmin=0, jmax=0; /* min, max spacing between 2 waves */
664: int ijmin=0, ijmax=0; /* Individuals having jmin and jmax */
665: int gipmx=0, gsw=0; /* Global variables on the number of contributions
666: to the likelihood and the sum of weights (done by funcone)*/
667: int mle=1, weightopt=0;
668: int **mw; /* mw[mi][i] is number of the mi wave for this individual */
669: int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
670: int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
671: * wave mi and wave mi+1 is not an exact multiple of stepm. */
672: int countcallfunc=0; /* Count the number of calls to func */
673: double jmean=1; /* Mean space between 2 waves */
674: double **matprod2(); /* test */
675: double **oldm, **newm, **savm; /* Working pointers to matrices */
676: double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
677: /*FILE *fic ; */ /* Used in readdata only */
678: FILE *ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
679: FILE *ficlog, *ficrespow;
680: int globpr=0; /* Global variable for printing or not */
681: double fretone; /* Only one call to likelihood */
682: long ipmx=0; /* Number of contributions */
683: double sw; /* Sum of weights */
684: char filerespow[FILENAMELENGTH];
685: char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
686: FILE *ficresilk;
687: FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
688: FILE *ficresprobmorprev;
689: FILE *fichtm, *fichtmcov; /* Html File */
690: FILE *ficreseij;
691: char filerese[FILENAMELENGTH];
692: FILE *ficresstdeij;
693: char fileresstde[FILENAMELENGTH];
694: FILE *ficrescveij;
695: char filerescve[FILENAMELENGTH];
696: FILE *ficresvij;
697: char fileresv[FILENAMELENGTH];
698: FILE *ficresvpl;
699: char fileresvpl[FILENAMELENGTH];
700: char title[MAXLINE];
701: char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH], filerespl[FILENAMELENGTH];
702: char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
703: char tmpout[FILENAMELENGTH], tmpout2[FILENAMELENGTH];
704: char command[FILENAMELENGTH];
705: int outcmd=0;
706:
707: char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
708:
709: char filelog[FILENAMELENGTH]; /* Log file */
710: char filerest[FILENAMELENGTH];
711: char fileregp[FILENAMELENGTH];
712: char popfile[FILENAMELENGTH];
713:
714: char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
715:
716: /* struct timeval start_time, end_time, curr_time, last_time, forecast_time; */
717: /* struct timezone tzp; */
718: /* extern int gettimeofday(); */
719: struct tm tml, *gmtime(), *localtime();
720:
721: extern time_t time();
722:
723: struct tm start_time, end_time, curr_time, last_time, forecast_time;
724: time_t rstart_time, rend_time, rcurr_time, rlast_time, rforecast_time; /* raw time */
725: struct tm tm;
726:
727: char strcurr[80], strfor[80];
728:
729: char *endptr;
730: long lval;
731: double dval;
732:
733: #define NR_END 1
734: #define FREE_ARG char*
735: #define FTOL 1.0e-10
736:
737: #define NRANSI
738: #define ITMAX 200
739:
740: #define TOL 2.0e-4
741:
742: #define CGOLD 0.3819660
743: #define ZEPS 1.0e-10
744: #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);
745:
746: #define GOLD 1.618034
747: #define GLIMIT 100.0
748: #define TINY 1.0e-20
749:
750: static double maxarg1,maxarg2;
751: #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
752: #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
753:
754: #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
755: #define rint(a) floor(a+0.5)
756: /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/myutils_8h-source.html */
757: /* #define mytinydouble 1.0e-16 */
758: /* #define DEQUAL(a,b) (fabs((a)-(b))<mytinydouble) */
759: /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/mynrutils_8h-source.html */
760: /* static double dsqrarg; */
761: /* #define DSQR(a) (DEQUAL((dsqrarg=(a)),0.0) ? 0.0 : dsqrarg*dsqrarg) */
762: static double sqrarg;
763: #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
764: #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}
765: int agegomp= AGEGOMP;
766:
767: int imx;
768: int stepm=1;
769: /* Stepm, step in month: minimum step interpolation*/
770:
771: int estepm;
772: /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
773:
774: int m,nb;
775: long *num;
776: int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
777: double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
778: double **pmmij, ***probs;
779: double *ageexmed,*agecens;
780: double dateintmean=0;
781:
782: double *weight;
783: int **s; /* Status */
784: double *agedc;
785: double **covar; /**< covar[j,i], value of jth covariate for individual i,
786: * covar=matrix(0,NCOVMAX,1,n);
787: * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; */
788: double idx;
789: int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */
790: int *Ndum; /** Freq of modality (tricode */
791: int **codtab; /**< codtab=imatrix(1,100,1,10); */
792: int **Tvard, *Tprod, cptcovprod, *Tvaraff;
793: double *lsurv, *lpop, *tpop;
794:
795: double ftol=FTOL; /**< Tolerance for computing Max Likelihood */
796: double ftolhess; /**< Tolerance for computing hessian */
797:
798: /**************** split *************************/
799: static int split( char *path, char *dirc, char *name, char *ext, char *finame )
800: {
801: /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
802: the name of the file (name), its extension only (ext) and its first part of the name (finame)
803: */
804: char *ss; /* pointer */
805: int l1, l2; /* length counters */
806:
807: l1 = strlen(path ); /* length of path */
808: if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
809: ss= strrchr( path, DIRSEPARATOR ); /* find last / */
810: if ( ss == NULL ) { /* no directory, so determine current directory */
811: strcpy( name, path ); /* we got the fullname name because no directory */
812: /*if(strrchr(path, ODIRSEPARATOR )==NULL)
813: printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
814: /* get current working directory */
815: /* extern char* getcwd ( char *buf , int len);*/
816: if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
817: return( GLOCK_ERROR_GETCWD );
818: }
819: /* got dirc from getcwd*/
820: printf(" DIRC = %s \n",dirc);
821: } else { /* strip direcotry from path */
822: ss++; /* after this, the filename */
823: l2 = strlen( ss ); /* length of filename */
824: if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
825: strcpy( name, ss ); /* save file name */
826: strncpy( dirc, path, l1 - l2 ); /* now the directory */
827: dirc[l1-l2] = 0; /* add zero */
828: printf(" DIRC2 = %s \n",dirc);
829: }
830: /* We add a separator at the end of dirc if not exists */
831: l1 = strlen( dirc ); /* length of directory */
832: if( dirc[l1-1] != DIRSEPARATOR ){
833: dirc[l1] = DIRSEPARATOR;
834: dirc[l1+1] = 0;
835: printf(" DIRC3 = %s \n",dirc);
836: }
837: ss = strrchr( name, '.' ); /* find last / */
838: if (ss >0){
839: ss++;
840: strcpy(ext,ss); /* save extension */
841: l1= strlen( name);
842: l2= strlen(ss)+1;
843: strncpy( finame, name, l1-l2);
844: finame[l1-l2]= 0;
845: }
846:
847: return( 0 ); /* we're done */
848: }
849:
850:
851: /******************************************/
852:
853: void replace_back_to_slash(char *s, char*t)
854: {
855: int i;
856: int lg=0;
857: i=0;
858: lg=strlen(t);
859: for(i=0; i<= lg; i++) {
860: (s[i] = t[i]);
861: if (t[i]== '\\') s[i]='/';
862: }
863: }
864:
865: char *trimbb(char *out, char *in)
866: { /* Trim multiple blanks in line but keeps first blanks if line starts with blanks */
867: char *s;
868: s=out;
869: while (*in != '\0'){
870: while( *in == ' ' && *(in+1) == ' '){ /* && *(in+1) != '\0'){*/
871: in++;
872: }
873: *out++ = *in++;
874: }
875: *out='\0';
876: return s;
877: }
878:
879: char *cutl(char *blocc, char *alocc, char *in, char occ)
880: {
881: /* cuts string in into blocc and alocc where blocc ends before first occurence of char 'occ'
882: and alocc starts after first occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
883: gives blocc="abcdef2ghi" and alocc="j".
884: If occ is not found blocc is null and alocc is equal to in. Returns blocc
885: */
886: char *s, *t;
887: t=in;s=in;
888: while ((*in != occ) && (*in != '\0')){
889: *alocc++ = *in++;
890: }
891: if( *in == occ){
892: *(alocc)='\0';
893: s=++in;
894: }
895:
896: if (s == t) {/* occ not found */
897: *(alocc-(in-s))='\0';
898: in=s;
899: }
900: while ( *in != '\0'){
901: *blocc++ = *in++;
902: }
903:
904: *blocc='\0';
905: return t;
906: }
907: char *cutv(char *blocc, char *alocc, char *in, char occ)
908: {
909: /* cuts string in into blocc and alocc where blocc ends before last occurence of char 'occ'
910: and alocc starts after last occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
911: gives blocc="abcdef2ghi" and alocc="j".
912: If occ is not found blocc is null and alocc is equal to in. Returns alocc
913: */
914: char *s, *t;
915: t=in;s=in;
916: while (*in != '\0'){
917: while( *in == occ){
918: *blocc++ = *in++;
919: s=in;
920: }
921: *blocc++ = *in++;
922: }
923: if (s == t) /* occ not found */
924: *(blocc-(in-s))='\0';
925: else
926: *(blocc-(in-s)-1)='\0';
927: in=s;
928: while ( *in != '\0'){
929: *alocc++ = *in++;
930: }
931:
932: *alocc='\0';
933: return s;
934: }
935:
936: int nbocc(char *s, char occ)
937: {
938: int i,j=0;
939: int lg=20;
940: i=0;
941: lg=strlen(s);
942: for(i=0; i<= lg; i++) {
943: if (s[i] == occ ) j++;
944: }
945: return j;
946: }
947:
948: /* void cutv(char *u,char *v, char*t, char occ) */
949: /* { */
950: /* /\* cuts string t into u and v where u ends before last occurence of char 'occ' */
951: /* and v starts after last occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2') */
952: /* gives u="abcdef2ghi" and v="j" *\/ */
953: /* int i,lg,j,p=0; */
954: /* i=0; */
955: /* lg=strlen(t); */
956: /* for(j=0; j<=lg-1; j++) { */
957: /* if((t[j]!= occ) && (t[j+1]== occ)) p=j+1; */
958: /* } */
959:
960: /* for(j=0; j<p; j++) { */
961: /* (u[j] = t[j]); */
962: /* } */
963: /* u[p]='\0'; */
964:
965: /* for(j=0; j<= lg; j++) { */
966: /* if (j>=(p+1))(v[j-p-1] = t[j]); */
967: /* } */
968: /* } */
969:
970: #ifdef _WIN32
971: char * strsep(char **pp, const char *delim)
972: {
973: char *p, *q;
974:
975: if ((p = *pp) == NULL)
976: return 0;
977: if ((q = strpbrk (p, delim)) != NULL)
978: {
979: *pp = q + 1;
980: *q = '\0';
981: }
982: else
983: *pp = 0;
984: return p;
985: }
986: #endif
987:
988: /********************** nrerror ********************/
989:
990: void nrerror(char error_text[])
991: {
992: fprintf(stderr,"ERREUR ...\n");
993: fprintf(stderr,"%s\n",error_text);
994: exit(EXIT_FAILURE);
995: }
996: /*********************** vector *******************/
997: double *vector(int nl, int nh)
998: {
999: double *v;
1000: v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
1001: if (!v) nrerror("allocation failure in vector");
1002: return v-nl+NR_END;
1003: }
1004:
1005: /************************ free vector ******************/
1006: void free_vector(double*v, int nl, int nh)
1007: {
1008: free((FREE_ARG)(v+nl-NR_END));
1009: }
1010:
1011: /************************ivector *******************************/
1012: int *ivector(long nl,long nh)
1013: {
1014: int *v;
1015: v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
1016: if (!v) nrerror("allocation failure in ivector");
1017: return v-nl+NR_END;
1018: }
1019:
1020: /******************free ivector **************************/
1021: void free_ivector(int *v, long nl, long nh)
1022: {
1023: free((FREE_ARG)(v+nl-NR_END));
1024: }
1025:
1026: /************************lvector *******************************/
1027: long *lvector(long nl,long nh)
1028: {
1029: long *v;
1030: v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
1031: if (!v) nrerror("allocation failure in ivector");
1032: return v-nl+NR_END;
1033: }
1034:
1035: /******************free lvector **************************/
1036: void free_lvector(long *v, long nl, long nh)
1037: {
1038: free((FREE_ARG)(v+nl-NR_END));
1039: }
1040:
1041: /******************* imatrix *******************************/
1042: int **imatrix(long nrl, long nrh, long ncl, long nch)
1043: /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */
1044: {
1045: long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;
1046: int **m;
1047:
1048: /* allocate pointers to rows */
1049: m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));
1050: if (!m) nrerror("allocation failure 1 in matrix()");
1051: m += NR_END;
1052: m -= nrl;
1053:
1054:
1055: /* allocate rows and set pointers to them */
1056: m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));
1057: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
1058: m[nrl] += NR_END;
1059: m[nrl] -= ncl;
1060:
1061: for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;
1062:
1063: /* return pointer to array of pointers to rows */
1064: return m;
1065: }
1066:
1067: /****************** free_imatrix *************************/
1068: void free_imatrix(m,nrl,nrh,ncl,nch)
1069: int **m;
1070: long nch,ncl,nrh,nrl;
1071: /* free an int matrix allocated by imatrix() */
1072: {
1073: free((FREE_ARG) (m[nrl]+ncl-NR_END));
1074: free((FREE_ARG) (m+nrl-NR_END));
1075: }
1076:
1077: /******************* matrix *******************************/
1078: double **matrix(long nrl, long nrh, long ncl, long nch)
1079: {
1080: long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
1081: double **m;
1082:
1083: m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
1084: if (!m) nrerror("allocation failure 1 in matrix()");
1085: m += NR_END;
1086: m -= nrl;
1087:
1088: m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
1089: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
1090: m[nrl] += NR_END;
1091: m[nrl] -= ncl;
1092:
1093: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
1094: return m;
1095: /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) or &(m[1][0])
1096: m[i] = address of ith row of the table. &(m[i]) is its value which is another adress
1097: that of m[i][0]. In order to get the value p m[i][0] but it is unitialized.
1098: */
1099: }
1100:
1101: /*************************free matrix ************************/
1102: void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
1103: {
1104: free((FREE_ARG)(m[nrl]+ncl-NR_END));
1105: free((FREE_ARG)(m+nrl-NR_END));
1106: }
1107:
1108: /******************* ma3x *******************************/
1109: double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
1110: {
1111: long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
1112: double ***m;
1113:
1114: m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
1115: if (!m) nrerror("allocation failure 1 in matrix()");
1116: m += NR_END;
1117: m -= nrl;
1118:
1119: m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
1120: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
1121: m[nrl] += NR_END;
1122: m[nrl] -= ncl;
1123:
1124: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
1125:
1126: m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
1127: if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
1128: m[nrl][ncl] += NR_END;
1129: m[nrl][ncl] -= nll;
1130: for (j=ncl+1; j<=nch; j++)
1131: m[nrl][j]=m[nrl][j-1]+nlay;
1132:
1133: for (i=nrl+1; i<=nrh; i++) {
1134: m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
1135: for (j=ncl+1; j<=nch; j++)
1136: m[i][j]=m[i][j-1]+nlay;
1137: }
1138: return m;
1139: /* gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
1140: &(m[i][j][k]) <=> *((*(m+i) + j)+k)
1141: */
1142: }
1143:
1144: /*************************free ma3x ************************/
1145: void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
1146: {
1147: free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
1148: free((FREE_ARG)(m[nrl]+ncl-NR_END));
1149: free((FREE_ARG)(m+nrl-NR_END));
1150: }
1151:
1152: /*************** function subdirf ***********/
1153: char *subdirf(char fileres[])
1154: {
1155: /* Caution optionfilefiname is hidden */
1156: strcpy(tmpout,optionfilefiname);
1157: strcat(tmpout,"/"); /* Add to the right */
1158: strcat(tmpout,fileres);
1159: return tmpout;
1160: }
1161:
1162: /*************** function subdirf2 ***********/
1163: char *subdirf2(char fileres[], char *preop)
1164: {
1165:
1166: /* Caution optionfilefiname is hidden */
1167: strcpy(tmpout,optionfilefiname);
1168: strcat(tmpout,"/");
1169: strcat(tmpout,preop);
1170: strcat(tmpout,fileres);
1171: return tmpout;
1172: }
1173:
1174: /*************** function subdirf3 ***********/
1175: char *subdirf3(char fileres[], char *preop, char *preop2)
1176: {
1177:
1178: /* Caution optionfilefiname is hidden */
1179: strcpy(tmpout,optionfilefiname);
1180: strcat(tmpout,"/");
1181: strcat(tmpout,preop);
1182: strcat(tmpout,preop2);
1183: strcat(tmpout,fileres);
1184: return tmpout;
1185: }
1186:
1187: char *asc_diff_time(long time_sec, char ascdiff[])
1188: {
1189: long sec_left, days, hours, minutes;
1190: days = (time_sec) / (60*60*24);
1191: sec_left = (time_sec) % (60*60*24);
1192: hours = (sec_left) / (60*60) ;
1193: sec_left = (sec_left) %(60*60);
1194: minutes = (sec_left) /60;
1195: sec_left = (sec_left) % (60);
1196: sprintf(ascdiff,"%ld day(s) %ld hour(s) %ld minute(s) %ld second(s)",days, hours, minutes, sec_left);
1197: return ascdiff;
1198: }
1199:
1200: /***************** f1dim *************************/
1201: extern int ncom;
1202: extern double *pcom,*xicom;
1203: extern double (*nrfunc)(double []);
1204:
1205: double f1dim(double x)
1206: {
1207: int j;
1208: double f;
1209: double *xt;
1210:
1211: xt=vector(1,ncom);
1212: for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];
1213: f=(*nrfunc)(xt);
1214: free_vector(xt,1,ncom);
1215: return f;
1216: }
1217:
1218: /*****************brent *************************/
1219: double brent(double ax, double bx, double cx, double (*f)(double), double tol, double *xmin)
1220: {
1221: int iter;
1222: double a,b,d,etemp;
1223: double fu=0,fv,fw,fx;
1224: double ftemp=0.;
1225: double p,q,r,tol1,tol2,u,v,w,x,xm;
1226: double e=0.0;
1227:
1228: a=(ax < cx ? ax : cx);
1229: b=(ax > cx ? ax : cx);
1230: x=w=v=bx;
1231: fw=fv=fx=(*f)(x);
1232: for (iter=1;iter<=ITMAX;iter++) {
1233: xm=0.5*(a+b);
1234: tol2=2.0*(tol1=tol*fabs(x)+ZEPS);
1235: /* if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
1236: printf(".");fflush(stdout);
1237: fprintf(ficlog,".");fflush(ficlog);
1238: #ifdef DEBUGBRENT
1239: 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);
1240: 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);
1241: /* if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
1242: #endif
1243: if (fabs(x-xm) <= (tol2-0.5*(b-a))){
1244: *xmin=x;
1245: return fx;
1246: }
1247: ftemp=fu;
1248: if (fabs(e) > tol1) {
1249: r=(x-w)*(fx-fv);
1250: q=(x-v)*(fx-fw);
1251: p=(x-v)*q-(x-w)*r;
1252: q=2.0*(q-r);
1253: if (q > 0.0) p = -p;
1254: q=fabs(q);
1255: etemp=e;
1256: e=d;
1257: if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))
1258: d=CGOLD*(e=(x >= xm ? a-x : b-x));
1259: else {
1260: d=p/q;
1261: u=x+d;
1262: if (u-a < tol2 || b-u < tol2)
1263: d=SIGN(tol1,xm-x);
1264: }
1265: } else {
1266: d=CGOLD*(e=(x >= xm ? a-x : b-x));
1267: }
1268: u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));
1269: fu=(*f)(u);
1270: if (fu <= fx) {
1271: if (u >= x) a=x; else b=x;
1272: SHFT(v,w,x,u)
1273: SHFT(fv,fw,fx,fu)
1274: } else {
1275: if (u < x) a=u; else b=u;
1276: if (fu <= fw || w == x) {
1277: v=w;
1278: w=u;
1279: fv=fw;
1280: fw=fu;
1281: } else if (fu <= fv || v == x || v == w) {
1282: v=u;
1283: fv=fu;
1284: }
1285: }
1286: }
1287: nrerror("Too many iterations in brent");
1288: *xmin=x;
1289: return fx;
1290: }
1291:
1292: /****************** mnbrak ***********************/
1293:
1294: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,
1295: double (*func)(double))
1296: {
1297: double ulim,u,r,q, dum;
1298: double fu;
1299:
1300: *fa=(*func)(*ax);
1301: *fb=(*func)(*bx);
1302: if (*fb > *fa) {
1303: SHFT(dum,*ax,*bx,dum)
1304: SHFT(dum,*fb,*fa,dum)
1305: }
1306: *cx=(*bx)+GOLD*(*bx-*ax);
1307: *fc=(*func)(*cx);
1308: while (*fb > *fc) { /* Declining fa, fb, fc */
1309: r=(*bx-*ax)*(*fb-*fc);
1310: q=(*bx-*cx)*(*fb-*fa);
1311: u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/
1312: (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); /* Minimum abscisse of a parabolic estimated from (a,fa), (b,fb) and (c,fc). */
1313: ulim=(*bx)+GLIMIT*(*cx-*bx); /* Maximum abscisse where function can be evaluated */
1314: if ((*bx-u)*(u-*cx) > 0.0) { /* if u between b and c */
1315: fu=(*func)(u);
1316: #ifdef DEBUG
1317: /* f(x)=A(x-u)**2+f(u) */
1318: double A, fparabu;
1319: A= (*fb - *fa)/(*bx-*ax)/(*bx+*ax-2*u);
1320: fparabu= *fa - A*(*ax-u)*(*ax-u);
1321: 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);
1322: 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);
1323: #endif
1324: } else if ((*cx-u)*(u-ulim) > 0.0) { /* u is after c but before ulim */
1325: fu=(*func)(u);
1326: if (fu < *fc) {
1327: SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))
1328: SHFT(*fb,*fc,fu,(*func)(u))
1329: }
1330: } else if ((u-ulim)*(ulim-*cx) >= 0.0) { /* u outside ulim (verifying that ulim is beyond c) */
1331: u=ulim;
1332: fu=(*func)(u);
1333: } else {
1334: u=(*cx)+GOLD*(*cx-*bx);
1335: fu=(*func)(u);
1336: }
1337: SHFT(*ax,*bx,*cx,u)
1338: SHFT(*fa,*fb,*fc,fu)
1339: }
1340: }
1341:
1342: /*************** linmin ************************/
1343: /* Given an n -dimensional point p[1..n] and an n -dimensional direction xi[1..n] , moves and
1344: resets p to where the function func(p) takes on a minimum along the direction xi from p ,
1345: and replaces xi by the actual vector displacement that p was moved. Also returns as fret
1346: the value of func at the returned location p . This is actually all accomplished by calling the
1347: routines mnbrak and brent .*/
1348: int ncom;
1349: double *pcom,*xicom;
1350: double (*nrfunc)(double []);
1351:
1352: void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))
1353: {
1354: double brent(double ax, double bx, double cx,
1355: double (*f)(double), double tol, double *xmin);
1356: double f1dim(double x);
1357: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,
1358: double *fc, double (*func)(double));
1359: int j;
1360: double xx,xmin,bx,ax;
1361: double fx,fb,fa;
1362:
1363: ncom=n;
1364: pcom=vector(1,n);
1365: xicom=vector(1,n);
1366: nrfunc=func;
1367: for (j=1;j<=n;j++) {
1368: pcom[j]=p[j];
1369: xicom[j]=xi[j];
1370: }
1371: ax=0.0;
1372: xx=1.0;
1373: mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); /* Find a bracket a,x,b in direction n=xi ie xicom */
1374: *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); /* Find a minimum P+lambda n in that direction (lambdamin), with TOL between abscisses */
1375: #ifdef DEBUG
1376: printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
1377: fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
1378: #endif
1379: for (j=1;j<=n;j++) {
1380: xi[j] *= xmin;
1381: p[j] += xi[j];
1382: }
1383: free_vector(xicom,1,n);
1384: free_vector(pcom,1,n);
1385: }
1386:
1387:
1388: /*************** powell ************************/
1389: /*
1390: Minimization of a function func of n variables. Input consists of an initial starting point
1391: p[1..n] ; an initial matrix xi[1..n][1..n] , whose columns contain the initial set of di-
1392: rections (usually the n unit vectors); and ftol , the fractional tolerance in the function value
1393: such that failure to decrease by more than this amount on one iteration signals doneness. On
1394: output, p is set to the best point found, xi is the then-current direction set, fret is the returned
1395: function value at p , and iter is the number of iterations taken. The routine linmin is used.
1396: */
1397: void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,
1398: double (*func)(double []))
1399: {
1400: void linmin(double p[], double xi[], int n, double *fret,
1401: double (*func)(double []));
1402: int i,ibig,j;
1403: double del,t,*pt,*ptt,*xit;
1404: double fp,fptt;
1405: double *xits;
1406: int niterf, itmp;
1407:
1408: pt=vector(1,n);
1409: ptt=vector(1,n);
1410: xit=vector(1,n);
1411: xits=vector(1,n);
1412: *fret=(*func)(p);
1413: for (j=1;j<=n;j++) pt[j]=p[j];
1414: rcurr_time = time(NULL);
1415: for (*iter=1;;++(*iter)) {
1416: fp=(*fret);
1417: ibig=0;
1418: del=0.0;
1419: rlast_time=rcurr_time;
1420: /* (void) gettimeofday(&curr_time,&tzp); */
1421: rcurr_time = time(NULL);
1422: curr_time = *localtime(&rcurr_time);
1423: printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, rcurr_time-rlast_time, rcurr_time-rstart_time);fflush(stdout);
1424: fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret,rcurr_time-rlast_time, rcurr_time-rstart_time); fflush(ficlog);
1425: /* fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tm_sec-start_time.tm_sec); */
1426: for (i=1;i<=n;i++) {
1427: printf(" %d %.12f",i, p[i]);
1428: fprintf(ficlog," %d %.12lf",i, p[i]);
1429: fprintf(ficrespow," %.12lf", p[i]);
1430: }
1431: printf("\n");
1432: fprintf(ficlog,"\n");
1433: fprintf(ficrespow,"\n");fflush(ficrespow);
1434: if(*iter <=3){
1435: tml = *localtime(&rcurr_time);
1436: strcpy(strcurr,asctime(&tml));
1437: rforecast_time=rcurr_time;
1438: itmp = strlen(strcurr);
1439: if(strcurr[itmp-1]=='\n') /* Windows outputs with a new line */
1440: strcurr[itmp-1]='\0';
1441: printf("\nConsidering the time needed for the last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
1442: fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
1443: for(niterf=10;niterf<=30;niterf+=10){
1444: rforecast_time=rcurr_time+(niterf-*iter)*(rcurr_time-rlast_time);
1445: forecast_time = *localtime(&rforecast_time);
1446: strcpy(strfor,asctime(&forecast_time));
1447: itmp = strlen(strfor);
1448: if(strfor[itmp-1]=='\n')
1449: strfor[itmp-1]='\0';
1450: 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);
1451: 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);
1452: }
1453: }
1454: for (i=1;i<=n;i++) {
1455: for (j=1;j<=n;j++) xit[j]=xi[j][i];
1456: fptt=(*fret);
1457: #ifdef DEBUG
1458: printf("fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
1459: fprintf(ficlog, "fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
1460: #endif
1461: printf("%d",i);fflush(stdout);
1462: fprintf(ficlog,"%d",i);fflush(ficlog);
1463: linmin(p,xit,n,fret,func);
1464: if (fabs(fptt-(*fret)) > del) {
1465: del=fabs(fptt-(*fret));
1466: ibig=i;
1467: }
1468: #ifdef DEBUG
1469: printf("%d %.12e",i,(*fret));
1470: fprintf(ficlog,"%d %.12e",i,(*fret));
1471: for (j=1;j<=n;j++) {
1472: xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
1473: printf(" x(%d)=%.12e",j,xit[j]);
1474: fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
1475: }
1476: for(j=1;j<=n;j++) {
1477: printf(" p(%d)=%.12e",j,p[j]);
1478: fprintf(ficlog," p(%d)=%.12e",j,p[j]);
1479: }
1480: printf("\n");
1481: fprintf(ficlog,"\n");
1482: #endif
1483: } /* end i */
1484: if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
1485: #ifdef DEBUG
1486: int k[2],l;
1487: k[0]=1;
1488: k[1]=-1;
1489: printf("Max: %.12e",(*func)(p));
1490: fprintf(ficlog,"Max: %.12e",(*func)(p));
1491: for (j=1;j<=n;j++) {
1492: printf(" %.12e",p[j]);
1493: fprintf(ficlog," %.12e",p[j]);
1494: }
1495: printf("\n");
1496: fprintf(ficlog,"\n");
1497: for(l=0;l<=1;l++) {
1498: for (j=1;j<=n;j++) {
1499: ptt[j]=p[j]+(p[j]-pt[j])*k[l];
1500: printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
1501: fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
1502: }
1503: printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
1504: fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
1505: }
1506: #endif
1507:
1508:
1509: free_vector(xit,1,n);
1510: free_vector(xits,1,n);
1511: free_vector(ptt,1,n);
1512: free_vector(pt,1,n);
1513: return;
1514: }
1515: if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");
1516: for (j=1;j<=n;j++) { /* Computes an extrapolated point */
1517: ptt[j]=2.0*p[j]-pt[j];
1518: xit[j]=p[j]-pt[j];
1519: pt[j]=p[j];
1520: }
1521: fptt=(*func)(ptt);
1522: if (fptt < fp) { /* If extrapolated point is better, decide if we keep that new direction or not */
1523: /* (x1 f1=fp), (x2 f2=*fret), (x3 f3=fptt), (xm fm) */
1524: /* From x1 (P0) distance of x2 is at h and x3 is 2h */
1525: /* Let f"(x2) be the 2nd derivative equal everywhere. */
1526: /* Then the parabolic through (x1,f1), (x2,f2) and (x3,f3) */
1527: /* will reach at f3 = fm + h^2/2 f"m ; f" = (f1 -2f2 +f3 ) / h**2 */
1528: /* f1-f3 = delta(2h) = 2 h**2 f'' = 2(f1- 2f2 +f3) */
1529: /* Thus we compare delta(2h) with observed f1-f3 */
1530: /* or best gain on one ancient line 'del' with total */
1531: /* gain f1-f2 = f1 - f2 - 'del' with del */
1532: /* t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); */
1533:
1534: t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del);
1535: t= t- del*SQR(fp-fptt);
1536: printf("t1= %.12lf, t2= %.12lf, t=%.12lf\n", 2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del),del*SQR(fp-fptt),t);
1537: 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);
1538: #ifdef DEBUG
1539: printf("t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
1540: (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
1541: fprintf(ficlog,"t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
1542: (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
1543: 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);
1544: 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);
1545: #endif
1546: if (t < 0.0) { /* Then we use it for last direction */
1547: linmin(p,xit,n,fret,func); /* computes mean on the extrapolated direction.*/
1548: for (j=1;j<=n;j++) {
1549: xi[j][ibig]=xi[j][n]; /* Replace the direction with biggest decrease by n */
1550: xi[j][n]=xit[j]; /* and nth direction by the extrapolated */
1551: }
1552: printf("Gaining to use average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
1553: fprintf(ficlog,"Gaining to use average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
1554:
1555: #ifdef DEBUG
1556: printf("Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
1557: fprintf(ficlog,"Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
1558: for(j=1;j<=n;j++){
1559: printf(" %.12e",xit[j]);
1560: fprintf(ficlog," %.12e",xit[j]);
1561: }
1562: printf("\n");
1563: fprintf(ficlog,"\n");
1564: #endif
1565: } /* end of t negative */
1566: } /* end if (fptt < fp) */
1567: }
1568: }
1569:
1570: /**** Prevalence limit (stable or period prevalence) ****************/
1571:
1572: double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
1573: {
1574: /* Computes the prevalence limit in each live state at age x by left multiplying the unit
1575: matrix by transitions matrix until convergence is reached */
1576:
1577: int i, ii,j,k;
1578: double min, max, maxmin, maxmax,sumnew=0.;
1579: /* double **matprod2(); */ /* test */
1580: double **out, cov[NCOVMAX+1], **pmij();
1581: double **newm;
1582: double agefin, delaymax=50 ; /* Max number of years to converge */
1583:
1584: for (ii=1;ii<=nlstate+ndeath;ii++)
1585: for (j=1;j<=nlstate+ndeath;j++){
1586: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1587: }
1588:
1589: cov[1]=1.;
1590:
1591: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
1592: for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
1593: newm=savm;
1594: /* Covariates have to be included here again */
1595: cov[2]=agefin;
1596:
1597: for (k=1; k<=cptcovn;k++) {
1598: cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
1599: /*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]]);*/
1600: }
1601: /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
1602: /* for (k=1; k<=cptcovprod;k++) /\* Useless *\/ */
1603: /* cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]] * nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]]; */
1604:
1605: /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
1606: /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
1607: /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
1608: /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
1609: /* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind *\/ */
1610: out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /* Bug Valgrind */
1611:
1612: savm=oldm;
1613: oldm=newm;
1614: maxmax=0.;
1615: for(j=1;j<=nlstate;j++){
1616: min=1.;
1617: max=0.;
1618: for(i=1; i<=nlstate; i++) {
1619: sumnew=0;
1620: for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
1621: prlim[i][j]= newm[i][j]/(1-sumnew);
1622: /*printf(" prevalim i=%d, j=%d, prmlim[%d][%d]=%f, agefin=%d \n", i, j, i, j, prlim[i][j],(int)agefin);*/
1623: max=FMAX(max,prlim[i][j]);
1624: min=FMIN(min,prlim[i][j]);
1625: }
1626: maxmin=max-min;
1627: maxmax=FMAX(maxmax,maxmin);
1628: } /* j loop */
1629: if(maxmax < ftolpl){
1630: return prlim;
1631: }
1632: } /* age loop */
1633: return prlim; /* should not reach here */
1634: }
1635:
1636: /*************** transition probabilities ***************/
1637:
1638: double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
1639: {
1640: /* According to parameters values stored in x and the covariate's values stored in cov,
1641: computes the probability to be observed in state j being in state i by appying the
1642: model to the ncovmodel covariates (including constant and age).
1643: lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc]
1644: and, according on how parameters are entered, the position of the coefficient xij(nc) of the
1645: ncth covariate in the global vector x is given by the formula:
1646: j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
1647: j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
1648: Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
1649: sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.
1650: Outputs ps[i][j] the probability to be observed in j being in j according to
1651: the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
1652: */
1653: double s1, lnpijopii;
1654: /*double t34;*/
1655: int i,j, nc, ii, jj;
1656:
1657: for(i=1; i<= nlstate; i++){
1658: for(j=1; j<i;j++){
1659: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
1660: /*lnpijopii += param[i][j][nc]*cov[nc];*/
1661: lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
1662: /* printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
1663: }
1664: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
1665: /* printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
1666: }
1667: for(j=i+1; j<=nlstate+ndeath;j++){
1668: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
1669: /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
1670: lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
1671: /* printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
1672: }
1673: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
1674: }
1675: }
1676:
1677: for(i=1; i<= nlstate; i++){
1678: s1=0;
1679: for(j=1; j<i; j++){
1680: s1+=exp(ps[i][j]); /* In fact sums pij/pii */
1681: /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
1682: }
1683: for(j=i+1; j<=nlstate+ndeath; j++){
1684: s1+=exp(ps[i][j]); /* In fact sums pij/pii */
1685: /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
1686: }
1687: /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
1688: ps[i][i]=1./(s1+1.);
1689: /* Computing other pijs */
1690: for(j=1; j<i; j++)
1691: ps[i][j]= exp(ps[i][j])*ps[i][i];
1692: for(j=i+1; j<=nlstate+ndeath; j++)
1693: ps[i][j]= exp(ps[i][j])*ps[i][i];
1694: /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
1695: } /* end i */
1696:
1697: for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
1698: for(jj=1; jj<= nlstate+ndeath; jj++){
1699: ps[ii][jj]=0;
1700: ps[ii][ii]=1;
1701: }
1702: }
1703:
1704:
1705: /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
1706: /* for(jj=1; jj<= nlstate+ndeath; jj++){ */
1707: /* printf(" pmij ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
1708: /* } */
1709: /* printf("\n "); */
1710: /* } */
1711: /* printf("\n ");printf("%lf ",cov[2]);*/
1712: /*
1713: for(i=1; i<= npar; i++) printf("%f ",x[i]);
1714: goto end;*/
1715: return ps;
1716: }
1717:
1718: /**************** Product of 2 matrices ******************/
1719:
1720: double **matprod2(double **out, double **in,int nrl, int nrh, int ncl, int nch, int ncolol, int ncoloh, double **b)
1721: {
1722: /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
1723: b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
1724: /* in, b, out are matrice of pointers which should have been initialized
1725: before: only the contents of out is modified. The function returns
1726: a pointer to pointers identical to out */
1727: int i, j, k;
1728: for(i=nrl; i<= nrh; i++)
1729: for(k=ncolol; k<=ncoloh; k++){
1730: out[i][k]=0.;
1731: for(j=ncl; j<=nch; j++)
1732: out[i][k] +=in[i][j]*b[j][k];
1733: }
1734: return out;
1735: }
1736:
1737:
1738: /************* Higher Matrix Product ***************/
1739:
1740: double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
1741: {
1742: /* Computes the transition matrix starting at age 'age' over
1743: 'nhstepm*hstepm*stepm' months (i.e. until
1744: age (in years) age+nhstepm*hstepm*stepm/12) by multiplying
1745: nhstepm*hstepm matrices.
1746: Output is stored in matrix po[i][j][h] for h every 'hstepm' step
1747: (typically every 2 years instead of every month which is too big
1748: for the memory).
1749: Model is determined by parameters x and covariates have to be
1750: included manually here.
1751:
1752: */
1753:
1754: int i, j, d, h, k;
1755: double **out, cov[NCOVMAX+1];
1756: double **newm;
1757:
1758: /* Hstepm could be zero and should return the unit matrix */
1759: for (i=1;i<=nlstate+ndeath;i++)
1760: for (j=1;j<=nlstate+ndeath;j++){
1761: oldm[i][j]=(i==j ? 1.0 : 0.0);
1762: po[i][j][0]=(i==j ? 1.0 : 0.0);
1763: }
1764: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
1765: for(h=1; h <=nhstepm; h++){
1766: for(d=1; d <=hstepm; d++){
1767: newm=savm;
1768: /* Covariates have to be included here again */
1769: cov[1]=1.;
1770: cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
1771: for (k=1; k<=cptcovn;k++)
1772: cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
1773: for (k=1; k<=cptcovage;k++)
1774: cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
1775: for (k=1; k<=cptcovprod;k++) /* Useless because included in cptcovn */
1776: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
1777:
1778:
1779: /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
1780: /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
1781: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
1782: pmij(pmmij,cov,ncovmodel,x,nlstate));
1783: savm=oldm;
1784: oldm=newm;
1785: }
1786: for(i=1; i<=nlstate+ndeath; i++)
1787: for(j=1;j<=nlstate+ndeath;j++) {
1788: po[i][j][h]=newm[i][j];
1789: /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
1790: }
1791: /*printf("h=%d ",h);*/
1792: } /* end h */
1793: /* printf("\n H=%d \n",h); */
1794: return po;
1795: }
1796:
1797: #ifdef NLOPT
1798: double myfunc(unsigned n, const double *p1, double *grad, void *pd){
1799: double fret;
1800: double *xt;
1801: int j;
1802: myfunc_data *d2 = (myfunc_data *) pd;
1803: /* xt = (p1-1); */
1804: xt=vector(1,n);
1805: for (j=1;j<=n;j++) xt[j]=p1[j-1]; /* xt[1]=p1[0] */
1806:
1807: fret=(d2->function)(xt); /* p xt[1]@8 is fine */
1808: /* fret=(*func)(xt); /\* p xt[1]@8 is fine *\/ */
1809: printf("Function = %.12lf ",fret);
1810: for (j=1;j<=n;j++) printf(" %d %.8lf", j, xt[j]);
1811: printf("\n");
1812: free_vector(xt,1,n);
1813: return fret;
1814: }
1815: #endif
1816:
1817: /*************** log-likelihood *************/
1818: double func( double *x)
1819: {
1820: int i, ii, j, k, mi, d, kk;
1821: double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
1822: double **out;
1823: double sw; /* Sum of weights */
1824: double lli; /* Individual log likelihood */
1825: int s1, s2;
1826: double bbh, survp;
1827: long ipmx;
1828: /*extern weight */
1829: /* We are differentiating ll according to initial status */
1830: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
1831: /*for(i=1;i<imx;i++)
1832: printf(" %d\n",s[4][i]);
1833: */
1834:
1835: ++countcallfunc;
1836:
1837: cov[1]=1.;
1838:
1839: for(k=1; k<=nlstate; k++) ll[k]=0.;
1840:
1841: if(mle==1){
1842: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1843: /* Computes the values of the ncovmodel covariates of the model
1844: depending if the covariates are fixed or variying (age dependent) and stores them in cov[]
1845: Then computes with function pmij which return a matrix p[i][j] giving the elementary probability
1846: to be observed in j being in i according to the model.
1847: */
1848: for (k=1; k<=cptcovn;k++){ /* Simple and product covariates without age* products */
1849: cov[2+k]=covar[Tvar[k]][i];
1850: }
1851: /* In model V2+V1*V4+age*V3+V3*V2 Tvar[1] is V2, Tvar[2=V1*V4]
1852: is 6, Tvar[3=age*V3] should not be computed because of age Tvar[4=V3*V2]
1853: has been calculated etc */
1854: for(mi=1; mi<= wav[i]-1; mi++){
1855: for (ii=1;ii<=nlstate+ndeath;ii++)
1856: for (j=1;j<=nlstate+ndeath;j++){
1857: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1858: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1859: }
1860: for(d=0; d<dh[mi][i]; d++){
1861: newm=savm;
1862: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1863: for (kk=1; kk<=cptcovage;kk++) {
1864: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; /* Tage[kk] gives the data-covariate associated with age */
1865: }
1866: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1867: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1868: savm=oldm;
1869: oldm=newm;
1870: } /* end mult */
1871:
1872: /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
1873: /* But now since version 0.9 we anticipate for bias at large stepm.
1874: * If stepm is larger than one month (smallest stepm) and if the exact delay
1875: * (in months) between two waves is not a multiple of stepm, we rounded to
1876: * the nearest (and in case of equal distance, to the lowest) interval but now
1877: * we keep into memory the bias bh[mi][i] and also the previous matrix product
1878: * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
1879: * probability in order to take into account the bias as a fraction of the way
1880: * from savm to out if bh is negative or even beyond if bh is positive. bh varies
1881: * -stepm/2 to stepm/2 .
1882: * For stepm=1 the results are the same as for previous versions of Imach.
1883: * For stepm > 1 the results are less biased than in previous versions.
1884: */
1885: s1=s[mw[mi][i]][i];
1886: s2=s[mw[mi+1][i]][i];
1887: bbh=(double)bh[mi][i]/(double)stepm;
1888: /* bias bh is positive if real duration
1889: * is higher than the multiple of stepm and negative otherwise.
1890: */
1891: /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
1892: if( s2 > nlstate){
1893: /* i.e. if s2 is a death state and if the date of death is known
1894: then the contribution to the likelihood is the probability to
1895: die between last step unit time and current step unit time,
1896: which is also equal to probability to die before dh
1897: minus probability to die before dh-stepm .
1898: In version up to 0.92 likelihood was computed
1899: as if date of death was unknown. Death was treated as any other
1900: health state: the date of the interview describes the actual state
1901: and not the date of a change in health state. The former idea was
1902: to consider that at each interview the state was recorded
1903: (healthy, disable or death) and IMaCh was corrected; but when we
1904: introduced the exact date of death then we should have modified
1905: the contribution of an exact death to the likelihood. This new
1906: contribution is smaller and very dependent of the step unit
1907: stepm. It is no more the probability to die between last interview
1908: and month of death but the probability to survive from last
1909: interview up to one month before death multiplied by the
1910: probability to die within a month. Thanks to Chris
1911: Jackson for correcting this bug. Former versions increased
1912: mortality artificially. The bad side is that we add another loop
1913: which slows down the processing. The difference can be up to 10%
1914: lower mortality.
1915: */
1916: lli=log(out[s1][s2] - savm[s1][s2]);
1917:
1918:
1919: } else if (s2==-2) {
1920: for (j=1,survp=0. ; j<=nlstate; j++)
1921: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
1922: /*survp += out[s1][j]; */
1923: lli= log(survp);
1924: }
1925:
1926: else if (s2==-4) {
1927: for (j=3,survp=0. ; j<=nlstate; j++)
1928: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
1929: lli= log(survp);
1930: }
1931:
1932: else if (s2==-5) {
1933: for (j=1,survp=0. ; j<=2; j++)
1934: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
1935: lli= log(survp);
1936: }
1937:
1938: else{
1939: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
1940: /* 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 */
1941: }
1942: /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
1943: /*if(lli ==000.0)*/
1944: /*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); */
1945: ipmx +=1;
1946: sw += weight[i];
1947: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1948: } /* end of wave */
1949: } /* end of individual */
1950: } else if(mle==2){
1951: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1952: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1953: for(mi=1; mi<= wav[i]-1; mi++){
1954: for (ii=1;ii<=nlstate+ndeath;ii++)
1955: for (j=1;j<=nlstate+ndeath;j++){
1956: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1957: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1958: }
1959: for(d=0; d<=dh[mi][i]; d++){
1960: newm=savm;
1961: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1962: for (kk=1; kk<=cptcovage;kk++) {
1963: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1964: }
1965: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1966: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1967: savm=oldm;
1968: oldm=newm;
1969: } /* end mult */
1970:
1971: s1=s[mw[mi][i]][i];
1972: s2=s[mw[mi+1][i]][i];
1973: bbh=(double)bh[mi][i]/(double)stepm;
1974: 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 */
1975: ipmx +=1;
1976: sw += weight[i];
1977: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1978: } /* end of wave */
1979: } /* end of individual */
1980: } else if(mle==3){ /* exponential inter-extrapolation */
1981: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1982: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1983: for(mi=1; mi<= wav[i]-1; mi++){
1984: for (ii=1;ii<=nlstate+ndeath;ii++)
1985: for (j=1;j<=nlstate+ndeath;j++){
1986: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1987: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1988: }
1989: for(d=0; d<dh[mi][i]; d++){
1990: newm=savm;
1991: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1992: for (kk=1; kk<=cptcovage;kk++) {
1993: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1994: }
1995: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1996: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1997: savm=oldm;
1998: oldm=newm;
1999: } /* end mult */
2000:
2001: s1=s[mw[mi][i]][i];
2002: s2=s[mw[mi+1][i]][i];
2003: bbh=(double)bh[mi][i]/(double)stepm;
2004: 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 */
2005: ipmx +=1;
2006: sw += weight[i];
2007: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
2008: } /* end of wave */
2009: } /* end of individual */
2010: }else if (mle==4){ /* ml=4 no inter-extrapolation */
2011: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
2012: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
2013: for(mi=1; mi<= wav[i]-1; mi++){
2014: for (ii=1;ii<=nlstate+ndeath;ii++)
2015: for (j=1;j<=nlstate+ndeath;j++){
2016: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2017: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2018: }
2019: for(d=0; d<dh[mi][i]; d++){
2020: newm=savm;
2021: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
2022: for (kk=1; kk<=cptcovage;kk++) {
2023: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
2024: }
2025:
2026: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2027: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
2028: savm=oldm;
2029: oldm=newm;
2030: } /* end mult */
2031:
2032: s1=s[mw[mi][i]][i];
2033: s2=s[mw[mi+1][i]][i];
2034: if( s2 > nlstate){
2035: lli=log(out[s1][s2] - savm[s1][s2]);
2036: }else{
2037: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
2038: }
2039: ipmx +=1;
2040: sw += weight[i];
2041: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
2042: /* 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]); */
2043: } /* end of wave */
2044: } /* end of individual */
2045: }else{ /* ml=5 no inter-extrapolation no jackson =0.8a */
2046: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
2047: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
2048: for(mi=1; mi<= wav[i]-1; mi++){
2049: for (ii=1;ii<=nlstate+ndeath;ii++)
2050: for (j=1;j<=nlstate+ndeath;j++){
2051: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2052: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2053: }
2054: for(d=0; d<dh[mi][i]; d++){
2055: newm=savm;
2056: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
2057: for (kk=1; kk<=cptcovage;kk++) {
2058: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
2059: }
2060:
2061: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2062: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
2063: savm=oldm;
2064: oldm=newm;
2065: } /* end mult */
2066:
2067: s1=s[mw[mi][i]][i];
2068: s2=s[mw[mi+1][i]][i];
2069: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
2070: ipmx +=1;
2071: sw += weight[i];
2072: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
2073: /*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]);*/
2074: } /* end of wave */
2075: } /* end of individual */
2076: } /* End of if */
2077: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
2078: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
2079: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
2080: return -l;
2081: }
2082:
2083: /*************** log-likelihood *************/
2084: double funcone( double *x)
2085: {
2086: /* Same as likeli but slower because of a lot of printf and if */
2087: int i, ii, j, k, mi, d, kk;
2088: double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
2089: double **out;
2090: double lli; /* Individual log likelihood */
2091: double llt;
2092: int s1, s2;
2093: double bbh, survp;
2094: /*extern weight */
2095: /* We are differentiating ll according to initial status */
2096: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
2097: /*for(i=1;i<imx;i++)
2098: printf(" %d\n",s[4][i]);
2099: */
2100: cov[1]=1.;
2101:
2102: for(k=1; k<=nlstate; k++) ll[k]=0.;
2103:
2104: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
2105: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
2106: for(mi=1; mi<= wav[i]-1; mi++){
2107: for (ii=1;ii<=nlstate+ndeath;ii++)
2108: for (j=1;j<=nlstate+ndeath;j++){
2109: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2110: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2111: }
2112: for(d=0; d<dh[mi][i]; d++){
2113: newm=savm;
2114: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
2115: for (kk=1; kk<=cptcovage;kk++) {
2116: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
2117: }
2118: /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
2119: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2120: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
2121: /* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, */
2122: /* 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); */
2123: savm=oldm;
2124: oldm=newm;
2125: } /* end mult */
2126:
2127: s1=s[mw[mi][i]][i];
2128: s2=s[mw[mi+1][i]][i];
2129: bbh=(double)bh[mi][i]/(double)stepm;
2130: /* bias is positive if real duration
2131: * is higher than the multiple of stepm and negative otherwise.
2132: */
2133: if( s2 > nlstate && (mle <5) ){ /* Jackson */
2134: lli=log(out[s1][s2] - savm[s1][s2]);
2135: } else if (s2==-2) {
2136: for (j=1,survp=0. ; j<=nlstate; j++)
2137: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
2138: lli= log(survp);
2139: }else if (mle==1){
2140: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
2141: } else if(mle==2){
2142: 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 */
2143: } else if(mle==3){ /* exponential inter-extrapolation */
2144: 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 */
2145: } else if (mle==4){ /* mle=4 no inter-extrapolation */
2146: lli=log(out[s1][s2]); /* Original formula */
2147: } else{ /* mle=0 back to 1 */
2148: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
2149: /*lli=log(out[s1][s2]); */ /* Original formula */
2150: } /* End of if */
2151: ipmx +=1;
2152: sw += weight[i];
2153: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
2154: /*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]); */
2155: if(globpr){
2156: fprintf(ficresilk,"%9ld %6d %2d %2d %1d %1d %3d %11.6f %8.4f\
2157: %11.6f %11.6f %11.6f ", \
2158: num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
2159: 2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
2160: for(k=1,llt=0.,l=0.; k<=nlstate; k++){
2161: llt +=ll[k]*gipmx/gsw;
2162: fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
2163: }
2164: fprintf(ficresilk," %10.6f\n", -llt);
2165: }
2166: } /* end of wave */
2167: } /* end of individual */
2168: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
2169: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
2170: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
2171: if(globpr==0){ /* First time we count the contributions and weights */
2172: gipmx=ipmx;
2173: gsw=sw;
2174: }
2175: return -l;
2176: }
2177:
2178:
2179: /*************** function likelione ***********/
2180: void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
2181: {
2182: /* This routine should help understanding what is done with
2183: the selection of individuals/waves and
2184: to check the exact contribution to the likelihood.
2185: Plotting could be done.
2186: */
2187: int k;
2188:
2189: if(*globpri !=0){ /* Just counts and sums, no printings */
2190: strcpy(fileresilk,"ilk");
2191: strcat(fileresilk,fileres);
2192: if((ficresilk=fopen(fileresilk,"w"))==NULL) {
2193: printf("Problem with resultfile: %s\n", fileresilk);
2194: fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
2195: }
2196: 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");
2197: fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
2198: /* i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
2199: for(k=1; k<=nlstate; k++)
2200: fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
2201: fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
2202: }
2203:
2204: *fretone=(*funcone)(p);
2205: if(*globpri !=0){
2206: fclose(ficresilk);
2207: fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
2208: fflush(fichtm);
2209: }
2210: return;
2211: }
2212:
2213:
2214: /*********** Maximum Likelihood Estimation ***************/
2215:
2216: void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
2217: {
2218: int i,j, iter=0;
2219: double **xi;
2220: double fret;
2221: double fretone; /* Only one call to likelihood */
2222: /* char filerespow[FILENAMELENGTH];*/
2223:
2224: #ifdef NLOPT
2225: int creturn;
2226: nlopt_opt opt;
2227: /* double lb[9] = { -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL }; /\* lower bounds *\/ */
2228: double *lb;
2229: double minf; /* the minimum objective value, upon return */
2230: double * p1; /* Shifted parameters from 0 instead of 1 */
2231: myfunc_data dinst, *d = &dinst;
2232: #endif
2233:
2234:
2235: xi=matrix(1,npar,1,npar);
2236: for (i=1;i<=npar;i++)
2237: for (j=1;j<=npar;j++)
2238: xi[i][j]=(i==j ? 1.0 : 0.0);
2239: printf("Powell\n"); fprintf(ficlog,"Powell\n");
2240: strcpy(filerespow,"pow");
2241: strcat(filerespow,fileres);
2242: if((ficrespow=fopen(filerespow,"w"))==NULL) {
2243: printf("Problem with resultfile: %s\n", filerespow);
2244: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
2245: }
2246: fprintf(ficrespow,"# Powell\n# iter -2*LL");
2247: for (i=1;i<=nlstate;i++)
2248: for(j=1;j<=nlstate+ndeath;j++)
2249: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
2250: fprintf(ficrespow,"\n");
2251: #ifdef POWELL
2252: powell(p,xi,npar,ftol,&iter,&fret,func);
2253: #endif
2254:
2255: #ifdef NLOPT
2256: #ifdef NEWUOA
2257: opt = nlopt_create(NLOPT_LN_NEWUOA,npar);
2258: #else
2259: opt = nlopt_create(NLOPT_LN_BOBYQA,npar);
2260: #endif
2261: lb=vector(0,npar-1);
2262: for (i=0;i<npar;i++) lb[i]= -HUGE_VAL;
2263: nlopt_set_lower_bounds(opt, lb);
2264: nlopt_set_initial_step1(opt, 0.1);
2265:
2266: p1= (p+1); /* p *(p+1)@8 and p *(p1)@8 are equal p1[0]=p[1] */
2267: d->function = func;
2268: printf(" Func %.12lf \n",myfunc(npar,p1,NULL,d));
2269: nlopt_set_min_objective(opt, myfunc, d);
2270: nlopt_set_xtol_rel(opt, ftol);
2271: if ((creturn=nlopt_optimize(opt, p1, &minf)) < 0) {
2272: printf("nlopt failed! %d\n",creturn);
2273: }
2274: else {
2275: printf("found minimum after %d evaluations (NLOPT=%d)\n", countcallfunc ,NLOPT);
2276: printf("found minimum at f(%g,%g) = %0.10g\n", p[0], p[1], minf);
2277: iter=1; /* not equal */
2278: }
2279: nlopt_destroy(opt);
2280: #endif
2281: free_matrix(xi,1,npar,1,npar);
2282: fclose(ficrespow);
2283: printf("\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
2284: fprintf(ficlog,"\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
2285: fprintf(ficres,"\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
2286:
2287: }
2288:
2289: /**** Computes Hessian and covariance matrix ***/
2290: void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
2291: {
2292: double **a,**y,*x,pd;
2293: double **hess;
2294: int i, j;
2295: int *indx;
2296:
2297: double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
2298: double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
2299: void lubksb(double **a, int npar, int *indx, double b[]) ;
2300: void ludcmp(double **a, int npar, int *indx, double *d) ;
2301: double gompertz(double p[]);
2302: hess=matrix(1,npar,1,npar);
2303:
2304: printf("\nCalculation of the hessian matrix. Wait...\n");
2305: fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
2306: for (i=1;i<=npar;i++){
2307: printf("%d",i);fflush(stdout);
2308: fprintf(ficlog,"%d",i);fflush(ficlog);
2309:
2310: hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
2311:
2312: /* printf(" %f ",p[i]);
2313: printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
2314: }
2315:
2316: for (i=1;i<=npar;i++) {
2317: for (j=1;j<=npar;j++) {
2318: if (j>i) {
2319: printf(".%d%d",i,j);fflush(stdout);
2320: fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
2321: hess[i][j]=hessij(p,delti,i,j,func,npar);
2322:
2323: hess[j][i]=hess[i][j];
2324: /*printf(" %lf ",hess[i][j]);*/
2325: }
2326: }
2327: }
2328: printf("\n");
2329: fprintf(ficlog,"\n");
2330:
2331: printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
2332: fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
2333:
2334: a=matrix(1,npar,1,npar);
2335: y=matrix(1,npar,1,npar);
2336: x=vector(1,npar);
2337: indx=ivector(1,npar);
2338: for (i=1;i<=npar;i++)
2339: for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
2340: ludcmp(a,npar,indx,&pd);
2341:
2342: for (j=1;j<=npar;j++) {
2343: for (i=1;i<=npar;i++) x[i]=0;
2344: x[j]=1;
2345: lubksb(a,npar,indx,x);
2346: for (i=1;i<=npar;i++){
2347: matcov[i][j]=x[i];
2348: }
2349: }
2350:
2351: printf("\n#Hessian matrix#\n");
2352: fprintf(ficlog,"\n#Hessian matrix#\n");
2353: for (i=1;i<=npar;i++) {
2354: for (j=1;j<=npar;j++) {
2355: printf("%.3e ",hess[i][j]);
2356: fprintf(ficlog,"%.3e ",hess[i][j]);
2357: }
2358: printf("\n");
2359: fprintf(ficlog,"\n");
2360: }
2361:
2362: /* Recompute Inverse */
2363: for (i=1;i<=npar;i++)
2364: for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
2365: ludcmp(a,npar,indx,&pd);
2366:
2367: /* printf("\n#Hessian matrix recomputed#\n");
2368:
2369: for (j=1;j<=npar;j++) {
2370: for (i=1;i<=npar;i++) x[i]=0;
2371: x[j]=1;
2372: lubksb(a,npar,indx,x);
2373: for (i=1;i<=npar;i++){
2374: y[i][j]=x[i];
2375: printf("%.3e ",y[i][j]);
2376: fprintf(ficlog,"%.3e ",y[i][j]);
2377: }
2378: printf("\n");
2379: fprintf(ficlog,"\n");
2380: }
2381: */
2382:
2383: free_matrix(a,1,npar,1,npar);
2384: free_matrix(y,1,npar,1,npar);
2385: free_vector(x,1,npar);
2386: free_ivector(indx,1,npar);
2387: free_matrix(hess,1,npar,1,npar);
2388:
2389:
2390: }
2391:
2392: /*************** hessian matrix ****************/
2393: double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
2394: {
2395: int i;
2396: int l=1, lmax=20;
2397: double k1,k2;
2398: double p2[MAXPARM+1]; /* identical to x */
2399: double res;
2400: double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
2401: double fx;
2402: int k=0,kmax=10;
2403: double l1;
2404:
2405: fx=func(x);
2406: for (i=1;i<=npar;i++) p2[i]=x[i];
2407: for(l=0 ; l <=lmax; l++){ /* Enlarging the zone around the Maximum */
2408: l1=pow(10,l);
2409: delts=delt;
2410: for(k=1 ; k <kmax; k=k+1){
2411: delt = delta*(l1*k);
2412: p2[theta]=x[theta] +delt;
2413: k1=func(p2)-fx; /* Might be negative if too close to the theoretical maximum */
2414: p2[theta]=x[theta]-delt;
2415: k2=func(p2)-fx;
2416: /*res= (k1-2.0*fx+k2)/delt/delt; */
2417: res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
2418:
2419: #ifdef DEBUGHESS
2420: 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);
2421: 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);
2422: #endif
2423: /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
2424: if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
2425: k=kmax;
2426: }
2427: else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
2428: k=kmax; l=lmax*10;
2429: }
2430: else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){
2431: delts=delt;
2432: }
2433: }
2434: }
2435: delti[theta]=delts;
2436: return res;
2437:
2438: }
2439:
2440: double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
2441: {
2442: int i;
2443: int l=1, lmax=20;
2444: double k1,k2,k3,k4,res,fx;
2445: double p2[MAXPARM+1];
2446: int k;
2447:
2448: fx=func(x);
2449: for (k=1; k<=2; k++) {
2450: for (i=1;i<=npar;i++) p2[i]=x[i];
2451: p2[thetai]=x[thetai]+delti[thetai]/k;
2452: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
2453: k1=func(p2)-fx;
2454:
2455: p2[thetai]=x[thetai]+delti[thetai]/k;
2456: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
2457: k2=func(p2)-fx;
2458:
2459: p2[thetai]=x[thetai]-delti[thetai]/k;
2460: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
2461: k3=func(p2)-fx;
2462:
2463: p2[thetai]=x[thetai]-delti[thetai]/k;
2464: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
2465: k4=func(p2)-fx;
2466: res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
2467: #ifdef DEBUG
2468: 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);
2469: 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);
2470: #endif
2471: }
2472: return res;
2473: }
2474:
2475: /************** Inverse of matrix **************/
2476: void ludcmp(double **a, int n, int *indx, double *d)
2477: {
2478: int i,imax,j,k;
2479: double big,dum,sum,temp;
2480: double *vv;
2481:
2482: vv=vector(1,n);
2483: *d=1.0;
2484: for (i=1;i<=n;i++) {
2485: big=0.0;
2486: for (j=1;j<=n;j++)
2487: if ((temp=fabs(a[i][j])) > big) big=temp;
2488: if (big == 0.0) nrerror("Singular matrix in routine ludcmp");
2489: vv[i]=1.0/big;
2490: }
2491: for (j=1;j<=n;j++) {
2492: for (i=1;i<j;i++) {
2493: sum=a[i][j];
2494: for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];
2495: a[i][j]=sum;
2496: }
2497: big=0.0;
2498: for (i=j;i<=n;i++) {
2499: sum=a[i][j];
2500: for (k=1;k<j;k++)
2501: sum -= a[i][k]*a[k][j];
2502: a[i][j]=sum;
2503: if ( (dum=vv[i]*fabs(sum)) >= big) {
2504: big=dum;
2505: imax=i;
2506: }
2507: }
2508: if (j != imax) {
2509: for (k=1;k<=n;k++) {
2510: dum=a[imax][k];
2511: a[imax][k]=a[j][k];
2512: a[j][k]=dum;
2513: }
2514: *d = -(*d);
2515: vv[imax]=vv[j];
2516: }
2517: indx[j]=imax;
2518: if (a[j][j] == 0.0) a[j][j]=TINY;
2519: if (j != n) {
2520: dum=1.0/(a[j][j]);
2521: for (i=j+1;i<=n;i++) a[i][j] *= dum;
2522: }
2523: }
2524: free_vector(vv,1,n); /* Doesn't work */
2525: ;
2526: }
2527:
2528: void lubksb(double **a, int n, int *indx, double b[])
2529: {
2530: int i,ii=0,ip,j;
2531: double sum;
2532:
2533: for (i=1;i<=n;i++) {
2534: ip=indx[i];
2535: sum=b[ip];
2536: b[ip]=b[i];
2537: if (ii)
2538: for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];
2539: else if (sum) ii=i;
2540: b[i]=sum;
2541: }
2542: for (i=n;i>=1;i--) {
2543: sum=b[i];
2544: for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];
2545: b[i]=sum/a[i][i];
2546: }
2547: }
2548:
2549: void pstamp(FILE *fichier)
2550: {
2551: fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart);
2552: }
2553:
2554: /************ Frequencies ********************/
2555: 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[])
2556: { /* Some frequencies */
2557:
2558: int i, m, jk, j1, bool, z1,j;
2559: int first;
2560: double ***freq; /* Frequencies */
2561: double *pp, **prop;
2562: double pos,posprop, k2, dateintsum=0,k2cpt=0;
2563: char fileresp[FILENAMELENGTH];
2564:
2565: pp=vector(1,nlstate);
2566: prop=matrix(1,nlstate,iagemin,iagemax+3);
2567: strcpy(fileresp,"p");
2568: strcat(fileresp,fileres);
2569: if((ficresp=fopen(fileresp,"w"))==NULL) {
2570: printf("Problem with prevalence resultfile: %s\n", fileresp);
2571: fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
2572: exit(0);
2573: }
2574: freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
2575: j1=0;
2576:
2577: j=cptcoveff;
2578: if (cptcovn<1) {j=1;ncodemax[1]=1;}
2579:
2580: first=1;
2581:
2582: /* for(k1=1; k1<=j ; k1++){ */ /* Loop on covariates */
2583: /* for(i1=1; i1<=ncodemax[k1];i1++){ */ /* Now it is 2 */
2584: /* j1++; */
2585: for (j1 = 1; j1 <= (int) pow(2,cptcoveff); j1++){
2586: /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
2587: scanf("%d", i);*/
2588: for (i=-5; i<=nlstate+ndeath; i++)
2589: for (jk=-5; jk<=nlstate+ndeath; jk++)
2590: for(m=iagemin; m <= iagemax+3; m++)
2591: freq[i][jk][m]=0;
2592:
2593: for (i=1; i<=nlstate; i++)
2594: for(m=iagemin; m <= iagemax+3; m++)
2595: prop[i][m]=0;
2596:
2597: dateintsum=0;
2598: k2cpt=0;
2599: for (i=1; i<=imx; i++) {
2600: bool=1;
2601: if (cptcovn>0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
2602: for (z1=1; z1<=cptcoveff; z1++)
2603: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]){
2604: /* Tests if the value of each of the covariates of i is equal to filter j1 */
2605: bool=0;
2606: /* 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",
2607: bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtab[j1][z1],
2608: j1,z1,nbcode[Tvaraff[z1]][codtab[j1][z1]],j1);*/
2609: /* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtab[7][3]=1 and nbcde[3][?]=1*/
2610: }
2611: }
2612:
2613: if (bool==1){
2614: for(m=firstpass; m<=lastpass; m++){
2615: k2=anint[m][i]+(mint[m][i]/12.);
2616: /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
2617: if(agev[m][i]==0) agev[m][i]=iagemax+1;
2618: if(agev[m][i]==1) agev[m][i]=iagemax+2;
2619: if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
2620: if (m<lastpass) {
2621: freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
2622: freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
2623: }
2624:
2625: if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
2626: dateintsum=dateintsum+k2;
2627: k2cpt++;
2628: }
2629: /*}*/
2630: }
2631: }
2632: } /* end i */
2633:
2634: /* fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
2635: pstamp(ficresp);
2636: if (cptcovn>0) {
2637: fprintf(ficresp, "\n#********** Variable ");
2638: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
2639: fprintf(ficresp, "**********\n#");
2640: fprintf(ficlog, "\n#********** Variable ");
2641: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficlog, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
2642: fprintf(ficlog, "**********\n#");
2643: }
2644: for(i=1; i<=nlstate;i++)
2645: fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
2646: fprintf(ficresp, "\n");
2647:
2648: for(i=iagemin; i <= iagemax+3; i++){
2649: if(i==iagemax+3){
2650: fprintf(ficlog,"Total");
2651: }else{
2652: if(first==1){
2653: first=0;
2654: printf("See log file for details...\n");
2655: }
2656: fprintf(ficlog,"Age %d", i);
2657: }
2658: for(jk=1; jk <=nlstate ; jk++){
2659: for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
2660: pp[jk] += freq[jk][m][i];
2661: }
2662: for(jk=1; jk <=nlstate ; jk++){
2663: for(m=-1, pos=0; m <=0 ; m++)
2664: pos += freq[jk][m][i];
2665: if(pp[jk]>=1.e-10){
2666: if(first==1){
2667: printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
2668: }
2669: fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
2670: }else{
2671: if(first==1)
2672: printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
2673: fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
2674: }
2675: }
2676:
2677: for(jk=1; jk <=nlstate ; jk++){
2678: for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
2679: pp[jk] += freq[jk][m][i];
2680: }
2681: for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
2682: pos += pp[jk];
2683: posprop += prop[jk][i];
2684: }
2685: for(jk=1; jk <=nlstate ; jk++){
2686: if(pos>=1.e-5){
2687: if(first==1)
2688: printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
2689: fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
2690: }else{
2691: if(first==1)
2692: printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
2693: fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
2694: }
2695: if( i <= iagemax){
2696: if(pos>=1.e-5){
2697: fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
2698: /*probs[i][jk][j1]= pp[jk]/pos;*/
2699: /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
2700: }
2701: else
2702: fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
2703: }
2704: }
2705:
2706: for(jk=-1; jk <=nlstate+ndeath; jk++)
2707: for(m=-1; m <=nlstate+ndeath; m++)
2708: if(freq[jk][m][i] !=0 ) {
2709: if(first==1)
2710: printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
2711: fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
2712: }
2713: if(i <= iagemax)
2714: fprintf(ficresp,"\n");
2715: if(first==1)
2716: printf("Others in log...\n");
2717: fprintf(ficlog,"\n");
2718: }
2719: /*}*/
2720: }
2721: dateintmean=dateintsum/k2cpt;
2722:
2723: fclose(ficresp);
2724: free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
2725: free_vector(pp,1,nlstate);
2726: free_matrix(prop,1,nlstate,iagemin, iagemax+3);
2727: /* End of Freq */
2728: }
2729:
2730: /************ Prevalence ********************/
2731: 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)
2732: {
2733: /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
2734: in each health status at the date of interview (if between dateprev1 and dateprev2).
2735: We still use firstpass and lastpass as another selection.
2736: */
2737:
2738: int i, m, jk, j1, bool, z1,j;
2739:
2740: double **prop;
2741: double posprop;
2742: double y2; /* in fractional years */
2743: int iagemin, iagemax;
2744: int first; /** to stop verbosity which is redirected to log file */
2745:
2746: iagemin= (int) agemin;
2747: iagemax= (int) agemax;
2748: /*pp=vector(1,nlstate);*/
2749: prop=matrix(1,nlstate,iagemin,iagemax+3);
2750: /* freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
2751: j1=0;
2752:
2753: /*j=cptcoveff;*/
2754: if (cptcovn<1) {j=1;ncodemax[1]=1;}
2755:
2756: first=1;
2757: for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){
2758: /*for(i1=1; i1<=ncodemax[k1];i1++){
2759: j1++;*/
2760:
2761: for (i=1; i<=nlstate; i++)
2762: for(m=iagemin; m <= iagemax+3; m++)
2763: prop[i][m]=0.0;
2764:
2765: for (i=1; i<=imx; i++) { /* Each individual */
2766: bool=1;
2767: if (cptcovn>0) {
2768: for (z1=1; z1<=cptcoveff; z1++)
2769: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
2770: bool=0;
2771: }
2772: if (bool==1) {
2773: for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
2774: y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
2775: if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
2776: if(agev[m][i]==0) agev[m][i]=iagemax+1;
2777: if(agev[m][i]==1) agev[m][i]=iagemax+2;
2778: 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);
2779: if (s[m][i]>0 && s[m][i]<=nlstate) {
2780: /*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]]);*/
2781: prop[s[m][i]][(int)agev[m][i]] += weight[i];
2782: prop[s[m][i]][iagemax+3] += weight[i];
2783: }
2784: }
2785: } /* end selection of waves */
2786: }
2787: }
2788: for(i=iagemin; i <= iagemax+3; i++){
2789: for(jk=1,posprop=0; jk <=nlstate ; jk++) {
2790: posprop += prop[jk][i];
2791: }
2792:
2793: for(jk=1; jk <=nlstate ; jk++){
2794: if( i <= iagemax){
2795: if(posprop>=1.e-5){
2796: probs[i][jk][j1]= prop[jk][i]/posprop;
2797: } else{
2798: if(first==1){
2799: first=0;
2800: 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]);
2801: }
2802: }
2803: }
2804: }/* end jk */
2805: }/* end i */
2806: /*} *//* end i1 */
2807: } /* end j1 */
2808:
2809: /* free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
2810: /*free_vector(pp,1,nlstate);*/
2811: free_matrix(prop,1,nlstate, iagemin,iagemax+3);
2812: } /* End of prevalence */
2813:
2814: /************* Waves Concatenation ***************/
2815:
2816: 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)
2817: {
2818: /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
2819: Death is a valid wave (if date is known).
2820: mw[mi][i] is the mi (mi=1 to wav[i]) effective wave of individual i
2821: dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
2822: and mw[mi+1][i]. dh depends on stepm.
2823: */
2824:
2825: int i, mi, m;
2826: /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
2827: double sum=0., jmean=0.;*/
2828: int first;
2829: int j, k=0,jk, ju, jl;
2830: double sum=0.;
2831: first=0;
2832: jmin=100000;
2833: jmax=-1;
2834: jmean=0.;
2835: for(i=1; i<=imx; i++){
2836: mi=0;
2837: m=firstpass;
2838: while(s[m][i] <= nlstate){
2839: if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
2840: mw[++mi][i]=m;
2841: if(m >=lastpass)
2842: break;
2843: else
2844: m++;
2845: }/* end while */
2846: if (s[m][i] > nlstate){
2847: mi++; /* Death is another wave */
2848: /* if(mi==0) never been interviewed correctly before death */
2849: /* Only death is a correct wave */
2850: mw[mi][i]=m;
2851: }
2852:
2853: wav[i]=mi;
2854: if(mi==0){
2855: nbwarn++;
2856: if(first==0){
2857: printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
2858: first=1;
2859: }
2860: if(first==1){
2861: fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
2862: }
2863: } /* end mi==0 */
2864: } /* End individuals */
2865:
2866: for(i=1; i<=imx; i++){
2867: for(mi=1; mi<wav[i];mi++){
2868: if (stepm <=0)
2869: dh[mi][i]=1;
2870: else{
2871: if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
2872: if (agedc[i] < 2*AGESUP) {
2873: j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);
2874: if(j==0) j=1; /* Survives at least one month after exam */
2875: else if(j<0){
2876: nberr++;
2877: 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]);
2878: j=1; /* Temporary Dangerous patch */
2879: 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);
2880: 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]);
2881: 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);
2882: }
2883: k=k+1;
2884: if (j >= jmax){
2885: jmax=j;
2886: ijmax=i;
2887: }
2888: if (j <= jmin){
2889: jmin=j;
2890: ijmin=i;
2891: }
2892: sum=sum+j;
2893: /*if (j<0) printf("j=%d num=%d \n",j,i);*/
2894: /* printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
2895: }
2896: }
2897: else{
2898: j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
2899: /* 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]); */
2900:
2901: k=k+1;
2902: if (j >= jmax) {
2903: jmax=j;
2904: ijmax=i;
2905: }
2906: else if (j <= jmin){
2907: jmin=j;
2908: ijmin=i;
2909: }
2910: /* if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
2911: /*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]);*/
2912: if(j<0){
2913: nberr++;
2914: 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]);
2915: 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]);
2916: }
2917: sum=sum+j;
2918: }
2919: jk= j/stepm;
2920: jl= j -jk*stepm;
2921: ju= j -(jk+1)*stepm;
2922: if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
2923: if(jl==0){
2924: dh[mi][i]=jk;
2925: bh[mi][i]=0;
2926: }else{ /* We want a negative bias in order to only have interpolation ie
2927: * to avoid the price of an extra matrix product in likelihood */
2928: dh[mi][i]=jk+1;
2929: bh[mi][i]=ju;
2930: }
2931: }else{
2932: if(jl <= -ju){
2933: dh[mi][i]=jk;
2934: bh[mi][i]=jl; /* bias is positive if real duration
2935: * is higher than the multiple of stepm and negative otherwise.
2936: */
2937: }
2938: else{
2939: dh[mi][i]=jk+1;
2940: bh[mi][i]=ju;
2941: }
2942: if(dh[mi][i]==0){
2943: dh[mi][i]=1; /* At least one step */
2944: bh[mi][i]=ju; /* At least one step */
2945: /* 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);*/
2946: }
2947: } /* end if mle */
2948: }
2949: } /* end wave */
2950: }
2951: jmean=sum/k;
2952: 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);
2953: 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);
2954: }
2955:
2956: /*********** Tricode ****************************/
2957: void tricode(int *Tvar, int **nbcode, int imx, int *Ndum)
2958: {
2959: /**< Uses cptcovn+2*cptcovprod as the number of covariates */
2960: /* Tvar[i]=atoi(stre); find 'n' in Vn and stores in Tvar. If model=V2+V1 Tvar[1]=2 and Tvar[2]=1
2961: * Boring subroutine which should only output nbcode[Tvar[j]][k]
2962: * Tvar[5] in V2+V1+V3*age+V2*V4 is 2 (V2)
2963: * nbcode[Tvar[j]][1]=
2964: */
2965:
2966: int ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
2967: int modmaxcovj=0; /* Modality max of covariates j */
2968: int cptcode=0; /* Modality max of covariates j */
2969: int modmincovj=0; /* Modality min of covariates j */
2970:
2971:
2972: cptcoveff=0;
2973:
2974: for (k=-1; k < maxncov; k++) Ndum[k]=0;
2975: for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */
2976:
2977: /* Loop on covariates without age and products */
2978: for (j=1; j<=(cptcovs); j++) { /* model V1 + V2*age+ V3 + V3*V4 : V1 + V3 = 2 only */
2979: for (i=1; i<=imx; i++) { /* Lopp on individuals: reads the data file to get the maximum value of the
2980: modality of this covariate Vj*/
2981: ij=(int)(covar[Tvar[j]][i]); /* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i
2982: * If product of Vn*Vm, still boolean *:
2983: * If it was coded 1, 2, 3, 4 should be splitted into 3 boolean variables
2984: * 1 => 0 0 0, 2 => 0 0 1, 3 => 0 1 1, 4=1 0 0 */
2985: /* Finds for covariate j, n=Tvar[j] of Vn . ij is the
2986: modality of the nth covariate of individual i. */
2987: if (ij > modmaxcovj)
2988: modmaxcovj=ij;
2989: else if (ij < modmincovj)
2990: modmincovj=ij;
2991: if ((ij < -1) && (ij > NCOVMAX)){
2992: printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX );
2993: exit(1);
2994: }else
2995: Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/
2996: /* If coded 1, 2, 3 , counts the number of 1 Ndum[1], number of 2, Ndum[2], etc */
2997: /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
2998: /* getting the maximum value of the modality of the covariate
2999: (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and
3000: female is 1, then modmaxcovj=1.*/
3001: }
3002: printf(" Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", j, Tvar[j], modmincovj, modmaxcovj);
3003: cptcode=modmaxcovj;
3004: /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */
3005: /*for (i=0; i<=cptcode; i++) {*/
3006: for (i=modmincovj; i<=modmaxcovj; i++) { /* i=-1 ? 0 and 1*//* For each value of the modality of model-cov j */
3007: printf("Frequencies of covariates %d V%d %d\n", j, Tvar[j], Ndum[i]);
3008: if( Ndum[i] != 0 ){ /* Counts if nobody answered, empty modality */
3009: ncodemax[j]++; /* ncodemax[j]= Number of non-null modalities of the j th covariate. */
3010: }
3011: /* In fact ncodemax[j]=2 (dichotom. variables only) but it could be more for
3012: historical reasons: 3 if coded 1, 2, 3 and 4 and Ndum[2]=0 */
3013: } /* Ndum[-1] number of undefined modalities */
3014:
3015: /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */
3016: /* For covariate j, modalities could be 1, 2, 3, 4. If Ndum[2]=0 ncodemax[j] is not 4 but 3 */
3017: /* If Ndum[3}= 635; Ndum[4]=0; Ndum[5]=0; Ndum[6]=27; Ndum[7]=125;
3018: modmincovj=3; modmaxcovj = 7;
3019: There are only 3 modalities non empty (or 2 if 27 is too few) : ncodemax[j]=3;
3020: which will be coded 0, 1, 2 which in binary on 3-1 digits are 0=00 1=01, 2=10; defining two dummy
3021: variables V1_1 and V1_2.
3022: nbcode[Tvar[j]][ij]=k;
3023: nbcode[Tvar[j]][1]=0;
3024: nbcode[Tvar[j]][2]=1;
3025: nbcode[Tvar[j]][3]=2;
3026: */
3027: ij=1; /* ij is similar to i but can jumps over null modalities */
3028: for (i=modmincovj; i<=modmaxcovj; i++) { /* i= 1 to 2 for dichotomous, or from 1 to 3 */
3029: for (k=0; k<= cptcode; k++) { /* k=-1 ? k=0 to 1 *//* Could be 1 to 4 */
3030: /*recode from 0 */
3031: if (Ndum[k] != 0) { /* If at least one individual responded to this modality k */
3032: nbcode[Tvar[j]][ij]=k; /* stores the modality in an array nbcode.
3033: k is a modality. If we have model=V1+V1*sex
3034: then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
3035: ij++;
3036: }
3037: if (ij > ncodemax[j]) break;
3038: } /* end of loop on */
3039: } /* end of loop on modality */
3040: } /* end of loop on model-covariate j. nbcode[Tvarj][1]=0 and nbcode[Tvarj][2]=1 sets the value of covariate j*/
3041:
3042: for (k=-1; k< maxncov; k++) Ndum[k]=0;
3043:
3044: for (i=1; i<=ncovmodel-2; i++) { /* -2, cste and age */
3045: /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
3046: ij=Tvar[i]; /* Tvar might be -1 if status was unknown */
3047: Ndum[ij]++;
3048: }
3049:
3050: ij=1;
3051: for (i=0; i<= maxncov-1; i++) { /* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) */
3052: /*printf("Ndum[%d]=%d\n",i, Ndum[i]);*/
3053: if((Ndum[i]!=0) && (i<=ncovcol)){
3054: /*printf("diff Ndum[%d]=%d\n",i, Ndum[i]);*/
3055: Tvaraff[ij]=i; /*For printing (unclear) */
3056: ij++;
3057: }else
3058: Tvaraff[ij]=0;
3059: }
3060: ij--;
3061: cptcoveff=ij; /*Number of total covariates*/
3062:
3063: }
3064:
3065:
3066: /*********** Health Expectancies ****************/
3067:
3068: void evsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,char strstart[] )
3069:
3070: {
3071: /* Health expectancies, no variances */
3072: int i, j, nhstepm, hstepm, h, nstepm;
3073: int nhstepma, nstepma; /* Decreasing with age */
3074: double age, agelim, hf;
3075: double ***p3mat;
3076: double eip;
3077:
3078: pstamp(ficreseij);
3079: fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
3080: fprintf(ficreseij,"# Age");
3081: for(i=1; i<=nlstate;i++){
3082: for(j=1; j<=nlstate;j++){
3083: fprintf(ficreseij," e%1d%1d ",i,j);
3084: }
3085: fprintf(ficreseij," e%1d. ",i);
3086: }
3087: fprintf(ficreseij,"\n");
3088:
3089:
3090: if(estepm < stepm){
3091: printf ("Problem %d lower than %d\n",estepm, stepm);
3092: }
3093: else hstepm=estepm;
3094: /* We compute the life expectancy from trapezoids spaced every estepm months
3095: * This is mainly to measure the difference between two models: for example
3096: * if stepm=24 months pijx are given only every 2 years and by summing them
3097: * we are calculating an estimate of the Life Expectancy assuming a linear
3098: * progression in between and thus overestimating or underestimating according
3099: * to the curvature of the survival function. If, for the same date, we
3100: * estimate the model with stepm=1 month, we can keep estepm to 24 months
3101: * to compare the new estimate of Life expectancy with the same linear
3102: * hypothesis. A more precise result, taking into account a more precise
3103: * curvature will be obtained if estepm is as small as stepm. */
3104:
3105: /* For example we decided to compute the life expectancy with the smallest unit */
3106: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
3107: nhstepm is the number of hstepm from age to agelim
3108: nstepm is the number of stepm from age to agelin.
3109: Look at hpijx to understand the reason of that which relies in memory size
3110: and note for a fixed period like estepm months */
3111: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
3112: survival function given by stepm (the optimization length). Unfortunately it
3113: means that if the survival funtion is printed only each two years of age and if
3114: you sum them up and add 1 year (area under the trapezoids) you won't get the same
3115: results. So we changed our mind and took the option of the best precision.
3116: */
3117: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
3118:
3119: agelim=AGESUP;
3120: /* If stepm=6 months */
3121: /* Computed by stepm unit matrices, product of hstepm matrices, stored
3122: in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
3123:
3124: /* nhstepm age range expressed in number of stepm */
3125: nstepm=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
3126: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
3127: /* if (stepm >= YEARM) hstepm=1;*/
3128: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
3129: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3130:
3131: for (age=bage; age<=fage; age ++){
3132: nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
3133: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
3134: /* if (stepm >= YEARM) hstepm=1;*/
3135: nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
3136:
3137: /* If stepm=6 months */
3138: /* Computed by stepm unit matrices, product of hstepma matrices, stored
3139: in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
3140:
3141: hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
3142:
3143: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
3144:
3145: printf("%d|",(int)age);fflush(stdout);
3146: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
3147:
3148: /* Computing expectancies */
3149: for(i=1; i<=nlstate;i++)
3150: for(j=1; j<=nlstate;j++)
3151: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
3152: eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
3153:
3154: /* 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]);*/
3155:
3156: }
3157:
3158: fprintf(ficreseij,"%3.0f",age );
3159: for(i=1; i<=nlstate;i++){
3160: eip=0;
3161: for(j=1; j<=nlstate;j++){
3162: eip +=eij[i][j][(int)age];
3163: fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
3164: }
3165: fprintf(ficreseij,"%9.4f", eip );
3166: }
3167: fprintf(ficreseij,"\n");
3168:
3169: }
3170: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3171: printf("\n");
3172: fprintf(ficlog,"\n");
3173:
3174: }
3175:
3176: 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[] )
3177:
3178: {
3179: /* Covariances of health expectancies eij and of total life expectancies according
3180: to initial status i, ei. .
3181: */
3182: int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
3183: int nhstepma, nstepma; /* Decreasing with age */
3184: double age, agelim, hf;
3185: double ***p3matp, ***p3matm, ***varhe;
3186: double **dnewm,**doldm;
3187: double *xp, *xm;
3188: double **gp, **gm;
3189: double ***gradg, ***trgradg;
3190: int theta;
3191:
3192: double eip, vip;
3193:
3194: varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
3195: xp=vector(1,npar);
3196: xm=vector(1,npar);
3197: dnewm=matrix(1,nlstate*nlstate,1,npar);
3198: doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
3199:
3200: pstamp(ficresstdeij);
3201: fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
3202: fprintf(ficresstdeij,"# Age");
3203: for(i=1; i<=nlstate;i++){
3204: for(j=1; j<=nlstate;j++)
3205: fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
3206: fprintf(ficresstdeij," e%1d. ",i);
3207: }
3208: fprintf(ficresstdeij,"\n");
3209:
3210: pstamp(ficrescveij);
3211: fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
3212: fprintf(ficrescveij,"# Age");
3213: for(i=1; i<=nlstate;i++)
3214: for(j=1; j<=nlstate;j++){
3215: cptj= (j-1)*nlstate+i;
3216: for(i2=1; i2<=nlstate;i2++)
3217: for(j2=1; j2<=nlstate;j2++){
3218: cptj2= (j2-1)*nlstate+i2;
3219: if(cptj2 <= cptj)
3220: fprintf(ficrescveij," %1d%1d,%1d%1d",i,j,i2,j2);
3221: }
3222: }
3223: fprintf(ficrescveij,"\n");
3224:
3225: if(estepm < stepm){
3226: printf ("Problem %d lower than %d\n",estepm, stepm);
3227: }
3228: else hstepm=estepm;
3229: /* We compute the life expectancy from trapezoids spaced every estepm months
3230: * This is mainly to measure the difference between two models: for example
3231: * if stepm=24 months pijx are given only every 2 years and by summing them
3232: * we are calculating an estimate of the Life Expectancy assuming a linear
3233: * progression in between and thus overestimating or underestimating according
3234: * to the curvature of the survival function. If, for the same date, we
3235: * estimate the model with stepm=1 month, we can keep estepm to 24 months
3236: * to compare the new estimate of Life expectancy with the same linear
3237: * hypothesis. A more precise result, taking into account a more precise
3238: * curvature will be obtained if estepm is as small as stepm. */
3239:
3240: /* For example we decided to compute the life expectancy with the smallest unit */
3241: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
3242: nhstepm is the number of hstepm from age to agelim
3243: nstepm is the number of stepm from age to agelin.
3244: Look at hpijx to understand the reason of that which relies in memory size
3245: and note for a fixed period like estepm months */
3246: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
3247: survival function given by stepm (the optimization length). Unfortunately it
3248: means that if the survival funtion is printed only each two years of age and if
3249: you sum them up and add 1 year (area under the trapezoids) you won't get the same
3250: results. So we changed our mind and took the option of the best precision.
3251: */
3252: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
3253:
3254: /* If stepm=6 months */
3255: /* nhstepm age range expressed in number of stepm */
3256: agelim=AGESUP;
3257: nstepm=(int) rint((agelim-bage)*YEARM/stepm);
3258: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
3259: /* if (stepm >= YEARM) hstepm=1;*/
3260: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
3261:
3262: p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3263: p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3264: gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
3265: trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
3266: gp=matrix(0,nhstepm,1,nlstate*nlstate);
3267: gm=matrix(0,nhstepm,1,nlstate*nlstate);
3268:
3269: for (age=bage; age<=fage; age ++){
3270: nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
3271: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
3272: /* if (stepm >= YEARM) hstepm=1;*/
3273: nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
3274:
3275: /* If stepm=6 months */
3276: /* Computed by stepm unit matrices, product of hstepma matrices, stored
3277: in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
3278:
3279: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
3280:
3281: /* Computing Variances of health expectancies */
3282: /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
3283: decrease memory allocation */
3284: for(theta=1; theta <=npar; theta++){
3285: for(i=1; i<=npar; i++){
3286: xp[i] = x[i] + (i==theta ?delti[theta]:0);
3287: xm[i] = x[i] - (i==theta ?delti[theta]:0);
3288: }
3289: hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);
3290: hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);
3291:
3292: for(j=1; j<= nlstate; j++){
3293: for(i=1; i<=nlstate; i++){
3294: for(h=0; h<=nhstepm-1; h++){
3295: gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
3296: gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
3297: }
3298: }
3299: }
3300:
3301: for(ij=1; ij<= nlstate*nlstate; ij++)
3302: for(h=0; h<=nhstepm-1; h++){
3303: gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
3304: }
3305: }/* End theta */
3306:
3307:
3308: for(h=0; h<=nhstepm-1; h++)
3309: for(j=1; j<=nlstate*nlstate;j++)
3310: for(theta=1; theta <=npar; theta++)
3311: trgradg[h][j][theta]=gradg[h][theta][j];
3312:
3313:
3314: for(ij=1;ij<=nlstate*nlstate;ij++)
3315: for(ji=1;ji<=nlstate*nlstate;ji++)
3316: varhe[ij][ji][(int)age] =0.;
3317:
3318: printf("%d|",(int)age);fflush(stdout);
3319: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
3320: for(h=0;h<=nhstepm-1;h++){
3321: for(k=0;k<=nhstepm-1;k++){
3322: matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
3323: matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
3324: for(ij=1;ij<=nlstate*nlstate;ij++)
3325: for(ji=1;ji<=nlstate*nlstate;ji++)
3326: varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
3327: }
3328: }
3329:
3330: /* Computing expectancies */
3331: hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
3332: for(i=1; i<=nlstate;i++)
3333: for(j=1; j<=nlstate;j++)
3334: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
3335: eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
3336:
3337: /* 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]);*/
3338:
3339: }
3340:
3341: fprintf(ficresstdeij,"%3.0f",age );
3342: for(i=1; i<=nlstate;i++){
3343: eip=0.;
3344: vip=0.;
3345: for(j=1; j<=nlstate;j++){
3346: eip += eij[i][j][(int)age];
3347: for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
3348: vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
3349: fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
3350: }
3351: fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
3352: }
3353: fprintf(ficresstdeij,"\n");
3354:
3355: fprintf(ficrescveij,"%3.0f",age );
3356: for(i=1; i<=nlstate;i++)
3357: for(j=1; j<=nlstate;j++){
3358: cptj= (j-1)*nlstate+i;
3359: for(i2=1; i2<=nlstate;i2++)
3360: for(j2=1; j2<=nlstate;j2++){
3361: cptj2= (j2-1)*nlstate+i2;
3362: if(cptj2 <= cptj)
3363: fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
3364: }
3365: }
3366: fprintf(ficrescveij,"\n");
3367:
3368: }
3369: free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
3370: free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
3371: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
3372: free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
3373: free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3374: free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3375: printf("\n");
3376: fprintf(ficlog,"\n");
3377:
3378: free_vector(xm,1,npar);
3379: free_vector(xp,1,npar);
3380: free_matrix(dnewm,1,nlstate*nlstate,1,npar);
3381: free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
3382: free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
3383: }
3384:
3385: /************ Variance ******************/
3386: 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[])
3387: {
3388: /* Variance of health expectancies */
3389: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
3390: /* double **newm;*/
3391: /* int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav)*/
3392:
3393: int movingaverage();
3394: double **dnewm,**doldm;
3395: double **dnewmp,**doldmp;
3396: int i, j, nhstepm, hstepm, h, nstepm ;
3397: int k;
3398: double *xp;
3399: double **gp, **gm; /* for var eij */
3400: double ***gradg, ***trgradg; /*for var eij */
3401: double **gradgp, **trgradgp; /* for var p point j */
3402: double *gpp, *gmp; /* for var p point j */
3403: double **varppt; /* for var p point j nlstate to nlstate+ndeath */
3404: double ***p3mat;
3405: double age,agelim, hf;
3406: double ***mobaverage;
3407: int theta;
3408: char digit[4];
3409: char digitp[25];
3410:
3411: char fileresprobmorprev[FILENAMELENGTH];
3412:
3413: if(popbased==1){
3414: if(mobilav!=0)
3415: strcpy(digitp,"-populbased-mobilav-");
3416: else strcpy(digitp,"-populbased-nomobil-");
3417: }
3418: else
3419: strcpy(digitp,"-stablbased-");
3420:
3421: if (mobilav!=0) {
3422: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3423: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
3424: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
3425: printf(" Error in movingaverage mobilav=%d\n",mobilav);
3426: }
3427: }
3428:
3429: strcpy(fileresprobmorprev,"prmorprev");
3430: sprintf(digit,"%-d",ij);
3431: /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
3432: strcat(fileresprobmorprev,digit); /* Tvar to be done */
3433: strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
3434: strcat(fileresprobmorprev,fileres);
3435: if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
3436: printf("Problem with resultfile: %s\n", fileresprobmorprev);
3437: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
3438: }
3439: printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
3440:
3441: fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
3442: pstamp(ficresprobmorprev);
3443: 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);
3444: fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
3445: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
3446: fprintf(ficresprobmorprev," p.%-d SE",j);
3447: for(i=1; i<=nlstate;i++)
3448: fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
3449: }
3450: fprintf(ficresprobmorprev,"\n");
3451: fprintf(ficgp,"\n# Routine varevsij");
3452: /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
3453: 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");
3454: fprintf(fichtm,"\n<br>%s <br>\n",digitp);
3455: /* } */
3456: varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
3457: pstamp(ficresvij);
3458: fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n# (weighted average of eij where weights are ");
3459: if(popbased==1)
3460: 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);
3461: else
3462: fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
3463: fprintf(ficresvij,"# Age");
3464: for(i=1; i<=nlstate;i++)
3465: for(j=1; j<=nlstate;j++)
3466: fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
3467: fprintf(ficresvij,"\n");
3468:
3469: xp=vector(1,npar);
3470: dnewm=matrix(1,nlstate,1,npar);
3471: doldm=matrix(1,nlstate,1,nlstate);
3472: dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
3473: doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
3474:
3475: gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
3476: gpp=vector(nlstate+1,nlstate+ndeath);
3477: gmp=vector(nlstate+1,nlstate+ndeath);
3478: trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
3479:
3480: if(estepm < stepm){
3481: printf ("Problem %d lower than %d\n",estepm, stepm);
3482: }
3483: else hstepm=estepm;
3484: /* For example we decided to compute the life expectancy with the smallest unit */
3485: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
3486: nhstepm is the number of hstepm from age to agelim
3487: nstepm is the number of stepm from age to agelin.
3488: Look at function hpijx to understand why (it is linked to memory size questions) */
3489: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
3490: survival function given by stepm (the optimization length). Unfortunately it
3491: means that if the survival funtion is printed every two years of age and if
3492: you sum them up and add 1 year (area under the trapezoids) you won't get the same
3493: results. So we changed our mind and took the option of the best precision.
3494: */
3495: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
3496: agelim = AGESUP;
3497: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
3498: nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
3499: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
3500: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3501: gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
3502: gp=matrix(0,nhstepm,1,nlstate);
3503: gm=matrix(0,nhstepm,1,nlstate);
3504:
3505:
3506: for(theta=1; theta <=npar; theta++){
3507: for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
3508: xp[i] = x[i] + (i==theta ?delti[theta]:0);
3509: }
3510: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
3511: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
3512:
3513: if (popbased==1) {
3514: if(mobilav ==0){
3515: for(i=1; i<=nlstate;i++)
3516: prlim[i][i]=probs[(int)age][i][ij];
3517: }else{ /* mobilav */
3518: for(i=1; i<=nlstate;i++)
3519: prlim[i][i]=mobaverage[(int)age][i][ij];
3520: }
3521: }
3522:
3523: for(j=1; j<= nlstate; j++){
3524: for(h=0; h<=nhstepm; h++){
3525: for(i=1, gp[h][j]=0.;i<=nlstate;i++)
3526: gp[h][j] += prlim[i][i]*p3mat[i][j][h];
3527: }
3528: }
3529: /* This for computing probability of death (h=1 means
3530: computed over hstepm matrices product = hstepm*stepm months)
3531: as a weighted average of prlim.
3532: */
3533: for(j=nlstate+1;j<=nlstate+ndeath;j++){
3534: for(i=1,gpp[j]=0.; i<= nlstate; i++)
3535: gpp[j] += prlim[i][i]*p3mat[i][j][1];
3536: }
3537: /* end probability of death */
3538:
3539: for(i=1; i<=npar; i++) /* Computes gradient x - delta */
3540: xp[i] = x[i] - (i==theta ?delti[theta]:0);
3541: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
3542: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
3543:
3544: if (popbased==1) {
3545: if(mobilav ==0){
3546: for(i=1; i<=nlstate;i++)
3547: prlim[i][i]=probs[(int)age][i][ij];
3548: }else{ /* mobilav */
3549: for(i=1; i<=nlstate;i++)
3550: prlim[i][i]=mobaverage[(int)age][i][ij];
3551: }
3552: }
3553:
3554: for(j=1; j<= nlstate; j++){ /* Sum of wi * eij = e.j */
3555: for(h=0; h<=nhstepm; h++){
3556: for(i=1, gm[h][j]=0.;i<=nlstate;i++)
3557: gm[h][j] += prlim[i][i]*p3mat[i][j][h];
3558: }
3559: }
3560: /* This for computing probability of death (h=1 means
3561: computed over hstepm matrices product = hstepm*stepm months)
3562: as a weighted average of prlim.
3563: */
3564: for(j=nlstate+1;j<=nlstate+ndeath;j++){
3565: for(i=1,gmp[j]=0.; i<= nlstate; i++)
3566: gmp[j] += prlim[i][i]*p3mat[i][j][1];
3567: }
3568: /* end probability of death */
3569:
3570: for(j=1; j<= nlstate; j++) /* vareij */
3571: for(h=0; h<=nhstepm; h++){
3572: gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
3573: }
3574:
3575: for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
3576: gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
3577: }
3578:
3579: } /* End theta */
3580:
3581: trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
3582:
3583: for(h=0; h<=nhstepm; h++) /* veij */
3584: for(j=1; j<=nlstate;j++)
3585: for(theta=1; theta <=npar; theta++)
3586: trgradg[h][j][theta]=gradg[h][theta][j];
3587:
3588: for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
3589: for(theta=1; theta <=npar; theta++)
3590: trgradgp[j][theta]=gradgp[theta][j];
3591:
3592:
3593: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
3594: for(i=1;i<=nlstate;i++)
3595: for(j=1;j<=nlstate;j++)
3596: vareij[i][j][(int)age] =0.;
3597:
3598: for(h=0;h<=nhstepm;h++){
3599: for(k=0;k<=nhstepm;k++){
3600: matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
3601: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
3602: for(i=1;i<=nlstate;i++)
3603: for(j=1;j<=nlstate;j++)
3604: vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
3605: }
3606: }
3607:
3608: /* pptj */
3609: matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
3610: matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
3611: for(j=nlstate+1;j<=nlstate+ndeath;j++)
3612: for(i=nlstate+1;i<=nlstate+ndeath;i++)
3613: varppt[j][i]=doldmp[j][i];
3614: /* end ppptj */
3615: /* x centered again */
3616: hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);
3617: prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
3618:
3619: if (popbased==1) {
3620: if(mobilav ==0){
3621: for(i=1; i<=nlstate;i++)
3622: prlim[i][i]=probs[(int)age][i][ij];
3623: }else{ /* mobilav */
3624: for(i=1; i<=nlstate;i++)
3625: prlim[i][i]=mobaverage[(int)age][i][ij];
3626: }
3627: }
3628:
3629: /* This for computing probability of death (h=1 means
3630: computed over hstepm (estepm) matrices product = hstepm*stepm months)
3631: as a weighted average of prlim.
3632: */
3633: for(j=nlstate+1;j<=nlstate+ndeath;j++){
3634: for(i=1,gmp[j]=0.;i<= nlstate; i++)
3635: gmp[j] += prlim[i][i]*p3mat[i][j][1];
3636: }
3637: /* end probability of death */
3638:
3639: fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
3640: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
3641: fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
3642: for(i=1; i<=nlstate;i++){
3643: fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
3644: }
3645: }
3646: fprintf(ficresprobmorprev,"\n");
3647:
3648: fprintf(ficresvij,"%.0f ",age );
3649: for(i=1; i<=nlstate;i++)
3650: for(j=1; j<=nlstate;j++){
3651: fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
3652: }
3653: fprintf(ficresvij,"\n");
3654: free_matrix(gp,0,nhstepm,1,nlstate);
3655: free_matrix(gm,0,nhstepm,1,nlstate);
3656: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
3657: free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
3658: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3659: } /* End age */
3660: free_vector(gpp,nlstate+1,nlstate+ndeath);
3661: free_vector(gmp,nlstate+1,nlstate+ndeath);
3662: free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
3663: free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
3664: fprintf(ficgp,"\nunset parametric;unset label; set ter png small size 320, 240");
3665: /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
3666: fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
3667: /* fprintf(ficgp,"\n plot \"%s\" u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
3668: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
3669: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
3670: fprintf(ficgp,"\n plot \"%s\" u 1:($3) not w l lt 1 ",subdirf(fileresprobmorprev));
3671: fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)) t \"95%% interval\" w l lt 2 ",subdirf(fileresprobmorprev));
3672: fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)) not w l lt 2 ",subdirf(fileresprobmorprev));
3673: fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
3674: 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);
3675: /* 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);
3676: */
3677: /* fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
3678: fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
3679:
3680: free_vector(xp,1,npar);
3681: free_matrix(doldm,1,nlstate,1,nlstate);
3682: free_matrix(dnewm,1,nlstate,1,npar);
3683: free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
3684: free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
3685: free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
3686: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3687: fclose(ficresprobmorprev);
3688: fflush(ficgp);
3689: fflush(fichtm);
3690: } /* end varevsij */
3691:
3692: /************ Variance of prevlim ******************/
3693: 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[])
3694: {
3695: /* Variance of prevalence limit */
3696: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
3697:
3698: double **dnewm,**doldm;
3699: int i, j, nhstepm, hstepm;
3700: double *xp;
3701: double *gp, *gm;
3702: double **gradg, **trgradg;
3703: double age,agelim;
3704: int theta;
3705:
3706: pstamp(ficresvpl);
3707: fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
3708: fprintf(ficresvpl,"# Age");
3709: for(i=1; i<=nlstate;i++)
3710: fprintf(ficresvpl," %1d-%1d",i,i);
3711: fprintf(ficresvpl,"\n");
3712:
3713: xp=vector(1,npar);
3714: dnewm=matrix(1,nlstate,1,npar);
3715: doldm=matrix(1,nlstate,1,nlstate);
3716:
3717: hstepm=1*YEARM; /* Every year of age */
3718: hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
3719: agelim = AGESUP;
3720: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
3721: nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
3722: if (stepm >= YEARM) hstepm=1;
3723: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
3724: gradg=matrix(1,npar,1,nlstate);
3725: gp=vector(1,nlstate);
3726: gm=vector(1,nlstate);
3727:
3728: for(theta=1; theta <=npar; theta++){
3729: for(i=1; i<=npar; i++){ /* Computes gradient */
3730: xp[i] = x[i] + (i==theta ?delti[theta]:0);
3731: }
3732: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
3733: for(i=1;i<=nlstate;i++)
3734: gp[i] = prlim[i][i];
3735:
3736: for(i=1; i<=npar; i++) /* Computes gradient */
3737: xp[i] = x[i] - (i==theta ?delti[theta]:0);
3738: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
3739: for(i=1;i<=nlstate;i++)
3740: gm[i] = prlim[i][i];
3741:
3742: for(i=1;i<=nlstate;i++)
3743: gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
3744: } /* End theta */
3745:
3746: trgradg =matrix(1,nlstate,1,npar);
3747:
3748: for(j=1; j<=nlstate;j++)
3749: for(theta=1; theta <=npar; theta++)
3750: trgradg[j][theta]=gradg[theta][j];
3751:
3752: for(i=1;i<=nlstate;i++)
3753: varpl[i][(int)age] =0.;
3754: matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
3755: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
3756: for(i=1;i<=nlstate;i++)
3757: varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
3758:
3759: fprintf(ficresvpl,"%.0f ",age );
3760: for(i=1; i<=nlstate;i++)
3761: fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
3762: fprintf(ficresvpl,"\n");
3763: free_vector(gp,1,nlstate);
3764: free_vector(gm,1,nlstate);
3765: free_matrix(gradg,1,npar,1,nlstate);
3766: free_matrix(trgradg,1,nlstate,1,npar);
3767: } /* End age */
3768:
3769: free_vector(xp,1,npar);
3770: free_matrix(doldm,1,nlstate,1,npar);
3771: free_matrix(dnewm,1,nlstate,1,nlstate);
3772:
3773: }
3774:
3775: /************ Variance of one-step probabilities ******************/
3776: 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[])
3777: {
3778: int i, j=0, k1, l1, tj;
3779: int k2, l2, j1, z1;
3780: int k=0, l;
3781: int first=1, first1, first2;
3782: double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
3783: double **dnewm,**doldm;
3784: double *xp;
3785: double *gp, *gm;
3786: double **gradg, **trgradg;
3787: double **mu;
3788: double age, cov[NCOVMAX+1];
3789: double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
3790: int theta;
3791: char fileresprob[FILENAMELENGTH];
3792: char fileresprobcov[FILENAMELENGTH];
3793: char fileresprobcor[FILENAMELENGTH];
3794: double ***varpij;
3795:
3796: strcpy(fileresprob,"prob");
3797: strcat(fileresprob,fileres);
3798: if((ficresprob=fopen(fileresprob,"w"))==NULL) {
3799: printf("Problem with resultfile: %s\n", fileresprob);
3800: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
3801: }
3802: strcpy(fileresprobcov,"probcov");
3803: strcat(fileresprobcov,fileres);
3804: if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
3805: printf("Problem with resultfile: %s\n", fileresprobcov);
3806: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
3807: }
3808: strcpy(fileresprobcor,"probcor");
3809: strcat(fileresprobcor,fileres);
3810: if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
3811: printf("Problem with resultfile: %s\n", fileresprobcor);
3812: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
3813: }
3814: printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
3815: fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
3816: printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
3817: fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
3818: printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
3819: fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
3820: pstamp(ficresprob);
3821: fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
3822: fprintf(ficresprob,"# Age");
3823: pstamp(ficresprobcov);
3824: fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
3825: fprintf(ficresprobcov,"# Age");
3826: pstamp(ficresprobcor);
3827: fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
3828: fprintf(ficresprobcor,"# Age");
3829:
3830:
3831: for(i=1; i<=nlstate;i++)
3832: for(j=1; j<=(nlstate+ndeath);j++){
3833: fprintf(ficresprob," p%1d-%1d (SE)",i,j);
3834: fprintf(ficresprobcov," p%1d-%1d ",i,j);
3835: fprintf(ficresprobcor," p%1d-%1d ",i,j);
3836: }
3837: /* fprintf(ficresprob,"\n");
3838: fprintf(ficresprobcov,"\n");
3839: fprintf(ficresprobcor,"\n");
3840: */
3841: xp=vector(1,npar);
3842: dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
3843: doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
3844: mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
3845: varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
3846: first=1;
3847: fprintf(ficgp,"\n# Routine varprob");
3848: fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
3849: fprintf(fichtm,"\n");
3850:
3851: fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
3852: fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
3853: file %s<br>\n",optionfilehtmcov);
3854: fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
3855: and drawn. It helps understanding how is the covariance between two incidences.\
3856: They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
3857: 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. \
3858: It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
3859: would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
3860: standard deviations wide on each axis. <br>\
3861: Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
3862: and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
3863: To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
3864:
3865: cov[1]=1;
3866: /* tj=cptcoveff; */
3867: tj = (int) pow(2,cptcoveff);
3868: if (cptcovn<1) {tj=1;ncodemax[1]=1;}
3869: j1=0;
3870: for(j1=1; j1<=tj;j1++){
3871: /*for(i1=1; i1<=ncodemax[t];i1++){ */
3872: /*j1++;*/
3873: if (cptcovn>0) {
3874: fprintf(ficresprob, "\n#********** Variable ");
3875: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3876: fprintf(ficresprob, "**********\n#\n");
3877: fprintf(ficresprobcov, "\n#********** Variable ");
3878: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3879: fprintf(ficresprobcov, "**********\n#\n");
3880:
3881: fprintf(ficgp, "\n#********** Variable ");
3882: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3883: fprintf(ficgp, "**********\n#\n");
3884:
3885:
3886: fprintf(fichtmcov, "\n<hr size=\"2\" color=\"#EC5E5E\">********** Variable ");
3887: for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3888: fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
3889:
3890: fprintf(ficresprobcor, "\n#********** Variable ");
3891: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3892: fprintf(ficresprobcor, "**********\n#");
3893: }
3894:
3895: gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
3896: trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
3897: gp=vector(1,(nlstate)*(nlstate+ndeath));
3898: gm=vector(1,(nlstate)*(nlstate+ndeath));
3899: for (age=bage; age<=fage; age ++){
3900: cov[2]=age;
3901: for (k=1; k<=cptcovn;k++) {
3902: cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];/* j1 1 2 3 4
3903: * 1 1 1 1 1
3904: * 2 2 1 1 1
3905: * 3 1 2 1 1
3906: */
3907: /* nbcode[1][1]=0 nbcode[1][2]=1;*/
3908: }
3909: for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
3910: for (k=1; k<=cptcovprod;k++)
3911: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
3912:
3913:
3914: for(theta=1; theta <=npar; theta++){
3915: for(i=1; i<=npar; i++)
3916: xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
3917:
3918: pmij(pmmij,cov,ncovmodel,xp,nlstate);
3919:
3920: k=0;
3921: for(i=1; i<= (nlstate); i++){
3922: for(j=1; j<=(nlstate+ndeath);j++){
3923: k=k+1;
3924: gp[k]=pmmij[i][j];
3925: }
3926: }
3927:
3928: for(i=1; i<=npar; i++)
3929: xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
3930:
3931: pmij(pmmij,cov,ncovmodel,xp,nlstate);
3932: k=0;
3933: for(i=1; i<=(nlstate); i++){
3934: for(j=1; j<=(nlstate+ndeath);j++){
3935: k=k+1;
3936: gm[k]=pmmij[i][j];
3937: }
3938: }
3939:
3940: for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)
3941: gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];
3942: }
3943:
3944: for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
3945: for(theta=1; theta <=npar; theta++)
3946: trgradg[j][theta]=gradg[theta][j];
3947:
3948: matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);
3949: matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
3950:
3951: pmij(pmmij,cov,ncovmodel,x,nlstate);
3952:
3953: k=0;
3954: for(i=1; i<=(nlstate); i++){
3955: for(j=1; j<=(nlstate+ndeath);j++){
3956: k=k+1;
3957: mu[k][(int) age]=pmmij[i][j];
3958: }
3959: }
3960: for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
3961: for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
3962: varpij[i][j][(int)age] = doldm[i][j];
3963:
3964: /*printf("\n%d ",(int)age);
3965: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
3966: printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
3967: fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
3968: }*/
3969:
3970: fprintf(ficresprob,"\n%d ",(int)age);
3971: fprintf(ficresprobcov,"\n%d ",(int)age);
3972: fprintf(ficresprobcor,"\n%d ",(int)age);
3973:
3974: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
3975: fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
3976: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
3977: fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
3978: fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
3979: }
3980: i=0;
3981: for (k=1; k<=(nlstate);k++){
3982: for (l=1; l<=(nlstate+ndeath);l++){
3983: i++;
3984: fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
3985: fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
3986: for (j=1; j<=i;j++){
3987: /* printf(" k=%d l=%d i=%d j=%d\n",k,l,i,j);fflush(stdout); */
3988: fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
3989: fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
3990: }
3991: }
3992: }/* end of loop for state */
3993: } /* end of loop for age */
3994: free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
3995: free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
3996: free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
3997: free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
3998:
3999: /* Confidence intervalle of pij */
4000: /*
4001: fprintf(ficgp,"\nunset parametric;unset label");
4002: fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
4003: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
4004: 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);
4005: fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
4006: fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
4007: fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
4008: */
4009:
4010: /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
4011: first1=1;first2=2;
4012: for (k2=1; k2<=(nlstate);k2++){
4013: for (l2=1; l2<=(nlstate+ndeath);l2++){
4014: if(l2==k2) continue;
4015: j=(k2-1)*(nlstate+ndeath)+l2;
4016: for (k1=1; k1<=(nlstate);k1++){
4017: for (l1=1; l1<=(nlstate+ndeath);l1++){
4018: if(l1==k1) continue;
4019: i=(k1-1)*(nlstate+ndeath)+l1;
4020: if(i<=j) continue;
4021: for (age=bage; age<=fage; age ++){
4022: if ((int)age %5==0){
4023: v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
4024: v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
4025: cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
4026: mu1=mu[i][(int) age]/stepm*YEARM ;
4027: mu2=mu[j][(int) age]/stepm*YEARM;
4028: c12=cv12/sqrt(v1*v2);
4029: /* Computing eigen value of matrix of covariance */
4030: lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
4031: lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
4032: if ((lc2 <0) || (lc1 <0) ){
4033: if(first2==1){
4034: first1=0;
4035: 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);
4036: }
4037: 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);
4038: /* lc1=fabs(lc1); */ /* If we want to have them positive */
4039: /* lc2=fabs(lc2); */
4040: }
4041:
4042: /* Eigen vectors */
4043: v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
4044: /*v21=sqrt(1.-v11*v11); *//* error */
4045: v21=(lc1-v1)/cv12*v11;
4046: v12=-v21;
4047: v22=v11;
4048: tnalp=v21/v11;
4049: if(first1==1){
4050: first1=0;
4051: 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);
4052: }
4053: 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);
4054: /*printf(fignu*/
4055: /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
4056: /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
4057: if(first==1){
4058: first=0;
4059: fprintf(ficgp,"\nset parametric;unset label");
4060: 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);
4061: fprintf(ficgp,"\nset ter png small size 320, 240");
4062: fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
4063: :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
4064: %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
4065: subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
4066: subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
4067: fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
4068: fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
4069: fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
4070: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
4071: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
4072: 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",\
4073: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
4074: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
4075: }else{
4076: first=0;
4077: fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
4078: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
4079: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
4080: 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",\
4081: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
4082: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
4083: }/* if first */
4084: } /* age mod 5 */
4085: } /* end loop age */
4086: fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
4087: first=1;
4088: } /*l12 */
4089: } /* k12 */
4090: } /*l1 */
4091: }/* k1 */
4092: /* } */ /* loop covariates */
4093: }
4094: free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
4095: free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
4096: free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
4097: free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
4098: free_vector(xp,1,npar);
4099: fclose(ficresprob);
4100: fclose(ficresprobcov);
4101: fclose(ficresprobcor);
4102: fflush(ficgp);
4103: fflush(fichtmcov);
4104: }
4105:
4106:
4107: /******************* Printing html file ***********/
4108: void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
4109: int lastpass, int stepm, int weightopt, char model[],\
4110: int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
4111: int popforecast, int estepm ,\
4112: double jprev1, double mprev1,double anprev1, \
4113: double jprev2, double mprev2,double anprev2){
4114: int jj1, k1, i1, cpt;
4115:
4116: fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
4117: <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
4118: </ul>");
4119: fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \
4120: - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
4121: jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
4122: fprintf(fichtm,"\
4123: - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
4124: stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
4125: fprintf(fichtm,"\
4126: - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
4127: subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
4128: fprintf(fichtm,"\
4129: - (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): \
4130: <a href=\"%s\">%s</a> <br>\n",
4131: estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
4132: fprintf(fichtm,"\
4133: - Population projections by age and states: \
4134: <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileres,"f"),subdirf2(fileres,"f"));
4135:
4136: fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
4137:
4138: m=pow(2,cptcoveff);
4139: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
4140:
4141: jj1=0;
4142: for(k1=1; k1<=m;k1++){
4143: for(i1=1; i1<=ncodemax[k1];i1++){
4144: jj1++;
4145: if (cptcovn > 0) {
4146: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
4147: for (cpt=1; cpt<=cptcoveff;cpt++)
4148: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
4149: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
4150: }
4151: /* Pij */
4152: 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> \
4153: <img src=\"%s%d_1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
4154: /* Quasi-incidences */
4155: fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
4156: 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> \
4157: <img src=\"%s%d_2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
4158: /* Period (stable) prevalence in each health state */
4159: for(cpt=1; cpt<=nlstate;cpt++){
4160: 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> \
4161: <img src=\"%s%d_%d.png\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
4162: }
4163: for(cpt=1; cpt<=nlstate;cpt++) {
4164: 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> \
4165: <img src=\"%s%d%d.png\">",cpt,nlstate,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
4166: }
4167: } /* end i1 */
4168: }/* End k1 */
4169: fprintf(fichtm,"</ul>");
4170:
4171:
4172: fprintf(fichtm,"\
4173: \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
4174: - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);
4175:
4176: fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
4177: subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
4178: fprintf(fichtm,"\
4179: - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
4180: subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
4181:
4182: fprintf(fichtm,"\
4183: - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
4184: subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
4185: fprintf(fichtm,"\
4186: - 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): \
4187: <a href=\"%s\">%s</a> <br>\n</li>",
4188: estepm,subdirf2(fileres,"cve"),subdirf2(fileres,"cve"));
4189: fprintf(fichtm,"\
4190: - (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): \
4191: <a href=\"%s\">%s</a> <br>\n</li>",
4192: estepm,subdirf2(fileres,"stde"),subdirf2(fileres,"stde"));
4193: fprintf(fichtm,"\
4194: - 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",
4195: estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
4196: fprintf(fichtm,"\
4197: - 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",
4198: estepm, subdirf2(fileres,"t"),subdirf2(fileres,"t"));
4199: fprintf(fichtm,"\
4200: - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
4201: subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
4202:
4203: /* if(popforecast==1) fprintf(fichtm,"\n */
4204: /* - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
4205: /* - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
4206: /* <br>",fileres,fileres,fileres,fileres); */
4207: /* else */
4208: /* 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); */
4209: fflush(fichtm);
4210: fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
4211:
4212: m=pow(2,cptcoveff);
4213: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
4214:
4215: jj1=0;
4216: for(k1=1; k1<=m;k1++){
4217: for(i1=1; i1<=ncodemax[k1];i1++){
4218: jj1++;
4219: if (cptcovn > 0) {
4220: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
4221: for (cpt=1; cpt<=cptcoveff;cpt++)
4222: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
4223: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
4224: }
4225: for(cpt=1; cpt<=nlstate;cpt++) {
4226: fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
4227: prevalence (with 95%% confidence interval) in state (%d): %s%d_%d.png <br>\
4228: <img src=\"%s%d_%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);
4229: }
4230: fprintf(fichtm,"\n<br>- Total life expectancy by age and \
4231: health expectancies in states (1) and (2). If popbased=1 the smooth (due to the model) \
4232: true period expectancies (those weighted with period prevalences are also\
4233: drawn in addition to the population based expectancies computed using\
4234: observed and cahotic prevalences: %s%d.png<br>\
4235: <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
4236: } /* end i1 */
4237: }/* End k1 */
4238: fprintf(fichtm,"</ul>");
4239: fflush(fichtm);
4240: }
4241:
4242: /******************* Gnuplot file **************/
4243: void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
4244:
4245: char dirfileres[132],optfileres[132];
4246: int cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,ij=0,l=0;
4247: int ng=0;
4248: /* if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
4249: /* printf("Problem with file %s",optionfilegnuplot); */
4250: /* fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
4251: /* } */
4252:
4253: /*#ifdef windows */
4254: fprintf(ficgp,"cd \"%s\" \n",pathc);
4255: /*#endif */
4256: m=pow(2,cptcoveff);
4257:
4258: strcpy(dirfileres,optionfilefiname);
4259: strcpy(optfileres,"vpl");
4260: /* 1eme*/
4261: fprintf(ficgp,"\n# 1st: Period (stable) prevalence with CI: 'vpl' files\n");
4262: for (cpt=1; cpt<= nlstate ; cpt ++) {
4263: for (k1=1; k1<= m ; k1 ++) { /* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */
4264: fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
4265: fprintf(ficgp,"\n#set out \"v%s%d_%d.png\" \n",optionfilefiname,cpt,k1);
4266: fprintf(ficgp,"set xlabel \"Age\" \n\
4267: set ylabel \"Probability\" \n\
4268: set ter png small size 320, 240\n\
4269: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
4270:
4271: for (i=1; i<= nlstate ; i ++) {
4272: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
4273: else fprintf(ficgp," %%*lf (%%*lf)");
4274: }
4275: 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);
4276: for (i=1; i<= nlstate ; i ++) {
4277: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
4278: else fprintf(ficgp," %%*lf (%%*lf)");
4279: }
4280: fprintf(ficgp,"\" t\"95%% CI\" w l lt 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
4281: for (i=1; i<= nlstate ; i ++) {
4282: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
4283: else fprintf(ficgp," %%*lf (%%*lf)");
4284: }
4285: fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l lt 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
4286: }
4287: }
4288: /*2 eme*/
4289: fprintf(ficgp,"\n# 2nd: Total life expectancy with CI: 't' files\n");
4290: for (k1=1; k1<= m ; k1 ++) {
4291: fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
4292: fprintf(ficgp,"set ylabel \"Years\" \nset ter png small size 320, 240\nplot [%.f:%.f] ",ageminpar,fage);
4293:
4294: for (i=1; i<= nlstate+1 ; i ++) {
4295: k=2*i;
4296: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
4297: for (j=1; j<= nlstate+1 ; j ++) {
4298: if (j==i) fprintf(ficgp," %%lf (%%lf)");
4299: else fprintf(ficgp," %%*lf (%%*lf)");
4300: }
4301: if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
4302: else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
4303: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
4304: for (j=1; j<= nlstate+1 ; j ++) {
4305: if (j==i) fprintf(ficgp," %%lf (%%lf)");
4306: else fprintf(ficgp," %%*lf (%%*lf)");
4307: }
4308: fprintf(ficgp,"\" t\"\" w l lt 0,");
4309: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
4310: for (j=1; j<= nlstate+1 ; j ++) {
4311: if (j==i) fprintf(ficgp," %%lf (%%lf)");
4312: else fprintf(ficgp," %%*lf (%%*lf)");
4313: }
4314: if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l lt 0");
4315: else fprintf(ficgp,"\" t\"\" w l lt 0,");
4316: }
4317: }
4318:
4319: /*3eme*/
4320:
4321: for (k1=1; k1<= m ; k1 ++) {
4322: for (cpt=1; cpt<= nlstate ; cpt ++) {
4323: /* k=2+nlstate*(2*cpt-2); */
4324: k=2+(nlstate+1)*(cpt-1);
4325: fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
4326: fprintf(ficgp,"set ter png small size 320, 240\n\
4327: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
4328: /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
4329: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
4330: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
4331: fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
4332: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
4333: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
4334:
4335: */
4336: for (i=1; i< nlstate ; i ++) {
4337: 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);
4338: /* 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);*/
4339:
4340: }
4341: fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+nlstate,cpt);
4342: }
4343: }
4344:
4345: /* CV preval stable (period) */
4346: for (k1=1; k1<= m ; k1 ++) { /* For each multivariate if any */
4347: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
4348: k=3;
4349: fprintf(ficgp,"\n#\n#\n#CV preval stable (period): 'pij' files, cov=%d state=%d",k1, cpt);
4350: fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
4351: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
4352: set ter png small size 320, 240\n\
4353: unset log y\n\
4354: plot [%.f:%.f] ", ageminpar, agemaxpar);
4355: for (i=1; i<= nlstate ; i ++){
4356: if(i==1)
4357: fprintf(ficgp,"\"%s\"",subdirf2(fileres,"pij"));
4358: else
4359: fprintf(ficgp,", '' ");
4360: l=(nlstate+ndeath)*(i-1)+1;
4361: fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
4362: for (j=1; j<= (nlstate-1) ; j ++)
4363: fprintf(ficgp,"+$%d",k+l+j);
4364: fprintf(ficgp,")) t \"prev(%d,%d)\" w l",i,cpt);
4365: } /* nlstate */
4366: fprintf(ficgp,"\n");
4367: } /* end cpt state*/
4368: } /* end covariate */
4369:
4370: /* proba elementaires */
4371: for(i=1,jk=1; i <=nlstate; i++){
4372: for(k=1; k <=(nlstate+ndeath); k++){
4373: if (k != i) {
4374: for(j=1; j <=ncovmodel; j++){
4375: fprintf(ficgp,"p%d=%f ",jk,p[jk]);
4376: jk++;
4377: fprintf(ficgp,"\n");
4378: }
4379: }
4380: }
4381: }
4382: /*goto avoid;*/
4383: for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
4384: for(jk=1; jk <=m; jk++) {
4385: fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng);
4386: if (ng==2)
4387: fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
4388: else
4389: fprintf(ficgp,"\nset title \"Probability\"\n");
4390: fprintf(ficgp,"\nset ter png small size 320, 240\nset log y\nplot [%.f:%.f] ",ageminpar,agemaxpar);
4391: i=1;
4392: for(k2=1; k2<=nlstate; k2++) {
4393: k3=i;
4394: for(k=1; k<=(nlstate+ndeath); k++) {
4395: if (k != k2){
4396: if(ng==2)
4397: fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
4398: else
4399: fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
4400: ij=1;/* To be checked else nbcode[0][0] wrong */
4401: for(j=3; j <=ncovmodel; j++) {
4402: /* if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) { /\* Bug valgrind *\/ */
4403: /* /\*fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);*\/ */
4404: /* ij++; */
4405: /* } */
4406: /* else */
4407: fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
4408: }
4409: fprintf(ficgp,")/(1");
4410:
4411: for(k1=1; k1 <=nlstate; k1++){
4412: fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
4413: ij=1;
4414: for(j=3; j <=ncovmodel; j++){
4415: /* if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) { */
4416: /* fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]); */
4417: /* ij++; */
4418: /* } */
4419: /* else */
4420: fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
4421: }
4422: fprintf(ficgp,")");
4423: }
4424: fprintf(ficgp,") t \"p%d%d\" ", k2,k);
4425: if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
4426: i=i+ncovmodel;
4427: }
4428: } /* end k */
4429: } /* end k2 */
4430: } /* end jk */
4431: } /* end ng */
4432: /* avoid: */
4433: fflush(ficgp);
4434: } /* end gnuplot */
4435:
4436:
4437: /*************** Moving average **************/
4438: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
4439:
4440: int i, cpt, cptcod;
4441: int modcovmax =1;
4442: int mobilavrange, mob;
4443: double age;
4444:
4445: modcovmax=2*cptcoveff;/* Max number of modalities. We suppose
4446: a covariate has 2 modalities */
4447: if (cptcovn<1) modcovmax=1; /* At least 1 pass */
4448:
4449: if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
4450: if(mobilav==1) mobilavrange=5; /* default */
4451: else mobilavrange=mobilav;
4452: for (age=bage; age<=fage; age++)
4453: for (i=1; i<=nlstate;i++)
4454: for (cptcod=1;cptcod<=modcovmax;cptcod++)
4455: mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
4456: /* We keep the original values on the extreme ages bage, fage and for
4457: fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
4458: we use a 5 terms etc. until the borders are no more concerned.
4459: */
4460: for (mob=3;mob <=mobilavrange;mob=mob+2){
4461: for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
4462: for (i=1; i<=nlstate;i++){
4463: for (cptcod=1;cptcod<=modcovmax;cptcod++){
4464: mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
4465: for (cpt=1;cpt<=(mob-1)/2;cpt++){
4466: mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
4467: mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
4468: }
4469: mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
4470: }
4471: }
4472: }/* end age */
4473: }/* end mob */
4474: }else return -1;
4475: return 0;
4476: }/* End movingaverage */
4477:
4478:
4479: /************** Forecasting ******************/
4480: 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){
4481: /* proj1, year, month, day of starting projection
4482: agemin, agemax range of age
4483: dateprev1 dateprev2 range of dates during which prevalence is computed
4484: anproj2 year of en of projection (same day and month as proj1).
4485: */
4486: int yearp, stepsize, hstepm, nhstepm, j, k, cptcod, i, h, i1;
4487: double agec; /* generic age */
4488: double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
4489: double *popeffectif,*popcount;
4490: double ***p3mat;
4491: double ***mobaverage;
4492: char fileresf[FILENAMELENGTH];
4493:
4494: agelim=AGESUP;
4495: prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
4496:
4497: strcpy(fileresf,"f");
4498: strcat(fileresf,fileres);
4499: if((ficresf=fopen(fileresf,"w"))==NULL) {
4500: printf("Problem with forecast resultfile: %s\n", fileresf);
4501: fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
4502: }
4503: printf("Computing forecasting: result on file '%s' \n", fileresf);
4504: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
4505:
4506: if (cptcoveff==0) ncodemax[cptcoveff]=1;
4507:
4508: if (mobilav!=0) {
4509: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4510: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
4511: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
4512: printf(" Error in movingaverage mobilav=%d\n",mobilav);
4513: }
4514: }
4515:
4516: stepsize=(int) (stepm+YEARM-1)/YEARM;
4517: if (stepm<=12) stepsize=1;
4518: if(estepm < stepm){
4519: printf ("Problem %d lower than %d\n",estepm, stepm);
4520: }
4521: else hstepm=estepm;
4522:
4523: hstepm=hstepm/stepm;
4524: yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp and
4525: fractional in yp1 */
4526: anprojmean=yp;
4527: yp2=modf((yp1*12),&yp);
4528: mprojmean=yp;
4529: yp1=modf((yp2*30.5),&yp);
4530: jprojmean=yp;
4531: if(jprojmean==0) jprojmean=1;
4532: if(mprojmean==0) jprojmean=1;
4533:
4534: i1=cptcoveff;
4535: if (cptcovn < 1){i1=1;}
4536:
4537: fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);
4538:
4539: fprintf(ficresf,"#****** Routine prevforecast **\n");
4540:
4541: /* if (h==(int)(YEARM*yearp)){ */
4542: for(cptcov=1, k=0;cptcov<=i1;cptcov++){
4543: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
4544: k=k+1;
4545: fprintf(ficresf,"\n#******");
4546: for(j=1;j<=cptcoveff;j++) {
4547: 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]]);
4548: }
4549: fprintf(ficresf,"******\n");
4550: fprintf(ficresf,"# Covariate valuofcovar yearproj age");
4551: for(j=1; j<=nlstate+ndeath;j++){
4552: for(i=1; i<=nlstate;i++)
4553: fprintf(ficresf," p%d%d",i,j);
4554: fprintf(ficresf," p.%d",j);
4555: }
4556: for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {
4557: fprintf(ficresf,"\n");
4558: fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);
4559:
4560: for (agec=fage; agec>=(ageminpar-1); agec--){
4561: nhstepm=(int) rint((agelim-agec)*YEARM/stepm);
4562: nhstepm = nhstepm/hstepm;
4563: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4564: oldm=oldms;savm=savms;
4565: hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);
4566:
4567: for (h=0; h<=nhstepm; h++){
4568: if (h*hstepm/YEARM*stepm ==yearp) {
4569: fprintf(ficresf,"\n");
4570: for(j=1;j<=cptcoveff;j++)
4571: fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4572: fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
4573: }
4574: for(j=1; j<=nlstate+ndeath;j++) {
4575: ppij=0.;
4576: for(i=1; i<=nlstate;i++) {
4577: if (mobilav==1)
4578: ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
4579: else {
4580: ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
4581: }
4582: if (h*hstepm/YEARM*stepm== yearp) {
4583: fprintf(ficresf," %.3f", p3mat[i][j][h]);
4584: }
4585: } /* end i */
4586: if (h*hstepm/YEARM*stepm==yearp) {
4587: fprintf(ficresf," %.3f", ppij);
4588: }
4589: }/* end j */
4590: } /* end h */
4591: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4592: } /* end agec */
4593: } /* end yearp */
4594: } /* end cptcod */
4595: } /* end cptcov */
4596:
4597: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4598:
4599: fclose(ficresf);
4600: }
4601:
4602: /************** Forecasting *****not tested NB*************/
4603: 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){
4604:
4605: int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
4606: int *popage;
4607: double calagedatem, agelim, kk1, kk2;
4608: double *popeffectif,*popcount;
4609: double ***p3mat,***tabpop,***tabpopprev;
4610: double ***mobaverage;
4611: char filerespop[FILENAMELENGTH];
4612:
4613: tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4614: tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4615: agelim=AGESUP;
4616: calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
4617:
4618: prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
4619:
4620:
4621: strcpy(filerespop,"pop");
4622: strcat(filerespop,fileres);
4623: if((ficrespop=fopen(filerespop,"w"))==NULL) {
4624: printf("Problem with forecast resultfile: %s\n", filerespop);
4625: fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
4626: }
4627: printf("Computing forecasting: result on file '%s' \n", filerespop);
4628: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
4629:
4630: if (cptcoveff==0) ncodemax[cptcoveff]=1;
4631:
4632: if (mobilav!=0) {
4633: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4634: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
4635: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
4636: printf(" Error in movingaverage mobilav=%d\n",mobilav);
4637: }
4638: }
4639:
4640: stepsize=(int) (stepm+YEARM-1)/YEARM;
4641: if (stepm<=12) stepsize=1;
4642:
4643: agelim=AGESUP;
4644:
4645: hstepm=1;
4646: hstepm=hstepm/stepm;
4647:
4648: if (popforecast==1) {
4649: if((ficpop=fopen(popfile,"r"))==NULL) {
4650: printf("Problem with population file : %s\n",popfile);exit(0);
4651: fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
4652: }
4653: popage=ivector(0,AGESUP);
4654: popeffectif=vector(0,AGESUP);
4655: popcount=vector(0,AGESUP);
4656:
4657: i=1;
4658: while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
4659:
4660: imx=i;
4661: for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
4662: }
4663:
4664: for(cptcov=1,k=0;cptcov<=i2;cptcov++){
4665: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
4666: k=k+1;
4667: fprintf(ficrespop,"\n#******");
4668: for(j=1;j<=cptcoveff;j++) {
4669: fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4670: }
4671: fprintf(ficrespop,"******\n");
4672: fprintf(ficrespop,"# Age");
4673: for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
4674: if (popforecast==1) fprintf(ficrespop," [Population]");
4675:
4676: for (cpt=0; cpt<=0;cpt++) {
4677: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
4678:
4679: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
4680: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
4681: nhstepm = nhstepm/hstepm;
4682:
4683: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4684: oldm=oldms;savm=savms;
4685: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
4686:
4687: for (h=0; h<=nhstepm; h++){
4688: if (h==(int) (calagedatem+YEARM*cpt)) {
4689: fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
4690: }
4691: for(j=1; j<=nlstate+ndeath;j++) {
4692: kk1=0.;kk2=0;
4693: for(i=1; i<=nlstate;i++) {
4694: if (mobilav==1)
4695: kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
4696: else {
4697: kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
4698: }
4699: }
4700: if (h==(int)(calagedatem+12*cpt)){
4701: tabpop[(int)(agedeb)][j][cptcod]=kk1;
4702: /*fprintf(ficrespop," %.3f", kk1);
4703: if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
4704: }
4705: }
4706: for(i=1; i<=nlstate;i++){
4707: kk1=0.;
4708: for(j=1; j<=nlstate;j++){
4709: kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];
4710: }
4711: tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
4712: }
4713:
4714: if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++)
4715: fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
4716: }
4717: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4718: }
4719: }
4720:
4721: /******/
4722:
4723: for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {
4724: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
4725: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
4726: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
4727: nhstepm = nhstepm/hstepm;
4728:
4729: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4730: oldm=oldms;savm=savms;
4731: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
4732: for (h=0; h<=nhstepm; h++){
4733: if (h==(int) (calagedatem+YEARM*cpt)) {
4734: fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
4735: }
4736: for(j=1; j<=nlstate+ndeath;j++) {
4737: kk1=0.;kk2=0;
4738: for(i=1; i<=nlstate;i++) {
4739: kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];
4740: }
4741: if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);
4742: }
4743: }
4744: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4745: }
4746: }
4747: }
4748: }
4749:
4750: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4751:
4752: if (popforecast==1) {
4753: free_ivector(popage,0,AGESUP);
4754: free_vector(popeffectif,0,AGESUP);
4755: free_vector(popcount,0,AGESUP);
4756: }
4757: free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4758: free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4759: fclose(ficrespop);
4760: } /* End of popforecast */
4761:
4762: int fileappend(FILE *fichier, char *optionfich)
4763: {
4764: if((fichier=fopen(optionfich,"a"))==NULL) {
4765: printf("Problem with file: %s\n", optionfich);
4766: fprintf(ficlog,"Problem with file: %s\n", optionfich);
4767: return (0);
4768: }
4769: fflush(fichier);
4770: return (1);
4771: }
4772:
4773:
4774: /**************** function prwizard **********************/
4775: void prwizard(int ncovmodel, int nlstate, int ndeath, char model[], FILE *ficparo)
4776: {
4777:
4778: /* Wizard to print covariance matrix template */
4779:
4780: char ca[32], cb[32];
4781: int i,j, k, li, lj, lk, ll, jj, npar, itimes;
4782: int numlinepar;
4783:
4784: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
4785: fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
4786: for(i=1; i <=nlstate; i++){
4787: jj=0;
4788: for(j=1; j <=nlstate+ndeath; j++){
4789: if(j==i) continue;
4790: jj++;
4791: /*ca[0]= k+'a'-1;ca[1]='\0';*/
4792: printf("%1d%1d",i,j);
4793: fprintf(ficparo,"%1d%1d",i,j);
4794: for(k=1; k<=ncovmodel;k++){
4795: /* printf(" %lf",param[i][j][k]); */
4796: /* fprintf(ficparo," %lf",param[i][j][k]); */
4797: printf(" 0.");
4798: fprintf(ficparo," 0.");
4799: }
4800: printf("\n");
4801: fprintf(ficparo,"\n");
4802: }
4803: }
4804: printf("# Scales (for hessian or gradient estimation)\n");
4805: fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
4806: npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
4807: for(i=1; i <=nlstate; i++){
4808: jj=0;
4809: for(j=1; j <=nlstate+ndeath; j++){
4810: if(j==i) continue;
4811: jj++;
4812: fprintf(ficparo,"%1d%1d",i,j);
4813: printf("%1d%1d",i,j);
4814: fflush(stdout);
4815: for(k=1; k<=ncovmodel;k++){
4816: /* printf(" %le",delti3[i][j][k]); */
4817: /* fprintf(ficparo," %le",delti3[i][j][k]); */
4818: printf(" 0.");
4819: fprintf(ficparo," 0.");
4820: }
4821: numlinepar++;
4822: printf("\n");
4823: fprintf(ficparo,"\n");
4824: }
4825: }
4826: printf("# Covariance matrix\n");
4827: /* # 121 Var(a12)\n\ */
4828: /* # 122 Cov(b12,a12) Var(b12)\n\ */
4829: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
4830: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
4831: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
4832: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
4833: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
4834: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
4835: fflush(stdout);
4836: fprintf(ficparo,"# Covariance matrix\n");
4837: /* # 121 Var(a12)\n\ */
4838: /* # 122 Cov(b12,a12) Var(b12)\n\ */
4839: /* # ...\n\ */
4840: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
4841:
4842: for(itimes=1;itimes<=2;itimes++){
4843: jj=0;
4844: for(i=1; i <=nlstate; i++){
4845: for(j=1; j <=nlstate+ndeath; j++){
4846: if(j==i) continue;
4847: for(k=1; k<=ncovmodel;k++){
4848: jj++;
4849: ca[0]= k+'a'-1;ca[1]='\0';
4850: if(itimes==1){
4851: printf("#%1d%1d%d",i,j,k);
4852: fprintf(ficparo,"#%1d%1d%d",i,j,k);
4853: }else{
4854: printf("%1d%1d%d",i,j,k);
4855: fprintf(ficparo,"%1d%1d%d",i,j,k);
4856: /* printf(" %.5le",matcov[i][j]); */
4857: }
4858: ll=0;
4859: for(li=1;li <=nlstate; li++){
4860: for(lj=1;lj <=nlstate+ndeath; lj++){
4861: if(lj==li) continue;
4862: for(lk=1;lk<=ncovmodel;lk++){
4863: ll++;
4864: if(ll<=jj){
4865: cb[0]= lk +'a'-1;cb[1]='\0';
4866: if(ll<jj){
4867: if(itimes==1){
4868: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
4869: fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
4870: }else{
4871: printf(" 0.");
4872: fprintf(ficparo," 0.");
4873: }
4874: }else{
4875: if(itimes==1){
4876: printf(" Var(%s%1d%1d)",ca,i,j);
4877: fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
4878: }else{
4879: printf(" 0.");
4880: fprintf(ficparo," 0.");
4881: }
4882: }
4883: }
4884: } /* end lk */
4885: } /* end lj */
4886: } /* end li */
4887: printf("\n");
4888: fprintf(ficparo,"\n");
4889: numlinepar++;
4890: } /* end k*/
4891: } /*end j */
4892: } /* end i */
4893: } /* end itimes */
4894:
4895: } /* end of prwizard */
4896: /******************* Gompertz Likelihood ******************************/
4897: double gompertz(double x[])
4898: {
4899: double A,B,L=0.0,sump=0.,num=0.;
4900: int i,n=0; /* n is the size of the sample */
4901:
4902: for (i=0;i<=imx-1 ; i++) {
4903: sump=sump+weight[i];
4904: /* sump=sump+1;*/
4905: num=num+1;
4906: }
4907:
4908:
4909: /* for (i=0; i<=imx; i++)
4910: 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]);*/
4911:
4912: for (i=1;i<=imx ; i++)
4913: {
4914: if (cens[i] == 1 && wav[i]>1)
4915: A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
4916:
4917: if (cens[i] == 0 && wav[i]>1)
4918: A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
4919: +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);
4920:
4921: /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
4922: if (wav[i] > 1 ) { /* ??? */
4923: L=L+A*weight[i];
4924: /* 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]);*/
4925: }
4926: }
4927:
4928: /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
4929:
4930: return -2*L*num/sump;
4931: }
4932:
4933: #ifdef GSL
4934: /******************* Gompertz_f Likelihood ******************************/
4935: double gompertz_f(const gsl_vector *v, void *params)
4936: {
4937: double A,B,LL=0.0,sump=0.,num=0.;
4938: double *x= (double *) v->data;
4939: int i,n=0; /* n is the size of the sample */
4940:
4941: for (i=0;i<=imx-1 ; i++) {
4942: sump=sump+weight[i];
4943: /* sump=sump+1;*/
4944: num=num+1;
4945: }
4946:
4947:
4948: /* for (i=0; i<=imx; i++)
4949: 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]);*/
4950: printf("x[0]=%lf x[1]=%lf\n",x[0],x[1]);
4951: for (i=1;i<=imx ; i++)
4952: {
4953: if (cens[i] == 1 && wav[i]>1)
4954: A=-x[0]/(x[1])*(exp(x[1]*(agecens[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)));
4955:
4956: if (cens[i] == 0 && wav[i]>1)
4957: A=-x[0]/(x[1])*(exp(x[1]*(agedc[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)))
4958: +log(x[0]/YEARM)+x[1]*(agedc[i]-agegomp)+log(YEARM);
4959:
4960: /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
4961: if (wav[i] > 1 ) { /* ??? */
4962: LL=LL+A*weight[i];
4963: /* 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]);*/
4964: }
4965: }
4966:
4967: /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
4968: printf("x[0]=%lf x[1]=%lf -2*LL*num/sump=%lf\n",x[0],x[1],-2*LL*num/sump);
4969:
4970: return -2*LL*num/sump;
4971: }
4972: #endif
4973:
4974: /******************* Printing html file ***********/
4975: void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \
4976: int lastpass, int stepm, int weightopt, char model[],\
4977: int imx, double p[],double **matcov,double agemortsup){
4978: int i,k;
4979:
4980: fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
4981: fprintf(fichtm," mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
4982: for (i=1;i<=2;i++)
4983: 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]));
4984: fprintf(fichtm,"<br><br><img src=\"graphmort.png\">");
4985: fprintf(fichtm,"</ul>");
4986:
4987: fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
4988:
4989: 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>");
4990:
4991: for (k=agegomp;k<(agemortsup-2);k++)
4992: 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]);
4993:
4994:
4995: fflush(fichtm);
4996: }
4997:
4998: /******************* Gnuplot file **************/
4999: void printinggnuplotmort(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
5000:
5001: char dirfileres[132],optfileres[132];
5002:
5003: int ng;
5004:
5005:
5006: /*#ifdef windows */
5007: fprintf(ficgp,"cd \"%s\" \n",pathc);
5008: /*#endif */
5009:
5010:
5011: strcpy(dirfileres,optionfilefiname);
5012: strcpy(optfileres,"vpl");
5013: fprintf(ficgp,"set out \"graphmort.png\"\n ");
5014: fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n ");
5015: fprintf(ficgp, "set ter png small size 320, 240\n set log y\n");
5016: /* fprintf(ficgp, "set size 0.65,0.65\n"); */
5017: fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
5018:
5019: }
5020:
5021: int readdata(char datafile[], int firstobs, int lastobs, int *imax)
5022: {
5023:
5024: /*-------- data file ----------*/
5025: FILE *fic;
5026: char dummy[]=" ";
5027: int i=0, j=0, n=0;
5028: int linei, month, year,iout;
5029: char line[MAXLINE], linetmp[MAXLINE];
5030: char stra[MAXLINE], strb[MAXLINE];
5031: char *stratrunc;
5032: int lstra;
5033:
5034:
5035: if((fic=fopen(datafile,"r"))==NULL) {
5036: printf("Problem while opening datafile: %s\n", datafile);return 1;
5037: fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);return 1;
5038: }
5039:
5040: i=1;
5041: linei=0;
5042: while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
5043: linei=linei+1;
5044: for(j=strlen(line); j>=0;j--){ /* Untabifies line */
5045: if(line[j] == '\t')
5046: line[j] = ' ';
5047: }
5048: for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){
5049: ;
5050: };
5051: line[j+1]=0; /* Trims blanks at end of line */
5052: if(line[0]=='#'){
5053: fprintf(ficlog,"Comment line\n%s\n",line);
5054: printf("Comment line\n%s\n",line);
5055: continue;
5056: }
5057: trimbb(linetmp,line); /* Trims multiple blanks in line */
5058: strcpy(line, linetmp);
5059:
5060:
5061: for (j=maxwav;j>=1;j--){
5062: cutv(stra, strb, line, ' ');
5063: if(strb[0]=='.') { /* Missing status */
5064: lval=-1;
5065: }else{
5066: errno=0;
5067: lval=strtol(strb,&endptr,10);
5068: /* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
5069: if( strb[0]=='\0' || (*endptr != '\0')){
5070: 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);
5071: 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);
5072: return 1;
5073: }
5074: }
5075: s[j][i]=lval;
5076:
5077: strcpy(line,stra);
5078: cutv(stra, strb,line,' ');
5079: if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
5080: }
5081: else if( (iout=sscanf(strb,"%s.",dummy)) != 0){
5082: month=99;
5083: year=9999;
5084: }else{
5085: 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);
5086: 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);
5087: return 1;
5088: }
5089: anint[j][i]= (double) year;
5090: mint[j][i]= (double)month;
5091: strcpy(line,stra);
5092: } /* ENd Waves */
5093:
5094: cutv(stra, strb,line,' ');
5095: if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
5096: }
5097: else if( (iout=sscanf(strb,"%s.",dummy)) != 0){
5098: month=99;
5099: year=9999;
5100: }else{
5101: 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);
5102: 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);
5103: return 1;
5104: }
5105: andc[i]=(double) year;
5106: moisdc[i]=(double) month;
5107: strcpy(line,stra);
5108:
5109: cutv(stra, strb,line,' ');
5110: if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
5111: }
5112: else if( (iout=sscanf(strb,"%s.", dummy)) != 0){
5113: month=99;
5114: year=9999;
5115: }else{
5116: 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);
5117: 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);
5118: return 1;
5119: }
5120: if (year==9999) {
5121: 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);
5122: 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);
5123: return 1;
5124:
5125: }
5126: annais[i]=(double)(year);
5127: moisnais[i]=(double)(month);
5128: strcpy(line,stra);
5129:
5130: cutv(stra, strb,line,' ');
5131: errno=0;
5132: dval=strtod(strb,&endptr);
5133: if( strb[0]=='\0' || (*endptr != '\0')){
5134: printf("Error reading data around '%f' at line number %d, \"%s\" for individual %d\nShould be a weight. Exiting.\n",dval, i,line,linei);
5135: 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);
5136: fflush(ficlog);
5137: return 1;
5138: }
5139: weight[i]=dval;
5140: strcpy(line,stra);
5141:
5142: for (j=ncovcol;j>=1;j--){
5143: cutv(stra, strb,line,' ');
5144: if(strb[0]=='.') { /* Missing status */
5145: lval=-1;
5146: }else{
5147: errno=0;
5148: lval=strtol(strb,&endptr,10);
5149: if( strb[0]=='\0' || (*endptr != '\0')){
5150: 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);
5151: 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);
5152: return 1;
5153: }
5154: }
5155: if(lval <-1 || lval >1){
5156: printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
5157: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
5158: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
5159: For example, for multinomial values like 1, 2 and 3,\n \
5160: build V1=0 V2=0 for the reference value (1),\n \
5161: V1=1 V2=0 for (2) \n \
5162: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
5163: output of IMaCh is often meaningless.\n \
5164: Exiting.\n",lval,linei, i,line,j);
5165: fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
5166: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
5167: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
5168: For example, for multinomial values like 1, 2 and 3,\n \
5169: build V1=0 V2=0 for the reference value (1),\n \
5170: V1=1 V2=0 for (2) \n \
5171: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
5172: output of IMaCh is often meaningless.\n \
5173: Exiting.\n",lval,linei, i,line,j);fflush(ficlog);
5174: return 1;
5175: }
5176: covar[j][i]=(double)(lval);
5177: strcpy(line,stra);
5178: }
5179: lstra=strlen(stra);
5180:
5181: if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
5182: stratrunc = &(stra[lstra-9]);
5183: num[i]=atol(stratrunc);
5184: }
5185: else
5186: num[i]=atol(stra);
5187: /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
5188: 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;}*/
5189:
5190: i=i+1;
5191: } /* End loop reading data */
5192:
5193: *imax=i-1; /* Number of individuals */
5194: fclose(fic);
5195:
5196: return (0);
5197: /* endread: */
5198: printf("Exiting readdata: ");
5199: fclose(fic);
5200: return (1);
5201:
5202:
5203:
5204: }
5205: void removespace(char *str) {
5206: char *p1 = str, *p2 = str;
5207: do
5208: while (*p2 == ' ')
5209: p2++;
5210: while (*p1++ == *p2++);
5211: }
5212:
5213: int decodemodel ( char model[], int lastobs) /**< This routine decode the model and returns:
5214: * Model V1+V2+V3+V8+V7*V8+V5*V6+V8*age+V3*age
5215: * - cptcovt total number of covariates of the model nbocc(+)+1 = 8
5216: * - cptcovn or number of covariates k of the models excluding age*products =6
5217: * - cptcovage number of covariates with age*products =2
5218: * - cptcovs number of simple covariates
5219: * - 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
5220: * which is a new column after the 9 (ncovcol) variables.
5221: * - if k is a product Vn*Vm covar[k][i] is filled with correct values for each individual
5222: * - Tprod[l] gives the kth covariates of the product Vn*Vm l=1 to cptcovprod-cptcovage
5223: * Tprod[1]@2 {5, 6}: position of first product V7*V8 is 5, and second V5*V6 is 6.
5224: * - Tvard[k] p Tvard[1][1]@4 {7, 8, 5, 6} for V7*V8 and V5*V6 .
5225: */
5226: {
5227: int i, j, k, ks;
5228: int j1, k1, k2;
5229: char modelsav[80];
5230: char stra[80], strb[80], strc[80], strd[80],stre[80];
5231:
5232: /*removespace(model);*/
5233: if (strlen(model) >1){ /* If there is at least 1 covariate */
5234: j=0, j1=0, k1=0, k2=-1, ks=0, cptcovn=0;
5235: j=nbocc(model,'+'); /**< j=Number of '+' */
5236: j1=nbocc(model,'*'); /**< j1=Number of '*' */
5237: cptcovs=j+1-j1; /**< Number of simple covariates V1+V2*age+V3 +V3*V4=> V1 + V3 =2 */
5238: cptcovt= j+1; /* Number of total covariates in the model V1 + V2*age+ V3 + V3*V4=> 4*/
5239: /* including age products which are counted in cptcovage.
5240: * but the covariates which are products must be treated separately: ncovn=4- 2=2 (V1+V3). */
5241: cptcovprod=j1; /**< Number of products V1*V2 +v3*age = 2 */
5242: cptcovprodnoage=0; /**< Number of covariate products without age: V3*V4 =1 */
5243: strcpy(modelsav,model);
5244: if (strstr(model,"AGE") !=0){
5245: printf("Error. AGE must be in lower case 'age' model=%s ",model);
5246: fprintf(ficlog,"Error. AGE must be in lower case model=%s ",model);fflush(ficlog);
5247: return 1;
5248: }
5249: if (strstr(model,"v") !=0){
5250: printf("Error. 'v' must be in upper case 'V' model=%s ",model);
5251: fprintf(ficlog,"Error. 'v' must be in upper case model=%s ",model);fflush(ficlog);
5252: return 1;
5253: }
5254:
5255: /* Design
5256: * V1 V2 V3 V4 V5 V6 V7 V8 V9 Weight
5257: * < ncovcol=8 >
5258: * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8
5259: * k= 1 2 3 4 5 6 7 8
5260: * cptcovn number of covariates (not including constant and age ) = # of + plus 1 = 7+1=8
5261: * covar[k,i], value of kth covariate if not including age for individual i:
5262: * covar[1][i]= (V2), covar[4][i]=(V3), covar[8][i]=(V8)
5263: * Tvar[k] # of the kth covariate: Tvar[1]=2 Tvar[4]=3 Tvar[8]=8
5264: * if multiplied by age: V3*age Tvar[3=V3*age]=3 (V3) Tvar[7]=8 and
5265: * Tage[++cptcovage]=k
5266: * if products, new covar are created after ncovcol with k1
5267: * Tvar[k]=ncovcol+k1; # of the kth covariate product: Tvar[5]=ncovcol+1=10 Tvar[6]=ncovcol+1=11
5268: * Tprod[k1]=k; Tprod[1]=5 Tprod[2]= 6; gives the position of the k1th product
5269: * 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
5270: * Tvar[cptcovn+k2]=Tvard[k1][1];Tvar[cptcovn+k2+1]=Tvard[k1][2];
5271: * Tvar[8+1]=5;Tvar[8+2]=6;Tvar[8+3]=7;Tvar[8+4]=8 inverted
5272: * V1 V2 V3 V4 V5 V6 V7 V8 V9 V10 V11
5273: * < ncovcol=8 >
5274: * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8 d1 d1 d2 d2
5275: * k= 1 2 3 4 5 6 7 8 9 10 11 12
5276: * Tvar[k]= 2 1 3 3 10 11 8 8 5 6 7 8
5277: * p Tvar[1]@12={2, 1, 3, 3, 11, 10, 8, 8, 7, 8, 5, 6}
5278: * p Tprod[1]@2={ 6, 5}
5279: *p Tvard[1][1]@4= {7, 8, 5, 6}
5280: * covar[k][i]= V2 V1 ? V3 V5*V6? V7*V8? ? V8
5281: * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
5282: *How to reorganize?
5283: * Model V1 + V2 + V3 + V8 + V5*V6 + V7*V8 + V3*age + V8*age
5284: * Tvars {2, 1, 3, 3, 11, 10, 8, 8, 7, 8, 5, 6}
5285: * {2, 1, 4, 8, 5, 6, 3, 7}
5286: * Struct []
5287: */
5288:
5289: /* This loop fills the array Tvar from the string 'model'.*/
5290: /* j is the number of + signs in the model V1+V2+V3 j=2 i=3 to 1 */
5291: /* modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4 */
5292: /* k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tage[cptcovage=1]=4 */
5293: /* k=3 V4 Tvar[k=3]= 4 (from V4) */
5294: /* k=2 V1 Tvar[k=2]= 1 (from V1) */
5295: /* k=1 Tvar[1]=2 (from V2) */
5296: /* k=5 Tvar[5] */
5297: /* for (k=1; k<=cptcovn;k++) { */
5298: /* cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]]; */
5299: /* } */
5300: /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
5301: /*
5302: * Treating invertedly V2+V1+V3*age+V2*V4 is as if written V2*V4 +V3*age + V1 + V2 */
5303: for(k=cptcovt; k>=1;k--) /**< Number of covariates */
5304: Tvar[k]=0;
5305: cptcovage=0;
5306: for(k=1; k<=cptcovt;k++){ /* Loop on total covariates of the model */
5307: cutl(stra,strb,modelsav,'+'); /* keeps in strb after the first '+'
5308: modelsav==V2+V1+V4+V3*age strb=V3*age stra=V2+V1+V4 */
5309: if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
5310: /* printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
5311: /*scanf("%d",i);*/
5312: if (strchr(strb,'*')) { /**< Model includes a product V2+V1+V4+V3*age strb=V3*age */
5313: cutl(strc,strd,strb,'*'); /**< strd*strc Vm*Vn: strb=V3*age(input) strc=age strd=V3 ; V3*V2 strc=V2, strd=V3 */
5314: if (strcmp(strc,"age")==0) { /**< Model includes age: Vn*age */
5315: /* covar is not filled and then is empty */
5316: cptcovprod--;
5317: cutl(stre,strb,strd,'V'); /* strd=V3(input): stre="3" */
5318: Tvar[k]=atoi(stre); /* V2+V1+V4+V3*age Tvar[4]=3 ; V1+V2*age Tvar[2]=2 */
5319: cptcovage++; /* Sums the number of covariates which include age as a product */
5320: Tage[cptcovage]=k; /* Tage[1] = 4 */
5321: /*printf("stre=%s ", stre);*/
5322: } else if (strcmp(strd,"age")==0) { /* or age*Vn */
5323: cptcovprod--;
5324: cutl(stre,strb,strc,'V');
5325: Tvar[k]=atoi(stre);
5326: cptcovage++;
5327: Tage[cptcovage]=k;
5328: } else { /* Age is not in the model product V2+V1+V1*V4+V3*age+V3*V2 strb=V3*V2*/
5329: /* loops on k1=1 (V3*V2) and k1=2 V4*V3 */
5330: cptcovn++;
5331: cptcovprodnoage++;k1++;
5332: cutl(stre,strb,strc,'V'); /* strc= Vn, stre is n; strb=V3*V2 stre=3 strc=*/
5333: Tvar[k]=ncovcol+k1; /* For model-covariate k tells which data-covariate to use but
5334: because this model-covariate is a construction we invent a new column
5335: ncovcol + k1
5336: If already ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2
5337: Tvar[3=V1*V4]=4+1 Tvar[5=V3*V2]=4 + 2= 6, etc */
5338: cutl(strc,strb,strd,'V'); /* strd was Vm, strc is m */
5339: Tprod[k1]=k; /* Tprod[1]=3(=V1*V4) for V2+V1+V1*V4+age*V3+V3*V2 */
5340: Tvard[k1][1] =atoi(strc); /* m 1 for V1*/
5341: Tvard[k1][2] =atoi(stre); /* n 4 for V4*/
5342: k2=k2+2;
5343: Tvar[cptcovt+k2]=Tvard[k1][1]; /* Tvar[(cptcovt=4+k2=1)=5]= 1 (V1) */
5344: Tvar[cptcovt+k2+1]=Tvard[k1][2]; /* Tvar[(cptcovt=4+(k2=1)+1)=6]= 4 (V4) */
5345: for (i=1; i<=lastobs;i++){
5346: /* Computes the new covariate which is a product of
5347: covar[n][i]* covar[m][i] and stores it at ncovol+k1 May not be defined */
5348: covar[ncovcol+k1][i]=covar[atoi(stre)][i]*covar[atoi(strc)][i];
5349: }
5350: } /* End age is not in the model */
5351: } /* End if model includes a product */
5352: else { /* no more sum */
5353: /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
5354: /* scanf("%d",i);*/
5355: cutl(strd,strc,strb,'V');
5356: ks++; /**< Number of simple covariates */
5357: cptcovn++;
5358: Tvar[k]=atoi(strd);
5359: }
5360: strcpy(modelsav,stra); /* modelsav=V2+V1+V4 stra=V2+V1+V4 */
5361: /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
5362: scanf("%d",i);*/
5363: } /* end of loop + */
5364: } /* end model */
5365:
5366: /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
5367: If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
5368:
5369: /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
5370: printf("cptcovprod=%d ", cptcovprod);
5371: fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
5372:
5373: scanf("%d ",i);*/
5374:
5375:
5376: return (0); /* with covar[new additional covariate if product] and Tage if age */
5377: /*endread:*/
5378: printf("Exiting decodemodel: ");
5379: return (1);
5380: }
5381:
5382: int calandcheckages(int imx, int maxwav, double *agemin, double *agemax, int *nberr, int *nbwarn )
5383: {
5384: int i, m;
5385:
5386: for (i=1; i<=imx; i++) {
5387: for(m=2; (m<= maxwav); m++) {
5388: if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
5389: anint[m][i]=9999;
5390: s[m][i]=-1;
5391: }
5392: if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
5393: *nberr = *nberr + 1;
5394: 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);
5395: 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);
5396: s[m][i]=-1;
5397: }
5398: if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
5399: (*nberr)++;
5400: 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]);
5401: 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]);
5402: s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
5403: }
5404: }
5405: }
5406:
5407: for (i=1; i<=imx; i++) {
5408: agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
5409: for(m=firstpass; (m<= lastpass); m++){
5410: if(s[m][i] >0 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){
5411: if (s[m][i] >= nlstate+1) {
5412: if(agedc[i]>0){
5413: if((int)moisdc[i]!=99 && (int)andc[i]!=9999){
5414: agev[m][i]=agedc[i];
5415: /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
5416: }else {
5417: if ((int)andc[i]!=9999){
5418: nbwarn++;
5419: printf("Warning negative age at death: %ld line:%d\n",num[i],i);
5420: fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
5421: agev[m][i]=-1;
5422: }
5423: }
5424: } /* agedc > 0 */
5425: }
5426: else if(s[m][i] !=9){ /* Standard case, age in fractional
5427: years but with the precision of a month */
5428: agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
5429: if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
5430: agev[m][i]=1;
5431: else if(agev[m][i] < *agemin){
5432: *agemin=agev[m][i];
5433: printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], *agemin);
5434: }
5435: else if(agev[m][i] >*agemax){
5436: *agemax=agev[m][i];
5437: /* printf(" Max anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.2f\n",m,i,anint[m][i], i,annais[i], *agemax);*/
5438: }
5439: /*agev[m][i]=anint[m][i]-annais[i];*/
5440: /* agev[m][i] = age[i]+2*m;*/
5441: }
5442: else { /* =9 */
5443: agev[m][i]=1;
5444: s[m][i]=-1;
5445: }
5446: }
5447: else /*= 0 Unknown */
5448: agev[m][i]=1;
5449: }
5450:
5451: }
5452: for (i=1; i<=imx; i++) {
5453: for(m=firstpass; (m<=lastpass); m++){
5454: if (s[m][i] > (nlstate+ndeath)) {
5455: (*nberr)++;
5456: 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);
5457: 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);
5458: return 1;
5459: }
5460: }
5461: }
5462:
5463: /*for (i=1; i<=imx; i++){
5464: for (m=firstpass; (m<lastpass); m++){
5465: printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
5466: }
5467:
5468: }*/
5469:
5470:
5471: printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
5472: fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
5473:
5474: return (0);
5475: /* endread:*/
5476: printf("Exiting calandcheckages: ");
5477: return (1);
5478: }
5479:
5480: #if defined(_MSC_VER)
5481: /*printf("Visual C++ compiler: %s \n;", _MSC_FULL_VER);*/
5482: /*fprintf(ficlog, "Visual C++ compiler: %s \n;", _MSC_FULL_VER);*/
5483: //#include "stdafx.h"
5484: //#include <stdio.h>
5485: //#include <tchar.h>
5486: //#include <windows.h>
5487: //#include <iostream>
5488: typedef BOOL(WINAPI *LPFN_ISWOW64PROCESS) (HANDLE, PBOOL);
5489:
5490: LPFN_ISWOW64PROCESS fnIsWow64Process;
5491:
5492: BOOL IsWow64()
5493: {
5494: BOOL bIsWow64 = FALSE;
5495:
5496: //typedef BOOL (APIENTRY *LPFN_ISWOW64PROCESS)
5497: // (HANDLE, PBOOL);
5498:
5499: //LPFN_ISWOW64PROCESS fnIsWow64Process;
5500:
5501: HMODULE module = GetModuleHandle(_T("kernel32"));
5502: const char funcName[] = "IsWow64Process";
5503: fnIsWow64Process = (LPFN_ISWOW64PROCESS)
5504: GetProcAddress(module, funcName);
5505:
5506: if (NULL != fnIsWow64Process)
5507: {
5508: if (!fnIsWow64Process(GetCurrentProcess(),
5509: &bIsWow64))
5510: //throw std::exception("Unknown error");
5511: printf("Unknown error\n");
5512: }
5513: return bIsWow64 != FALSE;
5514: }
5515: #endif
5516:
5517: void syscompilerinfo()
5518: {
5519: /* #include "syscompilerinfo.h"*/
5520:
5521: #if defined __INTEL_COMPILER
5522: #if defined(__GNUC__)
5523: struct utsname sysInfo; /* For Intel on Linux and OS/X */
5524: #endif
5525: #elif defined(__GNUC__)
5526: #ifndef __APPLE__
5527: #include <gnu/libc-version.h> /* Only on gnu */
5528: #endif
5529: struct utsname sysInfo;
5530: int cross = CROSS;
5531: if (cross){
5532: printf("Cross-");
5533: fprintf(ficlog, "Cross-");
5534: }
5535: #endif
5536:
5537: #include <stdint.h>
5538:
5539: printf("Compiled with:");fprintf(ficlog,"Compiled with:");
5540: #if defined(__clang__)
5541: printf(" Clang/LLVM");fprintf(ficlog," Clang/LLVM"); /* Clang/LLVM. ---------------------------------------------- */
5542: #endif
5543: #if defined(__ICC) || defined(__INTEL_COMPILER)
5544: printf(" Intel ICC/ICPC");fprintf(ficlog," Intel ICC/ICPC");/* Intel ICC/ICPC. ------------------------------------------ */
5545: #endif
5546: #if defined(__GNUC__) || defined(__GNUG__)
5547: printf(" GNU GCC/G++");fprintf(ficlog," GNU GCC/G++");/* GNU GCC/G++. --------------------------------------------- */
5548: #endif
5549: #if defined(__HP_cc) || defined(__HP_aCC)
5550: printf(" Hewlett-Packard C/aC++");fprintf(fcilog," Hewlett-Packard C/aC++"); /* Hewlett-Packard C/aC++. ---------------------------------- */
5551: #endif
5552: #if defined(__IBMC__) || defined(__IBMCPP__)
5553: printf(" IBM XL C/C++"); fprintf(ficlog," IBM XL C/C++");/* IBM XL C/C++. -------------------------------------------- */
5554: #endif
5555: #if defined(_MSC_VER)
5556: printf(" Microsoft Visual Studio");fprintf(ficlog," Microsoft Visual Studio");/* Microsoft Visual Studio. --------------------------------- */
5557: #endif
5558: #if defined(__PGI)
5559: printf(" Portland Group PGCC/PGCPP");fprintf(ficlog," Portland Group PGCC/PGCPP");/* Portland Group PGCC/PGCPP. ------------------------------- */
5560: #endif
5561: #if defined(__SUNPRO_C) || defined(__SUNPRO_CC)
5562: printf(" Oracle Solaris Studio");fprintf(ficlog," Oracle Solaris Studio\n");/* Oracle Solaris Studio. ----------------------------------- */
5563: #endif
5564: printf(" for ");fprintf(ficlog," for ");
5565:
5566: // http://stackoverflow.com/questions/4605842/how-to-identify-platform-compiler-from-preprocessor-macros
5567: #ifdef _WIN32 // note the underscore: without it, it's not msdn official!
5568: // Windows (x64 and x86)
5569: printf("Windows (x64 and x86) ");fprintf(ficlog,"Windows (x64 and x86) ");
5570: #elif __unix__ // all unices, not all compilers
5571: // Unix
5572: printf("Unix ");fprintf(ficlog,"Unix ");
5573: #elif __linux__
5574: // linux
5575: printf("linux ");fprintf(ficlog,"linux ");
5576: #elif __APPLE__
5577: // Mac OS, not sure if this is covered by __posix__ and/or __unix__ though..
5578: printf("Mac OS ");fprintf(ficlog,"Mac OS ");
5579: #endif
5580:
5581: /* __MINGW32__ */
5582: /* __CYGWIN__ */
5583: /* __MINGW64__ */
5584: // http://msdn.microsoft.com/en-us/library/b0084kay.aspx
5585: /* _MSC_VER //the Visual C++ compiler is 17.00.51106.1, the _MSC_VER macro evaluates to 1700. Type cl /? */
5586: /* _MSC_FULL_VER //the Visual C++ compiler is 15.00.20706.01, the _MSC_FULL_VER macro evaluates to 150020706 */
5587: /* _WIN64 // Defined for applications for Win64. */
5588: /* _M_X64 // Defined for compilations that target x64 processors. */
5589: /* _DEBUG // Defined when you compile with /LDd, /MDd, and /MTd. */
5590:
5591: #if UINTPTR_MAX == 0xffffffff
5592: printf(" 32-bit"); fprintf(ficlog," 32-bit");/* 32-bit */
5593: #elif UINTPTR_MAX == 0xffffffffffffffff
5594: printf(" 64-bit"); fprintf(ficlog," 64-bit");/* 64-bit */
5595: #else
5596: printf(" wtf-bit"); fprintf(ficlog," wtf-bit");/* wtf */
5597: #endif
5598:
5599: #if defined(__GNUC__)
5600: # if defined(__GNUC_PATCHLEVEL__)
5601: # define __GNUC_VERSION__ (__GNUC__ * 10000 \
5602: + __GNUC_MINOR__ * 100 \
5603: + __GNUC_PATCHLEVEL__)
5604: # else
5605: # define __GNUC_VERSION__ (__GNUC__ * 10000 \
5606: + __GNUC_MINOR__ * 100)
5607: # endif
5608: printf(" using GNU C version %d.\n", __GNUC_VERSION__);
5609: fprintf(ficlog, " using GNU C version %d.\n", __GNUC_VERSION__);
5610:
5611: if (uname(&sysInfo) != -1) {
5612: printf("Running on: %s %s %s %s %s\n",sysInfo.sysname, sysInfo.nodename, sysInfo.release, sysInfo.version, sysInfo.machine);
5613: fprintf(ficlog,"Running on: %s %s %s %s %s\n ",sysInfo.sysname, sysInfo.nodename, sysInfo.release, sysInfo.version, sysInfo.machine);
5614: }
5615: else
5616: perror("uname() error");
5617: //#ifndef __INTEL_COMPILER
5618: #if !defined (__INTEL_COMPILER) && !defined(__APPLE__)
5619: printf("GNU libc version: %s\n", gnu_get_libc_version());
5620: fprintf(ficlog,"GNU libc version: %s\n", gnu_get_libc_version());
5621: #endif
5622: #endif
5623:
5624: // void main()
5625: // {
5626: #if defined(_MSC_VER)
5627: if (IsWow64()){
5628: printf("The program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n");
5629: fprintf(ficlog, "The program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n");
5630: }
5631: else{
5632: printf("The process is not running under WOW64 (i.e probably on a 64bit Windows).\n");
5633: fprintf(ficlog,"The programm is not running under WOW64 (i.e probably on a 64bit Windows).\n");
5634: }
5635: // printf("\nPress Enter to continue...");
5636: // getchar();
5637: // }
5638:
5639: #endif
5640:
5641:
5642: }
5643:
5644: /***********************************************/
5645: /**************** Main Program *****************/
5646: /***********************************************/
5647:
5648: int main(int argc, char *argv[])
5649: {
5650: #ifdef GSL
5651: const gsl_multimin_fminimizer_type *T;
5652: size_t iteri = 0, it;
5653: int rval = GSL_CONTINUE;
5654: int status = GSL_SUCCESS;
5655: double ssval;
5656: #endif
5657: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
5658: int i,j, k, n=MAXN,iter=0,m,size=100, cptcod;
5659:
5660: int jj, ll, li, lj, lk;
5661: int numlinepar=0; /* Current linenumber of parameter file */
5662: int itimes;
5663: int NDIM=2;
5664: int vpopbased=0;
5665:
5666: char ca[32], cb[32];
5667: /* FILE *fichtm; *//* Html File */
5668: /* FILE *ficgp;*/ /*Gnuplot File */
5669: struct stat info;
5670: double agedeb;
5671: double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
5672:
5673: double fret;
5674: double dum; /* Dummy variable */
5675: double ***p3mat;
5676: double ***mobaverage;
5677:
5678: char line[MAXLINE];
5679: char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
5680: char pathr[MAXLINE], pathimach[MAXLINE];
5681: char *tok, *val; /* pathtot */
5682: int firstobs=1, lastobs=10;
5683: int c, h , cpt;
5684: int jl;
5685: int i1, j1, jk, stepsize;
5686: int *tab;
5687: int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
5688: int mobilav=0,popforecast=0;
5689: int hstepm, nhstepm;
5690: int agemortsup;
5691: float sumlpop=0.;
5692: double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
5693: double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
5694:
5695: double bage=0, fage=110, age, agelim, agebase;
5696: double ftolpl=FTOL;
5697: double **prlim;
5698: double ***param; /* Matrix of parameters */
5699: double *p;
5700: double **matcov; /* Matrix of covariance */
5701: double ***delti3; /* Scale */
5702: double *delti; /* Scale */
5703: double ***eij, ***vareij;
5704: double **varpl; /* Variances of prevalence limits by age */
5705: double *epj, vepp;
5706:
5707: double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
5708: double **ximort;
5709: char *alph[]={"a","a","b","c","d","e"}, str[4]="1234";
5710: int *dcwave;
5711:
5712: char z[1]="c";
5713:
5714: /*char *strt;*/
5715: char strtend[80];
5716:
5717:
5718: /* setlocale (LC_ALL, ""); */
5719: /* bindtextdomain (PACKAGE, LOCALEDIR); */
5720: /* textdomain (PACKAGE); */
5721: /* setlocale (LC_CTYPE, ""); */
5722: /* setlocale (LC_MESSAGES, ""); */
5723:
5724: /* gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
5725: rstart_time = time(NULL);
5726: /* (void) gettimeofday(&start_time,&tzp);*/
5727: start_time = *localtime(&rstart_time);
5728: curr_time=start_time;
5729: /*tml = *localtime(&start_time.tm_sec);*/
5730: /* strcpy(strstart,asctime(&tml)); */
5731: strcpy(strstart,asctime(&start_time));
5732:
5733: /* printf("Localtime (at start)=%s",strstart); */
5734: /* tp.tm_sec = tp.tm_sec +86400; */
5735: /* tm = *localtime(&start_time.tm_sec); */
5736: /* tmg.tm_year=tmg.tm_year +dsign*dyear; */
5737: /* tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
5738: /* tmg.tm_hour=tmg.tm_hour + 1; */
5739: /* tp.tm_sec = mktime(&tmg); */
5740: /* strt=asctime(&tmg); */
5741: /* printf("Time(after) =%s",strstart); */
5742: /* (void) time (&time_value);
5743: * printf("time=%d,t-=%d\n",time_value,time_value-86400);
5744: * tm = *localtime(&time_value);
5745: * strstart=asctime(&tm);
5746: * printf("tim_value=%d,asctime=%s\n",time_value,strstart);
5747: */
5748:
5749: nberr=0; /* Number of errors and warnings */
5750: nbwarn=0;
5751: getcwd(pathcd, size);
5752:
5753: printf("\n%s\n%s",version,fullversion);
5754: if(argc <=1){
5755: printf("\nEnter the parameter file name: ");
5756: fgets(pathr,FILENAMELENGTH,stdin);
5757: i=strlen(pathr);
5758: if(pathr[i-1]=='\n')
5759: pathr[i-1]='\0';
5760: i=strlen(pathr);
5761: if(pathr[i-1]==' ') /* This may happen when dragging on oS/X! */
5762: pathr[i-1]='\0';
5763: for (tok = pathr; tok != NULL; ){
5764: printf("Pathr |%s|\n",pathr);
5765: while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
5766: printf("val= |%s| pathr=%s\n",val,pathr);
5767: strcpy (pathtot, val);
5768: if(pathr[0] == '\0') break; /* Dirty */
5769: }
5770: }
5771: else{
5772: strcpy(pathtot,argv[1]);
5773: }
5774: /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
5775: /*cygwin_split_path(pathtot,path,optionfile);
5776: printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
5777: /* cutv(path,optionfile,pathtot,'\\');*/
5778:
5779: /* Split argv[0], imach program to get pathimach */
5780: printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
5781: split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
5782: printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
5783: /* strcpy(pathimach,argv[0]); */
5784: /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
5785: split(pathtot,path,optionfile,optionfilext,optionfilefiname);
5786: printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
5787: chdir(path); /* Can be a relative path */
5788: if(getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */
5789: printf("Current directory %s!\n",pathcd);
5790: strcpy(command,"mkdir ");
5791: strcat(command,optionfilefiname);
5792: if((outcmd=system(command)) != 0){
5793: printf("Directory already exists (or can't create it) %s%s, err=%d\n",path,optionfilefiname,outcmd);
5794: /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
5795: /* fclose(ficlog); */
5796: /* exit(1); */
5797: }
5798: /* if((imk=mkdir(optionfilefiname))<0){ */
5799: /* perror("mkdir"); */
5800: /* } */
5801:
5802: /*-------- arguments in the command line --------*/
5803:
5804: /* Log file */
5805: strcat(filelog, optionfilefiname);
5806: strcat(filelog,".log"); /* */
5807: if((ficlog=fopen(filelog,"w"))==NULL) {
5808: printf("Problem with logfile %s\n",filelog);
5809: goto end;
5810: }
5811: fprintf(ficlog,"Log filename:%s\n",filelog);
5812: fprintf(ficlog,"\n%s\n%s",version,fullversion);
5813: fprintf(ficlog,"\nEnter the parameter file name: \n");
5814: fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
5815: path=%s \n\
5816: optionfile=%s\n\
5817: optionfilext=%s\n\
5818: optionfilefiname='%s'\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
5819:
5820: syscompilerinfo();
5821:
5822: printf("Local time (at start):%s",strstart);
5823: fprintf(ficlog,"Local time (at start): %s",strstart);
5824: fflush(ficlog);
5825: /* (void) gettimeofday(&curr_time,&tzp); */
5826: /* printf("Elapsed time %d\n", asc_diff_time(curr_time.tm_sec-start_time.tm_sec,tmpout)); */
5827:
5828: /* */
5829: strcpy(fileres,"r");
5830: strcat(fileres, optionfilefiname);
5831: strcat(fileres,".txt"); /* Other files have txt extension */
5832:
5833: /*---------arguments file --------*/
5834:
5835: if((ficpar=fopen(optionfile,"r"))==NULL) {
5836: printf("Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
5837: fprintf(ficlog,"Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
5838: fflush(ficlog);
5839: /* goto end; */
5840: exit(70);
5841: }
5842:
5843:
5844:
5845: strcpy(filereso,"o");
5846: strcat(filereso,fileres);
5847: if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
5848: printf("Problem with Output resultfile: %s\n", filereso);
5849: fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
5850: fflush(ficlog);
5851: goto end;
5852: }
5853:
5854: /* Reads comments: lines beginning with '#' */
5855: numlinepar=0;
5856: while((c=getc(ficpar))=='#' && c!= EOF){
5857: ungetc(c,ficpar);
5858: fgets(line, MAXLINE, ficpar);
5859: numlinepar++;
5860: fputs(line,stdout);
5861: fputs(line,ficparo);
5862: fputs(line,ficlog);
5863: }
5864: ungetc(c,ficpar);
5865:
5866: 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);
5867: numlinepar++;
5868: 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);
5869: 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);
5870: 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);
5871: fflush(ficlog);
5872: while((c=getc(ficpar))=='#' && c!= EOF){
5873: ungetc(c,ficpar);
5874: fgets(line, MAXLINE, ficpar);
5875: numlinepar++;
5876: fputs(line, stdout);
5877: //puts(line);
5878: fputs(line,ficparo);
5879: fputs(line,ficlog);
5880: }
5881: ungetc(c,ficpar);
5882:
5883:
5884: covar=matrix(0,NCOVMAX,1,n); /**< used in readdata */
5885: cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement plus one, indepently of n in Vn*/
5886: /* v1+v2+v3+v2*v4+v5*age makes cptcovn = 5
5887: v1+v2*age+v2*v3 makes cptcovn = 3
5888: */
5889: if (strlen(model)>1)
5890: 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*/
5891: else
5892: ncovmodel=2;
5893: nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
5894: nforce= (nlstate+ndeath-1)*nlstate; /* Number of forces ij from state i to j */
5895: npar= nforce*ncovmodel; /* Number of parameters like aij*/
5896: if(npar >MAXPARM || nlstate >NLSTATEMAX || ndeath >NDEATHMAX || ncovmodel>NCOVMAX){
5897: 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);
5898: 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);
5899: fflush(stdout);
5900: fclose (ficlog);
5901: goto end;
5902: }
5903: delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
5904: delti=delti3[1][1];
5905: /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
5906: if(mle==-1){ /* Print a wizard for help writing covariance matrix */
5907: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
5908: printf(" You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
5909: fprintf(ficlog," You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
5910: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
5911: fclose (ficparo);
5912: fclose (ficlog);
5913: goto end;
5914: exit(0);
5915: }
5916: else if(mle==-3) {
5917: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
5918: printf(" You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
5919: fprintf(ficlog," You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
5920: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
5921: matcov=matrix(1,npar,1,npar);
5922: }
5923: else{
5924: /* Read guessed parameters */
5925: /* Reads comments: lines beginning with '#' */
5926: while((c=getc(ficpar))=='#' && c!= EOF){
5927: ungetc(c,ficpar);
5928: fgets(line, MAXLINE, ficpar);
5929: numlinepar++;
5930: fputs(line,stdout);
5931: fputs(line,ficparo);
5932: fputs(line,ficlog);
5933: }
5934: ungetc(c,ficpar);
5935:
5936: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
5937: for(i=1; i <=nlstate; i++){
5938: j=0;
5939: for(jj=1; jj <=nlstate+ndeath; jj++){
5940: if(jj==i) continue;
5941: j++;
5942: fscanf(ficpar,"%1d%1d",&i1,&j1);
5943: if ((i1 != i) && (j1 != j)){
5944: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \
5945: It might be a problem of design; if ncovcol and the model are correct\n \
5946: run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1);
5947: exit(1);
5948: }
5949: fprintf(ficparo,"%1d%1d",i1,j1);
5950: if(mle==1)
5951: printf("%1d%1d",i,j);
5952: fprintf(ficlog,"%1d%1d",i,j);
5953: for(k=1; k<=ncovmodel;k++){
5954: fscanf(ficpar," %lf",¶m[i][j][k]);
5955: if(mle==1){
5956: printf(" %lf",param[i][j][k]);
5957: fprintf(ficlog," %lf",param[i][j][k]);
5958: }
5959: else
5960: fprintf(ficlog," %lf",param[i][j][k]);
5961: fprintf(ficparo," %lf",param[i][j][k]);
5962: }
5963: fscanf(ficpar,"\n");
5964: numlinepar++;
5965: if(mle==1)
5966: printf("\n");
5967: fprintf(ficlog,"\n");
5968: fprintf(ficparo,"\n");
5969: }
5970: }
5971: fflush(ficlog);
5972:
5973: /* Reads scales values */
5974: p=param[1][1];
5975:
5976: /* Reads comments: lines beginning with '#' */
5977: while((c=getc(ficpar))=='#' && c!= EOF){
5978: ungetc(c,ficpar);
5979: fgets(line, MAXLINE, ficpar);
5980: numlinepar++;
5981: fputs(line,stdout);
5982: fputs(line,ficparo);
5983: fputs(line,ficlog);
5984: }
5985: ungetc(c,ficpar);
5986:
5987: for(i=1; i <=nlstate; i++){
5988: for(j=1; j <=nlstate+ndeath-1; j++){
5989: fscanf(ficpar,"%1d%1d",&i1,&j1);
5990: if ( (i1-i) * (j1-j) != 0){
5991: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
5992: exit(1);
5993: }
5994: printf("%1d%1d",i,j);
5995: fprintf(ficparo,"%1d%1d",i1,j1);
5996: fprintf(ficlog,"%1d%1d",i1,j1);
5997: for(k=1; k<=ncovmodel;k++){
5998: fscanf(ficpar,"%le",&delti3[i][j][k]);
5999: printf(" %le",delti3[i][j][k]);
6000: fprintf(ficparo," %le",delti3[i][j][k]);
6001: fprintf(ficlog," %le",delti3[i][j][k]);
6002: }
6003: fscanf(ficpar,"\n");
6004: numlinepar++;
6005: printf("\n");
6006: fprintf(ficparo,"\n");
6007: fprintf(ficlog,"\n");
6008: }
6009: }
6010: fflush(ficlog);
6011:
6012: /* Reads covariance matrix */
6013: delti=delti3[1][1];
6014:
6015:
6016: /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
6017:
6018: /* Reads comments: lines beginning with '#' */
6019: while((c=getc(ficpar))=='#' && c!= EOF){
6020: ungetc(c,ficpar);
6021: fgets(line, MAXLINE, ficpar);
6022: numlinepar++;
6023: fputs(line,stdout);
6024: fputs(line,ficparo);
6025: fputs(line,ficlog);
6026: }
6027: ungetc(c,ficpar);
6028:
6029: matcov=matrix(1,npar,1,npar);
6030: for(i=1; i <=npar; i++)
6031: for(j=1; j <=npar; j++) matcov[i][j]=0.;
6032:
6033: for(i=1; i <=npar; i++){
6034: fscanf(ficpar,"%s",str);
6035: if(mle==1)
6036: printf("%s",str);
6037: fprintf(ficlog,"%s",str);
6038: fprintf(ficparo,"%s",str);
6039: for(j=1; j <=i; j++){
6040: fscanf(ficpar," %le",&matcov[i][j]);
6041: if(mle==1){
6042: printf(" %.5le",matcov[i][j]);
6043: }
6044: fprintf(ficlog," %.5le",matcov[i][j]);
6045: fprintf(ficparo," %.5le",matcov[i][j]);
6046: }
6047: fscanf(ficpar,"\n");
6048: numlinepar++;
6049: if(mle==1)
6050: printf("\n");
6051: fprintf(ficlog,"\n");
6052: fprintf(ficparo,"\n");
6053: }
6054: for(i=1; i <=npar; i++)
6055: for(j=i+1;j<=npar;j++)
6056: matcov[i][j]=matcov[j][i];
6057:
6058: if(mle==1)
6059: printf("\n");
6060: fprintf(ficlog,"\n");
6061:
6062: fflush(ficlog);
6063:
6064: /*-------- Rewriting parameter file ----------*/
6065: strcpy(rfileres,"r"); /* "Rparameterfile */
6066: strcat(rfileres,optionfilefiname); /* Parameter file first name*/
6067: strcat(rfileres,"."); /* */
6068: strcat(rfileres,optionfilext); /* Other files have txt extension */
6069: if((ficres =fopen(rfileres,"w"))==NULL) {
6070: printf("Problem writing new parameter file: %s\n", fileres);goto end;
6071: fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
6072: }
6073: fprintf(ficres,"#%s\n",version);
6074: } /* End of mle != -3 */
6075:
6076:
6077: n= lastobs;
6078: num=lvector(1,n);
6079: moisnais=vector(1,n);
6080: annais=vector(1,n);
6081: moisdc=vector(1,n);
6082: andc=vector(1,n);
6083: agedc=vector(1,n);
6084: cod=ivector(1,n);
6085: weight=vector(1,n);
6086: for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
6087: mint=matrix(1,maxwav,1,n);
6088: anint=matrix(1,maxwav,1,n);
6089: s=imatrix(1,maxwav+1,1,n); /* s[i][j] health state for wave i and individual j */
6090: tab=ivector(1,NCOVMAX);
6091: ncodemax=ivector(1,NCOVMAX); /* Number of code per covariate; if O and 1 only, 2**ncov; V1+V2+V3+V4=>16 */
6092:
6093: /* Reads data from file datafile */
6094: if (readdata(datafile, firstobs, lastobs, &imx)==1)
6095: goto end;
6096:
6097: /* Calculation of the number of parameters from char model */
6098: /* modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4
6099: k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tag[cptcovage=1]=4
6100: k=3 V4 Tvar[k=3]= 4 (from V4)
6101: k=2 V1 Tvar[k=2]= 1 (from V1)
6102: k=1 Tvar[1]=2 (from V2)
6103: */
6104: Tvar=ivector(1,NCOVMAX); /* Was 15 changed to NCOVMAX. */
6105: /* V2+V1+V4+age*V3 is a model with 4 covariates (3 plus signs).
6106: For each model-covariate stores the data-covariate id. Tvar[1]=2, Tvar[2]=1, Tvar[3]=4,
6107: Tvar[4=age*V3] is 3 and 'age' is recorded in Tage.
6108: */
6109: /* For model-covariate k tells which data-covariate to use but
6110: because this model-covariate is a construction we invent a new column
6111: ncovcol + k1
6112: If already ncovcol=4 and model=V2+V1+V1*V4+age*V3
6113: Tvar[3=V1*V4]=4+1 etc */
6114: Tprod=ivector(1,NCOVMAX); /* Gives the position of a product */
6115: /* Tprod[k1=1]=3(=V1*V4) for V2+V1+V1*V4+age*V3
6116: if V2+V1+V1*V4+age*V3+V3*V2 TProd[k1=2]=5 (V3*V2)
6117: */
6118: Tvaraff=ivector(1,NCOVMAX); /* Unclear */
6119: 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
6120: * For V3*V2 (in V2+V1+V1*V4+age*V3+V3*V2), V3*V2 position is 2nd.
6121: * Tvard[k1=2][1]=3 (V3) Tvard[k1=2][2]=2(V2) */
6122: Tage=ivector(1,NCOVMAX); /* Gives the covariate id of covariates associated with age: V2 + V1 + age*V4 + V3*age
6123: 4 covariates (3 plus signs)
6124: Tage[1=V3*age]= 4; Tage[2=age*V4] = 3
6125: */
6126:
6127: if(decodemodel(model, lastobs) == 1)
6128: goto end;
6129:
6130: if((double)(lastobs-imx)/(double)imx > 1.10){
6131: nbwarn++;
6132: 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);
6133: 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);
6134: }
6135: /* if(mle==1){*/
6136: if (weightopt != 1) { /* Maximisation without weights. We can have weights different from 1 but want no weight*/
6137: for(i=1;i<=imx;i++) weight[i]=1.0; /* changed to imx */
6138: }
6139:
6140: /*-calculation of age at interview from date of interview and age at death -*/
6141: agev=matrix(1,maxwav,1,imx);
6142:
6143: if(calandcheckages(imx, maxwav, &agemin, &agemax, &nberr, &nbwarn) == 1)
6144: goto end;
6145:
6146:
6147: agegomp=(int)agemin;
6148: free_vector(moisnais,1,n);
6149: free_vector(annais,1,n);
6150: /* free_matrix(mint,1,maxwav,1,n);
6151: free_matrix(anint,1,maxwav,1,n);*/
6152: free_vector(moisdc,1,n);
6153: free_vector(andc,1,n);
6154: /* */
6155:
6156: wav=ivector(1,imx);
6157: dh=imatrix(1,lastpass-firstpass+1,1,imx);
6158: bh=imatrix(1,lastpass-firstpass+1,1,imx);
6159: mw=imatrix(1,lastpass-firstpass+1,1,imx);
6160:
6161: /* Concatenates waves */
6162: concatwav(wav, dh, bh, mw, s, agedc, agev, firstpass, lastpass, imx, nlstate, stepm);
6163: /* */
6164:
6165: /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
6166:
6167: nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
6168: ncodemax[1]=1;
6169: Ndum =ivector(-1,NCOVMAX);
6170: if (ncovmodel > 2)
6171: tricode(Tvar,nbcode,imx, Ndum); /**< Fills nbcode[Tvar[j]][l]; */
6172:
6173: codtab=imatrix(1,100,1,10); /* codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) */
6174: /*printf(" codtab[1,1],codtab[100,10]=%d,%d\n", codtab[1][1],codtab[100][10]);*/
6175: h=0;
6176:
6177:
6178: /*if (cptcovn > 0) */
6179:
6180:
6181: m=pow(2,cptcoveff);
6182:
6183: for(k=1;k<=cptcoveff; k++){ /* scans any effective covariate */
6184: 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 */
6185: for(j=1; j <= ncodemax[k]; j++){ /* For each modality of this covariate ncodemax=2*/
6186: for(cpt=1; cpt <=pow(2,k-1); cpt++){ /* cpt=1 to 8/2**(3+1-1 or 3+1-3) =1 or 4 */
6187: h++;
6188: if (h>m)
6189: h=1;
6190: /**< codtab(h,k) k = codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) + 1
6191: * h 1 2 3 4
6192: *______________________________
6193: * 1 i=1 1 i=1 1 i=1 1 i=1 1
6194: * 2 2 1 1 1
6195: * 3 i=2 1 2 1 1
6196: * 4 2 2 1 1
6197: * 5 i=3 1 i=2 1 2 1
6198: * 6 2 1 2 1
6199: * 7 i=4 1 2 2 1
6200: * 8 2 2 2 1
6201: * 9 i=5 1 i=3 1 i=2 1 1
6202: * 10 2 1 1 1
6203: * 11 i=6 1 2 1 1
6204: * 12 2 2 1 1
6205: * 13 i=7 1 i=4 1 2 1
6206: * 14 2 1 2 1
6207: * 15 i=8 1 2 2 1
6208: * 16 2 2 2 1
6209: */
6210: codtab[h][k]=j;
6211: /*codtab[h][Tvar[k]]=j;*/
6212: 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]]);
6213: }
6214: }
6215: }
6216: }
6217: /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);
6218: codtab[1][2]=1;codtab[2][2]=2; */
6219: /* for(i=1; i <=m ;i++){
6220: for(k=1; k <=cptcovn; k++){
6221: printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
6222: }
6223: printf("\n");
6224: }
6225: scanf("%d",i);*/
6226:
6227: free_ivector(Ndum,-1,NCOVMAX);
6228:
6229:
6230:
6231: /*------------ gnuplot -------------*/
6232: strcpy(optionfilegnuplot,optionfilefiname);
6233: if(mle==-3)
6234: strcat(optionfilegnuplot,"-mort");
6235: strcat(optionfilegnuplot,".gp");
6236:
6237: if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
6238: printf("Problem with file %s",optionfilegnuplot);
6239: }
6240: else{
6241: fprintf(ficgp,"\n# %s\n", version);
6242: fprintf(ficgp,"# %s\n", optionfilegnuplot);
6243: //fprintf(ficgp,"set missing 'NaNq'\n");
6244: fprintf(ficgp,"set datafile missing 'NaNq'\n");
6245: }
6246: /* fclose(ficgp);*/
6247: /*--------- index.htm --------*/
6248:
6249: strcpy(optionfilehtm,optionfilefiname); /* Main html file */
6250: if(mle==-3)
6251: strcat(optionfilehtm,"-mort");
6252: strcat(optionfilehtm,".htm");
6253: if((fichtm=fopen(optionfilehtm,"w"))==NULL) {
6254: printf("Problem with %s \n",optionfilehtm);
6255: exit(0);
6256: }
6257:
6258: strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
6259: strcat(optionfilehtmcov,"-cov.htm");
6260: if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL) {
6261: printf("Problem with %s \n",optionfilehtmcov), exit(0);
6262: }
6263: else{
6264: fprintf(fichtmcov,"<html><head>\n<title>IMaCh Cov %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
6265: <hr size=\"2\" color=\"#EC5E5E\"> \n\
6266: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n",\
6267: optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
6268: }
6269:
6270: fprintf(fichtm,"<html><head>\n<title>IMaCh %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
6271: <hr size=\"2\" color=\"#EC5E5E\"> \n\
6272: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
6273: \n\
6274: <hr size=\"2\" color=\"#EC5E5E\">\
6275: <ul><li><h4>Parameter files</h4>\n\
6276: - Parameter file: <a href=\"%s.%s\">%s.%s</a><br>\n\
6277: - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
6278: - Log file of the run: <a href=\"%s\">%s</a><br>\n\
6279: - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
6280: - Date and time at start: %s</ul>\n",\
6281: optionfilehtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
6282: optionfilefiname,optionfilext,optionfilefiname,optionfilext,\
6283: fileres,fileres,\
6284: filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
6285: fflush(fichtm);
6286:
6287: strcpy(pathr,path);
6288: strcat(pathr,optionfilefiname);
6289: chdir(optionfilefiname); /* Move to directory named optionfile */
6290:
6291: /* Calculates basic frequencies. Computes observed prevalence at single age
6292: and prints on file fileres'p'. */
6293: freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart);
6294:
6295: fprintf(fichtm,"\n");
6296: fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
6297: Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
6298: Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
6299: imx,agemin,agemax,jmin,jmax,jmean);
6300: pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
6301: oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
6302: newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
6303: savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
6304: oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
6305:
6306:
6307: /* For Powell, parameters are in a vector p[] starting at p[1]
6308: so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
6309: p=param[1][1]; /* *(*(*(param +1)+1)+0) */
6310:
6311: globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
6312:
6313: if (mle==-3){
6314: ximort=matrix(1,NDIM,1,NDIM);
6315: /* ximort=gsl_matrix_alloc(1,NDIM,1,NDIM); */
6316: cens=ivector(1,n);
6317: ageexmed=vector(1,n);
6318: agecens=vector(1,n);
6319: dcwave=ivector(1,n);
6320:
6321: for (i=1; i<=imx; i++){
6322: dcwave[i]=-1;
6323: for (m=firstpass; m<=lastpass; m++)
6324: if (s[m][i]>nlstate) {
6325: dcwave[i]=m;
6326: /* printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
6327: break;
6328: }
6329: }
6330:
6331: for (i=1; i<=imx; i++) {
6332: if (wav[i]>0){
6333: ageexmed[i]=agev[mw[1][i]][i];
6334: j=wav[i];
6335: agecens[i]=1.;
6336:
6337: if (ageexmed[i]> 1 && wav[i] > 0){
6338: agecens[i]=agev[mw[j][i]][i];
6339: cens[i]= 1;
6340: }else if (ageexmed[i]< 1)
6341: cens[i]= -1;
6342: if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
6343: cens[i]=0 ;
6344: }
6345: else cens[i]=-1;
6346: }
6347:
6348: for (i=1;i<=NDIM;i++) {
6349: for (j=1;j<=NDIM;j++)
6350: ximort[i][j]=(i == j ? 1.0 : 0.0);
6351: }
6352:
6353: /*p[1]=0.0268; p[NDIM]=0.083;*/
6354: /*printf("%lf %lf", p[1], p[2]);*/
6355:
6356:
6357: #ifdef GSL
6358: printf("GSL optimization\n"); fprintf(ficlog,"Powell\n");
6359: #else
6360: printf("Powell\n"); fprintf(ficlog,"Powell\n");
6361: #endif
6362: strcpy(filerespow,"pow-mort");
6363: strcat(filerespow,fileres);
6364: if((ficrespow=fopen(filerespow,"w"))==NULL) {
6365: printf("Problem with resultfile: %s\n", filerespow);
6366: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
6367: }
6368: #ifdef GSL
6369: fprintf(ficrespow,"# GSL optimization\n# iter -2*LL");
6370: #else
6371: fprintf(ficrespow,"# Powell\n# iter -2*LL");
6372: #endif
6373: /* for (i=1;i<=nlstate;i++)
6374: for(j=1;j<=nlstate+ndeath;j++)
6375: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
6376: */
6377: fprintf(ficrespow,"\n");
6378: #ifdef GSL
6379: /* gsl starts here */
6380: T = gsl_multimin_fminimizer_nmsimplex;
6381: gsl_multimin_fminimizer *sfm = NULL;
6382: gsl_vector *ss, *x;
6383: gsl_multimin_function minex_func;
6384:
6385: /* Initial vertex size vector */
6386: ss = gsl_vector_alloc (NDIM);
6387:
6388: if (ss == NULL){
6389: GSL_ERROR_VAL ("failed to allocate space for ss", GSL_ENOMEM, 0);
6390: }
6391: /* Set all step sizes to 1 */
6392: gsl_vector_set_all (ss, 0.001);
6393:
6394: /* Starting point */
6395:
6396: x = gsl_vector_alloc (NDIM);
6397:
6398: if (x == NULL){
6399: gsl_vector_free(ss);
6400: GSL_ERROR_VAL ("failed to allocate space for x", GSL_ENOMEM, 0);
6401: }
6402:
6403: /* Initialize method and iterate */
6404: /* p[1]=0.0268; p[NDIM]=0.083; */
6405: /* gsl_vector_set(x, 0, 0.0268); */
6406: /* gsl_vector_set(x, 1, 0.083); */
6407: gsl_vector_set(x, 0, p[1]);
6408: gsl_vector_set(x, 1, p[2]);
6409:
6410: minex_func.f = &gompertz_f;
6411: minex_func.n = NDIM;
6412: minex_func.params = (void *)&p; /* ??? */
6413:
6414: sfm = gsl_multimin_fminimizer_alloc (T, NDIM);
6415: gsl_multimin_fminimizer_set (sfm, &minex_func, x, ss);
6416:
6417: printf("Iterations beginning .....\n\n");
6418: printf("Iter. # Intercept Slope -Log Likelihood Simplex size\n");
6419:
6420: iteri=0;
6421: while (rval == GSL_CONTINUE){
6422: iteri++;
6423: status = gsl_multimin_fminimizer_iterate(sfm);
6424:
6425: if (status) printf("error: %s\n", gsl_strerror (status));
6426: fflush(0);
6427:
6428: if (status)
6429: break;
6430:
6431: rval = gsl_multimin_test_size (gsl_multimin_fminimizer_size (sfm), 1e-6);
6432: ssval = gsl_multimin_fminimizer_size (sfm);
6433:
6434: if (rval == GSL_SUCCESS)
6435: printf ("converged to a local maximum at\n");
6436:
6437: printf("%5d ", iteri);
6438: for (it = 0; it < NDIM; it++){
6439: printf ("%10.5f ", gsl_vector_get (sfm->x, it));
6440: }
6441: printf("f() = %-10.5f ssize = %.7f\n", sfm->fval, ssval);
6442: }
6443:
6444: printf("\n\n Please note: Program should be run many times with varying starting points to detemine global maximum\n\n");
6445:
6446: gsl_vector_free(x); /* initial values */
6447: gsl_vector_free(ss); /* inital step size */
6448: for (it=0; it<NDIM; it++){
6449: p[it+1]=gsl_vector_get(sfm->x,it);
6450: fprintf(ficrespow," %.12lf", p[it]);
6451: }
6452: gsl_multimin_fminimizer_free (sfm); /* p *(sfm.x.data) et p *(sfm.x.data+1) */
6453: #endif
6454: #ifdef POWELL
6455: powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
6456: #endif
6457: fclose(ficrespow);
6458:
6459: hesscov(matcov, p, NDIM, delti, 1e-4, gompertz);
6460:
6461: for(i=1; i <=NDIM; i++)
6462: for(j=i+1;j<=NDIM;j++)
6463: matcov[i][j]=matcov[j][i];
6464:
6465: printf("\nCovariance matrix\n ");
6466: for(i=1; i <=NDIM; i++) {
6467: for(j=1;j<=NDIM;j++){
6468: printf("%f ",matcov[i][j]);
6469: }
6470: printf("\n ");
6471: }
6472:
6473: printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
6474: for (i=1;i<=NDIM;i++)
6475: printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
6476:
6477: lsurv=vector(1,AGESUP);
6478: lpop=vector(1,AGESUP);
6479: tpop=vector(1,AGESUP);
6480: lsurv[agegomp]=100000;
6481:
6482: for (k=agegomp;k<=AGESUP;k++) {
6483: agemortsup=k;
6484: if (p[1]*exp(p[2]*(k-agegomp))>1) break;
6485: }
6486:
6487: for (k=agegomp;k<agemortsup;k++)
6488: lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
6489:
6490: for (k=agegomp;k<agemortsup;k++){
6491: lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
6492: sumlpop=sumlpop+lpop[k];
6493: }
6494:
6495: tpop[agegomp]=sumlpop;
6496: for (k=agegomp;k<(agemortsup-3);k++){
6497: /* tpop[k+1]=2;*/
6498: tpop[k+1]=tpop[k]-lpop[k];
6499: }
6500:
6501:
6502: printf("\nAge lx qx dx Lx Tx e(x)\n");
6503: for (k=agegomp;k<(agemortsup-2);k++)
6504: 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]);
6505:
6506:
6507: replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
6508: printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
6509:
6510: printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \
6511: stepm, weightopt,\
6512: model,imx,p,matcov,agemortsup);
6513:
6514: free_vector(lsurv,1,AGESUP);
6515: free_vector(lpop,1,AGESUP);
6516: free_vector(tpop,1,AGESUP);
6517: #ifdef GSL
6518: free_ivector(cens,1,n);
6519: free_vector(agecens,1,n);
6520: free_ivector(dcwave,1,n);
6521: free_matrix(ximort,1,NDIM,1,NDIM);
6522: #endif
6523: } /* Endof if mle==-3 */
6524:
6525: else{ /* For mle >=1 */
6526: globpr=0;/* debug */
6527: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
6528: printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
6529: for (k=1; k<=npar;k++)
6530: printf(" %d %8.5f",k,p[k]);
6531: printf("\n");
6532: globpr=1; /* to print the contributions */
6533: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
6534: printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
6535: for (k=1; k<=npar;k++)
6536: printf(" %d %8.5f",k,p[k]);
6537: printf("\n");
6538: if(mle>=1){ /* Could be 1 or 2 */
6539: mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
6540: }
6541:
6542: /*--------- results files --------------*/
6543: 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);
6544:
6545:
6546: fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
6547: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
6548: fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
6549: for(i=1,jk=1; i <=nlstate; i++){
6550: for(k=1; k <=(nlstate+ndeath); k++){
6551: if (k != i) {
6552: printf("%d%d ",i,k);
6553: fprintf(ficlog,"%d%d ",i,k);
6554: fprintf(ficres,"%1d%1d ",i,k);
6555: for(j=1; j <=ncovmodel; j++){
6556: printf("%lf ",p[jk]);
6557: fprintf(ficlog,"%lf ",p[jk]);
6558: fprintf(ficres,"%lf ",p[jk]);
6559: jk++;
6560: }
6561: printf("\n");
6562: fprintf(ficlog,"\n");
6563: fprintf(ficres,"\n");
6564: }
6565: }
6566: }
6567: if(mle!=0){
6568: /* Computing hessian and covariance matrix */
6569: ftolhess=ftol; /* Usually correct */
6570: hesscov(matcov, p, npar, delti, ftolhess, func);
6571: }
6572: fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
6573: printf("# Scales (for hessian or gradient estimation)\n");
6574: fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
6575: for(i=1,jk=1; i <=nlstate; i++){
6576: for(j=1; j <=nlstate+ndeath; j++){
6577: if (j!=i) {
6578: fprintf(ficres,"%1d%1d",i,j);
6579: printf("%1d%1d",i,j);
6580: fprintf(ficlog,"%1d%1d",i,j);
6581: for(k=1; k<=ncovmodel;k++){
6582: printf(" %.5e",delti[jk]);
6583: fprintf(ficlog," %.5e",delti[jk]);
6584: fprintf(ficres," %.5e",delti[jk]);
6585: jk++;
6586: }
6587: printf("\n");
6588: fprintf(ficlog,"\n");
6589: fprintf(ficres,"\n");
6590: }
6591: }
6592: }
6593:
6594: 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");
6595: if(mle>=1)
6596: 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");
6597: 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");
6598: /* # 121 Var(a12)\n\ */
6599: /* # 122 Cov(b12,a12) Var(b12)\n\ */
6600: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
6601: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
6602: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
6603: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
6604: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
6605: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
6606:
6607:
6608: /* Just to have a covariance matrix which will be more understandable
6609: even is we still don't want to manage dictionary of variables
6610: */
6611: for(itimes=1;itimes<=2;itimes++){
6612: jj=0;
6613: for(i=1; i <=nlstate; i++){
6614: for(j=1; j <=nlstate+ndeath; j++){
6615: if(j==i) continue;
6616: for(k=1; k<=ncovmodel;k++){
6617: jj++;
6618: ca[0]= k+'a'-1;ca[1]='\0';
6619: if(itimes==1){
6620: if(mle>=1)
6621: printf("#%1d%1d%d",i,j,k);
6622: fprintf(ficlog,"#%1d%1d%d",i,j,k);
6623: fprintf(ficres,"#%1d%1d%d",i,j,k);
6624: }else{
6625: if(mle>=1)
6626: printf("%1d%1d%d",i,j,k);
6627: fprintf(ficlog,"%1d%1d%d",i,j,k);
6628: fprintf(ficres,"%1d%1d%d",i,j,k);
6629: }
6630: ll=0;
6631: for(li=1;li <=nlstate; li++){
6632: for(lj=1;lj <=nlstate+ndeath; lj++){
6633: if(lj==li) continue;
6634: for(lk=1;lk<=ncovmodel;lk++){
6635: ll++;
6636: if(ll<=jj){
6637: cb[0]= lk +'a'-1;cb[1]='\0';
6638: if(ll<jj){
6639: if(itimes==1){
6640: if(mle>=1)
6641: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
6642: fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
6643: fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
6644: }else{
6645: if(mle>=1)
6646: printf(" %.5e",matcov[jj][ll]);
6647: fprintf(ficlog," %.5e",matcov[jj][ll]);
6648: fprintf(ficres," %.5e",matcov[jj][ll]);
6649: }
6650: }else{
6651: if(itimes==1){
6652: if(mle>=1)
6653: printf(" Var(%s%1d%1d)",ca,i,j);
6654: fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
6655: fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
6656: }else{
6657: if(mle>=1)
6658: printf(" %.5e",matcov[jj][ll]);
6659: fprintf(ficlog," %.5e",matcov[jj][ll]);
6660: fprintf(ficres," %.5e",matcov[jj][ll]);
6661: }
6662: }
6663: }
6664: } /* end lk */
6665: } /* end lj */
6666: } /* end li */
6667: if(mle>=1)
6668: printf("\n");
6669: fprintf(ficlog,"\n");
6670: fprintf(ficres,"\n");
6671: numlinepar++;
6672: } /* end k*/
6673: } /*end j */
6674: } /* end i */
6675: } /* end itimes */
6676:
6677: fflush(ficlog);
6678: fflush(ficres);
6679:
6680: while((c=getc(ficpar))=='#' && c!= EOF){
6681: ungetc(c,ficpar);
6682: fgets(line, MAXLINE, ficpar);
6683: fputs(line,stdout);
6684: fputs(line,ficparo);
6685: }
6686: ungetc(c,ficpar);
6687:
6688: estepm=0;
6689: fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
6690: if (estepm==0 || estepm < stepm) estepm=stepm;
6691: if (fage <= 2) {
6692: bage = ageminpar;
6693: fage = agemaxpar;
6694: }
6695:
6696: fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
6697: fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
6698: fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
6699:
6700: while((c=getc(ficpar))=='#' && c!= EOF){
6701: ungetc(c,ficpar);
6702: fgets(line, MAXLINE, ficpar);
6703: fputs(line,stdout);
6704: fputs(line,ficparo);
6705: }
6706: ungetc(c,ficpar);
6707:
6708: 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);
6709: 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);
6710: 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);
6711: printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
6712: 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);
6713:
6714: while((c=getc(ficpar))=='#' && c!= EOF){
6715: ungetc(c,ficpar);
6716: fgets(line, MAXLINE, ficpar);
6717: fputs(line,stdout);
6718: fputs(line,ficparo);
6719: }
6720: ungetc(c,ficpar);
6721:
6722:
6723: dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
6724: dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
6725:
6726: fscanf(ficpar,"pop_based=%d\n",&popbased);
6727: fprintf(ficparo,"pop_based=%d\n",popbased);
6728: fprintf(ficres,"pop_based=%d\n",popbased);
6729:
6730: while((c=getc(ficpar))=='#' && c!= EOF){
6731: ungetc(c,ficpar);
6732: fgets(line, MAXLINE, ficpar);
6733: fputs(line,stdout);
6734: fputs(line,ficparo);
6735: }
6736: ungetc(c,ficpar);
6737:
6738: 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);
6739: 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);
6740: 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);
6741: 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);
6742: 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);
6743: /* day and month of proj2 are not used but only year anproj2.*/
6744:
6745:
6746:
6747: /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint); */
6748: /* ,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2); */
6749:
6750: replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
6751: printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
6752:
6753: printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
6754: model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
6755: jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
6756:
6757: /*------------ free_vector -------------*/
6758: /* chdir(path); */
6759:
6760: free_ivector(wav,1,imx);
6761: free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
6762: free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
6763: free_imatrix(mw,1,lastpass-firstpass+1,1,imx);
6764: free_lvector(num,1,n);
6765: free_vector(agedc,1,n);
6766: /*free_matrix(covar,0,NCOVMAX,1,n);*/
6767: /*free_matrix(covar,1,NCOVMAX,1,n);*/
6768: fclose(ficparo);
6769: fclose(ficres);
6770:
6771:
6772: /*--------------- Prevalence limit (period or stable prevalence) --------------*/
6773: #include "prevlim.h" /* Use ficrespl, ficlog */
6774: fclose(ficrespl);
6775:
6776: #ifdef FREEEXIT2
6777: #include "freeexit2.h"
6778: #endif
6779:
6780: /*------------- h Pij x at various ages ------------*/
6781: #include "hpijx.h"
6782: fclose(ficrespij);
6783:
6784: /*-------------- Variance of one-step probabilities---*/
6785: k=1;
6786: varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
6787:
6788:
6789: probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
6790: for(i=1;i<=AGESUP;i++)
6791: for(j=1;j<=NCOVMAX;j++)
6792: for(k=1;k<=NCOVMAX;k++)
6793: probs[i][j][k]=0.;
6794:
6795: /*---------- Forecasting ------------------*/
6796: /*if((stepm == 1) && (strcmp(model,".")==0)){*/
6797: if(prevfcast==1){
6798: /* if(stepm ==1){*/
6799: prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
6800: /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
6801: /* } */
6802: /* else{ */
6803: /* erreur=108; */
6804: /* 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); */
6805: /* 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); */
6806: /* } */
6807: }
6808:
6809:
6810: /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
6811:
6812: prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
6813: /* 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",\
6814: ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
6815: */
6816:
6817: if (mobilav!=0) {
6818: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
6819: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
6820: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
6821: printf(" Error in movingaverage mobilav=%d\n",mobilav);
6822: }
6823: }
6824:
6825:
6826: /*---------- Health expectancies, no variances ------------*/
6827:
6828: strcpy(filerese,"e");
6829: strcat(filerese,fileres);
6830: if((ficreseij=fopen(filerese,"w"))==NULL) {
6831: printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
6832: fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
6833: }
6834: printf("Computing Health Expectancies: result on file '%s' \n", filerese);
6835: fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
6836: /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
6837: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
6838:
6839: for (k=1; k <= (int) pow(2,cptcoveff); k++){
6840: fprintf(ficreseij,"\n#****** ");
6841: for(j=1;j<=cptcoveff;j++) {
6842: fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6843: }
6844: fprintf(ficreseij,"******\n");
6845:
6846: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
6847: oldm=oldms;savm=savms;
6848: evsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart);
6849:
6850: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
6851: /*}*/
6852: }
6853: fclose(ficreseij);
6854:
6855:
6856: /*---------- Health expectancies and variances ------------*/
6857:
6858:
6859: strcpy(filerest,"t");
6860: strcat(filerest,fileres);
6861: if((ficrest=fopen(filerest,"w"))==NULL) {
6862: printf("Problem with total LE resultfile: %s\n", filerest);goto end;
6863: fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
6864: }
6865: printf("Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);
6866: fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);
6867:
6868:
6869: strcpy(fileresstde,"stde");
6870: strcat(fileresstde,fileres);
6871: if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {
6872: printf("Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
6873: fprintf(ficlog,"Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
6874: }
6875: printf("Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
6876: fprintf(ficlog,"Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
6877:
6878: strcpy(filerescve,"cve");
6879: strcat(filerescve,fileres);
6880: if((ficrescveij=fopen(filerescve,"w"))==NULL) {
6881: printf("Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
6882: fprintf(ficlog,"Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
6883: }
6884: printf("Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
6885: fprintf(ficlog,"Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
6886:
6887: strcpy(fileresv,"v");
6888: strcat(fileresv,fileres);
6889: if((ficresvij=fopen(fileresv,"w"))==NULL) {
6890: printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
6891: fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
6892: }
6893: printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
6894: fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
6895:
6896: /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
6897: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
6898:
6899: for (k=1; k <= (int) pow(2,cptcoveff); k++){
6900: fprintf(ficrest,"\n#****** ");
6901: for(j=1;j<=cptcoveff;j++)
6902: fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6903: fprintf(ficrest,"******\n");
6904:
6905: fprintf(ficresstdeij,"\n#****** ");
6906: fprintf(ficrescveij,"\n#****** ");
6907: for(j=1;j<=cptcoveff;j++) {
6908: fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6909: fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6910: }
6911: fprintf(ficresstdeij,"******\n");
6912: fprintf(ficrescveij,"******\n");
6913:
6914: fprintf(ficresvij,"\n#****** ");
6915: for(j=1;j<=cptcoveff;j++)
6916: fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6917: fprintf(ficresvij,"******\n");
6918:
6919: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
6920: oldm=oldms;savm=savms;
6921: cvevsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);
6922: /*
6923: */
6924: /* goto endfree; */
6925:
6926: vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
6927: pstamp(ficrest);
6928:
6929:
6930: for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
6931: oldm=oldms;savm=savms; /* Segmentation fault */
6932: cptcod= 0; /* To be deleted */
6933: 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 */
6934: 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 ");
6935: if(vpopbased==1)
6936: 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);
6937: else
6938: fprintf(ficrest,"the age specific period (stable) prevalences in each health state \n");
6939: fprintf(ficrest,"# Age e.. (std) ");
6940: for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
6941: fprintf(ficrest,"\n");
6942:
6943: epj=vector(1,nlstate+1);
6944: for(age=bage; age <=fage ;age++){
6945: prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
6946: if (vpopbased==1) {
6947: if(mobilav ==0){
6948: for(i=1; i<=nlstate;i++)
6949: prlim[i][i]=probs[(int)age][i][k];
6950: }else{ /* mobilav */
6951: for(i=1; i<=nlstate;i++)
6952: prlim[i][i]=mobaverage[(int)age][i][k];
6953: }
6954: }
6955:
6956: fprintf(ficrest," %4.0f",age);
6957: for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
6958: for(i=1, epj[j]=0.;i <=nlstate;i++) {
6959: epj[j] += prlim[i][i]*eij[i][j][(int)age];
6960: /* printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
6961: }
6962: epj[nlstate+1] +=epj[j];
6963: }
6964:
6965: for(i=1, vepp=0.;i <=nlstate;i++)
6966: for(j=1;j <=nlstate;j++)
6967: vepp += vareij[i][j][(int)age];
6968: fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
6969: for(j=1;j <=nlstate;j++){
6970: fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
6971: }
6972: fprintf(ficrest,"\n");
6973: }
6974: }
6975: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
6976: free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
6977: free_vector(epj,1,nlstate+1);
6978: /*}*/
6979: }
6980: free_vector(weight,1,n);
6981: free_imatrix(Tvard,1,NCOVMAX,1,2);
6982: free_imatrix(s,1,maxwav+1,1,n);
6983: free_matrix(anint,1,maxwav,1,n);
6984: free_matrix(mint,1,maxwav,1,n);
6985: free_ivector(cod,1,n);
6986: free_ivector(tab,1,NCOVMAX);
6987: fclose(ficresstdeij);
6988: fclose(ficrescveij);
6989: fclose(ficresvij);
6990: fclose(ficrest);
6991: fclose(ficpar);
6992:
6993: /*------- Variance of period (stable) prevalence------*/
6994:
6995: strcpy(fileresvpl,"vpl");
6996: strcat(fileresvpl,fileres);
6997: if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
6998: printf("Problem with variance of period (stable) prevalence resultfile: %s\n", fileresvpl);
6999: exit(0);
7000: }
7001: printf("Computing Variance-covariance of period (stable) prevalence: file '%s' \n", fileresvpl);
7002:
7003: /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
7004: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
7005:
7006: for (k=1; k <= (int) pow(2,cptcoveff); k++){
7007: fprintf(ficresvpl,"\n#****** ");
7008: for(j=1;j<=cptcoveff;j++)
7009: fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
7010: fprintf(ficresvpl,"******\n");
7011:
7012: varpl=matrix(1,nlstate,(int) bage, (int) fage);
7013: oldm=oldms;savm=savms;
7014: varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k,strstart);
7015: free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
7016: /*}*/
7017: }
7018:
7019: fclose(ficresvpl);
7020:
7021: /*---------- End : free ----------------*/
7022: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
7023: free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
7024: } /* mle==-3 arrives here for freeing */
7025: /* endfree:*/
7026: free_matrix(prlim,1,nlstate,1,nlstate); /*here or after loop ? */
7027: free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
7028: free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
7029: free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
7030: free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
7031: free_matrix(covar,0,NCOVMAX,1,n);
7032: free_matrix(matcov,1,npar,1,npar);
7033: /*free_vector(delti,1,npar);*/
7034: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
7035: free_matrix(agev,1,maxwav,1,imx);
7036: free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
7037:
7038: free_ivector(ncodemax,1,NCOVMAX);
7039: free_ivector(Tvar,1,NCOVMAX);
7040: free_ivector(Tprod,1,NCOVMAX);
7041: free_ivector(Tvaraff,1,NCOVMAX);
7042: free_ivector(Tage,1,NCOVMAX);
7043:
7044: free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
7045: free_imatrix(codtab,1,100,1,10);
7046: fflush(fichtm);
7047: fflush(ficgp);
7048:
7049:
7050: if((nberr >0) || (nbwarn>0)){
7051: printf("End of Imach with %d errors and/or %d warnings\n",nberr,nbwarn);
7052: fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
7053: }else{
7054: printf("End of Imach\n");
7055: fprintf(ficlog,"End of Imach\n");
7056: }
7057: printf("See log file on %s\n",filelog);
7058: /* gettimeofday(&end_time, (struct timezone*)0);*/ /* after time */
7059: /*(void) gettimeofday(&end_time,&tzp);*/
7060: rend_time = time(NULL);
7061: end_time = *localtime(&rend_time);
7062: /* tml = *localtime(&end_time.tm_sec); */
7063: strcpy(strtend,asctime(&end_time));
7064: printf("Local time at start %s\nLocal time at end %s",strstart, strtend);
7065: fprintf(ficlog,"Local time at start %s\nLocal time at end %s\n",strstart, strtend);
7066: printf("Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
7067:
7068: printf("Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
7069: fprintf(ficlog,"Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
7070: fprintf(ficlog,"Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
7071: /* printf("Total time was %d uSec.\n", total_usecs);*/
7072: /* if(fileappend(fichtm,optionfilehtm)){ */
7073: fprintf(fichtm,"<br>Local time at start %s<br>Local time at end %s<br>\n</body></html>",strstart, strtend);
7074: fclose(fichtm);
7075: fprintf(fichtmcov,"<br>Local time at start %s<br>Local time at end %s<br>\n</body></html>",strstart, strtend);
7076: fclose(fichtmcov);
7077: fclose(ficgp);
7078: fclose(ficlog);
7079: /*------ End -----------*/
7080:
7081:
7082: printf("Before Current directory %s!\n",pathcd);
7083: if(chdir(pathcd) != 0)
7084: printf("Can't move to directory %s!\n",path);
7085: if(getcwd(pathcd,MAXLINE) > 0)
7086: printf("Current directory %s!\n",pathcd);
7087: /*strcat(plotcmd,CHARSEPARATOR);*/
7088: sprintf(plotcmd,"gnuplot");
7089: #ifdef _WIN32
7090: sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
7091: #endif
7092: if(!stat(plotcmd,&info)){
7093: printf("Error or gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
7094: if(!stat(getenv("GNUPLOTBIN"),&info)){
7095: printf("Error or gnuplot program not found: '%s' Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);
7096: }else
7097: strcpy(pplotcmd,plotcmd);
7098: #ifdef __unix
7099: strcpy(plotcmd,GNUPLOTPROGRAM);
7100: if(!stat(plotcmd,&info)){
7101: printf("Error gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
7102: }else
7103: strcpy(pplotcmd,plotcmd);
7104: #endif
7105: }else
7106: strcpy(pplotcmd,plotcmd);
7107:
7108: sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
7109: printf("Starting graphs with: '%s'\n",plotcmd);fflush(stdout);
7110:
7111: if((outcmd=system(plotcmd)) != 0){
7112: printf("gnuplot command might not be in your path: '%s', err=%d\n", plotcmd, outcmd);
7113: printf("\n Trying if gnuplot resides on the same directory that IMaCh\n");
7114: sprintf(plotcmd,"%sgnuplot %s", pathimach, optionfilegnuplot);
7115: if((outcmd=system(plotcmd)) != 0)
7116: printf("\n Still a problem with gnuplot command %s, err=%d\n", plotcmd, outcmd);
7117: }
7118: printf(" Successful, please wait...");
7119: while (z[0] != 'q') {
7120: /* chdir(path); */
7121: printf("\nType e to edit results with your browser, g to graph again and q for exit: ");
7122: scanf("%s",z);
7123: /* if (z[0] == 'c') system("./imach"); */
7124: if (z[0] == 'e') {
7125: #ifdef __APPLE__
7126: sprintf(pplotcmd, "open %s", optionfilehtm);
7127: #elif __linux
7128: sprintf(pplotcmd, "xdg-open %s", optionfilehtm);
7129: #else
7130: sprintf(pplotcmd, "%s", optionfilehtm);
7131: #endif
7132: printf("Starting browser with: %s",pplotcmd);fflush(stdout);
7133: system(pplotcmd);
7134: }
7135: else if (z[0] == 'g') system(plotcmd);
7136: else if (z[0] == 'q') exit(0);
7137: }
7138: end:
7139: while (z[0] != 'q') {
7140: printf("\nType q for exiting: ");
7141: scanf("%s",z);
7142: }
7143: }
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