Annotation of imach/src/imach-nlopt.c, revision 1.1
1.1 ! brouard 1: /* $Id: imach.c,v 1.161 2014/09/15 20:41:41 brouard Exp $
! 2: $State: Exp $
! 3: $Log: imach.c,v $
! 4: Revision 1.161 2014/09/15 20:41:41 brouard
! 5: Summary: Problem with macro SQR on Intel compiler
! 6:
! 7: Revision 1.160 2014/09/02 09:24:05 brouard
! 8: *** empty log message ***
! 9:
! 10: Revision 1.159 2014/09/01 10:34:10 brouard
! 11: Summary: WIN32
! 12: Author: Brouard
! 13:
! 14: Revision 1.158 2014/08/27 17:11:51 brouard
! 15: *** empty log message ***
! 16:
! 17: Revision 1.157 2014/08/27 16:26:55 brouard
! 18: Summary: Preparing windows Visual studio version
! 19: Author: Brouard
! 20:
! 21: In order to compile on Visual studio, time.h is now correct and time_t
! 22: and tm struct should be used. difftime should be used but sometimes I
! 23: just make the differences in raw time format (time(&now).
! 24: Trying to suppress #ifdef LINUX
! 25: Add xdg-open for __linux in order to open default browser.
! 26:
! 27: Revision 1.156 2014/08/25 20:10:10 brouard
! 28: *** empty log message ***
! 29:
! 30: Revision 1.155 2014/08/25 18:32:34 brouard
! 31: Summary: New compile, minor changes
! 32: Author: Brouard
! 33:
! 34: Revision 1.154 2014/06/20 17:32:08 brouard
! 35: Summary: Outputs now all graphs of convergence to period prevalence
! 36:
! 37: Revision 1.153 2014/06/20 16:45:46 brouard
! 38: Summary: If 3 live state, convergence to period prevalence on same graph
! 39: Author: Brouard
! 40:
! 41: Revision 1.152 2014/06/18 17:54:09 brouard
! 42: Summary: open browser, use gnuplot on same dir than imach if not found in the path
! 43:
! 44: Revision 1.151 2014/06/18 16:43:30 brouard
! 45: *** empty log message ***
! 46:
! 47: Revision 1.150 2014/06/18 16:42:35 brouard
! 48: Summary: If gnuplot is not in the path try on same directory than imach binary (OSX)
! 49: Author: brouard
! 50:
! 51: Revision 1.149 2014/06/18 15:51:14 brouard
! 52: Summary: Some fixes in parameter files errors
! 53: Author: Nicolas Brouard
! 54:
! 55: Revision 1.148 2014/06/17 17:38:48 brouard
! 56: Summary: Nothing new
! 57: Author: Brouard
! 58:
! 59: Just a new packaging for OS/X version 0.98nS
! 60:
! 61: Revision 1.147 2014/06/16 10:33:11 brouard
! 62: *** empty log message ***
! 63:
! 64: Revision 1.146 2014/06/16 10:20:28 brouard
! 65: Summary: Merge
! 66: Author: Brouard
! 67:
! 68: Merge, before building revised version.
! 69:
! 70: Revision 1.145 2014/06/10 21:23:15 brouard
! 71: Summary: Debugging with valgrind
! 72: Author: Nicolas Brouard
! 73:
! 74: Lot of changes in order to output the results with some covariates
! 75: After the Edimburgh REVES conference 2014, it seems mandatory to
! 76: improve the code.
! 77: No more memory valgrind error but a lot has to be done in order to
! 78: continue the work of splitting the code into subroutines.
! 79: Also, decodemodel has been improved. Tricode is still not
! 80: optimal. nbcode should be improved. Documentation has been added in
! 81: the source code.
! 82:
! 83: Revision 1.143 2014/01/26 09:45:38 brouard
! 84: Summary: Version 0.98nR (to be improved, but gives same optimization results as 0.98k. Nice, promising
! 85:
! 86: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
! 87: (Module): Version 0.98nR Running ok, but output format still only works for three covariates.
! 88:
! 89: Revision 1.142 2014/01/26 03:57:36 brouard
! 90: Summary: gnuplot changed plot w l 1 has to be changed to plot w l lt 2
! 91:
! 92: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
! 93:
! 94: Revision 1.141 2014/01/26 02:42:01 brouard
! 95: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
! 96:
! 97: Revision 1.140 2011/09/02 10:37:54 brouard
! 98: Summary: times.h is ok with mingw32 now.
! 99:
! 100: Revision 1.139 2010/06/14 07:50:17 brouard
! 101: After the theft of my laptop, I probably lost some lines of codes which were not uploaded to the CVS tree.
! 102: I remember having already fixed agemin agemax which are pointers now but not cvs saved.
! 103:
! 104: Revision 1.138 2010/04/30 18:19:40 brouard
! 105: *** empty log message ***
! 106:
! 107: Revision 1.137 2010/04/29 18:11:38 brouard
! 108: (Module): Checking covariates for more complex models
! 109: than V1+V2. A lot of change to be done. Unstable.
! 110:
! 111: Revision 1.136 2010/04/26 20:30:53 brouard
! 112: (Module): merging some libgsl code. Fixing computation
! 113: of likelione (using inter/intrapolation if mle = 0) in order to
! 114: get same likelihood as if mle=1.
! 115: Some cleaning of code and comments added.
! 116:
! 117: Revision 1.135 2009/10/29 15:33:14 brouard
! 118: (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
! 119:
! 120: Revision 1.134 2009/10/29 13:18:53 brouard
! 121: (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
! 122:
! 123: Revision 1.133 2009/07/06 10:21:25 brouard
! 124: just nforces
! 125:
! 126: Revision 1.132 2009/07/06 08:22:05 brouard
! 127: Many tings
! 128:
! 129: Revision 1.131 2009/06/20 16:22:47 brouard
! 130: Some dimensions resccaled
! 131:
! 132: Revision 1.130 2009/05/26 06:44:34 brouard
! 133: (Module): Max Covariate is now set to 20 instead of 8. A
! 134: lot of cleaning with variables initialized to 0. Trying to make
! 135: V2+V3*age+V1+V4 strb=V3*age+V1+V4 working better.
! 136:
! 137: Revision 1.129 2007/08/31 13:49:27 lievre
! 138: Modification of the way of exiting when the covariate is not binary in order to see on the window the error message before exiting
! 139:
! 140: Revision 1.128 2006/06/30 13:02:05 brouard
! 141: (Module): Clarifications on computing e.j
! 142:
! 143: Revision 1.127 2006/04/28 18:11:50 brouard
! 144: (Module): Yes the sum of survivors was wrong since
! 145: imach-114 because nhstepm was no more computed in the age
! 146: loop. Now we define nhstepma in the age loop.
! 147: (Module): In order to speed up (in case of numerous covariates) we
! 148: compute health expectancies (without variances) in a first step
! 149: and then all the health expectancies with variances or standard
! 150: deviation (needs data from the Hessian matrices) which slows the
! 151: computation.
! 152: In the future we should be able to stop the program is only health
! 153: expectancies and graph are needed without standard deviations.
! 154:
! 155: Revision 1.126 2006/04/28 17:23:28 brouard
! 156: (Module): Yes the sum of survivors was wrong since
! 157: imach-114 because nhstepm was no more computed in the age
! 158: loop. Now we define nhstepma in the age loop.
! 159: Version 0.98h
! 160:
! 161: Revision 1.125 2006/04/04 15:20:31 lievre
! 162: Errors in calculation of health expectancies. Age was not initialized.
! 163: Forecasting file added.
! 164:
! 165: Revision 1.124 2006/03/22 17:13:53 lievre
! 166: Parameters are printed with %lf instead of %f (more numbers after the comma).
! 167: The log-likelihood is printed in the log file
! 168:
! 169: Revision 1.123 2006/03/20 10:52:43 brouard
! 170: * imach.c (Module): <title> changed, corresponds to .htm file
! 171: name. <head> headers where missing.
! 172:
! 173: * imach.c (Module): Weights can have a decimal point as for
! 174: English (a comma might work with a correct LC_NUMERIC environment,
! 175: otherwise the weight is truncated).
! 176: Modification of warning when the covariates values are not 0 or
! 177: 1.
! 178: Version 0.98g
! 179:
! 180: Revision 1.122 2006/03/20 09:45:41 brouard
! 181: (Module): Weights can have a decimal point as for
! 182: English (a comma might work with a correct LC_NUMERIC environment,
! 183: otherwise the weight is truncated).
! 184: Modification of warning when the covariates values are not 0 or
! 185: 1.
! 186: Version 0.98g
! 187:
! 188: Revision 1.121 2006/03/16 17:45:01 lievre
! 189: * imach.c (Module): Comments concerning covariates added
! 190:
! 191: * imach.c (Module): refinements in the computation of lli if
! 192: status=-2 in order to have more reliable computation if stepm is
! 193: not 1 month. Version 0.98f
! 194:
! 195: Revision 1.120 2006/03/16 15:10:38 lievre
! 196: (Module): refinements in the computation of lli if
! 197: status=-2 in order to have more reliable computation if stepm is
! 198: not 1 month. Version 0.98f
! 199:
! 200: Revision 1.119 2006/03/15 17:42:26 brouard
! 201: (Module): Bug if status = -2, the loglikelihood was
! 202: computed as likelihood omitting the logarithm. Version O.98e
! 203:
! 204: Revision 1.118 2006/03/14 18:20:07 brouard
! 205: (Module): varevsij Comments added explaining the second
! 206: table of variances if popbased=1 .
! 207: (Module): Covariances of eij, ekl added, graphs fixed, new html link.
! 208: (Module): Function pstamp added
! 209: (Module): Version 0.98d
! 210:
! 211: Revision 1.117 2006/03/14 17:16:22 brouard
! 212: (Module): varevsij Comments added explaining the second
! 213: table of variances if popbased=1 .
! 214: (Module): Covariances of eij, ekl added, graphs fixed, new html link.
! 215: (Module): Function pstamp added
! 216: (Module): Version 0.98d
! 217:
! 218: Revision 1.116 2006/03/06 10:29:27 brouard
! 219: (Module): Variance-covariance wrong links and
! 220: varian-covariance of ej. is needed (Saito).
! 221:
! 222: Revision 1.115 2006/02/27 12:17:45 brouard
! 223: (Module): One freematrix added in mlikeli! 0.98c
! 224:
! 225: Revision 1.114 2006/02/26 12:57:58 brouard
! 226: (Module): Some improvements in processing parameter
! 227: filename with strsep.
! 228:
! 229: Revision 1.113 2006/02/24 14:20:24 brouard
! 230: (Module): Memory leaks checks with valgrind and:
! 231: datafile was not closed, some imatrix were not freed and on matrix
! 232: allocation too.
! 233:
! 234: Revision 1.112 2006/01/30 09:55:26 brouard
! 235: (Module): Back to gnuplot.exe instead of wgnuplot.exe
! 236:
! 237: Revision 1.111 2006/01/25 20:38:18 brouard
! 238: (Module): Lots of cleaning and bugs added (Gompertz)
! 239: (Module): Comments can be added in data file. Missing date values
! 240: can be a simple dot '.'.
! 241:
! 242: Revision 1.110 2006/01/25 00:51:50 brouard
! 243: (Module): Lots of cleaning and bugs added (Gompertz)
! 244:
! 245: Revision 1.109 2006/01/24 19:37:15 brouard
! 246: (Module): Comments (lines starting with a #) are allowed in data.
! 247:
! 248: Revision 1.108 2006/01/19 18:05:42 lievre
! 249: Gnuplot problem appeared...
! 250: To be fixed
! 251:
! 252: Revision 1.107 2006/01/19 16:20:37 brouard
! 253: Test existence of gnuplot in imach path
! 254:
! 255: Revision 1.106 2006/01/19 13:24:36 brouard
! 256: Some cleaning and links added in html output
! 257:
! 258: Revision 1.105 2006/01/05 20:23:19 lievre
! 259: *** empty log message ***
! 260:
! 261: Revision 1.104 2005/09/30 16:11:43 lievre
! 262: (Module): sump fixed, loop imx fixed, and simplifications.
! 263: (Module): If the status is missing at the last wave but we know
! 264: that the person is alive, then we can code his/her status as -2
! 265: (instead of missing=-1 in earlier versions) and his/her
! 266: contributions to the likelihood is 1 - Prob of dying from last
! 267: health status (= 1-p13= p11+p12 in the easiest case of somebody in
! 268: the healthy state at last known wave). Version is 0.98
! 269:
! 270: Revision 1.103 2005/09/30 15:54:49 lievre
! 271: (Module): sump fixed, loop imx fixed, and simplifications.
! 272:
! 273: Revision 1.102 2004/09/15 17:31:30 brouard
! 274: Add the possibility to read data file including tab characters.
! 275:
! 276: Revision 1.101 2004/09/15 10:38:38 brouard
! 277: Fix on curr_time
! 278:
! 279: Revision 1.100 2004/07/12 18:29:06 brouard
! 280: Add version for Mac OS X. Just define UNIX in Makefile
! 281:
! 282: Revision 1.99 2004/06/05 08:57:40 brouard
! 283: *** empty log message ***
! 284:
! 285: Revision 1.98 2004/05/16 15:05:56 brouard
! 286: New version 0.97 . First attempt to estimate force of mortality
! 287: directly from the data i.e. without the need of knowing the health
! 288: state at each age, but using a Gompertz model: log u =a + b*age .
! 289: This is the basic analysis of mortality and should be done before any
! 290: other analysis, in order to test if the mortality estimated from the
! 291: cross-longitudinal survey is different from the mortality estimated
! 292: from other sources like vital statistic data.
! 293:
! 294: The same imach parameter file can be used but the option for mle should be -3.
! 295:
! 296: Agnès, who wrote this part of the code, tried to keep most of the
! 297: former routines in order to include the new code within the former code.
! 298:
! 299: The output is very simple: only an estimate of the intercept and of
! 300: the slope with 95% confident intervals.
! 301:
! 302: Current limitations:
! 303: A) Even if you enter covariates, i.e. with the
! 304: model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
! 305: B) There is no computation of Life Expectancy nor Life Table.
! 306:
! 307: Revision 1.97 2004/02/20 13:25:42 lievre
! 308: Version 0.96d. Population forecasting command line is (temporarily)
! 309: suppressed.
! 310:
! 311: Revision 1.96 2003/07/15 15:38:55 brouard
! 312: * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
! 313: rewritten within the same printf. Workaround: many printfs.
! 314:
! 315: Revision 1.95 2003/07/08 07:54:34 brouard
! 316: * imach.c (Repository):
! 317: (Repository): Using imachwizard code to output a more meaningful covariance
! 318: matrix (cov(a12,c31) instead of numbers.
! 319:
! 320: Revision 1.94 2003/06/27 13:00:02 brouard
! 321: Just cleaning
! 322:
! 323: Revision 1.93 2003/06/25 16:33:55 brouard
! 324: (Module): On windows (cygwin) function asctime_r doesn't
! 325: exist so I changed back to asctime which exists.
! 326: (Module): Version 0.96b
! 327:
! 328: Revision 1.92 2003/06/25 16:30:45 brouard
! 329: (Module): On windows (cygwin) function asctime_r doesn't
! 330: exist so I changed back to asctime which exists.
! 331:
! 332: Revision 1.91 2003/06/25 15:30:29 brouard
! 333: * imach.c (Repository): Duplicated warning errors corrected.
! 334: (Repository): Elapsed time after each iteration is now output. It
! 335: helps to forecast when convergence will be reached. Elapsed time
! 336: is stamped in powell. We created a new html file for the graphs
! 337: concerning matrix of covariance. It has extension -cov.htm.
! 338:
! 339: Revision 1.90 2003/06/24 12:34:15 brouard
! 340: (Module): Some bugs corrected for windows. Also, when
! 341: mle=-1 a template is output in file "or"mypar.txt with the design
! 342: of the covariance matrix to be input.
! 343:
! 344: Revision 1.89 2003/06/24 12:30:52 brouard
! 345: (Module): Some bugs corrected for windows. Also, when
! 346: mle=-1 a template is output in file "or"mypar.txt with the design
! 347: of the covariance matrix to be input.
! 348:
! 349: Revision 1.88 2003/06/23 17:54:56 brouard
! 350: * 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.
! 351:
! 352: Revision 1.87 2003/06/18 12:26:01 brouard
! 353: Version 0.96
! 354:
! 355: Revision 1.86 2003/06/17 20:04:08 brouard
! 356: (Module): Change position of html and gnuplot routines and added
! 357: routine fileappend.
! 358:
! 359: Revision 1.85 2003/06/17 13:12:43 brouard
! 360: * imach.c (Repository): Check when date of death was earlier that
! 361: current date of interview. It may happen when the death was just
! 362: prior to the death. In this case, dh was negative and likelihood
! 363: was wrong (infinity). We still send an "Error" but patch by
! 364: assuming that the date of death was just one stepm after the
! 365: interview.
! 366: (Repository): Because some people have very long ID (first column)
! 367: we changed int to long in num[] and we added a new lvector for
! 368: memory allocation. But we also truncated to 8 characters (left
! 369: truncation)
! 370: (Repository): No more line truncation errors.
! 371:
! 372: Revision 1.84 2003/06/13 21:44:43 brouard
! 373: * imach.c (Repository): Replace "freqsummary" at a correct
! 374: place. It differs from routine "prevalence" which may be called
! 375: many times. Probs is memory consuming and must be used with
! 376: parcimony.
! 377: Version 0.95a3 (should output exactly the same maximization than 0.8a2)
! 378:
! 379: Revision 1.83 2003/06/10 13:39:11 lievre
! 380: *** empty log message ***
! 381:
! 382: Revision 1.82 2003/06/05 15:57:20 brouard
! 383: Add log in imach.c and fullversion number is now printed.
! 384:
! 385: */
! 386: /*
! 387: Interpolated Markov Chain
! 388:
! 389: Short summary of the programme:
! 390:
! 391: This program computes Healthy Life Expectancies from
! 392: cross-longitudinal data. Cross-longitudinal data consist in: -1- a
! 393: first survey ("cross") where individuals from different ages are
! 394: interviewed on their health status or degree of disability (in the
! 395: case of a health survey which is our main interest) -2- at least a
! 396: second wave of interviews ("longitudinal") which measure each change
! 397: (if any) in individual health status. Health expectancies are
! 398: computed from the time spent in each health state according to a
! 399: model. More health states you consider, more time is necessary to reach the
! 400: Maximum Likelihood of the parameters involved in the model. The
! 401: simplest model is the multinomial logistic model where pij is the
! 402: probability to be observed in state j at the second wave
! 403: conditional to be observed in state i at the first wave. Therefore
! 404: the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
! 405: 'age' is age and 'sex' is a covariate. If you want to have a more
! 406: complex model than "constant and age", you should modify the program
! 407: where the markup *Covariates have to be included here again* invites
! 408: you to do it. More covariates you add, slower the
! 409: convergence.
! 410:
! 411: The advantage of this computer programme, compared to a simple
! 412: multinomial logistic model, is clear when the delay between waves is not
! 413: identical for each individual. Also, if a individual missed an
! 414: intermediate interview, the information is lost, but taken into
! 415: account using an interpolation or extrapolation.
! 416:
! 417: hPijx is the probability to be observed in state i at age x+h
! 418: conditional to the observed state i at age x. The delay 'h' can be
! 419: split into an exact number (nh*stepm) of unobserved intermediate
! 420: states. This elementary transition (by month, quarter,
! 421: semester or year) is modelled as a multinomial logistic. The hPx
! 422: matrix is simply the matrix product of nh*stepm elementary matrices
! 423: and the contribution of each individual to the likelihood is simply
! 424: hPijx.
! 425:
! 426: Also this programme outputs the covariance matrix of the parameters but also
! 427: of the life expectancies. It also computes the period (stable) prevalence.
! 428:
! 429: Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
! 430: Institut national d'études démographiques, Paris.
! 431: This software have been partly granted by Euro-REVES, a concerted action
! 432: from the European Union.
! 433: It is copyrighted identically to a GNU software product, ie programme and
! 434: software can be distributed freely for non commercial use. Latest version
! 435: can be accessed at http://euroreves.ined.fr/imach .
! 436:
! 437: Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
! 438: or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
! 439:
! 440: **********************************************************************/
! 441: /*
! 442: main
! 443: read parameterfile
! 444: read datafile
! 445: concatwav
! 446: freqsummary
! 447: if (mle >= 1)
! 448: mlikeli
! 449: print results files
! 450: if mle==1
! 451: computes hessian
! 452: read end of parameter file: agemin, agemax, bage, fage, estepm
! 453: begin-prev-date,...
! 454: open gnuplot file
! 455: open html file
! 456: period (stable) prevalence | pl_nom 1-1 2-2 etc by covariate
! 457: for age prevalim() | #****** V1=0 V2=1 V3=1 V4=0 ******
! 458: | 65 1 0 2 1 3 1 4 0 0.96326 0.03674
! 459: freexexit2 possible for memory heap.
! 460:
! 461: h Pij x | pij_nom ficrestpij
! 462: # Cov Agex agex+h hpijx with i,j= 1-1 1-2 1-3 2-1 2-2 2-3
! 463: 1 85 85 1.00000 0.00000 0.00000 0.00000 1.00000 0.00000
! 464: 1 85 86 0.68299 0.22291 0.09410 0.71093 0.00000 0.28907
! 465:
! 466: 1 65 99 0.00364 0.00322 0.99314 0.00350 0.00310 0.99340
! 467: 1 65 100 0.00214 0.00204 0.99581 0.00206 0.00196 0.99597
! 468: variance of p one-step probabilities varprob | prob_nom ficresprob #One-step probabilities and stand. devi in ()
! 469: Standard deviation of one-step probabilities | probcor_nom ficresprobcor #One-step probabilities and correlation matrix
! 470: Matrix of variance covariance of one-step probabilities | probcov_nom ficresprobcov #One-step probabilities and covariance matrix
! 471:
! 472: forecasting if prevfcast==1 prevforecast call prevalence()
! 473: health expectancies
! 474: Variance-covariance of DFLE
! 475: prevalence()
! 476: movingaverage()
! 477: varevsij()
! 478: if popbased==1 varevsij(,popbased)
! 479: total life expectancies
! 480: Variance of period (stable) prevalence
! 481: end
! 482: */
! 483:
! 484:
! 485:
! 486:
! 487: #include <math.h>
! 488: #include <stdio.h>
! 489: #include <stdlib.h>
! 490: #include <string.h>
! 491:
! 492: #ifdef _WIN32
! 493: #include <io.h>
! 494: #else
! 495: #include <unistd.h>
! 496: #endif
! 497:
! 498: #include <limits.h>
! 499: #include <sys/types.h>
! 500: #include <sys/stat.h>
! 501: #include <errno.h>
! 502: /* extern int errno; */
! 503:
! 504: /* #ifdef LINUX */
! 505: /* #include <time.h> */
! 506: /* #include "timeval.h" */
! 507: /* #else */
! 508: /* #include <sys/time.h> */
! 509: /* #endif */
! 510:
! 511: #include <time.h>
! 512:
! 513: #ifdef GSL
! 514: #include <gsl/gsl_errno.h>
! 515: #include <gsl/gsl_multimin.h>
! 516: #endif
! 517:
! 518: #ifdef NLOPT
! 519: #include <nlopt.h>
! 520: #endif
! 521:
! 522: /* #include <libintl.h> */
! 523: /* #define _(String) gettext (String) */
! 524:
! 525: #define MAXLINE 1024 /* Was 256. Overflow with 312 with 2 states and 4 covariates. Should be ok */
! 526:
! 527: #define GNUPLOTPROGRAM "gnuplot"
! 528: /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
! 529: #define FILENAMELENGTH 132
! 530:
! 531: #define GLOCK_ERROR_NOPATH -1 /* empty path */
! 532: #define GLOCK_ERROR_GETCWD -2 /* cannot get cwd */
! 533:
! 534: #define MAXPARM 128 /**< Maximum number of parameters for the optimization */
! 535: #define NPARMAX 64 /**< (nlstate+ndeath-1)*nlstate*ncovmodel */
! 536:
! 537: #define NINTERVMAX 8
! 538: #define NLSTATEMAX 8 /**< Maximum number of live states (for func) */
! 539: #define NDEATHMAX 8 /**< Maximum number of dead states (for func) */
! 540: #define NCOVMAX 20 /**< Maximum number of covariates, including generated covariates V1*V2 */
! 541: #define codtabm(h,k) 1 & (h-1) >> (k-1) ;
! 542: #define MAXN 20000
! 543: #define YEARM 12. /**< Number of months per year */
! 544: #define AGESUP 130
! 545: #define AGEBASE 40
! 546: #define AGEGOMP 10. /**< Minimal age for Gompertz adjustment */
! 547: #ifdef _WIN32
! 548: #define DIRSEPARATOR '\\'
! 549: #define CHARSEPARATOR "\\"
! 550: #define ODIRSEPARATOR '/'
! 551: #else
! 552: #define DIRSEPARATOR '/'
! 553: #define CHARSEPARATOR "/"
! 554: #define ODIRSEPARATOR '\\'
! 555: #endif
! 556:
! 557: /* $Id: imach.c,v 1.161 2014/09/15 20:41:41 brouard Exp $ */
! 558: /* $State: Exp $ */
! 559:
! 560: char version[]="Imach version 0.98nX, August 2014,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121)";
! 561: char fullversion[]="$Revision: 1.161 $ $Date: 2014/09/15 20:41:41 $";
! 562: char strstart[80];
! 563: char optionfilext[10], optionfilefiname[FILENAMELENGTH];
! 564: int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings */
! 565: int nvar=0, nforce=0; /* Number of variables, number of forces */
! 566: /* Number of covariates model=V2+V1+ V3*age+V2*V4 */
! 567: int cptcovn=0; /**< cptcovn number of covariates added in the model (excepting constant and age and age*product) */
! 568: int cptcovt=0; /**< cptcovt number of covariates added in the model (excepting constant and age) */
! 569: int cptcovs=0; /**< cptcovs number of simple covariates V2+V1 =2 */
! 570: int cptcovage=0; /**< Number of covariates with age: V3*age only =1 */
! 571: int cptcovprodnoage=0; /**< Number of covariate products without age */
! 572: int cptcoveff=0; /* Total number of covariates to vary for printing results */
! 573: int cptcov=0; /* Working variable */
! 574: int npar=NPARMAX;
! 575: int nlstate=2; /* Number of live states */
! 576: int ndeath=1; /* Number of dead states */
! 577: int ncovmodel=0, ncovcol=0; /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
! 578: int popbased=0;
! 579:
! 580: int *wav; /* Number of waves for this individuual 0 is possible */
! 581: int maxwav=0; /* Maxim number of waves */
! 582: int jmin=0, jmax=0; /* min, max spacing between 2 waves */
! 583: int ijmin=0, ijmax=0; /* Individuals having jmin and jmax */
! 584: int gipmx=0, gsw=0; /* Global variables on the number of contributions
! 585: to the likelihood and the sum of weights (done by funcone)*/
! 586: int mle=1, weightopt=0;
! 587: int **mw; /* mw[mi][i] is number of the mi wave for this individual */
! 588: int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
! 589: int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
! 590: * wave mi and wave mi+1 is not an exact multiple of stepm. */
! 591: int countcallfunc=0; /* Count the number of calls to func */
! 592: double jmean=1; /* Mean space between 2 waves */
! 593: double **matprod2(); /* test */
! 594: double **oldm, **newm, **savm; /* Working pointers to matrices */
! 595: double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
! 596: /*FILE *fic ; */ /* Used in readdata only */
! 597: FILE *ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
! 598: FILE *ficlog, *ficrespow;
! 599: int globpr=0; /* Global variable for printing or not */
! 600: double fretone; /* Only one call to likelihood */
! 601: long ipmx=0; /* Number of contributions */
! 602: double sw; /* Sum of weights */
! 603: char filerespow[FILENAMELENGTH];
! 604: char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
! 605: FILE *ficresilk;
! 606: FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
! 607: FILE *ficresprobmorprev;
! 608: FILE *fichtm, *fichtmcov; /* Html File */
! 609: FILE *ficreseij;
! 610: char filerese[FILENAMELENGTH];
! 611: FILE *ficresstdeij;
! 612: char fileresstde[FILENAMELENGTH];
! 613: FILE *ficrescveij;
! 614: char filerescve[FILENAMELENGTH];
! 615: FILE *ficresvij;
! 616: char fileresv[FILENAMELENGTH];
! 617: FILE *ficresvpl;
! 618: char fileresvpl[FILENAMELENGTH];
! 619: char title[MAXLINE];
! 620: char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH], filerespl[FILENAMELENGTH];
! 621: char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
! 622: char tmpout[FILENAMELENGTH], tmpout2[FILENAMELENGTH];
! 623: char command[FILENAMELENGTH];
! 624: int outcmd=0;
! 625:
! 626: char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
! 627:
! 628: char filelog[FILENAMELENGTH]; /* Log file */
! 629: char filerest[FILENAMELENGTH];
! 630: char fileregp[FILENAMELENGTH];
! 631: char popfile[FILENAMELENGTH];
! 632:
! 633: char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
! 634:
! 635: /* struct timeval start_time, end_time, curr_time, last_time, forecast_time; */
! 636: /* struct timezone tzp; */
! 637: /* extern int gettimeofday(); */
! 638: struct tm tml, *gmtime(), *localtime();
! 639:
! 640: extern time_t time();
! 641:
! 642: struct tm start_time, end_time, curr_time, last_time, forecast_time;
! 643: time_t rstart_time, rend_time, rcurr_time, rlast_time, rforecast_time; /* raw time */
! 644: struct tm tm;
! 645:
! 646: char strcurr[80], strfor[80];
! 647:
! 648: char *endptr;
! 649: long lval;
! 650: double dval;
! 651:
! 652: #define NR_END 1
! 653: #define FREE_ARG char*
! 654: #define FTOL 1.0e-10
! 655:
! 656: #define NRANSI
! 657: #define ITMAX 200
! 658:
! 659: #define TOL 2.0e-4
! 660:
! 661: #define CGOLD 0.3819660
! 662: #define ZEPS 1.0e-10
! 663: #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);
! 664:
! 665: #define GOLD 1.618034
! 666: #define GLIMIT 100.0
! 667: #define TINY 1.0e-20
! 668:
! 669: static double maxarg1,maxarg2;
! 670: #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
! 671: #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
! 672:
! 673: #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
! 674: #define rint(a) floor(a+0.5)
! 675:
! 676: static double sqrarg;
! 677: #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
! 678: #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}
! 679: int agegomp= AGEGOMP;
! 680:
! 681: int imx;
! 682: int stepm=1;
! 683: /* Stepm, step in month: minimum step interpolation*/
! 684:
! 685: int estepm;
! 686: /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
! 687:
! 688: int m,nb;
! 689: long *num;
! 690: int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
! 691: double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
! 692: double **pmmij, ***probs;
! 693: double *ageexmed,*agecens;
! 694: double dateintmean=0;
! 695:
! 696: double *weight;
! 697: int **s; /* Status */
! 698: double *agedc;
! 699: double **covar; /**< covar[j,i], value of jth covariate for individual i,
! 700: * covar=matrix(0,NCOVMAX,1,n);
! 701: * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; */
! 702: double idx;
! 703: int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */
! 704: int *Ndum; /** Freq of modality (tricode */
! 705: int **codtab; /**< codtab=imatrix(1,100,1,10); */
! 706: int **Tvard, *Tprod, cptcovprod, *Tvaraff;
! 707: double *lsurv, *lpop, *tpop;
! 708:
! 709: double ftol=FTOL; /**< Tolerance for computing Max Likelihood */
! 710: double ftolhess; /**< Tolerance for computing hessian */
! 711:
! 712: /**************** split *************************/
! 713: static int split( char *path, char *dirc, char *name, char *ext, char *finame )
! 714: {
! 715: /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
! 716: the name of the file (name), its extension only (ext) and its first part of the name (finame)
! 717: */
! 718: char *ss; /* pointer */
! 719: int l1, l2; /* length counters */
! 720:
! 721: l1 = strlen(path ); /* length of path */
! 722: if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
! 723: ss= strrchr( path, DIRSEPARATOR ); /* find last / */
! 724: if ( ss == NULL ) { /* no directory, so determine current directory */
! 725: strcpy( name, path ); /* we got the fullname name because no directory */
! 726: /*if(strrchr(path, ODIRSEPARATOR )==NULL)
! 727: printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
! 728: /* get current working directory */
! 729: /* extern char* getcwd ( char *buf , int len);*/
! 730: if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
! 731: return( GLOCK_ERROR_GETCWD );
! 732: }
! 733: /* got dirc from getcwd*/
! 734: printf(" DIRC = %s \n",dirc);
! 735: } else { /* strip direcotry from path */
! 736: ss++; /* after this, the filename */
! 737: l2 = strlen( ss ); /* length of filename */
! 738: if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
! 739: strcpy( name, ss ); /* save file name */
! 740: strncpy( dirc, path, l1 - l2 ); /* now the directory */
! 741: dirc[l1-l2] = 0; /* add zero */
! 742: printf(" DIRC2 = %s \n",dirc);
! 743: }
! 744: /* We add a separator at the end of dirc if not exists */
! 745: l1 = strlen( dirc ); /* length of directory */
! 746: if( dirc[l1-1] != DIRSEPARATOR ){
! 747: dirc[l1] = DIRSEPARATOR;
! 748: dirc[l1+1] = 0;
! 749: printf(" DIRC3 = %s \n",dirc);
! 750: }
! 751: ss = strrchr( name, '.' ); /* find last / */
! 752: if (ss >0){
! 753: ss++;
! 754: strcpy(ext,ss); /* save extension */
! 755: l1= strlen( name);
! 756: l2= strlen(ss)+1;
! 757: strncpy( finame, name, l1-l2);
! 758: finame[l1-l2]= 0;
! 759: }
! 760:
! 761: return( 0 ); /* we're done */
! 762: }
! 763:
! 764:
! 765: /******************************************/
! 766:
! 767: void replace_back_to_slash(char *s, char*t)
! 768: {
! 769: int i;
! 770: int lg=0;
! 771: i=0;
! 772: lg=strlen(t);
! 773: for(i=0; i<= lg; i++) {
! 774: (s[i] = t[i]);
! 775: if (t[i]== '\\') s[i]='/';
! 776: }
! 777: }
! 778:
! 779: char *trimbb(char *out, char *in)
! 780: { /* Trim multiple blanks in line but keeps first blanks if line starts with blanks */
! 781: char *s;
! 782: s=out;
! 783: while (*in != '\0'){
! 784: while( *in == ' ' && *(in+1) == ' '){ /* && *(in+1) != '\0'){*/
! 785: in++;
! 786: }
! 787: *out++ = *in++;
! 788: }
! 789: *out='\0';
! 790: return s;
! 791: }
! 792:
! 793: char *cutl(char *blocc, char *alocc, char *in, char occ)
! 794: {
! 795: /* cuts string in into blocc and alocc where blocc ends before first occurence of char 'occ'
! 796: and alocc starts after first occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
! 797: gives blocc="abcdef2ghi" and alocc="j".
! 798: If occ is not found blocc is null and alocc is equal to in. Returns blocc
! 799: */
! 800: char *s, *t;
! 801: t=in;s=in;
! 802: while ((*in != occ) && (*in != '\0')){
! 803: *alocc++ = *in++;
! 804: }
! 805: if( *in == occ){
! 806: *(alocc)='\0';
! 807: s=++in;
! 808: }
! 809:
! 810: if (s == t) {/* occ not found */
! 811: *(alocc-(in-s))='\0';
! 812: in=s;
! 813: }
! 814: while ( *in != '\0'){
! 815: *blocc++ = *in++;
! 816: }
! 817:
! 818: *blocc='\0';
! 819: return t;
! 820: }
! 821: char *cutv(char *blocc, char *alocc, char *in, char occ)
! 822: {
! 823: /* cuts string in into blocc and alocc where blocc ends before last occurence of char 'occ'
! 824: and alocc starts after last occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
! 825: gives blocc="abcdef2ghi" and alocc="j".
! 826: If occ is not found blocc is null and alocc is equal to in. Returns alocc
! 827: */
! 828: char *s, *t;
! 829: t=in;s=in;
! 830: while (*in != '\0'){
! 831: while( *in == occ){
! 832: *blocc++ = *in++;
! 833: s=in;
! 834: }
! 835: *blocc++ = *in++;
! 836: }
! 837: if (s == t) /* occ not found */
! 838: *(blocc-(in-s))='\0';
! 839: else
! 840: *(blocc-(in-s)-1)='\0';
! 841: in=s;
! 842: while ( *in != '\0'){
! 843: *alocc++ = *in++;
! 844: }
! 845:
! 846: *alocc='\0';
! 847: return s;
! 848: }
! 849:
! 850: int nbocc(char *s, char occ)
! 851: {
! 852: int i,j=0;
! 853: int lg=20;
! 854: i=0;
! 855: lg=strlen(s);
! 856: for(i=0; i<= lg; i++) {
! 857: if (s[i] == occ ) j++;
! 858: }
! 859: return j;
! 860: }
! 861:
! 862: /* void cutv(char *u,char *v, char*t, char occ) */
! 863: /* { */
! 864: /* /\* cuts string t into u and v where u ends before last occurence of char 'occ' */
! 865: /* and v starts after last occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2') */
! 866: /* gives u="abcdef2ghi" and v="j" *\/ */
! 867: /* int i,lg,j,p=0; */
! 868: /* i=0; */
! 869: /* lg=strlen(t); */
! 870: /* for(j=0; j<=lg-1; j++) { */
! 871: /* if((t[j]!= occ) && (t[j+1]== occ)) p=j+1; */
! 872: /* } */
! 873:
! 874: /* for(j=0; j<p; j++) { */
! 875: /* (u[j] = t[j]); */
! 876: /* } */
! 877: /* u[p]='\0'; */
! 878:
! 879: /* for(j=0; j<= lg; j++) { */
! 880: /* if (j>=(p+1))(v[j-p-1] = t[j]); */
! 881: /* } */
! 882: /* } */
! 883:
! 884: #ifdef _WIN32
! 885: char * strsep(char **pp, const char *delim)
! 886: {
! 887: char *p, *q;
! 888:
! 889: if ((p = *pp) == NULL)
! 890: return 0;
! 891: if ((q = strpbrk (p, delim)) != NULL)
! 892: {
! 893: *pp = q + 1;
! 894: *q = '\0';
! 895: }
! 896: else
! 897: *pp = 0;
! 898: return p;
! 899: }
! 900: #endif
! 901:
! 902: /********************** nrerror ********************/
! 903:
! 904: void nrerror(char error_text[])
! 905: {
! 906: fprintf(stderr,"ERREUR ...\n");
! 907: fprintf(stderr,"%s\n",error_text);
! 908: exit(EXIT_FAILURE);
! 909: }
! 910: /*********************** vector *******************/
! 911: double *vector(int nl, int nh)
! 912: {
! 913: double *v;
! 914: v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
! 915: if (!v) nrerror("allocation failure in vector");
! 916: return v-nl+NR_END;
! 917: }
! 918:
! 919: /************************ free vector ******************/
! 920: void free_vector(double*v, int nl, int nh)
! 921: {
! 922: free((FREE_ARG)(v+nl-NR_END));
! 923: }
! 924:
! 925: /************************ivector *******************************/
! 926: int *ivector(long nl,long nh)
! 927: {
! 928: int *v;
! 929: v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
! 930: if (!v) nrerror("allocation failure in ivector");
! 931: return v-nl+NR_END;
! 932: }
! 933:
! 934: /******************free ivector **************************/
! 935: void free_ivector(int *v, long nl, long nh)
! 936: {
! 937: free((FREE_ARG)(v+nl-NR_END));
! 938: }
! 939:
! 940: /************************lvector *******************************/
! 941: long *lvector(long nl,long nh)
! 942: {
! 943: long *v;
! 944: v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
! 945: if (!v) nrerror("allocation failure in ivector");
! 946: return v-nl+NR_END;
! 947: }
! 948:
! 949: /******************free lvector **************************/
! 950: void free_lvector(long *v, long nl, long nh)
! 951: {
! 952: free((FREE_ARG)(v+nl-NR_END));
! 953: }
! 954:
! 955: /******************* imatrix *******************************/
! 956: int **imatrix(long nrl, long nrh, long ncl, long nch)
! 957: /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */
! 958: {
! 959: long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;
! 960: int **m;
! 961:
! 962: /* allocate pointers to rows */
! 963: m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));
! 964: if (!m) nrerror("allocation failure 1 in matrix()");
! 965: m += NR_END;
! 966: m -= nrl;
! 967:
! 968:
! 969: /* allocate rows and set pointers to them */
! 970: m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));
! 971: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
! 972: m[nrl] += NR_END;
! 973: m[nrl] -= ncl;
! 974:
! 975: for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;
! 976:
! 977: /* return pointer to array of pointers to rows */
! 978: return m;
! 979: }
! 980:
! 981: /****************** free_imatrix *************************/
! 982: void free_imatrix(m,nrl,nrh,ncl,nch)
! 983: int **m;
! 984: long nch,ncl,nrh,nrl;
! 985: /* free an int matrix allocated by imatrix() */
! 986: {
! 987: free((FREE_ARG) (m[nrl]+ncl-NR_END));
! 988: free((FREE_ARG) (m+nrl-NR_END));
! 989: }
! 990:
! 991: /******************* matrix *******************************/
! 992: double **matrix(long nrl, long nrh, long ncl, long nch)
! 993: {
! 994: long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
! 995: double **m;
! 996:
! 997: m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
! 998: if (!m) nrerror("allocation failure 1 in matrix()");
! 999: m += NR_END;
! 1000: m -= nrl;
! 1001:
! 1002: m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
! 1003: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
! 1004: m[nrl] += NR_END;
! 1005: m[nrl] -= ncl;
! 1006:
! 1007: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
! 1008: return m;
! 1009: /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) or &(m[1][0])
! 1010: m[i] = address of ith row of the table. &(m[i]) is its value which is another adress
! 1011: that of m[i][0]. In order to get the value p m[i][0] but it is unitialized.
! 1012: */
! 1013: }
! 1014:
! 1015: /*************************free matrix ************************/
! 1016: void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
! 1017: {
! 1018: free((FREE_ARG)(m[nrl]+ncl-NR_END));
! 1019: free((FREE_ARG)(m+nrl-NR_END));
! 1020: }
! 1021:
! 1022: /******************* ma3x *******************************/
! 1023: double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
! 1024: {
! 1025: long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
! 1026: double ***m;
! 1027:
! 1028: m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
! 1029: if (!m) nrerror("allocation failure 1 in matrix()");
! 1030: m += NR_END;
! 1031: m -= nrl;
! 1032:
! 1033: m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
! 1034: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
! 1035: m[nrl] += NR_END;
! 1036: m[nrl] -= ncl;
! 1037:
! 1038: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
! 1039:
! 1040: m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
! 1041: if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
! 1042: m[nrl][ncl] += NR_END;
! 1043: m[nrl][ncl] -= nll;
! 1044: for (j=ncl+1; j<=nch; j++)
! 1045: m[nrl][j]=m[nrl][j-1]+nlay;
! 1046:
! 1047: for (i=nrl+1; i<=nrh; i++) {
! 1048: m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
! 1049: for (j=ncl+1; j<=nch; j++)
! 1050: m[i][j]=m[i][j-1]+nlay;
! 1051: }
! 1052: return m;
! 1053: /* gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
! 1054: &(m[i][j][k]) <=> *((*(m+i) + j)+k)
! 1055: */
! 1056: }
! 1057:
! 1058: /*************************free ma3x ************************/
! 1059: void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
! 1060: {
! 1061: free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
! 1062: free((FREE_ARG)(m[nrl]+ncl-NR_END));
! 1063: free((FREE_ARG)(m+nrl-NR_END));
! 1064: }
! 1065:
! 1066: /*************** function subdirf ***********/
! 1067: char *subdirf(char fileres[])
! 1068: {
! 1069: /* Caution optionfilefiname is hidden */
! 1070: strcpy(tmpout,optionfilefiname);
! 1071: strcat(tmpout,"/"); /* Add to the right */
! 1072: strcat(tmpout,fileres);
! 1073: return tmpout;
! 1074: }
! 1075:
! 1076: /*************** function subdirf2 ***********/
! 1077: char *subdirf2(char fileres[], char *preop)
! 1078: {
! 1079:
! 1080: /* Caution optionfilefiname is hidden */
! 1081: strcpy(tmpout,optionfilefiname);
! 1082: strcat(tmpout,"/");
! 1083: strcat(tmpout,preop);
! 1084: strcat(tmpout,fileres);
! 1085: return tmpout;
! 1086: }
! 1087:
! 1088: /*************** function subdirf3 ***********/
! 1089: char *subdirf3(char fileres[], char *preop, char *preop2)
! 1090: {
! 1091:
! 1092: /* Caution optionfilefiname is hidden */
! 1093: strcpy(tmpout,optionfilefiname);
! 1094: strcat(tmpout,"/");
! 1095: strcat(tmpout,preop);
! 1096: strcat(tmpout,preop2);
! 1097: strcat(tmpout,fileres);
! 1098: return tmpout;
! 1099: }
! 1100:
! 1101: /***************** f1dim *************************/
! 1102: extern int ncom;
! 1103: extern double *pcom,*xicom;
! 1104: extern double (*nrfunc)(double []);
! 1105:
! 1106: double f1dim(double x)
! 1107: {
! 1108: int j;
! 1109: double f;
! 1110: double *xt;
! 1111:
! 1112: xt=vector(1,ncom);
! 1113: for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];
! 1114: f=(*nrfunc)(xt);
! 1115: free_vector(xt,1,ncom);
! 1116: return f;
! 1117: }
! 1118:
! 1119: /*****************brent *************************/
! 1120: double brent(double ax, double bx, double cx, double (*f)(double), double tol, double *xmin)
! 1121: {
! 1122: int iter;
! 1123: double a,b,d,etemp;
! 1124: double fu=0,fv,fw,fx;
! 1125: double ftemp;
! 1126: double p,q,r,tol1,tol2,u,v,w,x,xm;
! 1127: double e=0.0;
! 1128:
! 1129: a=(ax < cx ? ax : cx);
! 1130: b=(ax > cx ? ax : cx);
! 1131: x=w=v=bx;
! 1132: fw=fv=fx=(*f)(x);
! 1133: for (iter=1;iter<=ITMAX;iter++) {
! 1134: xm=0.5*(a+b);
! 1135: tol2=2.0*(tol1=tol*fabs(x)+ZEPS);
! 1136: /* if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
! 1137: printf(".");fflush(stdout);
! 1138: fprintf(ficlog,".");fflush(ficlog);
! 1139: #ifdef DEBUG
! 1140: 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);
! 1141: 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);
! 1142: /* if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
! 1143: #endif
! 1144: if (fabs(x-xm) <= (tol2-0.5*(b-a))){
! 1145: *xmin=x;
! 1146: return fx;
! 1147: }
! 1148: ftemp=fu;
! 1149: if (fabs(e) > tol1) {
! 1150: r=(x-w)*(fx-fv);
! 1151: q=(x-v)*(fx-fw);
! 1152: p=(x-v)*q-(x-w)*r;
! 1153: q=2.0*(q-r);
! 1154: if (q > 0.0) p = -p;
! 1155: q=fabs(q);
! 1156: etemp=e;
! 1157: e=d;
! 1158: if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))
! 1159: d=CGOLD*(e=(x >= xm ? a-x : b-x));
! 1160: else {
! 1161: d=p/q;
! 1162: u=x+d;
! 1163: if (u-a < tol2 || b-u < tol2)
! 1164: d=SIGN(tol1,xm-x);
! 1165: }
! 1166: } else {
! 1167: d=CGOLD*(e=(x >= xm ? a-x : b-x));
! 1168: }
! 1169: u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));
! 1170: fu=(*f)(u);
! 1171: if (fu <= fx) {
! 1172: if (u >= x) a=x; else b=x;
! 1173: SHFT(v,w,x,u)
! 1174: SHFT(fv,fw,fx,fu)
! 1175: } else {
! 1176: if (u < x) a=u; else b=u;
! 1177: if (fu <= fw || w == x) {
! 1178: v=w;
! 1179: w=u;
! 1180: fv=fw;
! 1181: fw=fu;
! 1182: } else if (fu <= fv || v == x || v == w) {
! 1183: v=u;
! 1184: fv=fu;
! 1185: }
! 1186: }
! 1187: }
! 1188: nrerror("Too many iterations in brent");
! 1189: *xmin=x;
! 1190: return fx;
! 1191: }
! 1192:
! 1193: /****************** mnbrak ***********************/
! 1194:
! 1195: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,
! 1196: double (*func)(double))
! 1197: {
! 1198: double ulim,u,r,q, dum;
! 1199: double fu;
! 1200:
! 1201: *fa=(*func)(*ax);
! 1202: *fb=(*func)(*bx);
! 1203: if (*fb > *fa) {
! 1204: SHFT(dum,*ax,*bx,dum)
! 1205: SHFT(dum,*fb,*fa,dum)
! 1206: }
! 1207: *cx=(*bx)+GOLD*(*bx-*ax);
! 1208: *fc=(*func)(*cx);
! 1209: while (*fb > *fc) {
! 1210: r=(*bx-*ax)*(*fb-*fc);
! 1211: q=(*bx-*cx)*(*fb-*fa);
! 1212: u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/
! 1213: (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));
! 1214: ulim=(*bx)+GLIMIT*(*cx-*bx);
! 1215: if ((*bx-u)*(u-*cx) > 0.0) {
! 1216: fu=(*func)(u);
! 1217: } else if ((*cx-u)*(u-ulim) > 0.0) {
! 1218: fu=(*func)(u);
! 1219: if (fu < *fc) {
! 1220: SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))
! 1221: SHFT(*fb,*fc,fu,(*func)(u))
! 1222: }
! 1223: } else if ((u-ulim)*(ulim-*cx) >= 0.0) {
! 1224: u=ulim;
! 1225: fu=(*func)(u);
! 1226: } else {
! 1227: u=(*cx)+GOLD*(*cx-*bx);
! 1228: fu=(*func)(u);
! 1229: }
! 1230: SHFT(*ax,*bx,*cx,u)
! 1231: SHFT(*fa,*fb,*fc,fu)
! 1232: }
! 1233: }
! 1234:
! 1235: /*************** linmin ************************/
! 1236:
! 1237: int ncom;
! 1238: double *pcom,*xicom;
! 1239: double (*nrfunc)(double []);
! 1240:
! 1241: void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))
! 1242: {
! 1243: double brent(double ax, double bx, double cx,
! 1244: double (*f)(double), double tol, double *xmin);
! 1245: double f1dim(double x);
! 1246: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,
! 1247: double *fc, double (*func)(double));
! 1248: int j;
! 1249: double xx,xmin,bx,ax;
! 1250: double fx,fb,fa;
! 1251:
! 1252: ncom=n;
! 1253: pcom=vector(1,n);
! 1254: xicom=vector(1,n);
! 1255: nrfunc=func;
! 1256: for (j=1;j<=n;j++) {
! 1257: pcom[j]=p[j];
! 1258: xicom[j]=xi[j];
! 1259: }
! 1260: ax=0.0;
! 1261: xx=1.0;
! 1262: mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);
! 1263: *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);
! 1264: #ifdef DEBUG
! 1265: printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
! 1266: fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
! 1267: #endif
! 1268: for (j=1;j<=n;j++) {
! 1269: xi[j] *= xmin;
! 1270: p[j] += xi[j];
! 1271: }
! 1272: free_vector(xicom,1,n);
! 1273: free_vector(pcom,1,n);
! 1274: }
! 1275:
! 1276: char *asc_diff_time(long time_sec, char ascdiff[])
! 1277: {
! 1278: long sec_left, days, hours, minutes;
! 1279: days = (time_sec) / (60*60*24);
! 1280: sec_left = (time_sec) % (60*60*24);
! 1281: hours = (sec_left) / (60*60) ;
! 1282: sec_left = (sec_left) %(60*60);
! 1283: minutes = (sec_left) /60;
! 1284: sec_left = (sec_left) % (60);
! 1285: sprintf(ascdiff,"%ld day(s) %ld hour(s) %ld minute(s) %ld second(s)",days, hours, minutes, sec_left);
! 1286: return ascdiff;
! 1287: }
! 1288:
! 1289: /*************** powell ************************/
! 1290: void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,
! 1291: double (*func)(double []))
! 1292: {
! 1293: void linmin(double p[], double xi[], int n, double *fret,
! 1294: double (*func)(double []));
! 1295: int i,ibig,j;
! 1296: double del,t,*pt,*ptt,*xit;
! 1297: double fp,fptt;
! 1298: double *xits;
! 1299: int niterf, itmp;
! 1300:
! 1301: pt=vector(1,n);
! 1302: ptt=vector(1,n);
! 1303: xit=vector(1,n);
! 1304: xits=vector(1,n);
! 1305: *fret=(*func)(p);
! 1306: for (j=1;j<=n;j++) pt[j]=p[j];
! 1307: rcurr_time = time(NULL);
! 1308: for (*iter=1;;++(*iter)) {
! 1309: fp=(*fret);
! 1310: ibig=0;
! 1311: del=0.0;
! 1312: rlast_time=rcurr_time;
! 1313: /* (void) gettimeofday(&curr_time,&tzp); */
! 1314: rcurr_time = time(NULL);
! 1315: curr_time = *localtime(&rcurr_time);
! 1316: printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, rcurr_time-rlast_time, rcurr_time-rstart_time);fflush(stdout);
! 1317: fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret,rcurr_time-rlast_time, rcurr_time-rstart_time); fflush(ficlog);
! 1318: /* fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tm_sec-start_time.tm_sec); */
! 1319: for (i=1;i<=n;i++) {
! 1320: printf(" %d %.12f",i, p[i]);
! 1321: fprintf(ficlog," %d %.12lf",i, p[i]);
! 1322: fprintf(ficrespow," %.12lf", p[i]);
! 1323: }
! 1324: printf("\n");
! 1325: fprintf(ficlog,"\n");
! 1326: fprintf(ficrespow,"\n");fflush(ficrespow);
! 1327: if(*iter <=3){
! 1328: tml = *localtime(&rcurr_time);
! 1329: strcpy(strcurr,asctime(&tml));
! 1330: /* asctime_r(&tm,strcurr); */
! 1331: rforecast_time=rcurr_time;
! 1332: itmp = strlen(strcurr);
! 1333: if(strcurr[itmp-1]=='\n') /* Windows outputs with a new line */
! 1334: strcurr[itmp-1]='\0';
! 1335: printf("\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
! 1336: fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
! 1337: for(niterf=10;niterf<=30;niterf+=10){
! 1338: rforecast_time=rcurr_time+(niterf-*iter)*(rcurr_time-rlast_time);
! 1339: forecast_time = *localtime(&rforecast_time);
! 1340: /* asctime_r(&tmf,strfor); */
! 1341: strcpy(strfor,asctime(&forecast_time));
! 1342: itmp = strlen(strfor);
! 1343: if(strfor[itmp-1]=='\n')
! 1344: strfor[itmp-1]='\0';
! 1345: 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);
! 1346: 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);
! 1347: }
! 1348: }
! 1349: for (i=1;i<=n;i++) {
! 1350: for (j=1;j<=n;j++) xit[j]=xi[j][i];
! 1351: fptt=(*fret);
! 1352: #ifdef DEBUG
! 1353: printf("fret=%lf \n",*fret);
! 1354: fprintf(ficlog,"fret=%lf \n",*fret);
! 1355: #endif
! 1356: printf("%d",i);fflush(stdout);
! 1357: fprintf(ficlog,"%d",i);fflush(ficlog);
! 1358: linmin(p,xit,n,fret,func);
! 1359: if (fabs(fptt-(*fret)) > del) {
! 1360: del=fabs(fptt-(*fret));
! 1361: ibig=i;
! 1362: }
! 1363: #ifdef DEBUG
! 1364: printf("%d %.12e",i,(*fret));
! 1365: fprintf(ficlog,"%d %.12e",i,(*fret));
! 1366: for (j=1;j<=n;j++) {
! 1367: xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
! 1368: printf(" x(%d)=%.12e",j,xit[j]);
! 1369: fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
! 1370: }
! 1371: for(j=1;j<=n;j++) {
! 1372: printf(" p=%.12e",p[j]);
! 1373: fprintf(ficlog," p=%.12e",p[j]);
! 1374: }
! 1375: printf("\n");
! 1376: fprintf(ficlog,"\n");
! 1377: #endif
! 1378: }
! 1379: if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
! 1380: #ifdef DEBUG
! 1381: int k[2],l;
! 1382: k[0]=1;
! 1383: k[1]=-1;
! 1384: printf("Max: %.12e",(*func)(p));
! 1385: fprintf(ficlog,"Max: %.12e",(*func)(p));
! 1386: for (j=1;j<=n;j++) {
! 1387: printf(" %.12e",p[j]);
! 1388: fprintf(ficlog," %.12e",p[j]);
! 1389: }
! 1390: printf("\n");
! 1391: fprintf(ficlog,"\n");
! 1392: for(l=0;l<=1;l++) {
! 1393: for (j=1;j<=n;j++) {
! 1394: ptt[j]=p[j]+(p[j]-pt[j])*k[l];
! 1395: printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
! 1396: fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
! 1397: }
! 1398: printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
! 1399: fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
! 1400: }
! 1401: #endif
! 1402:
! 1403:
! 1404: free_vector(xit,1,n);
! 1405: free_vector(xits,1,n);
! 1406: free_vector(ptt,1,n);
! 1407: free_vector(pt,1,n);
! 1408: return;
! 1409: }
! 1410: if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");
! 1411: for (j=1;j<=n;j++) { /* Computes an extrapolated point */
! 1412: ptt[j]=2.0*p[j]-pt[j];
! 1413: xit[j]=p[j]-pt[j];
! 1414: pt[j]=p[j];
! 1415: }
! 1416: fptt=(*func)(ptt);
! 1417: if (fptt < fp) { /* If extrapolated point is better, decide if we keep that new direction or not */
! 1418: /* x1 f1=fp x2 f2=*fret x3 f3=fptt, xm fm */
! 1419: /* From x1 (P0) distance of x2 is at h and x3 is 2h */
! 1420: /* Let f"(x2) be the 2nd derivative equal everywhere. Then the parabolic through (x1,f1), (x2,f2) and (x3,f3)
! 1421: will reach at f3 = fm + h^2/2 f''m ; f" = (f1 -2f2 +f3 ) / h**2 */
! 1422: /* f1-f3 = delta(2h) = 2 h**2 f'' = 2(f1- 2f2 +f3) */
! 1423: /* Thus we compare delta(2h) with observed f1-f3 */
! 1424: /* or best gain on one ancient line 'del' with total gain f1-f2 = f1 - f2 - 'del' with del */
! 1425: /* t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); */
! 1426: t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del);
! 1427: t= t- del*SQR(fp-fptt);
! 1428: printf("t1= %.12lf, t2= %.12lf, t=%.12lf\n", 2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del),del*SQR(fp-fptt),t);
! 1429: 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);
! 1430: #ifdef DEBUG
! 1431: printf("t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
! 1432: (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
! 1433: fprintf(ficlog,"t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
! 1434: (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
! 1435: 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);
! 1436: 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);
! 1437: #endif
! 1438: if (t < 0.0) { /* Then we use it for last direction */
! 1439: linmin(p,xit,n,fret,func); /* computes mean on the extrapolated direction.*/
! 1440: for (j=1;j<=n;j++) {
! 1441: xi[j][ibig]=xi[j][n]; /* Replace the direction with biggest decrease by n */
! 1442: xi[j][n]=xit[j]; /* and nth direction by the extrapolated */
! 1443: }
! 1444: printf("Gaining to use average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
! 1445: fprintf(ficlog,"Gaining to use average direction of P0 P%d instead of biggest increase direction :\n",n,ibig);
! 1446:
! 1447: #ifdef DEBUG
! 1448: for(j=1;j<=n;j++){
! 1449: printf(" %.12e",xit[j]);
! 1450: fprintf(ficlog," %.12e",xit[j]);
! 1451: }
! 1452: printf("\n");
! 1453: fprintf(ficlog,"\n");
! 1454: #endif
! 1455: }
! 1456: }
! 1457: }
! 1458: }
! 1459:
! 1460: /**** Prevalence limit (stable or period prevalence) ****************/
! 1461:
! 1462: double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
! 1463: {
! 1464: /* Computes the prevalence limit in each live state at age x by left multiplying the unit
! 1465: matrix by transitions matrix until convergence is reached */
! 1466:
! 1467: int i, ii,j,k;
! 1468: double min, max, maxmin, maxmax,sumnew=0.;
! 1469: /* double **matprod2(); */ /* test */
! 1470: double **out, cov[NCOVMAX+1], **pmij();
! 1471: double **newm;
! 1472: double agefin, delaymax=50 ; /* Max number of years to converge */
! 1473:
! 1474: for (ii=1;ii<=nlstate+ndeath;ii++)
! 1475: for (j=1;j<=nlstate+ndeath;j++){
! 1476: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
! 1477: }
! 1478:
! 1479: cov[1]=1.;
! 1480:
! 1481: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
! 1482: for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
! 1483: newm=savm;
! 1484: /* Covariates have to be included here again */
! 1485: cov[2]=agefin;
! 1486:
! 1487: for (k=1; k<=cptcovn;k++) {
! 1488: cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
! 1489: /*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]]);*/
! 1490: }
! 1491: /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
! 1492: /* for (k=1; k<=cptcovprod;k++) /\* Useless *\/ */
! 1493: /* cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]] * nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]]; */
! 1494:
! 1495: /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
! 1496: /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
! 1497: /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
! 1498: /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
! 1499: /* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind *\/ */
! 1500: out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /* Bug Valgrind */
! 1501:
! 1502: savm=oldm;
! 1503: oldm=newm;
! 1504: maxmax=0.;
! 1505: for(j=1;j<=nlstate;j++){
! 1506: min=1.;
! 1507: max=0.;
! 1508: for(i=1; i<=nlstate; i++) {
! 1509: sumnew=0;
! 1510: for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
! 1511: prlim[i][j]= newm[i][j]/(1-sumnew);
! 1512: /*printf(" prevalim i=%d, j=%d, prmlim[%d][%d]=%f, agefin=%d \n", i, j, i, j, prlim[i][j],(int)agefin);*/
! 1513: max=FMAX(max,prlim[i][j]);
! 1514: min=FMIN(min,prlim[i][j]);
! 1515: }
! 1516: maxmin=max-min;
! 1517: maxmax=FMAX(maxmax,maxmin);
! 1518: }
! 1519: if(maxmax < ftolpl){
! 1520: return prlim;
! 1521: }
! 1522: }
! 1523: }
! 1524:
! 1525: /*************** transition probabilities ***************/
! 1526:
! 1527: double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
! 1528: {
! 1529: /* According to parameters values stored in x and the covariate's values stored in cov,
! 1530: computes the probability to be observed in state j being in state i by appying the
! 1531: model to the ncovmodel covariates (including constant and age).
! 1532: lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc]
! 1533: and, according on how parameters are entered, the position of the coefficient xij(nc) of the
! 1534: ncth covariate in the global vector x is given by the formula:
! 1535: j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
! 1536: j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
! 1537: Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
! 1538: sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.
! 1539: Outputs ps[i][j] the probability to be observed in j being in j according to
! 1540: the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
! 1541: */
! 1542: double s1, lnpijopii;
! 1543: /*double t34;*/
! 1544: int i,j,j1, nc, ii, jj;
! 1545:
! 1546: for(i=1; i<= nlstate; i++){
! 1547: for(j=1; j<i;j++){
! 1548: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
! 1549: /*lnpijopii += param[i][j][nc]*cov[nc];*/
! 1550: lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
! 1551: /* printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
! 1552: }
! 1553: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
! 1554: /* printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
! 1555: }
! 1556: for(j=i+1; j<=nlstate+ndeath;j++){
! 1557: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
! 1558: /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
! 1559: lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
! 1560: /* printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
! 1561: }
! 1562: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
! 1563: }
! 1564: }
! 1565:
! 1566: for(i=1; i<= nlstate; i++){
! 1567: s1=0;
! 1568: for(j=1; j<i; j++){
! 1569: s1+=exp(ps[i][j]); /* In fact sums pij/pii */
! 1570: /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
! 1571: }
! 1572: for(j=i+1; j<=nlstate+ndeath; j++){
! 1573: s1+=exp(ps[i][j]); /* In fact sums pij/pii */
! 1574: /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
! 1575: }
! 1576: /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
! 1577: ps[i][i]=1./(s1+1.);
! 1578: /* Computing other pijs */
! 1579: for(j=1; j<i; j++)
! 1580: ps[i][j]= exp(ps[i][j])*ps[i][i];
! 1581: for(j=i+1; j<=nlstate+ndeath; j++)
! 1582: ps[i][j]= exp(ps[i][j])*ps[i][i];
! 1583: /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
! 1584: } /* end i */
! 1585:
! 1586: for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
! 1587: for(jj=1; jj<= nlstate+ndeath; jj++){
! 1588: ps[ii][jj]=0;
! 1589: ps[ii][ii]=1;
! 1590: }
! 1591: }
! 1592:
! 1593:
! 1594: /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
! 1595: /* for(jj=1; jj<= nlstate+ndeath; jj++){ */
! 1596: /* printf(" pmij ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
! 1597: /* } */
! 1598: /* printf("\n "); */
! 1599: /* } */
! 1600: /* printf("\n ");printf("%lf ",cov[2]);*/
! 1601: /*
! 1602: for(i=1; i<= npar; i++) printf("%f ",x[i]);
! 1603: goto end;*/
! 1604: return ps;
! 1605: }
! 1606:
! 1607: /**************** Product of 2 matrices ******************/
! 1608:
! 1609: double **matprod2(double **out, double **in,int nrl, int nrh, int ncl, int nch, int ncolol, int ncoloh, double **b)
! 1610: {
! 1611: /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
! 1612: b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
! 1613: /* in, b, out are matrice of pointers which should have been initialized
! 1614: before: only the contents of out is modified. The function returns
! 1615: a pointer to pointers identical to out */
! 1616: int i, j, k;
! 1617: for(i=nrl; i<= nrh; i++)
! 1618: for(k=ncolol; k<=ncoloh; k++){
! 1619: out[i][k]=0.;
! 1620: for(j=ncl; j<=nch; j++)
! 1621: out[i][k] +=in[i][j]*b[j][k];
! 1622: }
! 1623: return out;
! 1624: }
! 1625:
! 1626:
! 1627: /************* Higher Matrix Product ***************/
! 1628:
! 1629: double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
! 1630: {
! 1631: /* Computes the transition matrix starting at age 'age' over
! 1632: 'nhstepm*hstepm*stepm' months (i.e. until
! 1633: age (in years) age+nhstepm*hstepm*stepm/12) by multiplying
! 1634: nhstepm*hstepm matrices.
! 1635: Output is stored in matrix po[i][j][h] for h every 'hstepm' step
! 1636: (typically every 2 years instead of every month which is too big
! 1637: for the memory).
! 1638: Model is determined by parameters x and covariates have to be
! 1639: included manually here.
! 1640:
! 1641: */
! 1642:
! 1643: int i, j, d, h, k;
! 1644: double **out, cov[NCOVMAX+1];
! 1645: double **newm;
! 1646:
! 1647: /* Hstepm could be zero and should return the unit matrix */
! 1648: for (i=1;i<=nlstate+ndeath;i++)
! 1649: for (j=1;j<=nlstate+ndeath;j++){
! 1650: oldm[i][j]=(i==j ? 1.0 : 0.0);
! 1651: po[i][j][0]=(i==j ? 1.0 : 0.0);
! 1652: }
! 1653: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
! 1654: for(h=1; h <=nhstepm; h++){
! 1655: for(d=1; d <=hstepm; d++){
! 1656: newm=savm;
! 1657: /* Covariates have to be included here again */
! 1658: cov[1]=1.;
! 1659: cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
! 1660: for (k=1; k<=cptcovn;k++)
! 1661: cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
! 1662: for (k=1; k<=cptcovage;k++)
! 1663: cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
! 1664: for (k=1; k<=cptcovprod;k++) /* Useless because included in cptcovn */
! 1665: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
! 1666:
! 1667:
! 1668: /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
! 1669: /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
! 1670: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
! 1671: pmij(pmmij,cov,ncovmodel,x,nlstate));
! 1672: savm=oldm;
! 1673: oldm=newm;
! 1674: }
! 1675: for(i=1; i<=nlstate+ndeath; i++)
! 1676: for(j=1;j<=nlstate+ndeath;j++) {
! 1677: po[i][j][h]=newm[i][j];
! 1678: /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
! 1679: }
! 1680: /*printf("h=%d ",h);*/
! 1681: } /* end h */
! 1682: /* printf("\n H=%d \n",h); */
! 1683: return po;
! 1684: }
! 1685:
! 1686: double myfunc(unsigned n, const double *p, double *grad, double (*func) (double [])){
! 1687: /* double (*nrfunc)(double []); */
! 1688: /* double myfunc(unsigned n, const double *p, double *grad, void *my_func_data){ */
! 1689: double fret;
! 1690: double *xt;
! 1691: int j;
! 1692:
! 1693: xt=vector(1,n);
! 1694: for (j=1;j<=n;j++)
! 1695: xt[j]=p[j];
! 1696: ++countcallfunc;
! 1697:
! 1698: fret=(*func)(xt);
! 1699: printf("Function = %.12lf ",fret);
! 1700: for (j=1;j<=n;j++)
! 1701: printf(" %d %.8lf", j, p[j]);
! 1702: printf("\n");
! 1703: free_vector(xt,1,n);
! 1704: return fret;
! 1705: }
! 1706: /*************** log-likelihood *************/
! 1707: double func( double *x)
! 1708: {
! 1709: int i, ii, j, k, mi, d, kk;
! 1710: double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
! 1711: double **out;
! 1712: double sw; /* Sum of weights */
! 1713: double lli; /* Individual log likelihood */
! 1714: int s1, s2;
! 1715: double bbh, survp;
! 1716: long ipmx;
! 1717: /*extern weight */
! 1718: /* We are differentiating ll according to initial status */
! 1719: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
! 1720: /*for(i=1;i<imx;i++)
! 1721: printf(" %d\n",s[4][i]);
! 1722: */
! 1723: cov[1]=1.;
! 1724:
! 1725: for(k=1; k<=nlstate; k++) ll[k]=0.;
! 1726:
! 1727: if(mle==1){
! 1728: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
! 1729: /* Computes the values of the ncovmodel covariates of the model
! 1730: depending if the covariates are fixed or variying (age dependent) and stores them in cov[]
! 1731: Then computes with function pmij which return a matrix p[i][j] giving the elementary probability
! 1732: to be observed in j being in i according to the model.
! 1733: */
! 1734: for (k=1; k<=cptcovn;k++){ /* Simple and product covariates without age* products */
! 1735: cov[2+k]=covar[Tvar[k]][i];
! 1736: }
! 1737: /* In model V2+V1*V4+age*V3+V3*V2 Tvar[1] is V2, Tvar[2=V1*V4]
! 1738: is 6, Tvar[3=age*V3] should not be computed because of age Tvar[4=V3*V2]
! 1739: has been calculated etc */
! 1740: for(mi=1; mi<= wav[i]-1; mi++){
! 1741: for (ii=1;ii<=nlstate+ndeath;ii++)
! 1742: for (j=1;j<=nlstate+ndeath;j++){
! 1743: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
! 1744: savm[ii][j]=(ii==j ? 1.0 : 0.0);
! 1745: }
! 1746: for(d=0; d<dh[mi][i]; d++){
! 1747: newm=savm;
! 1748: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
! 1749: for (kk=1; kk<=cptcovage;kk++) {
! 1750: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; /* Tage[kk] gives the data-covariate associated with age */
! 1751: }
! 1752: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
! 1753: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
! 1754: savm=oldm;
! 1755: oldm=newm;
! 1756: } /* end mult */
! 1757:
! 1758: /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
! 1759: /* But now since version 0.9 we anticipate for bias at large stepm.
! 1760: * If stepm is larger than one month (smallest stepm) and if the exact delay
! 1761: * (in months) between two waves is not a multiple of stepm, we rounded to
! 1762: * the nearest (and in case of equal distance, to the lowest) interval but now
! 1763: * we keep into memory the bias bh[mi][i] and also the previous matrix product
! 1764: * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
! 1765: * probability in order to take into account the bias as a fraction of the way
! 1766: * from savm to out if bh is negative or even beyond if bh is positive. bh varies
! 1767: * -stepm/2 to stepm/2 .
! 1768: * For stepm=1 the results are the same as for previous versions of Imach.
! 1769: * For stepm > 1 the results are less biased than in previous versions.
! 1770: */
! 1771: s1=s[mw[mi][i]][i];
! 1772: s2=s[mw[mi+1][i]][i];
! 1773: bbh=(double)bh[mi][i]/(double)stepm;
! 1774: /* bias bh is positive if real duration
! 1775: * is higher than the multiple of stepm and negative otherwise.
! 1776: */
! 1777: /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
! 1778: if( s2 > nlstate){
! 1779: /* i.e. if s2 is a death state and if the date of death is known
! 1780: then the contribution to the likelihood is the probability to
! 1781: die between last step unit time and current step unit time,
! 1782: which is also equal to probability to die before dh
! 1783: minus probability to die before dh-stepm .
! 1784: In version up to 0.92 likelihood was computed
! 1785: as if date of death was unknown. Death was treated as any other
! 1786: health state: the date of the interview describes the actual state
! 1787: and not the date of a change in health state. The former idea was
! 1788: to consider that at each interview the state was recorded
! 1789: (healthy, disable or death) and IMaCh was corrected; but when we
! 1790: introduced the exact date of death then we should have modified
! 1791: the contribution of an exact death to the likelihood. This new
! 1792: contribution is smaller and very dependent of the step unit
! 1793: stepm. It is no more the probability to die between last interview
! 1794: and month of death but the probability to survive from last
! 1795: interview up to one month before death multiplied by the
! 1796: probability to die within a month. Thanks to Chris
! 1797: Jackson for correcting this bug. Former versions increased
! 1798: mortality artificially. The bad side is that we add another loop
! 1799: which slows down the processing. The difference can be up to 10%
! 1800: lower mortality.
! 1801: */
! 1802: lli=log(out[s1][s2] - savm[s1][s2]);
! 1803:
! 1804:
! 1805: } else if (s2==-2) {
! 1806: for (j=1,survp=0. ; j<=nlstate; j++)
! 1807: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
! 1808: /*survp += out[s1][j]; */
! 1809: lli= log(survp);
! 1810: }
! 1811:
! 1812: else if (s2==-4) {
! 1813: for (j=3,survp=0. ; j<=nlstate; j++)
! 1814: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
! 1815: lli= log(survp);
! 1816: }
! 1817:
! 1818: else if (s2==-5) {
! 1819: for (j=1,survp=0. ; j<=2; j++)
! 1820: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
! 1821: lli= log(survp);
! 1822: }
! 1823:
! 1824: else{
! 1825: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
! 1826: /* 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 */
! 1827: }
! 1828: /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
! 1829: /*if(lli ==000.0)*/
! 1830: /*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); */
! 1831: ipmx +=1;
! 1832: sw += weight[i];
! 1833: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
! 1834: } /* end of wave */
! 1835: } /* end of individual */
! 1836: } else if(mle==2){
! 1837: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
! 1838: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
! 1839: for(mi=1; mi<= wav[i]-1; mi++){
! 1840: for (ii=1;ii<=nlstate+ndeath;ii++)
! 1841: for (j=1;j<=nlstate+ndeath;j++){
! 1842: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
! 1843: savm[ii][j]=(ii==j ? 1.0 : 0.0);
! 1844: }
! 1845: for(d=0; d<=dh[mi][i]; d++){
! 1846: newm=savm;
! 1847: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
! 1848: for (kk=1; kk<=cptcovage;kk++) {
! 1849: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
! 1850: }
! 1851: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
! 1852: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
! 1853: savm=oldm;
! 1854: oldm=newm;
! 1855: } /* end mult */
! 1856:
! 1857: s1=s[mw[mi][i]][i];
! 1858: s2=s[mw[mi+1][i]][i];
! 1859: bbh=(double)bh[mi][i]/(double)stepm;
! 1860: 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 */
! 1861: ipmx +=1;
! 1862: sw += weight[i];
! 1863: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
! 1864: } /* end of wave */
! 1865: } /* end of individual */
! 1866: } else if(mle==3){ /* exponential inter-extrapolation */
! 1867: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
! 1868: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
! 1869: for(mi=1; mi<= wav[i]-1; mi++){
! 1870: for (ii=1;ii<=nlstate+ndeath;ii++)
! 1871: for (j=1;j<=nlstate+ndeath;j++){
! 1872: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
! 1873: savm[ii][j]=(ii==j ? 1.0 : 0.0);
! 1874: }
! 1875: for(d=0; d<dh[mi][i]; d++){
! 1876: newm=savm;
! 1877: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
! 1878: for (kk=1; kk<=cptcovage;kk++) {
! 1879: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
! 1880: }
! 1881: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
! 1882: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
! 1883: savm=oldm;
! 1884: oldm=newm;
! 1885: } /* end mult */
! 1886:
! 1887: s1=s[mw[mi][i]][i];
! 1888: s2=s[mw[mi+1][i]][i];
! 1889: bbh=(double)bh[mi][i]/(double)stepm;
! 1890: 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 */
! 1891: ipmx +=1;
! 1892: sw += weight[i];
! 1893: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
! 1894: } /* end of wave */
! 1895: } /* end of individual */
! 1896: }else if (mle==4){ /* ml=4 no inter-extrapolation */
! 1897: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
! 1898: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
! 1899: for(mi=1; mi<= wav[i]-1; mi++){
! 1900: for (ii=1;ii<=nlstate+ndeath;ii++)
! 1901: for (j=1;j<=nlstate+ndeath;j++){
! 1902: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
! 1903: savm[ii][j]=(ii==j ? 1.0 : 0.0);
! 1904: }
! 1905: for(d=0; d<dh[mi][i]; d++){
! 1906: newm=savm;
! 1907: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
! 1908: for (kk=1; kk<=cptcovage;kk++) {
! 1909: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
! 1910: }
! 1911:
! 1912: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
! 1913: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
! 1914: savm=oldm;
! 1915: oldm=newm;
! 1916: } /* end mult */
! 1917:
! 1918: s1=s[mw[mi][i]][i];
! 1919: s2=s[mw[mi+1][i]][i];
! 1920: if( s2 > nlstate){
! 1921: lli=log(out[s1][s2] - savm[s1][s2]);
! 1922: }else{
! 1923: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
! 1924: }
! 1925: ipmx +=1;
! 1926: sw += weight[i];
! 1927: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
! 1928: /* 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]); */
! 1929: } /* end of wave */
! 1930: } /* end of individual */
! 1931: }else{ /* ml=5 no inter-extrapolation no jackson =0.8a */
! 1932: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
! 1933: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
! 1934: for(mi=1; mi<= wav[i]-1; mi++){
! 1935: for (ii=1;ii<=nlstate+ndeath;ii++)
! 1936: for (j=1;j<=nlstate+ndeath;j++){
! 1937: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
! 1938: savm[ii][j]=(ii==j ? 1.0 : 0.0);
! 1939: }
! 1940: for(d=0; d<dh[mi][i]; d++){
! 1941: newm=savm;
! 1942: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
! 1943: for (kk=1; kk<=cptcovage;kk++) {
! 1944: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
! 1945: }
! 1946:
! 1947: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
! 1948: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
! 1949: savm=oldm;
! 1950: oldm=newm;
! 1951: } /* end mult */
! 1952:
! 1953: s1=s[mw[mi][i]][i];
! 1954: s2=s[mw[mi+1][i]][i];
! 1955: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
! 1956: ipmx +=1;
! 1957: sw += weight[i];
! 1958: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
! 1959: /*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]);*/
! 1960: } /* end of wave */
! 1961: } /* end of individual */
! 1962: } /* End of if */
! 1963: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
! 1964: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
! 1965: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
! 1966: return -l;
! 1967: }
! 1968:
! 1969: /*************** log-likelihood *************/
! 1970: double funcone( double *x)
! 1971: {
! 1972: /* Same as likeli but slower because of a lot of printf and if */
! 1973: int i, ii, j, k, mi, d, kk;
! 1974: double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
! 1975: double **out;
! 1976: double lli; /* Individual log likelihood */
! 1977: double llt;
! 1978: int s1, s2;
! 1979: double bbh, survp;
! 1980: /*extern weight */
! 1981: /* We are differentiating ll according to initial status */
! 1982: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
! 1983: /*for(i=1;i<imx;i++)
! 1984: printf(" %d\n",s[4][i]);
! 1985: */
! 1986: cov[1]=1.;
! 1987:
! 1988: for(k=1; k<=nlstate; k++) ll[k]=0.;
! 1989:
! 1990: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
! 1991: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
! 1992: for(mi=1; mi<= wav[i]-1; mi++){
! 1993: for (ii=1;ii<=nlstate+ndeath;ii++)
! 1994: for (j=1;j<=nlstate+ndeath;j++){
! 1995: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
! 1996: savm[ii][j]=(ii==j ? 1.0 : 0.0);
! 1997: }
! 1998: for(d=0; d<dh[mi][i]; d++){
! 1999: newm=savm;
! 2000: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
! 2001: for (kk=1; kk<=cptcovage;kk++) {
! 2002: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
! 2003: }
! 2004: /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
! 2005: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
! 2006: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
! 2007: /* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, */
! 2008: /* 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); */
! 2009: savm=oldm;
! 2010: oldm=newm;
! 2011: } /* end mult */
! 2012:
! 2013: s1=s[mw[mi][i]][i];
! 2014: s2=s[mw[mi+1][i]][i];
! 2015: bbh=(double)bh[mi][i]/(double)stepm;
! 2016: /* bias is positive if real duration
! 2017: * is higher than the multiple of stepm and negative otherwise.
! 2018: */
! 2019: if( s2 > nlstate && (mle <5) ){ /* Jackson */
! 2020: lli=log(out[s1][s2] - savm[s1][s2]);
! 2021: } else if (s2==-2) {
! 2022: for (j=1,survp=0. ; j<=nlstate; j++)
! 2023: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
! 2024: lli= log(survp);
! 2025: }else if (mle==1){
! 2026: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
! 2027: } else if(mle==2){
! 2028: 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 */
! 2029: } else if(mle==3){ /* exponential inter-extrapolation */
! 2030: 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 */
! 2031: } else if (mle==4){ /* mle=4 no inter-extrapolation */
! 2032: lli=log(out[s1][s2]); /* Original formula */
! 2033: } else{ /* mle=0 back to 1 */
! 2034: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
! 2035: /*lli=log(out[s1][s2]); */ /* Original formula */
! 2036: } /* End of if */
! 2037: ipmx +=1;
! 2038: sw += weight[i];
! 2039: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
! 2040: /*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]); */
! 2041: if(globpr){
! 2042: fprintf(ficresilk,"%9ld %6d %2d %2d %1d %1d %3d %11.6f %8.4f\
! 2043: %11.6f %11.6f %11.6f ", \
! 2044: num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
! 2045: 2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
! 2046: for(k=1,llt=0.,l=0.; k<=nlstate; k++){
! 2047: llt +=ll[k]*gipmx/gsw;
! 2048: fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
! 2049: }
! 2050: fprintf(ficresilk," %10.6f\n", -llt);
! 2051: }
! 2052: } /* end of wave */
! 2053: } /* end of individual */
! 2054: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
! 2055: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
! 2056: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
! 2057: if(globpr==0){ /* First time we count the contributions and weights */
! 2058: gipmx=ipmx;
! 2059: gsw=sw;
! 2060: }
! 2061: return -l;
! 2062: }
! 2063:
! 2064:
! 2065: /*************** function likelione ***********/
! 2066: void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
! 2067: {
! 2068: /* This routine should help understanding what is done with
! 2069: the selection of individuals/waves and
! 2070: to check the exact contribution to the likelihood.
! 2071: Plotting could be done.
! 2072: */
! 2073: int k;
! 2074:
! 2075: if(*globpri !=0){ /* Just counts and sums, no printings */
! 2076: strcpy(fileresilk,"ilk");
! 2077: strcat(fileresilk,fileres);
! 2078: if((ficresilk=fopen(fileresilk,"w"))==NULL) {
! 2079: printf("Problem with resultfile: %s\n", fileresilk);
! 2080: fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
! 2081: }
! 2082: 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");
! 2083: fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
! 2084: /* i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
! 2085: for(k=1; k<=nlstate; k++)
! 2086: fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
! 2087: fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
! 2088: }
! 2089:
! 2090: *fretone=(*funcone)(p);
! 2091: if(*globpri !=0){
! 2092: fclose(ficresilk);
! 2093: fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
! 2094: fflush(fichtm);
! 2095: }
! 2096: return;
! 2097: }
! 2098:
! 2099:
! 2100: /*********** Maximum Likelihood Estimation ***************/
! 2101:
! 2102: void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
! 2103: {
! 2104: int i,j, iter;
! 2105: double **xi;
! 2106: double fret;
! 2107: double fretone; /* Only one call to likelihood */
! 2108: /* char filerespow[FILENAMELENGTH];*/
! 2109: xi=matrix(1,npar,1,npar);
! 2110: for (i=1;i<=npar;i++)
! 2111: for (j=1;j<=npar;j++)
! 2112: xi[i][j]=(i==j ? 1.0 : 0.0);
! 2113: printf("Powell\n"); fprintf(ficlog,"Powell\n");
! 2114: strcpy(filerespow,"pow");
! 2115: strcat(filerespow,fileres);
! 2116: if((ficrespow=fopen(filerespow,"w"))==NULL) {
! 2117: printf("Problem with resultfile: %s\n", filerespow);
! 2118: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
! 2119: }
! 2120: fprintf(ficrespow,"# Powell\n# iter -2*LL");
! 2121: for (i=1;i<=nlstate;i++)
! 2122: for(j=1;j<=nlstate+ndeath;j++)
! 2123: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
! 2124: fprintf(ficrespow,"\n");
! 2125: #ifdef POWELL
! 2126: powell(p,xi,npar,ftol,&iter,&fret,func);
! 2127: #endif
! 2128: #ifdef NLOPT
! 2129: int creturn;
! 2130: nlopt_opt opt;
! 2131: double lb[9] = { -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL }; /* lower bounds */
! 2132: double minf; /* the minimum objective value, upon return */
! 2133: /* opt = nlopt_create(NLOPT_LN_NEWUOA,npar); */
! 2134: opt = nlopt_create(NLOPT_LN_BOBYQA,npar);
! 2135: nlopt_set_lower_bounds(opt, lb);
! 2136: printf(" Func %.12lf \n",myfunc(npar,*(&p),NULL,func));
! 2137: /* printf(" Func %.12lf /n",myfunc(npar,p,NULL,NULL)); */
! 2138: /* nlopt_set_min_objective(opt, myfunc, NULL); */
! 2139: nlopt_set_min_objective(opt, myfunc, func);
! 2140: nlopt_set_xtol_rel(opt, ftol);
! 2141: /* printf(" Func %.12lf /n",myfunc(npar,p,NULL,func)); */
! 2142: if ((creturn=nlopt_optimize(opt, p, &minf)) < 0) {
! 2143: printf("nlopt failed! %d\n",creturn);
! 2144: }
! 2145: else {
! 2146: printf("found minimum after %d evaluations (NLOPT=%d)\n", countcallfunc ,NLOPT);
! 2147: printf("found minimum at f(%g,%g) = %0.10g\n", p[0], p[1], minf);
! 2148: iter=countcallfunc; /* not equal */
! 2149: }
! 2150: nlopt_destroy(opt);
! 2151: #endif
! 2152: free_matrix(xi,1,npar,1,npar);
! 2153: fclose(ficrespow);
! 2154: printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
! 2155: fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
! 2156: fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
! 2157:
! 2158: }
! 2159:
! 2160: /**** Computes Hessian and covariance matrix ***/
! 2161: void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
! 2162: {
! 2163: double **a,**y,*x,pd;
! 2164: double **hess;
! 2165: int i, j,jk;
! 2166: int *indx;
! 2167:
! 2168: double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
! 2169: double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
! 2170: void lubksb(double **a, int npar, int *indx, double b[]) ;
! 2171: void ludcmp(double **a, int npar, int *indx, double *d) ;
! 2172: double gompertz(double p[]);
! 2173: hess=matrix(1,npar,1,npar);
! 2174:
! 2175: printf("\nCalculation of the hessian matrix. Wait...\n");
! 2176: fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
! 2177: for (i=1;i<=npar;i++){
! 2178: printf("%d",i);fflush(stdout);
! 2179: fprintf(ficlog,"%d",i);fflush(ficlog);
! 2180:
! 2181: hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
! 2182:
! 2183: /* printf(" %f ",p[i]);
! 2184: printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
! 2185: }
! 2186:
! 2187: for (i=1;i<=npar;i++) {
! 2188: for (j=1;j<=npar;j++) {
! 2189: if (j>i) {
! 2190: printf(".%d%d",i,j);fflush(stdout);
! 2191: fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
! 2192: hess[i][j]=hessij(p,delti,i,j,func,npar);
! 2193:
! 2194: hess[j][i]=hess[i][j];
! 2195: /*printf(" %lf ",hess[i][j]);*/
! 2196: }
! 2197: }
! 2198: }
! 2199: printf("\n");
! 2200: fprintf(ficlog,"\n");
! 2201:
! 2202: printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
! 2203: fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
! 2204:
! 2205: a=matrix(1,npar,1,npar);
! 2206: y=matrix(1,npar,1,npar);
! 2207: x=vector(1,npar);
! 2208: indx=ivector(1,npar);
! 2209: for (i=1;i<=npar;i++)
! 2210: for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
! 2211: ludcmp(a,npar,indx,&pd);
! 2212:
! 2213: for (j=1;j<=npar;j++) {
! 2214: for (i=1;i<=npar;i++) x[i]=0;
! 2215: x[j]=1;
! 2216: lubksb(a,npar,indx,x);
! 2217: for (i=1;i<=npar;i++){
! 2218: matcov[i][j]=x[i];
! 2219: }
! 2220: }
! 2221:
! 2222: printf("\n#Hessian matrix#\n");
! 2223: fprintf(ficlog,"\n#Hessian matrix#\n");
! 2224: for (i=1;i<=npar;i++) {
! 2225: for (j=1;j<=npar;j++) {
! 2226: printf("%.3e ",hess[i][j]);
! 2227: fprintf(ficlog,"%.3e ",hess[i][j]);
! 2228: }
! 2229: printf("\n");
! 2230: fprintf(ficlog,"\n");
! 2231: }
! 2232:
! 2233: /* Recompute Inverse */
! 2234: for (i=1;i<=npar;i++)
! 2235: for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
! 2236: ludcmp(a,npar,indx,&pd);
! 2237:
! 2238: /* printf("\n#Hessian matrix recomputed#\n");
! 2239:
! 2240: for (j=1;j<=npar;j++) {
! 2241: for (i=1;i<=npar;i++) x[i]=0;
! 2242: x[j]=1;
! 2243: lubksb(a,npar,indx,x);
! 2244: for (i=1;i<=npar;i++){
! 2245: y[i][j]=x[i];
! 2246: printf("%.3e ",y[i][j]);
! 2247: fprintf(ficlog,"%.3e ",y[i][j]);
! 2248: }
! 2249: printf("\n");
! 2250: fprintf(ficlog,"\n");
! 2251: }
! 2252: */
! 2253:
! 2254: free_matrix(a,1,npar,1,npar);
! 2255: free_matrix(y,1,npar,1,npar);
! 2256: free_vector(x,1,npar);
! 2257: free_ivector(indx,1,npar);
! 2258: free_matrix(hess,1,npar,1,npar);
! 2259:
! 2260:
! 2261: }
! 2262:
! 2263: /*************** hessian matrix ****************/
! 2264: double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
! 2265: {
! 2266: int i;
! 2267: int l=1, lmax=20;
! 2268: double k1,k2;
! 2269: double p2[MAXPARM+1]; /* identical to x */
! 2270: double res;
! 2271: double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
! 2272: double fx;
! 2273: int k=0,kmax=10;
! 2274: double l1;
! 2275:
! 2276: fx=func(x);
! 2277: for (i=1;i<=npar;i++) p2[i]=x[i];
! 2278: for(l=0 ; l <=lmax; l++){ /* Enlarging the zone around the Maximum */
! 2279: l1=pow(10,l);
! 2280: delts=delt;
! 2281: for(k=1 ; k <kmax; k=k+1){
! 2282: delt = delta*(l1*k);
! 2283: p2[theta]=x[theta] +delt;
! 2284: k1=func(p2)-fx; /* Might be negative if too close to the theoretical maximum */
! 2285: p2[theta]=x[theta]-delt;
! 2286: k2=func(p2)-fx;
! 2287: /*res= (k1-2.0*fx+k2)/delt/delt; */
! 2288: res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
! 2289:
! 2290: #ifdef DEBUGHESS
! 2291: 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);
! 2292: 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);
! 2293: #endif
! 2294: /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
! 2295: if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
! 2296: k=kmax;
! 2297: }
! 2298: else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
! 2299: k=kmax; l=lmax*10.;
! 2300: }
! 2301: else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){
! 2302: delts=delt;
! 2303: }
! 2304: }
! 2305: }
! 2306: delti[theta]=delts;
! 2307: return res;
! 2308:
! 2309: }
! 2310:
! 2311: double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
! 2312: {
! 2313: int i;
! 2314: int l=1, l1, lmax=20;
! 2315: double k1,k2,k3,k4,res,fx;
! 2316: double p2[MAXPARM+1];
! 2317: int k;
! 2318:
! 2319: fx=func(x);
! 2320: for (k=1; k<=2; k++) {
! 2321: for (i=1;i<=npar;i++) p2[i]=x[i];
! 2322: p2[thetai]=x[thetai]+delti[thetai]/k;
! 2323: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
! 2324: k1=func(p2)-fx;
! 2325:
! 2326: p2[thetai]=x[thetai]+delti[thetai]/k;
! 2327: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
! 2328: k2=func(p2)-fx;
! 2329:
! 2330: p2[thetai]=x[thetai]-delti[thetai]/k;
! 2331: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
! 2332: k3=func(p2)-fx;
! 2333:
! 2334: p2[thetai]=x[thetai]-delti[thetai]/k;
! 2335: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
! 2336: k4=func(p2)-fx;
! 2337: res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
! 2338: #ifdef DEBUG
! 2339: 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);
! 2340: 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);
! 2341: #endif
! 2342: }
! 2343: return res;
! 2344: }
! 2345:
! 2346: /************** Inverse of matrix **************/
! 2347: void ludcmp(double **a, int n, int *indx, double *d)
! 2348: {
! 2349: int i,imax,j,k;
! 2350: double big,dum,sum,temp;
! 2351: double *vv;
! 2352:
! 2353: vv=vector(1,n);
! 2354: *d=1.0;
! 2355: for (i=1;i<=n;i++) {
! 2356: big=0.0;
! 2357: for (j=1;j<=n;j++)
! 2358: if ((temp=fabs(a[i][j])) > big) big=temp;
! 2359: if (big == 0.0) nrerror("Singular matrix in routine ludcmp");
! 2360: vv[i]=1.0/big;
! 2361: }
! 2362: for (j=1;j<=n;j++) {
! 2363: for (i=1;i<j;i++) {
! 2364: sum=a[i][j];
! 2365: for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];
! 2366: a[i][j]=sum;
! 2367: }
! 2368: big=0.0;
! 2369: for (i=j;i<=n;i++) {
! 2370: sum=a[i][j];
! 2371: for (k=1;k<j;k++)
! 2372: sum -= a[i][k]*a[k][j];
! 2373: a[i][j]=sum;
! 2374: if ( (dum=vv[i]*fabs(sum)) >= big) {
! 2375: big=dum;
! 2376: imax=i;
! 2377: }
! 2378: }
! 2379: if (j != imax) {
! 2380: for (k=1;k<=n;k++) {
! 2381: dum=a[imax][k];
! 2382: a[imax][k]=a[j][k];
! 2383: a[j][k]=dum;
! 2384: }
! 2385: *d = -(*d);
! 2386: vv[imax]=vv[j];
! 2387: }
! 2388: indx[j]=imax;
! 2389: if (a[j][j] == 0.0) a[j][j]=TINY;
! 2390: if (j != n) {
! 2391: dum=1.0/(a[j][j]);
! 2392: for (i=j+1;i<=n;i++) a[i][j] *= dum;
! 2393: }
! 2394: }
! 2395: free_vector(vv,1,n); /* Doesn't work */
! 2396: ;
! 2397: }
! 2398:
! 2399: void lubksb(double **a, int n, int *indx, double b[])
! 2400: {
! 2401: int i,ii=0,ip,j;
! 2402: double sum;
! 2403:
! 2404: for (i=1;i<=n;i++) {
! 2405: ip=indx[i];
! 2406: sum=b[ip];
! 2407: b[ip]=b[i];
! 2408: if (ii)
! 2409: for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];
! 2410: else if (sum) ii=i;
! 2411: b[i]=sum;
! 2412: }
! 2413: for (i=n;i>=1;i--) {
! 2414: sum=b[i];
! 2415: for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];
! 2416: b[i]=sum/a[i][i];
! 2417: }
! 2418: }
! 2419:
! 2420: void pstamp(FILE *fichier)
! 2421: {
! 2422: fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart);
! 2423: }
! 2424:
! 2425: /************ Frequencies ********************/
! 2426: 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[])
! 2427: { /* Some frequencies */
! 2428:
! 2429: int i, m, jk, k1,i1, j1, bool, z1,j;
! 2430: int first;
! 2431: double ***freq; /* Frequencies */
! 2432: double *pp, **prop;
! 2433: double pos,posprop, k2, dateintsum=0,k2cpt=0;
! 2434: char fileresp[FILENAMELENGTH];
! 2435:
! 2436: pp=vector(1,nlstate);
! 2437: prop=matrix(1,nlstate,iagemin,iagemax+3);
! 2438: strcpy(fileresp,"p");
! 2439: strcat(fileresp,fileres);
! 2440: if((ficresp=fopen(fileresp,"w"))==NULL) {
! 2441: printf("Problem with prevalence resultfile: %s\n", fileresp);
! 2442: fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
! 2443: exit(0);
! 2444: }
! 2445: freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
! 2446: j1=0;
! 2447:
! 2448: j=cptcoveff;
! 2449: if (cptcovn<1) {j=1;ncodemax[1]=1;}
! 2450:
! 2451: first=1;
! 2452:
! 2453: /* for(k1=1; k1<=j ; k1++){ /* Loop on covariates */
! 2454: /* for(i1=1; i1<=ncodemax[k1];i1++){ /* Now it is 2 */
! 2455: /* j1++;
! 2456: */
! 2457: for (j1 = 1; j1 <= (int) pow(2,cptcoveff); j1++){
! 2458: /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
! 2459: scanf("%d", i);*/
! 2460: for (i=-5; i<=nlstate+ndeath; i++)
! 2461: for (jk=-5; jk<=nlstate+ndeath; jk++)
! 2462: for(m=iagemin; m <= iagemax+3; m++)
! 2463: freq[i][jk][m]=0;
! 2464:
! 2465: for (i=1; i<=nlstate; i++)
! 2466: for(m=iagemin; m <= iagemax+3; m++)
! 2467: prop[i][m]=0;
! 2468:
! 2469: dateintsum=0;
! 2470: k2cpt=0;
! 2471: for (i=1; i<=imx; i++) {
! 2472: bool=1;
! 2473: if (cptcovn>0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
! 2474: for (z1=1; z1<=cptcoveff; z1++)
! 2475: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]){
! 2476: /* Tests if the value of each of the covariates of i is equal to filter j1 */
! 2477: bool=0;
! 2478: /* 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",
! 2479: bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtab[j1][z1],
! 2480: j1,z1,nbcode[Tvaraff[z1]][codtab[j1][z1]],j1);*/
! 2481: /* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtab[7][3]=1 and nbcde[3][?]=1*/
! 2482: }
! 2483: }
! 2484:
! 2485: if (bool==1){
! 2486: for(m=firstpass; m<=lastpass; m++){
! 2487: k2=anint[m][i]+(mint[m][i]/12.);
! 2488: /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
! 2489: if(agev[m][i]==0) agev[m][i]=iagemax+1;
! 2490: if(agev[m][i]==1) agev[m][i]=iagemax+2;
! 2491: if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
! 2492: if (m<lastpass) {
! 2493: freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
! 2494: freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
! 2495: }
! 2496:
! 2497: if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
! 2498: dateintsum=dateintsum+k2;
! 2499: k2cpt++;
! 2500: }
! 2501: /*}*/
! 2502: }
! 2503: }
! 2504: } /* end i */
! 2505:
! 2506: /* fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
! 2507: pstamp(ficresp);
! 2508: if (cptcovn>0) {
! 2509: fprintf(ficresp, "\n#********** Variable ");
! 2510: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
! 2511: fprintf(ficresp, "**********\n#");
! 2512: fprintf(ficlog, "\n#********** Variable ");
! 2513: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficlog, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
! 2514: fprintf(ficlog, "**********\n#");
! 2515: }
! 2516: for(i=1; i<=nlstate;i++)
! 2517: fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
! 2518: fprintf(ficresp, "\n");
! 2519:
! 2520: for(i=iagemin; i <= iagemax+3; i++){
! 2521: if(i==iagemax+3){
! 2522: fprintf(ficlog,"Total");
! 2523: }else{
! 2524: if(first==1){
! 2525: first=0;
! 2526: printf("See log file for details...\n");
! 2527: }
! 2528: fprintf(ficlog,"Age %d", i);
! 2529: }
! 2530: for(jk=1; jk <=nlstate ; jk++){
! 2531: for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
! 2532: pp[jk] += freq[jk][m][i];
! 2533: }
! 2534: for(jk=1; jk <=nlstate ; jk++){
! 2535: for(m=-1, pos=0; m <=0 ; m++)
! 2536: pos += freq[jk][m][i];
! 2537: if(pp[jk]>=1.e-10){
! 2538: if(first==1){
! 2539: printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
! 2540: }
! 2541: fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
! 2542: }else{
! 2543: if(first==1)
! 2544: printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
! 2545: fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
! 2546: }
! 2547: }
! 2548:
! 2549: for(jk=1; jk <=nlstate ; jk++){
! 2550: for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
! 2551: pp[jk] += freq[jk][m][i];
! 2552: }
! 2553: for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
! 2554: pos += pp[jk];
! 2555: posprop += prop[jk][i];
! 2556: }
! 2557: for(jk=1; jk <=nlstate ; jk++){
! 2558: if(pos>=1.e-5){
! 2559: if(first==1)
! 2560: printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
! 2561: fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
! 2562: }else{
! 2563: if(first==1)
! 2564: printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
! 2565: fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
! 2566: }
! 2567: if( i <= iagemax){
! 2568: if(pos>=1.e-5){
! 2569: fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
! 2570: /*probs[i][jk][j1]= pp[jk]/pos;*/
! 2571: /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
! 2572: }
! 2573: else
! 2574: fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
! 2575: }
! 2576: }
! 2577:
! 2578: for(jk=-1; jk <=nlstate+ndeath; jk++)
! 2579: for(m=-1; m <=nlstate+ndeath; m++)
! 2580: if(freq[jk][m][i] !=0 ) {
! 2581: if(first==1)
! 2582: printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
! 2583: fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
! 2584: }
! 2585: if(i <= iagemax)
! 2586: fprintf(ficresp,"\n");
! 2587: if(first==1)
! 2588: printf("Others in log...\n");
! 2589: fprintf(ficlog,"\n");
! 2590: }
! 2591: /*}*/
! 2592: }
! 2593: dateintmean=dateintsum/k2cpt;
! 2594:
! 2595: fclose(ficresp);
! 2596: free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
! 2597: free_vector(pp,1,nlstate);
! 2598: free_matrix(prop,1,nlstate,iagemin, iagemax+3);
! 2599: /* End of Freq */
! 2600: }
! 2601:
! 2602: /************ Prevalence ********************/
! 2603: 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)
! 2604: {
! 2605: /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
! 2606: in each health status at the date of interview (if between dateprev1 and dateprev2).
! 2607: We still use firstpass and lastpass as another selection.
! 2608: */
! 2609:
! 2610: int i, m, jk, k1, i1, j1, bool, z1,j;
! 2611: double ***freq; /* Frequencies */
! 2612: double *pp, **prop;
! 2613: double pos,posprop;
! 2614: double y2; /* in fractional years */
! 2615: int iagemin, iagemax;
! 2616: int first; /** to stop verbosity which is redirected to log file */
! 2617:
! 2618: iagemin= (int) agemin;
! 2619: iagemax= (int) agemax;
! 2620: /*pp=vector(1,nlstate);*/
! 2621: prop=matrix(1,nlstate,iagemin,iagemax+3);
! 2622: /* freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
! 2623: j1=0;
! 2624:
! 2625: /*j=cptcoveff;*/
! 2626: if (cptcovn<1) {j=1;ncodemax[1]=1;}
! 2627:
! 2628: first=1;
! 2629: for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){
! 2630: /*for(i1=1; i1<=ncodemax[k1];i1++){
! 2631: j1++;*/
! 2632:
! 2633: for (i=1; i<=nlstate; i++)
! 2634: for(m=iagemin; m <= iagemax+3; m++)
! 2635: prop[i][m]=0.0;
! 2636:
! 2637: for (i=1; i<=imx; i++) { /* Each individual */
! 2638: bool=1;
! 2639: if (cptcovn>0) {
! 2640: for (z1=1; z1<=cptcoveff; z1++)
! 2641: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
! 2642: bool=0;
! 2643: }
! 2644: if (bool==1) {
! 2645: for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
! 2646: y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
! 2647: if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
! 2648: if(agev[m][i]==0) agev[m][i]=iagemax+1;
! 2649: if(agev[m][i]==1) agev[m][i]=iagemax+2;
! 2650: 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);
! 2651: if (s[m][i]>0 && s[m][i]<=nlstate) {
! 2652: /*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]]);*/
! 2653: prop[s[m][i]][(int)agev[m][i]] += weight[i];
! 2654: prop[s[m][i]][iagemax+3] += weight[i];
! 2655: }
! 2656: }
! 2657: } /* end selection of waves */
! 2658: }
! 2659: }
! 2660: for(i=iagemin; i <= iagemax+3; i++){
! 2661: for(jk=1,posprop=0; jk <=nlstate ; jk++) {
! 2662: posprop += prop[jk][i];
! 2663: }
! 2664:
! 2665: for(jk=1; jk <=nlstate ; jk++){
! 2666: if( i <= iagemax){
! 2667: if(posprop>=1.e-5){
! 2668: probs[i][jk][j1]= prop[jk][i]/posprop;
! 2669: } else{
! 2670: if(first==1){
! 2671: first=0;
! 2672: 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]);
! 2673: }
! 2674: }
! 2675: }
! 2676: }/* end jk */
! 2677: }/* end i */
! 2678: /*} *//* end i1 */
! 2679: } /* end j1 */
! 2680:
! 2681: /* free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
! 2682: /*free_vector(pp,1,nlstate);*/
! 2683: free_matrix(prop,1,nlstate, iagemin,iagemax+3);
! 2684: } /* End of prevalence */
! 2685:
! 2686: /************* Waves Concatenation ***************/
! 2687:
! 2688: 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)
! 2689: {
! 2690: /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
! 2691: Death is a valid wave (if date is known).
! 2692: mw[mi][i] is the mi (mi=1 to wav[i]) effective wave of individual i
! 2693: dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
! 2694: and mw[mi+1][i]. dh depends on stepm.
! 2695: */
! 2696:
! 2697: int i, mi, m;
! 2698: /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
! 2699: double sum=0., jmean=0.;*/
! 2700: int first;
! 2701: int j, k=0,jk, ju, jl;
! 2702: double sum=0.;
! 2703: first=0;
! 2704: jmin=1e+5;
! 2705: jmax=-1;
! 2706: jmean=0.;
! 2707: for(i=1; i<=imx; i++){
! 2708: mi=0;
! 2709: m=firstpass;
! 2710: while(s[m][i] <= nlstate){
! 2711: if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
! 2712: mw[++mi][i]=m;
! 2713: if(m >=lastpass)
! 2714: break;
! 2715: else
! 2716: m++;
! 2717: }/* end while */
! 2718: if (s[m][i] > nlstate){
! 2719: mi++; /* Death is another wave */
! 2720: /* if(mi==0) never been interviewed correctly before death */
! 2721: /* Only death is a correct wave */
! 2722: mw[mi][i]=m;
! 2723: }
! 2724:
! 2725: wav[i]=mi;
! 2726: if(mi==0){
! 2727: nbwarn++;
! 2728: if(first==0){
! 2729: printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
! 2730: first=1;
! 2731: }
! 2732: if(first==1){
! 2733: fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
! 2734: }
! 2735: } /* end mi==0 */
! 2736: } /* End individuals */
! 2737:
! 2738: for(i=1; i<=imx; i++){
! 2739: for(mi=1; mi<wav[i];mi++){
! 2740: if (stepm <=0)
! 2741: dh[mi][i]=1;
! 2742: else{
! 2743: if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
! 2744: if (agedc[i] < 2*AGESUP) {
! 2745: j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);
! 2746: if(j==0) j=1; /* Survives at least one month after exam */
! 2747: else if(j<0){
! 2748: nberr++;
! 2749: 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]);
! 2750: j=1; /* Temporary Dangerous patch */
! 2751: 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);
! 2752: 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]);
! 2753: 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);
! 2754: }
! 2755: k=k+1;
! 2756: if (j >= jmax){
! 2757: jmax=j;
! 2758: ijmax=i;
! 2759: }
! 2760: if (j <= jmin){
! 2761: jmin=j;
! 2762: ijmin=i;
! 2763: }
! 2764: sum=sum+j;
! 2765: /*if (j<0) printf("j=%d num=%d \n",j,i);*/
! 2766: /* printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
! 2767: }
! 2768: }
! 2769: else{
! 2770: j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
! 2771: /* 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]); */
! 2772:
! 2773: k=k+1;
! 2774: if (j >= jmax) {
! 2775: jmax=j;
! 2776: ijmax=i;
! 2777: }
! 2778: else if (j <= jmin){
! 2779: jmin=j;
! 2780: ijmin=i;
! 2781: }
! 2782: /* if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
! 2783: /*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]);*/
! 2784: if(j<0){
! 2785: nberr++;
! 2786: 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]);
! 2787: 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]);
! 2788: }
! 2789: sum=sum+j;
! 2790: }
! 2791: jk= j/stepm;
! 2792: jl= j -jk*stepm;
! 2793: ju= j -(jk+1)*stepm;
! 2794: if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
! 2795: if(jl==0){
! 2796: dh[mi][i]=jk;
! 2797: bh[mi][i]=0;
! 2798: }else{ /* We want a negative bias in order to only have interpolation ie
! 2799: * to avoid the price of an extra matrix product in likelihood */
! 2800: dh[mi][i]=jk+1;
! 2801: bh[mi][i]=ju;
! 2802: }
! 2803: }else{
! 2804: if(jl <= -ju){
! 2805: dh[mi][i]=jk;
! 2806: bh[mi][i]=jl; /* bias is positive if real duration
! 2807: * is higher than the multiple of stepm and negative otherwise.
! 2808: */
! 2809: }
! 2810: else{
! 2811: dh[mi][i]=jk+1;
! 2812: bh[mi][i]=ju;
! 2813: }
! 2814: if(dh[mi][i]==0){
! 2815: dh[mi][i]=1; /* At least one step */
! 2816: bh[mi][i]=ju; /* At least one step */
! 2817: /* 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);*/
! 2818: }
! 2819: } /* end if mle */
! 2820: }
! 2821: } /* end wave */
! 2822: }
! 2823: jmean=sum/k;
! 2824: 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);
! 2825: 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);
! 2826: }
! 2827:
! 2828: /*********** Tricode ****************************/
! 2829: void tricode(int *Tvar, int **nbcode, int imx, int *Ndum)
! 2830: {
! 2831: /**< Uses cptcovn+2*cptcovprod as the number of covariates */
! 2832: /* Tvar[i]=atoi(stre); find 'n' in Vn and stores in Tvar. If model=V2+V1 Tvar[1]=2 and Tvar[2]=1
! 2833: /* Boring subroutine which should only output nbcode[Tvar[j]][k]
! 2834: * Tvar[5] in V2+V1+V3*age+V2*V4 is 2 (V2)
! 2835: /* nbcode[Tvar[j]][1]=
! 2836: */
! 2837:
! 2838: int ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
! 2839: int modmaxcovj=0; /* Modality max of covariates j */
! 2840: int cptcode=0; /* Modality max of covariates j */
! 2841: int modmincovj=0; /* Modality min of covariates j */
! 2842:
! 2843:
! 2844: cptcoveff=0;
! 2845:
! 2846: for (k=-1; k < maxncov; k++) Ndum[k]=0;
! 2847: for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */
! 2848:
! 2849: /* Loop on covariates without age and products */
! 2850: for (j=1; j<=(cptcovs); j++) { /* model V1 + V2*age+ V3 + V3*V4 : V1 + V3 = 2 only */
! 2851: for (i=1; i<=imx; i++) { /* Lopp on individuals: reads the data file to get the maximum value of the
! 2852: modality of this covariate Vj*/
! 2853: ij=(int)(covar[Tvar[j]][i]); /* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i
! 2854: * If product of Vn*Vm, still boolean *:
! 2855: * If it was coded 1, 2, 3, 4 should be splitted into 3 boolean variables
! 2856: * 1 => 0 0 0, 2 => 0 0 1, 3 => 0 1 1, 4=1 0 0 */
! 2857: /* Finds for covariate j, n=Tvar[j] of Vn . ij is the
! 2858: modality of the nth covariate of individual i. */
! 2859: if (ij > modmaxcovj)
! 2860: modmaxcovj=ij;
! 2861: else if (ij < modmincovj)
! 2862: modmincovj=ij;
! 2863: if ((ij < -1) && (ij > NCOVMAX)){
! 2864: printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX );
! 2865: exit(1);
! 2866: }else
! 2867: Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/
! 2868: /* If coded 1, 2, 3 , counts the number of 1 Ndum[1], number of 2, Ndum[2], etc */
! 2869: /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
! 2870: /* getting the maximum value of the modality of the covariate
! 2871: (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and
! 2872: female is 1, then modmaxcovj=1.*/
! 2873: }
! 2874: printf(" Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", j, Tvar[j], modmincovj, modmaxcovj);
! 2875: cptcode=modmaxcovj;
! 2876: /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */
! 2877: /*for (i=0; i<=cptcode; i++) {*/
! 2878: for (i=modmincovj; i<=modmaxcovj; i++) { /* i=-1 ? 0 and 1*//* For each value of the modality of model-cov j */
! 2879: printf("Frequencies of covariates %d V%d %d\n", j, Tvar[j], Ndum[i]);
! 2880: if( Ndum[i] != 0 ){ /* Counts if nobody answered, empty modality */
! 2881: ncodemax[j]++; /* ncodemax[j]= Number of non-null modalities of the j th covariate. */
! 2882: }
! 2883: /* In fact ncodemax[j]=2 (dichotom. variables only) but it could be more for
! 2884: historical reasons: 3 if coded 1, 2, 3 and 4 and Ndum[2]=0 */
! 2885: } /* Ndum[-1] number of undefined modalities */
! 2886:
! 2887: /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */
! 2888: /* For covariate j, modalities could be 1, 2, 3, 4. If Ndum[2]=0 ncodemax[j] is not 4 but 3 */
! 2889: /* If Ndum[3}= 635; Ndum[4]=0; Ndum[5]=0; Ndum[6]=27; Ndum[7]=125;
! 2890: modmincovj=3; modmaxcovj = 7;
! 2891: There are only 3 modalities non empty (or 2 if 27 is too few) : ncodemax[j]=3;
! 2892: which will be coded 0, 1, 2 which in binary on 3-1 digits are 0=00 1=01, 2=10; defining two dummy
! 2893: variables V1_1 and V1_2.
! 2894: nbcode[Tvar[j]][ij]=k;
! 2895: nbcode[Tvar[j]][1]=0;
! 2896: nbcode[Tvar[j]][2]=1;
! 2897: nbcode[Tvar[j]][3]=2;
! 2898: */
! 2899: ij=1; /* ij is similar to i but can jumps over null modalities */
! 2900: for (i=modmincovj; i<=modmaxcovj; i++) { /* i= 1 to 2 for dichotomous, or from 1 to 3 */
! 2901: for (k=0; k<= cptcode; k++) { /* k=-1 ? k=0 to 1 *//* Could be 1 to 4 */
! 2902: /*recode from 0 */
! 2903: if (Ndum[k] != 0) { /* If at least one individual responded to this modality k */
! 2904: nbcode[Tvar[j]][ij]=k; /* stores the modality in an array nbcode.
! 2905: k is a modality. If we have model=V1+V1*sex
! 2906: then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
! 2907: ij++;
! 2908: }
! 2909: if (ij > ncodemax[j]) break;
! 2910: } /* end of loop on */
! 2911: } /* end of loop on modality */
! 2912: } /* end of loop on model-covariate j. nbcode[Tvarj][1]=0 and nbcode[Tvarj][2]=1 sets the value of covariate j*/
! 2913:
! 2914: for (k=-1; k< maxncov; k++) Ndum[k]=0;
! 2915:
! 2916: for (i=1; i<=ncovmodel-2; i++) { /* -2, cste and age */
! 2917: /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
! 2918: ij=Tvar[i]; /* Tvar might be -1 if status was unknown */
! 2919: Ndum[ij]++;
! 2920: }
! 2921:
! 2922: ij=1;
! 2923: for (i=0; i<= maxncov-1; i++) { /* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) */
! 2924: /*printf("Ndum[%d]=%d\n",i, Ndum[i]);*/
! 2925: if((Ndum[i]!=0) && (i<=ncovcol)){
! 2926: /*printf("diff Ndum[%d]=%d\n",i, Ndum[i]);*/
! 2927: Tvaraff[ij]=i; /*For printing (unclear) */
! 2928: ij++;
! 2929: }else
! 2930: Tvaraff[ij]=0;
! 2931: }
! 2932: ij--;
! 2933: cptcoveff=ij; /*Number of total covariates*/
! 2934:
! 2935: }
! 2936:
! 2937:
! 2938: /*********** Health Expectancies ****************/
! 2939:
! 2940: void evsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,char strstart[] )
! 2941:
! 2942: {
! 2943: /* Health expectancies, no variances */
! 2944: int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2;
! 2945: int nhstepma, nstepma; /* Decreasing with age */
! 2946: double age, agelim, hf;
! 2947: double ***p3mat;
! 2948: double eip;
! 2949:
! 2950: pstamp(ficreseij);
! 2951: fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
! 2952: fprintf(ficreseij,"# Age");
! 2953: for(i=1; i<=nlstate;i++){
! 2954: for(j=1; j<=nlstate;j++){
! 2955: fprintf(ficreseij," e%1d%1d ",i,j);
! 2956: }
! 2957: fprintf(ficreseij," e%1d. ",i);
! 2958: }
! 2959: fprintf(ficreseij,"\n");
! 2960:
! 2961:
! 2962: if(estepm < stepm){
! 2963: printf ("Problem %d lower than %d\n",estepm, stepm);
! 2964: }
! 2965: else hstepm=estepm;
! 2966: /* We compute the life expectancy from trapezoids spaced every estepm months
! 2967: * This is mainly to measure the difference between two models: for example
! 2968: * if stepm=24 months pijx are given only every 2 years and by summing them
! 2969: * we are calculating an estimate of the Life Expectancy assuming a linear
! 2970: * progression in between and thus overestimating or underestimating according
! 2971: * to the curvature of the survival function. If, for the same date, we
! 2972: * estimate the model with stepm=1 month, we can keep estepm to 24 months
! 2973: * to compare the new estimate of Life expectancy with the same linear
! 2974: * hypothesis. A more precise result, taking into account a more precise
! 2975: * curvature will be obtained if estepm is as small as stepm. */
! 2976:
! 2977: /* For example we decided to compute the life expectancy with the smallest unit */
! 2978: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
! 2979: nhstepm is the number of hstepm from age to agelim
! 2980: nstepm is the number of stepm from age to agelin.
! 2981: Look at hpijx to understand the reason of that which relies in memory size
! 2982: and note for a fixed period like estepm months */
! 2983: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
! 2984: survival function given by stepm (the optimization length). Unfortunately it
! 2985: means that if the survival funtion is printed only each two years of age and if
! 2986: you sum them up and add 1 year (area under the trapezoids) you won't get the same
! 2987: results. So we changed our mind and took the option of the best precision.
! 2988: */
! 2989: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
! 2990:
! 2991: agelim=AGESUP;
! 2992: /* If stepm=6 months */
! 2993: /* Computed by stepm unit matrices, product of hstepm matrices, stored
! 2994: in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
! 2995:
! 2996: /* nhstepm age range expressed in number of stepm */
! 2997: nstepm=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
! 2998: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
! 2999: /* if (stepm >= YEARM) hstepm=1;*/
! 3000: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
! 3001: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
! 3002:
! 3003: for (age=bage; age<=fage; age ++){
! 3004: nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
! 3005: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
! 3006: /* if (stepm >= YEARM) hstepm=1;*/
! 3007: nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
! 3008:
! 3009: /* If stepm=6 months */
! 3010: /* Computed by stepm unit matrices, product of hstepma matrices, stored
! 3011: in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
! 3012:
! 3013: hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
! 3014:
! 3015: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
! 3016:
! 3017: printf("%d|",(int)age);fflush(stdout);
! 3018: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
! 3019:
! 3020: /* Computing expectancies */
! 3021: for(i=1; i<=nlstate;i++)
! 3022: for(j=1; j<=nlstate;j++)
! 3023: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
! 3024: eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
! 3025:
! 3026: /* 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]);*/
! 3027:
! 3028: }
! 3029:
! 3030: fprintf(ficreseij,"%3.0f",age );
! 3031: for(i=1; i<=nlstate;i++){
! 3032: eip=0;
! 3033: for(j=1; j<=nlstate;j++){
! 3034: eip +=eij[i][j][(int)age];
! 3035: fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
! 3036: }
! 3037: fprintf(ficreseij,"%9.4f", eip );
! 3038: }
! 3039: fprintf(ficreseij,"\n");
! 3040:
! 3041: }
! 3042: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
! 3043: printf("\n");
! 3044: fprintf(ficlog,"\n");
! 3045:
! 3046: }
! 3047:
! 3048: 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[] )
! 3049:
! 3050: {
! 3051: /* Covariances of health expectancies eij and of total life expectancies according
! 3052: to initial status i, ei. .
! 3053: */
! 3054: int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
! 3055: int nhstepma, nstepma; /* Decreasing with age */
! 3056: double age, agelim, hf;
! 3057: double ***p3matp, ***p3matm, ***varhe;
! 3058: double **dnewm,**doldm;
! 3059: double *xp, *xm;
! 3060: double **gp, **gm;
! 3061: double ***gradg, ***trgradg;
! 3062: int theta;
! 3063:
! 3064: double eip, vip;
! 3065:
! 3066: varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
! 3067: xp=vector(1,npar);
! 3068: xm=vector(1,npar);
! 3069: dnewm=matrix(1,nlstate*nlstate,1,npar);
! 3070: doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
! 3071:
! 3072: pstamp(ficresstdeij);
! 3073: fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
! 3074: fprintf(ficresstdeij,"# Age");
! 3075: for(i=1; i<=nlstate;i++){
! 3076: for(j=1; j<=nlstate;j++)
! 3077: fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
! 3078: fprintf(ficresstdeij," e%1d. ",i);
! 3079: }
! 3080: fprintf(ficresstdeij,"\n");
! 3081:
! 3082: pstamp(ficrescveij);
! 3083: fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
! 3084: fprintf(ficrescveij,"# Age");
! 3085: for(i=1; i<=nlstate;i++)
! 3086: for(j=1; j<=nlstate;j++){
! 3087: cptj= (j-1)*nlstate+i;
! 3088: for(i2=1; i2<=nlstate;i2++)
! 3089: for(j2=1; j2<=nlstate;j2++){
! 3090: cptj2= (j2-1)*nlstate+i2;
! 3091: if(cptj2 <= cptj)
! 3092: fprintf(ficrescveij," %1d%1d,%1d%1d",i,j,i2,j2);
! 3093: }
! 3094: }
! 3095: fprintf(ficrescveij,"\n");
! 3096:
! 3097: if(estepm < stepm){
! 3098: printf ("Problem %d lower than %d\n",estepm, stepm);
! 3099: }
! 3100: else hstepm=estepm;
! 3101: /* We compute the life expectancy from trapezoids spaced every estepm months
! 3102: * This is mainly to measure the difference between two models: for example
! 3103: * if stepm=24 months pijx are given only every 2 years and by summing them
! 3104: * we are calculating an estimate of the Life Expectancy assuming a linear
! 3105: * progression in between and thus overestimating or underestimating according
! 3106: * to the curvature of the survival function. If, for the same date, we
! 3107: * estimate the model with stepm=1 month, we can keep estepm to 24 months
! 3108: * to compare the new estimate of Life expectancy with the same linear
! 3109: * hypothesis. A more precise result, taking into account a more precise
! 3110: * curvature will be obtained if estepm is as small as stepm. */
! 3111:
! 3112: /* For example we decided to compute the life expectancy with the smallest unit */
! 3113: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
! 3114: nhstepm is the number of hstepm from age to agelim
! 3115: nstepm is the number of stepm from age to agelin.
! 3116: Look at hpijx to understand the reason of that which relies in memory size
! 3117: and note for a fixed period like estepm months */
! 3118: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
! 3119: survival function given by stepm (the optimization length). Unfortunately it
! 3120: means that if the survival funtion is printed only each two years of age and if
! 3121: you sum them up and add 1 year (area under the trapezoids) you won't get the same
! 3122: results. So we changed our mind and took the option of the best precision.
! 3123: */
! 3124: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
! 3125:
! 3126: /* If stepm=6 months */
! 3127: /* nhstepm age range expressed in number of stepm */
! 3128: agelim=AGESUP;
! 3129: nstepm=(int) rint((agelim-bage)*YEARM/stepm);
! 3130: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
! 3131: /* if (stepm >= YEARM) hstepm=1;*/
! 3132: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
! 3133:
! 3134: p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
! 3135: p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
! 3136: gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
! 3137: trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
! 3138: gp=matrix(0,nhstepm,1,nlstate*nlstate);
! 3139: gm=matrix(0,nhstepm,1,nlstate*nlstate);
! 3140:
! 3141: for (age=bage; age<=fage; age ++){
! 3142: nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
! 3143: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
! 3144: /* if (stepm >= YEARM) hstepm=1;*/
! 3145: nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
! 3146:
! 3147: /* If stepm=6 months */
! 3148: /* Computed by stepm unit matrices, product of hstepma matrices, stored
! 3149: in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
! 3150:
! 3151: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
! 3152:
! 3153: /* Computing Variances of health expectancies */
! 3154: /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
! 3155: decrease memory allocation */
! 3156: for(theta=1; theta <=npar; theta++){
! 3157: for(i=1; i<=npar; i++){
! 3158: xp[i] = x[i] + (i==theta ?delti[theta]:0);
! 3159: xm[i] = x[i] - (i==theta ?delti[theta]:0);
! 3160: }
! 3161: hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);
! 3162: hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);
! 3163:
! 3164: for(j=1; j<= nlstate; j++){
! 3165: for(i=1; i<=nlstate; i++){
! 3166: for(h=0; h<=nhstepm-1; h++){
! 3167: gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
! 3168: gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
! 3169: }
! 3170: }
! 3171: }
! 3172:
! 3173: for(ij=1; ij<= nlstate*nlstate; ij++)
! 3174: for(h=0; h<=nhstepm-1; h++){
! 3175: gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
! 3176: }
! 3177: }/* End theta */
! 3178:
! 3179:
! 3180: for(h=0; h<=nhstepm-1; h++)
! 3181: for(j=1; j<=nlstate*nlstate;j++)
! 3182: for(theta=1; theta <=npar; theta++)
! 3183: trgradg[h][j][theta]=gradg[h][theta][j];
! 3184:
! 3185:
! 3186: for(ij=1;ij<=nlstate*nlstate;ij++)
! 3187: for(ji=1;ji<=nlstate*nlstate;ji++)
! 3188: varhe[ij][ji][(int)age] =0.;
! 3189:
! 3190: printf("%d|",(int)age);fflush(stdout);
! 3191: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
! 3192: for(h=0;h<=nhstepm-1;h++){
! 3193: for(k=0;k<=nhstepm-1;k++){
! 3194: matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
! 3195: matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
! 3196: for(ij=1;ij<=nlstate*nlstate;ij++)
! 3197: for(ji=1;ji<=nlstate*nlstate;ji++)
! 3198: varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
! 3199: }
! 3200: }
! 3201:
! 3202: /* Computing expectancies */
! 3203: hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
! 3204: for(i=1; i<=nlstate;i++)
! 3205: for(j=1; j<=nlstate;j++)
! 3206: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
! 3207: eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
! 3208:
! 3209: /* 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]);*/
! 3210:
! 3211: }
! 3212:
! 3213: fprintf(ficresstdeij,"%3.0f",age );
! 3214: for(i=1; i<=nlstate;i++){
! 3215: eip=0.;
! 3216: vip=0.;
! 3217: for(j=1; j<=nlstate;j++){
! 3218: eip += eij[i][j][(int)age];
! 3219: for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
! 3220: vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
! 3221: fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
! 3222: }
! 3223: fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
! 3224: }
! 3225: fprintf(ficresstdeij,"\n");
! 3226:
! 3227: fprintf(ficrescveij,"%3.0f",age );
! 3228: for(i=1; i<=nlstate;i++)
! 3229: for(j=1; j<=nlstate;j++){
! 3230: cptj= (j-1)*nlstate+i;
! 3231: for(i2=1; i2<=nlstate;i2++)
! 3232: for(j2=1; j2<=nlstate;j2++){
! 3233: cptj2= (j2-1)*nlstate+i2;
! 3234: if(cptj2 <= cptj)
! 3235: fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
! 3236: }
! 3237: }
! 3238: fprintf(ficrescveij,"\n");
! 3239:
! 3240: }
! 3241: free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
! 3242: free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
! 3243: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
! 3244: free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
! 3245: free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
! 3246: free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
! 3247: printf("\n");
! 3248: fprintf(ficlog,"\n");
! 3249:
! 3250: free_vector(xm,1,npar);
! 3251: free_vector(xp,1,npar);
! 3252: free_matrix(dnewm,1,nlstate*nlstate,1,npar);
! 3253: free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
! 3254: free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
! 3255: }
! 3256:
! 3257: /************ Variance ******************/
! 3258: 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[])
! 3259: {
! 3260: /* Variance of health expectancies */
! 3261: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
! 3262: /* double **newm;*/
! 3263: double **dnewm,**doldm;
! 3264: double **dnewmp,**doldmp;
! 3265: int i, j, nhstepm, hstepm, h, nstepm ;
! 3266: int k, cptcode;
! 3267: double *xp;
! 3268: double **gp, **gm; /* for var eij */
! 3269: double ***gradg, ***trgradg; /*for var eij */
! 3270: double **gradgp, **trgradgp; /* for var p point j */
! 3271: double *gpp, *gmp; /* for var p point j */
! 3272: double **varppt; /* for var p point j nlstate to nlstate+ndeath */
! 3273: double ***p3mat;
! 3274: double age,agelim, hf;
! 3275: double ***mobaverage;
! 3276: int theta;
! 3277: char digit[4];
! 3278: char digitp[25];
! 3279:
! 3280: char fileresprobmorprev[FILENAMELENGTH];
! 3281:
! 3282: if(popbased==1){
! 3283: if(mobilav!=0)
! 3284: strcpy(digitp,"-populbased-mobilav-");
! 3285: else strcpy(digitp,"-populbased-nomobil-");
! 3286: }
! 3287: else
! 3288: strcpy(digitp,"-stablbased-");
! 3289:
! 3290: if (mobilav!=0) {
! 3291: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
! 3292: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
! 3293: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
! 3294: printf(" Error in movingaverage mobilav=%d\n",mobilav);
! 3295: }
! 3296: }
! 3297:
! 3298: strcpy(fileresprobmorprev,"prmorprev");
! 3299: sprintf(digit,"%-d",ij);
! 3300: /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
! 3301: strcat(fileresprobmorprev,digit); /* Tvar to be done */
! 3302: strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
! 3303: strcat(fileresprobmorprev,fileres);
! 3304: if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
! 3305: printf("Problem with resultfile: %s\n", fileresprobmorprev);
! 3306: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
! 3307: }
! 3308: printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
! 3309:
! 3310: fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
! 3311: pstamp(ficresprobmorprev);
! 3312: 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);
! 3313: fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
! 3314: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
! 3315: fprintf(ficresprobmorprev," p.%-d SE",j);
! 3316: for(i=1; i<=nlstate;i++)
! 3317: fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
! 3318: }
! 3319: fprintf(ficresprobmorprev,"\n");
! 3320: fprintf(ficgp,"\n# Routine varevsij");
! 3321: /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
! 3322: 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");
! 3323: fprintf(fichtm,"\n<br>%s <br>\n",digitp);
! 3324: /* } */
! 3325: varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
! 3326: pstamp(ficresvij);
! 3327: fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n# (weighted average of eij where weights are ");
! 3328: if(popbased==1)
! 3329: 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);
! 3330: else
! 3331: fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
! 3332: fprintf(ficresvij,"# Age");
! 3333: for(i=1; i<=nlstate;i++)
! 3334: for(j=1; j<=nlstate;j++)
! 3335: fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
! 3336: fprintf(ficresvij,"\n");
! 3337:
! 3338: xp=vector(1,npar);
! 3339: dnewm=matrix(1,nlstate,1,npar);
! 3340: doldm=matrix(1,nlstate,1,nlstate);
! 3341: dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
! 3342: doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
! 3343:
! 3344: gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
! 3345: gpp=vector(nlstate+1,nlstate+ndeath);
! 3346: gmp=vector(nlstate+1,nlstate+ndeath);
! 3347: trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
! 3348:
! 3349: if(estepm < stepm){
! 3350: printf ("Problem %d lower than %d\n",estepm, stepm);
! 3351: }
! 3352: else hstepm=estepm;
! 3353: /* For example we decided to compute the life expectancy with the smallest unit */
! 3354: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
! 3355: nhstepm is the number of hstepm from age to agelim
! 3356: nstepm is the number of stepm from age to agelin.
! 3357: Look at function hpijx to understand why (it is linked to memory size questions) */
! 3358: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
! 3359: survival function given by stepm (the optimization length). Unfortunately it
! 3360: means that if the survival funtion is printed every two years of age and if
! 3361: you sum them up and add 1 year (area under the trapezoids) you won't get the same
! 3362: results. So we changed our mind and took the option of the best precision.
! 3363: */
! 3364: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
! 3365: agelim = AGESUP;
! 3366: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
! 3367: nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
! 3368: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
! 3369: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
! 3370: gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
! 3371: gp=matrix(0,nhstepm,1,nlstate);
! 3372: gm=matrix(0,nhstepm,1,nlstate);
! 3373:
! 3374:
! 3375: for(theta=1; theta <=npar; theta++){
! 3376: for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
! 3377: xp[i] = x[i] + (i==theta ?delti[theta]:0);
! 3378: }
! 3379: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
! 3380: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
! 3381:
! 3382: if (popbased==1) {
! 3383: if(mobilav ==0){
! 3384: for(i=1; i<=nlstate;i++)
! 3385: prlim[i][i]=probs[(int)age][i][ij];
! 3386: }else{ /* mobilav */
! 3387: for(i=1; i<=nlstate;i++)
! 3388: prlim[i][i]=mobaverage[(int)age][i][ij];
! 3389: }
! 3390: }
! 3391:
! 3392: for(j=1; j<= nlstate; j++){
! 3393: for(h=0; h<=nhstepm; h++){
! 3394: for(i=1, gp[h][j]=0.;i<=nlstate;i++)
! 3395: gp[h][j] += prlim[i][i]*p3mat[i][j][h];
! 3396: }
! 3397: }
! 3398: /* This for computing probability of death (h=1 means
! 3399: computed over hstepm matrices product = hstepm*stepm months)
! 3400: as a weighted average of prlim.
! 3401: */
! 3402: for(j=nlstate+1;j<=nlstate+ndeath;j++){
! 3403: for(i=1,gpp[j]=0.; i<= nlstate; i++)
! 3404: gpp[j] += prlim[i][i]*p3mat[i][j][1];
! 3405: }
! 3406: /* end probability of death */
! 3407:
! 3408: for(i=1; i<=npar; i++) /* Computes gradient x - delta */
! 3409: xp[i] = x[i] - (i==theta ?delti[theta]:0);
! 3410: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
! 3411: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
! 3412:
! 3413: if (popbased==1) {
! 3414: if(mobilav ==0){
! 3415: for(i=1; i<=nlstate;i++)
! 3416: prlim[i][i]=probs[(int)age][i][ij];
! 3417: }else{ /* mobilav */
! 3418: for(i=1; i<=nlstate;i++)
! 3419: prlim[i][i]=mobaverage[(int)age][i][ij];
! 3420: }
! 3421: }
! 3422:
! 3423: for(j=1; j<= nlstate; j++){ /* Sum of wi * eij = e.j */
! 3424: for(h=0; h<=nhstepm; h++){
! 3425: for(i=1, gm[h][j]=0.;i<=nlstate;i++)
! 3426: gm[h][j] += prlim[i][i]*p3mat[i][j][h];
! 3427: }
! 3428: }
! 3429: /* This for computing probability of death (h=1 means
! 3430: computed over hstepm matrices product = hstepm*stepm months)
! 3431: as a weighted average of prlim.
! 3432: */
! 3433: for(j=nlstate+1;j<=nlstate+ndeath;j++){
! 3434: for(i=1,gmp[j]=0.; i<= nlstate; i++)
! 3435: gmp[j] += prlim[i][i]*p3mat[i][j][1];
! 3436: }
! 3437: /* end probability of death */
! 3438:
! 3439: for(j=1; j<= nlstate; j++) /* vareij */
! 3440: for(h=0; h<=nhstepm; h++){
! 3441: gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
! 3442: }
! 3443:
! 3444: for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
! 3445: gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
! 3446: }
! 3447:
! 3448: } /* End theta */
! 3449:
! 3450: trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
! 3451:
! 3452: for(h=0; h<=nhstepm; h++) /* veij */
! 3453: for(j=1; j<=nlstate;j++)
! 3454: for(theta=1; theta <=npar; theta++)
! 3455: trgradg[h][j][theta]=gradg[h][theta][j];
! 3456:
! 3457: for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
! 3458: for(theta=1; theta <=npar; theta++)
! 3459: trgradgp[j][theta]=gradgp[theta][j];
! 3460:
! 3461:
! 3462: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
! 3463: for(i=1;i<=nlstate;i++)
! 3464: for(j=1;j<=nlstate;j++)
! 3465: vareij[i][j][(int)age] =0.;
! 3466:
! 3467: for(h=0;h<=nhstepm;h++){
! 3468: for(k=0;k<=nhstepm;k++){
! 3469: matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
! 3470: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
! 3471: for(i=1;i<=nlstate;i++)
! 3472: for(j=1;j<=nlstate;j++)
! 3473: vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
! 3474: }
! 3475: }
! 3476:
! 3477: /* pptj */
! 3478: matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
! 3479: matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
! 3480: for(j=nlstate+1;j<=nlstate+ndeath;j++)
! 3481: for(i=nlstate+1;i<=nlstate+ndeath;i++)
! 3482: varppt[j][i]=doldmp[j][i];
! 3483: /* end ppptj */
! 3484: /* x centered again */
! 3485: hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);
! 3486: prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
! 3487:
! 3488: if (popbased==1) {
! 3489: if(mobilav ==0){
! 3490: for(i=1; i<=nlstate;i++)
! 3491: prlim[i][i]=probs[(int)age][i][ij];
! 3492: }else{ /* mobilav */
! 3493: for(i=1; i<=nlstate;i++)
! 3494: prlim[i][i]=mobaverage[(int)age][i][ij];
! 3495: }
! 3496: }
! 3497:
! 3498: /* This for computing probability of death (h=1 means
! 3499: computed over hstepm (estepm) matrices product = hstepm*stepm months)
! 3500: as a weighted average of prlim.
! 3501: */
! 3502: for(j=nlstate+1;j<=nlstate+ndeath;j++){
! 3503: for(i=1,gmp[j]=0.;i<= nlstate; i++)
! 3504: gmp[j] += prlim[i][i]*p3mat[i][j][1];
! 3505: }
! 3506: /* end probability of death */
! 3507:
! 3508: fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
! 3509: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
! 3510: fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
! 3511: for(i=1; i<=nlstate;i++){
! 3512: fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
! 3513: }
! 3514: }
! 3515: fprintf(ficresprobmorprev,"\n");
! 3516:
! 3517: fprintf(ficresvij,"%.0f ",age );
! 3518: for(i=1; i<=nlstate;i++)
! 3519: for(j=1; j<=nlstate;j++){
! 3520: fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
! 3521: }
! 3522: fprintf(ficresvij,"\n");
! 3523: free_matrix(gp,0,nhstepm,1,nlstate);
! 3524: free_matrix(gm,0,nhstepm,1,nlstate);
! 3525: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
! 3526: free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
! 3527: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
! 3528: } /* End age */
! 3529: free_vector(gpp,nlstate+1,nlstate+ndeath);
! 3530: free_vector(gmp,nlstate+1,nlstate+ndeath);
! 3531: free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
! 3532: free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
! 3533: fprintf(ficgp,"\nunset parametric;unset label; set ter png small size 320, 240");
! 3534: /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
! 3535: fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
! 3536: /* fprintf(ficgp,"\n plot \"%s\" u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
! 3537: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
! 3538: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
! 3539: fprintf(ficgp,"\n plot \"%s\" u 1:($3) not w l lt 1 ",subdirf(fileresprobmorprev));
! 3540: fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)) t \"95\%% interval\" w l lt 2 ",subdirf(fileresprobmorprev));
! 3541: fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)) not w l lt 2 ",subdirf(fileresprobmorprev));
! 3542: fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
! 3543: 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);
! 3544: /* 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);
! 3545: */
! 3546: /* fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
! 3547: fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
! 3548:
! 3549: free_vector(xp,1,npar);
! 3550: free_matrix(doldm,1,nlstate,1,nlstate);
! 3551: free_matrix(dnewm,1,nlstate,1,npar);
! 3552: free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
! 3553: free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
! 3554: free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
! 3555: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
! 3556: fclose(ficresprobmorprev);
! 3557: fflush(ficgp);
! 3558: fflush(fichtm);
! 3559: } /* end varevsij */
! 3560:
! 3561: /************ Variance of prevlim ******************/
! 3562: 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[])
! 3563: {
! 3564: /* Variance of prevalence limit */
! 3565: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
! 3566: double **newm;
! 3567: double **dnewm,**doldm;
! 3568: int i, j, nhstepm, hstepm;
! 3569: int k, cptcode;
! 3570: double *xp;
! 3571: double *gp, *gm;
! 3572: double **gradg, **trgradg;
! 3573: double age,agelim;
! 3574: int theta;
! 3575:
! 3576: pstamp(ficresvpl);
! 3577: fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
! 3578: fprintf(ficresvpl,"# Age");
! 3579: for(i=1; i<=nlstate;i++)
! 3580: fprintf(ficresvpl," %1d-%1d",i,i);
! 3581: fprintf(ficresvpl,"\n");
! 3582:
! 3583: xp=vector(1,npar);
! 3584: dnewm=matrix(1,nlstate,1,npar);
! 3585: doldm=matrix(1,nlstate,1,nlstate);
! 3586:
! 3587: hstepm=1*YEARM; /* Every year of age */
! 3588: hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
! 3589: agelim = AGESUP;
! 3590: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
! 3591: nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
! 3592: if (stepm >= YEARM) hstepm=1;
! 3593: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
! 3594: gradg=matrix(1,npar,1,nlstate);
! 3595: gp=vector(1,nlstate);
! 3596: gm=vector(1,nlstate);
! 3597:
! 3598: for(theta=1; theta <=npar; theta++){
! 3599: for(i=1; i<=npar; i++){ /* Computes gradient */
! 3600: xp[i] = x[i] + (i==theta ?delti[theta]:0);
! 3601: }
! 3602: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
! 3603: for(i=1;i<=nlstate;i++)
! 3604: gp[i] = prlim[i][i];
! 3605:
! 3606: for(i=1; i<=npar; i++) /* Computes gradient */
! 3607: xp[i] = x[i] - (i==theta ?delti[theta]:0);
! 3608: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
! 3609: for(i=1;i<=nlstate;i++)
! 3610: gm[i] = prlim[i][i];
! 3611:
! 3612: for(i=1;i<=nlstate;i++)
! 3613: gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
! 3614: } /* End theta */
! 3615:
! 3616: trgradg =matrix(1,nlstate,1,npar);
! 3617:
! 3618: for(j=1; j<=nlstate;j++)
! 3619: for(theta=1; theta <=npar; theta++)
! 3620: trgradg[j][theta]=gradg[theta][j];
! 3621:
! 3622: for(i=1;i<=nlstate;i++)
! 3623: varpl[i][(int)age] =0.;
! 3624: matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
! 3625: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
! 3626: for(i=1;i<=nlstate;i++)
! 3627: varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
! 3628:
! 3629: fprintf(ficresvpl,"%.0f ",age );
! 3630: for(i=1; i<=nlstate;i++)
! 3631: fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
! 3632: fprintf(ficresvpl,"\n");
! 3633: free_vector(gp,1,nlstate);
! 3634: free_vector(gm,1,nlstate);
! 3635: free_matrix(gradg,1,npar,1,nlstate);
! 3636: free_matrix(trgradg,1,nlstate,1,npar);
! 3637: } /* End age */
! 3638:
! 3639: free_vector(xp,1,npar);
! 3640: free_matrix(doldm,1,nlstate,1,npar);
! 3641: free_matrix(dnewm,1,nlstate,1,nlstate);
! 3642:
! 3643: }
! 3644:
! 3645: /************ Variance of one-step probabilities ******************/
! 3646: 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[])
! 3647: {
! 3648: int i, j=0, i1, k1, l1, t, tj;
! 3649: int k2, l2, j1, z1;
! 3650: int k=0,l, cptcode;
! 3651: int first=1, first1, first2;
! 3652: double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
! 3653: double **dnewm,**doldm;
! 3654: double *xp;
! 3655: double *gp, *gm;
! 3656: double **gradg, **trgradg;
! 3657: double **mu;
! 3658: double age,agelim, cov[NCOVMAX+1];
! 3659: double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
! 3660: int theta;
! 3661: char fileresprob[FILENAMELENGTH];
! 3662: char fileresprobcov[FILENAMELENGTH];
! 3663: char fileresprobcor[FILENAMELENGTH];
! 3664: double ***varpij;
! 3665:
! 3666: strcpy(fileresprob,"prob");
! 3667: strcat(fileresprob,fileres);
! 3668: if((ficresprob=fopen(fileresprob,"w"))==NULL) {
! 3669: printf("Problem with resultfile: %s\n", fileresprob);
! 3670: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
! 3671: }
! 3672: strcpy(fileresprobcov,"probcov");
! 3673: strcat(fileresprobcov,fileres);
! 3674: if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
! 3675: printf("Problem with resultfile: %s\n", fileresprobcov);
! 3676: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
! 3677: }
! 3678: strcpy(fileresprobcor,"probcor");
! 3679: strcat(fileresprobcor,fileres);
! 3680: if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
! 3681: printf("Problem with resultfile: %s\n", fileresprobcor);
! 3682: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
! 3683: }
! 3684: printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
! 3685: fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
! 3686: printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
! 3687: fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
! 3688: printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
! 3689: fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
! 3690: pstamp(ficresprob);
! 3691: fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
! 3692: fprintf(ficresprob,"# Age");
! 3693: pstamp(ficresprobcov);
! 3694: fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
! 3695: fprintf(ficresprobcov,"# Age");
! 3696: pstamp(ficresprobcor);
! 3697: fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
! 3698: fprintf(ficresprobcor,"# Age");
! 3699:
! 3700:
! 3701: for(i=1; i<=nlstate;i++)
! 3702: for(j=1; j<=(nlstate+ndeath);j++){
! 3703: fprintf(ficresprob," p%1d-%1d (SE)",i,j);
! 3704: fprintf(ficresprobcov," p%1d-%1d ",i,j);
! 3705: fprintf(ficresprobcor," p%1d-%1d ",i,j);
! 3706: }
! 3707: /* fprintf(ficresprob,"\n");
! 3708: fprintf(ficresprobcov,"\n");
! 3709: fprintf(ficresprobcor,"\n");
! 3710: */
! 3711: xp=vector(1,npar);
! 3712: dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
! 3713: doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
! 3714: mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
! 3715: varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
! 3716: first=1;
! 3717: fprintf(ficgp,"\n# Routine varprob");
! 3718: fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
! 3719: fprintf(fichtm,"\n");
! 3720:
! 3721: fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
! 3722: fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
! 3723: file %s<br>\n",optionfilehtmcov);
! 3724: fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
! 3725: and drawn. It helps understanding how is the covariance between two incidences.\
! 3726: They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
! 3727: 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. \
! 3728: It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
! 3729: would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
! 3730: standard deviations wide on each axis. <br>\
! 3731: Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
! 3732: and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
! 3733: To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
! 3734:
! 3735: cov[1]=1;
! 3736: /* tj=cptcoveff; */
! 3737: tj = (int) pow(2,cptcoveff);
! 3738: if (cptcovn<1) {tj=1;ncodemax[1]=1;}
! 3739: j1=0;
! 3740: for(j1=1; j1<=tj;j1++){
! 3741: /*for(i1=1; i1<=ncodemax[t];i1++){ */
! 3742: /*j1++;*/
! 3743: if (cptcovn>0) {
! 3744: fprintf(ficresprob, "\n#********** Variable ");
! 3745: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
! 3746: fprintf(ficresprob, "**********\n#\n");
! 3747: fprintf(ficresprobcov, "\n#********** Variable ");
! 3748: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
! 3749: fprintf(ficresprobcov, "**********\n#\n");
! 3750:
! 3751: fprintf(ficgp, "\n#********** Variable ");
! 3752: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
! 3753: fprintf(ficgp, "**********\n#\n");
! 3754:
! 3755:
! 3756: fprintf(fichtmcov, "\n<hr size=\"2\" color=\"#EC5E5E\">********** Variable ");
! 3757: for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
! 3758: fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
! 3759:
! 3760: fprintf(ficresprobcor, "\n#********** Variable ");
! 3761: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
! 3762: fprintf(ficresprobcor, "**********\n#");
! 3763: }
! 3764:
! 3765: gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
! 3766: trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
! 3767: gp=vector(1,(nlstate)*(nlstate+ndeath));
! 3768: gm=vector(1,(nlstate)*(nlstate+ndeath));
! 3769: for (age=bage; age<=fage; age ++){
! 3770: cov[2]=age;
! 3771: for (k=1; k<=cptcovn;k++) {
! 3772: cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];/* j1 1 2 3 4
! 3773: * 1 1 1 1 1
! 3774: * 2 2 1 1 1
! 3775: * 3 1 2 1 1
! 3776: */
! 3777: /* nbcode[1][1]=0 nbcode[1][2]=1;*/
! 3778: }
! 3779: for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
! 3780: for (k=1; k<=cptcovprod;k++)
! 3781: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
! 3782:
! 3783:
! 3784: for(theta=1; theta <=npar; theta++){
! 3785: for(i=1; i<=npar; i++)
! 3786: xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
! 3787:
! 3788: pmij(pmmij,cov,ncovmodel,xp,nlstate);
! 3789:
! 3790: k=0;
! 3791: for(i=1; i<= (nlstate); i++){
! 3792: for(j=1; j<=(nlstate+ndeath);j++){
! 3793: k=k+1;
! 3794: gp[k]=pmmij[i][j];
! 3795: }
! 3796: }
! 3797:
! 3798: for(i=1; i<=npar; i++)
! 3799: xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
! 3800:
! 3801: pmij(pmmij,cov,ncovmodel,xp,nlstate);
! 3802: k=0;
! 3803: for(i=1; i<=(nlstate); i++){
! 3804: for(j=1; j<=(nlstate+ndeath);j++){
! 3805: k=k+1;
! 3806: gm[k]=pmmij[i][j];
! 3807: }
! 3808: }
! 3809:
! 3810: for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)
! 3811: gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];
! 3812: }
! 3813:
! 3814: for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
! 3815: for(theta=1; theta <=npar; theta++)
! 3816: trgradg[j][theta]=gradg[theta][j];
! 3817:
! 3818: matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);
! 3819: matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
! 3820:
! 3821: pmij(pmmij,cov,ncovmodel,x,nlstate);
! 3822:
! 3823: k=0;
! 3824: for(i=1; i<=(nlstate); i++){
! 3825: for(j=1; j<=(nlstate+ndeath);j++){
! 3826: k=k+1;
! 3827: mu[k][(int) age]=pmmij[i][j];
! 3828: }
! 3829: }
! 3830: for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
! 3831: for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
! 3832: varpij[i][j][(int)age] = doldm[i][j];
! 3833:
! 3834: /*printf("\n%d ",(int)age);
! 3835: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
! 3836: printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
! 3837: fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
! 3838: }*/
! 3839:
! 3840: fprintf(ficresprob,"\n%d ",(int)age);
! 3841: fprintf(ficresprobcov,"\n%d ",(int)age);
! 3842: fprintf(ficresprobcor,"\n%d ",(int)age);
! 3843:
! 3844: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
! 3845: fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
! 3846: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
! 3847: fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
! 3848: fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
! 3849: }
! 3850: i=0;
! 3851: for (k=1; k<=(nlstate);k++){
! 3852: for (l=1; l<=(nlstate+ndeath);l++){
! 3853: i++;
! 3854: fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
! 3855: fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
! 3856: for (j=1; j<=i;j++){
! 3857: /* printf(" k=%d l=%d i=%d j=%d\n",k,l,i,j);fflush(stdout); */
! 3858: fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
! 3859: fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
! 3860: }
! 3861: }
! 3862: }/* end of loop for state */
! 3863: } /* end of loop for age */
! 3864: free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
! 3865: free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
! 3866: free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
! 3867: free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
! 3868:
! 3869: /* Confidence intervalle of pij */
! 3870: /*
! 3871: fprintf(ficgp,"\nunset parametric;unset label");
! 3872: fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
! 3873: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
! 3874: 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);
! 3875: fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
! 3876: fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
! 3877: fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
! 3878: */
! 3879:
! 3880: /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
! 3881: first1=1;first2=2;
! 3882: for (k2=1; k2<=(nlstate);k2++){
! 3883: for (l2=1; l2<=(nlstate+ndeath);l2++){
! 3884: if(l2==k2) continue;
! 3885: j=(k2-1)*(nlstate+ndeath)+l2;
! 3886: for (k1=1; k1<=(nlstate);k1++){
! 3887: for (l1=1; l1<=(nlstate+ndeath);l1++){
! 3888: if(l1==k1) continue;
! 3889: i=(k1-1)*(nlstate+ndeath)+l1;
! 3890: if(i<=j) continue;
! 3891: for (age=bage; age<=fage; age ++){
! 3892: if ((int)age %5==0){
! 3893: v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
! 3894: v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
! 3895: cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
! 3896: mu1=mu[i][(int) age]/stepm*YEARM ;
! 3897: mu2=mu[j][(int) age]/stepm*YEARM;
! 3898: c12=cv12/sqrt(v1*v2);
! 3899: /* Computing eigen value of matrix of covariance */
! 3900: lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
! 3901: lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
! 3902: if ((lc2 <0) || (lc1 <0) ){
! 3903: if(first2==1){
! 3904: first1=0;
! 3905: 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);
! 3906: }
! 3907: 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);
! 3908: /* lc1=fabs(lc1); */ /* If we want to have them positive */
! 3909: /* lc2=fabs(lc2); */
! 3910: }
! 3911:
! 3912: /* Eigen vectors */
! 3913: v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
! 3914: /*v21=sqrt(1.-v11*v11); *//* error */
! 3915: v21=(lc1-v1)/cv12*v11;
! 3916: v12=-v21;
! 3917: v22=v11;
! 3918: tnalp=v21/v11;
! 3919: if(first1==1){
! 3920: first1=0;
! 3921: 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);
! 3922: }
! 3923: 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);
! 3924: /*printf(fignu*/
! 3925: /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
! 3926: /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
! 3927: if(first==1){
! 3928: first=0;
! 3929: fprintf(ficgp,"\nset parametric;unset label");
! 3930: 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);
! 3931: fprintf(ficgp,"\nset ter png small size 320, 240");
! 3932: fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
! 3933: :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
! 3934: %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
! 3935: subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
! 3936: subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
! 3937: fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
! 3938: fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
! 3939: fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
! 3940: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
! 3941: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
! 3942: 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",\
! 3943: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
! 3944: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
! 3945: }else{
! 3946: first=0;
! 3947: fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
! 3948: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
! 3949: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
! 3950: 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",\
! 3951: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
! 3952: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
! 3953: }/* if first */
! 3954: } /* age mod 5 */
! 3955: } /* end loop age */
! 3956: fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
! 3957: first=1;
! 3958: } /*l12 */
! 3959: } /* k12 */
! 3960: } /*l1 */
! 3961: }/* k1 */
! 3962: /* } /* loop covariates */
! 3963: }
! 3964: free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
! 3965: free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
! 3966: free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
! 3967: free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
! 3968: free_vector(xp,1,npar);
! 3969: fclose(ficresprob);
! 3970: fclose(ficresprobcov);
! 3971: fclose(ficresprobcor);
! 3972: fflush(ficgp);
! 3973: fflush(fichtmcov);
! 3974: }
! 3975:
! 3976:
! 3977: /******************* Printing html file ***********/
! 3978: void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
! 3979: int lastpass, int stepm, int weightopt, char model[],\
! 3980: int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
! 3981: int popforecast, int estepm ,\
! 3982: double jprev1, double mprev1,double anprev1, \
! 3983: double jprev2, double mprev2,double anprev2){
! 3984: int jj1, k1, i1, cpt;
! 3985:
! 3986: fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
! 3987: <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
! 3988: </ul>");
! 3989: fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \
! 3990: - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
! 3991: jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
! 3992: fprintf(fichtm,"\
! 3993: - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
! 3994: stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
! 3995: fprintf(fichtm,"\
! 3996: - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
! 3997: subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
! 3998: fprintf(fichtm,"\
! 3999: - (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): \
! 4000: <a href=\"%s\">%s</a> <br>\n",
! 4001: estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
! 4002: fprintf(fichtm,"\
! 4003: - Population projections by age and states: \
! 4004: <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileres,"f"),subdirf2(fileres,"f"));
! 4005:
! 4006: fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
! 4007:
! 4008: m=pow(2,cptcoveff);
! 4009: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
! 4010:
! 4011: jj1=0;
! 4012: for(k1=1; k1<=m;k1++){
! 4013: for(i1=1; i1<=ncodemax[k1];i1++){
! 4014: jj1++;
! 4015: if (cptcovn > 0) {
! 4016: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
! 4017: for (cpt=1; cpt<=cptcoveff;cpt++)
! 4018: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
! 4019: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
! 4020: }
! 4021: /* Pij */
! 4022: 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> \
! 4023: <img src=\"%s%d_1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
! 4024: /* Quasi-incidences */
! 4025: fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
! 4026: 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> \
! 4027: <img src=\"%s%d_2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
! 4028: /* Period (stable) prevalence in each health state */
! 4029: for(cpt=1; cpt<=nlstate;cpt++){
! 4030: fprintf(fichtm,"<br>- Convergence from each state (1 to %d) to period (stable) prevalence in state %d <a href=\"%s%d_%d.png\">%s%d_%d.png</a><br> \
! 4031: <img src=\"%s%d_%d.png\">",nlstate, cpt, subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
! 4032: }
! 4033: for(cpt=1; cpt<=nlstate;cpt++) {
! 4034: 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> \
! 4035: <img src=\"%s%d%d.png\">",cpt,nlstate,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
! 4036: }
! 4037: } /* end i1 */
! 4038: }/* End k1 */
! 4039: fprintf(fichtm,"</ul>");
! 4040:
! 4041:
! 4042: fprintf(fichtm,"\
! 4043: \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
! 4044: - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);
! 4045:
! 4046: fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
! 4047: subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
! 4048: fprintf(fichtm,"\
! 4049: - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
! 4050: subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
! 4051:
! 4052: fprintf(fichtm,"\
! 4053: - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
! 4054: subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
! 4055: fprintf(fichtm,"\
! 4056: - 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): \
! 4057: <a href=\"%s\">%s</a> <br>\n</li>",
! 4058: estepm,subdirf2(fileres,"cve"),subdirf2(fileres,"cve"));
! 4059: fprintf(fichtm,"\
! 4060: - (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): \
! 4061: <a href=\"%s\">%s</a> <br>\n</li>",
! 4062: estepm,subdirf2(fileres,"stde"),subdirf2(fileres,"stde"));
! 4063: fprintf(fichtm,"\
! 4064: - 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",
! 4065: estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
! 4066: fprintf(fichtm,"\
! 4067: - 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",
! 4068: estepm, subdirf2(fileres,"t"),subdirf2(fileres,"t"));
! 4069: fprintf(fichtm,"\
! 4070: - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
! 4071: subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
! 4072:
! 4073: /* if(popforecast==1) fprintf(fichtm,"\n */
! 4074: /* - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
! 4075: /* - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
! 4076: /* <br>",fileres,fileres,fileres,fileres); */
! 4077: /* else */
! 4078: /* 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); */
! 4079: fflush(fichtm);
! 4080: fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
! 4081:
! 4082: m=pow(2,cptcoveff);
! 4083: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
! 4084:
! 4085: jj1=0;
! 4086: for(k1=1; k1<=m;k1++){
! 4087: for(i1=1; i1<=ncodemax[k1];i1++){
! 4088: jj1++;
! 4089: if (cptcovn > 0) {
! 4090: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
! 4091: for (cpt=1; cpt<=cptcoveff;cpt++)
! 4092: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
! 4093: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
! 4094: }
! 4095: for(cpt=1; cpt<=nlstate;cpt++) {
! 4096: fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
! 4097: prevalence (with 95%% confidence interval) in state (%d): %s%d_%d.png <br>\
! 4098: <img src=\"%s%d_%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);
! 4099: }
! 4100: fprintf(fichtm,"\n<br>- Total life expectancy by age and \
! 4101: health expectancies in states (1) and (2). If popbased=1 the smooth (due to the model) \
! 4102: true period expectancies (those weighted with period prevalences are also\
! 4103: drawn in addition to the population based expectancies computed using\
! 4104: observed and cahotic prevalences: %s%d.png<br>\
! 4105: <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
! 4106: } /* end i1 */
! 4107: }/* End k1 */
! 4108: fprintf(fichtm,"</ul>");
! 4109: fflush(fichtm);
! 4110: }
! 4111:
! 4112: /******************* Gnuplot file **************/
! 4113: void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
! 4114:
! 4115: char dirfileres[132],optfileres[132];
! 4116: int m0,cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,ij=0,l=0;
! 4117: int ng=0;
! 4118: /* if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
! 4119: /* printf("Problem with file %s",optionfilegnuplot); */
! 4120: /* fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
! 4121: /* } */
! 4122:
! 4123: /*#ifdef windows */
! 4124: fprintf(ficgp,"cd \"%s\" \n",pathc);
! 4125: /*#endif */
! 4126: m=pow(2,cptcoveff);
! 4127:
! 4128: strcpy(dirfileres,optionfilefiname);
! 4129: strcpy(optfileres,"vpl");
! 4130: /* 1eme*/
! 4131: fprintf(ficgp,"\n# 1st: Period (stable) prevalence with CI: 'vpl' files\n");
! 4132: for (cpt=1; cpt<= nlstate ; cpt ++) {
! 4133: for (k1=1; k1<= m ; k1 ++) { /* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */
! 4134: fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
! 4135: fprintf(ficgp,"\n#set out \"v%s%d_%d.png\" \n",optionfilefiname,cpt,k1);
! 4136: fprintf(ficgp,"set xlabel \"Age\" \n\
! 4137: set ylabel \"Probability\" \n\
! 4138: set ter png small size 320, 240\n\
! 4139: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
! 4140:
! 4141: for (i=1; i<= nlstate ; i ++) {
! 4142: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
! 4143: else fprintf(ficgp," \%%*lf (\%%*lf)");
! 4144: }
! 4145: 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);
! 4146: for (i=1; i<= nlstate ; i ++) {
! 4147: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
! 4148: else fprintf(ficgp," \%%*lf (\%%*lf)");
! 4149: }
! 4150: fprintf(ficgp,"\" t\"95\%% CI\" w l lt 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
! 4151: for (i=1; i<= nlstate ; i ++) {
! 4152: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
! 4153: else fprintf(ficgp," \%%*lf (\%%*lf)");
! 4154: }
! 4155: fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l lt 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
! 4156: }
! 4157: }
! 4158: /*2 eme*/
! 4159: fprintf(ficgp,"\n# 2nd: Total life expectancy with CI: 't' files\n");
! 4160: for (k1=1; k1<= m ; k1 ++) {
! 4161: fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
! 4162: fprintf(ficgp,"set ylabel \"Years\" \nset ter png small size 320, 240\nplot [%.f:%.f] ",ageminpar,fage);
! 4163:
! 4164: for (i=1; i<= nlstate+1 ; i ++) {
! 4165: k=2*i;
! 4166: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
! 4167: for (j=1; j<= nlstate+1 ; j ++) {
! 4168: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
! 4169: else fprintf(ficgp," \%%*lf (\%%*lf)");
! 4170: }
! 4171: if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
! 4172: else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
! 4173: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
! 4174: for (j=1; j<= nlstate+1 ; j ++) {
! 4175: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
! 4176: else fprintf(ficgp," \%%*lf (\%%*lf)");
! 4177: }
! 4178: fprintf(ficgp,"\" t\"\" w l lt 0,");
! 4179: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
! 4180: for (j=1; j<= nlstate+1 ; j ++) {
! 4181: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
! 4182: else fprintf(ficgp," \%%*lf (\%%*lf)");
! 4183: }
! 4184: if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l lt 0");
! 4185: else fprintf(ficgp,"\" t\"\" w l lt 0,");
! 4186: }
! 4187: }
! 4188:
! 4189: /*3eme*/
! 4190:
! 4191: for (k1=1; k1<= m ; k1 ++) {
! 4192: for (cpt=1; cpt<= nlstate ; cpt ++) {
! 4193: /* k=2+nlstate*(2*cpt-2); */
! 4194: k=2+(nlstate+1)*(cpt-1);
! 4195: fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
! 4196: fprintf(ficgp,"set ter png small size 320, 240\n\
! 4197: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
! 4198: /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
! 4199: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
! 4200: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
! 4201: fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
! 4202: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
! 4203: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
! 4204:
! 4205: */
! 4206: for (i=1; i< nlstate ; i ++) {
! 4207: 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);
! 4208: /* 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);*/
! 4209:
! 4210: }
! 4211: fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+nlstate,cpt);
! 4212: }
! 4213: }
! 4214:
! 4215: /* CV preval stable (period) */
! 4216: for (k1=1; k1<= m ; k1 ++) { /* For each multivariate if any */
! 4217: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
! 4218: k=3;
! 4219: fprintf(ficgp,"\n#\n#\n#CV preval stable (period): 'pij' files, cov=%d state=%d",k1, cpt);
! 4220: fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
! 4221: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
! 4222: set ter png small size 320, 240\n\
! 4223: unset log y\n\
! 4224: plot [%.f:%.f] ", ageminpar, agemaxpar);
! 4225: for (i=1; i<= nlstate ; i ++){
! 4226: if(i==1)
! 4227: fprintf(ficgp,"\"%s\"",subdirf2(fileres,"pij"));
! 4228: else
! 4229: fprintf(ficgp,", '' ");
! 4230: l=(nlstate+ndeath)*(i-1)+1;
! 4231: fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
! 4232: for (j=1; j<= (nlstate-1) ; j ++)
! 4233: fprintf(ficgp,"+$%d",k+l+j);
! 4234: fprintf(ficgp,")) t \"prev(%d,%d)\" w l",i,cpt);
! 4235: } /* nlstate */
! 4236: fprintf(ficgp,"\n");
! 4237: } /* end cpt state*/
! 4238: } /* end covariate */
! 4239:
! 4240: /* proba elementaires */
! 4241: for(i=1,jk=1; i <=nlstate; i++){
! 4242: for(k=1; k <=(nlstate+ndeath); k++){
! 4243: if (k != i) {
! 4244: for(j=1; j <=ncovmodel; j++){
! 4245: fprintf(ficgp,"p%d=%f ",jk,p[jk]);
! 4246: jk++;
! 4247: fprintf(ficgp,"\n");
! 4248: }
! 4249: }
! 4250: }
! 4251: }
! 4252: /*goto avoid;*/
! 4253: for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
! 4254: for(jk=1; jk <=m; jk++) {
! 4255: fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng);
! 4256: if (ng==2)
! 4257: fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
! 4258: else
! 4259: fprintf(ficgp,"\nset title \"Probability\"\n");
! 4260: fprintf(ficgp,"\nset ter png small size 320, 240\nset log y\nplot [%.f:%.f] ",ageminpar,agemaxpar);
! 4261: i=1;
! 4262: for(k2=1; k2<=nlstate; k2++) {
! 4263: k3=i;
! 4264: for(k=1; k<=(nlstate+ndeath); k++) {
! 4265: if (k != k2){
! 4266: if(ng==2)
! 4267: fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
! 4268: else
! 4269: fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
! 4270: ij=1;/* To be checked else nbcode[0][0] wrong */
! 4271: for(j=3; j <=ncovmodel; j++) {
! 4272: /* if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) { /\* Bug valgrind *\/ */
! 4273: /* /\*fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);*\/ */
! 4274: /* ij++; */
! 4275: /* } */
! 4276: /* else */
! 4277: fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
! 4278: }
! 4279: fprintf(ficgp,")/(1");
! 4280:
! 4281: for(k1=1; k1 <=nlstate; k1++){
! 4282: fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
! 4283: ij=1;
! 4284: for(j=3; j <=ncovmodel; j++){
! 4285: /* if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) { */
! 4286: /* fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]); */
! 4287: /* ij++; */
! 4288: /* } */
! 4289: /* else */
! 4290: fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
! 4291: }
! 4292: fprintf(ficgp,")");
! 4293: }
! 4294: fprintf(ficgp,") t \"p%d%d\" ", k2,k);
! 4295: if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
! 4296: i=i+ncovmodel;
! 4297: }
! 4298: } /* end k */
! 4299: } /* end k2 */
! 4300: } /* end jk */
! 4301: } /* end ng */
! 4302: avoid:
! 4303: fflush(ficgp);
! 4304: } /* end gnuplot */
! 4305:
! 4306:
! 4307: /*************** Moving average **************/
! 4308: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
! 4309:
! 4310: int i, cpt, cptcod;
! 4311: int modcovmax =1;
! 4312: int mobilavrange, mob;
! 4313: double age;
! 4314:
! 4315: modcovmax=2*cptcoveff;/* Max number of modalities. We suppose
! 4316: a covariate has 2 modalities */
! 4317: if (cptcovn<1) modcovmax=1; /* At least 1 pass */
! 4318:
! 4319: if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
! 4320: if(mobilav==1) mobilavrange=5; /* default */
! 4321: else mobilavrange=mobilav;
! 4322: for (age=bage; age<=fage; age++)
! 4323: for (i=1; i<=nlstate;i++)
! 4324: for (cptcod=1;cptcod<=modcovmax;cptcod++)
! 4325: mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
! 4326: /* We keep the original values on the extreme ages bage, fage and for
! 4327: fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
! 4328: we use a 5 terms etc. until the borders are no more concerned.
! 4329: */
! 4330: for (mob=3;mob <=mobilavrange;mob=mob+2){
! 4331: for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
! 4332: for (i=1; i<=nlstate;i++){
! 4333: for (cptcod=1;cptcod<=modcovmax;cptcod++){
! 4334: mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
! 4335: for (cpt=1;cpt<=(mob-1)/2;cpt++){
! 4336: mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
! 4337: mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
! 4338: }
! 4339: mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
! 4340: }
! 4341: }
! 4342: }/* end age */
! 4343: }/* end mob */
! 4344: }else return -1;
! 4345: return 0;
! 4346: }/* End movingaverage */
! 4347:
! 4348:
! 4349: /************** Forecasting ******************/
! 4350: 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){
! 4351: /* proj1, year, month, day of starting projection
! 4352: agemin, agemax range of age
! 4353: dateprev1 dateprev2 range of dates during which prevalence is computed
! 4354: anproj2 year of en of projection (same day and month as proj1).
! 4355: */
! 4356: int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;
! 4357: int *popage;
! 4358: double agec; /* generic age */
! 4359: double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
! 4360: double *popeffectif,*popcount;
! 4361: double ***p3mat;
! 4362: double ***mobaverage;
! 4363: char fileresf[FILENAMELENGTH];
! 4364:
! 4365: agelim=AGESUP;
! 4366: prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
! 4367:
! 4368: strcpy(fileresf,"f");
! 4369: strcat(fileresf,fileres);
! 4370: if((ficresf=fopen(fileresf,"w"))==NULL) {
! 4371: printf("Problem with forecast resultfile: %s\n", fileresf);
! 4372: fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
! 4373: }
! 4374: printf("Computing forecasting: result on file '%s' \n", fileresf);
! 4375: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
! 4376:
! 4377: if (cptcoveff==0) ncodemax[cptcoveff]=1;
! 4378:
! 4379: if (mobilav!=0) {
! 4380: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
! 4381: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
! 4382: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
! 4383: printf(" Error in movingaverage mobilav=%d\n",mobilav);
! 4384: }
! 4385: }
! 4386:
! 4387: stepsize=(int) (stepm+YEARM-1)/YEARM;
! 4388: if (stepm<=12) stepsize=1;
! 4389: if(estepm < stepm){
! 4390: printf ("Problem %d lower than %d\n",estepm, stepm);
! 4391: }
! 4392: else hstepm=estepm;
! 4393:
! 4394: hstepm=hstepm/stepm;
! 4395: yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp and
! 4396: fractional in yp1 */
! 4397: anprojmean=yp;
! 4398: yp2=modf((yp1*12),&yp);
! 4399: mprojmean=yp;
! 4400: yp1=modf((yp2*30.5),&yp);
! 4401: jprojmean=yp;
! 4402: if(jprojmean==0) jprojmean=1;
! 4403: if(mprojmean==0) jprojmean=1;
! 4404:
! 4405: i1=cptcoveff;
! 4406: if (cptcovn < 1){i1=1;}
! 4407:
! 4408: fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);
! 4409:
! 4410: fprintf(ficresf,"#****** Routine prevforecast **\n");
! 4411:
! 4412: /* if (h==(int)(YEARM*yearp)){ */
! 4413: for(cptcov=1, k=0;cptcov<=i1;cptcov++){
! 4414: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
! 4415: k=k+1;
! 4416: fprintf(ficresf,"\n#******");
! 4417: for(j=1;j<=cptcoveff;j++) {
! 4418: 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]]);
! 4419: }
! 4420: fprintf(ficresf,"******\n");
! 4421: fprintf(ficresf,"# Covariate valuofcovar yearproj age");
! 4422: for(j=1; j<=nlstate+ndeath;j++){
! 4423: for(i=1; i<=nlstate;i++)
! 4424: fprintf(ficresf," p%d%d",i,j);
! 4425: fprintf(ficresf," p.%d",j);
! 4426: }
! 4427: for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {
! 4428: fprintf(ficresf,"\n");
! 4429: fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);
! 4430:
! 4431: for (agec=fage; agec>=(ageminpar-1); agec--){
! 4432: nhstepm=(int) rint((agelim-agec)*YEARM/stepm);
! 4433: nhstepm = nhstepm/hstepm;
! 4434: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
! 4435: oldm=oldms;savm=savms;
! 4436: hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);
! 4437:
! 4438: for (h=0; h<=nhstepm; h++){
! 4439: if (h*hstepm/YEARM*stepm ==yearp) {
! 4440: fprintf(ficresf,"\n");
! 4441: for(j=1;j<=cptcoveff;j++)
! 4442: fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
! 4443: fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
! 4444: }
! 4445: for(j=1; j<=nlstate+ndeath;j++) {
! 4446: ppij=0.;
! 4447: for(i=1; i<=nlstate;i++) {
! 4448: if (mobilav==1)
! 4449: ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
! 4450: else {
! 4451: ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
! 4452: }
! 4453: if (h*hstepm/YEARM*stepm== yearp) {
! 4454: fprintf(ficresf," %.3f", p3mat[i][j][h]);
! 4455: }
! 4456: } /* end i */
! 4457: if (h*hstepm/YEARM*stepm==yearp) {
! 4458: fprintf(ficresf," %.3f", ppij);
! 4459: }
! 4460: }/* end j */
! 4461: } /* end h */
! 4462: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
! 4463: } /* end agec */
! 4464: } /* end yearp */
! 4465: } /* end cptcod */
! 4466: } /* end cptcov */
! 4467:
! 4468: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
! 4469:
! 4470: fclose(ficresf);
! 4471: }
! 4472:
! 4473: /************** Forecasting *****not tested NB*************/
! 4474: 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){
! 4475:
! 4476: int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
! 4477: int *popage;
! 4478: double calagedatem, agelim, kk1, kk2;
! 4479: double *popeffectif,*popcount;
! 4480: double ***p3mat,***tabpop,***tabpopprev;
! 4481: double ***mobaverage;
! 4482: char filerespop[FILENAMELENGTH];
! 4483:
! 4484: tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
! 4485: tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
! 4486: agelim=AGESUP;
! 4487: calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
! 4488:
! 4489: prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
! 4490:
! 4491:
! 4492: strcpy(filerespop,"pop");
! 4493: strcat(filerespop,fileres);
! 4494: if((ficrespop=fopen(filerespop,"w"))==NULL) {
! 4495: printf("Problem with forecast resultfile: %s\n", filerespop);
! 4496: fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
! 4497: }
! 4498: printf("Computing forecasting: result on file '%s' \n", filerespop);
! 4499: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
! 4500:
! 4501: if (cptcoveff==0) ncodemax[cptcoveff]=1;
! 4502:
! 4503: if (mobilav!=0) {
! 4504: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
! 4505: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
! 4506: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
! 4507: printf(" Error in movingaverage mobilav=%d\n",mobilav);
! 4508: }
! 4509: }
! 4510:
! 4511: stepsize=(int) (stepm+YEARM-1)/YEARM;
! 4512: if (stepm<=12) stepsize=1;
! 4513:
! 4514: agelim=AGESUP;
! 4515:
! 4516: hstepm=1;
! 4517: hstepm=hstepm/stepm;
! 4518:
! 4519: if (popforecast==1) {
! 4520: if((ficpop=fopen(popfile,"r"))==NULL) {
! 4521: printf("Problem with population file : %s\n",popfile);exit(0);
! 4522: fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
! 4523: }
! 4524: popage=ivector(0,AGESUP);
! 4525: popeffectif=vector(0,AGESUP);
! 4526: popcount=vector(0,AGESUP);
! 4527:
! 4528: i=1;
! 4529: while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
! 4530:
! 4531: imx=i;
! 4532: for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
! 4533: }
! 4534:
! 4535: for(cptcov=1,k=0;cptcov<=i2;cptcov++){
! 4536: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
! 4537: k=k+1;
! 4538: fprintf(ficrespop,"\n#******");
! 4539: for(j=1;j<=cptcoveff;j++) {
! 4540: fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
! 4541: }
! 4542: fprintf(ficrespop,"******\n");
! 4543: fprintf(ficrespop,"# Age");
! 4544: for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
! 4545: if (popforecast==1) fprintf(ficrespop," [Population]");
! 4546:
! 4547: for (cpt=0; cpt<=0;cpt++) {
! 4548: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
! 4549:
! 4550: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
! 4551: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
! 4552: nhstepm = nhstepm/hstepm;
! 4553:
! 4554: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
! 4555: oldm=oldms;savm=savms;
! 4556: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
! 4557:
! 4558: for (h=0; h<=nhstepm; h++){
! 4559: if (h==(int) (calagedatem+YEARM*cpt)) {
! 4560: fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
! 4561: }
! 4562: for(j=1; j<=nlstate+ndeath;j++) {
! 4563: kk1=0.;kk2=0;
! 4564: for(i=1; i<=nlstate;i++) {
! 4565: if (mobilav==1)
! 4566: kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
! 4567: else {
! 4568: kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
! 4569: }
! 4570: }
! 4571: if (h==(int)(calagedatem+12*cpt)){
! 4572: tabpop[(int)(agedeb)][j][cptcod]=kk1;
! 4573: /*fprintf(ficrespop," %.3f", kk1);
! 4574: if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
! 4575: }
! 4576: }
! 4577: for(i=1; i<=nlstate;i++){
! 4578: kk1=0.;
! 4579: for(j=1; j<=nlstate;j++){
! 4580: kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];
! 4581: }
! 4582: tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
! 4583: }
! 4584:
! 4585: if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++)
! 4586: fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
! 4587: }
! 4588: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
! 4589: }
! 4590: }
! 4591:
! 4592: /******/
! 4593:
! 4594: for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {
! 4595: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
! 4596: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
! 4597: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
! 4598: nhstepm = nhstepm/hstepm;
! 4599:
! 4600: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
! 4601: oldm=oldms;savm=savms;
! 4602: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
! 4603: for (h=0; h<=nhstepm; h++){
! 4604: if (h==(int) (calagedatem+YEARM*cpt)) {
! 4605: fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
! 4606: }
! 4607: for(j=1; j<=nlstate+ndeath;j++) {
! 4608: kk1=0.;kk2=0;
! 4609: for(i=1; i<=nlstate;i++) {
! 4610: kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];
! 4611: }
! 4612: if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);
! 4613: }
! 4614: }
! 4615: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
! 4616: }
! 4617: }
! 4618: }
! 4619: }
! 4620:
! 4621: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
! 4622:
! 4623: if (popforecast==1) {
! 4624: free_ivector(popage,0,AGESUP);
! 4625: free_vector(popeffectif,0,AGESUP);
! 4626: free_vector(popcount,0,AGESUP);
! 4627: }
! 4628: free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
! 4629: free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
! 4630: fclose(ficrespop);
! 4631: } /* End of popforecast */
! 4632:
! 4633: int fileappend(FILE *fichier, char *optionfich)
! 4634: {
! 4635: if((fichier=fopen(optionfich,"a"))==NULL) {
! 4636: printf("Problem with file: %s\n", optionfich);
! 4637: fprintf(ficlog,"Problem with file: %s\n", optionfich);
! 4638: return (0);
! 4639: }
! 4640: fflush(fichier);
! 4641: return (1);
! 4642: }
! 4643:
! 4644:
! 4645: /**************** function prwizard **********************/
! 4646: void prwizard(int ncovmodel, int nlstate, int ndeath, char model[], FILE *ficparo)
! 4647: {
! 4648:
! 4649: /* Wizard to print covariance matrix template */
! 4650:
! 4651: char ca[32], cb[32], cc[32];
! 4652: int i,j, k, l, li, lj, lk, ll, jj, npar, itimes;
! 4653: int numlinepar;
! 4654:
! 4655: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
! 4656: fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
! 4657: for(i=1; i <=nlstate; i++){
! 4658: jj=0;
! 4659: for(j=1; j <=nlstate+ndeath; j++){
! 4660: if(j==i) continue;
! 4661: jj++;
! 4662: /*ca[0]= k+'a'-1;ca[1]='\0';*/
! 4663: printf("%1d%1d",i,j);
! 4664: fprintf(ficparo,"%1d%1d",i,j);
! 4665: for(k=1; k<=ncovmodel;k++){
! 4666: /* printf(" %lf",param[i][j][k]); */
! 4667: /* fprintf(ficparo," %lf",param[i][j][k]); */
! 4668: printf(" 0.");
! 4669: fprintf(ficparo," 0.");
! 4670: }
! 4671: printf("\n");
! 4672: fprintf(ficparo,"\n");
! 4673: }
! 4674: }
! 4675: printf("# Scales (for hessian or gradient estimation)\n");
! 4676: fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
! 4677: npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
! 4678: for(i=1; i <=nlstate; i++){
! 4679: jj=0;
! 4680: for(j=1; j <=nlstate+ndeath; j++){
! 4681: if(j==i) continue;
! 4682: jj++;
! 4683: fprintf(ficparo,"%1d%1d",i,j);
! 4684: printf("%1d%1d",i,j);
! 4685: fflush(stdout);
! 4686: for(k=1; k<=ncovmodel;k++){
! 4687: /* printf(" %le",delti3[i][j][k]); */
! 4688: /* fprintf(ficparo," %le",delti3[i][j][k]); */
! 4689: printf(" 0.");
! 4690: fprintf(ficparo," 0.");
! 4691: }
! 4692: numlinepar++;
! 4693: printf("\n");
! 4694: fprintf(ficparo,"\n");
! 4695: }
! 4696: }
! 4697: printf("# Covariance matrix\n");
! 4698: /* # 121 Var(a12)\n\ */
! 4699: /* # 122 Cov(b12,a12) Var(b12)\n\ */
! 4700: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
! 4701: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
! 4702: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
! 4703: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
! 4704: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
! 4705: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
! 4706: fflush(stdout);
! 4707: fprintf(ficparo,"# Covariance matrix\n");
! 4708: /* # 121 Var(a12)\n\ */
! 4709: /* # 122 Cov(b12,a12) Var(b12)\n\ */
! 4710: /* # ...\n\ */
! 4711: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
! 4712:
! 4713: for(itimes=1;itimes<=2;itimes++){
! 4714: jj=0;
! 4715: for(i=1; i <=nlstate; i++){
! 4716: for(j=1; j <=nlstate+ndeath; j++){
! 4717: if(j==i) continue;
! 4718: for(k=1; k<=ncovmodel;k++){
! 4719: jj++;
! 4720: ca[0]= k+'a'-1;ca[1]='\0';
! 4721: if(itimes==1){
! 4722: printf("#%1d%1d%d",i,j,k);
! 4723: fprintf(ficparo,"#%1d%1d%d",i,j,k);
! 4724: }else{
! 4725: printf("%1d%1d%d",i,j,k);
! 4726: fprintf(ficparo,"%1d%1d%d",i,j,k);
! 4727: /* printf(" %.5le",matcov[i][j]); */
! 4728: }
! 4729: ll=0;
! 4730: for(li=1;li <=nlstate; li++){
! 4731: for(lj=1;lj <=nlstate+ndeath; lj++){
! 4732: if(lj==li) continue;
! 4733: for(lk=1;lk<=ncovmodel;lk++){
! 4734: ll++;
! 4735: if(ll<=jj){
! 4736: cb[0]= lk +'a'-1;cb[1]='\0';
! 4737: if(ll<jj){
! 4738: if(itimes==1){
! 4739: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
! 4740: fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
! 4741: }else{
! 4742: printf(" 0.");
! 4743: fprintf(ficparo," 0.");
! 4744: }
! 4745: }else{
! 4746: if(itimes==1){
! 4747: printf(" Var(%s%1d%1d)",ca,i,j);
! 4748: fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
! 4749: }else{
! 4750: printf(" 0.");
! 4751: fprintf(ficparo," 0.");
! 4752: }
! 4753: }
! 4754: }
! 4755: } /* end lk */
! 4756: } /* end lj */
! 4757: } /* end li */
! 4758: printf("\n");
! 4759: fprintf(ficparo,"\n");
! 4760: numlinepar++;
! 4761: } /* end k*/
! 4762: } /*end j */
! 4763: } /* end i */
! 4764: } /* end itimes */
! 4765:
! 4766: } /* end of prwizard */
! 4767: /******************* Gompertz Likelihood ******************************/
! 4768: double gompertz(double x[])
! 4769: {
! 4770: double A,B,L=0.0,sump=0.,num=0.;
! 4771: int i,n=0; /* n is the size of the sample */
! 4772:
! 4773: for (i=0;i<=imx-1 ; i++) {
! 4774: sump=sump+weight[i];
! 4775: /* sump=sump+1;*/
! 4776: num=num+1;
! 4777: }
! 4778:
! 4779:
! 4780: /* for (i=0; i<=imx; i++)
! 4781: 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]);*/
! 4782:
! 4783: for (i=1;i<=imx ; i++)
! 4784: {
! 4785: if (cens[i] == 1 && wav[i]>1)
! 4786: A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
! 4787:
! 4788: if (cens[i] == 0 && wav[i]>1)
! 4789: A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
! 4790: +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);
! 4791:
! 4792: /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
! 4793: if (wav[i] > 1 ) { /* ??? */
! 4794: L=L+A*weight[i];
! 4795: /* 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]);*/
! 4796: }
! 4797: }
! 4798:
! 4799: /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
! 4800:
! 4801: return -2*L*num/sump;
! 4802: }
! 4803:
! 4804: #ifdef GSL
! 4805: /******************* Gompertz_f Likelihood ******************************/
! 4806: double gompertz_f(const gsl_vector *v, void *params)
! 4807: {
! 4808: double A,B,LL=0.0,sump=0.,num=0.;
! 4809: double *x= (double *) v->data;
! 4810: int i,n=0; /* n is the size of the sample */
! 4811:
! 4812: for (i=0;i<=imx-1 ; i++) {
! 4813: sump=sump+weight[i];
! 4814: /* sump=sump+1;*/
! 4815: num=num+1;
! 4816: }
! 4817:
! 4818:
! 4819: /* for (i=0; i<=imx; i++)
! 4820: 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]);*/
! 4821: printf("x[0]=%lf x[1]=%lf\n",x[0],x[1]);
! 4822: for (i=1;i<=imx ; i++)
! 4823: {
! 4824: if (cens[i] == 1 && wav[i]>1)
! 4825: A=-x[0]/(x[1])*(exp(x[1]*(agecens[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)));
! 4826:
! 4827: if (cens[i] == 0 && wav[i]>1)
! 4828: A=-x[0]/(x[1])*(exp(x[1]*(agedc[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)))
! 4829: +log(x[0]/YEARM)+x[1]*(agedc[i]-agegomp)+log(YEARM);
! 4830:
! 4831: /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
! 4832: if (wav[i] > 1 ) { /* ??? */
! 4833: LL=LL+A*weight[i];
! 4834: /* 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]);*/
! 4835: }
! 4836: }
! 4837:
! 4838: /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
! 4839: printf("x[0]=%lf x[1]=%lf -2*LL*num/sump=%lf\n",x[0],x[1],-2*LL*num/sump);
! 4840:
! 4841: return -2*LL*num/sump;
! 4842: }
! 4843: #endif
! 4844:
! 4845: /******************* Printing html file ***********/
! 4846: void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \
! 4847: int lastpass, int stepm, int weightopt, char model[],\
! 4848: int imx, double p[],double **matcov,double agemortsup){
! 4849: int i,k;
! 4850:
! 4851: fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
! 4852: fprintf(fichtm," mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
! 4853: for (i=1;i<=2;i++)
! 4854: 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]));
! 4855: fprintf(fichtm,"<br><br><img src=\"graphmort.png\">");
! 4856: fprintf(fichtm,"</ul>");
! 4857:
! 4858: fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
! 4859:
! 4860: 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>");
! 4861:
! 4862: for (k=agegomp;k<(agemortsup-2);k++)
! 4863: 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]);
! 4864:
! 4865:
! 4866: fflush(fichtm);
! 4867: }
! 4868:
! 4869: /******************* Gnuplot file **************/
! 4870: void printinggnuplotmort(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
! 4871:
! 4872: char dirfileres[132],optfileres[132];
! 4873: int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
! 4874: int ng;
! 4875:
! 4876:
! 4877: /*#ifdef windows */
! 4878: fprintf(ficgp,"cd \"%s\" \n",pathc);
! 4879: /*#endif */
! 4880:
! 4881:
! 4882: strcpy(dirfileres,optionfilefiname);
! 4883: strcpy(optfileres,"vpl");
! 4884: fprintf(ficgp,"set out \"graphmort.png\"\n ");
! 4885: fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n ");
! 4886: fprintf(ficgp, "set ter png small size 320, 240\n set log y\n");
! 4887: /* fprintf(ficgp, "set size 0.65,0.65\n"); */
! 4888: fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
! 4889:
! 4890: }
! 4891:
! 4892: int readdata(char datafile[], int firstobs, int lastobs, int *imax)
! 4893: {
! 4894:
! 4895: /*-------- data file ----------*/
! 4896: FILE *fic;
! 4897: char dummy[]=" ";
! 4898: int i, j, n;
! 4899: int linei, month, year,iout;
! 4900: char line[MAXLINE], linetmp[MAXLINE];
! 4901: char stra[80], strb[80];
! 4902: char *stratrunc;
! 4903: int lstra;
! 4904:
! 4905:
! 4906: if((fic=fopen(datafile,"r"))==NULL) {
! 4907: printf("Problem while opening datafile: %s\n", datafile);return 1;
! 4908: fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);return 1;
! 4909: }
! 4910:
! 4911: i=1;
! 4912: linei=0;
! 4913: while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
! 4914: linei=linei+1;
! 4915: for(j=strlen(line); j>=0;j--){ /* Untabifies line */
! 4916: if(line[j] == '\t')
! 4917: line[j] = ' ';
! 4918: }
! 4919: for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){
! 4920: ;
! 4921: };
! 4922: line[j+1]=0; /* Trims blanks at end of line */
! 4923: if(line[0]=='#'){
! 4924: fprintf(ficlog,"Comment line\n%s\n",line);
! 4925: printf("Comment line\n%s\n",line);
! 4926: continue;
! 4927: }
! 4928: trimbb(linetmp,line); /* Trims multiple blanks in line */
! 4929: for (j=0; line[j]!='\0';j++){
! 4930: line[j]=linetmp[j];
! 4931: }
! 4932:
! 4933:
! 4934: for (j=maxwav;j>=1;j--){
! 4935: cutv(stra, strb, line, ' ');
! 4936: if(strb[0]=='.') { /* Missing status */
! 4937: lval=-1;
! 4938: }else{
! 4939: errno=0;
! 4940: lval=strtol(strb,&endptr,10);
! 4941: /* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
! 4942: if( strb[0]=='\0' || (*endptr != '\0')){
! 4943: 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);
! 4944: 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);
! 4945: return 1;
! 4946: }
! 4947: }
! 4948: s[j][i]=lval;
! 4949:
! 4950: strcpy(line,stra);
! 4951: cutv(stra, strb,line,' ');
! 4952: if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
! 4953: }
! 4954: else if(iout=sscanf(strb,"%s.",dummy) != 0){
! 4955: month=99;
! 4956: year=9999;
! 4957: }else{
! 4958: 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);
! 4959: 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);
! 4960: return 1;
! 4961: }
! 4962: anint[j][i]= (double) year;
! 4963: mint[j][i]= (double)month;
! 4964: strcpy(line,stra);
! 4965: } /* ENd Waves */
! 4966:
! 4967: cutv(stra, strb,line,' ');
! 4968: if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
! 4969: }
! 4970: else if(iout=sscanf(strb,"%s.",dummy) != 0){
! 4971: month=99;
! 4972: year=9999;
! 4973: }else{
! 4974: 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);
! 4975: 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);
! 4976: return 1;
! 4977: }
! 4978: andc[i]=(double) year;
! 4979: moisdc[i]=(double) month;
! 4980: strcpy(line,stra);
! 4981:
! 4982: cutv(stra, strb,line,' ');
! 4983: if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
! 4984: }
! 4985: else if(iout=sscanf(strb,"%s.", dummy) != 0){
! 4986: month=99;
! 4987: year=9999;
! 4988: }else{
! 4989: 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);
! 4990: 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);
! 4991: return 1;
! 4992: }
! 4993: if (year==9999) {
! 4994: 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);
! 4995: 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);
! 4996: return 1;
! 4997:
! 4998: }
! 4999: annais[i]=(double)(year);
! 5000: moisnais[i]=(double)(month);
! 5001: strcpy(line,stra);
! 5002:
! 5003: cutv(stra, strb,line,' ');
! 5004: errno=0;
! 5005: dval=strtod(strb,&endptr);
! 5006: if( strb[0]=='\0' || (*endptr != '\0')){
! 5007: printf("Error reading data around '%f' at line number %d, \"%s\" for individual %d\nShould be a weight. Exiting.\n",dval, i,line,linei);
! 5008: 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);
! 5009: fflush(ficlog);
! 5010: return 1;
! 5011: }
! 5012: weight[i]=dval;
! 5013: strcpy(line,stra);
! 5014:
! 5015: for (j=ncovcol;j>=1;j--){
! 5016: cutv(stra, strb,line,' ');
! 5017: if(strb[0]=='.') { /* Missing status */
! 5018: lval=-1;
! 5019: }else{
! 5020: errno=0;
! 5021: lval=strtol(strb,&endptr,10);
! 5022: if( strb[0]=='\0' || (*endptr != '\0')){
! 5023: 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);
! 5024: 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);
! 5025: return 1;
! 5026: }
! 5027: }
! 5028: if(lval <-1 || lval >1){
! 5029: printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
! 5030: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
! 5031: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
! 5032: For example, for multinomial values like 1, 2 and 3,\n \
! 5033: build V1=0 V2=0 for the reference value (1),\n \
! 5034: V1=1 V2=0 for (2) \n \
! 5035: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
! 5036: output of IMaCh is often meaningless.\n \
! 5037: Exiting.\n",lval,linei, i,line,j);
! 5038: fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
! 5039: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
! 5040: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
! 5041: For example, for multinomial values like 1, 2 and 3,\n \
! 5042: build V1=0 V2=0 for the reference value (1),\n \
! 5043: V1=1 V2=0 for (2) \n \
! 5044: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
! 5045: output of IMaCh is often meaningless.\n \
! 5046: Exiting.\n",lval,linei, i,line,j);fflush(ficlog);
! 5047: return 1;
! 5048: }
! 5049: covar[j][i]=(double)(lval);
! 5050: strcpy(line,stra);
! 5051: }
! 5052: lstra=strlen(stra);
! 5053:
! 5054: if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
! 5055: stratrunc = &(stra[lstra-9]);
! 5056: num[i]=atol(stratrunc);
! 5057: }
! 5058: else
! 5059: num[i]=atol(stra);
! 5060: /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
! 5061: 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;}*/
! 5062:
! 5063: i=i+1;
! 5064: } /* End loop reading data */
! 5065:
! 5066: *imax=i-1; /* Number of individuals */
! 5067: fclose(fic);
! 5068:
! 5069: return (0);
! 5070: endread:
! 5071: printf("Exiting readdata: ");
! 5072: fclose(fic);
! 5073: return (1);
! 5074:
! 5075:
! 5076:
! 5077: }
! 5078: void removespace(char *str) {
! 5079: char *p1 = str, *p2 = str;
! 5080: do
! 5081: while (*p2 == ' ')
! 5082: p2++;
! 5083: while (*p1++ = *p2++);
! 5084: }
! 5085:
! 5086: int decodemodel ( char model[], int lastobs) /**< This routine decode the model and returns:
! 5087: * Model V1+V2+V3+V8+V7*V8+V5*V6+V8*age+V3*age
! 5088: * - cptcovt total number of covariates of the model nbocc(+)+1 = 8
! 5089: * - cptcovn or number of covariates k of the models excluding age*products =6
! 5090: * - cptcovage number of covariates with age*products =2
! 5091: * - cptcovs number of simple covariates
! 5092: * - 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
! 5093: * which is a new column after the 9 (ncovcol) variables.
! 5094: * - if k is a product Vn*Vm covar[k][i] is filled with correct values for each individual
! 5095: * - Tprod[l] gives the kth covariates of the product Vn*Vm l=1 to cptcovprod-cptcovage
! 5096: * Tprod[1]@2 {5, 6}: position of first product V7*V8 is 5, and second V5*V6 is 6.
! 5097: * - Tvard[k] p Tvard[1][1]@4 {7, 8, 5, 6} for V7*V8 and V5*V6 .
! 5098: */
! 5099: {
! 5100: int i, j, k, ks;
! 5101: int i1, j1, k1, k2;
! 5102: char modelsav[80];
! 5103: char stra[80], strb[80], strc[80], strd[80],stre[80];
! 5104:
! 5105: /*removespace(model);*/
! 5106: if (strlen(model) >1){ /* If there is at least 1 covariate */
! 5107: j=0, j1=0, k1=0, k2=-1, ks=0, cptcovn=0;
! 5108: j=nbocc(model,'+'); /**< j=Number of '+' */
! 5109: j1=nbocc(model,'*'); /**< j1=Number of '*' */
! 5110: cptcovs=j+1-j1; /**< Number of simple covariates V1+V2*age+V3 +V3*V4=> V1 + V3 =2 */
! 5111: cptcovt= j+1; /* Number of total covariates in the model V1 + V2*age+ V3 + V3*V4=> 4*/
! 5112: /* including age products which are counted in cptcovage.
! 5113: /* but the covariates which are products must be treated separately: ncovn=4- 2=2 (V1+V3). */
! 5114: cptcovprod=j1; /**< Number of products V1*V2 +v3*age = 2 */
! 5115: cptcovprodnoage=0; /**< Number of covariate products without age: V3*V4 =1 */
! 5116: strcpy(modelsav,model);
! 5117: if (strstr(model,"AGE") !=0){
! 5118: printf("Error. AGE must be in lower case 'age' model=%s ",model);
! 5119: fprintf(ficlog,"Error. AGE must be in lower case model=%s ",model);fflush(ficlog);
! 5120: return 1;
! 5121: }
! 5122: if (strstr(model,"v") !=0){
! 5123: printf("Error. 'v' must be in upper case 'V' model=%s ",model);
! 5124: fprintf(ficlog,"Error. 'v' must be in upper case model=%s ",model);fflush(ficlog);
! 5125: return 1;
! 5126: }
! 5127:
! 5128: /* Design
! 5129: * V1 V2 V3 V4 V5 V6 V7 V8 V9 Weight
! 5130: * < ncovcol=8 >
! 5131: * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8
! 5132: * k= 1 2 3 4 5 6 7 8
! 5133: * cptcovn number of covariates (not including constant and age ) = # of + plus 1 = 7+1=8
! 5134: * covar[k,i], value of kth covariate if not including age for individual i:
! 5135: * covar[1][i]= (V2), covar[4][i]=(V3), covar[8][i]=(V8)
! 5136: * Tvar[k] # of the kth covariate: Tvar[1]=2 Tvar[4]=3 Tvar[8]=8
! 5137: * if multiplied by age: V3*age Tvar[3=V3*age]=3 (V3) Tvar[7]=8 and
! 5138: * Tage[++cptcovage]=k
! 5139: * if products, new covar are created after ncovcol with k1
! 5140: * Tvar[k]=ncovcol+k1; # of the kth covariate product: Tvar[5]=ncovcol+1=10 Tvar[6]=ncovcol+1=11
! 5141: * Tprod[k1]=k; Tprod[1]=5 Tprod[2]= 6; gives the position of the k1th product
! 5142: * 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
! 5143: * Tvar[cptcovn+k2]=Tvard[k1][1];Tvar[cptcovn+k2+1]=Tvard[k1][2];
! 5144: * Tvar[8+1]=5;Tvar[8+2]=6;Tvar[8+3]=7;Tvar[8+4]=8 inverted
! 5145: * V1 V2 V3 V4 V5 V6 V7 V8 V9 V10 V11
! 5146: * < ncovcol=8 >
! 5147: * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8 d1 d1 d2 d2
! 5148: * k= 1 2 3 4 5 6 7 8 9 10 11 12
! 5149: * Tvar[k]= 2 1 3 3 10 11 8 8 5 6 7 8
! 5150: * p Tvar[1]@12={2, 1, 3, 3, 11, 10, 8, 8, 7, 8, 5, 6}
! 5151: * p Tprod[1]@2={ 6, 5}
! 5152: *p Tvard[1][1]@4= {7, 8, 5, 6}
! 5153: * covar[k][i]= V2 V1 ? V3 V5*V6? V7*V8? ? V8
! 5154: * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
! 5155: *How to reorganize?
! 5156: * Model V1 + V2 + V3 + V8 + V5*V6 + V7*V8 + V3*age + V8*age
! 5157: * Tvars {2, 1, 3, 3, 11, 10, 8, 8, 7, 8, 5, 6}
! 5158: * {2, 1, 4, 8, 5, 6, 3, 7}
! 5159: * Struct []
! 5160: */
! 5161:
! 5162: /* This loop fills the array Tvar from the string 'model'.*/
! 5163: /* j is the number of + signs in the model V1+V2+V3 j=2 i=3 to 1 */
! 5164: /* modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4 */
! 5165: /* k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tage[cptcovage=1]=4 */
! 5166: /* k=3 V4 Tvar[k=3]= 4 (from V4) */
! 5167: /* k=2 V1 Tvar[k=2]= 1 (from V1) */
! 5168: /* k=1 Tvar[1]=2 (from V2) */
! 5169: /* k=5 Tvar[5] */
! 5170: /* for (k=1; k<=cptcovn;k++) { */
! 5171: /* cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]]; */
! 5172: /* } */
! 5173: /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
! 5174: /*
! 5175: * Treating invertedly V2+V1+V3*age+V2*V4 is as if written V2*V4 +V3*age + V1 + V2 */
! 5176: for(k=cptcovt; k>=1;k--) /**< Number of covariates */
! 5177: Tvar[k]=0;
! 5178: cptcovage=0;
! 5179: for(k=1; k<=cptcovt;k++){ /* Loop on total covariates of the model */
! 5180: cutl(stra,strb,modelsav,'+'); /* keeps in strb after the first '+'
! 5181: modelsav==V2+V1+V4+V3*age strb=V3*age stra=V2+V1+V4 */
! 5182: if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
! 5183: /* printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
! 5184: /*scanf("%d",i);*/
! 5185: if (strchr(strb,'*')) { /**< Model includes a product V2+V1+V4+V3*age strb=V3*age */
! 5186: cutl(strc,strd,strb,'*'); /**< strd*strc Vm*Vn: strb=V3*age(input) strc=age strd=V3 ; V3*V2 strc=V2, strd=V3 */
! 5187: if (strcmp(strc,"age")==0) { /**< Model includes age: Vn*age */
! 5188: /* covar is not filled and then is empty */
! 5189: cptcovprod--;
! 5190: cutl(stre,strb,strd,'V'); /* strd=V3(input): stre="3" */
! 5191: Tvar[k]=atoi(stre); /* V2+V1+V4+V3*age Tvar[4]=3 ; V1+V2*age Tvar[2]=2 */
! 5192: cptcovage++; /* Sums the number of covariates which include age as a product */
! 5193: Tage[cptcovage]=k; /* Tage[1] = 4 */
! 5194: /*printf("stre=%s ", stre);*/
! 5195: } else if (strcmp(strd,"age")==0) { /* or age*Vn */
! 5196: cptcovprod--;
! 5197: cutl(stre,strb,strc,'V');
! 5198: Tvar[k]=atoi(stre);
! 5199: cptcovage++;
! 5200: Tage[cptcovage]=k;
! 5201: } else { /* Age is not in the model product V2+V1+V1*V4+V3*age+V3*V2 strb=V3*V2*/
! 5202: /* loops on k1=1 (V3*V2) and k1=2 V4*V3 */
! 5203: cptcovn++;
! 5204: cptcovprodnoage++;k1++;
! 5205: cutl(stre,strb,strc,'V'); /* strc= Vn, stre is n; strb=V3*V2 stre=3 strc=*/
! 5206: Tvar[k]=ncovcol+k1; /* For model-covariate k tells which data-covariate to use but
! 5207: because this model-covariate is a construction we invent a new column
! 5208: ncovcol + k1
! 5209: If already ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2
! 5210: Tvar[3=V1*V4]=4+1 Tvar[5=V3*V2]=4 + 2= 6, etc */
! 5211: cutl(strc,strb,strd,'V'); /* strd was Vm, strc is m */
! 5212: Tprod[k1]=k; /* Tprod[1]=3(=V1*V4) for V2+V1+V1*V4+age*V3+V3*V2 */
! 5213: Tvard[k1][1] =atoi(strc); /* m 1 for V1*/
! 5214: Tvard[k1][2] =atoi(stre); /* n 4 for V4*/
! 5215: k2=k2+2;
! 5216: Tvar[cptcovt+k2]=Tvard[k1][1]; /* Tvar[(cptcovt=4+k2=1)=5]= 1 (V1) */
! 5217: Tvar[cptcovt+k2+1]=Tvard[k1][2]; /* Tvar[(cptcovt=4+(k2=1)+1)=6]= 4 (V4) */
! 5218: for (i=1; i<=lastobs;i++){
! 5219: /* Computes the new covariate which is a product of
! 5220: covar[n][i]* covar[m][i] and stores it at ncovol+k1 May not be defined */
! 5221: covar[ncovcol+k1][i]=covar[atoi(stre)][i]*covar[atoi(strc)][i];
! 5222: }
! 5223: } /* End age is not in the model */
! 5224: } /* End if model includes a product */
! 5225: else { /* no more sum */
! 5226: /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
! 5227: /* scanf("%d",i);*/
! 5228: cutl(strd,strc,strb,'V');
! 5229: ks++; /**< Number of simple covariates */
! 5230: cptcovn++;
! 5231: Tvar[k]=atoi(strd);
! 5232: }
! 5233: strcpy(modelsav,stra); /* modelsav=V2+V1+V4 stra=V2+V1+V4 */
! 5234: /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
! 5235: scanf("%d",i);*/
! 5236: } /* end of loop + */
! 5237: } /* end model */
! 5238:
! 5239: /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
! 5240: If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
! 5241:
! 5242: /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
! 5243: printf("cptcovprod=%d ", cptcovprod);
! 5244: fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
! 5245:
! 5246: scanf("%d ",i);*/
! 5247:
! 5248:
! 5249: return (0); /* with covar[new additional covariate if product] and Tage if age */
! 5250: endread:
! 5251: printf("Exiting decodemodel: ");
! 5252: return (1);
! 5253: }
! 5254:
! 5255: calandcheckages(int imx, int maxwav, double *agemin, double *agemax, int *nberr, int *nbwarn )
! 5256: {
! 5257: int i, m;
! 5258:
! 5259: for (i=1; i<=imx; i++) {
! 5260: for(m=2; (m<= maxwav); m++) {
! 5261: if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
! 5262: anint[m][i]=9999;
! 5263: s[m][i]=-1;
! 5264: }
! 5265: if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
! 5266: *nberr++;
! 5267: 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\n",(int)moisdc[i],(int)andc[i],num[i],i);
! 5268: 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\n",(int)moisdc[i],(int)andc[i],num[i],i);
! 5269: s[m][i]=-1;
! 5270: }
! 5271: if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
! 5272: *nberr++;
! 5273: 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]);
! 5274: 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]);
! 5275: s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
! 5276: }
! 5277: }
! 5278: }
! 5279:
! 5280: for (i=1; i<=imx; i++) {
! 5281: agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
! 5282: for(m=firstpass; (m<= lastpass); m++){
! 5283: if(s[m][i] >0 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){
! 5284: if (s[m][i] >= nlstate+1) {
! 5285: if(agedc[i]>0)
! 5286: if((int)moisdc[i]!=99 && (int)andc[i]!=9999)
! 5287: agev[m][i]=agedc[i];
! 5288: /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
! 5289: else {
! 5290: if ((int)andc[i]!=9999){
! 5291: nbwarn++;
! 5292: printf("Warning negative age at death: %ld line:%d\n",num[i],i);
! 5293: fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
! 5294: agev[m][i]=-1;
! 5295: }
! 5296: }
! 5297: }
! 5298: else if(s[m][i] !=9){ /* Standard case, age in fractional
! 5299: years but with the precision of a month */
! 5300: agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
! 5301: if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
! 5302: agev[m][i]=1;
! 5303: else if(agev[m][i] < *agemin){
! 5304: *agemin=agev[m][i];
! 5305: printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], *agemin);
! 5306: }
! 5307: else if(agev[m][i] >*agemax){
! 5308: *agemax=agev[m][i];
! 5309: /* printf(" Max anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.2f\n",m,i,anint[m][i], i,annais[i], *agemax);*/
! 5310: }
! 5311: /*agev[m][i]=anint[m][i]-annais[i];*/
! 5312: /* agev[m][i] = age[i]+2*m;*/
! 5313: }
! 5314: else { /* =9 */
! 5315: agev[m][i]=1;
! 5316: s[m][i]=-1;
! 5317: }
! 5318: }
! 5319: else /*= 0 Unknown */
! 5320: agev[m][i]=1;
! 5321: }
! 5322:
! 5323: }
! 5324: for (i=1; i<=imx; i++) {
! 5325: for(m=firstpass; (m<=lastpass); m++){
! 5326: if (s[m][i] > (nlstate+ndeath)) {
! 5327: *nberr++;
! 5328: 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);
! 5329: 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);
! 5330: return 1;
! 5331: }
! 5332: }
! 5333: }
! 5334:
! 5335: /*for (i=1; i<=imx; i++){
! 5336: for (m=firstpass; (m<lastpass); m++){
! 5337: printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
! 5338: }
! 5339:
! 5340: }*/
! 5341:
! 5342:
! 5343: printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
! 5344: fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
! 5345:
! 5346: return (0);
! 5347: endread:
! 5348: printf("Exiting calandcheckages: ");
! 5349: return (1);
! 5350: }
! 5351:
! 5352:
! 5353: /***********************************************/
! 5354: /**************** Main Program *****************/
! 5355: /***********************************************/
! 5356:
! 5357: int main(int argc, char *argv[])
! 5358: {
! 5359: #ifdef GSL
! 5360: const gsl_multimin_fminimizer_type *T;
! 5361: size_t iteri = 0, it;
! 5362: int rval = GSL_CONTINUE;
! 5363: int status = GSL_SUCCESS;
! 5364: double ssval;
! 5365: #endif
! 5366: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
! 5367: int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod;
! 5368: int linei, month, year,iout;
! 5369: int jj, ll, li, lj, lk, imk;
! 5370: int numlinepar=0; /* Current linenumber of parameter file */
! 5371: int itimes;
! 5372: int NDIM=2;
! 5373: int vpopbased=0;
! 5374:
! 5375: char ca[32], cb[32], cc[32];
! 5376: /* FILE *fichtm; *//* Html File */
! 5377: /* FILE *ficgp;*/ /*Gnuplot File */
! 5378: struct stat info;
! 5379: double agedeb, agefin,hf;
! 5380: double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
! 5381:
! 5382: double fret;
! 5383: double **xi,tmp,delta;
! 5384:
! 5385: double dum; /* Dummy variable */
! 5386: double ***p3mat;
! 5387: double ***mobaverage;
! 5388: int *indx;
! 5389: char line[MAXLINE], linepar[MAXLINE];
! 5390: char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
! 5391: char pathr[MAXLINE], pathimach[MAXLINE];
! 5392: char **bp, *tok, *val; /* pathtot */
! 5393: int firstobs=1, lastobs=10;
! 5394: int sdeb, sfin; /* Status at beginning and end */
! 5395: int c, h , cpt,l;
! 5396: int ju,jl, mi;
! 5397: int i1,j1, jk,aa,bb, stepsize, ij;
! 5398: int jnais,jdc,jint4,jint1,jint2,jint3,*tab;
! 5399: int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
! 5400: int mobilav=0,popforecast=0;
! 5401: int hstepm, nhstepm;
! 5402: int agemortsup;
! 5403: float sumlpop=0.;
! 5404: double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
! 5405: double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
! 5406:
! 5407: double bage, fage, age, agelim, agebase;
! 5408: double ftolpl=FTOL;
! 5409: double **prlim;
! 5410: double ***param; /* Matrix of parameters */
! 5411: double *p;
! 5412: double **matcov; /* Matrix of covariance */
! 5413: double ***delti3; /* Scale */
! 5414: double *delti; /* Scale */
! 5415: double ***eij, ***vareij;
! 5416: double **varpl; /* Variances of prevalence limits by age */
! 5417: double *epj, vepp;
! 5418: double kk1, kk2;
! 5419: double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
! 5420: double **ximort;
! 5421: char *alph[]={"a","a","b","c","d","e"}, str[4]="1234";
! 5422: int *dcwave;
! 5423:
! 5424: char z[1]="c", occ;
! 5425:
! 5426: /*char *strt;*/
! 5427: char strtend[80];
! 5428:
! 5429: long total_usecs;
! 5430:
! 5431: /* setlocale (LC_ALL, ""); */
! 5432: /* bindtextdomain (PACKAGE, LOCALEDIR); */
! 5433: /* textdomain (PACKAGE); */
! 5434: /* setlocale (LC_CTYPE, ""); */
! 5435: /* setlocale (LC_MESSAGES, ""); */
! 5436:
! 5437: /* gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
! 5438: rstart_time = time(NULL);
! 5439: /* (void) gettimeofday(&start_time,&tzp);*/
! 5440: start_time = *localtime(&rstart_time);
! 5441: curr_time=start_time;
! 5442: /*tml = *localtime(&start_time.tm_sec);*/
! 5443: /* strcpy(strstart,asctime(&tml)); */
! 5444: strcpy(strstart,asctime(&start_time));
! 5445:
! 5446: /* printf("Localtime (at start)=%s",strstart); */
! 5447: /* tp.tm_sec = tp.tm_sec +86400; */
! 5448: /* tm = *localtime(&start_time.tm_sec); */
! 5449: /* tmg.tm_year=tmg.tm_year +dsign*dyear; */
! 5450: /* tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
! 5451: /* tmg.tm_hour=tmg.tm_hour + 1; */
! 5452: /* tp.tm_sec = mktime(&tmg); */
! 5453: /* strt=asctime(&tmg); */
! 5454: /* printf("Time(after) =%s",strstart); */
! 5455: /* (void) time (&time_value);
! 5456: * printf("time=%d,t-=%d\n",time_value,time_value-86400);
! 5457: * tm = *localtime(&time_value);
! 5458: * strstart=asctime(&tm);
! 5459: * printf("tim_value=%d,asctime=%s\n",time_value,strstart);
! 5460: */
! 5461:
! 5462: nberr=0; /* Number of errors and warnings */
! 5463: nbwarn=0;
! 5464: getcwd(pathcd, size);
! 5465:
! 5466: printf("\n%s\n%s",version,fullversion);
! 5467: if(argc <=1){
! 5468: printf("\nEnter the parameter file name: ");
! 5469: fgets(pathr,FILENAMELENGTH,stdin);
! 5470: i=strlen(pathr);
! 5471: if(pathr[i-1]=='\n')
! 5472: pathr[i-1]='\0';
! 5473: i=strlen(pathr);
! 5474: if(pathr[i-1]==' ') /* This may happen when dragging on oS/X! */
! 5475: pathr[i-1]='\0';
! 5476: for (tok = pathr; tok != NULL; ){
! 5477: printf("Pathr |%s|\n",pathr);
! 5478: while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
! 5479: printf("val= |%s| pathr=%s\n",val,pathr);
! 5480: strcpy (pathtot, val);
! 5481: if(pathr[0] == '\0') break; /* Dirty */
! 5482: }
! 5483: }
! 5484: else{
! 5485: strcpy(pathtot,argv[1]);
! 5486: }
! 5487: /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
! 5488: /*cygwin_split_path(pathtot,path,optionfile);
! 5489: printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
! 5490: /* cutv(path,optionfile,pathtot,'\\');*/
! 5491:
! 5492: /* Split argv[0], imach program to get pathimach */
! 5493: printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
! 5494: split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
! 5495: printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
! 5496: /* strcpy(pathimach,argv[0]); */
! 5497: /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
! 5498: split(pathtot,path,optionfile,optionfilext,optionfilefiname);
! 5499: printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
! 5500: chdir(path); /* Can be a relative path */
! 5501: if(getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */
! 5502: printf("Current directory %s!\n",pathcd);
! 5503: strcpy(command,"mkdir ");
! 5504: strcat(command,optionfilefiname);
! 5505: if((outcmd=system(command)) != 0){
! 5506: printf("Problem creating directory or it already exists %s%s, err=%d\n",path,optionfilefiname,outcmd);
! 5507: /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
! 5508: /* fclose(ficlog); */
! 5509: /* exit(1); */
! 5510: }
! 5511: /* if((imk=mkdir(optionfilefiname))<0){ */
! 5512: /* perror("mkdir"); */
! 5513: /* } */
! 5514:
! 5515: /*-------- arguments in the command line --------*/
! 5516:
! 5517: /* Log file */
! 5518: strcat(filelog, optionfilefiname);
! 5519: strcat(filelog,".log"); /* */
! 5520: if((ficlog=fopen(filelog,"w"))==NULL) {
! 5521: printf("Problem with logfile %s\n",filelog);
! 5522: goto end;
! 5523: }
! 5524: fprintf(ficlog,"Log filename:%s\n",filelog);
! 5525: fprintf(ficlog,"\n%s\n%s",version,fullversion);
! 5526: fprintf(ficlog,"\nEnter the parameter file name: \n");
! 5527: fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
! 5528: path=%s \n\
! 5529: optionfile=%s\n\
! 5530: optionfilext=%s\n\
! 5531: optionfilefiname='%s'\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
! 5532:
! 5533: printf("Local time (at start):%s",strstart);
! 5534: fprintf(ficlog,"Local time (at start): %s",strstart);
! 5535: fflush(ficlog);
! 5536: /* (void) gettimeofday(&curr_time,&tzp); */
! 5537: /* printf("Elapsed time %d\n", asc_diff_time(curr_time.tm_sec-start_time.tm_sec,tmpout)); */
! 5538:
! 5539: /* */
! 5540: strcpy(fileres,"r");
! 5541: strcat(fileres, optionfilefiname);
! 5542: strcat(fileres,".txt"); /* Other files have txt extension */
! 5543:
! 5544: /*---------arguments file --------*/
! 5545:
! 5546: if((ficpar=fopen(optionfile,"r"))==NULL) {
! 5547: printf("Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
! 5548: fprintf(ficlog,"Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
! 5549: fflush(ficlog);
! 5550: /* goto end; */
! 5551: exit(70);
! 5552: }
! 5553:
! 5554:
! 5555:
! 5556: strcpy(filereso,"o");
! 5557: strcat(filereso,fileres);
! 5558: if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
! 5559: printf("Problem with Output resultfile: %s\n", filereso);
! 5560: fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
! 5561: fflush(ficlog);
! 5562: goto end;
! 5563: }
! 5564:
! 5565: /* Reads comments: lines beginning with '#' */
! 5566: numlinepar=0;
! 5567: while((c=getc(ficpar))=='#' && c!= EOF){
! 5568: ungetc(c,ficpar);
! 5569: fgets(line, MAXLINE, ficpar);
! 5570: numlinepar++;
! 5571: fputs(line,stdout);
! 5572: fputs(line,ficparo);
! 5573: fputs(line,ficlog);
! 5574: }
! 5575: ungetc(c,ficpar);
! 5576:
! 5577: 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);
! 5578: numlinepar++;
! 5579: 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);
! 5580: 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);
! 5581: 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);
! 5582: fflush(ficlog);
! 5583: while((c=getc(ficpar))=='#' && c!= EOF){
! 5584: ungetc(c,ficpar);
! 5585: fgets(line, MAXLINE, ficpar);
! 5586: numlinepar++;
! 5587: fputs(line, stdout);
! 5588: //puts(line);
! 5589: fputs(line,ficparo);
! 5590: fputs(line,ficlog);
! 5591: }
! 5592: ungetc(c,ficpar);
! 5593:
! 5594:
! 5595: covar=matrix(0,NCOVMAX,1,n); /**< used in readdata */
! 5596: cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement plus one, indepently of n in Vn*/
! 5597: /* v1+v2+v3+v2*v4+v5*age makes cptcovn = 5
! 5598: v1+v2*age+v2*v3 makes cptcovn = 3
! 5599: */
! 5600: if (strlen(model)>1)
! 5601: 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*/
! 5602: else
! 5603: ncovmodel=2;
! 5604: nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
! 5605: nforce= (nlstate+ndeath-1)*nlstate; /* Number of forces ij from state i to j */
! 5606: npar= nforce*ncovmodel; /* Number of parameters like aij*/
! 5607: if(npar >MAXPARM || nlstate >NLSTATEMAX || ndeath >NDEATHMAX || ncovmodel>NCOVMAX){
! 5608: 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);
! 5609: 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);
! 5610: fflush(stdout);
! 5611: fclose (ficlog);
! 5612: goto end;
! 5613: }
! 5614: delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
! 5615: delti=delti3[1][1];
! 5616: /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
! 5617: if(mle==-1){ /* Print a wizard for help writing covariance matrix */
! 5618: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
! 5619: printf(" You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
! 5620: fprintf(ficlog," You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
! 5621: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
! 5622: fclose (ficparo);
! 5623: fclose (ficlog);
! 5624: goto end;
! 5625: exit(0);
! 5626: }
! 5627: else if(mle==-3) {
! 5628: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
! 5629: printf(" You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
! 5630: fprintf(ficlog," You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
! 5631: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
! 5632: matcov=matrix(1,npar,1,npar);
! 5633: }
! 5634: else{
! 5635: /* Read guessed parameters */
! 5636: /* Reads comments: lines beginning with '#' */
! 5637: while((c=getc(ficpar))=='#' && c!= EOF){
! 5638: ungetc(c,ficpar);
! 5639: fgets(line, MAXLINE, ficpar);
! 5640: numlinepar++;
! 5641: fputs(line,stdout);
! 5642: fputs(line,ficparo);
! 5643: fputs(line,ficlog);
! 5644: }
! 5645: ungetc(c,ficpar);
! 5646:
! 5647: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
! 5648: for(i=1; i <=nlstate; i++){
! 5649: j=0;
! 5650: for(jj=1; jj <=nlstate+ndeath; jj++){
! 5651: if(jj==i) continue;
! 5652: j++;
! 5653: fscanf(ficpar,"%1d%1d",&i1,&j1);
! 5654: if ((i1 != i) && (j1 != j)){
! 5655: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \
! 5656: It might be a problem of design; if ncovcol and the model are correct\n \
! 5657: run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1);
! 5658: exit(1);
! 5659: }
! 5660: fprintf(ficparo,"%1d%1d",i1,j1);
! 5661: if(mle==1)
! 5662: printf("%1d%1d",i,j);
! 5663: fprintf(ficlog,"%1d%1d",i,j);
! 5664: for(k=1; k<=ncovmodel;k++){
! 5665: fscanf(ficpar," %lf",¶m[i][j][k]);
! 5666: if(mle==1){
! 5667: printf(" %lf",param[i][j][k]);
! 5668: fprintf(ficlog," %lf",param[i][j][k]);
! 5669: }
! 5670: else
! 5671: fprintf(ficlog," %lf",param[i][j][k]);
! 5672: fprintf(ficparo," %lf",param[i][j][k]);
! 5673: }
! 5674: fscanf(ficpar,"\n");
! 5675: numlinepar++;
! 5676: if(mle==1)
! 5677: printf("\n");
! 5678: fprintf(ficlog,"\n");
! 5679: fprintf(ficparo,"\n");
! 5680: }
! 5681: }
! 5682: fflush(ficlog);
! 5683:
! 5684: /* Reads scales values */
! 5685: p=param[1][1];
! 5686:
! 5687: /* Reads comments: lines beginning with '#' */
! 5688: while((c=getc(ficpar))=='#' && c!= EOF){
! 5689: ungetc(c,ficpar);
! 5690: fgets(line, MAXLINE, ficpar);
! 5691: numlinepar++;
! 5692: fputs(line,stdout);
! 5693: fputs(line,ficparo);
! 5694: fputs(line,ficlog);
! 5695: }
! 5696: ungetc(c,ficpar);
! 5697:
! 5698: for(i=1; i <=nlstate; i++){
! 5699: for(j=1; j <=nlstate+ndeath-1; j++){
! 5700: fscanf(ficpar,"%1d%1d",&i1,&j1);
! 5701: if ((i1-i)*(j1-j)!=0){
! 5702: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
! 5703: exit(1);
! 5704: }
! 5705: printf("%1d%1d",i,j);
! 5706: fprintf(ficparo,"%1d%1d",i1,j1);
! 5707: fprintf(ficlog,"%1d%1d",i1,j1);
! 5708: for(k=1; k<=ncovmodel;k++){
! 5709: fscanf(ficpar,"%le",&delti3[i][j][k]);
! 5710: printf(" %le",delti3[i][j][k]);
! 5711: fprintf(ficparo," %le",delti3[i][j][k]);
! 5712: fprintf(ficlog," %le",delti3[i][j][k]);
! 5713: }
! 5714: fscanf(ficpar,"\n");
! 5715: numlinepar++;
! 5716: printf("\n");
! 5717: fprintf(ficparo,"\n");
! 5718: fprintf(ficlog,"\n");
! 5719: }
! 5720: }
! 5721: fflush(ficlog);
! 5722:
! 5723: /* Reads covariance matrix */
! 5724: delti=delti3[1][1];
! 5725:
! 5726:
! 5727: /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
! 5728:
! 5729: /* Reads comments: lines beginning with '#' */
! 5730: while((c=getc(ficpar))=='#' && c!= EOF){
! 5731: ungetc(c,ficpar);
! 5732: fgets(line, MAXLINE, ficpar);
! 5733: numlinepar++;
! 5734: fputs(line,stdout);
! 5735: fputs(line,ficparo);
! 5736: fputs(line,ficlog);
! 5737: }
! 5738: ungetc(c,ficpar);
! 5739:
! 5740: matcov=matrix(1,npar,1,npar);
! 5741: for(i=1; i <=npar; i++)
! 5742: for(j=1; j <=npar; j++) matcov[i][j]=0.;
! 5743:
! 5744: for(i=1; i <=npar; i++){
! 5745: fscanf(ficpar,"%s",str);
! 5746: if(mle==1)
! 5747: printf("%s",str);
! 5748: fprintf(ficlog,"%s",str);
! 5749: fprintf(ficparo,"%s",str);
! 5750: for(j=1; j <=i; j++){
! 5751: fscanf(ficpar," %le",&matcov[i][j]);
! 5752: if(mle==1){
! 5753: printf(" %.5le",matcov[i][j]);
! 5754: }
! 5755: fprintf(ficlog," %.5le",matcov[i][j]);
! 5756: fprintf(ficparo," %.5le",matcov[i][j]);
! 5757: }
! 5758: fscanf(ficpar,"\n");
! 5759: numlinepar++;
! 5760: if(mle==1)
! 5761: printf("\n");
! 5762: fprintf(ficlog,"\n");
! 5763: fprintf(ficparo,"\n");
! 5764: }
! 5765: for(i=1; i <=npar; i++)
! 5766: for(j=i+1;j<=npar;j++)
! 5767: matcov[i][j]=matcov[j][i];
! 5768:
! 5769: if(mle==1)
! 5770: printf("\n");
! 5771: fprintf(ficlog,"\n");
! 5772:
! 5773: fflush(ficlog);
! 5774:
! 5775: /*-------- Rewriting parameter file ----------*/
! 5776: strcpy(rfileres,"r"); /* "Rparameterfile */
! 5777: strcat(rfileres,optionfilefiname); /* Parameter file first name*/
! 5778: strcat(rfileres,"."); /* */
! 5779: strcat(rfileres,optionfilext); /* Other files have txt extension */
! 5780: if((ficres =fopen(rfileres,"w"))==NULL) {
! 5781: printf("Problem writing new parameter file: %s\n", fileres);goto end;
! 5782: fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
! 5783: }
! 5784: fprintf(ficres,"#%s\n",version);
! 5785: } /* End of mle != -3 */
! 5786:
! 5787:
! 5788: n= lastobs;
! 5789: num=lvector(1,n);
! 5790: moisnais=vector(1,n);
! 5791: annais=vector(1,n);
! 5792: moisdc=vector(1,n);
! 5793: andc=vector(1,n);
! 5794: agedc=vector(1,n);
! 5795: cod=ivector(1,n);
! 5796: weight=vector(1,n);
! 5797: for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
! 5798: mint=matrix(1,maxwav,1,n);
! 5799: anint=matrix(1,maxwav,1,n);
! 5800: s=imatrix(1,maxwav+1,1,n); /* s[i][j] health state for wave i and individual j */
! 5801: tab=ivector(1,NCOVMAX);
! 5802: ncodemax=ivector(1,NCOVMAX); /* Number of code per covariate; if O and 1 only, 2**ncov; V1+V2+V3+V4=>16 */
! 5803:
! 5804: /* Reads data from file datafile */
! 5805: if (readdata(datafile, firstobs, lastobs, &imx)==1)
! 5806: goto end;
! 5807:
! 5808: /* Calculation of the number of parameters from char model */
! 5809: /* modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4
! 5810: k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tag[cptcovage=1]=4
! 5811: k=3 V4 Tvar[k=3]= 4 (from V4)
! 5812: k=2 V1 Tvar[k=2]= 1 (from V1)
! 5813: k=1 Tvar[1]=2 (from V2)
! 5814: */
! 5815: Tvar=ivector(1,NCOVMAX); /* Was 15 changed to NCOVMAX. */
! 5816: /* V2+V1+V4+age*V3 is a model with 4 covariates (3 plus signs).
! 5817: For each model-covariate stores the data-covariate id. Tvar[1]=2, Tvar[2]=1, Tvar[3]=4,
! 5818: Tvar[4=age*V3] is 3 and 'age' is recorded in Tage.
! 5819: */
! 5820: /* For model-covariate k tells which data-covariate to use but
! 5821: because this model-covariate is a construction we invent a new column
! 5822: ncovcol + k1
! 5823: If already ncovcol=4 and model=V2+V1+V1*V4+age*V3
! 5824: Tvar[3=V1*V4]=4+1 etc */
! 5825: Tprod=ivector(1,NCOVMAX); /* Gives the position of a product */
! 5826: /* Tprod[k1=1]=3(=V1*V4) for V2+V1+V1*V4+age*V3
! 5827: if V2+V1+V1*V4+age*V3+V3*V2 TProd[k1=2]=5 (V3*V2)
! 5828: */
! 5829: Tvaraff=ivector(1,NCOVMAX); /* Unclear */
! 5830: 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
! 5831: * For V3*V2 (in V2+V1+V1*V4+age*V3+V3*V2), V3*V2 position is 2nd.
! 5832: * Tvard[k1=2][1]=3 (V3) Tvard[k1=2][2]=2(V2) */
! 5833: Tage=ivector(1,NCOVMAX); /* Gives the covariate id of covariates associated with age: V2 + V1 + age*V4 + V3*age
! 5834: 4 covariates (3 plus signs)
! 5835: Tage[1=V3*age]= 4; Tage[2=age*V4] = 3
! 5836: */
! 5837:
! 5838: if(decodemodel(model, lastobs) == 1)
! 5839: goto end;
! 5840:
! 5841: if((double)(lastobs-imx)/(double)imx > 1.10){
! 5842: nbwarn++;
! 5843: 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);
! 5844: 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);
! 5845: }
! 5846: /* if(mle==1){*/
! 5847: if (weightopt != 1) { /* Maximisation without weights. We can have weights different from 1 but want no weight*/
! 5848: for(i=1;i<=imx;i++) weight[i]=1.0; /* changed to imx */
! 5849: }
! 5850:
! 5851: /*-calculation of age at interview from date of interview and age at death -*/
! 5852: agev=matrix(1,maxwav,1,imx);
! 5853:
! 5854: if(calandcheckages(imx, maxwav, &agemin, &agemax, &nberr, &nbwarn) == 1)
! 5855: goto end;
! 5856:
! 5857:
! 5858: agegomp=(int)agemin;
! 5859: free_vector(moisnais,1,n);
! 5860: free_vector(annais,1,n);
! 5861: /* free_matrix(mint,1,maxwav,1,n);
! 5862: free_matrix(anint,1,maxwav,1,n);*/
! 5863: free_vector(moisdc,1,n);
! 5864: free_vector(andc,1,n);
! 5865: /* */
! 5866:
! 5867: wav=ivector(1,imx);
! 5868: dh=imatrix(1,lastpass-firstpass+1,1,imx);
! 5869: bh=imatrix(1,lastpass-firstpass+1,1,imx);
! 5870: mw=imatrix(1,lastpass-firstpass+1,1,imx);
! 5871:
! 5872: /* Concatenates waves */
! 5873: concatwav(wav, dh, bh, mw, s, agedc, agev, firstpass, lastpass, imx, nlstate, stepm);
! 5874: /* */
! 5875:
! 5876: /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
! 5877:
! 5878: nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
! 5879: ncodemax[1]=1;
! 5880: Ndum =ivector(-1,NCOVMAX);
! 5881: if (ncovmodel > 2)
! 5882: tricode(Tvar,nbcode,imx, Ndum); /**< Fills nbcode[Tvar[j]][l]; */
! 5883:
! 5884: codtab=imatrix(1,100,1,10); /* codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) */
! 5885: /*printf(" codtab[1,1],codtab[100,10]=%d,%d\n", codtab[1][1],codtab[100][10]);*/
! 5886: h=0;
! 5887:
! 5888:
! 5889: /*if (cptcovn > 0) */
! 5890:
! 5891:
! 5892: m=pow(2,cptcoveff);
! 5893:
! 5894: for(k=1;k<=cptcoveff; k++){ /* scans any effective covariate */
! 5895: 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 */
! 5896: for(j=1; j <= ncodemax[k]; j++){ /* For each modality of this covariate ncodemax=2*/
! 5897: for(cpt=1; cpt <=pow(2,k-1); cpt++){ /* cpt=1 to 8/2**(3+1-1 or 3+1-3) =1 or 4 */
! 5898: h++;
! 5899: if (h>m)
! 5900: h=1;
! 5901: /**< codtab(h,k) k = codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) + 1
! 5902: * h 1 2 3 4
! 5903: *______________________________
! 5904: * 1 i=1 1 i=1 1 i=1 1 i=1 1
! 5905: * 2 2 1 1 1
! 5906: * 3 i=2 1 2 1 1
! 5907: * 4 2 2 1 1
! 5908: * 5 i=3 1 i=2 1 2 1
! 5909: * 6 2 1 2 1
! 5910: * 7 i=4 1 2 2 1
! 5911: * 8 2 2 2 1
! 5912: * 9 i=5 1 i=3 1 i=2 1 1
! 5913: * 10 2 1 1 1
! 5914: * 11 i=6 1 2 1 1
! 5915: * 12 2 2 1 1
! 5916: * 13 i=7 1 i=4 1 2 1
! 5917: * 14 2 1 2 1
! 5918: * 15 i=8 1 2 2 1
! 5919: * 16 2 2 2 1
! 5920: */
! 5921: codtab[h][k]=j;
! 5922: /*codtab[h][Tvar[k]]=j;*/
! 5923: 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]]);
! 5924: }
! 5925: }
! 5926: }
! 5927: }
! 5928: /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);
! 5929: codtab[1][2]=1;codtab[2][2]=2; */
! 5930: /* for(i=1; i <=m ;i++){
! 5931: for(k=1; k <=cptcovn; k++){
! 5932: printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
! 5933: }
! 5934: printf("\n");
! 5935: }
! 5936: scanf("%d",i);*/
! 5937:
! 5938: free_ivector(Ndum,-1,NCOVMAX);
! 5939:
! 5940:
! 5941:
! 5942: /*------------ gnuplot -------------*/
! 5943: strcpy(optionfilegnuplot,optionfilefiname);
! 5944: if(mle==-3)
! 5945: strcat(optionfilegnuplot,"-mort");
! 5946: strcat(optionfilegnuplot,".gp");
! 5947:
! 5948: if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
! 5949: printf("Problem with file %s",optionfilegnuplot);
! 5950: }
! 5951: else{
! 5952: fprintf(ficgp,"\n# %s\n", version);
! 5953: fprintf(ficgp,"# %s\n", optionfilegnuplot);
! 5954: //fprintf(ficgp,"set missing 'NaNq'\n");
! 5955: fprintf(ficgp,"set datafile missing 'NaNq'\n");
! 5956: }
! 5957: /* fclose(ficgp);*/
! 5958: /*--------- index.htm --------*/
! 5959:
! 5960: strcpy(optionfilehtm,optionfilefiname); /* Main html file */
! 5961: if(mle==-3)
! 5962: strcat(optionfilehtm,"-mort");
! 5963: strcat(optionfilehtm,".htm");
! 5964: if((fichtm=fopen(optionfilehtm,"w"))==NULL) {
! 5965: printf("Problem with %s \n",optionfilehtm);
! 5966: exit(0);
! 5967: }
! 5968:
! 5969: strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
! 5970: strcat(optionfilehtmcov,"-cov.htm");
! 5971: if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL) {
! 5972: printf("Problem with %s \n",optionfilehtmcov), exit(0);
! 5973: }
! 5974: else{
! 5975: fprintf(fichtmcov,"<html><head>\n<title>IMaCh Cov %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
! 5976: <hr size=\"2\" color=\"#EC5E5E\"> \n\
! 5977: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n",\
! 5978: optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
! 5979: }
! 5980:
! 5981: fprintf(fichtm,"<html><head>\n<title>IMaCh %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
! 5982: <hr size=\"2\" color=\"#EC5E5E\"> \n\
! 5983: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
! 5984: \n\
! 5985: <hr size=\"2\" color=\"#EC5E5E\">\
! 5986: <ul><li><h4>Parameter files</h4>\n\
! 5987: - Parameter file: <a href=\"%s.%s\">%s.%s</a><br>\n\
! 5988: - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
! 5989: - Log file of the run: <a href=\"%s\">%s</a><br>\n\
! 5990: - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
! 5991: - Date and time at start: %s</ul>\n",\
! 5992: optionfilehtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
! 5993: optionfilefiname,optionfilext,optionfilefiname,optionfilext,\
! 5994: fileres,fileres,\
! 5995: filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
! 5996: fflush(fichtm);
! 5997:
! 5998: strcpy(pathr,path);
! 5999: strcat(pathr,optionfilefiname);
! 6000: chdir(optionfilefiname); /* Move to directory named optionfile */
! 6001:
! 6002: /* Calculates basic frequencies. Computes observed prevalence at single age
! 6003: and prints on file fileres'p'. */
! 6004: freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart);
! 6005:
! 6006: fprintf(fichtm,"\n");
! 6007: fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
! 6008: Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
! 6009: Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
! 6010: imx,agemin,agemax,jmin,jmax,jmean);
! 6011: pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
! 6012: oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
! 6013: newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
! 6014: savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
! 6015: oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
! 6016:
! 6017:
! 6018: /* For Powell, parameters are in a vector p[] starting at p[1]
! 6019: so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
! 6020: p=param[1][1]; /* *(*(*(param +1)+1)+0) */
! 6021:
! 6022: globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
! 6023:
! 6024: if (mle==-3){
! 6025: ximort=matrix(1,NDIM,1,NDIM);
! 6026: /* ximort=gsl_matrix_alloc(1,NDIM,1,NDIM); */
! 6027: cens=ivector(1,n);
! 6028: ageexmed=vector(1,n);
! 6029: agecens=vector(1,n);
! 6030: dcwave=ivector(1,n);
! 6031:
! 6032: for (i=1; i<=imx; i++){
! 6033: dcwave[i]=-1;
! 6034: for (m=firstpass; m<=lastpass; m++)
! 6035: if (s[m][i]>nlstate) {
! 6036: dcwave[i]=m;
! 6037: /* printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
! 6038: break;
! 6039: }
! 6040: }
! 6041:
! 6042: for (i=1; i<=imx; i++) {
! 6043: if (wav[i]>0){
! 6044: ageexmed[i]=agev[mw[1][i]][i];
! 6045: j=wav[i];
! 6046: agecens[i]=1.;
! 6047:
! 6048: if (ageexmed[i]> 1 && wav[i] > 0){
! 6049: agecens[i]=agev[mw[j][i]][i];
! 6050: cens[i]= 1;
! 6051: }else if (ageexmed[i]< 1)
! 6052: cens[i]= -1;
! 6053: if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
! 6054: cens[i]=0 ;
! 6055: }
! 6056: else cens[i]=-1;
! 6057: }
! 6058:
! 6059: for (i=1;i<=NDIM;i++) {
! 6060: for (j=1;j<=NDIM;j++)
! 6061: ximort[i][j]=(i == j ? 1.0 : 0.0);
! 6062: }
! 6063:
! 6064: /*p[1]=0.0268; p[NDIM]=0.083;*/
! 6065: /*printf("%lf %lf", p[1], p[2]);*/
! 6066:
! 6067:
! 6068: #ifdef GSL
! 6069: printf("GSL optimization\n"); fprintf(ficlog,"Powell\n");
! 6070: #else
! 6071: printf("Powell\n"); fprintf(ficlog,"Powell\n");
! 6072: #endif
! 6073: strcpy(filerespow,"pow-mort");
! 6074: strcat(filerespow,fileres);
! 6075: if((ficrespow=fopen(filerespow,"w"))==NULL) {
! 6076: printf("Problem with resultfile: %s\n", filerespow);
! 6077: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
! 6078: }
! 6079: #ifdef GSL
! 6080: fprintf(ficrespow,"# GSL optimization\n# iter -2*LL");
! 6081: #else
! 6082: fprintf(ficrespow,"# Powell\n# iter -2*LL");
! 6083: #endif
! 6084: /* for (i=1;i<=nlstate;i++)
! 6085: for(j=1;j<=nlstate+ndeath;j++)
! 6086: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
! 6087: */
! 6088: fprintf(ficrespow,"\n");
! 6089: #ifdef GSL
! 6090: /* gsl starts here */
! 6091: T = gsl_multimin_fminimizer_nmsimplex;
! 6092: gsl_multimin_fminimizer *sfm = NULL;
! 6093: gsl_vector *ss, *x;
! 6094: gsl_multimin_function minex_func;
! 6095:
! 6096: /* Initial vertex size vector */
! 6097: ss = gsl_vector_alloc (NDIM);
! 6098:
! 6099: if (ss == NULL){
! 6100: GSL_ERROR_VAL ("failed to allocate space for ss", GSL_ENOMEM, 0);
! 6101: }
! 6102: /* Set all step sizes to 1 */
! 6103: gsl_vector_set_all (ss, 0.001);
! 6104:
! 6105: /* Starting point */
! 6106:
! 6107: x = gsl_vector_alloc (NDIM);
! 6108:
! 6109: if (x == NULL){
! 6110: gsl_vector_free(ss);
! 6111: GSL_ERROR_VAL ("failed to allocate space for x", GSL_ENOMEM, 0);
! 6112: }
! 6113:
! 6114: /* Initialize method and iterate */
! 6115: /* p[1]=0.0268; p[NDIM]=0.083; */
! 6116: /* gsl_vector_set(x, 0, 0.0268); */
! 6117: /* gsl_vector_set(x, 1, 0.083); */
! 6118: gsl_vector_set(x, 0, p[1]);
! 6119: gsl_vector_set(x, 1, p[2]);
! 6120:
! 6121: minex_func.f = &gompertz_f;
! 6122: minex_func.n = NDIM;
! 6123: minex_func.params = (void *)&p; /* ??? */
! 6124:
! 6125: sfm = gsl_multimin_fminimizer_alloc (T, NDIM);
! 6126: gsl_multimin_fminimizer_set (sfm, &minex_func, x, ss);
! 6127:
! 6128: printf("Iterations beginning .....\n\n");
! 6129: printf("Iter. # Intercept Slope -Log Likelihood Simplex size\n");
! 6130:
! 6131: iteri=0;
! 6132: while (rval == GSL_CONTINUE){
! 6133: iteri++;
! 6134: status = gsl_multimin_fminimizer_iterate(sfm);
! 6135:
! 6136: if (status) printf("error: %s\n", gsl_strerror (status));
! 6137: fflush(0);
! 6138:
! 6139: if (status)
! 6140: break;
! 6141:
! 6142: rval = gsl_multimin_test_size (gsl_multimin_fminimizer_size (sfm), 1e-6);
! 6143: ssval = gsl_multimin_fminimizer_size (sfm);
! 6144:
! 6145: if (rval == GSL_SUCCESS)
! 6146: printf ("converged to a local maximum at\n");
! 6147:
! 6148: printf("%5d ", iteri);
! 6149: for (it = 0; it < NDIM; it++){
! 6150: printf ("%10.5f ", gsl_vector_get (sfm->x, it));
! 6151: }
! 6152: printf("f() = %-10.5f ssize = %.7f\n", sfm->fval, ssval);
! 6153: }
! 6154:
! 6155: printf("\n\n Please note: Program should be run many times with varying starting points to detemine global maximum\n\n");
! 6156:
! 6157: gsl_vector_free(x); /* initial values */
! 6158: gsl_vector_free(ss); /* inital step size */
! 6159: for (it=0; it<NDIM; it++){
! 6160: p[it+1]=gsl_vector_get(sfm->x,it);
! 6161: fprintf(ficrespow," %.12lf", p[it]);
! 6162: }
! 6163: gsl_multimin_fminimizer_free (sfm); /* p *(sfm.x.data) et p *(sfm.x.data+1) */
! 6164: #endif
! 6165: #ifdef POWELL
! 6166: powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
! 6167: #endif
! 6168: fclose(ficrespow);
! 6169:
! 6170: hesscov(matcov, p, NDIM, delti, 1e-4, gompertz);
! 6171:
! 6172: for(i=1; i <=NDIM; i++)
! 6173: for(j=i+1;j<=NDIM;j++)
! 6174: matcov[i][j]=matcov[j][i];
! 6175:
! 6176: printf("\nCovariance matrix\n ");
! 6177: for(i=1; i <=NDIM; i++) {
! 6178: for(j=1;j<=NDIM;j++){
! 6179: printf("%f ",matcov[i][j]);
! 6180: }
! 6181: printf("\n ");
! 6182: }
! 6183:
! 6184: printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
! 6185: for (i=1;i<=NDIM;i++)
! 6186: printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
! 6187:
! 6188: lsurv=vector(1,AGESUP);
! 6189: lpop=vector(1,AGESUP);
! 6190: tpop=vector(1,AGESUP);
! 6191: lsurv[agegomp]=100000;
! 6192:
! 6193: for (k=agegomp;k<=AGESUP;k++) {
! 6194: agemortsup=k;
! 6195: if (p[1]*exp(p[2]*(k-agegomp))>1) break;
! 6196: }
! 6197:
! 6198: for (k=agegomp;k<agemortsup;k++)
! 6199: lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
! 6200:
! 6201: for (k=agegomp;k<agemortsup;k++){
! 6202: lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
! 6203: sumlpop=sumlpop+lpop[k];
! 6204: }
! 6205:
! 6206: tpop[agegomp]=sumlpop;
! 6207: for (k=agegomp;k<(agemortsup-3);k++){
! 6208: /* tpop[k+1]=2;*/
! 6209: tpop[k+1]=tpop[k]-lpop[k];
! 6210: }
! 6211:
! 6212:
! 6213: printf("\nAge lx qx dx Lx Tx e(x)\n");
! 6214: for (k=agegomp;k<(agemortsup-2);k++)
! 6215: 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]);
! 6216:
! 6217:
! 6218: replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
! 6219: printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
! 6220:
! 6221: printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \
! 6222: stepm, weightopt,\
! 6223: model,imx,p,matcov,agemortsup);
! 6224:
! 6225: free_vector(lsurv,1,AGESUP);
! 6226: free_vector(lpop,1,AGESUP);
! 6227: free_vector(tpop,1,AGESUP);
! 6228: #ifdef GSL
! 6229: free_ivector(cens,1,n);
! 6230: free_vector(agecens,1,n);
! 6231: free_ivector(dcwave,1,n);
! 6232: free_matrix(ximort,1,NDIM,1,NDIM);
! 6233: #endif
! 6234: } /* Endof if mle==-3 */
! 6235:
! 6236: else{ /* For mle >=1 */
! 6237: globpr=0;/* debug */
! 6238: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
! 6239: printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
! 6240: for (k=1; k<=npar;k++)
! 6241: printf(" %d %8.5f",k,p[k]);
! 6242: printf("\n");
! 6243: globpr=1; /* to print the contributions */
! 6244: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
! 6245: printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
! 6246: for (k=1; k<=npar;k++)
! 6247: printf(" %d %8.5f",k,p[k]);
! 6248: printf("\n");
! 6249: if(mle>=1){ /* Could be 1 or 2 */
! 6250: mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
! 6251: }
! 6252:
! 6253: /*--------- results files --------------*/
! 6254: 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);
! 6255:
! 6256:
! 6257: fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
! 6258: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
! 6259: fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
! 6260: for(i=1,jk=1; i <=nlstate; i++){
! 6261: for(k=1; k <=(nlstate+ndeath); k++){
! 6262: if (k != i) {
! 6263: printf("%d%d ",i,k);
! 6264: fprintf(ficlog,"%d%d ",i,k);
! 6265: fprintf(ficres,"%1d%1d ",i,k);
! 6266: for(j=1; j <=ncovmodel; j++){
! 6267: printf("%lf ",p[jk]);
! 6268: fprintf(ficlog,"%lf ",p[jk]);
! 6269: fprintf(ficres,"%lf ",p[jk]);
! 6270: jk++;
! 6271: }
! 6272: printf("\n");
! 6273: fprintf(ficlog,"\n");
! 6274: fprintf(ficres,"\n");
! 6275: }
! 6276: }
! 6277: }
! 6278: if(mle!=0){
! 6279: /* Computing hessian and covariance matrix */
! 6280: ftolhess=ftol; /* Usually correct */
! 6281: hesscov(matcov, p, npar, delti, ftolhess, func);
! 6282: }
! 6283: fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
! 6284: printf("# Scales (for hessian or gradient estimation)\n");
! 6285: fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
! 6286: for(i=1,jk=1; i <=nlstate; i++){
! 6287: for(j=1; j <=nlstate+ndeath; j++){
! 6288: if (j!=i) {
! 6289: fprintf(ficres,"%1d%1d",i,j);
! 6290: printf("%1d%1d",i,j);
! 6291: fprintf(ficlog,"%1d%1d",i,j);
! 6292: for(k=1; k<=ncovmodel;k++){
! 6293: printf(" %.5e",delti[jk]);
! 6294: fprintf(ficlog," %.5e",delti[jk]);
! 6295: fprintf(ficres," %.5e",delti[jk]);
! 6296: jk++;
! 6297: }
! 6298: printf("\n");
! 6299: fprintf(ficlog,"\n");
! 6300: fprintf(ficres,"\n");
! 6301: }
! 6302: }
! 6303: }
! 6304:
! 6305: 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");
! 6306: if(mle>=1)
! 6307: 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");
! 6308: 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");
! 6309: /* # 121 Var(a12)\n\ */
! 6310: /* # 122 Cov(b12,a12) Var(b12)\n\ */
! 6311: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
! 6312: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
! 6313: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
! 6314: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
! 6315: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
! 6316: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
! 6317:
! 6318:
! 6319: /* Just to have a covariance matrix which will be more understandable
! 6320: even is we still don't want to manage dictionary of variables
! 6321: */
! 6322: for(itimes=1;itimes<=2;itimes++){
! 6323: jj=0;
! 6324: for(i=1; i <=nlstate; i++){
! 6325: for(j=1; j <=nlstate+ndeath; j++){
! 6326: if(j==i) continue;
! 6327: for(k=1; k<=ncovmodel;k++){
! 6328: jj++;
! 6329: ca[0]= k+'a'-1;ca[1]='\0';
! 6330: if(itimes==1){
! 6331: if(mle>=1)
! 6332: printf("#%1d%1d%d",i,j,k);
! 6333: fprintf(ficlog,"#%1d%1d%d",i,j,k);
! 6334: fprintf(ficres,"#%1d%1d%d",i,j,k);
! 6335: }else{
! 6336: if(mle>=1)
! 6337: printf("%1d%1d%d",i,j,k);
! 6338: fprintf(ficlog,"%1d%1d%d",i,j,k);
! 6339: fprintf(ficres,"%1d%1d%d",i,j,k);
! 6340: }
! 6341: ll=0;
! 6342: for(li=1;li <=nlstate; li++){
! 6343: for(lj=1;lj <=nlstate+ndeath; lj++){
! 6344: if(lj==li) continue;
! 6345: for(lk=1;lk<=ncovmodel;lk++){
! 6346: ll++;
! 6347: if(ll<=jj){
! 6348: cb[0]= lk +'a'-1;cb[1]='\0';
! 6349: if(ll<jj){
! 6350: if(itimes==1){
! 6351: if(mle>=1)
! 6352: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
! 6353: fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
! 6354: fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
! 6355: }else{
! 6356: if(mle>=1)
! 6357: printf(" %.5e",matcov[jj][ll]);
! 6358: fprintf(ficlog," %.5e",matcov[jj][ll]);
! 6359: fprintf(ficres," %.5e",matcov[jj][ll]);
! 6360: }
! 6361: }else{
! 6362: if(itimes==1){
! 6363: if(mle>=1)
! 6364: printf(" Var(%s%1d%1d)",ca,i,j);
! 6365: fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
! 6366: fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
! 6367: }else{
! 6368: if(mle>=1)
! 6369: printf(" %.5e",matcov[jj][ll]);
! 6370: fprintf(ficlog," %.5e",matcov[jj][ll]);
! 6371: fprintf(ficres," %.5e",matcov[jj][ll]);
! 6372: }
! 6373: }
! 6374: }
! 6375: } /* end lk */
! 6376: } /* end lj */
! 6377: } /* end li */
! 6378: if(mle>=1)
! 6379: printf("\n");
! 6380: fprintf(ficlog,"\n");
! 6381: fprintf(ficres,"\n");
! 6382: numlinepar++;
! 6383: } /* end k*/
! 6384: } /*end j */
! 6385: } /* end i */
! 6386: } /* end itimes */
! 6387:
! 6388: fflush(ficlog);
! 6389: fflush(ficres);
! 6390:
! 6391: while((c=getc(ficpar))=='#' && c!= EOF){
! 6392: ungetc(c,ficpar);
! 6393: fgets(line, MAXLINE, ficpar);
! 6394: fputs(line,stdout);
! 6395: fputs(line,ficparo);
! 6396: }
! 6397: ungetc(c,ficpar);
! 6398:
! 6399: estepm=0;
! 6400: fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
! 6401: if (estepm==0 || estepm < stepm) estepm=stepm;
! 6402: if (fage <= 2) {
! 6403: bage = ageminpar;
! 6404: fage = agemaxpar;
! 6405: }
! 6406:
! 6407: fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
! 6408: fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
! 6409: fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
! 6410:
! 6411: while((c=getc(ficpar))=='#' && c!= EOF){
! 6412: ungetc(c,ficpar);
! 6413: fgets(line, MAXLINE, ficpar);
! 6414: fputs(line,stdout);
! 6415: fputs(line,ficparo);
! 6416: }
! 6417: ungetc(c,ficpar);
! 6418:
! 6419: 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);
! 6420: 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);
! 6421: 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);
! 6422: printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
! 6423: 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);
! 6424:
! 6425: while((c=getc(ficpar))=='#' && c!= EOF){
! 6426: ungetc(c,ficpar);
! 6427: fgets(line, MAXLINE, ficpar);
! 6428: fputs(line,stdout);
! 6429: fputs(line,ficparo);
! 6430: }
! 6431: ungetc(c,ficpar);
! 6432:
! 6433:
! 6434: dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
! 6435: dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
! 6436:
! 6437: fscanf(ficpar,"pop_based=%d\n",&popbased);
! 6438: fprintf(ficparo,"pop_based=%d\n",popbased);
! 6439: fprintf(ficres,"pop_based=%d\n",popbased);
! 6440:
! 6441: while((c=getc(ficpar))=='#' && c!= EOF){
! 6442: ungetc(c,ficpar);
! 6443: fgets(line, MAXLINE, ficpar);
! 6444: fputs(line,stdout);
! 6445: fputs(line,ficparo);
! 6446: }
! 6447: ungetc(c,ficpar);
! 6448:
! 6449: 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);
! 6450: 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);
! 6451: 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);
! 6452: 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);
! 6453: 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);
! 6454: /* day and month of proj2 are not used but only year anproj2.*/
! 6455:
! 6456:
! 6457:
! 6458: /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint); */
! 6459: /* ,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2); */
! 6460:
! 6461: replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
! 6462: printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
! 6463:
! 6464: printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
! 6465: model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
! 6466: jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
! 6467:
! 6468: /*------------ free_vector -------------*/
! 6469: /* chdir(path); */
! 6470:
! 6471: free_ivector(wav,1,imx);
! 6472: free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
! 6473: free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
! 6474: free_imatrix(mw,1,lastpass-firstpass+1,1,imx);
! 6475: free_lvector(num,1,n);
! 6476: free_vector(agedc,1,n);
! 6477: /*free_matrix(covar,0,NCOVMAX,1,n);*/
! 6478: /*free_matrix(covar,1,NCOVMAX,1,n);*/
! 6479: fclose(ficparo);
! 6480: fclose(ficres);
! 6481:
! 6482:
! 6483: /*--------------- Prevalence limit (period or stable prevalence) --------------*/
! 6484: #include "prevlim.h" /* Use ficrespl, ficlog */
! 6485: fclose(ficrespl);
! 6486:
! 6487: #ifdef FREEEXIT2
! 6488: #include "freeexit2.h"
! 6489: #endif
! 6490:
! 6491: /*------------- h Pij x at various ages ------------*/
! 6492: #include "hpijx.h"
! 6493: fclose(ficrespij);
! 6494:
! 6495: /*-------------- Variance of one-step probabilities---*/
! 6496: k=1;
! 6497: varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
! 6498:
! 6499:
! 6500: probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
! 6501: for(i=1;i<=AGESUP;i++)
! 6502: for(j=1;j<=NCOVMAX;j++)
! 6503: for(k=1;k<=NCOVMAX;k++)
! 6504: probs[i][j][k]=0.;
! 6505:
! 6506: /*---------- Forecasting ------------------*/
! 6507: /*if((stepm == 1) && (strcmp(model,".")==0)){*/
! 6508: if(prevfcast==1){
! 6509: /* if(stepm ==1){*/
! 6510: prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
! 6511: /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
! 6512: /* } */
! 6513: /* else{ */
! 6514: /* erreur=108; */
! 6515: /* 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); */
! 6516: /* 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); */
! 6517: /* } */
! 6518: }
! 6519:
! 6520:
! 6521: /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
! 6522:
! 6523: prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
! 6524: /* 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",\
! 6525: ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
! 6526: */
! 6527:
! 6528: if (mobilav!=0) {
! 6529: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
! 6530: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
! 6531: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
! 6532: printf(" Error in movingaverage mobilav=%d\n",mobilav);
! 6533: }
! 6534: }
! 6535:
! 6536:
! 6537: /*---------- Health expectancies, no variances ------------*/
! 6538:
! 6539: strcpy(filerese,"e");
! 6540: strcat(filerese,fileres);
! 6541: if((ficreseij=fopen(filerese,"w"))==NULL) {
! 6542: printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
! 6543: fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
! 6544: }
! 6545: printf("Computing Health Expectancies: result on file '%s' \n", filerese);
! 6546: fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
! 6547: /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
! 6548: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
! 6549:
! 6550: for (k=1; k <= (int) pow(2,cptcoveff); k++){
! 6551: fprintf(ficreseij,"\n#****** ");
! 6552: for(j=1;j<=cptcoveff;j++) {
! 6553: fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
! 6554: }
! 6555: fprintf(ficreseij,"******\n");
! 6556:
! 6557: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
! 6558: oldm=oldms;savm=savms;
! 6559: evsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart);
! 6560:
! 6561: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
! 6562: /*}*/
! 6563: }
! 6564: fclose(ficreseij);
! 6565:
! 6566:
! 6567: /*---------- Health expectancies and variances ------------*/
! 6568:
! 6569:
! 6570: strcpy(filerest,"t");
! 6571: strcat(filerest,fileres);
! 6572: if((ficrest=fopen(filerest,"w"))==NULL) {
! 6573: printf("Problem with total LE resultfile: %s\n", filerest);goto end;
! 6574: fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
! 6575: }
! 6576: printf("Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);
! 6577: fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);
! 6578:
! 6579:
! 6580: strcpy(fileresstde,"stde");
! 6581: strcat(fileresstde,fileres);
! 6582: if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {
! 6583: printf("Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
! 6584: fprintf(ficlog,"Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
! 6585: }
! 6586: printf("Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
! 6587: fprintf(ficlog,"Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
! 6588:
! 6589: strcpy(filerescve,"cve");
! 6590: strcat(filerescve,fileres);
! 6591: if((ficrescveij=fopen(filerescve,"w"))==NULL) {
! 6592: printf("Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
! 6593: fprintf(ficlog,"Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
! 6594: }
! 6595: printf("Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
! 6596: fprintf(ficlog,"Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
! 6597:
! 6598: strcpy(fileresv,"v");
! 6599: strcat(fileresv,fileres);
! 6600: if((ficresvij=fopen(fileresv,"w"))==NULL) {
! 6601: printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
! 6602: fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
! 6603: }
! 6604: printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
! 6605: fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
! 6606:
! 6607: /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
! 6608: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
! 6609:
! 6610: for (k=1; k <= (int) pow(2,cptcoveff); k++){
! 6611: fprintf(ficrest,"\n#****** ");
! 6612: for(j=1;j<=cptcoveff;j++)
! 6613: fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
! 6614: fprintf(ficrest,"******\n");
! 6615:
! 6616: fprintf(ficresstdeij,"\n#****** ");
! 6617: fprintf(ficrescveij,"\n#****** ");
! 6618: for(j=1;j<=cptcoveff;j++) {
! 6619: fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
! 6620: fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
! 6621: }
! 6622: fprintf(ficresstdeij,"******\n");
! 6623: fprintf(ficrescveij,"******\n");
! 6624:
! 6625: fprintf(ficresvij,"\n#****** ");
! 6626: for(j=1;j<=cptcoveff;j++)
! 6627: fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
! 6628: fprintf(ficresvij,"******\n");
! 6629:
! 6630: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
! 6631: oldm=oldms;savm=savms;
! 6632: cvevsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);
! 6633: /*
! 6634: */
! 6635: /* goto endfree; */
! 6636:
! 6637: vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
! 6638: pstamp(ficrest);
! 6639:
! 6640:
! 6641: for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
! 6642: oldm=oldms;savm=savms; /* Segmentation fault */
! 6643: cptcod= 0; /* To be deleted */
! 6644: 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 */
! 6645: 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 ");
! 6646: if(vpopbased==1)
! 6647: 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);
! 6648: else
! 6649: fprintf(ficrest,"the age specific period (stable) prevalences in each health state \n");
! 6650: fprintf(ficrest,"# Age e.. (std) ");
! 6651: for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
! 6652: fprintf(ficrest,"\n");
! 6653:
! 6654: epj=vector(1,nlstate+1);
! 6655: for(age=bage; age <=fage ;age++){
! 6656: prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
! 6657: if (vpopbased==1) {
! 6658: if(mobilav ==0){
! 6659: for(i=1; i<=nlstate;i++)
! 6660: prlim[i][i]=probs[(int)age][i][k];
! 6661: }else{ /* mobilav */
! 6662: for(i=1; i<=nlstate;i++)
! 6663: prlim[i][i]=mobaverage[(int)age][i][k];
! 6664: }
! 6665: }
! 6666:
! 6667: fprintf(ficrest," %4.0f",age);
! 6668: for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
! 6669: for(i=1, epj[j]=0.;i <=nlstate;i++) {
! 6670: epj[j] += prlim[i][i]*eij[i][j][(int)age];
! 6671: /* printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
! 6672: }
! 6673: epj[nlstate+1] +=epj[j];
! 6674: }
! 6675:
! 6676: for(i=1, vepp=0.;i <=nlstate;i++)
! 6677: for(j=1;j <=nlstate;j++)
! 6678: vepp += vareij[i][j][(int)age];
! 6679: fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
! 6680: for(j=1;j <=nlstate;j++){
! 6681: fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
! 6682: }
! 6683: fprintf(ficrest,"\n");
! 6684: }
! 6685: }
! 6686: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
! 6687: free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
! 6688: free_vector(epj,1,nlstate+1);
! 6689: /*}*/
! 6690: }
! 6691: free_vector(weight,1,n);
! 6692: free_imatrix(Tvard,1,NCOVMAX,1,2);
! 6693: free_imatrix(s,1,maxwav+1,1,n);
! 6694: free_matrix(anint,1,maxwav,1,n);
! 6695: free_matrix(mint,1,maxwav,1,n);
! 6696: free_ivector(cod,1,n);
! 6697: free_ivector(tab,1,NCOVMAX);
! 6698: fclose(ficresstdeij);
! 6699: fclose(ficrescveij);
! 6700: fclose(ficresvij);
! 6701: fclose(ficrest);
! 6702: fclose(ficpar);
! 6703:
! 6704: /*------- Variance of period (stable) prevalence------*/
! 6705:
! 6706: strcpy(fileresvpl,"vpl");
! 6707: strcat(fileresvpl,fileres);
! 6708: if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
! 6709: printf("Problem with variance of period (stable) prevalence resultfile: %s\n", fileresvpl);
! 6710: exit(0);
! 6711: }
! 6712: printf("Computing Variance-covariance of period (stable) prevalence: file '%s' \n", fileresvpl);
! 6713:
! 6714: /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
! 6715: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
! 6716:
! 6717: for (k=1; k <= (int) pow(2,cptcoveff); k++){
! 6718: fprintf(ficresvpl,"\n#****** ");
! 6719: for(j=1;j<=cptcoveff;j++)
! 6720: fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
! 6721: fprintf(ficresvpl,"******\n");
! 6722:
! 6723: varpl=matrix(1,nlstate,(int) bage, (int) fage);
! 6724: oldm=oldms;savm=savms;
! 6725: varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k,strstart);
! 6726: free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
! 6727: /*}*/
! 6728: }
! 6729:
! 6730: fclose(ficresvpl);
! 6731:
! 6732: /*---------- End : free ----------------*/
! 6733: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
! 6734: free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
! 6735: } /* mle==-3 arrives here for freeing */
! 6736: endfree:
! 6737: free_matrix(prlim,1,nlstate,1,nlstate); /*here or after loop ? */
! 6738: free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
! 6739: free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
! 6740: free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
! 6741: free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
! 6742: free_matrix(covar,0,NCOVMAX,1,n);
! 6743: free_matrix(matcov,1,npar,1,npar);
! 6744: /*free_vector(delti,1,npar);*/
! 6745: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
! 6746: free_matrix(agev,1,maxwav,1,imx);
! 6747: free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
! 6748:
! 6749: free_ivector(ncodemax,1,NCOVMAX);
! 6750: free_ivector(Tvar,1,NCOVMAX);
! 6751: free_ivector(Tprod,1,NCOVMAX);
! 6752: free_ivector(Tvaraff,1,NCOVMAX);
! 6753: free_ivector(Tage,1,NCOVMAX);
! 6754:
! 6755: free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
! 6756: free_imatrix(codtab,1,100,1,10);
! 6757: fflush(fichtm);
! 6758: fflush(ficgp);
! 6759:
! 6760:
! 6761: if((nberr >0) || (nbwarn>0)){
! 6762: printf("End of Imach with %d errors and/or %d warnings\n",nberr,nbwarn);
! 6763: fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
! 6764: }else{
! 6765: printf("End of Imach\n");
! 6766: fprintf(ficlog,"End of Imach\n");
! 6767: }
! 6768: printf("See log file on %s\n",filelog);
! 6769: /* gettimeofday(&end_time, (struct timezone*)0);*/ /* after time */
! 6770: /*(void) gettimeofday(&end_time,&tzp);*/
! 6771: rend_time = time(NULL);
! 6772: end_time = *localtime(&rend_time);
! 6773: /* tml = *localtime(&end_time.tm_sec); */
! 6774: strcpy(strtend,asctime(&end_time));
! 6775: printf("Local time at start %s\nLocal time at end %s",strstart, strtend);
! 6776: fprintf(ficlog,"Local time at start %s\nLocal time at end %s\n",strstart, strtend);
! 6777: printf("Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
! 6778:
! 6779: printf("Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
! 6780: fprintf(ficlog,"Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
! 6781: fprintf(ficlog,"Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
! 6782: /* printf("Total time was %d uSec.\n", total_usecs);*/
! 6783: /* if(fileappend(fichtm,optionfilehtm)){ */
! 6784: fprintf(fichtm,"<br>Local time at start %s<br>Local time at end %s<br>\n</body></html>",strstart, strtend);
! 6785: fclose(fichtm);
! 6786: fprintf(fichtmcov,"<br>Local time at start %s<br>Local time at end %s<br>\n</body></html>",strstart, strtend);
! 6787: fclose(fichtmcov);
! 6788: fclose(ficgp);
! 6789: fclose(ficlog);
! 6790: /*------ End -----------*/
! 6791:
! 6792:
! 6793: printf("Before Current directory %s!\n",pathcd);
! 6794: if(chdir(pathcd) != 0)
! 6795: printf("Can't move to directory %s!\n",path);
! 6796: if(getcwd(pathcd,MAXLINE) > 0)
! 6797: printf("Current directory %s!\n",pathcd);
! 6798: /*strcat(plotcmd,CHARSEPARATOR);*/
! 6799: sprintf(plotcmd,"gnuplot");
! 6800: #ifdef _WIN32
! 6801: sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
! 6802: #endif
! 6803: if(!stat(plotcmd,&info)){
! 6804: printf("Error or gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
! 6805: if(!stat(getenv("GNUPLOTBIN"),&info)){
! 6806: printf("Error or gnuplot program not found: '%s' Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);
! 6807: }else
! 6808: strcpy(pplotcmd,plotcmd);
! 6809: #ifdef __unix
! 6810: strcpy(plotcmd,GNUPLOTPROGRAM);
! 6811: if(!stat(plotcmd,&info)){
! 6812: printf("Error gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
! 6813: }else
! 6814: strcpy(pplotcmd,plotcmd);
! 6815: #endif
! 6816: }else
! 6817: strcpy(pplotcmd,plotcmd);
! 6818:
! 6819: sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
! 6820: printf("Starting graphs with: '%s'\n",plotcmd);fflush(stdout);
! 6821:
! 6822: if((outcmd=system(plotcmd)) != 0){
! 6823: printf("gnuplot command might not be in your path: '%s', err=%d\n", plotcmd, outcmd);
! 6824: printf("\n Trying if gnuplot resides on the same directory that IMaCh\n");
! 6825: sprintf(plotcmd,"%sgnuplot %s", pathimach, optionfilegnuplot);
! 6826: if((outcmd=system(plotcmd)) != 0)
! 6827: printf("\n Still a problem with gnuplot command %s, err=%d\n", plotcmd, outcmd);
! 6828: }
! 6829: printf(" Successful, please wait...");
! 6830: while (z[0] != 'q') {
! 6831: /* chdir(path); */
! 6832: printf("\nType e to edit results with your browser, g to graph again and q for exit: ");
! 6833: scanf("%s",z);
! 6834: /* if (z[0] == 'c') system("./imach"); */
! 6835: if (z[0] == 'e') {
! 6836: #ifdef __APPLE__
! 6837: sprintf(pplotcmd, "open %s", optionfilehtm);
! 6838: #elif __linux
! 6839: sprintf(pplotcmd, "xdg-open %s", optionfilehtm);
! 6840: #else
! 6841: sprintf(pplotcmd, "%s", optionfilehtm);
! 6842: #endif
! 6843: printf("Starting browser with: %s",pplotcmd);fflush(stdout);
! 6844: system(pplotcmd);
! 6845: }
! 6846: else if (z[0] == 'g') system(plotcmd);
! 6847: else if (z[0] == 'q') exit(0);
! 6848: }
! 6849: end:
! 6850: while (z[0] != 'q') {
! 6851: printf("\nType q for exiting: ");
! 6852: scanf("%s",z);
! 6853: }
! 6854: }
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