Annotation of imach/src/imach.c, revision 1.169
1.169 ! brouard 1: /* $Id: imach.c,v 1.168 2014/12/22 15:17:42 brouard Exp $
1.126 brouard 2: $State: Exp $
1.163 brouard 3: $Log: imach.c,v $
1.169 ! brouard 4: Revision 1.168 2014/12/22 15:17:42 brouard
! 5: Summary: udate
! 6:
1.168 brouard 7: Revision 1.167 2014/12/22 13:50:56 brouard
8: Summary: Testing uname and compiler version and if compiled 32 or 64
9:
10: Testing on Linux 64
11:
1.167 brouard 12: Revision 1.166 2014/12/22 11:40:47 brouard
13: *** empty log message ***
14:
1.166 brouard 15: Revision 1.165 2014/12/16 11:20:36 brouard
16: Summary: After compiling on Visual C
17:
18: * imach.c (Module): Merging 1.61 to 1.162
19:
1.165 brouard 20: Revision 1.164 2014/12/16 10:52:11 brouard
21: Summary: Merging with Visual C after suppressing some warnings for unused variables. Also fixing Saito's bug 0.98Xn
22:
23: * imach.c (Module): Merging 1.61 to 1.162
24:
1.164 brouard 25: Revision 1.163 2014/12/16 10:30:11 brouard
26: * imach.c (Module): Merging 1.61 to 1.162
27:
1.163 brouard 28: Revision 1.162 2014/09/25 11:43:39 brouard
29: Summary: temporary backup 0.99!
30:
1.162 brouard 31: Revision 1.1 2014/09/16 11:06:58 brouard
32: Summary: With some code (wrong) for nlopt
33:
34: Author:
35:
36: Revision 1.161 2014/09/15 20:41:41 brouard
37: Summary: Problem with macro SQR on Intel compiler
38:
1.161 brouard 39: Revision 1.160 2014/09/02 09:24:05 brouard
40: *** empty log message ***
41:
1.160 brouard 42: Revision 1.159 2014/09/01 10:34:10 brouard
43: Summary: WIN32
44: Author: Brouard
45:
1.159 brouard 46: Revision 1.158 2014/08/27 17:11:51 brouard
47: *** empty log message ***
48:
1.158 brouard 49: Revision 1.157 2014/08/27 16:26:55 brouard
50: Summary: Preparing windows Visual studio version
51: Author: Brouard
52:
53: In order to compile on Visual studio, time.h is now correct and time_t
54: and tm struct should be used. difftime should be used but sometimes I
55: just make the differences in raw time format (time(&now).
56: Trying to suppress #ifdef LINUX
57: Add xdg-open for __linux in order to open default browser.
58:
1.157 brouard 59: Revision 1.156 2014/08/25 20:10:10 brouard
60: *** empty log message ***
61:
1.156 brouard 62: Revision 1.155 2014/08/25 18:32:34 brouard
63: Summary: New compile, minor changes
64: Author: Brouard
65:
1.155 brouard 66: Revision 1.154 2014/06/20 17:32:08 brouard
67: Summary: Outputs now all graphs of convergence to period prevalence
68:
1.154 brouard 69: Revision 1.153 2014/06/20 16:45:46 brouard
70: Summary: If 3 live state, convergence to period prevalence on same graph
71: Author: Brouard
72:
1.153 brouard 73: Revision 1.152 2014/06/18 17:54:09 brouard
74: Summary: open browser, use gnuplot on same dir than imach if not found in the path
75:
1.152 brouard 76: Revision 1.151 2014/06/18 16:43:30 brouard
77: *** empty log message ***
78:
1.151 brouard 79: Revision 1.150 2014/06/18 16:42:35 brouard
80: Summary: If gnuplot is not in the path try on same directory than imach binary (OSX)
81: Author: brouard
82:
1.150 brouard 83: Revision 1.149 2014/06/18 15:51:14 brouard
84: Summary: Some fixes in parameter files errors
85: Author: Nicolas Brouard
86:
1.149 brouard 87: Revision 1.148 2014/06/17 17:38:48 brouard
88: Summary: Nothing new
89: Author: Brouard
90:
91: Just a new packaging for OS/X version 0.98nS
92:
1.148 brouard 93: Revision 1.147 2014/06/16 10:33:11 brouard
94: *** empty log message ***
95:
1.147 brouard 96: Revision 1.146 2014/06/16 10:20:28 brouard
97: Summary: Merge
98: Author: Brouard
99:
100: Merge, before building revised version.
101:
1.146 brouard 102: Revision 1.145 2014/06/10 21:23:15 brouard
103: Summary: Debugging with valgrind
104: Author: Nicolas Brouard
105:
106: Lot of changes in order to output the results with some covariates
107: After the Edimburgh REVES conference 2014, it seems mandatory to
108: improve the code.
109: No more memory valgrind error but a lot has to be done in order to
110: continue the work of splitting the code into subroutines.
111: Also, decodemodel has been improved. Tricode is still not
112: optimal. nbcode should be improved. Documentation has been added in
113: the source code.
114:
1.144 brouard 115: Revision 1.143 2014/01/26 09:45:38 brouard
116: Summary: Version 0.98nR (to be improved, but gives same optimization results as 0.98k. Nice, promising
117:
118: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
119: (Module): Version 0.98nR Running ok, but output format still only works for three covariates.
120:
1.143 brouard 121: Revision 1.142 2014/01/26 03:57:36 brouard
122: Summary: gnuplot changed plot w l 1 has to be changed to plot w l lt 2
123:
124: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
125:
1.142 brouard 126: Revision 1.141 2014/01/26 02:42:01 brouard
127: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
128:
1.141 brouard 129: Revision 1.140 2011/09/02 10:37:54 brouard
130: Summary: times.h is ok with mingw32 now.
131:
1.140 brouard 132: Revision 1.139 2010/06/14 07:50:17 brouard
133: After the theft of my laptop, I probably lost some lines of codes which were not uploaded to the CVS tree.
134: I remember having already fixed agemin agemax which are pointers now but not cvs saved.
135:
1.139 brouard 136: Revision 1.138 2010/04/30 18:19:40 brouard
137: *** empty log message ***
138:
1.138 brouard 139: Revision 1.137 2010/04/29 18:11:38 brouard
140: (Module): Checking covariates for more complex models
141: than V1+V2. A lot of change to be done. Unstable.
142:
1.137 brouard 143: Revision 1.136 2010/04/26 20:30:53 brouard
144: (Module): merging some libgsl code. Fixing computation
145: of likelione (using inter/intrapolation if mle = 0) in order to
146: get same likelihood as if mle=1.
147: Some cleaning of code and comments added.
148:
1.136 brouard 149: Revision 1.135 2009/10/29 15:33:14 brouard
150: (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
151:
1.135 brouard 152: Revision 1.134 2009/10/29 13:18:53 brouard
153: (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
154:
1.134 brouard 155: Revision 1.133 2009/07/06 10:21:25 brouard
156: just nforces
157:
1.133 brouard 158: Revision 1.132 2009/07/06 08:22:05 brouard
159: Many tings
160:
1.132 brouard 161: Revision 1.131 2009/06/20 16:22:47 brouard
162: Some dimensions resccaled
163:
1.131 brouard 164: Revision 1.130 2009/05/26 06:44:34 brouard
165: (Module): Max Covariate is now set to 20 instead of 8. A
166: lot of cleaning with variables initialized to 0. Trying to make
167: V2+V3*age+V1+V4 strb=V3*age+V1+V4 working better.
168:
1.130 brouard 169: Revision 1.129 2007/08/31 13:49:27 lievre
170: Modification of the way of exiting when the covariate is not binary in order to see on the window the error message before exiting
171:
1.129 lievre 172: Revision 1.128 2006/06/30 13:02:05 brouard
173: (Module): Clarifications on computing e.j
174:
1.128 brouard 175: Revision 1.127 2006/04/28 18:11:50 brouard
176: (Module): Yes the sum of survivors was wrong since
177: imach-114 because nhstepm was no more computed in the age
178: loop. Now we define nhstepma in the age loop.
179: (Module): In order to speed up (in case of numerous covariates) we
180: compute health expectancies (without variances) in a first step
181: and then all the health expectancies with variances or standard
182: deviation (needs data from the Hessian matrices) which slows the
183: computation.
184: In the future we should be able to stop the program is only health
185: expectancies and graph are needed without standard deviations.
186:
1.127 brouard 187: Revision 1.126 2006/04/28 17:23:28 brouard
188: (Module): Yes the sum of survivors was wrong since
189: imach-114 because nhstepm was no more computed in the age
190: loop. Now we define nhstepma in the age loop.
191: Version 0.98h
192:
1.126 brouard 193: Revision 1.125 2006/04/04 15:20:31 lievre
194: Errors in calculation of health expectancies. Age was not initialized.
195: Forecasting file added.
196:
197: Revision 1.124 2006/03/22 17:13:53 lievre
198: Parameters are printed with %lf instead of %f (more numbers after the comma).
199: The log-likelihood is printed in the log file
200:
201: Revision 1.123 2006/03/20 10:52:43 brouard
202: * imach.c (Module): <title> changed, corresponds to .htm file
203: name. <head> headers where missing.
204:
205: * imach.c (Module): Weights can have a decimal point as for
206: English (a comma might work with a correct LC_NUMERIC environment,
207: otherwise the weight is truncated).
208: Modification of warning when the covariates values are not 0 or
209: 1.
210: Version 0.98g
211:
212: Revision 1.122 2006/03/20 09:45:41 brouard
213: (Module): Weights can have a decimal point as for
214: English (a comma might work with a correct LC_NUMERIC environment,
215: otherwise the weight is truncated).
216: Modification of warning when the covariates values are not 0 or
217: 1.
218: Version 0.98g
219:
220: Revision 1.121 2006/03/16 17:45:01 lievre
221: * imach.c (Module): Comments concerning covariates added
222:
223: * imach.c (Module): refinements in the computation of lli if
224: status=-2 in order to have more reliable computation if stepm is
225: not 1 month. Version 0.98f
226:
227: Revision 1.120 2006/03/16 15:10:38 lievre
228: (Module): refinements in the computation of lli if
229: status=-2 in order to have more reliable computation if stepm is
230: not 1 month. Version 0.98f
231:
232: Revision 1.119 2006/03/15 17:42:26 brouard
233: (Module): Bug if status = -2, the loglikelihood was
234: computed as likelihood omitting the logarithm. Version O.98e
235:
236: Revision 1.118 2006/03/14 18:20:07 brouard
237: (Module): varevsij Comments added explaining the second
238: table of variances if popbased=1 .
239: (Module): Covariances of eij, ekl added, graphs fixed, new html link.
240: (Module): Function pstamp added
241: (Module): Version 0.98d
242:
243: Revision 1.117 2006/03/14 17:16:22 brouard
244: (Module): varevsij Comments added explaining the second
245: table of variances if popbased=1 .
246: (Module): Covariances of eij, ekl added, graphs fixed, new html link.
247: (Module): Function pstamp added
248: (Module): Version 0.98d
249:
250: Revision 1.116 2006/03/06 10:29:27 brouard
251: (Module): Variance-covariance wrong links and
252: varian-covariance of ej. is needed (Saito).
253:
254: Revision 1.115 2006/02/27 12:17:45 brouard
255: (Module): One freematrix added in mlikeli! 0.98c
256:
257: Revision 1.114 2006/02/26 12:57:58 brouard
258: (Module): Some improvements in processing parameter
259: filename with strsep.
260:
261: Revision 1.113 2006/02/24 14:20:24 brouard
262: (Module): Memory leaks checks with valgrind and:
263: datafile was not closed, some imatrix were not freed and on matrix
264: allocation too.
265:
266: Revision 1.112 2006/01/30 09:55:26 brouard
267: (Module): Back to gnuplot.exe instead of wgnuplot.exe
268:
269: Revision 1.111 2006/01/25 20:38:18 brouard
270: (Module): Lots of cleaning and bugs added (Gompertz)
271: (Module): Comments can be added in data file. Missing date values
272: can be a simple dot '.'.
273:
274: Revision 1.110 2006/01/25 00:51:50 brouard
275: (Module): Lots of cleaning and bugs added (Gompertz)
276:
277: Revision 1.109 2006/01/24 19:37:15 brouard
278: (Module): Comments (lines starting with a #) are allowed in data.
279:
280: Revision 1.108 2006/01/19 18:05:42 lievre
281: Gnuplot problem appeared...
282: To be fixed
283:
284: Revision 1.107 2006/01/19 16:20:37 brouard
285: Test existence of gnuplot in imach path
286:
287: Revision 1.106 2006/01/19 13:24:36 brouard
288: Some cleaning and links added in html output
289:
290: Revision 1.105 2006/01/05 20:23:19 lievre
291: *** empty log message ***
292:
293: Revision 1.104 2005/09/30 16:11:43 lievre
294: (Module): sump fixed, loop imx fixed, and simplifications.
295: (Module): If the status is missing at the last wave but we know
296: that the person is alive, then we can code his/her status as -2
297: (instead of missing=-1 in earlier versions) and his/her
298: contributions to the likelihood is 1 - Prob of dying from last
299: health status (= 1-p13= p11+p12 in the easiest case of somebody in
300: the healthy state at last known wave). Version is 0.98
301:
302: Revision 1.103 2005/09/30 15:54:49 lievre
303: (Module): sump fixed, loop imx fixed, and simplifications.
304:
305: Revision 1.102 2004/09/15 17:31:30 brouard
306: Add the possibility to read data file including tab characters.
307:
308: Revision 1.101 2004/09/15 10:38:38 brouard
309: Fix on curr_time
310:
311: Revision 1.100 2004/07/12 18:29:06 brouard
312: Add version for Mac OS X. Just define UNIX in Makefile
313:
314: Revision 1.99 2004/06/05 08:57:40 brouard
315: *** empty log message ***
316:
317: Revision 1.98 2004/05/16 15:05:56 brouard
318: New version 0.97 . First attempt to estimate force of mortality
319: directly from the data i.e. without the need of knowing the health
320: state at each age, but using a Gompertz model: log u =a + b*age .
321: This is the basic analysis of mortality and should be done before any
322: other analysis, in order to test if the mortality estimated from the
323: cross-longitudinal survey is different from the mortality estimated
324: from other sources like vital statistic data.
325:
326: The same imach parameter file can be used but the option for mle should be -3.
327:
1.133 brouard 328: Agnès, who wrote this part of the code, tried to keep most of the
1.126 brouard 329: former routines in order to include the new code within the former code.
330:
331: The output is very simple: only an estimate of the intercept and of
332: the slope with 95% confident intervals.
333:
334: Current limitations:
335: A) Even if you enter covariates, i.e. with the
336: model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
337: B) There is no computation of Life Expectancy nor Life Table.
338:
339: Revision 1.97 2004/02/20 13:25:42 lievre
340: Version 0.96d. Population forecasting command line is (temporarily)
341: suppressed.
342:
343: Revision 1.96 2003/07/15 15:38:55 brouard
344: * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
345: rewritten within the same printf. Workaround: many printfs.
346:
347: Revision 1.95 2003/07/08 07:54:34 brouard
348: * imach.c (Repository):
349: (Repository): Using imachwizard code to output a more meaningful covariance
350: matrix (cov(a12,c31) instead of numbers.
351:
352: Revision 1.94 2003/06/27 13:00:02 brouard
353: Just cleaning
354:
355: Revision 1.93 2003/06/25 16:33:55 brouard
356: (Module): On windows (cygwin) function asctime_r doesn't
357: exist so I changed back to asctime which exists.
358: (Module): Version 0.96b
359:
360: Revision 1.92 2003/06/25 16:30:45 brouard
361: (Module): On windows (cygwin) function asctime_r doesn't
362: exist so I changed back to asctime which exists.
363:
364: Revision 1.91 2003/06/25 15:30:29 brouard
365: * imach.c (Repository): Duplicated warning errors corrected.
366: (Repository): Elapsed time after each iteration is now output. It
367: helps to forecast when convergence will be reached. Elapsed time
368: is stamped in powell. We created a new html file for the graphs
369: concerning matrix of covariance. It has extension -cov.htm.
370:
371: Revision 1.90 2003/06/24 12:34:15 brouard
372: (Module): Some bugs corrected for windows. Also, when
373: mle=-1 a template is output in file "or"mypar.txt with the design
374: of the covariance matrix to be input.
375:
376: Revision 1.89 2003/06/24 12:30:52 brouard
377: (Module): Some bugs corrected for windows. Also, when
378: mle=-1 a template is output in file "or"mypar.txt with the design
379: of the covariance matrix to be input.
380:
381: Revision 1.88 2003/06/23 17:54:56 brouard
382: * 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.
383:
384: Revision 1.87 2003/06/18 12:26:01 brouard
385: Version 0.96
386:
387: Revision 1.86 2003/06/17 20:04:08 brouard
388: (Module): Change position of html and gnuplot routines and added
389: routine fileappend.
390:
391: Revision 1.85 2003/06/17 13:12:43 brouard
392: * imach.c (Repository): Check when date of death was earlier that
393: current date of interview. It may happen when the death was just
394: prior to the death. In this case, dh was negative and likelihood
395: was wrong (infinity). We still send an "Error" but patch by
396: assuming that the date of death was just one stepm after the
397: interview.
398: (Repository): Because some people have very long ID (first column)
399: we changed int to long in num[] and we added a new lvector for
400: memory allocation. But we also truncated to 8 characters (left
401: truncation)
402: (Repository): No more line truncation errors.
403:
404: Revision 1.84 2003/06/13 21:44:43 brouard
405: * imach.c (Repository): Replace "freqsummary" at a correct
406: place. It differs from routine "prevalence" which may be called
407: many times. Probs is memory consuming and must be used with
408: parcimony.
409: Version 0.95a3 (should output exactly the same maximization than 0.8a2)
410:
411: Revision 1.83 2003/06/10 13:39:11 lievre
412: *** empty log message ***
413:
414: Revision 1.82 2003/06/05 15:57:20 brouard
415: Add log in imach.c and fullversion number is now printed.
416:
417: */
418: /*
419: Interpolated Markov Chain
420:
421: Short summary of the programme:
422:
423: This program computes Healthy Life Expectancies from
424: cross-longitudinal data. Cross-longitudinal data consist in: -1- a
425: first survey ("cross") where individuals from different ages are
426: interviewed on their health status or degree of disability (in the
427: case of a health survey which is our main interest) -2- at least a
428: second wave of interviews ("longitudinal") which measure each change
429: (if any) in individual health status. Health expectancies are
430: computed from the time spent in each health state according to a
431: model. More health states you consider, more time is necessary to reach the
432: Maximum Likelihood of the parameters involved in the model. The
433: simplest model is the multinomial logistic model where pij is the
434: probability to be observed in state j at the second wave
435: conditional to be observed in state i at the first wave. Therefore
436: the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
437: 'age' is age and 'sex' is a covariate. If you want to have a more
438: complex model than "constant and age", you should modify the program
439: where the markup *Covariates have to be included here again* invites
440: you to do it. More covariates you add, slower the
441: convergence.
442:
443: The advantage of this computer programme, compared to a simple
444: multinomial logistic model, is clear when the delay between waves is not
445: identical for each individual. Also, if a individual missed an
446: intermediate interview, the information is lost, but taken into
447: account using an interpolation or extrapolation.
448:
449: hPijx is the probability to be observed in state i at age x+h
450: conditional to the observed state i at age x. The delay 'h' can be
451: split into an exact number (nh*stepm) of unobserved intermediate
452: states. This elementary transition (by month, quarter,
453: semester or year) is modelled as a multinomial logistic. The hPx
454: matrix is simply the matrix product of nh*stepm elementary matrices
455: and the contribution of each individual to the likelihood is simply
456: hPijx.
457:
458: Also this programme outputs the covariance matrix of the parameters but also
459: of the life expectancies. It also computes the period (stable) prevalence.
460:
1.133 brouard 461: Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
462: Institut national d'études démographiques, Paris.
1.126 brouard 463: This software have been partly granted by Euro-REVES, a concerted action
464: from the European Union.
465: It is copyrighted identically to a GNU software product, ie programme and
466: software can be distributed freely for non commercial use. Latest version
467: can be accessed at http://euroreves.ined.fr/imach .
468:
469: Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
470: or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
471:
472: **********************************************************************/
473: /*
474: main
475: read parameterfile
476: read datafile
477: concatwav
478: freqsummary
479: if (mle >= 1)
480: mlikeli
481: print results files
482: if mle==1
483: computes hessian
484: read end of parameter file: agemin, agemax, bage, fage, estepm
485: begin-prev-date,...
486: open gnuplot file
487: open html file
1.145 brouard 488: period (stable) prevalence | pl_nom 1-1 2-2 etc by covariate
489: for age prevalim() | #****** V1=0 V2=1 V3=1 V4=0 ******
490: | 65 1 0 2 1 3 1 4 0 0.96326 0.03674
491: freexexit2 possible for memory heap.
492:
493: h Pij x | pij_nom ficrestpij
494: # Cov Agex agex+h hpijx with i,j= 1-1 1-2 1-3 2-1 2-2 2-3
495: 1 85 85 1.00000 0.00000 0.00000 0.00000 1.00000 0.00000
496: 1 85 86 0.68299 0.22291 0.09410 0.71093 0.00000 0.28907
497:
498: 1 65 99 0.00364 0.00322 0.99314 0.00350 0.00310 0.99340
499: 1 65 100 0.00214 0.00204 0.99581 0.00206 0.00196 0.99597
500: variance of p one-step probabilities varprob | prob_nom ficresprob #One-step probabilities and stand. devi in ()
501: Standard deviation of one-step probabilities | probcor_nom ficresprobcor #One-step probabilities and correlation matrix
502: Matrix of variance covariance of one-step probabilities | probcov_nom ficresprobcov #One-step probabilities and covariance matrix
503:
1.126 brouard 504: forecasting if prevfcast==1 prevforecast call prevalence()
505: health expectancies
506: Variance-covariance of DFLE
507: prevalence()
508: movingaverage()
509: varevsij()
510: if popbased==1 varevsij(,popbased)
511: total life expectancies
512: Variance of period (stable) prevalence
513: end
514: */
515:
1.165 brouard 516: #define POWELL /* Instead of NLOPT */
1.126 brouard 517:
518: #include <math.h>
519: #include <stdio.h>
520: #include <stdlib.h>
521: #include <string.h>
1.159 brouard 522:
523: #ifdef _WIN32
524: #include <io.h>
525: #else
1.126 brouard 526: #include <unistd.h>
1.159 brouard 527: #endif
1.126 brouard 528:
529: #include <limits.h>
530: #include <sys/types.h>
1.167 brouard 531: #include <sys/utsname.h>
1.126 brouard 532: #include <sys/stat.h>
533: #include <errno.h>
1.159 brouard 534: /* extern int errno; */
1.126 brouard 535:
1.157 brouard 536: /* #ifdef LINUX */
537: /* #include <time.h> */
538: /* #include "timeval.h" */
539: /* #else */
540: /* #include <sys/time.h> */
541: /* #endif */
542:
1.126 brouard 543: #include <time.h>
544:
1.136 brouard 545: #ifdef GSL
546: #include <gsl/gsl_errno.h>
547: #include <gsl/gsl_multimin.h>
548: #endif
549:
1.167 brouard 550:
1.162 brouard 551: #ifdef NLOPT
552: #include <nlopt.h>
553: typedef struct {
554: double (* function)(double [] );
555: } myfunc_data ;
556: #endif
557:
1.126 brouard 558: /* #include <libintl.h> */
559: /* #define _(String) gettext (String) */
560:
1.141 brouard 561: #define MAXLINE 1024 /* Was 256. Overflow with 312 with 2 states and 4 covariates. Should be ok */
1.126 brouard 562:
563: #define GNUPLOTPROGRAM "gnuplot"
564: /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
565: #define FILENAMELENGTH 132
566:
567: #define GLOCK_ERROR_NOPATH -1 /* empty path */
568: #define GLOCK_ERROR_GETCWD -2 /* cannot get cwd */
569:
1.144 brouard 570: #define MAXPARM 128 /**< Maximum number of parameters for the optimization */
571: #define NPARMAX 64 /**< (nlstate+ndeath-1)*nlstate*ncovmodel */
1.126 brouard 572:
573: #define NINTERVMAX 8
1.144 brouard 574: #define NLSTATEMAX 8 /**< Maximum number of live states (for func) */
575: #define NDEATHMAX 8 /**< Maximum number of dead states (for func) */
576: #define NCOVMAX 20 /**< Maximum number of covariates, including generated covariates V1*V2 */
1.145 brouard 577: #define codtabm(h,k) 1 & (h-1) >> (k-1) ;
1.126 brouard 578: #define MAXN 20000
1.144 brouard 579: #define YEARM 12. /**< Number of months per year */
1.126 brouard 580: #define AGESUP 130
581: #define AGEBASE 40
1.164 brouard 582: #define AGEGOMP 10 /**< Minimal age for Gompertz adjustment */
1.157 brouard 583: #ifdef _WIN32
584: #define DIRSEPARATOR '\\'
585: #define CHARSEPARATOR "\\"
586: #define ODIRSEPARATOR '/'
587: #else
1.126 brouard 588: #define DIRSEPARATOR '/'
589: #define CHARSEPARATOR "/"
590: #define ODIRSEPARATOR '\\'
591: #endif
592:
1.169 ! brouard 593: /* $Id: imach.c,v 1.168 2014/12/22 15:17:42 brouard Exp $ */
1.126 brouard 594: /* $State: Exp $ */
595:
1.169 ! brouard 596: 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";
! 597: char fullversion[]="$Revision: 1.168 $ $Date: 2014/12/22 15:17:42 $";
1.126 brouard 598: char strstart[80];
599: char optionfilext[10], optionfilefiname[FILENAMELENGTH];
1.130 brouard 600: int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings */
1.133 brouard 601: int nvar=0, nforce=0; /* Number of variables, number of forces */
1.145 brouard 602: /* Number of covariates model=V2+V1+ V3*age+V2*V4 */
603: int cptcovn=0; /**< cptcovn number of covariates added in the model (excepting constant and age and age*product) */
604: int cptcovt=0; /**< cptcovt number of covariates added in the model (excepting constant and age) */
605: int cptcovs=0; /**< cptcovs number of simple covariates V2+V1 =2 */
606: int cptcovage=0; /**< Number of covariates with age: V3*age only =1 */
607: int cptcovprodnoage=0; /**< Number of covariate products without age */
608: int cptcoveff=0; /* Total number of covariates to vary for printing results */
609: int cptcov=0; /* Working variable */
1.126 brouard 610: int npar=NPARMAX;
611: int nlstate=2; /* Number of live states */
612: int ndeath=1; /* Number of dead states */
1.130 brouard 613: int ncovmodel=0, ncovcol=0; /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
1.126 brouard 614: int popbased=0;
615:
616: int *wav; /* Number of waves for this individuual 0 is possible */
1.130 brouard 617: int maxwav=0; /* Maxim number of waves */
618: int jmin=0, jmax=0; /* min, max spacing between 2 waves */
619: int ijmin=0, ijmax=0; /* Individuals having jmin and jmax */
620: int gipmx=0, gsw=0; /* Global variables on the number of contributions
1.126 brouard 621: to the likelihood and the sum of weights (done by funcone)*/
1.130 brouard 622: int mle=1, weightopt=0;
1.126 brouard 623: int **mw; /* mw[mi][i] is number of the mi wave for this individual */
624: int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
625: int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
626: * wave mi and wave mi+1 is not an exact multiple of stepm. */
1.162 brouard 627: int countcallfunc=0; /* Count the number of calls to func */
1.130 brouard 628: double jmean=1; /* Mean space between 2 waves */
1.145 brouard 629: double **matprod2(); /* test */
1.126 brouard 630: double **oldm, **newm, **savm; /* Working pointers to matrices */
631: double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
1.136 brouard 632: /*FILE *fic ; */ /* Used in readdata only */
633: FILE *ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
1.126 brouard 634: FILE *ficlog, *ficrespow;
1.130 brouard 635: int globpr=0; /* Global variable for printing or not */
1.126 brouard 636: double fretone; /* Only one call to likelihood */
1.130 brouard 637: long ipmx=0; /* Number of contributions */
1.126 brouard 638: double sw; /* Sum of weights */
639: char filerespow[FILENAMELENGTH];
640: char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
641: FILE *ficresilk;
642: FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
643: FILE *ficresprobmorprev;
644: FILE *fichtm, *fichtmcov; /* Html File */
645: FILE *ficreseij;
646: char filerese[FILENAMELENGTH];
647: FILE *ficresstdeij;
648: char fileresstde[FILENAMELENGTH];
649: FILE *ficrescveij;
650: char filerescve[FILENAMELENGTH];
651: FILE *ficresvij;
652: char fileresv[FILENAMELENGTH];
653: FILE *ficresvpl;
654: char fileresvpl[FILENAMELENGTH];
655: char title[MAXLINE];
656: char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH], filerespl[FILENAMELENGTH];
657: char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
658: char tmpout[FILENAMELENGTH], tmpout2[FILENAMELENGTH];
659: char command[FILENAMELENGTH];
660: int outcmd=0;
661:
662: char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
663:
664: char filelog[FILENAMELENGTH]; /* Log file */
665: char filerest[FILENAMELENGTH];
666: char fileregp[FILENAMELENGTH];
667: char popfile[FILENAMELENGTH];
668:
669: char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
670:
1.157 brouard 671: /* struct timeval start_time, end_time, curr_time, last_time, forecast_time; */
672: /* struct timezone tzp; */
673: /* extern int gettimeofday(); */
674: struct tm tml, *gmtime(), *localtime();
675:
676: extern time_t time();
677:
678: struct tm start_time, end_time, curr_time, last_time, forecast_time;
679: time_t rstart_time, rend_time, rcurr_time, rlast_time, rforecast_time; /* raw time */
680: struct tm tm;
681:
1.126 brouard 682: char strcurr[80], strfor[80];
683:
684: char *endptr;
685: long lval;
686: double dval;
687:
688: #define NR_END 1
689: #define FREE_ARG char*
690: #define FTOL 1.0e-10
691:
692: #define NRANSI
693: #define ITMAX 200
694:
695: #define TOL 2.0e-4
696:
697: #define CGOLD 0.3819660
698: #define ZEPS 1.0e-10
699: #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);
700:
701: #define GOLD 1.618034
702: #define GLIMIT 100.0
703: #define TINY 1.0e-20
704:
705: static double maxarg1,maxarg2;
706: #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
707: #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
708:
709: #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
710: #define rint(a) floor(a+0.5)
1.166 brouard 711: /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/myutils_8h-source.html */
712: /* #define mytinydouble 1.0e-16 */
713: /* #define DEQUAL(a,b) (fabs((a)-(b))<mytinydouble) */
714: /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/mynrutils_8h-source.html */
715: /* static double dsqrarg; */
716: /* #define DSQR(a) (DEQUAL((dsqrarg=(a)),0.0) ? 0.0 : dsqrarg*dsqrarg) */
1.126 brouard 717: static double sqrarg;
718: #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
719: #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}
720: int agegomp= AGEGOMP;
721:
722: int imx;
723: int stepm=1;
724: /* Stepm, step in month: minimum step interpolation*/
725:
726: int estepm;
727: /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
728:
729: int m,nb;
730: long *num;
731: int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
732: double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
733: double **pmmij, ***probs;
734: double *ageexmed,*agecens;
735: double dateintmean=0;
736:
737: double *weight;
738: int **s; /* Status */
1.141 brouard 739: double *agedc;
1.145 brouard 740: double **covar; /**< covar[j,i], value of jth covariate for individual i,
1.141 brouard 741: * covar=matrix(0,NCOVMAX,1,n);
742: * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; */
743: double idx;
744: int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */
1.145 brouard 745: int *Ndum; /** Freq of modality (tricode */
1.141 brouard 746: int **codtab; /**< codtab=imatrix(1,100,1,10); */
747: int **Tvard, *Tprod, cptcovprod, *Tvaraff;
1.126 brouard 748: double *lsurv, *lpop, *tpop;
749:
1.143 brouard 750: double ftol=FTOL; /**< Tolerance for computing Max Likelihood */
751: double ftolhess; /**< Tolerance for computing hessian */
1.126 brouard 752:
753: /**************** split *************************/
754: static int split( char *path, char *dirc, char *name, char *ext, char *finame )
755: {
756: /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
757: the name of the file (name), its extension only (ext) and its first part of the name (finame)
758: */
759: char *ss; /* pointer */
760: int l1, l2; /* length counters */
761:
762: l1 = strlen(path ); /* length of path */
763: if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
764: ss= strrchr( path, DIRSEPARATOR ); /* find last / */
765: if ( ss == NULL ) { /* no directory, so determine current directory */
766: strcpy( name, path ); /* we got the fullname name because no directory */
767: /*if(strrchr(path, ODIRSEPARATOR )==NULL)
768: printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
769: /* get current working directory */
770: /* extern char* getcwd ( char *buf , int len);*/
771: if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
772: return( GLOCK_ERROR_GETCWD );
773: }
774: /* got dirc from getcwd*/
775: printf(" DIRC = %s \n",dirc);
776: } else { /* strip direcotry from path */
777: ss++; /* after this, the filename */
778: l2 = strlen( ss ); /* length of filename */
779: if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
780: strcpy( name, ss ); /* save file name */
781: strncpy( dirc, path, l1 - l2 ); /* now the directory */
782: dirc[l1-l2] = 0; /* add zero */
783: printf(" DIRC2 = %s \n",dirc);
784: }
785: /* We add a separator at the end of dirc if not exists */
786: l1 = strlen( dirc ); /* length of directory */
787: if( dirc[l1-1] != DIRSEPARATOR ){
788: dirc[l1] = DIRSEPARATOR;
789: dirc[l1+1] = 0;
790: printf(" DIRC3 = %s \n",dirc);
791: }
792: ss = strrchr( name, '.' ); /* find last / */
793: if (ss >0){
794: ss++;
795: strcpy(ext,ss); /* save extension */
796: l1= strlen( name);
797: l2= strlen(ss)+1;
798: strncpy( finame, name, l1-l2);
799: finame[l1-l2]= 0;
800: }
801:
802: return( 0 ); /* we're done */
803: }
804:
805:
806: /******************************************/
807:
808: void replace_back_to_slash(char *s, char*t)
809: {
810: int i;
811: int lg=0;
812: i=0;
813: lg=strlen(t);
814: for(i=0; i<= lg; i++) {
815: (s[i] = t[i]);
816: if (t[i]== '\\') s[i]='/';
817: }
818: }
819:
1.132 brouard 820: char *trimbb(char *out, char *in)
1.137 brouard 821: { /* Trim multiple blanks in line but keeps first blanks if line starts with blanks */
1.132 brouard 822: char *s;
823: s=out;
824: while (*in != '\0'){
1.137 brouard 825: while( *in == ' ' && *(in+1) == ' '){ /* && *(in+1) != '\0'){*/
1.132 brouard 826: in++;
827: }
828: *out++ = *in++;
829: }
830: *out='\0';
831: return s;
832: }
833:
1.145 brouard 834: char *cutl(char *blocc, char *alocc, char *in, char occ)
835: {
836: /* cuts string in into blocc and alocc where blocc ends before first occurence of char 'occ'
837: and alocc starts after first occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
838: gives blocc="abcdef2ghi" and alocc="j".
839: If occ is not found blocc is null and alocc is equal to in. Returns blocc
840: */
1.160 brouard 841: char *s, *t;
1.145 brouard 842: t=in;s=in;
843: while ((*in != occ) && (*in != '\0')){
844: *alocc++ = *in++;
845: }
846: if( *in == occ){
847: *(alocc)='\0';
848: s=++in;
849: }
850:
851: if (s == t) {/* occ not found */
852: *(alocc-(in-s))='\0';
853: in=s;
854: }
855: while ( *in != '\0'){
856: *blocc++ = *in++;
857: }
858:
859: *blocc='\0';
860: return t;
861: }
1.137 brouard 862: char *cutv(char *blocc, char *alocc, char *in, char occ)
863: {
864: /* cuts string in into blocc and alocc where blocc ends before last occurence of char 'occ'
865: and alocc starts after last occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
866: gives blocc="abcdef2ghi" and alocc="j".
867: If occ is not found blocc is null and alocc is equal to in. Returns alocc
868: */
869: char *s, *t;
870: t=in;s=in;
871: while (*in != '\0'){
872: while( *in == occ){
873: *blocc++ = *in++;
874: s=in;
875: }
876: *blocc++ = *in++;
877: }
878: if (s == t) /* occ not found */
879: *(blocc-(in-s))='\0';
880: else
881: *(blocc-(in-s)-1)='\0';
882: in=s;
883: while ( *in != '\0'){
884: *alocc++ = *in++;
885: }
886:
887: *alocc='\0';
888: return s;
889: }
890:
1.126 brouard 891: int nbocc(char *s, char occ)
892: {
893: int i,j=0;
894: int lg=20;
895: i=0;
896: lg=strlen(s);
897: for(i=0; i<= lg; i++) {
898: if (s[i] == occ ) j++;
899: }
900: return j;
901: }
902:
1.137 brouard 903: /* void cutv(char *u,char *v, char*t, char occ) */
904: /* { */
905: /* /\* cuts string t into u and v where u ends before last occurence of char 'occ' */
906: /* and v starts after last occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2') */
907: /* gives u="abcdef2ghi" and v="j" *\/ */
908: /* int i,lg,j,p=0; */
909: /* i=0; */
910: /* lg=strlen(t); */
911: /* for(j=0; j<=lg-1; j++) { */
912: /* if((t[j]!= occ) && (t[j+1]== occ)) p=j+1; */
913: /* } */
1.126 brouard 914:
1.137 brouard 915: /* for(j=0; j<p; j++) { */
916: /* (u[j] = t[j]); */
917: /* } */
918: /* u[p]='\0'; */
1.126 brouard 919:
1.137 brouard 920: /* for(j=0; j<= lg; j++) { */
921: /* if (j>=(p+1))(v[j-p-1] = t[j]); */
922: /* } */
923: /* } */
1.126 brouard 924:
1.160 brouard 925: #ifdef _WIN32
926: char * strsep(char **pp, const char *delim)
927: {
928: char *p, *q;
929:
930: if ((p = *pp) == NULL)
931: return 0;
932: if ((q = strpbrk (p, delim)) != NULL)
933: {
934: *pp = q + 1;
935: *q = '\0';
936: }
937: else
938: *pp = 0;
939: return p;
940: }
941: #endif
942:
1.126 brouard 943: /********************** nrerror ********************/
944:
945: void nrerror(char error_text[])
946: {
947: fprintf(stderr,"ERREUR ...\n");
948: fprintf(stderr,"%s\n",error_text);
949: exit(EXIT_FAILURE);
950: }
951: /*********************** vector *******************/
952: double *vector(int nl, int nh)
953: {
954: double *v;
955: v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
956: if (!v) nrerror("allocation failure in vector");
957: return v-nl+NR_END;
958: }
959:
960: /************************ free vector ******************/
961: void free_vector(double*v, int nl, int nh)
962: {
963: free((FREE_ARG)(v+nl-NR_END));
964: }
965:
966: /************************ivector *******************************/
967: int *ivector(long nl,long nh)
968: {
969: int *v;
970: v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
971: if (!v) nrerror("allocation failure in ivector");
972: return v-nl+NR_END;
973: }
974:
975: /******************free ivector **************************/
976: void free_ivector(int *v, long nl, long nh)
977: {
978: free((FREE_ARG)(v+nl-NR_END));
979: }
980:
981: /************************lvector *******************************/
982: long *lvector(long nl,long nh)
983: {
984: long *v;
985: v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
986: if (!v) nrerror("allocation failure in ivector");
987: return v-nl+NR_END;
988: }
989:
990: /******************free lvector **************************/
991: void free_lvector(long *v, long nl, long nh)
992: {
993: free((FREE_ARG)(v+nl-NR_END));
994: }
995:
996: /******************* imatrix *******************************/
997: int **imatrix(long nrl, long nrh, long ncl, long nch)
998: /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */
999: {
1000: long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;
1001: int **m;
1002:
1003: /* allocate pointers to rows */
1004: m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));
1005: if (!m) nrerror("allocation failure 1 in matrix()");
1006: m += NR_END;
1007: m -= nrl;
1008:
1009:
1010: /* allocate rows and set pointers to them */
1011: m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));
1012: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
1013: m[nrl] += NR_END;
1014: m[nrl] -= ncl;
1015:
1016: for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;
1017:
1018: /* return pointer to array of pointers to rows */
1019: return m;
1020: }
1021:
1022: /****************** free_imatrix *************************/
1023: void free_imatrix(m,nrl,nrh,ncl,nch)
1024: int **m;
1025: long nch,ncl,nrh,nrl;
1026: /* free an int matrix allocated by imatrix() */
1027: {
1028: free((FREE_ARG) (m[nrl]+ncl-NR_END));
1029: free((FREE_ARG) (m+nrl-NR_END));
1030: }
1031:
1032: /******************* matrix *******************************/
1033: double **matrix(long nrl, long nrh, long ncl, long nch)
1034: {
1035: long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
1036: double **m;
1037:
1038: m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
1039: if (!m) nrerror("allocation failure 1 in matrix()");
1040: m += NR_END;
1041: m -= nrl;
1042:
1043: m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
1044: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
1045: m[nrl] += NR_END;
1046: m[nrl] -= ncl;
1047:
1048: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
1049: return m;
1.145 brouard 1050: /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) or &(m[1][0])
1051: m[i] = address of ith row of the table. &(m[i]) is its value which is another adress
1052: that of m[i][0]. In order to get the value p m[i][0] but it is unitialized.
1.126 brouard 1053: */
1054: }
1055:
1056: /*************************free matrix ************************/
1057: void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
1058: {
1059: free((FREE_ARG)(m[nrl]+ncl-NR_END));
1060: free((FREE_ARG)(m+nrl-NR_END));
1061: }
1062:
1063: /******************* ma3x *******************************/
1064: double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
1065: {
1066: long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
1067: double ***m;
1068:
1069: m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
1070: if (!m) nrerror("allocation failure 1 in matrix()");
1071: m += NR_END;
1072: m -= nrl;
1073:
1074: m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
1075: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
1076: m[nrl] += NR_END;
1077: m[nrl] -= ncl;
1078:
1079: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
1080:
1081: m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
1082: if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
1083: m[nrl][ncl] += NR_END;
1084: m[nrl][ncl] -= nll;
1085: for (j=ncl+1; j<=nch; j++)
1086: m[nrl][j]=m[nrl][j-1]+nlay;
1087:
1088: for (i=nrl+1; i<=nrh; i++) {
1089: m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
1090: for (j=ncl+1; j<=nch; j++)
1091: m[i][j]=m[i][j-1]+nlay;
1092: }
1093: return m;
1094: /* gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
1095: &(m[i][j][k]) <=> *((*(m+i) + j)+k)
1096: */
1097: }
1098:
1099: /*************************free ma3x ************************/
1100: void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
1101: {
1102: free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
1103: free((FREE_ARG)(m[nrl]+ncl-NR_END));
1104: free((FREE_ARG)(m+nrl-NR_END));
1105: }
1106:
1107: /*************** function subdirf ***********/
1108: char *subdirf(char fileres[])
1109: {
1110: /* Caution optionfilefiname is hidden */
1111: strcpy(tmpout,optionfilefiname);
1112: strcat(tmpout,"/"); /* Add to the right */
1113: strcat(tmpout,fileres);
1114: return tmpout;
1115: }
1116:
1117: /*************** function subdirf2 ***********/
1118: char *subdirf2(char fileres[], char *preop)
1119: {
1120:
1121: /* Caution optionfilefiname is hidden */
1122: strcpy(tmpout,optionfilefiname);
1123: strcat(tmpout,"/");
1124: strcat(tmpout,preop);
1125: strcat(tmpout,fileres);
1126: return tmpout;
1127: }
1128:
1129: /*************** function subdirf3 ***********/
1130: char *subdirf3(char fileres[], char *preop, char *preop2)
1131: {
1132:
1133: /* Caution optionfilefiname is hidden */
1134: strcpy(tmpout,optionfilefiname);
1135: strcat(tmpout,"/");
1136: strcat(tmpout,preop);
1137: strcat(tmpout,preop2);
1138: strcat(tmpout,fileres);
1139: return tmpout;
1140: }
1141:
1.162 brouard 1142: char *asc_diff_time(long time_sec, char ascdiff[])
1143: {
1144: long sec_left, days, hours, minutes;
1145: days = (time_sec) / (60*60*24);
1146: sec_left = (time_sec) % (60*60*24);
1147: hours = (sec_left) / (60*60) ;
1148: sec_left = (sec_left) %(60*60);
1149: minutes = (sec_left) /60;
1150: sec_left = (sec_left) % (60);
1151: sprintf(ascdiff,"%ld day(s) %ld hour(s) %ld minute(s) %ld second(s)",days, hours, minutes, sec_left);
1152: return ascdiff;
1153: }
1154:
1.126 brouard 1155: /***************** f1dim *************************/
1156: extern int ncom;
1157: extern double *pcom,*xicom;
1158: extern double (*nrfunc)(double []);
1159:
1160: double f1dim(double x)
1161: {
1162: int j;
1163: double f;
1164: double *xt;
1165:
1166: xt=vector(1,ncom);
1167: for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];
1168: f=(*nrfunc)(xt);
1169: free_vector(xt,1,ncom);
1170: return f;
1171: }
1172:
1173: /*****************brent *************************/
1174: double brent(double ax, double bx, double cx, double (*f)(double), double tol, double *xmin)
1175: {
1176: int iter;
1177: double a,b,d,etemp;
1.159 brouard 1178: double fu=0,fv,fw,fx;
1.164 brouard 1179: double ftemp=0.;
1.126 brouard 1180: double p,q,r,tol1,tol2,u,v,w,x,xm;
1181: double e=0.0;
1182:
1183: a=(ax < cx ? ax : cx);
1184: b=(ax > cx ? ax : cx);
1185: x=w=v=bx;
1186: fw=fv=fx=(*f)(x);
1187: for (iter=1;iter<=ITMAX;iter++) {
1188: xm=0.5*(a+b);
1189: tol2=2.0*(tol1=tol*fabs(x)+ZEPS);
1190: /* if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
1191: printf(".");fflush(stdout);
1192: fprintf(ficlog,".");fflush(ficlog);
1.162 brouard 1193: #ifdef DEBUGBRENT
1.126 brouard 1194: 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);
1195: 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);
1196: /* if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
1197: #endif
1198: if (fabs(x-xm) <= (tol2-0.5*(b-a))){
1199: *xmin=x;
1200: return fx;
1201: }
1202: ftemp=fu;
1203: if (fabs(e) > tol1) {
1204: r=(x-w)*(fx-fv);
1205: q=(x-v)*(fx-fw);
1206: p=(x-v)*q-(x-w)*r;
1207: q=2.0*(q-r);
1208: if (q > 0.0) p = -p;
1209: q=fabs(q);
1210: etemp=e;
1211: e=d;
1212: if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))
1213: d=CGOLD*(e=(x >= xm ? a-x : b-x));
1214: else {
1215: d=p/q;
1216: u=x+d;
1217: if (u-a < tol2 || b-u < tol2)
1218: d=SIGN(tol1,xm-x);
1219: }
1220: } else {
1221: d=CGOLD*(e=(x >= xm ? a-x : b-x));
1222: }
1223: u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));
1224: fu=(*f)(u);
1225: if (fu <= fx) {
1226: if (u >= x) a=x; else b=x;
1227: SHFT(v,w,x,u)
1228: SHFT(fv,fw,fx,fu)
1229: } else {
1230: if (u < x) a=u; else b=u;
1231: if (fu <= fw || w == x) {
1232: v=w;
1233: w=u;
1234: fv=fw;
1235: fw=fu;
1236: } else if (fu <= fv || v == x || v == w) {
1237: v=u;
1238: fv=fu;
1239: }
1240: }
1241: }
1242: nrerror("Too many iterations in brent");
1243: *xmin=x;
1244: return fx;
1245: }
1246:
1247: /****************** mnbrak ***********************/
1248:
1249: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,
1250: double (*func)(double))
1251: {
1252: double ulim,u,r,q, dum;
1253: double fu;
1254:
1255: *fa=(*func)(*ax);
1256: *fb=(*func)(*bx);
1257: if (*fb > *fa) {
1258: SHFT(dum,*ax,*bx,dum)
1259: SHFT(dum,*fb,*fa,dum)
1260: }
1261: *cx=(*bx)+GOLD*(*bx-*ax);
1262: *fc=(*func)(*cx);
1.162 brouard 1263: while (*fb > *fc) { /* Declining fa, fb, fc */
1.126 brouard 1264: r=(*bx-*ax)*(*fb-*fc);
1265: q=(*bx-*cx)*(*fb-*fa);
1266: u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/
1.162 brouard 1267: (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); /* Minimum abscisse of a parabolic estimated from (a,fa), (b,fb) and (c,fc). */
1268: ulim=(*bx)+GLIMIT*(*cx-*bx); /* Maximum abscisse where function can be evaluated */
1269: if ((*bx-u)*(u-*cx) > 0.0) { /* if u between b and c */
1.126 brouard 1270: fu=(*func)(u);
1.163 brouard 1271: #ifdef DEBUG
1272: /* f(x)=A(x-u)**2+f(u) */
1273: double A, fparabu;
1274: A= (*fb - *fa)/(*bx-*ax)/(*bx+*ax-2*u);
1275: fparabu= *fa - A*(*ax-u)*(*ax-u);
1276: 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);
1277: 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);
1278: #endif
1.162 brouard 1279: } else if ((*cx-u)*(u-ulim) > 0.0) { /* u is after c but before ulim */
1.126 brouard 1280: fu=(*func)(u);
1281: if (fu < *fc) {
1282: SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))
1283: SHFT(*fb,*fc,fu,(*func)(u))
1284: }
1.162 brouard 1285: } else if ((u-ulim)*(ulim-*cx) >= 0.0) { /* u outside ulim (verifying that ulim is beyond c) */
1.126 brouard 1286: u=ulim;
1287: fu=(*func)(u);
1288: } else {
1289: u=(*cx)+GOLD*(*cx-*bx);
1290: fu=(*func)(u);
1291: }
1292: SHFT(*ax,*bx,*cx,u)
1293: SHFT(*fa,*fb,*fc,fu)
1294: }
1295: }
1296:
1297: /*************** linmin ************************/
1.162 brouard 1298: /* Given an n -dimensional point p[1..n] and an n -dimensional direction xi[1..n] , moves and
1299: resets p to where the function func(p) takes on a minimum along the direction xi from p ,
1300: and replaces xi by the actual vector displacement that p was moved. Also returns as fret
1301: the value of func at the returned location p . This is actually all accomplished by calling the
1302: routines mnbrak and brent .*/
1.126 brouard 1303: int ncom;
1304: double *pcom,*xicom;
1305: double (*nrfunc)(double []);
1306:
1307: void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))
1308: {
1309: double brent(double ax, double bx, double cx,
1310: double (*f)(double), double tol, double *xmin);
1311: double f1dim(double x);
1312: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,
1313: double *fc, double (*func)(double));
1314: int j;
1315: double xx,xmin,bx,ax;
1316: double fx,fb,fa;
1317:
1318: ncom=n;
1319: pcom=vector(1,n);
1320: xicom=vector(1,n);
1321: nrfunc=func;
1322: for (j=1;j<=n;j++) {
1323: pcom[j]=p[j];
1324: xicom[j]=xi[j];
1325: }
1326: ax=0.0;
1327: xx=1.0;
1.162 brouard 1328: mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); /* Find a bracket a,x,b in direction n=xi ie xicom */
1329: *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); /* Find a minimum P+lambda n in that direction (lambdamin), with TOL between abscisses */
1.126 brouard 1330: #ifdef DEBUG
1331: printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
1332: fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
1333: #endif
1334: for (j=1;j<=n;j++) {
1335: xi[j] *= xmin;
1336: p[j] += xi[j];
1337: }
1338: free_vector(xicom,1,n);
1339: free_vector(pcom,1,n);
1340: }
1341:
1342:
1343: /*************** powell ************************/
1.162 brouard 1344: /*
1345: Minimization of a function func of n variables. Input consists of an initial starting point
1346: p[1..n] ; an initial matrix xi[1..n][1..n] , whose columns contain the initial set of di-
1347: rections (usually the n unit vectors); and ftol , the fractional tolerance in the function value
1348: such that failure to decrease by more than this amount on one iteration signals doneness. On
1349: output, p is set to the best point found, xi is the then-current direction set, fret is the returned
1350: function value at p , and iter is the number of iterations taken. The routine linmin is used.
1351: */
1.126 brouard 1352: void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,
1353: double (*func)(double []))
1354: {
1355: void linmin(double p[], double xi[], int n, double *fret,
1356: double (*func)(double []));
1357: int i,ibig,j;
1358: double del,t,*pt,*ptt,*xit;
1359: double fp,fptt;
1360: double *xits;
1361: int niterf, itmp;
1362:
1363: pt=vector(1,n);
1364: ptt=vector(1,n);
1365: xit=vector(1,n);
1366: xits=vector(1,n);
1367: *fret=(*func)(p);
1368: for (j=1;j<=n;j++) pt[j]=p[j];
1.157 brouard 1369: rcurr_time = time(NULL);
1.126 brouard 1370: for (*iter=1;;++(*iter)) {
1371: fp=(*fret);
1372: ibig=0;
1373: del=0.0;
1.157 brouard 1374: rlast_time=rcurr_time;
1375: /* (void) gettimeofday(&curr_time,&tzp); */
1376: rcurr_time = time(NULL);
1377: curr_time = *localtime(&rcurr_time);
1378: printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, rcurr_time-rlast_time, rcurr_time-rstart_time);fflush(stdout);
1379: fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret,rcurr_time-rlast_time, rcurr_time-rstart_time); fflush(ficlog);
1380: /* fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tm_sec-start_time.tm_sec); */
1.126 brouard 1381: for (i=1;i<=n;i++) {
1382: printf(" %d %.12f",i, p[i]);
1383: fprintf(ficlog," %d %.12lf",i, p[i]);
1384: fprintf(ficrespow," %.12lf", p[i]);
1385: }
1386: printf("\n");
1387: fprintf(ficlog,"\n");
1388: fprintf(ficrespow,"\n");fflush(ficrespow);
1389: if(*iter <=3){
1.157 brouard 1390: tml = *localtime(&rcurr_time);
1391: strcpy(strcurr,asctime(&tml));
1392: rforecast_time=rcurr_time;
1.126 brouard 1393: itmp = strlen(strcurr);
1394: if(strcurr[itmp-1]=='\n') /* Windows outputs with a new line */
1395: strcurr[itmp-1]='\0';
1.162 brouard 1396: printf("\nConsidering the time needed for the last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
1.157 brouard 1397: fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
1.126 brouard 1398: for(niterf=10;niterf<=30;niterf+=10){
1.157 brouard 1399: rforecast_time=rcurr_time+(niterf-*iter)*(rcurr_time-rlast_time);
1400: forecast_time = *localtime(&rforecast_time);
1401: strcpy(strfor,asctime(&forecast_time));
1.126 brouard 1402: itmp = strlen(strfor);
1403: if(strfor[itmp-1]=='\n')
1404: strfor[itmp-1]='\0';
1.157 brouard 1405: 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);
1406: fprintf(ficlog," - if your program needs %d iterations to converge, convergence will be \n reached in %s i.e.\n on %s (current time is %s);\n",niterf, asc_diff_time(rforecast_time-rcurr_time,tmpout),strfor,strcurr);
1.126 brouard 1407: }
1408: }
1409: for (i=1;i<=n;i++) {
1410: for (j=1;j<=n;j++) xit[j]=xi[j][i];
1411: fptt=(*fret);
1412: #ifdef DEBUG
1.164 brouard 1413: printf("fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
1414: fprintf(ficlog, "fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
1.126 brouard 1415: #endif
1416: printf("%d",i);fflush(stdout);
1417: fprintf(ficlog,"%d",i);fflush(ficlog);
1418: linmin(p,xit,n,fret,func);
1419: if (fabs(fptt-(*fret)) > del) {
1420: del=fabs(fptt-(*fret));
1421: ibig=i;
1422: }
1423: #ifdef DEBUG
1424: printf("%d %.12e",i,(*fret));
1425: fprintf(ficlog,"%d %.12e",i,(*fret));
1426: for (j=1;j<=n;j++) {
1427: xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
1428: printf(" x(%d)=%.12e",j,xit[j]);
1429: fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
1430: }
1431: for(j=1;j<=n;j++) {
1.162 brouard 1432: printf(" p(%d)=%.12e",j,p[j]);
1433: fprintf(ficlog," p(%d)=%.12e",j,p[j]);
1.126 brouard 1434: }
1435: printf("\n");
1436: fprintf(ficlog,"\n");
1437: #endif
1.162 brouard 1438: } /* end i */
1.126 brouard 1439: if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
1440: #ifdef DEBUG
1441: int k[2],l;
1442: k[0]=1;
1443: k[1]=-1;
1444: printf("Max: %.12e",(*func)(p));
1445: fprintf(ficlog,"Max: %.12e",(*func)(p));
1446: for (j=1;j<=n;j++) {
1447: printf(" %.12e",p[j]);
1448: fprintf(ficlog," %.12e",p[j]);
1449: }
1450: printf("\n");
1451: fprintf(ficlog,"\n");
1452: for(l=0;l<=1;l++) {
1453: for (j=1;j<=n;j++) {
1454: ptt[j]=p[j]+(p[j]-pt[j])*k[l];
1455: printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
1456: fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
1457: }
1458: printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
1459: fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
1460: }
1461: #endif
1462:
1463:
1464: free_vector(xit,1,n);
1465: free_vector(xits,1,n);
1466: free_vector(ptt,1,n);
1467: free_vector(pt,1,n);
1468: return;
1469: }
1470: if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");
1.161 brouard 1471: for (j=1;j<=n;j++) { /* Computes an extrapolated point */
1.126 brouard 1472: ptt[j]=2.0*p[j]-pt[j];
1473: xit[j]=p[j]-pt[j];
1474: pt[j]=p[j];
1475: }
1476: fptt=(*func)(ptt);
1.161 brouard 1477: if (fptt < fp) { /* If extrapolated point is better, decide if we keep that new direction or not */
1.162 brouard 1478: /* (x1 f1=fp), (x2 f2=*fret), (x3 f3=fptt), (xm fm) */
1.161 brouard 1479: /* From x1 (P0) distance of x2 is at h and x3 is 2h */
1.162 brouard 1480: /* Let f"(x2) be the 2nd derivative equal everywhere. */
1481: /* Then the parabolic through (x1,f1), (x2,f2) and (x3,f3) */
1482: /* will reach at f3 = fm + h^2/2 f"m ; f" = (f1 -2f2 +f3 ) / h**2 */
1.161 brouard 1483: /* f1-f3 = delta(2h) = 2 h**2 f'' = 2(f1- 2f2 +f3) */
1484: /* Thus we compare delta(2h) with observed f1-f3 */
1.162 brouard 1485: /* or best gain on one ancient line 'del' with total */
1486: /* gain f1-f2 = f1 - f2 - 'del' with del */
1.161 brouard 1487: /* t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); */
1.162 brouard 1488:
1.161 brouard 1489: t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del);
1490: t= t- del*SQR(fp-fptt);
1491: printf("t1= %.12lf, t2= %.12lf, t=%.12lf\n", 2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del),del*SQR(fp-fptt),t);
1492: 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);
1493: #ifdef DEBUG
1494: printf("t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
1495: (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
1496: fprintf(ficlog,"t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
1497: (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
1498: 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);
1499: 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);
1500: #endif
1501: if (t < 0.0) { /* Then we use it for last direction */
1502: linmin(p,xit,n,fret,func); /* computes mean on the extrapolated direction.*/
1.126 brouard 1503: for (j=1;j<=n;j++) {
1.161 brouard 1504: xi[j][ibig]=xi[j][n]; /* Replace the direction with biggest decrease by n */
1505: xi[j][n]=xit[j]; /* and nth direction by the extrapolated */
1.126 brouard 1506: }
1.161 brouard 1507: printf("Gaining to use average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
1.169 ! brouard 1508: fprintf(ficlog,"Gaining to use average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
1.161 brouard 1509:
1.126 brouard 1510: #ifdef DEBUG
1.164 brouard 1511: printf("Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
1512: fprintf(ficlog,"Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
1.126 brouard 1513: for(j=1;j<=n;j++){
1514: printf(" %.12e",xit[j]);
1515: fprintf(ficlog," %.12e",xit[j]);
1516: }
1517: printf("\n");
1518: fprintf(ficlog,"\n");
1519: #endif
1.162 brouard 1520: } /* end of t negative */
1521: } /* end if (fptt < fp) */
1.126 brouard 1522: }
1523: }
1524:
1525: /**** Prevalence limit (stable or period prevalence) ****************/
1526:
1527: double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
1528: {
1529: /* Computes the prevalence limit in each live state at age x by left multiplying the unit
1530: matrix by transitions matrix until convergence is reached */
1.169 ! brouard 1531:
1.126 brouard 1532: int i, ii,j,k;
1533: double min, max, maxmin, maxmax,sumnew=0.;
1.145 brouard 1534: /* double **matprod2(); */ /* test */
1.131 brouard 1535: double **out, cov[NCOVMAX+1], **pmij();
1.126 brouard 1536: double **newm;
1537: double agefin, delaymax=50 ; /* Max number of years to converge */
1.169 ! brouard 1538:
1.126 brouard 1539: for (ii=1;ii<=nlstate+ndeath;ii++)
1540: for (j=1;j<=nlstate+ndeath;j++){
1541: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1542: }
1.169 ! brouard 1543:
! 1544: cov[1]=1.;
! 1545:
! 1546: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
1.126 brouard 1547: for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
1548: newm=savm;
1549: /* Covariates have to be included here again */
1.138 brouard 1550: cov[2]=agefin;
1551:
1552: for (k=1; k<=cptcovn;k++) {
1553: cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
1.145 brouard 1554: /*printf("prevalim ij=%d k=%d Tvar[%d]=%d nbcode=%d cov=%lf codtab[%d][Tvar[%d]]=%d \n",ij,k, k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], ij, k, codtab[ij][Tvar[k]]);*/
1.138 brouard 1555: }
1.145 brouard 1556: /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
1557: /* for (k=1; k<=cptcovprod;k++) /\* Useless *\/ */
1558: /* cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]] * nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]]; */
1.138 brouard 1559:
1560: /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
1561: /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
1562: /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
1.145 brouard 1563: /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
1564: /* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind *\/ */
1.142 brouard 1565: out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /* Bug Valgrind */
1.138 brouard 1566:
1.126 brouard 1567: savm=oldm;
1568: oldm=newm;
1569: maxmax=0.;
1570: for(j=1;j<=nlstate;j++){
1571: min=1.;
1572: max=0.;
1573: for(i=1; i<=nlstate; i++) {
1574: sumnew=0;
1575: for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
1576: prlim[i][j]= newm[i][j]/(1-sumnew);
1.145 brouard 1577: /*printf(" prevalim i=%d, j=%d, prmlim[%d][%d]=%f, agefin=%d \n", i, j, i, j, prlim[i][j],(int)agefin);*/
1.126 brouard 1578: max=FMAX(max,prlim[i][j]);
1579: min=FMIN(min,prlim[i][j]);
1580: }
1581: maxmin=max-min;
1582: maxmax=FMAX(maxmax,maxmin);
1.169 ! brouard 1583: } /* j loop */
1.126 brouard 1584: if(maxmax < ftolpl){
1585: return prlim;
1586: }
1.169 ! brouard 1587: } /* age loop */
! 1588: return prlim; /* should not reach here */
1.126 brouard 1589: }
1590:
1591: /*************** transition probabilities ***************/
1592:
1593: double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
1594: {
1.138 brouard 1595: /* According to parameters values stored in x and the covariate's values stored in cov,
1596: computes the probability to be observed in state j being in state i by appying the
1597: model to the ncovmodel covariates (including constant and age).
1598: lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc]
1599: and, according on how parameters are entered, the position of the coefficient xij(nc) of the
1600: ncth covariate in the global vector x is given by the formula:
1601: j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
1602: j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
1603: Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
1604: sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.
1605: Outputs ps[i][j] the probability to be observed in j being in j according to
1606: the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
1607: */
1608: double s1, lnpijopii;
1.126 brouard 1609: /*double t34;*/
1.164 brouard 1610: int i,j, nc, ii, jj;
1.126 brouard 1611:
1612: for(i=1; i<= nlstate; i++){
1613: for(j=1; j<i;j++){
1.138 brouard 1614: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
1615: /*lnpijopii += param[i][j][nc]*cov[nc];*/
1616: lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
1617: /* printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
1.126 brouard 1618: }
1.138 brouard 1619: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
1620: /* printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
1.126 brouard 1621: }
1622: for(j=i+1; j<=nlstate+ndeath;j++){
1.138 brouard 1623: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
1624: /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
1625: lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
1626: /* printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
1.126 brouard 1627: }
1.138 brouard 1628: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
1.126 brouard 1629: }
1630: }
1631:
1632: for(i=1; i<= nlstate; i++){
1633: s1=0;
1.131 brouard 1634: for(j=1; j<i; j++){
1.138 brouard 1635: s1+=exp(ps[i][j]); /* In fact sums pij/pii */
1.131 brouard 1636: /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
1637: }
1638: for(j=i+1; j<=nlstate+ndeath; j++){
1.138 brouard 1639: s1+=exp(ps[i][j]); /* In fact sums pij/pii */
1.131 brouard 1640: /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
1641: }
1.138 brouard 1642: /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
1.126 brouard 1643: ps[i][i]=1./(s1+1.);
1.138 brouard 1644: /* Computing other pijs */
1.126 brouard 1645: for(j=1; j<i; j++)
1646: ps[i][j]= exp(ps[i][j])*ps[i][i];
1647: for(j=i+1; j<=nlstate+ndeath; j++)
1648: ps[i][j]= exp(ps[i][j])*ps[i][i];
1649: /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
1650: } /* end i */
1651:
1652: for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
1653: for(jj=1; jj<= nlstate+ndeath; jj++){
1654: ps[ii][jj]=0;
1655: ps[ii][ii]=1;
1656: }
1657: }
1658:
1.145 brouard 1659:
1660: /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
1661: /* for(jj=1; jj<= nlstate+ndeath; jj++){ */
1662: /* printf(" pmij ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
1663: /* } */
1664: /* printf("\n "); */
1665: /* } */
1666: /* printf("\n ");printf("%lf ",cov[2]);*/
1667: /*
1.126 brouard 1668: for(i=1; i<= npar; i++) printf("%f ",x[i]);
1669: goto end;*/
1670: return ps;
1671: }
1672:
1673: /**************** Product of 2 matrices ******************/
1674:
1.145 brouard 1675: double **matprod2(double **out, double **in,int nrl, int nrh, int ncl, int nch, int ncolol, int ncoloh, double **b)
1.126 brouard 1676: {
1677: /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
1678: b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
1679: /* in, b, out are matrice of pointers which should have been initialized
1680: before: only the contents of out is modified. The function returns
1681: a pointer to pointers identical to out */
1.145 brouard 1682: int i, j, k;
1.126 brouard 1683: for(i=nrl; i<= nrh; i++)
1.145 brouard 1684: for(k=ncolol; k<=ncoloh; k++){
1685: out[i][k]=0.;
1686: for(j=ncl; j<=nch; j++)
1687: out[i][k] +=in[i][j]*b[j][k];
1688: }
1.126 brouard 1689: return out;
1690: }
1691:
1692:
1693: /************* Higher Matrix Product ***************/
1694:
1695: double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
1696: {
1697: /* Computes the transition matrix starting at age 'age' over
1698: 'nhstepm*hstepm*stepm' months (i.e. until
1699: age (in years) age+nhstepm*hstepm*stepm/12) by multiplying
1700: nhstepm*hstepm matrices.
1701: Output is stored in matrix po[i][j][h] for h every 'hstepm' step
1702: (typically every 2 years instead of every month which is too big
1703: for the memory).
1704: Model is determined by parameters x and covariates have to be
1705: included manually here.
1706:
1707: */
1708:
1709: int i, j, d, h, k;
1.131 brouard 1710: double **out, cov[NCOVMAX+1];
1.126 brouard 1711: double **newm;
1712:
1713: /* Hstepm could be zero and should return the unit matrix */
1714: for (i=1;i<=nlstate+ndeath;i++)
1715: for (j=1;j<=nlstate+ndeath;j++){
1716: oldm[i][j]=(i==j ? 1.0 : 0.0);
1717: po[i][j][0]=(i==j ? 1.0 : 0.0);
1718: }
1719: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
1720: for(h=1; h <=nhstepm; h++){
1721: for(d=1; d <=hstepm; d++){
1722: newm=savm;
1723: /* Covariates have to be included here again */
1724: cov[1]=1.;
1725: cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
1.131 brouard 1726: for (k=1; k<=cptcovn;k++)
1727: cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
1.126 brouard 1728: for (k=1; k<=cptcovage;k++)
1729: cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
1.145 brouard 1730: for (k=1; k<=cptcovprod;k++) /* Useless because included in cptcovn */
1.126 brouard 1731: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
1732:
1733:
1734: /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
1735: /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
1736: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
1737: pmij(pmmij,cov,ncovmodel,x,nlstate));
1738: savm=oldm;
1739: oldm=newm;
1740: }
1741: for(i=1; i<=nlstate+ndeath; i++)
1742: for(j=1;j<=nlstate+ndeath;j++) {
1743: po[i][j][h]=newm[i][j];
1.128 brouard 1744: /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
1.126 brouard 1745: }
1.128 brouard 1746: /*printf("h=%d ",h);*/
1.126 brouard 1747: } /* end h */
1.128 brouard 1748: /* printf("\n H=%d \n",h); */
1.126 brouard 1749: return po;
1750: }
1751:
1.162 brouard 1752: #ifdef NLOPT
1753: double myfunc(unsigned n, const double *p1, double *grad, void *pd){
1754: double fret;
1755: double *xt;
1756: int j;
1757: myfunc_data *d2 = (myfunc_data *) pd;
1758: /* xt = (p1-1); */
1759: xt=vector(1,n);
1760: for (j=1;j<=n;j++) xt[j]=p1[j-1]; /* xt[1]=p1[0] */
1761:
1762: fret=(d2->function)(xt); /* p xt[1]@8 is fine */
1763: /* fret=(*func)(xt); /\* p xt[1]@8 is fine *\/ */
1764: printf("Function = %.12lf ",fret);
1765: for (j=1;j<=n;j++) printf(" %d %.8lf", j, xt[j]);
1766: printf("\n");
1767: free_vector(xt,1,n);
1768: return fret;
1769: }
1770: #endif
1.126 brouard 1771:
1772: /*************** log-likelihood *************/
1773: double func( double *x)
1774: {
1775: int i, ii, j, k, mi, d, kk;
1.131 brouard 1776: double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
1.126 brouard 1777: double **out;
1778: double sw; /* Sum of weights */
1779: double lli; /* Individual log likelihood */
1780: int s1, s2;
1781: double bbh, survp;
1782: long ipmx;
1783: /*extern weight */
1784: /* We are differentiating ll according to initial status */
1785: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
1786: /*for(i=1;i<imx;i++)
1787: printf(" %d\n",s[4][i]);
1788: */
1.162 brouard 1789:
1790: ++countcallfunc;
1791:
1.126 brouard 1792: cov[1]=1.;
1793:
1794: for(k=1; k<=nlstate; k++) ll[k]=0.;
1795:
1796: if(mle==1){
1797: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1.138 brouard 1798: /* Computes the values of the ncovmodel covariates of the model
1799: depending if the covariates are fixed or variying (age dependent) and stores them in cov[]
1800: Then computes with function pmij which return a matrix p[i][j] giving the elementary probability
1801: to be observed in j being in i according to the model.
1802: */
1.145 brouard 1803: for (k=1; k<=cptcovn;k++){ /* Simple and product covariates without age* products */
1804: cov[2+k]=covar[Tvar[k]][i];
1805: }
1.137 brouard 1806: /* In model V2+V1*V4+age*V3+V3*V2 Tvar[1] is V2, Tvar[2=V1*V4]
1.138 brouard 1807: is 6, Tvar[3=age*V3] should not be computed because of age Tvar[4=V3*V2]
1.137 brouard 1808: has been calculated etc */
1.126 brouard 1809: for(mi=1; mi<= wav[i]-1; mi++){
1810: for (ii=1;ii<=nlstate+ndeath;ii++)
1811: for (j=1;j<=nlstate+ndeath;j++){
1812: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1813: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1814: }
1815: for(d=0; d<dh[mi][i]; d++){
1816: newm=savm;
1817: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1818: for (kk=1; kk<=cptcovage;kk++) {
1.137 brouard 1819: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; /* Tage[kk] gives the data-covariate associated with age */
1.126 brouard 1820: }
1821: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1822: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1823: savm=oldm;
1824: oldm=newm;
1825: } /* end mult */
1826:
1827: /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
1828: /* But now since version 0.9 we anticipate for bias at large stepm.
1829: * If stepm is larger than one month (smallest stepm) and if the exact delay
1830: * (in months) between two waves is not a multiple of stepm, we rounded to
1831: * the nearest (and in case of equal distance, to the lowest) interval but now
1832: * we keep into memory the bias bh[mi][i] and also the previous matrix product
1833: * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
1834: * probability in order to take into account the bias as a fraction of the way
1835: * from savm to out if bh is negative or even beyond if bh is positive. bh varies
1836: * -stepm/2 to stepm/2 .
1837: * For stepm=1 the results are the same as for previous versions of Imach.
1838: * For stepm > 1 the results are less biased than in previous versions.
1839: */
1840: s1=s[mw[mi][i]][i];
1841: s2=s[mw[mi+1][i]][i];
1842: bbh=(double)bh[mi][i]/(double)stepm;
1843: /* bias bh is positive if real duration
1844: * is higher than the multiple of stepm and negative otherwise.
1845: */
1846: /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
1847: if( s2 > nlstate){
1848: /* i.e. if s2 is a death state and if the date of death is known
1849: then the contribution to the likelihood is the probability to
1850: die between last step unit time and current step unit time,
1851: which is also equal to probability to die before dh
1852: minus probability to die before dh-stepm .
1853: In version up to 0.92 likelihood was computed
1854: as if date of death was unknown. Death was treated as any other
1855: health state: the date of the interview describes the actual state
1856: and not the date of a change in health state. The former idea was
1857: to consider that at each interview the state was recorded
1858: (healthy, disable or death) and IMaCh was corrected; but when we
1859: introduced the exact date of death then we should have modified
1860: the contribution of an exact death to the likelihood. This new
1861: contribution is smaller and very dependent of the step unit
1862: stepm. It is no more the probability to die between last interview
1863: and month of death but the probability to survive from last
1864: interview up to one month before death multiplied by the
1865: probability to die within a month. Thanks to Chris
1866: Jackson for correcting this bug. Former versions increased
1867: mortality artificially. The bad side is that we add another loop
1868: which slows down the processing. The difference can be up to 10%
1869: lower mortality.
1870: */
1871: lli=log(out[s1][s2] - savm[s1][s2]);
1872:
1873:
1874: } else if (s2==-2) {
1875: for (j=1,survp=0. ; j<=nlstate; j++)
1876: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
1877: /*survp += out[s1][j]; */
1878: lli= log(survp);
1879: }
1880:
1881: else if (s2==-4) {
1882: for (j=3,survp=0. ; j<=nlstate; j++)
1883: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
1884: lli= log(survp);
1885: }
1886:
1887: else if (s2==-5) {
1888: for (j=1,survp=0. ; j<=2; j++)
1889: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
1890: lli= log(survp);
1891: }
1892:
1893: else{
1894: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
1895: /* 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 */
1896: }
1897: /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
1898: /*if(lli ==000.0)*/
1899: /*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); */
1900: ipmx +=1;
1901: sw += weight[i];
1902: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1903: } /* end of wave */
1904: } /* end of individual */
1905: } else if(mle==2){
1906: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1907: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1908: for(mi=1; mi<= wav[i]-1; mi++){
1909: for (ii=1;ii<=nlstate+ndeath;ii++)
1910: for (j=1;j<=nlstate+ndeath;j++){
1911: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1912: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1913: }
1914: for(d=0; d<=dh[mi][i]; d++){
1915: newm=savm;
1916: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1917: for (kk=1; kk<=cptcovage;kk++) {
1918: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1919: }
1920: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1921: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1922: savm=oldm;
1923: oldm=newm;
1924: } /* end mult */
1925:
1926: s1=s[mw[mi][i]][i];
1927: s2=s[mw[mi+1][i]][i];
1928: bbh=(double)bh[mi][i]/(double)stepm;
1929: 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 */
1930: ipmx +=1;
1931: sw += weight[i];
1932: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1933: } /* end of wave */
1934: } /* end of individual */
1935: } else if(mle==3){ /* exponential inter-extrapolation */
1936: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1937: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1938: for(mi=1; mi<= wav[i]-1; mi++){
1939: for (ii=1;ii<=nlstate+ndeath;ii++)
1940: for (j=1;j<=nlstate+ndeath;j++){
1941: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1942: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1943: }
1944: for(d=0; d<dh[mi][i]; d++){
1945: newm=savm;
1946: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1947: for (kk=1; kk<=cptcovage;kk++) {
1948: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1949: }
1950: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1951: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1952: savm=oldm;
1953: oldm=newm;
1954: } /* end mult */
1955:
1956: s1=s[mw[mi][i]][i];
1957: s2=s[mw[mi+1][i]][i];
1958: bbh=(double)bh[mi][i]/(double)stepm;
1959: 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 */
1960: ipmx +=1;
1961: sw += weight[i];
1962: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1963: } /* end of wave */
1964: } /* end of individual */
1965: }else if (mle==4){ /* ml=4 no inter-extrapolation */
1966: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1967: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1968: for(mi=1; mi<= wav[i]-1; mi++){
1969: for (ii=1;ii<=nlstate+ndeath;ii++)
1970: for (j=1;j<=nlstate+ndeath;j++){
1971: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1972: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1973: }
1974: for(d=0; d<dh[mi][i]; d++){
1975: newm=savm;
1976: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1977: for (kk=1; kk<=cptcovage;kk++) {
1978: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1979: }
1980:
1981: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1982: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1983: savm=oldm;
1984: oldm=newm;
1985: } /* end mult */
1986:
1987: s1=s[mw[mi][i]][i];
1988: s2=s[mw[mi+1][i]][i];
1989: if( s2 > nlstate){
1990: lli=log(out[s1][s2] - savm[s1][s2]);
1991: }else{
1992: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
1993: }
1994: ipmx +=1;
1995: sw += weight[i];
1996: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1997: /* 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]); */
1998: } /* end of wave */
1999: } /* end of individual */
2000: }else{ /* ml=5 no inter-extrapolation no jackson =0.8a */
2001: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
2002: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
2003: for(mi=1; mi<= wav[i]-1; mi++){
2004: for (ii=1;ii<=nlstate+ndeath;ii++)
2005: for (j=1;j<=nlstate+ndeath;j++){
2006: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2007: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2008: }
2009: for(d=0; d<dh[mi][i]; d++){
2010: newm=savm;
2011: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
2012: for (kk=1; kk<=cptcovage;kk++) {
2013: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
2014: }
2015:
2016: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2017: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
2018: savm=oldm;
2019: oldm=newm;
2020: } /* end mult */
2021:
2022: s1=s[mw[mi][i]][i];
2023: s2=s[mw[mi+1][i]][i];
2024: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
2025: ipmx +=1;
2026: sw += weight[i];
2027: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
2028: /*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]);*/
2029: } /* end of wave */
2030: } /* end of individual */
2031: } /* End of if */
2032: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
2033: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
2034: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
2035: return -l;
2036: }
2037:
2038: /*************** log-likelihood *************/
2039: double funcone( double *x)
2040: {
2041: /* Same as likeli but slower because of a lot of printf and if */
2042: int i, ii, j, k, mi, d, kk;
1.131 brouard 2043: double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
1.126 brouard 2044: double **out;
2045: double lli; /* Individual log likelihood */
2046: double llt;
2047: int s1, s2;
2048: double bbh, survp;
2049: /*extern weight */
2050: /* We are differentiating ll according to initial status */
2051: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
2052: /*for(i=1;i<imx;i++)
2053: printf(" %d\n",s[4][i]);
2054: */
2055: cov[1]=1.;
2056:
2057: for(k=1; k<=nlstate; k++) ll[k]=0.;
2058:
2059: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
2060: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
2061: for(mi=1; mi<= wav[i]-1; mi++){
2062: for (ii=1;ii<=nlstate+ndeath;ii++)
2063: for (j=1;j<=nlstate+ndeath;j++){
2064: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2065: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2066: }
2067: for(d=0; d<dh[mi][i]; d++){
2068: newm=savm;
2069: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
2070: for (kk=1; kk<=cptcovage;kk++) {
2071: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
2072: }
1.145 brouard 2073: /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
1.126 brouard 2074: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2075: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1.145 brouard 2076: /* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, */
2077: /* 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); */
1.126 brouard 2078: savm=oldm;
2079: oldm=newm;
2080: } /* end mult */
2081:
2082: s1=s[mw[mi][i]][i];
2083: s2=s[mw[mi+1][i]][i];
2084: bbh=(double)bh[mi][i]/(double)stepm;
2085: /* bias is positive if real duration
2086: * is higher than the multiple of stepm and negative otherwise.
2087: */
2088: if( s2 > nlstate && (mle <5) ){ /* Jackson */
2089: lli=log(out[s1][s2] - savm[s1][s2]);
2090: } else if (s2==-2) {
2091: for (j=1,survp=0. ; j<=nlstate; j++)
2092: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
2093: lli= log(survp);
2094: }else if (mle==1){
2095: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
2096: } else if(mle==2){
2097: 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 */
2098: } else if(mle==3){ /* exponential inter-extrapolation */
2099: 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 */
2100: } else if (mle==4){ /* mle=4 no inter-extrapolation */
2101: lli=log(out[s1][s2]); /* Original formula */
1.136 brouard 2102: } else{ /* mle=0 back to 1 */
2103: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
2104: /*lli=log(out[s1][s2]); */ /* Original formula */
1.126 brouard 2105: } /* End of if */
2106: ipmx +=1;
2107: sw += weight[i];
2108: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1.132 brouard 2109: /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
1.126 brouard 2110: if(globpr){
1.141 brouard 2111: fprintf(ficresilk,"%9ld %6d %2d %2d %1d %1d %3d %11.6f %8.4f\
1.126 brouard 2112: %11.6f %11.6f %11.6f ", \
2113: num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
2114: 2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
2115: for(k=1,llt=0.,l=0.; k<=nlstate; k++){
2116: llt +=ll[k]*gipmx/gsw;
2117: fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
2118: }
2119: fprintf(ficresilk," %10.6f\n", -llt);
2120: }
2121: } /* end of wave */
2122: } /* end of individual */
2123: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
2124: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
2125: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
2126: if(globpr==0){ /* First time we count the contributions and weights */
2127: gipmx=ipmx;
2128: gsw=sw;
2129: }
2130: return -l;
2131: }
2132:
2133:
2134: /*************** function likelione ***********/
2135: void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
2136: {
2137: /* This routine should help understanding what is done with
2138: the selection of individuals/waves and
2139: to check the exact contribution to the likelihood.
2140: Plotting could be done.
2141: */
2142: int k;
2143:
2144: if(*globpri !=0){ /* Just counts and sums, no printings */
2145: strcpy(fileresilk,"ilk");
2146: strcat(fileresilk,fileres);
2147: if((ficresilk=fopen(fileresilk,"w"))==NULL) {
2148: printf("Problem with resultfile: %s\n", fileresilk);
2149: fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
2150: }
2151: 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");
2152: fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
2153: /* i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
2154: for(k=1; k<=nlstate; k++)
2155: fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
2156: fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
2157: }
2158:
2159: *fretone=(*funcone)(p);
2160: if(*globpri !=0){
2161: fclose(ficresilk);
2162: fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
2163: fflush(fichtm);
2164: }
2165: return;
2166: }
2167:
2168:
2169: /*********** Maximum Likelihood Estimation ***************/
2170:
2171: void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
2172: {
1.165 brouard 2173: int i,j, iter=0;
1.126 brouard 2174: double **xi;
2175: double fret;
2176: double fretone; /* Only one call to likelihood */
2177: /* char filerespow[FILENAMELENGTH];*/
1.162 brouard 2178:
2179: #ifdef NLOPT
2180: int creturn;
2181: nlopt_opt opt;
2182: /* double lb[9] = { -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL }; /\* lower bounds *\/ */
2183: double *lb;
2184: double minf; /* the minimum objective value, upon return */
2185: double * p1; /* Shifted parameters from 0 instead of 1 */
2186: myfunc_data dinst, *d = &dinst;
2187: #endif
2188:
2189:
1.126 brouard 2190: xi=matrix(1,npar,1,npar);
2191: for (i=1;i<=npar;i++)
2192: for (j=1;j<=npar;j++)
2193: xi[i][j]=(i==j ? 1.0 : 0.0);
2194: printf("Powell\n"); fprintf(ficlog,"Powell\n");
2195: strcpy(filerespow,"pow");
2196: strcat(filerespow,fileres);
2197: if((ficrespow=fopen(filerespow,"w"))==NULL) {
2198: printf("Problem with resultfile: %s\n", filerespow);
2199: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
2200: }
2201: fprintf(ficrespow,"# Powell\n# iter -2*LL");
2202: for (i=1;i<=nlstate;i++)
2203: for(j=1;j<=nlstate+ndeath;j++)
2204: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
2205: fprintf(ficrespow,"\n");
1.162 brouard 2206: #ifdef POWELL
1.126 brouard 2207: powell(p,xi,npar,ftol,&iter,&fret,func);
1.162 brouard 2208: #endif
1.126 brouard 2209:
1.162 brouard 2210: #ifdef NLOPT
2211: #ifdef NEWUOA
2212: opt = nlopt_create(NLOPT_LN_NEWUOA,npar);
2213: #else
2214: opt = nlopt_create(NLOPT_LN_BOBYQA,npar);
2215: #endif
2216: lb=vector(0,npar-1);
2217: for (i=0;i<npar;i++) lb[i]= -HUGE_VAL;
2218: nlopt_set_lower_bounds(opt, lb);
2219: nlopt_set_initial_step1(opt, 0.1);
2220:
2221: p1= (p+1); /* p *(p+1)@8 and p *(p1)@8 are equal p1[0]=p[1] */
2222: d->function = func;
2223: printf(" Func %.12lf \n",myfunc(npar,p1,NULL,d));
2224: nlopt_set_min_objective(opt, myfunc, d);
2225: nlopt_set_xtol_rel(opt, ftol);
2226: if ((creturn=nlopt_optimize(opt, p1, &minf)) < 0) {
2227: printf("nlopt failed! %d\n",creturn);
2228: }
2229: else {
2230: printf("found minimum after %d evaluations (NLOPT=%d)\n", countcallfunc ,NLOPT);
2231: printf("found minimum at f(%g,%g) = %0.10g\n", p[0], p[1], minf);
2232: iter=1; /* not equal */
2233: }
2234: nlopt_destroy(opt);
2235: #endif
1.126 brouard 2236: free_matrix(xi,1,npar,1,npar);
2237: fclose(ficrespow);
1.162 brouard 2238: printf("\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
2239: fprintf(ficlog,"\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
2240: fprintf(ficres,"\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
1.126 brouard 2241:
2242: }
2243:
2244: /**** Computes Hessian and covariance matrix ***/
2245: void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
2246: {
2247: double **a,**y,*x,pd;
2248: double **hess;
1.164 brouard 2249: int i, j;
1.126 brouard 2250: int *indx;
2251:
2252: double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
2253: double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
2254: void lubksb(double **a, int npar, int *indx, double b[]) ;
2255: void ludcmp(double **a, int npar, int *indx, double *d) ;
2256: double gompertz(double p[]);
2257: hess=matrix(1,npar,1,npar);
2258:
2259: printf("\nCalculation of the hessian matrix. Wait...\n");
2260: fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
2261: for (i=1;i<=npar;i++){
2262: printf("%d",i);fflush(stdout);
2263: fprintf(ficlog,"%d",i);fflush(ficlog);
2264:
2265: hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
2266:
2267: /* printf(" %f ",p[i]);
2268: printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
2269: }
2270:
2271: for (i=1;i<=npar;i++) {
2272: for (j=1;j<=npar;j++) {
2273: if (j>i) {
2274: printf(".%d%d",i,j);fflush(stdout);
2275: fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
2276: hess[i][j]=hessij(p,delti,i,j,func,npar);
2277:
2278: hess[j][i]=hess[i][j];
2279: /*printf(" %lf ",hess[i][j]);*/
2280: }
2281: }
2282: }
2283: printf("\n");
2284: fprintf(ficlog,"\n");
2285:
2286: printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
2287: fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
2288:
2289: a=matrix(1,npar,1,npar);
2290: y=matrix(1,npar,1,npar);
2291: x=vector(1,npar);
2292: indx=ivector(1,npar);
2293: for (i=1;i<=npar;i++)
2294: for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
2295: ludcmp(a,npar,indx,&pd);
2296:
2297: for (j=1;j<=npar;j++) {
2298: for (i=1;i<=npar;i++) x[i]=0;
2299: x[j]=1;
2300: lubksb(a,npar,indx,x);
2301: for (i=1;i<=npar;i++){
2302: matcov[i][j]=x[i];
2303: }
2304: }
2305:
2306: printf("\n#Hessian matrix#\n");
2307: fprintf(ficlog,"\n#Hessian matrix#\n");
2308: for (i=1;i<=npar;i++) {
2309: for (j=1;j<=npar;j++) {
2310: printf("%.3e ",hess[i][j]);
2311: fprintf(ficlog,"%.3e ",hess[i][j]);
2312: }
2313: printf("\n");
2314: fprintf(ficlog,"\n");
2315: }
2316:
2317: /* Recompute Inverse */
2318: for (i=1;i<=npar;i++)
2319: for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
2320: ludcmp(a,npar,indx,&pd);
2321:
2322: /* printf("\n#Hessian matrix recomputed#\n");
2323:
2324: for (j=1;j<=npar;j++) {
2325: for (i=1;i<=npar;i++) x[i]=0;
2326: x[j]=1;
2327: lubksb(a,npar,indx,x);
2328: for (i=1;i<=npar;i++){
2329: y[i][j]=x[i];
2330: printf("%.3e ",y[i][j]);
2331: fprintf(ficlog,"%.3e ",y[i][j]);
2332: }
2333: printf("\n");
2334: fprintf(ficlog,"\n");
2335: }
2336: */
2337:
2338: free_matrix(a,1,npar,1,npar);
2339: free_matrix(y,1,npar,1,npar);
2340: free_vector(x,1,npar);
2341: free_ivector(indx,1,npar);
2342: free_matrix(hess,1,npar,1,npar);
2343:
2344:
2345: }
2346:
2347: /*************** hessian matrix ****************/
2348: double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
2349: {
2350: int i;
2351: int l=1, lmax=20;
2352: double k1,k2;
1.132 brouard 2353: double p2[MAXPARM+1]; /* identical to x */
1.126 brouard 2354: double res;
2355: double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
2356: double fx;
2357: int k=0,kmax=10;
2358: double l1;
2359:
2360: fx=func(x);
2361: for (i=1;i<=npar;i++) p2[i]=x[i];
1.145 brouard 2362: for(l=0 ; l <=lmax; l++){ /* Enlarging the zone around the Maximum */
1.126 brouard 2363: l1=pow(10,l);
2364: delts=delt;
2365: for(k=1 ; k <kmax; k=k+1){
2366: delt = delta*(l1*k);
2367: p2[theta]=x[theta] +delt;
1.145 brouard 2368: k1=func(p2)-fx; /* Might be negative if too close to the theoretical maximum */
1.126 brouard 2369: p2[theta]=x[theta]-delt;
2370: k2=func(p2)-fx;
2371: /*res= (k1-2.0*fx+k2)/delt/delt; */
2372: res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
2373:
1.132 brouard 2374: #ifdef DEBUGHESS
1.126 brouard 2375: 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);
2376: 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);
2377: #endif
2378: /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
2379: if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
2380: k=kmax;
2381: }
2382: else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
1.164 brouard 2383: k=kmax; l=lmax*10;
1.126 brouard 2384: }
2385: else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){
2386: delts=delt;
2387: }
2388: }
2389: }
2390: delti[theta]=delts;
2391: return res;
2392:
2393: }
2394:
2395: double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
2396: {
2397: int i;
1.164 brouard 2398: int l=1, lmax=20;
1.126 brouard 2399: double k1,k2,k3,k4,res,fx;
1.132 brouard 2400: double p2[MAXPARM+1];
1.126 brouard 2401: int k;
2402:
2403: fx=func(x);
2404: for (k=1; k<=2; k++) {
2405: for (i=1;i<=npar;i++) p2[i]=x[i];
2406: p2[thetai]=x[thetai]+delti[thetai]/k;
2407: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
2408: k1=func(p2)-fx;
2409:
2410: p2[thetai]=x[thetai]+delti[thetai]/k;
2411: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
2412: k2=func(p2)-fx;
2413:
2414: p2[thetai]=x[thetai]-delti[thetai]/k;
2415: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
2416: k3=func(p2)-fx;
2417:
2418: p2[thetai]=x[thetai]-delti[thetai]/k;
2419: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
2420: k4=func(p2)-fx;
2421: res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
2422: #ifdef DEBUG
2423: 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);
2424: 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);
2425: #endif
2426: }
2427: return res;
2428: }
2429:
2430: /************** Inverse of matrix **************/
2431: void ludcmp(double **a, int n, int *indx, double *d)
2432: {
2433: int i,imax,j,k;
2434: double big,dum,sum,temp;
2435: double *vv;
2436:
2437: vv=vector(1,n);
2438: *d=1.0;
2439: for (i=1;i<=n;i++) {
2440: big=0.0;
2441: for (j=1;j<=n;j++)
2442: if ((temp=fabs(a[i][j])) > big) big=temp;
2443: if (big == 0.0) nrerror("Singular matrix in routine ludcmp");
2444: vv[i]=1.0/big;
2445: }
2446: for (j=1;j<=n;j++) {
2447: for (i=1;i<j;i++) {
2448: sum=a[i][j];
2449: for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];
2450: a[i][j]=sum;
2451: }
2452: big=0.0;
2453: for (i=j;i<=n;i++) {
2454: sum=a[i][j];
2455: for (k=1;k<j;k++)
2456: sum -= a[i][k]*a[k][j];
2457: a[i][j]=sum;
2458: if ( (dum=vv[i]*fabs(sum)) >= big) {
2459: big=dum;
2460: imax=i;
2461: }
2462: }
2463: if (j != imax) {
2464: for (k=1;k<=n;k++) {
2465: dum=a[imax][k];
2466: a[imax][k]=a[j][k];
2467: a[j][k]=dum;
2468: }
2469: *d = -(*d);
2470: vv[imax]=vv[j];
2471: }
2472: indx[j]=imax;
2473: if (a[j][j] == 0.0) a[j][j]=TINY;
2474: if (j != n) {
2475: dum=1.0/(a[j][j]);
2476: for (i=j+1;i<=n;i++) a[i][j] *= dum;
2477: }
2478: }
2479: free_vector(vv,1,n); /* Doesn't work */
2480: ;
2481: }
2482:
2483: void lubksb(double **a, int n, int *indx, double b[])
2484: {
2485: int i,ii=0,ip,j;
2486: double sum;
2487:
2488: for (i=1;i<=n;i++) {
2489: ip=indx[i];
2490: sum=b[ip];
2491: b[ip]=b[i];
2492: if (ii)
2493: for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];
2494: else if (sum) ii=i;
2495: b[i]=sum;
2496: }
2497: for (i=n;i>=1;i--) {
2498: sum=b[i];
2499: for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];
2500: b[i]=sum/a[i][i];
2501: }
2502: }
2503:
2504: void pstamp(FILE *fichier)
2505: {
2506: fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart);
2507: }
2508:
2509: /************ Frequencies ********************/
2510: 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[])
2511: { /* Some frequencies */
2512:
1.164 brouard 2513: int i, m, jk, j1, bool, z1,j;
1.126 brouard 2514: int first;
2515: double ***freq; /* Frequencies */
2516: double *pp, **prop;
2517: double pos,posprop, k2, dateintsum=0,k2cpt=0;
2518: char fileresp[FILENAMELENGTH];
2519:
2520: pp=vector(1,nlstate);
2521: prop=matrix(1,nlstate,iagemin,iagemax+3);
2522: strcpy(fileresp,"p");
2523: strcat(fileresp,fileres);
2524: if((ficresp=fopen(fileresp,"w"))==NULL) {
2525: printf("Problem with prevalence resultfile: %s\n", fileresp);
2526: fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
2527: exit(0);
2528: }
2529: freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
2530: j1=0;
2531:
2532: j=cptcoveff;
2533: if (cptcovn<1) {j=1;ncodemax[1]=1;}
2534:
2535: first=1;
2536:
1.169 ! brouard 2537: /* for(k1=1; k1<=j ; k1++){ */ /* Loop on covariates */
! 2538: /* for(i1=1; i1<=ncodemax[k1];i1++){ */ /* Now it is 2 */
! 2539: /* j1++; */
1.145 brouard 2540: for (j1 = 1; j1 <= (int) pow(2,cptcoveff); j1++){
1.126 brouard 2541: /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
2542: scanf("%d", i);*/
2543: for (i=-5; i<=nlstate+ndeath; i++)
2544: for (jk=-5; jk<=nlstate+ndeath; jk++)
2545: for(m=iagemin; m <= iagemax+3; m++)
2546: freq[i][jk][m]=0;
1.143 brouard 2547:
2548: for (i=1; i<=nlstate; i++)
2549: for(m=iagemin; m <= iagemax+3; m++)
2550: prop[i][m]=0;
1.126 brouard 2551:
2552: dateintsum=0;
2553: k2cpt=0;
2554: for (i=1; i<=imx; i++) {
2555: bool=1;
1.144 brouard 2556: if (cptcovn>0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
2557: for (z1=1; z1<=cptcoveff; z1++)
2558: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]){
1.145 brouard 2559: /* Tests if the value of each of the covariates of i is equal to filter j1 */
1.144 brouard 2560: bool=0;
1.145 brouard 2561: /* 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",
2562: bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtab[j1][z1],
2563: j1,z1,nbcode[Tvaraff[z1]][codtab[j1][z1]],j1);*/
1.144 brouard 2564: /* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtab[7][3]=1 and nbcde[3][?]=1*/
2565: }
1.126 brouard 2566: }
1.144 brouard 2567:
1.126 brouard 2568: if (bool==1){
2569: for(m=firstpass; m<=lastpass; m++){
2570: k2=anint[m][i]+(mint[m][i]/12.);
2571: /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
2572: if(agev[m][i]==0) agev[m][i]=iagemax+1;
2573: if(agev[m][i]==1) agev[m][i]=iagemax+2;
2574: if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
2575: if (m<lastpass) {
2576: freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
2577: freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
2578: }
2579:
2580: if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
2581: dateintsum=dateintsum+k2;
2582: k2cpt++;
2583: }
2584: /*}*/
2585: }
2586: }
1.145 brouard 2587: } /* end i */
1.126 brouard 2588:
2589: /* fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
2590: pstamp(ficresp);
2591: if (cptcovn>0) {
2592: fprintf(ficresp, "\n#********** Variable ");
2593: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
2594: fprintf(ficresp, "**********\n#");
1.143 brouard 2595: fprintf(ficlog, "\n#********** Variable ");
2596: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficlog, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
2597: fprintf(ficlog, "**********\n#");
1.126 brouard 2598: }
2599: for(i=1; i<=nlstate;i++)
2600: fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
2601: fprintf(ficresp, "\n");
2602:
2603: for(i=iagemin; i <= iagemax+3; i++){
2604: if(i==iagemax+3){
2605: fprintf(ficlog,"Total");
2606: }else{
2607: if(first==1){
2608: first=0;
2609: printf("See log file for details...\n");
2610: }
2611: fprintf(ficlog,"Age %d", i);
2612: }
2613: for(jk=1; jk <=nlstate ; jk++){
2614: for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
2615: pp[jk] += freq[jk][m][i];
2616: }
2617: for(jk=1; jk <=nlstate ; jk++){
2618: for(m=-1, pos=0; m <=0 ; m++)
2619: pos += freq[jk][m][i];
2620: if(pp[jk]>=1.e-10){
2621: if(first==1){
1.132 brouard 2622: printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
1.126 brouard 2623: }
2624: fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
2625: }else{
2626: if(first==1)
2627: printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
2628: fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
2629: }
2630: }
2631:
2632: for(jk=1; jk <=nlstate ; jk++){
2633: for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
2634: pp[jk] += freq[jk][m][i];
2635: }
2636: for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
2637: pos += pp[jk];
2638: posprop += prop[jk][i];
2639: }
2640: for(jk=1; jk <=nlstate ; jk++){
2641: if(pos>=1.e-5){
2642: if(first==1)
2643: printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
2644: fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
2645: }else{
2646: if(first==1)
2647: printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
2648: fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
2649: }
2650: if( i <= iagemax){
2651: if(pos>=1.e-5){
2652: fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
2653: /*probs[i][jk][j1]= pp[jk]/pos;*/
2654: /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
2655: }
2656: else
2657: fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
2658: }
2659: }
2660:
2661: for(jk=-1; jk <=nlstate+ndeath; jk++)
2662: for(m=-1; m <=nlstate+ndeath; m++)
2663: if(freq[jk][m][i] !=0 ) {
2664: if(first==1)
2665: printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
2666: fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
2667: }
2668: if(i <= iagemax)
2669: fprintf(ficresp,"\n");
2670: if(first==1)
2671: printf("Others in log...\n");
2672: fprintf(ficlog,"\n");
2673: }
1.145 brouard 2674: /*}*/
1.126 brouard 2675: }
2676: dateintmean=dateintsum/k2cpt;
2677:
2678: fclose(ficresp);
2679: free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
2680: free_vector(pp,1,nlstate);
2681: free_matrix(prop,1,nlstate,iagemin, iagemax+3);
2682: /* End of Freq */
2683: }
2684:
2685: /************ Prevalence ********************/
2686: 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)
2687: {
2688: /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
2689: in each health status at the date of interview (if between dateprev1 and dateprev2).
2690: We still use firstpass and lastpass as another selection.
2691: */
2692:
1.164 brouard 2693: int i, m, jk, j1, bool, z1,j;
2694:
2695: double **prop;
2696: double posprop;
1.126 brouard 2697: double y2; /* in fractional years */
2698: int iagemin, iagemax;
1.145 brouard 2699: int first; /** to stop verbosity which is redirected to log file */
1.126 brouard 2700:
2701: iagemin= (int) agemin;
2702: iagemax= (int) agemax;
2703: /*pp=vector(1,nlstate);*/
2704: prop=matrix(1,nlstate,iagemin,iagemax+3);
2705: /* freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
2706: j1=0;
2707:
1.145 brouard 2708: /*j=cptcoveff;*/
1.126 brouard 2709: if (cptcovn<1) {j=1;ncodemax[1]=1;}
2710:
1.145 brouard 2711: first=1;
2712: for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){
2713: /*for(i1=1; i1<=ncodemax[k1];i1++){
2714: j1++;*/
1.126 brouard 2715:
2716: for (i=1; i<=nlstate; i++)
2717: for(m=iagemin; m <= iagemax+3; m++)
2718: prop[i][m]=0.0;
2719:
2720: for (i=1; i<=imx; i++) { /* Each individual */
2721: bool=1;
2722: if (cptcovn>0) {
2723: for (z1=1; z1<=cptcoveff; z1++)
2724: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
2725: bool=0;
2726: }
2727: if (bool==1) {
2728: for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
2729: y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
2730: if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
2731: if(agev[m][i]==0) agev[m][i]=iagemax+1;
2732: if(agev[m][i]==1) agev[m][i]=iagemax+2;
2733: 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);
2734: if (s[m][i]>0 && s[m][i]<=nlstate) {
2735: /*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]]);*/
2736: prop[s[m][i]][(int)agev[m][i]] += weight[i];
2737: prop[s[m][i]][iagemax+3] += weight[i];
2738: }
2739: }
2740: } /* end selection of waves */
2741: }
2742: }
2743: for(i=iagemin; i <= iagemax+3; i++){
2744: for(jk=1,posprop=0; jk <=nlstate ; jk++) {
2745: posprop += prop[jk][i];
2746: }
1.145 brouard 2747:
1.126 brouard 2748: for(jk=1; jk <=nlstate ; jk++){
2749: if( i <= iagemax){
2750: if(posprop>=1.e-5){
2751: probs[i][jk][j1]= prop[jk][i]/posprop;
1.145 brouard 2752: } else{
2753: if(first==1){
2754: first=0;
2755: 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]);
2756: }
2757: }
1.126 brouard 2758: }
2759: }/* end jk */
2760: }/* end i */
1.145 brouard 2761: /*} *//* end i1 */
2762: } /* end j1 */
1.126 brouard 2763:
2764: /* free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
2765: /*free_vector(pp,1,nlstate);*/
2766: free_matrix(prop,1,nlstate, iagemin,iagemax+3);
2767: } /* End of prevalence */
2768:
2769: /************* Waves Concatenation ***************/
2770:
2771: 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)
2772: {
2773: /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
2774: Death is a valid wave (if date is known).
2775: mw[mi][i] is the mi (mi=1 to wav[i]) effective wave of individual i
2776: dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
2777: and mw[mi+1][i]. dh depends on stepm.
2778: */
2779:
2780: int i, mi, m;
2781: /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
2782: double sum=0., jmean=0.;*/
2783: int first;
2784: int j, k=0,jk, ju, jl;
2785: double sum=0.;
2786: first=0;
1.164 brouard 2787: jmin=100000;
1.126 brouard 2788: jmax=-1;
2789: jmean=0.;
2790: for(i=1; i<=imx; i++){
2791: mi=0;
2792: m=firstpass;
2793: while(s[m][i] <= nlstate){
2794: if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
2795: mw[++mi][i]=m;
2796: if(m >=lastpass)
2797: break;
2798: else
2799: m++;
2800: }/* end while */
2801: if (s[m][i] > nlstate){
2802: mi++; /* Death is another wave */
2803: /* if(mi==0) never been interviewed correctly before death */
2804: /* Only death is a correct wave */
2805: mw[mi][i]=m;
2806: }
2807:
2808: wav[i]=mi;
2809: if(mi==0){
2810: nbwarn++;
2811: if(first==0){
2812: printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
2813: first=1;
2814: }
2815: if(first==1){
2816: fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
2817: }
2818: } /* end mi==0 */
2819: } /* End individuals */
2820:
2821: for(i=1; i<=imx; i++){
2822: for(mi=1; mi<wav[i];mi++){
2823: if (stepm <=0)
2824: dh[mi][i]=1;
2825: else{
2826: if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
2827: if (agedc[i] < 2*AGESUP) {
2828: j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);
2829: if(j==0) j=1; /* Survives at least one month after exam */
2830: else if(j<0){
2831: nberr++;
2832: 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]);
2833: j=1; /* Temporary Dangerous patch */
2834: 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);
2835: 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]);
2836: 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);
2837: }
2838: k=k+1;
2839: if (j >= jmax){
2840: jmax=j;
2841: ijmax=i;
2842: }
2843: if (j <= jmin){
2844: jmin=j;
2845: ijmin=i;
2846: }
2847: sum=sum+j;
2848: /*if (j<0) printf("j=%d num=%d \n",j,i);*/
2849: /* printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
2850: }
2851: }
2852: else{
2853: j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
2854: /* 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]); */
2855:
2856: k=k+1;
2857: if (j >= jmax) {
2858: jmax=j;
2859: ijmax=i;
2860: }
2861: else if (j <= jmin){
2862: jmin=j;
2863: ijmin=i;
2864: }
2865: /* if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
2866: /*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]);*/
2867: if(j<0){
2868: nberr++;
2869: 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]);
2870: 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]);
2871: }
2872: sum=sum+j;
2873: }
2874: jk= j/stepm;
2875: jl= j -jk*stepm;
2876: ju= j -(jk+1)*stepm;
2877: if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
2878: if(jl==0){
2879: dh[mi][i]=jk;
2880: bh[mi][i]=0;
2881: }else{ /* We want a negative bias in order to only have interpolation ie
1.136 brouard 2882: * to avoid the price of an extra matrix product in likelihood */
1.126 brouard 2883: dh[mi][i]=jk+1;
2884: bh[mi][i]=ju;
2885: }
2886: }else{
2887: if(jl <= -ju){
2888: dh[mi][i]=jk;
2889: bh[mi][i]=jl; /* bias is positive if real duration
2890: * is higher than the multiple of stepm and negative otherwise.
2891: */
2892: }
2893: else{
2894: dh[mi][i]=jk+1;
2895: bh[mi][i]=ju;
2896: }
2897: if(dh[mi][i]==0){
2898: dh[mi][i]=1; /* At least one step */
2899: bh[mi][i]=ju; /* At least one step */
2900: /* 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);*/
2901: }
2902: } /* end if mle */
2903: }
2904: } /* end wave */
2905: }
2906: jmean=sum/k;
2907: printf("Delay (in months) between two waves Min=%d (for indiviudal %ld) Max=%d (%ld) Mean=%f\n\n ",jmin, num[ijmin], jmax, num[ijmax], jmean);
1.141 brouard 2908: fprintf(ficlog,"Delay (in months) between two waves Min=%d (for indiviudal %d) Max=%d (%d) Mean=%f\n\n ",jmin, ijmin, jmax, ijmax, jmean);
1.126 brouard 2909: }
2910:
2911: /*********** Tricode ****************************/
1.145 brouard 2912: void tricode(int *Tvar, int **nbcode, int imx, int *Ndum)
1.126 brouard 2913: {
1.144 brouard 2914: /**< Uses cptcovn+2*cptcovprod as the number of covariates */
2915: /* Tvar[i]=atoi(stre); find 'n' in Vn and stores in Tvar. If model=V2+V1 Tvar[1]=2 and Tvar[2]=1
1.169 ! brouard 2916: * Boring subroutine which should only output nbcode[Tvar[j]][k]
1.145 brouard 2917: * Tvar[5] in V2+V1+V3*age+V2*V4 is 2 (V2)
1.169 ! brouard 2918: * nbcode[Tvar[j]][1]=
1.144 brouard 2919: */
1.130 brouard 2920:
1.145 brouard 2921: int ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
1.136 brouard 2922: int modmaxcovj=0; /* Modality max of covariates j */
1.145 brouard 2923: int cptcode=0; /* Modality max of covariates j */
2924: int modmincovj=0; /* Modality min of covariates j */
2925:
2926:
1.126 brouard 2927: cptcoveff=0;
2928:
1.145 brouard 2929: for (k=-1; k < maxncov; k++) Ndum[k]=0;
1.144 brouard 2930: for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */
1.126 brouard 2931:
1.145 brouard 2932: /* Loop on covariates without age and products */
2933: for (j=1; j<=(cptcovs); j++) { /* model V1 + V2*age+ V3 + V3*V4 : V1 + V3 = 2 only */
2934: for (i=1; i<=imx; i++) { /* Lopp on individuals: reads the data file to get the maximum value of the
1.136 brouard 2935: modality of this covariate Vj*/
1.145 brouard 2936: ij=(int)(covar[Tvar[j]][i]); /* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i
2937: * If product of Vn*Vm, still boolean *:
2938: * If it was coded 1, 2, 3, 4 should be splitted into 3 boolean variables
2939: * 1 => 0 0 0, 2 => 0 0 1, 3 => 0 1 1, 4=1 0 0 */
2940: /* Finds for covariate j, n=Tvar[j] of Vn . ij is the
1.136 brouard 2941: modality of the nth covariate of individual i. */
1.145 brouard 2942: if (ij > modmaxcovj)
2943: modmaxcovj=ij;
2944: else if (ij < modmincovj)
2945: modmincovj=ij;
2946: if ((ij < -1) && (ij > NCOVMAX)){
2947: printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX );
2948: exit(1);
2949: }else
1.136 brouard 2950: Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/
1.145 brouard 2951: /* If coded 1, 2, 3 , counts the number of 1 Ndum[1], number of 2, Ndum[2], etc */
1.126 brouard 2952: /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
1.136 brouard 2953: /* getting the maximum value of the modality of the covariate
2954: (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and
2955: female is 1, then modmaxcovj=1.*/
1.126 brouard 2956: }
1.145 brouard 2957: printf(" Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", j, Tvar[j], modmincovj, modmaxcovj);
2958: cptcode=modmaxcovj;
1.137 brouard 2959: /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */
1.145 brouard 2960: /*for (i=0; i<=cptcode; i++) {*/
2961: for (i=modmincovj; i<=modmaxcovj; i++) { /* i=-1 ? 0 and 1*//* For each value of the modality of model-cov j */
2962: printf("Frequencies of covariates %d V%d %d\n", j, Tvar[j], Ndum[i]);
2963: if( Ndum[i] != 0 ){ /* Counts if nobody answered, empty modality */
2964: ncodemax[j]++; /* ncodemax[j]= Number of non-null modalities of the j th covariate. */
2965: }
2966: /* In fact ncodemax[j]=2 (dichotom. variables only) but it could be more for
2967: historical reasons: 3 if coded 1, 2, 3 and 4 and Ndum[2]=0 */
1.131 brouard 2968: } /* Ndum[-1] number of undefined modalities */
1.126 brouard 2969:
1.136 brouard 2970: /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */
1.145 brouard 2971: /* For covariate j, modalities could be 1, 2, 3, 4. If Ndum[2]=0 ncodemax[j] is not 4 but 3 */
2972: /* If Ndum[3}= 635; Ndum[4]=0; Ndum[5]=0; Ndum[6]=27; Ndum[7]=125;
2973: modmincovj=3; modmaxcovj = 7;
2974: There are only 3 modalities non empty (or 2 if 27 is too few) : ncodemax[j]=3;
2975: which will be coded 0, 1, 2 which in binary on 3-1 digits are 0=00 1=01, 2=10; defining two dummy
2976: variables V1_1 and V1_2.
2977: nbcode[Tvar[j]][ij]=k;
2978: nbcode[Tvar[j]][1]=0;
2979: nbcode[Tvar[j]][2]=1;
2980: nbcode[Tvar[j]][3]=2;
2981: */
2982: ij=1; /* ij is similar to i but can jumps over null modalities */
2983: for (i=modmincovj; i<=modmaxcovj; i++) { /* i= 1 to 2 for dichotomous, or from 1 to 3 */
2984: for (k=0; k<= cptcode; k++) { /* k=-1 ? k=0 to 1 *//* Could be 1 to 4 */
2985: /*recode from 0 */
1.131 brouard 2986: if (Ndum[k] != 0) { /* If at least one individual responded to this modality k */
2987: nbcode[Tvar[j]][ij]=k; /* stores the modality in an array nbcode.
2988: k is a modality. If we have model=V1+V1*sex
2989: then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
1.126 brouard 2990: ij++;
2991: }
2992: if (ij > ncodemax[j]) break;
1.137 brouard 2993: } /* end of loop on */
2994: } /* end of loop on modality */
2995: } /* end of loop on model-covariate j. nbcode[Tvarj][1]=0 and nbcode[Tvarj][2]=1 sets the value of covariate j*/
2996:
1.145 brouard 2997: for (k=-1; k< maxncov; k++) Ndum[k]=0;
1.137 brouard 2998:
1.145 brouard 2999: for (i=1; i<=ncovmodel-2; i++) { /* -2, cste and age */
3000: /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
3001: ij=Tvar[i]; /* Tvar might be -1 if status was unknown */
3002: Ndum[ij]++;
3003: }
1.126 brouard 3004:
3005: ij=1;
1.145 brouard 3006: for (i=0; i<= maxncov-1; i++) { /* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) */
3007: /*printf("Ndum[%d]=%d\n",i, Ndum[i]);*/
1.126 brouard 3008: if((Ndum[i]!=0) && (i<=ncovcol)){
1.145 brouard 3009: /*printf("diff Ndum[%d]=%d\n",i, Ndum[i]);*/
3010: Tvaraff[ij]=i; /*For printing (unclear) */
1.126 brouard 3011: ij++;
1.145 brouard 3012: }else
3013: Tvaraff[ij]=0;
1.126 brouard 3014: }
1.131 brouard 3015: ij--;
1.144 brouard 3016: cptcoveff=ij; /*Number of total covariates*/
1.145 brouard 3017:
1.126 brouard 3018: }
3019:
1.145 brouard 3020:
1.126 brouard 3021: /*********** Health Expectancies ****************/
3022:
1.127 brouard 3023: void evsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,char strstart[] )
1.126 brouard 3024:
3025: {
3026: /* Health expectancies, no variances */
1.164 brouard 3027: int i, j, nhstepm, hstepm, h, nstepm;
1.126 brouard 3028: int nhstepma, nstepma; /* Decreasing with age */
3029: double age, agelim, hf;
3030: double ***p3mat;
3031: double eip;
3032:
3033: pstamp(ficreseij);
3034: fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
3035: fprintf(ficreseij,"# Age");
3036: for(i=1; i<=nlstate;i++){
3037: for(j=1; j<=nlstate;j++){
3038: fprintf(ficreseij," e%1d%1d ",i,j);
3039: }
3040: fprintf(ficreseij," e%1d. ",i);
3041: }
3042: fprintf(ficreseij,"\n");
3043:
3044:
3045: if(estepm < stepm){
3046: printf ("Problem %d lower than %d\n",estepm, stepm);
3047: }
3048: else hstepm=estepm;
3049: /* We compute the life expectancy from trapezoids spaced every estepm months
3050: * This is mainly to measure the difference between two models: for example
3051: * if stepm=24 months pijx are given only every 2 years and by summing them
3052: * we are calculating an estimate of the Life Expectancy assuming a linear
3053: * progression in between and thus overestimating or underestimating according
3054: * to the curvature of the survival function. If, for the same date, we
3055: * estimate the model with stepm=1 month, we can keep estepm to 24 months
3056: * to compare the new estimate of Life expectancy with the same linear
3057: * hypothesis. A more precise result, taking into account a more precise
3058: * curvature will be obtained if estepm is as small as stepm. */
3059:
3060: /* For example we decided to compute the life expectancy with the smallest unit */
3061: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
3062: nhstepm is the number of hstepm from age to agelim
3063: nstepm is the number of stepm from age to agelin.
3064: Look at hpijx to understand the reason of that which relies in memory size
3065: and note for a fixed period like estepm months */
3066: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
3067: survival function given by stepm (the optimization length). Unfortunately it
3068: means that if the survival funtion is printed only each two years of age and if
3069: you sum them up and add 1 year (area under the trapezoids) you won't get the same
3070: results. So we changed our mind and took the option of the best precision.
3071: */
3072: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
3073:
3074: agelim=AGESUP;
3075: /* If stepm=6 months */
3076: /* Computed by stepm unit matrices, product of hstepm matrices, stored
3077: in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
3078:
3079: /* nhstepm age range expressed in number of stepm */
3080: nstepm=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
3081: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
3082: /* if (stepm >= YEARM) hstepm=1;*/
3083: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
3084: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3085:
3086: for (age=bage; age<=fage; age ++){
3087: nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
3088: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
3089: /* if (stepm >= YEARM) hstepm=1;*/
3090: nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
3091:
3092: /* If stepm=6 months */
3093: /* Computed by stepm unit matrices, product of hstepma matrices, stored
3094: in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
3095:
3096: hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
3097:
3098: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
3099:
3100: printf("%d|",(int)age);fflush(stdout);
3101: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
3102:
3103: /* Computing expectancies */
3104: for(i=1; i<=nlstate;i++)
3105: for(j=1; j<=nlstate;j++)
3106: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
3107: eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
3108:
3109: /* 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]);*/
3110:
3111: }
3112:
3113: fprintf(ficreseij,"%3.0f",age );
3114: for(i=1; i<=nlstate;i++){
3115: eip=0;
3116: for(j=1; j<=nlstate;j++){
3117: eip +=eij[i][j][(int)age];
3118: fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
3119: }
3120: fprintf(ficreseij,"%9.4f", eip );
3121: }
3122: fprintf(ficreseij,"\n");
3123:
3124: }
3125: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3126: printf("\n");
3127: fprintf(ficlog,"\n");
3128:
3129: }
3130:
1.127 brouard 3131: void cvevsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,double delti[],double **matcov,char strstart[] )
1.126 brouard 3132:
3133: {
3134: /* Covariances of health expectancies eij and of total life expectancies according
3135: to initial status i, ei. .
3136: */
3137: int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
3138: int nhstepma, nstepma; /* Decreasing with age */
3139: double age, agelim, hf;
3140: double ***p3matp, ***p3matm, ***varhe;
3141: double **dnewm,**doldm;
3142: double *xp, *xm;
3143: double **gp, **gm;
3144: double ***gradg, ***trgradg;
3145: int theta;
3146:
3147: double eip, vip;
3148:
3149: varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
3150: xp=vector(1,npar);
3151: xm=vector(1,npar);
3152: dnewm=matrix(1,nlstate*nlstate,1,npar);
3153: doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
3154:
3155: pstamp(ficresstdeij);
3156: fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
3157: fprintf(ficresstdeij,"# Age");
3158: for(i=1; i<=nlstate;i++){
3159: for(j=1; j<=nlstate;j++)
3160: fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
3161: fprintf(ficresstdeij," e%1d. ",i);
3162: }
3163: fprintf(ficresstdeij,"\n");
3164:
3165: pstamp(ficrescveij);
3166: fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
3167: fprintf(ficrescveij,"# Age");
3168: for(i=1; i<=nlstate;i++)
3169: for(j=1; j<=nlstate;j++){
3170: cptj= (j-1)*nlstate+i;
3171: for(i2=1; i2<=nlstate;i2++)
3172: for(j2=1; j2<=nlstate;j2++){
3173: cptj2= (j2-1)*nlstate+i2;
3174: if(cptj2 <= cptj)
3175: fprintf(ficrescveij," %1d%1d,%1d%1d",i,j,i2,j2);
3176: }
3177: }
3178: fprintf(ficrescveij,"\n");
3179:
3180: if(estepm < stepm){
3181: printf ("Problem %d lower than %d\n",estepm, stepm);
3182: }
3183: else hstepm=estepm;
3184: /* We compute the life expectancy from trapezoids spaced every estepm months
3185: * This is mainly to measure the difference between two models: for example
3186: * if stepm=24 months pijx are given only every 2 years and by summing them
3187: * we are calculating an estimate of the Life Expectancy assuming a linear
3188: * progression in between and thus overestimating or underestimating according
3189: * to the curvature of the survival function. If, for the same date, we
3190: * estimate the model with stepm=1 month, we can keep estepm to 24 months
3191: * to compare the new estimate of Life expectancy with the same linear
3192: * hypothesis. A more precise result, taking into account a more precise
3193: * curvature will be obtained if estepm is as small as stepm. */
3194:
3195: /* For example we decided to compute the life expectancy with the smallest unit */
3196: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
3197: nhstepm is the number of hstepm from age to agelim
3198: nstepm is the number of stepm from age to agelin.
3199: Look at hpijx to understand the reason of that which relies in memory size
3200: and note for a fixed period like estepm months */
3201: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
3202: survival function given by stepm (the optimization length). Unfortunately it
3203: means that if the survival funtion is printed only each two years of age and if
3204: you sum them up and add 1 year (area under the trapezoids) you won't get the same
3205: results. So we changed our mind and took the option of the best precision.
3206: */
3207: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
3208:
3209: /* If stepm=6 months */
3210: /* nhstepm age range expressed in number of stepm */
3211: agelim=AGESUP;
3212: nstepm=(int) rint((agelim-bage)*YEARM/stepm);
3213: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
3214: /* if (stepm >= YEARM) hstepm=1;*/
3215: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
3216:
3217: p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3218: p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3219: gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
3220: trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
3221: gp=matrix(0,nhstepm,1,nlstate*nlstate);
3222: gm=matrix(0,nhstepm,1,nlstate*nlstate);
3223:
3224: for (age=bage; age<=fage; age ++){
3225: nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
3226: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
3227: /* if (stepm >= YEARM) hstepm=1;*/
3228: nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
3229:
3230: /* If stepm=6 months */
3231: /* Computed by stepm unit matrices, product of hstepma matrices, stored
3232: in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
3233:
3234: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
3235:
3236: /* Computing Variances of health expectancies */
3237: /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
3238: decrease memory allocation */
3239: for(theta=1; theta <=npar; theta++){
3240: for(i=1; i<=npar; i++){
3241: xp[i] = x[i] + (i==theta ?delti[theta]:0);
3242: xm[i] = x[i] - (i==theta ?delti[theta]:0);
3243: }
3244: hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);
3245: hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);
3246:
3247: for(j=1; j<= nlstate; j++){
3248: for(i=1; i<=nlstate; i++){
3249: for(h=0; h<=nhstepm-1; h++){
3250: gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
3251: gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
3252: }
3253: }
3254: }
3255:
3256: for(ij=1; ij<= nlstate*nlstate; ij++)
3257: for(h=0; h<=nhstepm-1; h++){
3258: gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
3259: }
3260: }/* End theta */
3261:
3262:
3263: for(h=0; h<=nhstepm-1; h++)
3264: for(j=1; j<=nlstate*nlstate;j++)
3265: for(theta=1; theta <=npar; theta++)
3266: trgradg[h][j][theta]=gradg[h][theta][j];
3267:
3268:
3269: for(ij=1;ij<=nlstate*nlstate;ij++)
3270: for(ji=1;ji<=nlstate*nlstate;ji++)
3271: varhe[ij][ji][(int)age] =0.;
3272:
3273: printf("%d|",(int)age);fflush(stdout);
3274: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
3275: for(h=0;h<=nhstepm-1;h++){
3276: for(k=0;k<=nhstepm-1;k++){
3277: matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
3278: matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
3279: for(ij=1;ij<=nlstate*nlstate;ij++)
3280: for(ji=1;ji<=nlstate*nlstate;ji++)
3281: varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
3282: }
3283: }
3284:
3285: /* Computing expectancies */
3286: hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
3287: for(i=1; i<=nlstate;i++)
3288: for(j=1; j<=nlstate;j++)
3289: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
3290: eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
3291:
3292: /* 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]);*/
3293:
3294: }
3295:
3296: fprintf(ficresstdeij,"%3.0f",age );
3297: for(i=1; i<=nlstate;i++){
3298: eip=0.;
3299: vip=0.;
3300: for(j=1; j<=nlstate;j++){
3301: eip += eij[i][j][(int)age];
3302: for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
3303: vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
3304: fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
3305: }
3306: fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
3307: }
3308: fprintf(ficresstdeij,"\n");
3309:
3310: fprintf(ficrescveij,"%3.0f",age );
3311: for(i=1; i<=nlstate;i++)
3312: for(j=1; j<=nlstate;j++){
3313: cptj= (j-1)*nlstate+i;
3314: for(i2=1; i2<=nlstate;i2++)
3315: for(j2=1; j2<=nlstate;j2++){
3316: cptj2= (j2-1)*nlstate+i2;
3317: if(cptj2 <= cptj)
3318: fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
3319: }
3320: }
3321: fprintf(ficrescveij,"\n");
3322:
3323: }
3324: free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
3325: free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
3326: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
3327: free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
3328: free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3329: free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3330: printf("\n");
3331: fprintf(ficlog,"\n");
3332:
3333: free_vector(xm,1,npar);
3334: free_vector(xp,1,npar);
3335: free_matrix(dnewm,1,nlstate*nlstate,1,npar);
3336: free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
3337: free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
3338: }
3339:
3340: /************ Variance ******************/
3341: 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[])
3342: {
3343: /* Variance of health expectancies */
3344: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
3345: /* double **newm;*/
1.169 ! brouard 3346: /* int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav)*/
! 3347:
! 3348: int movingaverage();
1.126 brouard 3349: double **dnewm,**doldm;
3350: double **dnewmp,**doldmp;
3351: int i, j, nhstepm, hstepm, h, nstepm ;
1.164 brouard 3352: int k;
1.126 brouard 3353: double *xp;
3354: double **gp, **gm; /* for var eij */
3355: double ***gradg, ***trgradg; /*for var eij */
3356: double **gradgp, **trgradgp; /* for var p point j */
3357: double *gpp, *gmp; /* for var p point j */
3358: double **varppt; /* for var p point j nlstate to nlstate+ndeath */
3359: double ***p3mat;
3360: double age,agelim, hf;
3361: double ***mobaverage;
3362: int theta;
3363: char digit[4];
3364: char digitp[25];
3365:
3366: char fileresprobmorprev[FILENAMELENGTH];
3367:
3368: if(popbased==1){
3369: if(mobilav!=0)
3370: strcpy(digitp,"-populbased-mobilav-");
3371: else strcpy(digitp,"-populbased-nomobil-");
3372: }
3373: else
3374: strcpy(digitp,"-stablbased-");
3375:
3376: if (mobilav!=0) {
3377: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3378: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
3379: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
3380: printf(" Error in movingaverage mobilav=%d\n",mobilav);
3381: }
3382: }
3383:
3384: strcpy(fileresprobmorprev,"prmorprev");
3385: sprintf(digit,"%-d",ij);
3386: /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
3387: strcat(fileresprobmorprev,digit); /* Tvar to be done */
3388: strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
3389: strcat(fileresprobmorprev,fileres);
3390: if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
3391: printf("Problem with resultfile: %s\n", fileresprobmorprev);
3392: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
3393: }
3394: printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
3395:
3396: fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
3397: pstamp(ficresprobmorprev);
3398: 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);
3399: fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
3400: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
3401: fprintf(ficresprobmorprev," p.%-d SE",j);
3402: for(i=1; i<=nlstate;i++)
3403: fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
3404: }
3405: fprintf(ficresprobmorprev,"\n");
3406: fprintf(ficgp,"\n# Routine varevsij");
3407: /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
3408: 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");
3409: fprintf(fichtm,"\n<br>%s <br>\n",digitp);
3410: /* } */
3411: varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
3412: pstamp(ficresvij);
3413: fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n# (weighted average of eij where weights are ");
3414: if(popbased==1)
1.128 brouard 3415: fprintf(ficresvij,"the age specific prevalence observed (cross-sectionally) in the population i.e cross-sectionally\n in each health state (popbased=1) (mobilav=%d\n",mobilav);
1.126 brouard 3416: else
3417: fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
3418: fprintf(ficresvij,"# Age");
3419: for(i=1; i<=nlstate;i++)
3420: for(j=1; j<=nlstate;j++)
3421: fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
3422: fprintf(ficresvij,"\n");
3423:
3424: xp=vector(1,npar);
3425: dnewm=matrix(1,nlstate,1,npar);
3426: doldm=matrix(1,nlstate,1,nlstate);
3427: dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
3428: doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
3429:
3430: gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
3431: gpp=vector(nlstate+1,nlstate+ndeath);
3432: gmp=vector(nlstate+1,nlstate+ndeath);
3433: trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
3434:
3435: if(estepm < stepm){
3436: printf ("Problem %d lower than %d\n",estepm, stepm);
3437: }
3438: else hstepm=estepm;
3439: /* For example we decided to compute the life expectancy with the smallest unit */
3440: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
3441: nhstepm is the number of hstepm from age to agelim
3442: nstepm is the number of stepm from age to agelin.
1.128 brouard 3443: Look at function hpijx to understand why (it is linked to memory size questions) */
1.126 brouard 3444: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
3445: survival function given by stepm (the optimization length). Unfortunately it
3446: means that if the survival funtion is printed every two years of age and if
3447: you sum them up and add 1 year (area under the trapezoids) you won't get the same
3448: results. So we changed our mind and took the option of the best precision.
3449: */
3450: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
3451: agelim = AGESUP;
3452: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
3453: nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
3454: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
3455: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3456: gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
3457: gp=matrix(0,nhstepm,1,nlstate);
3458: gm=matrix(0,nhstepm,1,nlstate);
3459:
3460:
3461: for(theta=1; theta <=npar; theta++){
3462: for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
3463: xp[i] = x[i] + (i==theta ?delti[theta]:0);
3464: }
3465: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
3466: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
3467:
3468: if (popbased==1) {
3469: if(mobilav ==0){
3470: for(i=1; i<=nlstate;i++)
3471: prlim[i][i]=probs[(int)age][i][ij];
3472: }else{ /* mobilav */
3473: for(i=1; i<=nlstate;i++)
3474: prlim[i][i]=mobaverage[(int)age][i][ij];
3475: }
3476: }
3477:
3478: for(j=1; j<= nlstate; j++){
3479: for(h=0; h<=nhstepm; h++){
3480: for(i=1, gp[h][j]=0.;i<=nlstate;i++)
3481: gp[h][j] += prlim[i][i]*p3mat[i][j][h];
3482: }
3483: }
3484: /* This for computing probability of death (h=1 means
3485: computed over hstepm matrices product = hstepm*stepm months)
3486: as a weighted average of prlim.
3487: */
3488: for(j=nlstate+1;j<=nlstate+ndeath;j++){
3489: for(i=1,gpp[j]=0.; i<= nlstate; i++)
3490: gpp[j] += prlim[i][i]*p3mat[i][j][1];
3491: }
3492: /* end probability of death */
3493:
3494: for(i=1; i<=npar; i++) /* Computes gradient x - delta */
3495: xp[i] = x[i] - (i==theta ?delti[theta]:0);
3496: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
3497: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
3498:
3499: if (popbased==1) {
3500: if(mobilav ==0){
3501: for(i=1; i<=nlstate;i++)
3502: prlim[i][i]=probs[(int)age][i][ij];
3503: }else{ /* mobilav */
3504: for(i=1; i<=nlstate;i++)
3505: prlim[i][i]=mobaverage[(int)age][i][ij];
3506: }
3507: }
3508:
1.128 brouard 3509: for(j=1; j<= nlstate; j++){ /* Sum of wi * eij = e.j */
1.126 brouard 3510: for(h=0; h<=nhstepm; h++){
3511: for(i=1, gm[h][j]=0.;i<=nlstate;i++)
3512: gm[h][j] += prlim[i][i]*p3mat[i][j][h];
3513: }
3514: }
3515: /* This for computing probability of death (h=1 means
3516: computed over hstepm matrices product = hstepm*stepm months)
3517: as a weighted average of prlim.
3518: */
3519: for(j=nlstate+1;j<=nlstate+ndeath;j++){
3520: for(i=1,gmp[j]=0.; i<= nlstate; i++)
3521: gmp[j] += prlim[i][i]*p3mat[i][j][1];
3522: }
3523: /* end probability of death */
3524:
3525: for(j=1; j<= nlstate; j++) /* vareij */
3526: for(h=0; h<=nhstepm; h++){
3527: gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
3528: }
3529:
3530: for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
3531: gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
3532: }
3533:
3534: } /* End theta */
3535:
3536: trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
3537:
3538: for(h=0; h<=nhstepm; h++) /* veij */
3539: for(j=1; j<=nlstate;j++)
3540: for(theta=1; theta <=npar; theta++)
3541: trgradg[h][j][theta]=gradg[h][theta][j];
3542:
3543: for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
3544: for(theta=1; theta <=npar; theta++)
3545: trgradgp[j][theta]=gradgp[theta][j];
3546:
3547:
3548: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
3549: for(i=1;i<=nlstate;i++)
3550: for(j=1;j<=nlstate;j++)
3551: vareij[i][j][(int)age] =0.;
3552:
3553: for(h=0;h<=nhstepm;h++){
3554: for(k=0;k<=nhstepm;k++){
3555: matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
3556: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
3557: for(i=1;i<=nlstate;i++)
3558: for(j=1;j<=nlstate;j++)
3559: vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
3560: }
3561: }
3562:
3563: /* pptj */
3564: matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
3565: matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
3566: for(j=nlstate+1;j<=nlstate+ndeath;j++)
3567: for(i=nlstate+1;i<=nlstate+ndeath;i++)
3568: varppt[j][i]=doldmp[j][i];
3569: /* end ppptj */
3570: /* x centered again */
3571: hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);
3572: prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
3573:
3574: if (popbased==1) {
3575: if(mobilav ==0){
3576: for(i=1; i<=nlstate;i++)
3577: prlim[i][i]=probs[(int)age][i][ij];
3578: }else{ /* mobilav */
3579: for(i=1; i<=nlstate;i++)
3580: prlim[i][i]=mobaverage[(int)age][i][ij];
3581: }
3582: }
3583:
3584: /* This for computing probability of death (h=1 means
3585: computed over hstepm (estepm) matrices product = hstepm*stepm months)
3586: as a weighted average of prlim.
3587: */
3588: for(j=nlstate+1;j<=nlstate+ndeath;j++){
3589: for(i=1,gmp[j]=0.;i<= nlstate; i++)
3590: gmp[j] += prlim[i][i]*p3mat[i][j][1];
3591: }
3592: /* end probability of death */
3593:
3594: fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
3595: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
3596: fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
3597: for(i=1; i<=nlstate;i++){
3598: fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
3599: }
3600: }
3601: fprintf(ficresprobmorprev,"\n");
3602:
3603: fprintf(ficresvij,"%.0f ",age );
3604: for(i=1; i<=nlstate;i++)
3605: for(j=1; j<=nlstate;j++){
3606: fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
3607: }
3608: fprintf(ficresvij,"\n");
3609: free_matrix(gp,0,nhstepm,1,nlstate);
3610: free_matrix(gm,0,nhstepm,1,nlstate);
3611: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
3612: free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
3613: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3614: } /* End age */
3615: free_vector(gpp,nlstate+1,nlstate+ndeath);
3616: free_vector(gmp,nlstate+1,nlstate+ndeath);
3617: free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
3618: free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
1.145 brouard 3619: fprintf(ficgp,"\nunset parametric;unset label; set ter png small size 320, 240");
1.126 brouard 3620: /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
1.131 brouard 3621: fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
1.126 brouard 3622: /* fprintf(ficgp,"\n plot \"%s\" u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
3623: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
3624: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
1.145 brouard 3625: fprintf(ficgp,"\n plot \"%s\" u 1:($3) not w l lt 1 ",subdirf(fileresprobmorprev));
3626: fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)) t \"95\%% interval\" w l lt 2 ",subdirf(fileresprobmorprev));
3627: fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)) not w l lt 2 ",subdirf(fileresprobmorprev));
1.126 brouard 3628: fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
3629: 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);
3630: /* 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);
3631: */
3632: /* fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
3633: fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
3634:
3635: free_vector(xp,1,npar);
3636: free_matrix(doldm,1,nlstate,1,nlstate);
3637: free_matrix(dnewm,1,nlstate,1,npar);
3638: free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
3639: free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
3640: free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
3641: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3642: fclose(ficresprobmorprev);
3643: fflush(ficgp);
3644: fflush(fichtm);
3645: } /* end varevsij */
3646:
3647: /************ Variance of prevlim ******************/
3648: 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[])
3649: {
3650: /* Variance of prevalence limit */
3651: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
1.164 brouard 3652:
1.126 brouard 3653: double **dnewm,**doldm;
3654: int i, j, nhstepm, hstepm;
3655: double *xp;
3656: double *gp, *gm;
3657: double **gradg, **trgradg;
3658: double age,agelim;
3659: int theta;
3660:
3661: pstamp(ficresvpl);
3662: fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
3663: fprintf(ficresvpl,"# Age");
3664: for(i=1; i<=nlstate;i++)
3665: fprintf(ficresvpl," %1d-%1d",i,i);
3666: fprintf(ficresvpl,"\n");
3667:
3668: xp=vector(1,npar);
3669: dnewm=matrix(1,nlstate,1,npar);
3670: doldm=matrix(1,nlstate,1,nlstate);
3671:
3672: hstepm=1*YEARM; /* Every year of age */
3673: hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
3674: agelim = AGESUP;
3675: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
3676: nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
3677: if (stepm >= YEARM) hstepm=1;
3678: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
3679: gradg=matrix(1,npar,1,nlstate);
3680: gp=vector(1,nlstate);
3681: gm=vector(1,nlstate);
3682:
3683: for(theta=1; theta <=npar; theta++){
3684: for(i=1; i<=npar; i++){ /* Computes gradient */
3685: xp[i] = x[i] + (i==theta ?delti[theta]:0);
3686: }
3687: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
3688: for(i=1;i<=nlstate;i++)
3689: gp[i] = prlim[i][i];
3690:
3691: for(i=1; i<=npar; i++) /* Computes gradient */
3692: xp[i] = x[i] - (i==theta ?delti[theta]:0);
3693: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
3694: for(i=1;i<=nlstate;i++)
3695: gm[i] = prlim[i][i];
3696:
3697: for(i=1;i<=nlstate;i++)
3698: gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
3699: } /* End theta */
3700:
3701: trgradg =matrix(1,nlstate,1,npar);
3702:
3703: for(j=1; j<=nlstate;j++)
3704: for(theta=1; theta <=npar; theta++)
3705: trgradg[j][theta]=gradg[theta][j];
3706:
3707: for(i=1;i<=nlstate;i++)
3708: varpl[i][(int)age] =0.;
3709: matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
3710: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
3711: for(i=1;i<=nlstate;i++)
3712: varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
3713:
3714: fprintf(ficresvpl,"%.0f ",age );
3715: for(i=1; i<=nlstate;i++)
3716: fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
3717: fprintf(ficresvpl,"\n");
3718: free_vector(gp,1,nlstate);
3719: free_vector(gm,1,nlstate);
3720: free_matrix(gradg,1,npar,1,nlstate);
3721: free_matrix(trgradg,1,nlstate,1,npar);
3722: } /* End age */
3723:
3724: free_vector(xp,1,npar);
3725: free_matrix(doldm,1,nlstate,1,npar);
3726: free_matrix(dnewm,1,nlstate,1,nlstate);
3727:
3728: }
3729:
3730: /************ Variance of one-step probabilities ******************/
3731: 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[])
3732: {
1.164 brouard 3733: int i, j=0, k1, l1, tj;
1.126 brouard 3734: int k2, l2, j1, z1;
1.164 brouard 3735: int k=0, l;
1.145 brouard 3736: int first=1, first1, first2;
1.126 brouard 3737: double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
3738: double **dnewm,**doldm;
3739: double *xp;
3740: double *gp, *gm;
3741: double **gradg, **trgradg;
3742: double **mu;
1.164 brouard 3743: double age, cov[NCOVMAX+1];
1.126 brouard 3744: double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
3745: int theta;
3746: char fileresprob[FILENAMELENGTH];
3747: char fileresprobcov[FILENAMELENGTH];
3748: char fileresprobcor[FILENAMELENGTH];
3749: double ***varpij;
3750:
3751: strcpy(fileresprob,"prob");
3752: strcat(fileresprob,fileres);
3753: if((ficresprob=fopen(fileresprob,"w"))==NULL) {
3754: printf("Problem with resultfile: %s\n", fileresprob);
3755: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
3756: }
3757: strcpy(fileresprobcov,"probcov");
3758: strcat(fileresprobcov,fileres);
3759: if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
3760: printf("Problem with resultfile: %s\n", fileresprobcov);
3761: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
3762: }
3763: strcpy(fileresprobcor,"probcor");
3764: strcat(fileresprobcor,fileres);
3765: if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
3766: printf("Problem with resultfile: %s\n", fileresprobcor);
3767: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
3768: }
3769: printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
3770: fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
3771: printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
3772: fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
3773: printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
3774: fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
3775: pstamp(ficresprob);
3776: fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
3777: fprintf(ficresprob,"# Age");
3778: pstamp(ficresprobcov);
3779: fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
3780: fprintf(ficresprobcov,"# Age");
3781: pstamp(ficresprobcor);
3782: fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
3783: fprintf(ficresprobcor,"# Age");
3784:
3785:
3786: for(i=1; i<=nlstate;i++)
3787: for(j=1; j<=(nlstate+ndeath);j++){
3788: fprintf(ficresprob," p%1d-%1d (SE)",i,j);
3789: fprintf(ficresprobcov," p%1d-%1d ",i,j);
3790: fprintf(ficresprobcor," p%1d-%1d ",i,j);
3791: }
3792: /* fprintf(ficresprob,"\n");
3793: fprintf(ficresprobcov,"\n");
3794: fprintf(ficresprobcor,"\n");
3795: */
1.131 brouard 3796: xp=vector(1,npar);
1.126 brouard 3797: dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
3798: doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
3799: mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
3800: varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
3801: first=1;
3802: fprintf(ficgp,"\n# Routine varprob");
3803: fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
3804: fprintf(fichtm,"\n");
3805:
3806: fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
3807: fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
3808: file %s<br>\n",optionfilehtmcov);
3809: fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
3810: and drawn. It helps understanding how is the covariance between two incidences.\
3811: They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
3812: 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. \
3813: It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
3814: would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
3815: standard deviations wide on each axis. <br>\
3816: Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
3817: and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
3818: To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
3819:
3820: cov[1]=1;
1.145 brouard 3821: /* tj=cptcoveff; */
3822: tj = (int) pow(2,cptcoveff);
1.126 brouard 3823: if (cptcovn<1) {tj=1;ncodemax[1]=1;}
3824: j1=0;
1.145 brouard 3825: for(j1=1; j1<=tj;j1++){
3826: /*for(i1=1; i1<=ncodemax[t];i1++){ */
3827: /*j1++;*/
1.126 brouard 3828: if (cptcovn>0) {
3829: fprintf(ficresprob, "\n#********** Variable ");
3830: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3831: fprintf(ficresprob, "**********\n#\n");
3832: fprintf(ficresprobcov, "\n#********** Variable ");
3833: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3834: fprintf(ficresprobcov, "**********\n#\n");
3835:
3836: fprintf(ficgp, "\n#********** Variable ");
3837: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3838: fprintf(ficgp, "**********\n#\n");
3839:
3840:
3841: fprintf(fichtmcov, "\n<hr size=\"2\" color=\"#EC5E5E\">********** Variable ");
3842: for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3843: fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
3844:
3845: fprintf(ficresprobcor, "\n#********** Variable ");
3846: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3847: fprintf(ficresprobcor, "**********\n#");
3848: }
3849:
1.145 brouard 3850: gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
3851: trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
3852: gp=vector(1,(nlstate)*(nlstate+ndeath));
3853: gm=vector(1,(nlstate)*(nlstate+ndeath));
1.126 brouard 3854: for (age=bage; age<=fage; age ++){
3855: cov[2]=age;
3856: for (k=1; k<=cptcovn;k++) {
1.145 brouard 3857: cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];/* j1 1 2 3 4
3858: * 1 1 1 1 1
3859: * 2 2 1 1 1
3860: * 3 1 2 1 1
3861: */
3862: /* nbcode[1][1]=0 nbcode[1][2]=1;*/
1.126 brouard 3863: }
3864: for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
3865: for (k=1; k<=cptcovprod;k++)
3866: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
3867:
3868:
3869: for(theta=1; theta <=npar; theta++){
3870: for(i=1; i<=npar; i++)
3871: xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
3872:
3873: pmij(pmmij,cov,ncovmodel,xp,nlstate);
3874:
3875: k=0;
3876: for(i=1; i<= (nlstate); i++){
3877: for(j=1; j<=(nlstate+ndeath);j++){
3878: k=k+1;
3879: gp[k]=pmmij[i][j];
3880: }
3881: }
3882:
3883: for(i=1; i<=npar; i++)
3884: xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
3885:
3886: pmij(pmmij,cov,ncovmodel,xp,nlstate);
3887: k=0;
3888: for(i=1; i<=(nlstate); i++){
3889: for(j=1; j<=(nlstate+ndeath);j++){
3890: k=k+1;
3891: gm[k]=pmmij[i][j];
3892: }
3893: }
3894:
3895: for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)
3896: gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];
3897: }
3898:
3899: for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
3900: for(theta=1; theta <=npar; theta++)
3901: trgradg[j][theta]=gradg[theta][j];
3902:
3903: matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);
3904: matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
3905:
3906: pmij(pmmij,cov,ncovmodel,x,nlstate);
3907:
3908: k=0;
3909: for(i=1; i<=(nlstate); i++){
3910: for(j=1; j<=(nlstate+ndeath);j++){
3911: k=k+1;
3912: mu[k][(int) age]=pmmij[i][j];
3913: }
3914: }
3915: for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
3916: for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
3917: varpij[i][j][(int)age] = doldm[i][j];
3918:
3919: /*printf("\n%d ",(int)age);
3920: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
3921: printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
3922: fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
3923: }*/
3924:
3925: fprintf(ficresprob,"\n%d ",(int)age);
3926: fprintf(ficresprobcov,"\n%d ",(int)age);
3927: fprintf(ficresprobcor,"\n%d ",(int)age);
3928:
3929: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
3930: fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
3931: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
3932: fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
3933: fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
3934: }
3935: i=0;
3936: for (k=1; k<=(nlstate);k++){
3937: for (l=1; l<=(nlstate+ndeath);l++){
1.145 brouard 3938: i++;
1.126 brouard 3939: fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
3940: fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
3941: for (j=1; j<=i;j++){
1.145 brouard 3942: /* printf(" k=%d l=%d i=%d j=%d\n",k,l,i,j);fflush(stdout); */
1.126 brouard 3943: fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
3944: fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
3945: }
3946: }
3947: }/* end of loop for state */
3948: } /* end of loop for age */
1.145 brouard 3949: free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
3950: free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
3951: free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
3952: free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
3953:
1.126 brouard 3954: /* Confidence intervalle of pij */
3955: /*
1.131 brouard 3956: fprintf(ficgp,"\nunset parametric;unset label");
1.126 brouard 3957: fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
3958: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
3959: 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);
3960: fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
3961: fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
3962: fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
3963: */
3964:
3965: /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
1.145 brouard 3966: first1=1;first2=2;
1.126 brouard 3967: for (k2=1; k2<=(nlstate);k2++){
3968: for (l2=1; l2<=(nlstate+ndeath);l2++){
3969: if(l2==k2) continue;
3970: j=(k2-1)*(nlstate+ndeath)+l2;
3971: for (k1=1; k1<=(nlstate);k1++){
3972: for (l1=1; l1<=(nlstate+ndeath);l1++){
3973: if(l1==k1) continue;
3974: i=(k1-1)*(nlstate+ndeath)+l1;
3975: if(i<=j) continue;
3976: for (age=bage; age<=fage; age ++){
3977: if ((int)age %5==0){
3978: v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
3979: v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
3980: cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
3981: mu1=mu[i][(int) age]/stepm*YEARM ;
3982: mu2=mu[j][(int) age]/stepm*YEARM;
3983: c12=cv12/sqrt(v1*v2);
3984: /* Computing eigen value of matrix of covariance */
3985: lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
3986: lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
1.135 brouard 3987: if ((lc2 <0) || (lc1 <0) ){
1.145 brouard 3988: if(first2==1){
3989: first1=0;
3990: 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);
3991: }
3992: 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);
3993: /* lc1=fabs(lc1); */ /* If we want to have them positive */
3994: /* lc2=fabs(lc2); */
1.135 brouard 3995: }
3996:
1.126 brouard 3997: /* Eigen vectors */
3998: v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
3999: /*v21=sqrt(1.-v11*v11); *//* error */
4000: v21=(lc1-v1)/cv12*v11;
4001: v12=-v21;
4002: v22=v11;
4003: tnalp=v21/v11;
4004: if(first1==1){
4005: first1=0;
4006: 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);
4007: }
4008: 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);
4009: /*printf(fignu*/
4010: /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
4011: /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
4012: if(first==1){
4013: first=0;
4014: fprintf(ficgp,"\nset parametric;unset label");
4015: fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k1,l1,k2,l2);
1.145 brouard 4016: fprintf(ficgp,"\nset ter png small size 320, 240");
1.126 brouard 4017: fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
4018: :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
4019: %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
4020: subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
4021: subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
4022: fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
4023: fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
4024: fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
4025: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
4026: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
4027: 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",\
4028: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
4029: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
4030: }else{
4031: first=0;
4032: fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
4033: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
4034: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
4035: 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",\
4036: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
4037: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
4038: }/* if first */
4039: } /* age mod 5 */
4040: } /* end loop age */
4041: fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
4042: first=1;
4043: } /*l12 */
4044: } /* k12 */
4045: } /*l1 */
4046: }/* k1 */
1.169 ! brouard 4047: /* } */ /* loop covariates */
1.126 brouard 4048: }
4049: free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
4050: free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
4051: free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
4052: free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
4053: free_vector(xp,1,npar);
4054: fclose(ficresprob);
4055: fclose(ficresprobcov);
4056: fclose(ficresprobcor);
4057: fflush(ficgp);
4058: fflush(fichtmcov);
4059: }
4060:
4061:
4062: /******************* Printing html file ***********/
4063: void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
4064: int lastpass, int stepm, int weightopt, char model[],\
4065: int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
4066: int popforecast, int estepm ,\
4067: double jprev1, double mprev1,double anprev1, \
4068: double jprev2, double mprev2,double anprev2){
4069: int jj1, k1, i1, cpt;
4070:
4071: fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
4072: <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
4073: </ul>");
4074: fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \
4075: - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
4076: jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
4077: fprintf(fichtm,"\
4078: - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
4079: stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
4080: fprintf(fichtm,"\
4081: - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
4082: subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
4083: fprintf(fichtm,"\
1.128 brouard 4084: - (a) Life expectancies by health status at initial age, ei. (b) health expectancies by health status at initial age, eij . If one or more covariates are included, specific tables for each value of the covariate are output in sequences within the same file (estepm=%2d months): \
1.126 brouard 4085: <a href=\"%s\">%s</a> <br>\n",
4086: estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
4087: fprintf(fichtm,"\
4088: - Population projections by age and states: \
4089: <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileres,"f"),subdirf2(fileres,"f"));
4090:
4091: fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
4092:
1.145 brouard 4093: m=pow(2,cptcoveff);
1.126 brouard 4094: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
4095:
4096: jj1=0;
4097: for(k1=1; k1<=m;k1++){
4098: for(i1=1; i1<=ncodemax[k1];i1++){
4099: jj1++;
4100: if (cptcovn > 0) {
4101: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
4102: for (cpt=1; cpt<=cptcoveff;cpt++)
4103: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
4104: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
4105: }
4106: /* Pij */
1.145 brouard 4107: 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> \
4108: <img src=\"%s%d_1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
1.126 brouard 4109: /* Quasi-incidences */
4110: fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
1.145 brouard 4111: 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> \
4112: <img src=\"%s%d_2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
1.126 brouard 4113: /* Period (stable) prevalence in each health state */
1.154 brouard 4114: for(cpt=1; cpt<=nlstate;cpt++){
1.166 brouard 4115: 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> \
4116: <img src=\"%s%d_%d.png\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
1.126 brouard 4117: }
4118: for(cpt=1; cpt<=nlstate;cpt++) {
1.154 brouard 4119: 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> \
4120: <img src=\"%s%d%d.png\">",cpt,nlstate,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
1.126 brouard 4121: }
4122: } /* end i1 */
4123: }/* End k1 */
4124: fprintf(fichtm,"</ul>");
4125:
4126:
4127: fprintf(fichtm,"\
4128: \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
4129: - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);
4130:
4131: fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
4132: subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
4133: fprintf(fichtm,"\
4134: - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
4135: subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
4136:
4137: fprintf(fichtm,"\
4138: - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
4139: subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
4140: fprintf(fichtm,"\
4141: - 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): \
4142: <a href=\"%s\">%s</a> <br>\n</li>",
4143: estepm,subdirf2(fileres,"cve"),subdirf2(fileres,"cve"));
4144: fprintf(fichtm,"\
4145: - (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): \
4146: <a href=\"%s\">%s</a> <br>\n</li>",
4147: estepm,subdirf2(fileres,"stde"),subdirf2(fileres,"stde"));
4148: fprintf(fichtm,"\
1.128 brouard 4149: - Variances and covariances of health expectancies by age. Status (i) based health expectancies (in state j), e<sup>ij</sup> are weighted by the period prevalences in each state i (if popbased=1, an additional computation is done using the cross-sectional prevalences, i.e population based) (estepm=%d months): <a href=\"%s\">%s</a><br>\n",
1.126 brouard 4150: estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
4151: fprintf(fichtm,"\
1.128 brouard 4152: - 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",
4153: estepm, subdirf2(fileres,"t"),subdirf2(fileres,"t"));
1.126 brouard 4154: fprintf(fichtm,"\
4155: - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
4156: subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
4157:
4158: /* if(popforecast==1) fprintf(fichtm,"\n */
4159: /* - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
4160: /* - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
4161: /* <br>",fileres,fileres,fileres,fileres); */
4162: /* else */
4163: /* 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); */
4164: fflush(fichtm);
4165: fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
4166:
1.145 brouard 4167: m=pow(2,cptcoveff);
1.126 brouard 4168: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
4169:
4170: jj1=0;
4171: for(k1=1; k1<=m;k1++){
4172: for(i1=1; i1<=ncodemax[k1];i1++){
4173: jj1++;
4174: if (cptcovn > 0) {
4175: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
4176: for (cpt=1; cpt<=cptcoveff;cpt++)
4177: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
4178: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
4179: }
4180: for(cpt=1; cpt<=nlstate;cpt++) {
4181: fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
1.145 brouard 4182: prevalence (with 95%% confidence interval) in state (%d): %s%d_%d.png <br>\
4183: <img src=\"%s%d_%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);
1.126 brouard 4184: }
4185: fprintf(fichtm,"\n<br>- Total life expectancy by age and \
1.128 brouard 4186: health expectancies in states (1) and (2). If popbased=1 the smooth (due to the model) \
4187: true period expectancies (those weighted with period prevalences are also\
4188: drawn in addition to the population based expectancies computed using\
4189: observed and cahotic prevalences: %s%d.png<br>\
1.126 brouard 4190: <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
4191: } /* end i1 */
4192: }/* End k1 */
4193: fprintf(fichtm,"</ul>");
4194: fflush(fichtm);
4195: }
4196:
4197: /******************* Gnuplot file **************/
4198: void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
4199:
4200: char dirfileres[132],optfileres[132];
1.164 brouard 4201: int cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,ij=0,l=0;
1.130 brouard 4202: int ng=0;
1.126 brouard 4203: /* if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
4204: /* printf("Problem with file %s",optionfilegnuplot); */
4205: /* fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
4206: /* } */
4207:
4208: /*#ifdef windows */
4209: fprintf(ficgp,"cd \"%s\" \n",pathc);
4210: /*#endif */
4211: m=pow(2,cptcoveff);
4212:
4213: strcpy(dirfileres,optionfilefiname);
4214: strcpy(optfileres,"vpl");
4215: /* 1eme*/
1.153 brouard 4216: fprintf(ficgp,"\n# 1st: Period (stable) prevalence with CI: 'vpl' files\n");
1.126 brouard 4217: for (cpt=1; cpt<= nlstate ; cpt ++) {
1.145 brouard 4218: for (k1=1; k1<= m ; k1 ++) { /* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */
4219: fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
4220: fprintf(ficgp,"\n#set out \"v%s%d_%d.png\" \n",optionfilefiname,cpt,k1);
1.126 brouard 4221: fprintf(ficgp,"set xlabel \"Age\" \n\
4222: set ylabel \"Probability\" \n\
1.145 brouard 4223: set ter png small size 320, 240\n\
1.126 brouard 4224: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
4225:
4226: for (i=1; i<= nlstate ; i ++) {
4227: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
1.131 brouard 4228: else fprintf(ficgp," \%%*lf (\%%*lf)");
1.126 brouard 4229: }
1.145 brouard 4230: fprintf(ficgp,"\" t\"Period (stable) prevalence\" w l lt 0,\"%s\" every :::%d::%d u 1:($2+1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
1.126 brouard 4231: for (i=1; i<= nlstate ; i ++) {
4232: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
4233: else fprintf(ficgp," \%%*lf (\%%*lf)");
4234: }
1.145 brouard 4235: fprintf(ficgp,"\" t\"95\%% CI\" w l lt 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
1.126 brouard 4236: for (i=1; i<= nlstate ; i ++) {
4237: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
4238: else fprintf(ficgp," \%%*lf (\%%*lf)");
4239: }
1.145 brouard 4240: fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l lt 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
1.126 brouard 4241: }
4242: }
4243: /*2 eme*/
1.153 brouard 4244: fprintf(ficgp,"\n# 2nd: Total life expectancy with CI: 't' files\n");
1.126 brouard 4245: for (k1=1; k1<= m ; k1 ++) {
4246: fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
1.145 brouard 4247: fprintf(ficgp,"set ylabel \"Years\" \nset ter png small size 320, 240\nplot [%.f:%.f] ",ageminpar,fage);
1.126 brouard 4248:
4249: for (i=1; i<= nlstate+1 ; i ++) {
4250: k=2*i;
4251: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
4252: for (j=1; j<= nlstate+1 ; j ++) {
4253: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
4254: else fprintf(ficgp," \%%*lf (\%%*lf)");
4255: }
4256: if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
4257: else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
4258: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
4259: for (j=1; j<= nlstate+1 ; j ++) {
4260: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
4261: else fprintf(ficgp," \%%*lf (\%%*lf)");
4262: }
1.145 brouard 4263: fprintf(ficgp,"\" t\"\" w l lt 0,");
1.126 brouard 4264: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
4265: for (j=1; j<= nlstate+1 ; j ++) {
4266: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
4267: else fprintf(ficgp," \%%*lf (\%%*lf)");
4268: }
1.145 brouard 4269: if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l lt 0");
4270: else fprintf(ficgp,"\" t\"\" w l lt 0,");
1.126 brouard 4271: }
4272: }
4273:
4274: /*3eme*/
4275:
4276: for (k1=1; k1<= m ; k1 ++) {
4277: for (cpt=1; cpt<= nlstate ; cpt ++) {
4278: /* k=2+nlstate*(2*cpt-2); */
4279: k=2+(nlstate+1)*(cpt-1);
4280: fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
1.145 brouard 4281: fprintf(ficgp,"set ter png small size 320, 240\n\
1.126 brouard 4282: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
4283: /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
4284: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
4285: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
4286: fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
4287: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
4288: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
4289:
4290: */
4291: for (i=1; i< nlstate ; i ++) {
4292: 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);
4293: /* 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);*/
4294:
4295: }
4296: fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+nlstate,cpt);
4297: }
4298: }
4299:
4300: /* CV preval stable (period) */
1.153 brouard 4301: for (k1=1; k1<= m ; k1 ++) { /* For each multivariate if any */
4302: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
1.126 brouard 4303: k=3;
1.153 brouard 4304: fprintf(ficgp,"\n#\n#\n#CV preval stable (period): 'pij' files, cov=%d state=%d",k1, cpt);
1.145 brouard 4305: fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
1.126 brouard 4306: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
1.145 brouard 4307: set ter png small size 320, 240\n\
1.126 brouard 4308: unset log y\n\
1.153 brouard 4309: plot [%.f:%.f] ", ageminpar, agemaxpar);
4310: for (i=1; i<= nlstate ; i ++){
4311: if(i==1)
4312: fprintf(ficgp,"\"%s\"",subdirf2(fileres,"pij"));
4313: else
4314: fprintf(ficgp,", '' ");
1.154 brouard 4315: l=(nlstate+ndeath)*(i-1)+1;
4316: fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
1.153 brouard 4317: for (j=1; j<= (nlstate-1) ; j ++)
4318: fprintf(ficgp,"+$%d",k+l+j);
4319: fprintf(ficgp,")) t \"prev(%d,%d)\" w l",i,cpt);
4320: } /* nlstate */
4321: fprintf(ficgp,"\n");
4322: } /* end cpt state*/
4323: } /* end covariate */
1.126 brouard 4324:
4325: /* proba elementaires */
4326: for(i=1,jk=1; i <=nlstate; i++){
4327: for(k=1; k <=(nlstate+ndeath); k++){
4328: if (k != i) {
4329: for(j=1; j <=ncovmodel; j++){
4330: fprintf(ficgp,"p%d=%f ",jk,p[jk]);
4331: jk++;
4332: fprintf(ficgp,"\n");
4333: }
4334: }
4335: }
4336: }
1.145 brouard 4337: /*goto avoid;*/
1.126 brouard 4338: for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
4339: for(jk=1; jk <=m; jk++) {
1.145 brouard 4340: fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng);
1.126 brouard 4341: if (ng==2)
4342: fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
4343: else
4344: fprintf(ficgp,"\nset title \"Probability\"\n");
1.145 brouard 4345: fprintf(ficgp,"\nset ter png small size 320, 240\nset log y\nplot [%.f:%.f] ",ageminpar,agemaxpar);
1.126 brouard 4346: i=1;
4347: for(k2=1; k2<=nlstate; k2++) {
4348: k3=i;
4349: for(k=1; k<=(nlstate+ndeath); k++) {
4350: if (k != k2){
4351: if(ng==2)
4352: fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
4353: else
4354: fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
1.141 brouard 4355: ij=1;/* To be checked else nbcode[0][0] wrong */
1.126 brouard 4356: for(j=3; j <=ncovmodel; j++) {
1.145 brouard 4357: /* if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) { /\* Bug valgrind *\/ */
4358: /* /\*fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);*\/ */
4359: /* ij++; */
4360: /* } */
4361: /* else */
1.126 brouard 4362: fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
4363: }
4364: fprintf(ficgp,")/(1");
4365:
4366: for(k1=1; k1 <=nlstate; k1++){
4367: fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
4368: ij=1;
4369: for(j=3; j <=ncovmodel; j++){
1.145 brouard 4370: /* if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) { */
4371: /* fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]); */
4372: /* ij++; */
4373: /* } */
4374: /* else */
1.126 brouard 4375: fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
4376: }
4377: fprintf(ficgp,")");
4378: }
4379: fprintf(ficgp,") t \"p%d%d\" ", k2,k);
4380: if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
4381: i=i+ncovmodel;
4382: }
4383: } /* end k */
4384: } /* end k2 */
4385: } /* end jk */
4386: } /* end ng */
1.164 brouard 4387: /* avoid: */
1.126 brouard 4388: fflush(ficgp);
4389: } /* end gnuplot */
4390:
4391:
4392: /*************** Moving average **************/
4393: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
4394:
4395: int i, cpt, cptcod;
4396: int modcovmax =1;
4397: int mobilavrange, mob;
4398: double age;
4399:
4400: modcovmax=2*cptcoveff;/* Max number of modalities. We suppose
4401: a covariate has 2 modalities */
4402: if (cptcovn<1) modcovmax=1; /* At least 1 pass */
4403:
4404: if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
4405: if(mobilav==1) mobilavrange=5; /* default */
4406: else mobilavrange=mobilav;
4407: for (age=bage; age<=fage; age++)
4408: for (i=1; i<=nlstate;i++)
4409: for (cptcod=1;cptcod<=modcovmax;cptcod++)
4410: mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
4411: /* We keep the original values on the extreme ages bage, fage and for
4412: fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
4413: we use a 5 terms etc. until the borders are no more concerned.
4414: */
4415: for (mob=3;mob <=mobilavrange;mob=mob+2){
4416: for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
4417: for (i=1; i<=nlstate;i++){
4418: for (cptcod=1;cptcod<=modcovmax;cptcod++){
4419: mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
4420: for (cpt=1;cpt<=(mob-1)/2;cpt++){
4421: mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
4422: mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
4423: }
4424: mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
4425: }
4426: }
4427: }/* end age */
4428: }/* end mob */
4429: }else return -1;
4430: return 0;
4431: }/* End movingaverage */
4432:
4433:
4434: /************** Forecasting ******************/
1.169 ! brouard 4435: void prevforecast(char fileres[], double anproj1, double mproj1, double jproj1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double anproj2, double p[], int cptcoveff){
1.126 brouard 4436: /* proj1, year, month, day of starting projection
4437: agemin, agemax range of age
4438: dateprev1 dateprev2 range of dates during which prevalence is computed
4439: anproj2 year of en of projection (same day and month as proj1).
4440: */
1.164 brouard 4441: int yearp, stepsize, hstepm, nhstepm, j, k, cptcod, i, h, i1;
1.126 brouard 4442: double agec; /* generic age */
4443: double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
4444: double *popeffectif,*popcount;
4445: double ***p3mat;
4446: double ***mobaverage;
4447: char fileresf[FILENAMELENGTH];
4448:
4449: agelim=AGESUP;
4450: prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
4451:
4452: strcpy(fileresf,"f");
4453: strcat(fileresf,fileres);
4454: if((ficresf=fopen(fileresf,"w"))==NULL) {
4455: printf("Problem with forecast resultfile: %s\n", fileresf);
4456: fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
4457: }
4458: printf("Computing forecasting: result on file '%s' \n", fileresf);
4459: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
4460:
4461: if (cptcoveff==0) ncodemax[cptcoveff]=1;
4462:
4463: if (mobilav!=0) {
4464: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4465: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
4466: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
4467: printf(" Error in movingaverage mobilav=%d\n",mobilav);
4468: }
4469: }
4470:
4471: stepsize=(int) (stepm+YEARM-1)/YEARM;
4472: if (stepm<=12) stepsize=1;
4473: if(estepm < stepm){
4474: printf ("Problem %d lower than %d\n",estepm, stepm);
4475: }
4476: else hstepm=estepm;
4477:
4478: hstepm=hstepm/stepm;
4479: yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp and
4480: fractional in yp1 */
4481: anprojmean=yp;
4482: yp2=modf((yp1*12),&yp);
4483: mprojmean=yp;
4484: yp1=modf((yp2*30.5),&yp);
4485: jprojmean=yp;
4486: if(jprojmean==0) jprojmean=1;
4487: if(mprojmean==0) jprojmean=1;
4488:
4489: i1=cptcoveff;
4490: if (cptcovn < 1){i1=1;}
4491:
4492: fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);
4493:
4494: fprintf(ficresf,"#****** Routine prevforecast **\n");
4495:
4496: /* if (h==(int)(YEARM*yearp)){ */
4497: for(cptcov=1, k=0;cptcov<=i1;cptcov++){
4498: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
4499: k=k+1;
4500: fprintf(ficresf,"\n#******");
4501: for(j=1;j<=cptcoveff;j++) {
4502: 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]]);
4503: }
4504: fprintf(ficresf,"******\n");
4505: fprintf(ficresf,"# Covariate valuofcovar yearproj age");
4506: for(j=1; j<=nlstate+ndeath;j++){
4507: for(i=1; i<=nlstate;i++)
4508: fprintf(ficresf," p%d%d",i,j);
4509: fprintf(ficresf," p.%d",j);
4510: }
4511: for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {
4512: fprintf(ficresf,"\n");
4513: fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);
4514:
4515: for (agec=fage; agec>=(ageminpar-1); agec--){
4516: nhstepm=(int) rint((agelim-agec)*YEARM/stepm);
4517: nhstepm = nhstepm/hstepm;
4518: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4519: oldm=oldms;savm=savms;
4520: hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);
4521:
4522: for (h=0; h<=nhstepm; h++){
4523: if (h*hstepm/YEARM*stepm ==yearp) {
4524: fprintf(ficresf,"\n");
4525: for(j=1;j<=cptcoveff;j++)
4526: fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4527: fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
4528: }
4529: for(j=1; j<=nlstate+ndeath;j++) {
4530: ppij=0.;
4531: for(i=1; i<=nlstate;i++) {
4532: if (mobilav==1)
4533: ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
4534: else {
4535: ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
4536: }
4537: if (h*hstepm/YEARM*stepm== yearp) {
4538: fprintf(ficresf," %.3f", p3mat[i][j][h]);
4539: }
4540: } /* end i */
4541: if (h*hstepm/YEARM*stepm==yearp) {
4542: fprintf(ficresf," %.3f", ppij);
4543: }
4544: }/* end j */
4545: } /* end h */
4546: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4547: } /* end agec */
4548: } /* end yearp */
4549: } /* end cptcod */
4550: } /* end cptcov */
4551:
4552: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4553:
4554: fclose(ficresf);
4555: }
4556:
4557: /************** Forecasting *****not tested NB*************/
1.169 ! brouard 4558: void populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){
1.126 brouard 4559:
4560: int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
4561: int *popage;
4562: double calagedatem, agelim, kk1, kk2;
4563: double *popeffectif,*popcount;
4564: double ***p3mat,***tabpop,***tabpopprev;
4565: double ***mobaverage;
4566: char filerespop[FILENAMELENGTH];
4567:
4568: tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4569: tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4570: agelim=AGESUP;
4571: calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
4572:
4573: prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
4574:
4575:
4576: strcpy(filerespop,"pop");
4577: strcat(filerespop,fileres);
4578: if((ficrespop=fopen(filerespop,"w"))==NULL) {
4579: printf("Problem with forecast resultfile: %s\n", filerespop);
4580: fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
4581: }
4582: printf("Computing forecasting: result on file '%s' \n", filerespop);
4583: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
4584:
4585: if (cptcoveff==0) ncodemax[cptcoveff]=1;
4586:
4587: if (mobilav!=0) {
4588: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4589: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
4590: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
4591: printf(" Error in movingaverage mobilav=%d\n",mobilav);
4592: }
4593: }
4594:
4595: stepsize=(int) (stepm+YEARM-1)/YEARM;
4596: if (stepm<=12) stepsize=1;
4597:
4598: agelim=AGESUP;
4599:
4600: hstepm=1;
4601: hstepm=hstepm/stepm;
4602:
4603: if (popforecast==1) {
4604: if((ficpop=fopen(popfile,"r"))==NULL) {
4605: printf("Problem with population file : %s\n",popfile);exit(0);
4606: fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
4607: }
4608: popage=ivector(0,AGESUP);
4609: popeffectif=vector(0,AGESUP);
4610: popcount=vector(0,AGESUP);
4611:
4612: i=1;
4613: while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
4614:
4615: imx=i;
4616: for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
4617: }
4618:
4619: for(cptcov=1,k=0;cptcov<=i2;cptcov++){
4620: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
4621: k=k+1;
4622: fprintf(ficrespop,"\n#******");
4623: for(j=1;j<=cptcoveff;j++) {
4624: fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4625: }
4626: fprintf(ficrespop,"******\n");
4627: fprintf(ficrespop,"# Age");
4628: for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
4629: if (popforecast==1) fprintf(ficrespop," [Population]");
4630:
4631: for (cpt=0; cpt<=0;cpt++) {
4632: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
4633:
4634: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
4635: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
4636: nhstepm = nhstepm/hstepm;
4637:
4638: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4639: oldm=oldms;savm=savms;
4640: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
4641:
4642: for (h=0; h<=nhstepm; h++){
4643: if (h==(int) (calagedatem+YEARM*cpt)) {
4644: fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
4645: }
4646: for(j=1; j<=nlstate+ndeath;j++) {
4647: kk1=0.;kk2=0;
4648: for(i=1; i<=nlstate;i++) {
4649: if (mobilav==1)
4650: kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
4651: else {
4652: kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
4653: }
4654: }
4655: if (h==(int)(calagedatem+12*cpt)){
4656: tabpop[(int)(agedeb)][j][cptcod]=kk1;
4657: /*fprintf(ficrespop," %.3f", kk1);
4658: if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
4659: }
4660: }
4661: for(i=1; i<=nlstate;i++){
4662: kk1=0.;
4663: for(j=1; j<=nlstate;j++){
4664: kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];
4665: }
4666: tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
4667: }
4668:
4669: if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++)
4670: fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
4671: }
4672: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4673: }
4674: }
4675:
4676: /******/
4677:
4678: for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {
4679: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
4680: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
4681: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
4682: nhstepm = nhstepm/hstepm;
4683:
4684: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4685: oldm=oldms;savm=savms;
4686: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
4687: for (h=0; h<=nhstepm; h++){
4688: if (h==(int) (calagedatem+YEARM*cpt)) {
4689: fprintf(ficresf,"\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: kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];
4695: }
4696: if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);
4697: }
4698: }
4699: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4700: }
4701: }
4702: }
4703: }
4704:
4705: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4706:
4707: if (popforecast==1) {
4708: free_ivector(popage,0,AGESUP);
4709: free_vector(popeffectif,0,AGESUP);
4710: free_vector(popcount,0,AGESUP);
4711: }
4712: free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4713: free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4714: fclose(ficrespop);
4715: } /* End of popforecast */
4716:
4717: int fileappend(FILE *fichier, char *optionfich)
4718: {
4719: if((fichier=fopen(optionfich,"a"))==NULL) {
4720: printf("Problem with file: %s\n", optionfich);
4721: fprintf(ficlog,"Problem with file: %s\n", optionfich);
4722: return (0);
4723: }
4724: fflush(fichier);
4725: return (1);
4726: }
4727:
4728:
4729: /**************** function prwizard **********************/
4730: void prwizard(int ncovmodel, int nlstate, int ndeath, char model[], FILE *ficparo)
4731: {
4732:
4733: /* Wizard to print covariance matrix template */
4734:
1.164 brouard 4735: char ca[32], cb[32];
4736: int i,j, k, li, lj, lk, ll, jj, npar, itimes;
1.126 brouard 4737: int numlinepar;
4738:
4739: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
4740: fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
4741: for(i=1; i <=nlstate; i++){
4742: jj=0;
4743: for(j=1; j <=nlstate+ndeath; j++){
4744: if(j==i) continue;
4745: jj++;
4746: /*ca[0]= k+'a'-1;ca[1]='\0';*/
4747: printf("%1d%1d",i,j);
4748: fprintf(ficparo,"%1d%1d",i,j);
4749: for(k=1; k<=ncovmodel;k++){
4750: /* printf(" %lf",param[i][j][k]); */
4751: /* fprintf(ficparo," %lf",param[i][j][k]); */
4752: printf(" 0.");
4753: fprintf(ficparo," 0.");
4754: }
4755: printf("\n");
4756: fprintf(ficparo,"\n");
4757: }
4758: }
4759: printf("# Scales (for hessian or gradient estimation)\n");
4760: fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
4761: npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
4762: for(i=1; i <=nlstate; i++){
4763: jj=0;
4764: for(j=1; j <=nlstate+ndeath; j++){
4765: if(j==i) continue;
4766: jj++;
4767: fprintf(ficparo,"%1d%1d",i,j);
4768: printf("%1d%1d",i,j);
4769: fflush(stdout);
4770: for(k=1; k<=ncovmodel;k++){
4771: /* printf(" %le",delti3[i][j][k]); */
4772: /* fprintf(ficparo," %le",delti3[i][j][k]); */
4773: printf(" 0.");
4774: fprintf(ficparo," 0.");
4775: }
4776: numlinepar++;
4777: printf("\n");
4778: fprintf(ficparo,"\n");
4779: }
4780: }
4781: printf("# Covariance matrix\n");
4782: /* # 121 Var(a12)\n\ */
4783: /* # 122 Cov(b12,a12) Var(b12)\n\ */
4784: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
4785: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
4786: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
4787: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
4788: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
4789: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
4790: fflush(stdout);
4791: fprintf(ficparo,"# Covariance matrix\n");
4792: /* # 121 Var(a12)\n\ */
4793: /* # 122 Cov(b12,a12) Var(b12)\n\ */
4794: /* # ...\n\ */
4795: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
4796:
4797: for(itimes=1;itimes<=2;itimes++){
4798: jj=0;
4799: for(i=1; i <=nlstate; i++){
4800: for(j=1; j <=nlstate+ndeath; j++){
4801: if(j==i) continue;
4802: for(k=1; k<=ncovmodel;k++){
4803: jj++;
4804: ca[0]= k+'a'-1;ca[1]='\0';
4805: if(itimes==1){
4806: printf("#%1d%1d%d",i,j,k);
4807: fprintf(ficparo,"#%1d%1d%d",i,j,k);
4808: }else{
4809: printf("%1d%1d%d",i,j,k);
4810: fprintf(ficparo,"%1d%1d%d",i,j,k);
4811: /* printf(" %.5le",matcov[i][j]); */
4812: }
4813: ll=0;
4814: for(li=1;li <=nlstate; li++){
4815: for(lj=1;lj <=nlstate+ndeath; lj++){
4816: if(lj==li) continue;
4817: for(lk=1;lk<=ncovmodel;lk++){
4818: ll++;
4819: if(ll<=jj){
4820: cb[0]= lk +'a'-1;cb[1]='\0';
4821: if(ll<jj){
4822: if(itimes==1){
4823: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
4824: fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
4825: }else{
4826: printf(" 0.");
4827: fprintf(ficparo," 0.");
4828: }
4829: }else{
4830: if(itimes==1){
4831: printf(" Var(%s%1d%1d)",ca,i,j);
4832: fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
4833: }else{
4834: printf(" 0.");
4835: fprintf(ficparo," 0.");
4836: }
4837: }
4838: }
4839: } /* end lk */
4840: } /* end lj */
4841: } /* end li */
4842: printf("\n");
4843: fprintf(ficparo,"\n");
4844: numlinepar++;
4845: } /* end k*/
4846: } /*end j */
4847: } /* end i */
4848: } /* end itimes */
4849:
4850: } /* end of prwizard */
4851: /******************* Gompertz Likelihood ******************************/
4852: double gompertz(double x[])
4853: {
4854: double A,B,L=0.0,sump=0.,num=0.;
4855: int i,n=0; /* n is the size of the sample */
4856:
4857: for (i=0;i<=imx-1 ; i++) {
4858: sump=sump+weight[i];
4859: /* sump=sump+1;*/
4860: num=num+1;
4861: }
4862:
4863:
4864: /* for (i=0; i<=imx; i++)
4865: 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]);*/
4866:
4867: for (i=1;i<=imx ; i++)
4868: {
4869: if (cens[i] == 1 && wav[i]>1)
4870: A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
4871:
4872: if (cens[i] == 0 && wav[i]>1)
4873: A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
4874: +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);
4875:
4876: /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
4877: if (wav[i] > 1 ) { /* ??? */
4878: L=L+A*weight[i];
4879: /* 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]);*/
4880: }
4881: }
4882:
4883: /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
4884:
4885: return -2*L*num/sump;
4886: }
4887:
1.136 brouard 4888: #ifdef GSL
4889: /******************* Gompertz_f Likelihood ******************************/
4890: double gompertz_f(const gsl_vector *v, void *params)
4891: {
4892: double A,B,LL=0.0,sump=0.,num=0.;
4893: double *x= (double *) v->data;
4894: int i,n=0; /* n is the size of the sample */
4895:
4896: for (i=0;i<=imx-1 ; i++) {
4897: sump=sump+weight[i];
4898: /* sump=sump+1;*/
4899: num=num+1;
4900: }
4901:
4902:
4903: /* for (i=0; i<=imx; i++)
4904: 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]);*/
4905: printf("x[0]=%lf x[1]=%lf\n",x[0],x[1]);
4906: for (i=1;i<=imx ; i++)
4907: {
4908: if (cens[i] == 1 && wav[i]>1)
4909: A=-x[0]/(x[1])*(exp(x[1]*(agecens[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)));
4910:
4911: if (cens[i] == 0 && wav[i]>1)
4912: A=-x[0]/(x[1])*(exp(x[1]*(agedc[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)))
4913: +log(x[0]/YEARM)+x[1]*(agedc[i]-agegomp)+log(YEARM);
4914:
4915: /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
4916: if (wav[i] > 1 ) { /* ??? */
4917: LL=LL+A*weight[i];
4918: /* 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]);*/
4919: }
4920: }
4921:
4922: /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
4923: printf("x[0]=%lf x[1]=%lf -2*LL*num/sump=%lf\n",x[0],x[1],-2*LL*num/sump);
4924:
4925: return -2*LL*num/sump;
4926: }
4927: #endif
4928:
1.126 brouard 4929: /******************* Printing html file ***********/
4930: void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \
4931: int lastpass, int stepm, int weightopt, char model[],\
4932: int imx, double p[],double **matcov,double agemortsup){
4933: int i,k;
4934:
4935: fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
4936: fprintf(fichtm," mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
4937: for (i=1;i<=2;i++)
4938: 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]));
4939: fprintf(fichtm,"<br><br><img src=\"graphmort.png\">");
4940: fprintf(fichtm,"</ul>");
4941:
4942: fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
4943:
4944: 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>");
4945:
4946: for (k=agegomp;k<(agemortsup-2);k++)
4947: 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]);
4948:
4949:
4950: fflush(fichtm);
4951: }
4952:
4953: /******************* Gnuplot file **************/
4954: void printinggnuplotmort(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
4955:
4956: char dirfileres[132],optfileres[132];
1.164 brouard 4957:
1.126 brouard 4958: int ng;
4959:
4960:
4961: /*#ifdef windows */
4962: fprintf(ficgp,"cd \"%s\" \n",pathc);
4963: /*#endif */
4964:
4965:
4966: strcpy(dirfileres,optionfilefiname);
4967: strcpy(optfileres,"vpl");
4968: fprintf(ficgp,"set out \"graphmort.png\"\n ");
4969: fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n ");
1.145 brouard 4970: fprintf(ficgp, "set ter png small size 320, 240\n set log y\n");
4971: /* fprintf(ficgp, "set size 0.65,0.65\n"); */
1.126 brouard 4972: fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
4973:
4974: }
4975:
1.136 brouard 4976: int readdata(char datafile[], int firstobs, int lastobs, int *imax)
4977: {
1.126 brouard 4978:
1.136 brouard 4979: /*-------- data file ----------*/
4980: FILE *fic;
4981: char dummy[]=" ";
1.164 brouard 4982: int i=0, j=0, n=0;
1.136 brouard 4983: int linei, month, year,iout;
4984: char line[MAXLINE], linetmp[MAXLINE];
1.164 brouard 4985: char stra[MAXLINE], strb[MAXLINE];
1.136 brouard 4986: char *stratrunc;
4987: int lstra;
1.126 brouard 4988:
4989:
1.136 brouard 4990: if((fic=fopen(datafile,"r"))==NULL) {
4991: printf("Problem while opening datafile: %s\n", datafile);return 1;
4992: fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);return 1;
4993: }
1.126 brouard 4994:
1.136 brouard 4995: i=1;
4996: linei=0;
4997: while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
4998: linei=linei+1;
4999: for(j=strlen(line); j>=0;j--){ /* Untabifies line */
5000: if(line[j] == '\t')
5001: line[j] = ' ';
5002: }
5003: for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){
5004: ;
5005: };
5006: line[j+1]=0; /* Trims blanks at end of line */
5007: if(line[0]=='#'){
5008: fprintf(ficlog,"Comment line\n%s\n",line);
5009: printf("Comment line\n%s\n",line);
5010: continue;
5011: }
5012: trimbb(linetmp,line); /* Trims multiple blanks in line */
1.164 brouard 5013: strcpy(line, linetmp);
1.136 brouard 5014:
1.126 brouard 5015:
1.136 brouard 5016: for (j=maxwav;j>=1;j--){
1.137 brouard 5017: cutv(stra, strb, line, ' ');
1.136 brouard 5018: if(strb[0]=='.') { /* Missing status */
5019: lval=-1;
5020: }else{
5021: errno=0;
5022: lval=strtol(strb,&endptr,10);
5023: /* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
5024: if( strb[0]=='\0' || (*endptr != '\0')){
1.141 brouard 5025: 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);
5026: fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong. Exiting.\n", strb, linei,i,line,j,maxwav);fflush(ficlog);
1.136 brouard 5027: return 1;
5028: }
5029: }
5030: s[j][i]=lval;
5031:
5032: strcpy(line,stra);
5033: cutv(stra, strb,line,' ');
1.169 ! brouard 5034: if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
1.136 brouard 5035: }
1.169 ! brouard 5036: else if( (iout=sscanf(strb,"%s.",dummy)) != 0){
1.136 brouard 5037: month=99;
5038: year=9999;
5039: }else{
1.141 brouard 5040: 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);
5041: fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of interview (mm/yyyy or .) at wave %d. Exiting.\n",strb, linei,i, line,j);fflush(ficlog);
1.136 brouard 5042: return 1;
5043: }
5044: anint[j][i]= (double) year;
5045: mint[j][i]= (double)month;
5046: strcpy(line,stra);
5047: } /* ENd Waves */
5048:
5049: cutv(stra, strb,line,' ');
1.169 ! brouard 5050: if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
1.136 brouard 5051: }
1.169 ! brouard 5052: else if( (iout=sscanf(strb,"%s.",dummy)) != 0){
1.136 brouard 5053: month=99;
5054: year=9999;
5055: }else{
1.141 brouard 5056: 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);
5057: fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of death (mm/yyyy or .). Exiting.\n",strb, linei,i,line);fflush(ficlog);
1.136 brouard 5058: return 1;
5059: }
5060: andc[i]=(double) year;
5061: moisdc[i]=(double) month;
5062: strcpy(line,stra);
5063:
5064: cutv(stra, strb,line,' ');
1.169 ! brouard 5065: if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
1.136 brouard 5066: }
1.169 ! brouard 5067: else if( (iout=sscanf(strb,"%s.", dummy)) != 0){
1.136 brouard 5068: month=99;
5069: year=9999;
5070: }else{
1.141 brouard 5071: 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);
5072: fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .). Exiting.\n",strb, linei,i,line);fflush(ficlog);
1.136 brouard 5073: return 1;
5074: }
5075: if (year==9999) {
1.141 brouard 5076: 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);
5077: fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy) but at least the year of birth should be given. Exiting.\n",strb, linei,i,line);fflush(ficlog);
1.136 brouard 5078: return 1;
1.126 brouard 5079:
1.136 brouard 5080: }
5081: annais[i]=(double)(year);
5082: moisnais[i]=(double)(month);
5083: strcpy(line,stra);
5084:
5085: cutv(stra, strb,line,' ');
5086: errno=0;
5087: dval=strtod(strb,&endptr);
5088: if( strb[0]=='\0' || (*endptr != '\0')){
1.141 brouard 5089: printf("Error reading data around '%f' at line number %d, \"%s\" for individual %d\nShould be a weight. Exiting.\n",dval, i,line,linei);
5090: fprintf(ficlog,"Error reading data around '%f' at line number %d, \"%s\" for individual %d\nShould be a weight. Exiting.\n",dval, i,line,linei);
1.136 brouard 5091: fflush(ficlog);
5092: return 1;
5093: }
5094: weight[i]=dval;
5095: strcpy(line,stra);
5096:
5097: for (j=ncovcol;j>=1;j--){
5098: cutv(stra, strb,line,' ');
5099: if(strb[0]=='.') { /* Missing status */
5100: lval=-1;
5101: }else{
5102: errno=0;
5103: lval=strtol(strb,&endptr,10);
5104: if( strb[0]=='\0' || (*endptr != '\0')){
1.141 brouard 5105: 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);
5106: fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\nShould be a covariate value (=0 for the reference or 1 for alternative). Exiting.\n",lval, linei,i, line);fflush(ficlog);
1.136 brouard 5107: return 1;
5108: }
5109: }
5110: if(lval <-1 || lval >1){
1.141 brouard 5111: printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
1.136 brouard 5112: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
5113: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
5114: For example, for multinomial values like 1, 2 and 3,\n \
5115: build V1=0 V2=0 for the reference value (1),\n \
5116: V1=1 V2=0 for (2) \n \
5117: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
5118: output of IMaCh is often meaningless.\n \
5119: Exiting.\n",lval,linei, i,line,j);
1.141 brouard 5120: fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
1.136 brouard 5121: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
5122: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
5123: For example, for multinomial values like 1, 2 and 3,\n \
5124: build V1=0 V2=0 for the reference value (1),\n \
5125: V1=1 V2=0 for (2) \n \
5126: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
5127: output of IMaCh is often meaningless.\n \
5128: Exiting.\n",lval,linei, i,line,j);fflush(ficlog);
5129: return 1;
5130: }
5131: covar[j][i]=(double)(lval);
5132: strcpy(line,stra);
5133: }
5134: lstra=strlen(stra);
5135:
5136: if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
5137: stratrunc = &(stra[lstra-9]);
5138: num[i]=atol(stratrunc);
5139: }
5140: else
5141: num[i]=atol(stra);
5142: /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
5143: 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;}*/
5144:
5145: i=i+1;
5146: } /* End loop reading data */
1.126 brouard 5147:
1.136 brouard 5148: *imax=i-1; /* Number of individuals */
5149: fclose(fic);
5150:
5151: return (0);
1.164 brouard 5152: /* endread: */
1.136 brouard 5153: printf("Exiting readdata: ");
5154: fclose(fic);
5155: return (1);
1.126 brouard 5156:
5157:
5158:
1.136 brouard 5159: }
1.145 brouard 5160: void removespace(char *str) {
5161: char *p1 = str, *p2 = str;
5162: do
5163: while (*p2 == ' ')
5164: p2++;
1.169 ! brouard 5165: while (*p1++ == *p2++);
1.145 brouard 5166: }
5167:
5168: int decodemodel ( char model[], int lastobs) /**< This routine decode the model and returns:
5169: * Model V1+V2+V3+V8+V7*V8+V5*V6+V8*age+V3*age
5170: * - cptcovt total number of covariates of the model nbocc(+)+1 = 8
5171: * - cptcovn or number of covariates k of the models excluding age*products =6
5172: * - cptcovage number of covariates with age*products =2
5173: * - cptcovs number of simple covariates
5174: * - 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
5175: * which is a new column after the 9 (ncovcol) variables.
5176: * - if k is a product Vn*Vm covar[k][i] is filled with correct values for each individual
5177: * - Tprod[l] gives the kth covariates of the product Vn*Vm l=1 to cptcovprod-cptcovage
5178: * Tprod[1]@2 {5, 6}: position of first product V7*V8 is 5, and second V5*V6 is 6.
5179: * - Tvard[k] p Tvard[1][1]@4 {7, 8, 5, 6} for V7*V8 and V5*V6 .
5180: */
1.136 brouard 5181: {
1.145 brouard 5182: int i, j, k, ks;
1.164 brouard 5183: int j1, k1, k2;
1.136 brouard 5184: char modelsav[80];
1.145 brouard 5185: char stra[80], strb[80], strc[80], strd[80],stre[80];
1.136 brouard 5186:
1.145 brouard 5187: /*removespace(model);*/
1.136 brouard 5188: if (strlen(model) >1){ /* If there is at least 1 covariate */
1.145 brouard 5189: j=0, j1=0, k1=0, k2=-1, ks=0, cptcovn=0;
5190: j=nbocc(model,'+'); /**< j=Number of '+' */
5191: j1=nbocc(model,'*'); /**< j1=Number of '*' */
5192: cptcovs=j+1-j1; /**< Number of simple covariates V1+V2*age+V3 +V3*V4=> V1 + V3 =2 */
5193: cptcovt= j+1; /* Number of total covariates in the model V1 + V2*age+ V3 + V3*V4=> 4*/
5194: /* including age products which are counted in cptcovage.
1.169 ! brouard 5195: * but the covariates which are products must be treated separately: ncovn=4- 2=2 (V1+V3). */
1.145 brouard 5196: cptcovprod=j1; /**< Number of products V1*V2 +v3*age = 2 */
5197: cptcovprodnoage=0; /**< Number of covariate products without age: V3*V4 =1 */
1.136 brouard 5198: strcpy(modelsav,model);
1.137 brouard 5199: if (strstr(model,"AGE") !=0){
5200: printf("Error. AGE must be in lower case 'age' model=%s ",model);
5201: fprintf(ficlog,"Error. AGE must be in lower case model=%s ",model);fflush(ficlog);
1.136 brouard 5202: return 1;
5203: }
1.141 brouard 5204: if (strstr(model,"v") !=0){
5205: printf("Error. 'v' must be in upper case 'V' model=%s ",model);
5206: fprintf(ficlog,"Error. 'v' must be in upper case model=%s ",model);fflush(ficlog);
5207: return 1;
5208: }
1.136 brouard 5209:
1.145 brouard 5210: /* Design
5211: * V1 V2 V3 V4 V5 V6 V7 V8 V9 Weight
5212: * < ncovcol=8 >
5213: * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8
5214: * k= 1 2 3 4 5 6 7 8
5215: * cptcovn number of covariates (not including constant and age ) = # of + plus 1 = 7+1=8
5216: * covar[k,i], value of kth covariate if not including age for individual i:
5217: * covar[1][i]= (V2), covar[4][i]=(V3), covar[8][i]=(V8)
5218: * Tvar[k] # of the kth covariate: Tvar[1]=2 Tvar[4]=3 Tvar[8]=8
5219: * if multiplied by age: V3*age Tvar[3=V3*age]=3 (V3) Tvar[7]=8 and
5220: * Tage[++cptcovage]=k
5221: * if products, new covar are created after ncovcol with k1
5222: * Tvar[k]=ncovcol+k1; # of the kth covariate product: Tvar[5]=ncovcol+1=10 Tvar[6]=ncovcol+1=11
5223: * Tprod[k1]=k; Tprod[1]=5 Tprod[2]= 6; gives the position of the k1th product
5224: * 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
5225: * Tvar[cptcovn+k2]=Tvard[k1][1];Tvar[cptcovn+k2+1]=Tvard[k1][2];
5226: * Tvar[8+1]=5;Tvar[8+2]=6;Tvar[8+3]=7;Tvar[8+4]=8 inverted
5227: * V1 V2 V3 V4 V5 V6 V7 V8 V9 V10 V11
5228: * < ncovcol=8 >
5229: * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8 d1 d1 d2 d2
5230: * k= 1 2 3 4 5 6 7 8 9 10 11 12
5231: * Tvar[k]= 2 1 3 3 10 11 8 8 5 6 7 8
5232: * p Tvar[1]@12={2, 1, 3, 3, 11, 10, 8, 8, 7, 8, 5, 6}
5233: * p Tprod[1]@2={ 6, 5}
5234: *p Tvard[1][1]@4= {7, 8, 5, 6}
5235: * covar[k][i]= V2 V1 ? V3 V5*V6? V7*V8? ? V8
5236: * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
5237: *How to reorganize?
5238: * Model V1 + V2 + V3 + V8 + V5*V6 + V7*V8 + V3*age + V8*age
5239: * Tvars {2, 1, 3, 3, 11, 10, 8, 8, 7, 8, 5, 6}
5240: * {2, 1, 4, 8, 5, 6, 3, 7}
5241: * Struct []
5242: */
5243:
1.136 brouard 5244: /* This loop fills the array Tvar from the string 'model'.*/
5245: /* j is the number of + signs in the model V1+V2+V3 j=2 i=3 to 1 */
1.137 brouard 5246: /* modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4 */
5247: /* k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tage[cptcovage=1]=4 */
5248: /* k=3 V4 Tvar[k=3]= 4 (from V4) */
5249: /* k=2 V1 Tvar[k=2]= 1 (from V1) */
5250: /* k=1 Tvar[1]=2 (from V2) */
5251: /* k=5 Tvar[5] */
5252: /* for (k=1; k<=cptcovn;k++) { */
5253: /* cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]]; */
5254: /* } */
5255: /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
1.145 brouard 5256: /*
5257: * Treating invertedly V2+V1+V3*age+V2*V4 is as if written V2*V4 +V3*age + V1 + V2 */
5258: for(k=cptcovt; k>=1;k--) /**< Number of covariates */
5259: Tvar[k]=0;
5260: cptcovage=0;
5261: for(k=1; k<=cptcovt;k++){ /* Loop on total covariates of the model */
5262: cutl(stra,strb,modelsav,'+'); /* keeps in strb after the first '+'
5263: modelsav==V2+V1+V4+V3*age strb=V3*age stra=V2+V1+V4 */
1.137 brouard 5264: if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
1.136 brouard 5265: /* printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
5266: /*scanf("%d",i);*/
1.145 brouard 5267: if (strchr(strb,'*')) { /**< Model includes a product V2+V1+V4+V3*age strb=V3*age */
5268: cutl(strc,strd,strb,'*'); /**< strd*strc Vm*Vn: strb=V3*age(input) strc=age strd=V3 ; V3*V2 strc=V2, strd=V3 */
5269: if (strcmp(strc,"age")==0) { /**< Model includes age: Vn*age */
5270: /* covar is not filled and then is empty */
1.136 brouard 5271: cptcovprod--;
1.145 brouard 5272: cutl(stre,strb,strd,'V'); /* strd=V3(input): stre="3" */
5273: Tvar[k]=atoi(stre); /* V2+V1+V4+V3*age Tvar[4]=3 ; V1+V2*age Tvar[2]=2 */
1.136 brouard 5274: cptcovage++; /* Sums the number of covariates which include age as a product */
1.137 brouard 5275: Tage[cptcovage]=k; /* Tage[1] = 4 */
1.136 brouard 5276: /*printf("stre=%s ", stre);*/
1.137 brouard 5277: } else if (strcmp(strd,"age")==0) { /* or age*Vn */
1.136 brouard 5278: cptcovprod--;
1.145 brouard 5279: cutl(stre,strb,strc,'V');
1.136 brouard 5280: Tvar[k]=atoi(stre);
5281: cptcovage++;
5282: Tage[cptcovage]=k;
1.137 brouard 5283: } else { /* Age is not in the model product V2+V1+V1*V4+V3*age+V3*V2 strb=V3*V2*/
5284: /* loops on k1=1 (V3*V2) and k1=2 V4*V3 */
1.145 brouard 5285: cptcovn++;
5286: cptcovprodnoage++;k1++;
5287: cutl(stre,strb,strc,'V'); /* strc= Vn, stre is n; strb=V3*V2 stre=3 strc=*/
5288: Tvar[k]=ncovcol+k1; /* For model-covariate k tells which data-covariate to use but
1.137 brouard 5289: because this model-covariate is a construction we invent a new column
5290: ncovcol + k1
5291: If already ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2
5292: Tvar[3=V1*V4]=4+1 Tvar[5=V3*V2]=4 + 2= 6, etc */
1.145 brouard 5293: cutl(strc,strb,strd,'V'); /* strd was Vm, strc is m */
1.137 brouard 5294: Tprod[k1]=k; /* Tprod[1]=3(=V1*V4) for V2+V1+V1*V4+age*V3+V3*V2 */
1.145 brouard 5295: Tvard[k1][1] =atoi(strc); /* m 1 for V1*/
5296: Tvard[k1][2] =atoi(stre); /* n 4 for V4*/
5297: k2=k2+2;
5298: Tvar[cptcovt+k2]=Tvard[k1][1]; /* Tvar[(cptcovt=4+k2=1)=5]= 1 (V1) */
5299: Tvar[cptcovt+k2+1]=Tvard[k1][2]; /* Tvar[(cptcovt=4+(k2=1)+1)=6]= 4 (V4) */
1.137 brouard 5300: for (i=1; i<=lastobs;i++){
5301: /* Computes the new covariate which is a product of
1.145 brouard 5302: covar[n][i]* covar[m][i] and stores it at ncovol+k1 May not be defined */
1.136 brouard 5303: covar[ncovcol+k1][i]=covar[atoi(stre)][i]*covar[atoi(strc)][i];
1.137 brouard 5304: }
5305: } /* End age is not in the model */
5306: } /* End if model includes a product */
1.136 brouard 5307: else { /* no more sum */
5308: /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
5309: /* scanf("%d",i);*/
1.145 brouard 5310: cutl(strd,strc,strb,'V');
5311: ks++; /**< Number of simple covariates */
5312: cptcovn++;
5313: Tvar[k]=atoi(strd);
1.136 brouard 5314: }
1.137 brouard 5315: strcpy(modelsav,stra); /* modelsav=V2+V1+V4 stra=V2+V1+V4 */
1.136 brouard 5316: /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
5317: scanf("%d",i);*/
5318: } /* end of loop + */
5319: } /* end model */
5320:
5321: /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
5322: If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
5323:
5324: /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
5325: printf("cptcovprod=%d ", cptcovprod);
5326: fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
5327:
5328: scanf("%d ",i);*/
5329:
5330:
1.137 brouard 5331: return (0); /* with covar[new additional covariate if product] and Tage if age */
1.164 brouard 5332: /*endread:*/
1.136 brouard 5333: printf("Exiting decodemodel: ");
5334: return (1);
5335: }
5336:
1.169 ! brouard 5337: int calandcheckages(int imx, int maxwav, double *agemin, double *agemax, int *nberr, int *nbwarn )
1.136 brouard 5338: {
5339: int i, m;
5340:
5341: for (i=1; i<=imx; i++) {
5342: for(m=2; (m<= maxwav); m++) {
5343: if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
5344: anint[m][i]=9999;
5345: s[m][i]=-1;
5346: }
5347: if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
1.169 ! brouard 5348: *nberr = *nberr + 1;
! 5349: 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);
! 5350: fprintf(ficlog,"Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased (%d)\n",(int)moisdc[i],(int)andc[i],num[i],i, *nberr);
1.136 brouard 5351: s[m][i]=-1;
5352: }
5353: if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
1.169 ! brouard 5354: (*nberr)++;
1.136 brouard 5355: 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]);
5356: 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]);
5357: s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
5358: }
5359: }
5360: }
5361:
5362: for (i=1; i<=imx; i++) {
5363: agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
5364: for(m=firstpass; (m<= lastpass); m++){
5365: if(s[m][i] >0 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){
5366: if (s[m][i] >= nlstate+1) {
1.169 ! brouard 5367: if(agedc[i]>0){
! 5368: if((int)moisdc[i]!=99 && (int)andc[i]!=9999){
1.136 brouard 5369: agev[m][i]=agedc[i];
5370: /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
1.169 ! brouard 5371: }else {
1.136 brouard 5372: if ((int)andc[i]!=9999){
5373: nbwarn++;
5374: printf("Warning negative age at death: %ld line:%d\n",num[i],i);
5375: fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
5376: agev[m][i]=-1;
5377: }
5378: }
1.169 ! brouard 5379: } /* agedc > 0 */
1.136 brouard 5380: }
5381: else if(s[m][i] !=9){ /* Standard case, age in fractional
5382: years but with the precision of a month */
5383: agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
5384: if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
5385: agev[m][i]=1;
5386: else if(agev[m][i] < *agemin){
5387: *agemin=agev[m][i];
5388: printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], *agemin);
5389: }
5390: else if(agev[m][i] >*agemax){
5391: *agemax=agev[m][i];
1.156 brouard 5392: /* printf(" Max anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.2f\n",m,i,anint[m][i], i,annais[i], *agemax);*/
1.136 brouard 5393: }
5394: /*agev[m][i]=anint[m][i]-annais[i];*/
5395: /* agev[m][i] = age[i]+2*m;*/
5396: }
5397: else { /* =9 */
5398: agev[m][i]=1;
5399: s[m][i]=-1;
5400: }
5401: }
5402: else /*= 0 Unknown */
5403: agev[m][i]=1;
5404: }
5405:
5406: }
5407: for (i=1; i<=imx; i++) {
5408: for(m=firstpass; (m<=lastpass); m++){
5409: if (s[m][i] > (nlstate+ndeath)) {
1.169 ! brouard 5410: (*nberr)++;
1.136 brouard 5411: 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);
5412: 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);
5413: return 1;
5414: }
5415: }
5416: }
5417:
5418: /*for (i=1; i<=imx; i++){
5419: for (m=firstpass; (m<lastpass); m++){
5420: printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
5421: }
5422:
5423: }*/
5424:
5425:
1.139 brouard 5426: printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
5427: fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
1.136 brouard 5428:
5429: return (0);
1.164 brouard 5430: /* endread:*/
1.136 brouard 5431: printf("Exiting calandcheckages: ");
5432: return (1);
5433: }
5434:
1.169 ! brouard 5435: void syscompilerinfo()
1.167 brouard 5436: {
5437: /* #include "syscompilerinfo.h"*/
1.169 ! brouard 5438: /* #include <gnu/libc-version.h> */ /* Only on gnu */
! 5439:
! 5440: printf("Compiled with:");fprintf(ficlog,"Compiled with:");
! 5441: #if defined(__clang__)
! 5442: printf(" Clang/LLVM");fprintf(ficlog," Clang/LLVM"); /* Clang/LLVM. ---------------------------------------------- */
! 5443: #endif
! 5444: #if defined(__ICC) || defined(__INTEL_COMPILER)
! 5445: printf(" Intel ICC/ICPC");fprintf(ficlog," Intel ICC/ICPC");/* Intel ICC/ICPC. ------------------------------------------ */
! 5446: #endif
! 5447: #if defined(__GNUC__) || defined(__GNUG__)
! 5448: printf(" GNU GCC/G++");fprintf(ficlog," GNU GCC/G++");/* GNU GCC/G++. --------------------------------------------- */
! 5449: #endif
! 5450: #if defined(__HP_cc) || defined(__HP_aCC)
! 5451: printf(" Hewlett-Packard C/aC++");fprintf(fcilog," Hewlett-Packard C/aC++"); /* Hewlett-Packard C/aC++. ---------------------------------- */
! 5452: #endif
! 5453: #if defined(__IBMC__) || defined(__IBMCPP__)
! 5454: printf(" IBM XL C/C++"); fprintf(ficlog," IBM XL C/C++");/* IBM XL C/C++. -------------------------------------------- */
! 5455: #endif
! 5456: #if defined(_MSC_VER)
! 5457: printf(" Microsoft Visual Studio");fprintf(ficlog," Microsoft Visual Studio");/* Microsoft Visual Studio. --------------------------------- */
! 5458: #endif
! 5459: #if defined(__PGI)
! 5460: printf(" Portland Group PGCC/PGCPP");fprintf(ficlog," Portland Group PGCC/PGCPP");/* Portland Group PGCC/PGCPP. ------------------------------- */
! 5461: #endif
! 5462: #if defined(__SUNPRO_C) || defined(__SUNPRO_CC)
! 5463: printf(" Oracle Solaris Studio");fprintf(ficlog," Oracle Solaris Studio\n");/* Oracle Solaris Studio. ----------------------------------- */
1.167 brouard 5464: #endif
1.169 ! brouard 5465: printf(". ");fprintf(ficlog,". ");
! 5466:
1.167 brouard 5467: // http://stackoverflow.com/questions/4605842/how-to-identify-platform-compiler-from-preprocessor-macros
5468: #ifdef _WIN32 // note the underscore: without it, it's not msdn official!
5469: // Windows (x64 and x86)
5470: #elif __unix__ // all unices, not all compilers
5471: // Unix
5472: #elif __linux__
5473: // linux
5474: #elif __APPLE__
5475: // Mac OS, not sure if this is covered by __posix__ and/or __unix__ though...
5476: #endif
5477:
5478: /* __MINGW32__ */
5479: /* __CYGWIN__ */
5480: /* __MINGW64__ */
5481: // http://msdn.microsoft.com/en-us/library/b0084kay.aspx
5482: /* _MSC_VER //the Visual C++ compiler is 17.00.51106.1, the _MSC_VER macro evaluates to 1700. Type cl /? */
5483: /* _MSC_FULL_VER //the Visual C++ compiler is 15.00.20706.01, the _MSC_FULL_VER macro evaluates to 150020706 */
5484: /* _WIN64 // Defined for applications for Win64. */
5485: /* _M_X64 // Defined for compilations that target x64 processors. */
5486: /* _DEBUG // Defined when you compile with /LDd, /MDd, and /MTd. */
5487: #include <stdint.h>
5488: #if UINTPTR_MAX == 0xffffffff
1.169 ! brouard 5489: printf(" 32-bit."); /* 32-bit */
1.167 brouard 5490: #elif UINTPTR_MAX == 0xffffffffffffffff
1.169 ! brouard 5491: printf(" 64-bit.");/* 64-bit */
1.167 brouard 5492: #else
1.169 ! brouard 5493: printf(" wtf-bit."); /* wtf */
1.167 brouard 5494: #endif
5495:
5496: struct utsname sysInfo;
5497:
5498: if (uname(&sysInfo) != -1) {
1.169 ! brouard 5499: printf(" %s %s %s %s %s\n",sysInfo.sysname, sysInfo.nodename, sysInfo.release, sysInfo.version, sysInfo.machine);
! 5500: fprintf(ficlog," %s %s %s %s %s\n ",sysInfo.sysname, sysInfo.nodename, sysInfo.release, sysInfo.version, sysInfo.machine);
1.167 brouard 5501: }
5502: else
5503: perror("uname() error");
1.169 ! brouard 5504: #if defined(__GNUC__)
! 5505: # if defined(__GNUC_PATCHLEVEL__)
! 5506: # define __GNUC_VERSION__ (__GNUC__ * 10000 \
! 5507: + __GNUC_MINOR__ * 100 \
! 5508: + __GNUC_PATCHLEVEL__)
! 5509: # else
! 5510: # define __GNUC_VERSION__ (__GNUC__ * 10000 \
! 5511: + __GNUC_MINOR__ * 100)
! 5512: # endif
! 5513: printf("GNU C version %d.\n", __GNUC_VERSION__);
! 5514: fprintf(ficlog, "GNU C version %d.\n", __GNUC_VERSION__);
! 5515: #endif
! 5516: #if defined(_MSC_VER)
! 5517: printf("Visual C++ compiler: %s \n;", _MSC_FULL_VER);
! 5518: fprintf(ficlog, "Visual C++ compiler: %s \n;", _MSC_FULL_VER);
! 5519: #endif
! 5520:
! 5521: /* printf("GNU libc version: %s\n", gnu_get_libc_version()); */
1.167 brouard 5522:
5523: }
1.136 brouard 5524:
5525: /***********************************************/
5526: /**************** Main Program *****************/
5527: /***********************************************/
5528:
5529: int main(int argc, char *argv[])
5530: {
5531: #ifdef GSL
5532: const gsl_multimin_fminimizer_type *T;
5533: size_t iteri = 0, it;
5534: int rval = GSL_CONTINUE;
5535: int status = GSL_SUCCESS;
5536: double ssval;
5537: #endif
5538: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
1.164 brouard 5539: int i,j, k, n=MAXN,iter=0,m,size=100, cptcod;
5540:
5541: int jj, ll, li, lj, lk;
1.136 brouard 5542: int numlinepar=0; /* Current linenumber of parameter file */
5543: int itimes;
5544: int NDIM=2;
5545: int vpopbased=0;
5546:
1.164 brouard 5547: char ca[32], cb[32];
1.136 brouard 5548: /* FILE *fichtm; *//* Html File */
5549: /* FILE *ficgp;*/ /*Gnuplot File */
5550: struct stat info;
1.164 brouard 5551: double agedeb;
1.136 brouard 5552: double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
5553:
1.165 brouard 5554: double fret;
1.136 brouard 5555: double dum; /* Dummy variable */
5556: double ***p3mat;
5557: double ***mobaverage;
1.164 brouard 5558:
5559: char line[MAXLINE];
1.136 brouard 5560: char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
5561: char pathr[MAXLINE], pathimach[MAXLINE];
1.164 brouard 5562: char *tok, *val; /* pathtot */
1.136 brouard 5563: int firstobs=1, lastobs=10;
1.164 brouard 5564: int c, h , cpt;
5565: int jl;
5566: int i1, j1, jk, stepsize;
5567: int *tab;
1.136 brouard 5568: int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
5569: int mobilav=0,popforecast=0;
5570: int hstepm, nhstepm;
5571: int agemortsup;
5572: float sumlpop=0.;
5573: double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
5574: double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
5575:
1.164 brouard 5576: double bage=0, fage=110, age, agelim, agebase;
1.136 brouard 5577: double ftolpl=FTOL;
5578: double **prlim;
5579: double ***param; /* Matrix of parameters */
5580: double *p;
5581: double **matcov; /* Matrix of covariance */
5582: double ***delti3; /* Scale */
5583: double *delti; /* Scale */
5584: double ***eij, ***vareij;
5585: double **varpl; /* Variances of prevalence limits by age */
5586: double *epj, vepp;
1.164 brouard 5587:
1.136 brouard 5588: double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
5589: double **ximort;
1.145 brouard 5590: char *alph[]={"a","a","b","c","d","e"}, str[4]="1234";
1.136 brouard 5591: int *dcwave;
5592:
1.164 brouard 5593: char z[1]="c";
1.136 brouard 5594:
5595: /*char *strt;*/
5596: char strtend[80];
1.126 brouard 5597:
1.164 brouard 5598:
1.126 brouard 5599: /* setlocale (LC_ALL, ""); */
5600: /* bindtextdomain (PACKAGE, LOCALEDIR); */
5601: /* textdomain (PACKAGE); */
5602: /* setlocale (LC_CTYPE, ""); */
5603: /* setlocale (LC_MESSAGES, ""); */
5604:
5605: /* gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
1.157 brouard 5606: rstart_time = time(NULL);
5607: /* (void) gettimeofday(&start_time,&tzp);*/
5608: start_time = *localtime(&rstart_time);
1.126 brouard 5609: curr_time=start_time;
1.157 brouard 5610: /*tml = *localtime(&start_time.tm_sec);*/
5611: /* strcpy(strstart,asctime(&tml)); */
5612: strcpy(strstart,asctime(&start_time));
1.126 brouard 5613:
5614: /* printf("Localtime (at start)=%s",strstart); */
1.157 brouard 5615: /* tp.tm_sec = tp.tm_sec +86400; */
5616: /* tm = *localtime(&start_time.tm_sec); */
1.126 brouard 5617: /* tmg.tm_year=tmg.tm_year +dsign*dyear; */
5618: /* tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
5619: /* tmg.tm_hour=tmg.tm_hour + 1; */
1.157 brouard 5620: /* tp.tm_sec = mktime(&tmg); */
1.126 brouard 5621: /* strt=asctime(&tmg); */
5622: /* printf("Time(after) =%s",strstart); */
5623: /* (void) time (&time_value);
5624: * printf("time=%d,t-=%d\n",time_value,time_value-86400);
5625: * tm = *localtime(&time_value);
5626: * strstart=asctime(&tm);
5627: * printf("tim_value=%d,asctime=%s\n",time_value,strstart);
5628: */
5629:
5630: nberr=0; /* Number of errors and warnings */
5631: nbwarn=0;
5632: getcwd(pathcd, size);
5633:
5634: printf("\n%s\n%s",version,fullversion);
5635: if(argc <=1){
5636: printf("\nEnter the parameter file name: ");
5637: fgets(pathr,FILENAMELENGTH,stdin);
5638: i=strlen(pathr);
5639: if(pathr[i-1]=='\n')
5640: pathr[i-1]='\0';
1.156 brouard 5641: i=strlen(pathr);
5642: if(pathr[i-1]==' ') /* This may happen when dragging on oS/X! */
5643: pathr[i-1]='\0';
1.126 brouard 5644: for (tok = pathr; tok != NULL; ){
5645: printf("Pathr |%s|\n",pathr);
5646: while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
5647: printf("val= |%s| pathr=%s\n",val,pathr);
5648: strcpy (pathtot, val);
5649: if(pathr[0] == '\0') break; /* Dirty */
5650: }
5651: }
5652: else{
5653: strcpy(pathtot,argv[1]);
5654: }
5655: /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
5656: /*cygwin_split_path(pathtot,path,optionfile);
5657: printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
5658: /* cutv(path,optionfile,pathtot,'\\');*/
5659:
5660: /* Split argv[0], imach program to get pathimach */
5661: printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
5662: split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
5663: printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
5664: /* strcpy(pathimach,argv[0]); */
5665: /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
5666: split(pathtot,path,optionfile,optionfilext,optionfilefiname);
5667: printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
5668: chdir(path); /* Can be a relative path */
5669: if(getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */
5670: printf("Current directory %s!\n",pathcd);
5671: strcpy(command,"mkdir ");
5672: strcat(command,optionfilefiname);
5673: if((outcmd=system(command)) != 0){
1.169 ! brouard 5674: printf("Directory already exists (or can't create it) %s%s, err=%d\n",path,optionfilefiname,outcmd);
1.126 brouard 5675: /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
5676: /* fclose(ficlog); */
5677: /* exit(1); */
5678: }
5679: /* if((imk=mkdir(optionfilefiname))<0){ */
5680: /* perror("mkdir"); */
5681: /* } */
5682:
5683: /*-------- arguments in the command line --------*/
5684:
5685: /* Log file */
5686: strcat(filelog, optionfilefiname);
5687: strcat(filelog,".log"); /* */
5688: if((ficlog=fopen(filelog,"w"))==NULL) {
5689: printf("Problem with logfile %s\n",filelog);
5690: goto end;
5691: }
5692: fprintf(ficlog,"Log filename:%s\n",filelog);
5693: fprintf(ficlog,"\n%s\n%s",version,fullversion);
5694: fprintf(ficlog,"\nEnter the parameter file name: \n");
5695: fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
5696: path=%s \n\
5697: optionfile=%s\n\
5698: optionfilext=%s\n\
1.156 brouard 5699: optionfilefiname='%s'\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
1.126 brouard 5700:
1.167 brouard 5701: syscompilerinfo();
5702:
1.126 brouard 5703: printf("Local time (at start):%s",strstart);
5704: fprintf(ficlog,"Local time (at start): %s",strstart);
5705: fflush(ficlog);
5706: /* (void) gettimeofday(&curr_time,&tzp); */
1.157 brouard 5707: /* printf("Elapsed time %d\n", asc_diff_time(curr_time.tm_sec-start_time.tm_sec,tmpout)); */
1.126 brouard 5708:
5709: /* */
5710: strcpy(fileres,"r");
5711: strcat(fileres, optionfilefiname);
5712: strcat(fileres,".txt"); /* Other files have txt extension */
5713:
5714: /*---------arguments file --------*/
5715:
5716: if((ficpar=fopen(optionfile,"r"))==NULL) {
1.155 brouard 5717: printf("Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
5718: fprintf(ficlog,"Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
1.126 brouard 5719: fflush(ficlog);
1.149 brouard 5720: /* goto end; */
5721: exit(70);
1.126 brouard 5722: }
5723:
5724:
5725:
5726: strcpy(filereso,"o");
5727: strcat(filereso,fileres);
5728: if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
5729: printf("Problem with Output resultfile: %s\n", filereso);
5730: fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
5731: fflush(ficlog);
5732: goto end;
5733: }
5734:
5735: /* Reads comments: lines beginning with '#' */
5736: numlinepar=0;
5737: while((c=getc(ficpar))=='#' && c!= EOF){
5738: ungetc(c,ficpar);
5739: fgets(line, MAXLINE, ficpar);
5740: numlinepar++;
1.141 brouard 5741: fputs(line,stdout);
1.126 brouard 5742: fputs(line,ficparo);
5743: fputs(line,ficlog);
5744: }
5745: ungetc(c,ficpar);
5746:
5747: 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);
5748: numlinepar++;
5749: 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);
5750: 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);
5751: 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);
5752: fflush(ficlog);
5753: while((c=getc(ficpar))=='#' && c!= EOF){
5754: ungetc(c,ficpar);
5755: fgets(line, MAXLINE, ficpar);
5756: numlinepar++;
1.141 brouard 5757: fputs(line, stdout);
5758: //puts(line);
1.126 brouard 5759: fputs(line,ficparo);
5760: fputs(line,ficlog);
5761: }
5762: ungetc(c,ficpar);
5763:
5764:
1.145 brouard 5765: covar=matrix(0,NCOVMAX,1,n); /**< used in readdata */
1.136 brouard 5766: cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement plus one, indepently of n in Vn*/
5767: /* v1+v2+v3+v2*v4+v5*age makes cptcovn = 5
5768: v1+v2*age+v2*v3 makes cptcovn = 3
5769: */
5770: if (strlen(model)>1)
1.145 brouard 5771: 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*/
5772: else
5773: ncovmodel=2;
1.126 brouard 5774: nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
1.133 brouard 5775: nforce= (nlstate+ndeath-1)*nlstate; /* Number of forces ij from state i to j */
5776: npar= nforce*ncovmodel; /* Number of parameters like aij*/
1.131 brouard 5777: if(npar >MAXPARM || nlstate >NLSTATEMAX || ndeath >NDEATHMAX || ncovmodel>NCOVMAX){
5778: 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);
5779: 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);
5780: fflush(stdout);
5781: fclose (ficlog);
5782: goto end;
5783: }
1.126 brouard 5784: delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
5785: delti=delti3[1][1];
5786: /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
5787: if(mle==-1){ /* Print a wizard for help writing covariance matrix */
5788: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
5789: printf(" You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
5790: fprintf(ficlog," You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
5791: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
5792: fclose (ficparo);
5793: fclose (ficlog);
5794: goto end;
5795: exit(0);
5796: }
5797: else if(mle==-3) {
5798: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
5799: printf(" You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
5800: fprintf(ficlog," You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
5801: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
5802: matcov=matrix(1,npar,1,npar);
5803: }
5804: else{
1.145 brouard 5805: /* Read guessed parameters */
1.126 brouard 5806: /* Reads comments: lines beginning with '#' */
5807: while((c=getc(ficpar))=='#' && c!= EOF){
5808: ungetc(c,ficpar);
5809: fgets(line, MAXLINE, ficpar);
5810: numlinepar++;
1.141 brouard 5811: fputs(line,stdout);
1.126 brouard 5812: fputs(line,ficparo);
5813: fputs(line,ficlog);
5814: }
5815: ungetc(c,ficpar);
5816:
5817: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
5818: for(i=1; i <=nlstate; i++){
5819: j=0;
5820: for(jj=1; jj <=nlstate+ndeath; jj++){
5821: if(jj==i) continue;
5822: j++;
5823: fscanf(ficpar,"%1d%1d",&i1,&j1);
5824: if ((i1 != i) && (j1 != j)){
5825: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \
5826: It might be a problem of design; if ncovcol and the model are correct\n \
5827: run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1);
5828: exit(1);
5829: }
5830: fprintf(ficparo,"%1d%1d",i1,j1);
5831: if(mle==1)
5832: printf("%1d%1d",i,j);
5833: fprintf(ficlog,"%1d%1d",i,j);
5834: for(k=1; k<=ncovmodel;k++){
5835: fscanf(ficpar," %lf",¶m[i][j][k]);
5836: if(mle==1){
5837: printf(" %lf",param[i][j][k]);
5838: fprintf(ficlog," %lf",param[i][j][k]);
5839: }
5840: else
5841: fprintf(ficlog," %lf",param[i][j][k]);
5842: fprintf(ficparo," %lf",param[i][j][k]);
5843: }
5844: fscanf(ficpar,"\n");
5845: numlinepar++;
5846: if(mle==1)
5847: printf("\n");
5848: fprintf(ficlog,"\n");
5849: fprintf(ficparo,"\n");
5850: }
5851: }
5852: fflush(ficlog);
5853:
1.145 brouard 5854: /* Reads scales values */
1.126 brouard 5855: p=param[1][1];
5856:
5857: /* Reads comments: lines beginning with '#' */
5858: while((c=getc(ficpar))=='#' && c!= EOF){
5859: ungetc(c,ficpar);
5860: fgets(line, MAXLINE, ficpar);
5861: numlinepar++;
1.141 brouard 5862: fputs(line,stdout);
1.126 brouard 5863: fputs(line,ficparo);
5864: fputs(line,ficlog);
5865: }
5866: ungetc(c,ficpar);
5867:
5868: for(i=1; i <=nlstate; i++){
5869: for(j=1; j <=nlstate+ndeath-1; j++){
5870: fscanf(ficpar,"%1d%1d",&i1,&j1);
1.164 brouard 5871: if ( (i1-i) * (j1-j) != 0){
1.126 brouard 5872: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
5873: exit(1);
5874: }
5875: printf("%1d%1d",i,j);
5876: fprintf(ficparo,"%1d%1d",i1,j1);
5877: fprintf(ficlog,"%1d%1d",i1,j1);
5878: for(k=1; k<=ncovmodel;k++){
5879: fscanf(ficpar,"%le",&delti3[i][j][k]);
5880: printf(" %le",delti3[i][j][k]);
5881: fprintf(ficparo," %le",delti3[i][j][k]);
5882: fprintf(ficlog," %le",delti3[i][j][k]);
5883: }
5884: fscanf(ficpar,"\n");
5885: numlinepar++;
5886: printf("\n");
5887: fprintf(ficparo,"\n");
5888: fprintf(ficlog,"\n");
5889: }
5890: }
5891: fflush(ficlog);
5892:
1.145 brouard 5893: /* Reads covariance matrix */
1.126 brouard 5894: delti=delti3[1][1];
5895:
5896:
5897: /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
5898:
5899: /* Reads comments: lines beginning with '#' */
5900: while((c=getc(ficpar))=='#' && c!= EOF){
5901: ungetc(c,ficpar);
5902: fgets(line, MAXLINE, ficpar);
5903: numlinepar++;
1.141 brouard 5904: fputs(line,stdout);
1.126 brouard 5905: fputs(line,ficparo);
5906: fputs(line,ficlog);
5907: }
5908: ungetc(c,ficpar);
5909:
5910: matcov=matrix(1,npar,1,npar);
1.131 brouard 5911: for(i=1; i <=npar; i++)
5912: for(j=1; j <=npar; j++) matcov[i][j]=0.;
5913:
1.126 brouard 5914: for(i=1; i <=npar; i++){
1.145 brouard 5915: fscanf(ficpar,"%s",str);
1.126 brouard 5916: if(mle==1)
5917: printf("%s",str);
5918: fprintf(ficlog,"%s",str);
5919: fprintf(ficparo,"%s",str);
5920: for(j=1; j <=i; j++){
5921: fscanf(ficpar," %le",&matcov[i][j]);
5922: if(mle==1){
5923: printf(" %.5le",matcov[i][j]);
5924: }
5925: fprintf(ficlog," %.5le",matcov[i][j]);
5926: fprintf(ficparo," %.5le",matcov[i][j]);
5927: }
5928: fscanf(ficpar,"\n");
5929: numlinepar++;
5930: if(mle==1)
5931: printf("\n");
5932: fprintf(ficlog,"\n");
5933: fprintf(ficparo,"\n");
5934: }
5935: for(i=1; i <=npar; i++)
5936: for(j=i+1;j<=npar;j++)
5937: matcov[i][j]=matcov[j][i];
5938:
5939: if(mle==1)
5940: printf("\n");
5941: fprintf(ficlog,"\n");
5942:
5943: fflush(ficlog);
5944:
5945: /*-------- Rewriting parameter file ----------*/
5946: strcpy(rfileres,"r"); /* "Rparameterfile */
5947: strcat(rfileres,optionfilefiname); /* Parameter file first name*/
5948: strcat(rfileres,"."); /* */
5949: strcat(rfileres,optionfilext); /* Other files have txt extension */
5950: if((ficres =fopen(rfileres,"w"))==NULL) {
5951: printf("Problem writing new parameter file: %s\n", fileres);goto end;
5952: fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
5953: }
5954: fprintf(ficres,"#%s\n",version);
5955: } /* End of mle != -3 */
5956:
5957:
5958: n= lastobs;
5959: num=lvector(1,n);
5960: moisnais=vector(1,n);
5961: annais=vector(1,n);
5962: moisdc=vector(1,n);
5963: andc=vector(1,n);
5964: agedc=vector(1,n);
5965: cod=ivector(1,n);
5966: weight=vector(1,n);
5967: for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
5968: mint=matrix(1,maxwav,1,n);
5969: anint=matrix(1,maxwav,1,n);
1.131 brouard 5970: s=imatrix(1,maxwav+1,1,n); /* s[i][j] health state for wave i and individual j */
1.126 brouard 5971: tab=ivector(1,NCOVMAX);
1.144 brouard 5972: ncodemax=ivector(1,NCOVMAX); /* Number of code per covariate; if O and 1 only, 2**ncov; V1+V2+V3+V4=>16 */
1.126 brouard 5973:
1.136 brouard 5974: /* Reads data from file datafile */
5975: if (readdata(datafile, firstobs, lastobs, &imx)==1)
5976: goto end;
5977:
5978: /* Calculation of the number of parameters from char model */
1.137 brouard 5979: /* modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4
5980: k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tag[cptcovage=1]=4
5981: k=3 V4 Tvar[k=3]= 4 (from V4)
5982: k=2 V1 Tvar[k=2]= 1 (from V1)
5983: k=1 Tvar[1]=2 (from V2)
5984: */
5985: Tvar=ivector(1,NCOVMAX); /* Was 15 changed to NCOVMAX. */
5986: /* V2+V1+V4+age*V3 is a model with 4 covariates (3 plus signs).
5987: For each model-covariate stores the data-covariate id. Tvar[1]=2, Tvar[2]=1, Tvar[3]=4,
5988: Tvar[4=age*V3] is 3 and 'age' is recorded in Tage.
5989: */
5990: /* For model-covariate k tells which data-covariate to use but
5991: because this model-covariate is a construction we invent a new column
5992: ncovcol + k1
5993: If already ncovcol=4 and model=V2+V1+V1*V4+age*V3
5994: Tvar[3=V1*V4]=4+1 etc */
1.145 brouard 5995: Tprod=ivector(1,NCOVMAX); /* Gives the position of a product */
1.137 brouard 5996: /* Tprod[k1=1]=3(=V1*V4) for V2+V1+V1*V4+age*V3
5997: if V2+V1+V1*V4+age*V3+V3*V2 TProd[k1=2]=5 (V3*V2)
5998: */
1.145 brouard 5999: Tvaraff=ivector(1,NCOVMAX); /* Unclear */
6000: Tvard=imatrix(1,NCOVMAX,1,2); /* n=Tvard[k1][1] and m=Tvard[k1][2] gives the couple n,m of the k1 th product Vn*Vm
1.141 brouard 6001: * For V3*V2 (in V2+V1+V1*V4+age*V3+V3*V2), V3*V2 position is 2nd.
6002: * Tvard[k1=2][1]=3 (V3) Tvard[k1=2][2]=2(V2) */
1.145 brouard 6003: Tage=ivector(1,NCOVMAX); /* Gives the covariate id of covariates associated with age: V2 + V1 + age*V4 + V3*age
1.137 brouard 6004: 4 covariates (3 plus signs)
6005: Tage[1=V3*age]= 4; Tage[2=age*V4] = 3
6006: */
1.136 brouard 6007:
6008: if(decodemodel(model, lastobs) == 1)
6009: goto end;
6010:
1.137 brouard 6011: if((double)(lastobs-imx)/(double)imx > 1.10){
6012: nbwarn++;
6013: 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);
6014: 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);
6015: }
1.136 brouard 6016: /* if(mle==1){*/
1.137 brouard 6017: if (weightopt != 1) { /* Maximisation without weights. We can have weights different from 1 but want no weight*/
6018: for(i=1;i<=imx;i++) weight[i]=1.0; /* changed to imx */
1.136 brouard 6019: }
6020:
6021: /*-calculation of age at interview from date of interview and age at death -*/
6022: agev=matrix(1,maxwav,1,imx);
6023:
6024: if(calandcheckages(imx, maxwav, &agemin, &agemax, &nberr, &nbwarn) == 1)
6025: goto end;
6026:
1.126 brouard 6027:
1.136 brouard 6028: agegomp=(int)agemin;
6029: free_vector(moisnais,1,n);
6030: free_vector(annais,1,n);
1.126 brouard 6031: /* free_matrix(mint,1,maxwav,1,n);
6032: free_matrix(anint,1,maxwav,1,n);*/
6033: free_vector(moisdc,1,n);
6034: free_vector(andc,1,n);
1.145 brouard 6035: /* */
6036:
1.126 brouard 6037: wav=ivector(1,imx);
6038: dh=imatrix(1,lastpass-firstpass+1,1,imx);
6039: bh=imatrix(1,lastpass-firstpass+1,1,imx);
6040: mw=imatrix(1,lastpass-firstpass+1,1,imx);
6041:
6042: /* Concatenates waves */
6043: concatwav(wav, dh, bh, mw, s, agedc, agev, firstpass, lastpass, imx, nlstate, stepm);
1.145 brouard 6044: /* */
6045:
1.126 brouard 6046: /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
6047:
6048: nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
6049: ncodemax[1]=1;
1.145 brouard 6050: Ndum =ivector(-1,NCOVMAX);
6051: if (ncovmodel > 2)
6052: tricode(Tvar,nbcode,imx, Ndum); /**< Fills nbcode[Tvar[j]][l]; */
6053:
6054: codtab=imatrix(1,100,1,10); /* codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) */
6055: /*printf(" codtab[1,1],codtab[100,10]=%d,%d\n", codtab[1][1],codtab[100][10]);*/
6056: h=0;
6057:
6058:
6059: /*if (cptcovn > 0) */
1.126 brouard 6060:
1.145 brouard 6061:
1.126 brouard 6062: m=pow(2,cptcoveff);
6063:
1.131 brouard 6064: for(k=1;k<=cptcoveff; k++){ /* scans any effective covariate */
1.143 brouard 6065: 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 */
6066: for(j=1; j <= ncodemax[k]; j++){ /* For each modality of this covariate ncodemax=2*/
6067: for(cpt=1; cpt <=pow(2,k-1); cpt++){ /* cpt=1 to 8/2**(3+1-1 or 3+1-3) =1 or 4 */
1.126 brouard 6068: h++;
1.141 brouard 6069: if (h>m)
1.136 brouard 6070: h=1;
1.144 brouard 6071: /**< codtab(h,k) k = codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) + 1
1.143 brouard 6072: * h 1 2 3 4
6073: *______________________________
6074: * 1 i=1 1 i=1 1 i=1 1 i=1 1
6075: * 2 2 1 1 1
6076: * 3 i=2 1 2 1 1
6077: * 4 2 2 1 1
6078: * 5 i=3 1 i=2 1 2 1
6079: * 6 2 1 2 1
6080: * 7 i=4 1 2 2 1
6081: * 8 2 2 2 1
6082: * 9 i=5 1 i=3 1 i=2 1 1
6083: * 10 2 1 1 1
6084: * 11 i=6 1 2 1 1
6085: * 12 2 2 1 1
6086: * 13 i=7 1 i=4 1 2 1
6087: * 14 2 1 2 1
6088: * 15 i=8 1 2 2 1
6089: * 16 2 2 2 1
6090: */
1.141 brouard 6091: codtab[h][k]=j;
1.145 brouard 6092: /*codtab[h][Tvar[k]]=j;*/
1.130 brouard 6093: printf("h=%d k=%d j=%d codtab[h][k]=%d Tvar[k]=%d codtab[h][Tvar[k]]=%d \n",h, k,j,codtab[h][k],Tvar[k],codtab[h][Tvar[k]]);
1.126 brouard 6094: }
6095: }
6096: }
6097: }
6098: /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);
6099: codtab[1][2]=1;codtab[2][2]=2; */
6100: /* for(i=1; i <=m ;i++){
6101: for(k=1; k <=cptcovn; k++){
1.131 brouard 6102: printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
1.126 brouard 6103: }
6104: printf("\n");
6105: }
6106: scanf("%d",i);*/
1.145 brouard 6107:
6108: free_ivector(Ndum,-1,NCOVMAX);
6109:
6110:
1.126 brouard 6111:
6112: /*------------ gnuplot -------------*/
6113: strcpy(optionfilegnuplot,optionfilefiname);
6114: if(mle==-3)
6115: strcat(optionfilegnuplot,"-mort");
6116: strcat(optionfilegnuplot,".gp");
6117:
6118: if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
6119: printf("Problem with file %s",optionfilegnuplot);
6120: }
6121: else{
6122: fprintf(ficgp,"\n# %s\n", version);
6123: fprintf(ficgp,"# %s\n", optionfilegnuplot);
1.141 brouard 6124: //fprintf(ficgp,"set missing 'NaNq'\n");
6125: fprintf(ficgp,"set datafile missing 'NaNq'\n");
1.126 brouard 6126: }
6127: /* fclose(ficgp);*/
6128: /*--------- index.htm --------*/
6129:
6130: strcpy(optionfilehtm,optionfilefiname); /* Main html file */
6131: if(mle==-3)
6132: strcat(optionfilehtm,"-mort");
6133: strcat(optionfilehtm,".htm");
6134: if((fichtm=fopen(optionfilehtm,"w"))==NULL) {
1.131 brouard 6135: printf("Problem with %s \n",optionfilehtm);
6136: exit(0);
1.126 brouard 6137: }
6138:
6139: strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
6140: strcat(optionfilehtmcov,"-cov.htm");
6141: if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL) {
6142: printf("Problem with %s \n",optionfilehtmcov), exit(0);
6143: }
6144: else{
6145: fprintf(fichtmcov,"<html><head>\n<title>IMaCh Cov %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
6146: <hr size=\"2\" color=\"#EC5E5E\"> \n\
6147: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n",\
6148: optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
6149: }
6150:
6151: fprintf(fichtm,"<html><head>\n<title>IMaCh %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
6152: <hr size=\"2\" color=\"#EC5E5E\"> \n\
6153: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
6154: \n\
6155: <hr size=\"2\" color=\"#EC5E5E\">\
6156: <ul><li><h4>Parameter files</h4>\n\
6157: - Parameter file: <a href=\"%s.%s\">%s.%s</a><br>\n\
6158: - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
6159: - Log file of the run: <a href=\"%s\">%s</a><br>\n\
6160: - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
6161: - Date and time at start: %s</ul>\n",\
6162: optionfilehtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
6163: optionfilefiname,optionfilext,optionfilefiname,optionfilext,\
6164: fileres,fileres,\
6165: filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
6166: fflush(fichtm);
6167:
6168: strcpy(pathr,path);
6169: strcat(pathr,optionfilefiname);
6170: chdir(optionfilefiname); /* Move to directory named optionfile */
6171:
6172: /* Calculates basic frequencies. Computes observed prevalence at single age
6173: and prints on file fileres'p'. */
6174: freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart);
6175:
6176: fprintf(fichtm,"\n");
6177: fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
6178: Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
6179: Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
6180: imx,agemin,agemax,jmin,jmax,jmean);
6181: pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
6182: oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
6183: newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
6184: savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
6185: oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
6186:
6187:
6188: /* For Powell, parameters are in a vector p[] starting at p[1]
6189: so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
6190: p=param[1][1]; /* *(*(*(param +1)+1)+0) */
6191:
6192: globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
6193:
6194: if (mle==-3){
1.136 brouard 6195: ximort=matrix(1,NDIM,1,NDIM);
6196: /* ximort=gsl_matrix_alloc(1,NDIM,1,NDIM); */
1.126 brouard 6197: cens=ivector(1,n);
6198: ageexmed=vector(1,n);
6199: agecens=vector(1,n);
6200: dcwave=ivector(1,n);
6201:
6202: for (i=1; i<=imx; i++){
6203: dcwave[i]=-1;
6204: for (m=firstpass; m<=lastpass; m++)
6205: if (s[m][i]>nlstate) {
6206: dcwave[i]=m;
6207: /* printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
6208: break;
6209: }
6210: }
6211:
6212: for (i=1; i<=imx; i++) {
6213: if (wav[i]>0){
6214: ageexmed[i]=agev[mw[1][i]][i];
6215: j=wav[i];
6216: agecens[i]=1.;
6217:
6218: if (ageexmed[i]> 1 && wav[i] > 0){
6219: agecens[i]=agev[mw[j][i]][i];
6220: cens[i]= 1;
6221: }else if (ageexmed[i]< 1)
6222: cens[i]= -1;
6223: if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
6224: cens[i]=0 ;
6225: }
6226: else cens[i]=-1;
6227: }
6228:
6229: for (i=1;i<=NDIM;i++) {
6230: for (j=1;j<=NDIM;j++)
6231: ximort[i][j]=(i == j ? 1.0 : 0.0);
6232: }
6233:
1.145 brouard 6234: /*p[1]=0.0268; p[NDIM]=0.083;*/
1.126 brouard 6235: /*printf("%lf %lf", p[1], p[2]);*/
6236:
6237:
1.136 brouard 6238: #ifdef GSL
6239: printf("GSL optimization\n"); fprintf(ficlog,"Powell\n");
1.162 brouard 6240: #else
1.126 brouard 6241: printf("Powell\n"); fprintf(ficlog,"Powell\n");
1.136 brouard 6242: #endif
1.126 brouard 6243: strcpy(filerespow,"pow-mort");
6244: strcat(filerespow,fileres);
6245: if((ficrespow=fopen(filerespow,"w"))==NULL) {
6246: printf("Problem with resultfile: %s\n", filerespow);
6247: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
6248: }
1.136 brouard 6249: #ifdef GSL
6250: fprintf(ficrespow,"# GSL optimization\n# iter -2*LL");
1.162 brouard 6251: #else
1.126 brouard 6252: fprintf(ficrespow,"# Powell\n# iter -2*LL");
1.136 brouard 6253: #endif
1.126 brouard 6254: /* for (i=1;i<=nlstate;i++)
6255: for(j=1;j<=nlstate+ndeath;j++)
6256: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
6257: */
6258: fprintf(ficrespow,"\n");
1.136 brouard 6259: #ifdef GSL
6260: /* gsl starts here */
6261: T = gsl_multimin_fminimizer_nmsimplex;
6262: gsl_multimin_fminimizer *sfm = NULL;
6263: gsl_vector *ss, *x;
6264: gsl_multimin_function minex_func;
6265:
6266: /* Initial vertex size vector */
6267: ss = gsl_vector_alloc (NDIM);
6268:
6269: if (ss == NULL){
6270: GSL_ERROR_VAL ("failed to allocate space for ss", GSL_ENOMEM, 0);
6271: }
6272: /* Set all step sizes to 1 */
6273: gsl_vector_set_all (ss, 0.001);
6274:
6275: /* Starting point */
1.126 brouard 6276:
1.136 brouard 6277: x = gsl_vector_alloc (NDIM);
6278:
6279: if (x == NULL){
6280: gsl_vector_free(ss);
6281: GSL_ERROR_VAL ("failed to allocate space for x", GSL_ENOMEM, 0);
6282: }
6283:
6284: /* Initialize method and iterate */
6285: /* p[1]=0.0268; p[NDIM]=0.083; */
6286: /* gsl_vector_set(x, 0, 0.0268); */
6287: /* gsl_vector_set(x, 1, 0.083); */
6288: gsl_vector_set(x, 0, p[1]);
6289: gsl_vector_set(x, 1, p[2]);
6290:
6291: minex_func.f = &gompertz_f;
6292: minex_func.n = NDIM;
6293: minex_func.params = (void *)&p; /* ??? */
6294:
6295: sfm = gsl_multimin_fminimizer_alloc (T, NDIM);
6296: gsl_multimin_fminimizer_set (sfm, &minex_func, x, ss);
6297:
6298: printf("Iterations beginning .....\n\n");
6299: printf("Iter. # Intercept Slope -Log Likelihood Simplex size\n");
6300:
6301: iteri=0;
6302: while (rval == GSL_CONTINUE){
6303: iteri++;
6304: status = gsl_multimin_fminimizer_iterate(sfm);
6305:
6306: if (status) printf("error: %s\n", gsl_strerror (status));
6307: fflush(0);
6308:
6309: if (status)
6310: break;
6311:
6312: rval = gsl_multimin_test_size (gsl_multimin_fminimizer_size (sfm), 1e-6);
6313: ssval = gsl_multimin_fminimizer_size (sfm);
6314:
6315: if (rval == GSL_SUCCESS)
6316: printf ("converged to a local maximum at\n");
6317:
6318: printf("%5d ", iteri);
6319: for (it = 0; it < NDIM; it++){
6320: printf ("%10.5f ", gsl_vector_get (sfm->x, it));
6321: }
6322: printf("f() = %-10.5f ssize = %.7f\n", sfm->fval, ssval);
6323: }
6324:
6325: printf("\n\n Please note: Program should be run many times with varying starting points to detemine global maximum\n\n");
6326:
6327: gsl_vector_free(x); /* initial values */
6328: gsl_vector_free(ss); /* inital step size */
6329: for (it=0; it<NDIM; it++){
6330: p[it+1]=gsl_vector_get(sfm->x,it);
6331: fprintf(ficrespow," %.12lf", p[it]);
6332: }
6333: gsl_multimin_fminimizer_free (sfm); /* p *(sfm.x.data) et p *(sfm.x.data+1) */
6334: #endif
6335: #ifdef POWELL
6336: powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
6337: #endif
1.126 brouard 6338: fclose(ficrespow);
6339:
6340: hesscov(matcov, p, NDIM, delti, 1e-4, gompertz);
6341:
6342: for(i=1; i <=NDIM; i++)
6343: for(j=i+1;j<=NDIM;j++)
6344: matcov[i][j]=matcov[j][i];
6345:
6346: printf("\nCovariance matrix\n ");
6347: for(i=1; i <=NDIM; i++) {
6348: for(j=1;j<=NDIM;j++){
6349: printf("%f ",matcov[i][j]);
6350: }
6351: printf("\n ");
6352: }
6353:
6354: printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
6355: for (i=1;i<=NDIM;i++)
6356: printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
6357:
6358: lsurv=vector(1,AGESUP);
6359: lpop=vector(1,AGESUP);
6360: tpop=vector(1,AGESUP);
6361: lsurv[agegomp]=100000;
6362:
6363: for (k=agegomp;k<=AGESUP;k++) {
6364: agemortsup=k;
6365: if (p[1]*exp(p[2]*(k-agegomp))>1) break;
6366: }
6367:
6368: for (k=agegomp;k<agemortsup;k++)
6369: lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
6370:
6371: for (k=agegomp;k<agemortsup;k++){
6372: lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
6373: sumlpop=sumlpop+lpop[k];
6374: }
6375:
6376: tpop[agegomp]=sumlpop;
6377: for (k=agegomp;k<(agemortsup-3);k++){
6378: /* tpop[k+1]=2;*/
6379: tpop[k+1]=tpop[k]-lpop[k];
6380: }
6381:
6382:
6383: printf("\nAge lx qx dx Lx Tx e(x)\n");
6384: for (k=agegomp;k<(agemortsup-2);k++)
6385: 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]);
6386:
6387:
6388: replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
6389: printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
6390:
6391: printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \
6392: stepm, weightopt,\
6393: model,imx,p,matcov,agemortsup);
6394:
6395: free_vector(lsurv,1,AGESUP);
6396: free_vector(lpop,1,AGESUP);
6397: free_vector(tpop,1,AGESUP);
1.136 brouard 6398: #ifdef GSL
6399: free_ivector(cens,1,n);
6400: free_vector(agecens,1,n);
6401: free_ivector(dcwave,1,n);
6402: free_matrix(ximort,1,NDIM,1,NDIM);
6403: #endif
1.126 brouard 6404: } /* Endof if mle==-3 */
6405:
6406: else{ /* For mle >=1 */
1.132 brouard 6407: globpr=0;/* debug */
6408: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
1.126 brouard 6409: printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
6410: for (k=1; k<=npar;k++)
6411: printf(" %d %8.5f",k,p[k]);
6412: printf("\n");
6413: globpr=1; /* to print the contributions */
6414: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
6415: printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
6416: for (k=1; k<=npar;k++)
6417: printf(" %d %8.5f",k,p[k]);
6418: printf("\n");
6419: if(mle>=1){ /* Could be 1 or 2 */
6420: mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
6421: }
6422:
6423: /*--------- results files --------------*/
6424: 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);
6425:
6426:
6427: fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
6428: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
6429: fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
6430: for(i=1,jk=1; i <=nlstate; i++){
6431: for(k=1; k <=(nlstate+ndeath); k++){
6432: if (k != i) {
6433: printf("%d%d ",i,k);
6434: fprintf(ficlog,"%d%d ",i,k);
6435: fprintf(ficres,"%1d%1d ",i,k);
6436: for(j=1; j <=ncovmodel; j++){
6437: printf("%lf ",p[jk]);
6438: fprintf(ficlog,"%lf ",p[jk]);
6439: fprintf(ficres,"%lf ",p[jk]);
6440: jk++;
6441: }
6442: printf("\n");
6443: fprintf(ficlog,"\n");
6444: fprintf(ficres,"\n");
6445: }
6446: }
6447: }
6448: if(mle!=0){
6449: /* Computing hessian and covariance matrix */
6450: ftolhess=ftol; /* Usually correct */
6451: hesscov(matcov, p, npar, delti, ftolhess, func);
6452: }
6453: fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
6454: printf("# Scales (for hessian or gradient estimation)\n");
6455: fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
6456: for(i=1,jk=1; i <=nlstate; i++){
6457: for(j=1; j <=nlstate+ndeath; j++){
6458: if (j!=i) {
6459: fprintf(ficres,"%1d%1d",i,j);
6460: printf("%1d%1d",i,j);
6461: fprintf(ficlog,"%1d%1d",i,j);
6462: for(k=1; k<=ncovmodel;k++){
6463: printf(" %.5e",delti[jk]);
6464: fprintf(ficlog," %.5e",delti[jk]);
6465: fprintf(ficres," %.5e",delti[jk]);
6466: jk++;
6467: }
6468: printf("\n");
6469: fprintf(ficlog,"\n");
6470: fprintf(ficres,"\n");
6471: }
6472: }
6473: }
6474:
6475: 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");
6476: if(mle>=1)
6477: 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");
6478: 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");
6479: /* # 121 Var(a12)\n\ */
6480: /* # 122 Cov(b12,a12) Var(b12)\n\ */
6481: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
6482: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
6483: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
6484: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
6485: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
6486: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
6487:
6488:
6489: /* Just to have a covariance matrix which will be more understandable
6490: even is we still don't want to manage dictionary of variables
6491: */
6492: for(itimes=1;itimes<=2;itimes++){
6493: jj=0;
6494: for(i=1; i <=nlstate; i++){
6495: for(j=1; j <=nlstate+ndeath; j++){
6496: if(j==i) continue;
6497: for(k=1; k<=ncovmodel;k++){
6498: jj++;
6499: ca[0]= k+'a'-1;ca[1]='\0';
6500: if(itimes==1){
6501: if(mle>=1)
6502: printf("#%1d%1d%d",i,j,k);
6503: fprintf(ficlog,"#%1d%1d%d",i,j,k);
6504: fprintf(ficres,"#%1d%1d%d",i,j,k);
6505: }else{
6506: if(mle>=1)
6507: printf("%1d%1d%d",i,j,k);
6508: fprintf(ficlog,"%1d%1d%d",i,j,k);
6509: fprintf(ficres,"%1d%1d%d",i,j,k);
6510: }
6511: ll=0;
6512: for(li=1;li <=nlstate; li++){
6513: for(lj=1;lj <=nlstate+ndeath; lj++){
6514: if(lj==li) continue;
6515: for(lk=1;lk<=ncovmodel;lk++){
6516: ll++;
6517: if(ll<=jj){
6518: cb[0]= lk +'a'-1;cb[1]='\0';
6519: if(ll<jj){
6520: if(itimes==1){
6521: if(mle>=1)
6522: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
6523: fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
6524: fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
6525: }else{
6526: if(mle>=1)
6527: printf(" %.5e",matcov[jj][ll]);
6528: fprintf(ficlog," %.5e",matcov[jj][ll]);
6529: fprintf(ficres," %.5e",matcov[jj][ll]);
6530: }
6531: }else{
6532: if(itimes==1){
6533: if(mle>=1)
6534: printf(" Var(%s%1d%1d)",ca,i,j);
6535: fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
6536: fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
6537: }else{
6538: if(mle>=1)
6539: printf(" %.5e",matcov[jj][ll]);
6540: fprintf(ficlog," %.5e",matcov[jj][ll]);
6541: fprintf(ficres," %.5e",matcov[jj][ll]);
6542: }
6543: }
6544: }
6545: } /* end lk */
6546: } /* end lj */
6547: } /* end li */
6548: if(mle>=1)
6549: printf("\n");
6550: fprintf(ficlog,"\n");
6551: fprintf(ficres,"\n");
6552: numlinepar++;
6553: } /* end k*/
6554: } /*end j */
6555: } /* end i */
6556: } /* end itimes */
6557:
6558: fflush(ficlog);
6559: fflush(ficres);
6560:
6561: while((c=getc(ficpar))=='#' && c!= EOF){
6562: ungetc(c,ficpar);
6563: fgets(line, MAXLINE, ficpar);
1.141 brouard 6564: fputs(line,stdout);
1.126 brouard 6565: fputs(line,ficparo);
6566: }
6567: ungetc(c,ficpar);
6568:
6569: estepm=0;
6570: fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
6571: if (estepm==0 || estepm < stepm) estepm=stepm;
6572: if (fage <= 2) {
6573: bage = ageminpar;
6574: fage = agemaxpar;
6575: }
6576:
6577: fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
6578: fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
6579: fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
6580:
6581: while((c=getc(ficpar))=='#' && c!= EOF){
6582: ungetc(c,ficpar);
6583: fgets(line, MAXLINE, ficpar);
1.141 brouard 6584: fputs(line,stdout);
1.126 brouard 6585: fputs(line,ficparo);
6586: }
6587: ungetc(c,ficpar);
6588:
6589: 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);
6590: 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);
6591: 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);
6592: printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
6593: 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);
6594:
6595: while((c=getc(ficpar))=='#' && c!= EOF){
6596: ungetc(c,ficpar);
6597: fgets(line, MAXLINE, ficpar);
1.141 brouard 6598: fputs(line,stdout);
1.126 brouard 6599: fputs(line,ficparo);
6600: }
6601: ungetc(c,ficpar);
6602:
6603:
6604: dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
6605: dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
6606:
6607: fscanf(ficpar,"pop_based=%d\n",&popbased);
6608: fprintf(ficparo,"pop_based=%d\n",popbased);
6609: fprintf(ficres,"pop_based=%d\n",popbased);
6610:
6611: while((c=getc(ficpar))=='#' && c!= EOF){
6612: ungetc(c,ficpar);
6613: fgets(line, MAXLINE, ficpar);
1.141 brouard 6614: fputs(line,stdout);
1.126 brouard 6615: fputs(line,ficparo);
6616: }
6617: ungetc(c,ficpar);
6618:
6619: 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);
6620: 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);
6621: 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);
6622: 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);
6623: 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);
6624: /* day and month of proj2 are not used but only year anproj2.*/
6625:
6626:
6627:
1.145 brouard 6628: /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint); */
6629: /* ,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2); */
1.126 brouard 6630:
6631: replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
6632: printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
6633:
6634: printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
6635: model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
6636: jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
6637:
6638: /*------------ free_vector -------------*/
6639: /* chdir(path); */
6640:
6641: free_ivector(wav,1,imx);
6642: free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
6643: free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
6644: free_imatrix(mw,1,lastpass-firstpass+1,1,imx);
6645: free_lvector(num,1,n);
6646: free_vector(agedc,1,n);
6647: /*free_matrix(covar,0,NCOVMAX,1,n);*/
6648: /*free_matrix(covar,1,NCOVMAX,1,n);*/
6649: fclose(ficparo);
6650: fclose(ficres);
6651:
6652:
6653: /*--------------- Prevalence limit (period or stable prevalence) --------------*/
1.145 brouard 6654: #include "prevlim.h" /* Use ficrespl, ficlog */
1.126 brouard 6655: fclose(ficrespl);
6656:
1.145 brouard 6657: #ifdef FREEEXIT2
6658: #include "freeexit2.h"
6659: #endif
6660:
1.126 brouard 6661: /*------------- h Pij x at various ages ------------*/
1.145 brouard 6662: #include "hpijx.h"
6663: fclose(ficrespij);
1.126 brouard 6664:
1.145 brouard 6665: /*-------------- Variance of one-step probabilities---*/
6666: k=1;
1.126 brouard 6667: varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
6668:
6669:
6670: probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
6671: for(i=1;i<=AGESUP;i++)
6672: for(j=1;j<=NCOVMAX;j++)
6673: for(k=1;k<=NCOVMAX;k++)
6674: probs[i][j][k]=0.;
6675:
6676: /*---------- Forecasting ------------------*/
6677: /*if((stepm == 1) && (strcmp(model,".")==0)){*/
6678: if(prevfcast==1){
6679: /* if(stepm ==1){*/
6680: prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
6681: /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
6682: /* } */
6683: /* else{ */
6684: /* erreur=108; */
6685: /* 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); */
6686: /* 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); */
6687: /* } */
6688: }
6689:
6690:
1.127 brouard 6691: /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
6692:
6693: prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
6694: /* 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",\
6695: ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
6696: */
1.126 brouard 6697:
1.127 brouard 6698: if (mobilav!=0) {
6699: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
6700: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
6701: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
6702: printf(" Error in movingaverage mobilav=%d\n",mobilav);
6703: }
1.126 brouard 6704: }
6705:
6706:
1.127 brouard 6707: /*---------- Health expectancies, no variances ------------*/
6708:
1.126 brouard 6709: strcpy(filerese,"e");
6710: strcat(filerese,fileres);
6711: if((ficreseij=fopen(filerese,"w"))==NULL) {
6712: printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
6713: fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
6714: }
6715: printf("Computing Health Expectancies: result on file '%s' \n", filerese);
6716: fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
1.145 brouard 6717: /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
6718: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
6719:
6720: for (k=1; k <= (int) pow(2,cptcoveff); k++){
1.127 brouard 6721: fprintf(ficreseij,"\n#****** ");
6722: for(j=1;j<=cptcoveff;j++) {
6723: fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6724: }
6725: fprintf(ficreseij,"******\n");
6726:
6727: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
6728: oldm=oldms;savm=savms;
6729: evsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart);
6730:
6731: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
1.145 brouard 6732: /*}*/
1.127 brouard 6733: }
6734: fclose(ficreseij);
6735:
6736:
6737: /*---------- Health expectancies and variances ------------*/
6738:
6739:
6740: strcpy(filerest,"t");
6741: strcat(filerest,fileres);
6742: if((ficrest=fopen(filerest,"w"))==NULL) {
6743: printf("Problem with total LE resultfile: %s\n", filerest);goto end;
6744: fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
6745: }
6746: printf("Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);
6747: fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);
6748:
1.126 brouard 6749:
6750: strcpy(fileresstde,"stde");
6751: strcat(fileresstde,fileres);
6752: if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {
6753: printf("Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
6754: fprintf(ficlog,"Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
6755: }
6756: printf("Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
6757: fprintf(ficlog,"Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
6758:
6759: strcpy(filerescve,"cve");
6760: strcat(filerescve,fileres);
6761: if((ficrescveij=fopen(filerescve,"w"))==NULL) {
6762: printf("Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
6763: fprintf(ficlog,"Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
6764: }
6765: printf("Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
6766: fprintf(ficlog,"Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
6767:
6768: strcpy(fileresv,"v");
6769: strcat(fileresv,fileres);
6770: if((ficresvij=fopen(fileresv,"w"))==NULL) {
6771: printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
6772: fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
6773: }
6774: printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
6775: fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
6776:
1.145 brouard 6777: /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
6778: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
6779:
6780: for (k=1; k <= (int) pow(2,cptcoveff); k++){
6781: fprintf(ficrest,"\n#****** ");
1.126 brouard 6782: for(j=1;j<=cptcoveff;j++)
6783: fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6784: fprintf(ficrest,"******\n");
6785:
6786: fprintf(ficresstdeij,"\n#****** ");
6787: fprintf(ficrescveij,"\n#****** ");
6788: for(j=1;j<=cptcoveff;j++) {
6789: fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6790: fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6791: }
6792: fprintf(ficresstdeij,"******\n");
6793: fprintf(ficrescveij,"******\n");
6794:
6795: fprintf(ficresvij,"\n#****** ");
6796: for(j=1;j<=cptcoveff;j++)
6797: fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6798: fprintf(ficresvij,"******\n");
6799:
6800: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
6801: oldm=oldms;savm=savms;
1.127 brouard 6802: cvevsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);
1.145 brouard 6803: /*
6804: */
6805: /* goto endfree; */
1.126 brouard 6806:
6807: vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
6808: pstamp(ficrest);
1.145 brouard 6809:
6810:
1.128 brouard 6811: for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
1.145 brouard 6812: oldm=oldms;savm=savms; /* Segmentation fault */
1.161 brouard 6813: cptcod= 0; /* To be deleted */
6814: varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,vpopbased,mobilav, strstart); /* cptcod not initialized Intel */
1.145 brouard 6815: fprintf(ficrest,"# Total life expectancy with std error and decomposition into time to be expected in each health state\n# (weighted average of eij where weights are ");
1.128 brouard 6816: if(vpopbased==1)
6817: 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);
6818: else
6819: fprintf(ficrest,"the age specific period (stable) prevalences in each health state \n");
6820: fprintf(ficrest,"# Age e.. (std) ");
6821: for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
6822: fprintf(ficrest,"\n");
1.126 brouard 6823:
1.128 brouard 6824: epj=vector(1,nlstate+1);
6825: for(age=bage; age <=fage ;age++){
6826: prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
6827: if (vpopbased==1) {
6828: if(mobilav ==0){
6829: for(i=1; i<=nlstate;i++)
6830: prlim[i][i]=probs[(int)age][i][k];
6831: }else{ /* mobilav */
6832: for(i=1; i<=nlstate;i++)
6833: prlim[i][i]=mobaverage[(int)age][i][k];
6834: }
1.126 brouard 6835: }
6836:
1.128 brouard 6837: fprintf(ficrest," %4.0f",age);
6838: for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
6839: for(i=1, epj[j]=0.;i <=nlstate;i++) {
6840: epj[j] += prlim[i][i]*eij[i][j][(int)age];
6841: /* printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
6842: }
6843: epj[nlstate+1] +=epj[j];
1.126 brouard 6844: }
6845:
1.128 brouard 6846: for(i=1, vepp=0.;i <=nlstate;i++)
6847: for(j=1;j <=nlstate;j++)
6848: vepp += vareij[i][j][(int)age];
6849: fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
6850: for(j=1;j <=nlstate;j++){
6851: fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
6852: }
6853: fprintf(ficrest,"\n");
1.126 brouard 6854: }
6855: }
6856: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
6857: free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
6858: free_vector(epj,1,nlstate+1);
1.145 brouard 6859: /*}*/
1.126 brouard 6860: }
6861: free_vector(weight,1,n);
1.145 brouard 6862: free_imatrix(Tvard,1,NCOVMAX,1,2);
1.126 brouard 6863: free_imatrix(s,1,maxwav+1,1,n);
6864: free_matrix(anint,1,maxwav,1,n);
6865: free_matrix(mint,1,maxwav,1,n);
6866: free_ivector(cod,1,n);
6867: free_ivector(tab,1,NCOVMAX);
6868: fclose(ficresstdeij);
6869: fclose(ficrescveij);
6870: fclose(ficresvij);
6871: fclose(ficrest);
6872: fclose(ficpar);
6873:
6874: /*------- Variance of period (stable) prevalence------*/
6875:
6876: strcpy(fileresvpl,"vpl");
6877: strcat(fileresvpl,fileres);
6878: if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
6879: printf("Problem with variance of period (stable) prevalence resultfile: %s\n", fileresvpl);
6880: exit(0);
6881: }
6882: printf("Computing Variance-covariance of period (stable) prevalence: file '%s' \n", fileresvpl);
6883:
1.145 brouard 6884: /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
6885: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
6886:
6887: for (k=1; k <= (int) pow(2,cptcoveff); k++){
6888: fprintf(ficresvpl,"\n#****** ");
1.126 brouard 6889: for(j=1;j<=cptcoveff;j++)
6890: fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6891: fprintf(ficresvpl,"******\n");
6892:
6893: varpl=matrix(1,nlstate,(int) bage, (int) fage);
6894: oldm=oldms;savm=savms;
6895: varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k,strstart);
6896: free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
1.145 brouard 6897: /*}*/
1.126 brouard 6898: }
6899:
6900: fclose(ficresvpl);
6901:
6902: /*---------- End : free ----------------*/
6903: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
6904: free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
6905: } /* mle==-3 arrives here for freeing */
1.164 brouard 6906: /* endfree:*/
1.141 brouard 6907: free_matrix(prlim,1,nlstate,1,nlstate); /*here or after loop ? */
1.126 brouard 6908: free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
6909: free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
6910: free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
6911: free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
6912: free_matrix(covar,0,NCOVMAX,1,n);
6913: free_matrix(matcov,1,npar,1,npar);
6914: /*free_vector(delti,1,npar);*/
6915: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
6916: free_matrix(agev,1,maxwav,1,imx);
6917: free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
6918:
1.145 brouard 6919: free_ivector(ncodemax,1,NCOVMAX);
6920: free_ivector(Tvar,1,NCOVMAX);
6921: free_ivector(Tprod,1,NCOVMAX);
6922: free_ivector(Tvaraff,1,NCOVMAX);
6923: free_ivector(Tage,1,NCOVMAX);
1.126 brouard 6924:
6925: free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
6926: free_imatrix(codtab,1,100,1,10);
6927: fflush(fichtm);
6928: fflush(ficgp);
6929:
6930:
6931: if((nberr >0) || (nbwarn>0)){
6932: printf("End of Imach with %d errors and/or %d warnings\n",nberr,nbwarn);
6933: fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
6934: }else{
6935: printf("End of Imach\n");
6936: fprintf(ficlog,"End of Imach\n");
6937: }
6938: printf("See log file on %s\n",filelog);
6939: /* gettimeofday(&end_time, (struct timezone*)0);*/ /* after time */
1.157 brouard 6940: /*(void) gettimeofday(&end_time,&tzp);*/
6941: rend_time = time(NULL);
6942: end_time = *localtime(&rend_time);
6943: /* tml = *localtime(&end_time.tm_sec); */
6944: strcpy(strtend,asctime(&end_time));
1.126 brouard 6945: printf("Local time at start %s\nLocal time at end %s",strstart, strtend);
6946: fprintf(ficlog,"Local time at start %s\nLocal time at end %s\n",strstart, strtend);
1.157 brouard 6947: printf("Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
1.126 brouard 6948:
1.157 brouard 6949: printf("Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
6950: fprintf(ficlog,"Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
6951: fprintf(ficlog,"Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
1.126 brouard 6952: /* printf("Total time was %d uSec.\n", total_usecs);*/
6953: /* if(fileappend(fichtm,optionfilehtm)){ */
6954: fprintf(fichtm,"<br>Local time at start %s<br>Local time at end %s<br>\n</body></html>",strstart, strtend);
6955: fclose(fichtm);
6956: fprintf(fichtmcov,"<br>Local time at start %s<br>Local time at end %s<br>\n</body></html>",strstart, strtend);
6957: fclose(fichtmcov);
6958: fclose(ficgp);
6959: fclose(ficlog);
6960: /*------ End -----------*/
6961:
6962:
6963: printf("Before Current directory %s!\n",pathcd);
6964: if(chdir(pathcd) != 0)
6965: printf("Can't move to directory %s!\n",path);
6966: if(getcwd(pathcd,MAXLINE) > 0)
6967: printf("Current directory %s!\n",pathcd);
6968: /*strcat(plotcmd,CHARSEPARATOR);*/
6969: sprintf(plotcmd,"gnuplot");
1.157 brouard 6970: #ifdef _WIN32
1.126 brouard 6971: sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
6972: #endif
6973: if(!stat(plotcmd,&info)){
1.158 brouard 6974: printf("Error or gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
1.126 brouard 6975: if(!stat(getenv("GNUPLOTBIN"),&info)){
1.158 brouard 6976: printf("Error or gnuplot program not found: '%s' Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);
1.126 brouard 6977: }else
6978: strcpy(pplotcmd,plotcmd);
1.157 brouard 6979: #ifdef __unix
1.126 brouard 6980: strcpy(plotcmd,GNUPLOTPROGRAM);
6981: if(!stat(plotcmd,&info)){
1.158 brouard 6982: printf("Error gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
1.126 brouard 6983: }else
6984: strcpy(pplotcmd,plotcmd);
6985: #endif
6986: }else
6987: strcpy(pplotcmd,plotcmd);
6988:
6989: sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
1.158 brouard 6990: printf("Starting graphs with: '%s'\n",plotcmd);fflush(stdout);
1.126 brouard 6991:
6992: if((outcmd=system(plotcmd)) != 0){
1.158 brouard 6993: printf("gnuplot command might not be in your path: '%s', err=%d\n", plotcmd, outcmd);
1.154 brouard 6994: printf("\n Trying if gnuplot resides on the same directory that IMaCh\n");
1.152 brouard 6995: sprintf(plotcmd,"%sgnuplot %s", pathimach, optionfilegnuplot);
1.150 brouard 6996: if((outcmd=system(plotcmd)) != 0)
1.153 brouard 6997: printf("\n Still a problem with gnuplot command %s, err=%d\n", plotcmd, outcmd);
1.126 brouard 6998: }
1.158 brouard 6999: printf(" Successful, please wait...");
1.126 brouard 7000: while (z[0] != 'q') {
7001: /* chdir(path); */
1.154 brouard 7002: printf("\nType e to edit results with your browser, g to graph again and q for exit: ");
1.126 brouard 7003: scanf("%s",z);
7004: /* if (z[0] == 'c') system("./imach"); */
7005: if (z[0] == 'e') {
1.158 brouard 7006: #ifdef __APPLE__
1.152 brouard 7007: sprintf(pplotcmd, "open %s", optionfilehtm);
1.157 brouard 7008: #elif __linux
7009: sprintf(pplotcmd, "xdg-open %s", optionfilehtm);
1.153 brouard 7010: #else
1.152 brouard 7011: sprintf(pplotcmd, "%s", optionfilehtm);
1.153 brouard 7012: #endif
7013: printf("Starting browser with: %s",pplotcmd);fflush(stdout);
7014: system(pplotcmd);
1.126 brouard 7015: }
7016: else if (z[0] == 'g') system(plotcmd);
7017: else if (z[0] == 'q') exit(0);
7018: }
7019: end:
7020: while (z[0] != 'q') {
7021: printf("\nType q for exiting: ");
7022: scanf("%s",z);
7023: }
7024: }
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