imach/src/imach.c - view

File: [Local Repository] / imach / src / imach.c
Revision 1.194: download - view: text, annotated - select for diffs
Tue Aug 18 13:32:00 2015 UTC (8 years, 10 months ago) by brouard
Branches: MAIN
CVS tags: HEAD

Summary:  Adding error when the covariance matrix doesn't contain the exact number of lines required by the model line.

1: /* $Id: imach.c,v 1.194 2015/08/18 13:32:00 brouard Exp $ 2: $State: Exp $ 3: $Log: imach.c,v $ 4: Revision 1.194 2015/08/18 13:32:00 brouard 5: Summary: Adding error when the covariance matrix doesn't contain the exact number of lines required by the model line. 6: 7: Revision 1.193 2015/08/04 07:17:42 brouard 8: Summary: 0.98q4 9: 10: Revision 1.192 2015/07/16 16:49:02 brouard 11: Summary: Fixing some outputs 12: 13: Revision 1.191 2015/07/14 10:00:33 brouard 14: Summary: Some fixes 15: 16: Revision 1.190 2015/05/05 08:51:13 brouard 17: Summary: Adding digits in output parameters (7 digits instead of 6) 18: 19: Fix 1+age+. 20: 21: Revision 1.189 2015/04/30 14:45:16 brouard 22: Summary: 0.98q2 23: 24: Revision 1.188 2015/04/30 08:27:53 brouard 25: *** empty log message *** 26: 27: Revision 1.187 2015/04/29 09:11:15 brouard 28: *** empty log message *** 29: 30: Revision 1.186 2015/04/23 12:01:52 brouard 31: Summary: V1*age is working now, version 0.98q1 32: 33: Some codes had been disabled in order to simplify and Vn*age was 34: working in the optimization phase, ie, giving correct MLE parameters, 35: but, as usual, outputs were not correct and program core dumped. 36: 37: Revision 1.185 2015/03/11 13:26:42 brouard 38: Summary: Inclusion of compile and links command line for Intel Compiler 39: 40: Revision 1.184 2015/03/11 11:52:39 brouard 41: Summary: Back from Windows 8. Intel Compiler 42: 43: Revision 1.183 2015/03/10 20:34:32 brouard 44: Summary: 0.98q0, trying with directest, mnbrak fixed 45: 46: We use directest instead of original Powell test; probably no 47: incidence on the results, but better justifications; 48: We fixed Numerical Recipes mnbrak routine which was wrong and gave 49: wrong results. 50: 51: Revision 1.182 2015/02/12 08:19:57 brouard 52: Summary: Trying to keep directest which seems simpler and more general 53: Author: Nicolas Brouard 54: 55: Revision 1.181 2015/02/11 23:22:24 brouard 56: Summary: Comments on Powell added 57: 58: Author: 59: 60: Revision 1.180 2015/02/11 17:33:45 brouard 61: Summary: Finishing move from main to function (hpijx and prevalence_limit) 62: 63: Revision 1.179 2015/01/04 09:57:06 brouard 64: Summary: back to OS/X 65: 66: Revision 1.178 2015/01/04 09:35:48 brouard 67: *** empty log message *** 68: 69: Revision 1.177 2015/01/03 18:40:56 brouard 70: Summary: Still testing ilc32 on OSX 71: 72: Revision 1.176 2015/01/03 16:45:04 brouard 73: *** empty log message *** 74: 75: Revision 1.175 2015/01/03 16:33:42 brouard 76: *** empty log message *** 77: 78: Revision 1.174 2015/01/03 16:15:49 brouard 79: Summary: Still in cross-compilation 80: 81: Revision 1.173 2015/01/03 12:06:26 brouard 82: Summary: trying to detect cross-compilation 83: 84: Revision 1.172 2014/12/27 12:07:47 brouard 85: Summary: Back from Visual Studio and Intel, options for compiling for Windows XP 86: 87: Revision 1.171 2014/12/23 13:26:59 brouard 88: Summary: Back from Visual C 89: 90: Still problem with utsname.h on Windows 91: 92: Revision 1.170 2014/12/23 11:17:12 brouard 93: Summary: Cleaning some \%% back to %% 94: 95: The escape was mandatory for a specific compiler (which one?), but too many warnings. 96: 97: Revision 1.169 2014/12/22 23:08:31 brouard 98: Summary: 0.98p 99: 100: Outputs some informations on compiler used, OS etc. Testing on different platforms. 101: 102: Revision 1.168 2014/12/22 15:17:42 brouard 103: Summary: update 104: 105: Revision 1.167 2014/12/22 13:50:56 brouard 106: Summary: Testing uname and compiler version and if compiled 32 or 64 107: 108: Testing on Linux 64 109: 110: Revision 1.166 2014/12/22 11:40:47 brouard 111: *** empty log message *** 112: 113: Revision 1.165 2014/12/16 11:20:36 brouard 114: Summary: After compiling on Visual C 115: 116: * imach.c (Module): Merging 1.61 to 1.162 117: 118: Revision 1.164 2014/12/16 10:52:11 brouard 119: Summary: Merging with Visual C after suppressing some warnings for unused variables. Also fixing Saito's bug 0.98Xn 120: 121: * imach.c (Module): Merging 1.61 to 1.162 122: 123: Revision 1.163 2014/12/16 10:30:11 brouard 124: * imach.c (Module): Merging 1.61 to 1.162 125: 126: Revision 1.162 2014/09/25 11:43:39 brouard 127: Summary: temporary backup 0.99! 128: 129: Revision 1.1 2014/09/16 11:06:58 brouard 130: Summary: With some code (wrong) for nlopt 131: 132: Author: 133: 134: Revision 1.161 2014/09/15 20:41:41 brouard 135: Summary: Problem with macro SQR on Intel compiler 136: 137: Revision 1.160 2014/09/02 09:24:05 brouard 138: *** empty log message *** 139: 140: Revision 1.159 2014/09/01 10:34:10 brouard 141: Summary: WIN32 142: Author: Brouard 143: 144: Revision 1.158 2014/08/27 17:11:51 brouard 145: *** empty log message *** 146: 147: Revision 1.157 2014/08/27 16:26:55 brouard 148: Summary: Preparing windows Visual studio version 149: Author: Brouard 150: 151: In order to compile on Visual studio, time.h is now correct and time_t 152: and tm struct should be used. difftime should be used but sometimes I 153: just make the differences in raw time format (time(&now). 154: Trying to suppress #ifdef LINUX 155: Add xdg-open for __linux in order to open default browser. 156: 157: Revision 1.156 2014/08/25 20:10:10 brouard 158: *** empty log message *** 159: 160: Revision 1.155 2014/08/25 18:32:34 brouard 161: Summary: New compile, minor changes 162: Author: Brouard 163: 164: Revision 1.154 2014/06/20 17:32:08 brouard 165: Summary: Outputs now all graphs of convergence to period prevalence 166: 167: Revision 1.153 2014/06/20 16:45:46 brouard 168: Summary: If 3 live state, convergence to period prevalence on same graph 169: Author: Brouard 170: 171: Revision 1.152 2014/06/18 17:54:09 brouard 172: Summary: open browser, use gnuplot on same dir than imach if not found in the path 173: 174: Revision 1.151 2014/06/18 16:43:30 brouard 175: *** empty log message *** 176: 177: Revision 1.150 2014/06/18 16:42:35 brouard 178: Summary: If gnuplot is not in the path try on same directory than imach binary (OSX) 179: Author: brouard 180: 181: Revision 1.149 2014/06/18 15:51:14 brouard 182: Summary: Some fixes in parameter files errors 183: Author: Nicolas Brouard 184: 185: Revision 1.148 2014/06/17 17:38:48 brouard 186: Summary: Nothing new 187: Author: Brouard 188: 189: Just a new packaging for OS/X version 0.98nS 190: 191: Revision 1.147 2014/06/16 10:33:11 brouard 192: *** empty log message *** 193: 194: Revision 1.146 2014/06/16 10:20:28 brouard 195: Summary: Merge 196: Author: Brouard 197: 198: Merge, before building revised version. 199: 200: Revision 1.145 2014/06/10 21:23:15 brouard 201: Summary: Debugging with valgrind 202: Author: Nicolas Brouard 203: 204: Lot of changes in order to output the results with some covariates 205: After the Edimburgh REVES conference 2014, it seems mandatory to 206: improve the code. 207: No more memory valgrind error but a lot has to be done in order to 208: continue the work of splitting the code into subroutines. 209: Also, decodemodel has been improved. Tricode is still not 210: optimal. nbcode should be improved. Documentation has been added in 211: the source code. 212: 213: Revision 1.143 2014/01/26 09:45:38 brouard 214: Summary: Version 0.98nR (to be improved, but gives same optimization results as 0.98k. Nice, promising 215: 216: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested... 217: (Module): Version 0.98nR Running ok, but output format still only works for three covariates. 218: 219: Revision 1.142 2014/01/26 03:57:36 brouard 220: Summary: gnuplot changed plot w l 1 has to be changed to plot w l lt 2 221: 222: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested... 223: 224: Revision 1.141 2014/01/26 02:42:01 brouard 225: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested... 226: 227: Revision 1.140 2011/09/02 10:37:54 brouard 228: Summary: times.h is ok with mingw32 now. 229: 230: Revision 1.139 2010/06/14 07:50:17 brouard 231: After the theft of my laptop, I probably lost some lines of codes which were not uploaded to the CVS tree. 232: I remember having already fixed agemin agemax which are pointers now but not cvs saved. 233: 234: Revision 1.138 2010/04/30 18:19:40 brouard 235: *** empty log message *** 236: 237: Revision 1.137 2010/04/29 18:11:38 brouard 238: (Module): Checking covariates for more complex models 239: than V1+V2. A lot of change to be done. Unstable. 240: 241: Revision 1.136 2010/04/26 20:30:53 brouard 242: (Module): merging some libgsl code. Fixing computation 243: of likelione (using inter/intrapolation if mle = 0) in order to 244: get same likelihood as if mle=1. 245: Some cleaning of code and comments added. 246: 247: Revision 1.135 2009/10/29 15:33:14 brouard 248: (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code. 249: 250: Revision 1.134 2009/10/29 13:18:53 brouard 251: (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code. 252: 253: Revision 1.133 2009/07/06 10:21:25 brouard 254: just nforces 255: 256: Revision 1.132 2009/07/06 08:22:05 brouard 257: Many tings 258: 259: Revision 1.131 2009/06/20 16:22:47 brouard 260: Some dimensions resccaled 261: 262: Revision 1.130 2009/05/26 06:44:34 brouard 263: (Module): Max Covariate is now set to 20 instead of 8. A 264: lot of cleaning with variables initialized to 0. Trying to make 265: V2+V3*age+V1+V4 strb=V3*age+V1+V4 working better. 266: 267: Revision 1.129 2007/08/31 13:49:27 lievre 268: Modification of the way of exiting when the covariate is not binary in order to see on the window the error message before exiting 269: 270: Revision 1.128 2006/06/30 13:02:05 brouard 271: (Module): Clarifications on computing e.j 272: 273: Revision 1.127 2006/04/28 18:11:50 brouard 274: (Module): Yes the sum of survivors was wrong since 275: imach-114 because nhstepm was no more computed in the age 276: loop. Now we define nhstepma in the age loop. 277: (Module): In order to speed up (in case of numerous covariates) we 278: compute health expectancies (without variances) in a first step 279: and then all the health expectancies with variances or standard 280: deviation (needs data from the Hessian matrices) which slows the 281: computation. 282: In the future we should be able to stop the program is only health 283: expectancies and graph are needed without standard deviations. 284: 285: Revision 1.126 2006/04/28 17:23:28 brouard 286: (Module): Yes the sum of survivors was wrong since 287: imach-114 because nhstepm was no more computed in the age 288: loop. Now we define nhstepma in the age loop. 289: Version 0.98h 290: 291: Revision 1.125 2006/04/04 15:20:31 lievre 292: Errors in calculation of health expectancies. Age was not initialized. 293: Forecasting file added. 294: 295: Revision 1.124 2006/03/22 17:13:53 lievre 296: Parameters are printed with %lf instead of %f (more numbers after the comma). 297: The log-likelihood is printed in the log file 298: 299: Revision 1.123 2006/03/20 10:52:43 brouard 300: * imach.c (Module): <title> changed, corresponds to .htm file 301: name. <head> headers where missing. 302: 303: * imach.c (Module): Weights can have a decimal point as for 304: English (a comma might work with a correct LC_NUMERIC environment, 305: otherwise the weight is truncated). 306: Modification of warning when the covariates values are not 0 or 307: 1. 308: Version 0.98g 309: 310: Revision 1.122 2006/03/20 09:45:41 brouard 311: (Module): Weights can have a decimal point as for 312: English (a comma might work with a correct LC_NUMERIC environment, 313: otherwise the weight is truncated). 314: Modification of warning when the covariates values are not 0 or 315: 1. 316: Version 0.98g 317: 318: Revision 1.121 2006/03/16 17:45:01 lievre 319: * imach.c (Module): Comments concerning covariates added 320: 321: * imach.c (Module): refinements in the computation of lli if 322: status=-2 in order to have more reliable computation if stepm is 323: not 1 month. Version 0.98f 324: 325: Revision 1.120 2006/03/16 15:10:38 lievre 326: (Module): refinements in the computation of lli if 327: status=-2 in order to have more reliable computation if stepm is 328: not 1 month. Version 0.98f 329: 330: Revision 1.119 2006/03/15 17:42:26 brouard 331: (Module): Bug if status = -2, the loglikelihood was 332: computed as likelihood omitting the logarithm. Version O.98e 333: 334: Revision 1.118 2006/03/14 18:20:07 brouard 335: (Module): varevsij Comments added explaining the second 336: table of variances if popbased=1 . 337: (Module): Covariances of eij, ekl added, graphs fixed, new html link. 338: (Module): Function pstamp added 339: (Module): Version 0.98d 340: 341: Revision 1.117 2006/03/14 17:16:22 brouard 342: (Module): varevsij Comments added explaining the second 343: table of variances if popbased=1 . 344: (Module): Covariances of eij, ekl added, graphs fixed, new html link. 345: (Module): Function pstamp added 346: (Module): Version 0.98d 347: 348: Revision 1.116 2006/03/06 10:29:27 brouard 349: (Module): Variance-covariance wrong links and 350: varian-covariance of ej. is needed (Saito). 351: 352: Revision 1.115 2006/02/27 12:17:45 brouard 353: (Module): One freematrix added in mlikeli! 0.98c 354: 355: Revision 1.114 2006/02/26 12:57:58 brouard 356: (Module): Some improvements in processing parameter 357: filename with strsep. 358: 359: Revision 1.113 2006/02/24 14:20:24 brouard 360: (Module): Memory leaks checks with valgrind and: 361: datafile was not closed, some imatrix were not freed and on matrix 362: allocation too. 363: 364: Revision 1.112 2006/01/30 09:55:26 brouard 365: (Module): Back to gnuplot.exe instead of wgnuplot.exe 366: 367: Revision 1.111 2006/01/25 20:38:18 brouard 368: (Module): Lots of cleaning and bugs added (Gompertz) 369: (Module): Comments can be added in data file. Missing date values 370: can be a simple dot '.'. 371: 372: Revision 1.110 2006/01/25 00:51:50 brouard 373: (Module): Lots of cleaning and bugs added (Gompertz) 374: 375: Revision 1.109 2006/01/24 19:37:15 brouard 376: (Module): Comments (lines starting with a #) are allowed in data. 377: 378: Revision 1.108 2006/01/19 18:05:42 lievre 379: Gnuplot problem appeared... 380: To be fixed 381: 382: Revision 1.107 2006/01/19 16:20:37 brouard 383: Test existence of gnuplot in imach path 384: 385: Revision 1.106 2006/01/19 13:24:36 brouard 386: Some cleaning and links added in html output 387: 388: Revision 1.105 2006/01/05 20:23:19 lievre 389: *** empty log message *** 390: 391: Revision 1.104 2005/09/30 16:11:43 lievre 392: (Module): sump fixed, loop imx fixed, and simplifications. 393: (Module): If the status is missing at the last wave but we know 394: that the person is alive, then we can code his/her status as -2 395: (instead of missing=-1 in earlier versions) and his/her 396: contributions to the likelihood is 1 - Prob of dying from last 397: health status (= 1-p13= p11+p12 in the easiest case of somebody in 398: the healthy state at last known wave). Version is 0.98 399: 400: Revision 1.103 2005/09/30 15:54:49 lievre 401: (Module): sump fixed, loop imx fixed, and simplifications. 402: 403: Revision 1.102 2004/09/15 17:31:30 brouard 404: Add the possibility to read data file including tab characters. 405: 406: Revision 1.101 2004/09/15 10:38:38 brouard 407: Fix on curr_time 408: 409: Revision 1.100 2004/07/12 18:29:06 brouard 410: Add version for Mac OS X. Just define UNIX in Makefile 411: 412: Revision 1.99 2004/06/05 08:57:40 brouard 413: *** empty log message *** 414: 415: Revision 1.98 2004/05/16 15:05:56 brouard 416: New version 0.97 . First attempt to estimate force of mortality 417: directly from the data i.e. without the need of knowing the health 418: state at each age, but using a Gompertz model: log u =a + b*age . 419: This is the basic analysis of mortality and should be done before any 420: other analysis, in order to test if the mortality estimated from the 421: cross-longitudinal survey is different from the mortality estimated 422: from other sources like vital statistic data. 423: 424: The same imach parameter file can be used but the option for mle should be -3. 425: 426: Agnès, who wrote this part of the code, tried to keep most of the 427: former routines in order to include the new code within the former code. 428: 429: The output is very simple: only an estimate of the intercept and of 430: the slope with 95% confident intervals. 431: 432: Current limitations: 433: A) Even if you enter covariates, i.e. with the 434: model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates. 435: B) There is no computation of Life Expectancy nor Life Table. 436: 437: Revision 1.97 2004/02/20 13:25:42 lievre 438: Version 0.96d. Population forecasting command line is (temporarily) 439: suppressed. 440: 441: Revision 1.96 2003/07/15 15:38:55 brouard 442: * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is 443: rewritten within the same printf. Workaround: many printfs. 444: 445: Revision 1.95 2003/07/08 07:54:34 brouard 446: * imach.c (Repository): 447: (Repository): Using imachwizard code to output a more meaningful covariance 448: matrix (cov(a12,c31) instead of numbers. 449: 450: Revision 1.94 2003/06/27 13:00:02 brouard 451: Just cleaning 452: 453: Revision 1.93 2003/06/25 16:33:55 brouard 454: (Module): On windows (cygwin) function asctime_r doesn't 455: exist so I changed back to asctime which exists. 456: (Module): Version 0.96b 457: 458: Revision 1.92 2003/06/25 16:30:45 brouard 459: (Module): On windows (cygwin) function asctime_r doesn't 460: exist so I changed back to asctime which exists. 461: 462: Revision 1.91 2003/06/25 15:30:29 brouard 463: * imach.c (Repository): Duplicated warning errors corrected. 464: (Repository): Elapsed time after each iteration is now output. It 465: helps to forecast when convergence will be reached. Elapsed time 466: is stamped in powell. We created a new html file for the graphs 467: concerning matrix of covariance. It has extension -cov.htm. 468: 469: Revision 1.90 2003/06/24 12:34:15 brouard 470: (Module): Some bugs corrected for windows. Also, when 471: mle=-1 a template is output in file "or"mypar.txt with the design 472: of the covariance matrix to be input. 473: 474: Revision 1.89 2003/06/24 12:30:52 brouard 475: (Module): Some bugs corrected for windows. Also, when 476: mle=-1 a template is output in file "or"mypar.txt with the design 477: of the covariance matrix to be input. 478: 479: Revision 1.88 2003/06/23 17:54:56 brouard 480: * 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. 481: 482: Revision 1.87 2003/06/18 12:26:01 brouard 483: Version 0.96 484: 485: Revision 1.86 2003/06/17 20:04:08 brouard 486: (Module): Change position of html and gnuplot routines and added 487: routine fileappend. 488: 489: Revision 1.85 2003/06/17 13:12:43 brouard 490: * imach.c (Repository): Check when date of death was earlier that 491: current date of interview. It may happen when the death was just 492: prior to the death. In this case, dh was negative and likelihood 493: was wrong (infinity). We still send an "Error" but patch by 494: assuming that the date of death was just one stepm after the 495: interview. 496: (Repository): Because some people have very long ID (first column) 497: we changed int to long in num[] and we added a new lvector for 498: memory allocation. But we also truncated to 8 characters (left 499: truncation) 500: (Repository): No more line truncation errors. 501: 502: Revision 1.84 2003/06/13 21:44:43 brouard 503: * imach.c (Repository): Replace "freqsummary" at a correct 504: place. It differs from routine "prevalence" which may be called 505: many times. Probs is memory consuming and must be used with 506: parcimony. 507: Version 0.95a3 (should output exactly the same maximization than 0.8a2) 508: 509: Revision 1.83 2003/06/10 13:39:11 lievre 510: *** empty log message *** 511: 512: Revision 1.82 2003/06/05 15:57:20 brouard 513: Add log in imach.c and fullversion number is now printed. 514: 515: */ 516: /* 517: Interpolated Markov Chain 518: 519: Short summary of the programme: 520: 521: This program computes Healthy Life Expectancies from 522: cross-longitudinal data. Cross-longitudinal data consist in: -1- a 523: first survey ("cross") where individuals from different ages are 524: interviewed on their health status or degree of disability (in the 525: case of a health survey which is our main interest) -2- at least a 526: second wave of interviews ("longitudinal") which measure each change 527: (if any) in individual health status. Health expectancies are 528: computed from the time spent in each health state according to a 529: model. More health states you consider, more time is necessary to reach the 530: Maximum Likelihood of the parameters involved in the model. The 531: simplest model is the multinomial logistic model where pij is the 532: probability to be observed in state j at the second wave 533: conditional to be observed in state i at the first wave. Therefore 534: the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where 535: 'age' is age and 'sex' is a covariate. If you want to have a more 536: complex model than "constant and age", you should modify the program 537: where the markup *Covariates have to be included here again* invites 538: you to do it. More covariates you add, slower the 539: convergence. 540: 541: The advantage of this computer programme, compared to a simple 542: multinomial logistic model, is clear when the delay between waves is not 543: identical for each individual. Also, if a individual missed an 544: intermediate interview, the information is lost, but taken into 545: account using an interpolation or extrapolation. 546: 547: hPijx is the probability to be observed in state i at age x+h 548: conditional to the observed state i at age x. The delay 'h' can be 549: split into an exact number (nh*stepm) of unobserved intermediate 550: states. This elementary transition (by month, quarter, 551: semester or year) is modelled as a multinomial logistic. The hPx 552: matrix is simply the matrix product of nh*stepm elementary matrices 553: and the contribution of each individual to the likelihood is simply 554: hPijx. 555: 556: Also this programme outputs the covariance matrix of the parameters but also 557: of the life expectancies. It also computes the period (stable) prevalence. 558: 559: Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr). 560: Institut national d'études démographiques, Paris. 561: This software have been partly granted by Euro-REVES, a concerted action 562: from the European Union. 563: It is copyrighted identically to a GNU software product, ie programme and 564: software can be distributed freely for non commercial use. Latest version 565: can be accessed at http://euroreves.ined.fr/imach . 566: 567: Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach 568: or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so 569: 570: **********************************************************************/ 571: /* 572: main 573: read parameterfile 574: read datafile 575: concatwav 576: freqsummary 577: if (mle >= 1) 578: mlikeli 579: print results files 580: if mle==1 581: computes hessian 582: read end of parameter file: agemin, agemax, bage, fage, estepm 583: begin-prev-date,... 584: open gnuplot file 585: open html file 586: period (stable) prevalence | pl_nom 1-1 2-2 etc by covariate 587: for age prevalim() | #****** V1=0 V2=1 V3=1 V4=0 ****** 588: | 65 1 0 2 1 3 1 4 0 0.96326 0.03674 589: freexexit2 possible for memory heap. 590: 591: h Pij x | pij_nom ficrestpij 592: # Cov Agex agex+h hpijx with i,j= 1-1 1-2 1-3 2-1 2-2 2-3 593: 1 85 85 1.00000 0.00000 0.00000 0.00000 1.00000 0.00000 594: 1 85 86 0.68299 0.22291 0.09410 0.71093 0.00000 0.28907 595: 596: 1 65 99 0.00364 0.00322 0.99314 0.00350 0.00310 0.99340 597: 1 65 100 0.00214 0.00204 0.99581 0.00206 0.00196 0.99597 598: variance of p one-step probabilities varprob | prob_nom ficresprob #One-step probabilities and stand. devi in () 599: Standard deviation of one-step probabilities | probcor_nom ficresprobcor #One-step probabilities and correlation matrix 600: Matrix of variance covariance of one-step probabilities | probcov_nom ficresprobcov #One-step probabilities and covariance matrix 601: 602: forecasting if prevfcast==1 prevforecast call prevalence() 603: health expectancies 604: Variance-covariance of DFLE 605: prevalence() 606: movingaverage() 607: varevsij() 608: if popbased==1 varevsij(,popbased) 609: total life expectancies 610: Variance of period (stable) prevalence 611: end 612: */ 613: 614: /* #define DEBUG */ 615: /* #define DEBUGBRENT */ 616: #define POWELL /* Instead of NLOPT */ 617: #define POWELLF1F3 /* Skip test */ 618: /* #define POWELLORIGINAL /\* Don't use Directest to decide new direction but original Powell test *\/ */ 619: /* #define MNBRAKORIGINAL /\* Don't use mnbrak fix *\/ */ 620: 621: #include <math.h> 622: #include <stdio.h> 623: #include <stdlib.h> 624: #include <string.h> 625: 626: #ifdef _WIN32 627: #include <io.h> 628: #include <windows.h> 629: #include <tchar.h> 630: #else 631: #include <unistd.h> 632: #endif 633: 634: #include <limits.h> 635: #include <sys/types.h> 636: 637: #if defined(__GNUC__) 638: #include <sys/utsname.h> /* Doesn't work on Windows */ 639: #endif 640: 641: #include <sys/stat.h> 642: #include <errno.h> 643: /* extern int errno; */ 644: 645: /* #ifdef LINUX */ 646: /* #include <time.h> */ 647: /* #include "timeval.h" */ 648: /* #else */ 649: /* #include <sys/time.h> */ 650: /* #endif */ 651: 652: #include <time.h> 653: 654: #ifdef GSL 655: #include <gsl/gsl_errno.h> 656: #include <gsl/gsl_multimin.h> 657: #endif 658: 659: 660: #ifdef NLOPT 661: #include <nlopt.h> 662: typedef struct { 663: double (* function)(double [] ); 664: } myfunc_data ; 665: #endif 666: 667: /* #include <libintl.h> */ 668: /* #define _(String) gettext (String) */ 669: 670: #define MAXLINE 1024 /* Was 256. Overflow with 312 with 2 states and 4 covariates. Should be ok */ 671: 672: #define GNUPLOTPROGRAM "gnuplot" 673: /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/ 674: #define FILENAMELENGTH 132 675: 676: #define GLOCK_ERROR_NOPATH -1 /* empty path */ 677: #define GLOCK_ERROR_GETCWD -2 /* cannot get cwd */ 678: 679: #define MAXPARM 128 /**< Maximum number of parameters for the optimization */ 680: #define NPARMAX 64 /**< (nlstate+ndeath-1)*nlstate*ncovmodel */ 681: 682: #define NINTERVMAX 8 683: #define NLSTATEMAX 8 /**< Maximum number of live states (for func) */ 684: #define NDEATHMAX 8 /**< Maximum number of dead states (for func) */ 685: #define NCOVMAX 20 /**< Maximum number of covariates, including generated covariates V1*V2 */ 686: #define codtabm(h,k) 1 & (h-1) >> (k-1) ; 687: #define MAXN 20000 688: #define YEARM 12. /**< Number of months per year */ 689: #define AGESUP 130 690: #define AGEBASE 40 691: #define AGEOVERFLOW 1.e20 692: #define AGEGOMP 10 /**< Minimal age for Gompertz adjustment */ 693: #ifdef _WIN32 694: #define DIRSEPARATOR '\\' 695: #define CHARSEPARATOR "\\" 696: #define ODIRSEPARATOR '/' 697: #else 698: #define DIRSEPARATOR '/' 699: #define CHARSEPARATOR "/" 700: #define ODIRSEPARATOR '\\' 701: #endif 702: 703: /* $Id: imach.c,v 1.194 2015/08/18 13:32:00 brouard Exp $ */ 704: /* $State: Exp $ */ 705: 706: char version[]="Imach version 0.98q5, August 2015,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121), Intel Software 2015"; 707: char fullversion[]="$Revision: 1.194 $ $Date: 2015/08/18 13:32:00 $"; 708: char strstart[80]; 709: char optionfilext[10], optionfilefiname[FILENAMELENGTH]; 710: int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings */ 711: int nagesqr=0, nforce=0; /* nagesqr=1 if model is including age*age, number of forces */ 712: /* Number of covariates model=V2+V1+ V3*age+V2*V4 */ 713: int cptcovn=0; /**< cptcovn number of covariates added in the model (excepting constant and age and age*product) */ 714: int cptcovt=0; /**< cptcovt number of covariates added in the model (excepting constant and age) */ 715: int cptcovs=0; /**< cptcovs number of simple covariates V2+V1 =2 */ 716: int cptcovage=0; /**< Number of covariates with age: V3*age only =1 */ 717: int cptcovprodnoage=0; /**< Number of covariate products without age */ 718: int cptcoveff=0; /* Total number of covariates to vary for printing results */ 719: int cptcov=0; /* Working variable */ 720: int npar=NPARMAX; 721: int nlstate=2; /* Number of live states */ 722: int ndeath=1; /* Number of dead states */ 723: int ncovmodel=0, ncovcol=0; /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */ 724: int popbased=0; 725: 726: int *wav; /* Number of waves for this individuual 0 is possible */ 727: int maxwav=0; /* Maxim number of waves */ 728: int jmin=0, jmax=0; /* min, max spacing between 2 waves */ 729: int ijmin=0, ijmax=0; /* Individuals having jmin and jmax */ 730: int gipmx=0, gsw=0; /* Global variables on the number of contributions 731: to the likelihood and the sum of weights (done by funcone)*/ 732: int mle=1, weightopt=0; 733: int **mw; /* mw[mi][i] is number of the mi wave for this individual */ 734: int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */ 735: int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between 736: * wave mi and wave mi+1 is not an exact multiple of stepm. */ 737: int countcallfunc=0; /* Count the number of calls to func */ 738: double jmean=1; /* Mean space between 2 waves */ 739: double **matprod2(); /* test */ 740: double **oldm, **newm, **savm; /* Working pointers to matrices */ 741: double **oldms, **newms, **savms; /* Fixed working pointers to matrices */ 742: /*FILE *fic ; */ /* Used in readdata only */ 743: FILE *ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop; 744: FILE *ficlog, *ficrespow; 745: int globpr=0; /* Global variable for printing or not */ 746: double fretone; /* Only one call to likelihood */ 747: long ipmx=0; /* Number of contributions */ 748: double sw; /* Sum of weights */ 749: char filerespow[FILENAMELENGTH]; 750: char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */ 751: FILE *ficresilk; 752: FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor; 753: FILE *ficresprobmorprev; 754: FILE *fichtm, *fichtmcov; /* Html File */ 755: FILE *ficreseij; 756: char filerese[FILENAMELENGTH]; 757: FILE *ficresstdeij; 758: char fileresstde[FILENAMELENGTH]; 759: FILE *ficrescveij; 760: char filerescve[FILENAMELENGTH]; 761: FILE *ficresvij; 762: char fileresv[FILENAMELENGTH]; 763: FILE *ficresvpl; 764: char fileresvpl[FILENAMELENGTH]; 765: char title[MAXLINE]; 766: char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH], filerespl[FILENAMELENGTH]; 767: char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH]; 768: char tmpout[FILENAMELENGTH], tmpout2[FILENAMELENGTH]; 769: char command[FILENAMELENGTH]; 770: int outcmd=0; 771: 772: char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH]; 773: 774: char filelog[FILENAMELENGTH]; /* Log file */ 775: char filerest[FILENAMELENGTH]; 776: char fileregp[FILENAMELENGTH]; 777: char popfile[FILENAMELENGTH]; 778: 779: char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ; 780: 781: /* struct timeval start_time, end_time, curr_time, last_time, forecast_time; */ 782: /* struct timezone tzp; */ 783: /* extern int gettimeofday(); */ 784: struct tm tml, *gmtime(), *localtime(); 785: 786: extern time_t time(); 787: 788: struct tm start_time, end_time, curr_time, last_time, forecast_time; 789: time_t rstart_time, rend_time, rcurr_time, rlast_time, rforecast_time; /* raw time */ 790: struct tm tm; 791: 792: char strcurr[80], strfor[80]; 793: 794: char *endptr; 795: long lval; 796: double dval; 797: 798: #define NR_END 1 799: #define FREE_ARG char* 800: #define FTOL 1.0e-10 801: 802: #define NRANSI 803: #define ITMAX 200 804: 805: #define TOL 2.0e-4 806: 807: #define CGOLD 0.3819660 808: #define ZEPS 1.0e-10 809: #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 810: 811: #define GOLD 1.618034 812: #define GLIMIT 100.0 813: #define TINY 1.0e-20 814: 815: static double maxarg1,maxarg2; 816: #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2)) 817: #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2)) 818: 819: #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a)) 820: #define rint(a) floor(a+0.5) 821: /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/myutils_8h-source.html */ 822: #define mytinydouble 1.0e-16 823: /* #define DEQUAL(a,b) (fabs((a)-(b))<mytinydouble) */ 824: /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/mynrutils_8h-source.html */ 825: /* static double dsqrarg; */ 826: /* #define DSQR(a) (DEQUAL((dsqrarg=(a)),0.0) ? 0.0 : dsqrarg*dsqrarg) */ 827: static double sqrarg; 828: #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg) 829: #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 830: int agegomp= AGEGOMP; 831: 832: int imx; 833: int stepm=1; 834: /* Stepm, step in month: minimum step interpolation*/ 835: 836: int estepm; 837: /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/ 838: 839: int m,nb; 840: long *num; 841: int firstpass=0, lastpass=4,*cod, *Tage,*cens; 842: int *ncodemax; /* ncodemax[j]= Number of modalities of the j th 843: covariate for which somebody answered excluding 844: undefined. Usually 2: 0 and 1. */ 845: int *ncodemaxwundef; /* ncodemax[j]= Number of modalities of the j th 846: covariate for which somebody answered including 847: undefined. Usually 3: -1, 0 and 1. */ 848: double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint; 849: double **pmmij, ***probs; 850: double *ageexmed,*agecens; 851: double dateintmean=0; 852: 853: double *weight; 854: int **s; /* Status */ 855: double *agedc; 856: double **covar; /**< covar[j,i], value of jth covariate for individual i, 857: * covar=matrix(0,NCOVMAX,1,n); 858: * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*age; */ 859: double idx; 860: int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */ 861: int *Ndum; /** Freq of modality (tricode */ 862: int **codtab; /**< codtab=imatrix(1,100,1,10); */ 863: int **Tvard, *Tprod, cptcovprod, *Tvaraff; 864: double *lsurv, *lpop, *tpop; 865: 866: double ftol=FTOL; /**< Tolerance for computing Max Likelihood */ 867: double ftolhess; /**< Tolerance for computing hessian */ 868: 869: /**************** split *************************/ 870: static int split( char *path, char *dirc, char *name, char *ext, char *finame ) 871: { 872: /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc) 873: the name of the file (name), its extension only (ext) and its first part of the name (finame) 874: */ 875: char *ss; /* pointer */ 876: int l1=0, l2=0; /* length counters */ 877: 878: l1 = strlen(path ); /* length of path */ 879: if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH ); 880: ss= strrchr( path, DIRSEPARATOR ); /* find last / */ 881: if ( ss == NULL ) { /* no directory, so determine current directory */ 882: strcpy( name, path ); /* we got the fullname name because no directory */ 883: /*if(strrchr(path, ODIRSEPARATOR )==NULL) 884: printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/ 885: /* get current working directory */ 886: /* extern char* getcwd ( char *buf , int len);*/ 887: #ifdef WIN32 888: if (_getcwd( dirc, FILENAME_MAX ) == NULL ) { 889: #else 890: if (getcwd(dirc, FILENAME_MAX) == NULL) { 891: #endif 892: return( GLOCK_ERROR_GETCWD ); 893: } 894: /* got dirc from getcwd*/ 895: printf(" DIRC = %s \n",dirc); 896: } else { /* strip direcotry from path */ 897: ss++; /* after this, the filename */ 898: l2 = strlen( ss ); /* length of filename */ 899: if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH ); 900: strcpy( name, ss ); /* save file name */ 901: strncpy( dirc, path, l1 - l2 ); /* now the directory */ 902: dirc[l1-l2] = '\0'; /* add zero */ 903: printf(" DIRC2 = %s \n",dirc); 904: } 905: /* We add a separator at the end of dirc if not exists */ 906: l1 = strlen( dirc ); /* length of directory */ 907: if( dirc[l1-1] != DIRSEPARATOR ){ 908: dirc[l1] = DIRSEPARATOR; 909: dirc[l1+1] = 0; 910: printf(" DIRC3 = %s \n",dirc); 911: } 912: ss = strrchr( name, '.' ); /* find last / */ 913: if (ss >0){ 914: ss++; 915: strcpy(ext,ss); /* save extension */ 916: l1= strlen( name); 917: l2= strlen(ss)+1; 918: strncpy( finame, name, l1-l2); 919: finame[l1-l2]= 0; 920: } 921: 922: return( 0 ); /* we're done */ 923: } 924: 925: 926: /******************************************/ 927: 928: void replace_back_to_slash(char *s, char*t) 929: { 930: int i; 931: int lg=0; 932: i=0; 933: lg=strlen(t); 934: for(i=0; i<= lg; i++) { 935: (s[i] = t[i]); 936: if (t[i]== '\\') s[i]='/'; 937: } 938: } 939: 940: char *trimbb(char *out, char *in) 941: { /* Trim multiple blanks in line but keeps first blanks if line starts with blanks */ 942: char *s; 943: s=out; 944: while (*in != '\0'){ 945: while( *in == ' ' && *(in+1) == ' '){ /* && *(in+1) != '\0'){*/ 946: in++; 947: } 948: *out++ = *in++; 949: } 950: *out='\0'; 951: return s; 952: } 953: 954: /* char *substrchaine(char *out, char *in, char *chain) */ 955: /* { */ 956: /* /\* Substract chain 'chain' from 'in', return and output 'out' *\/ */ 957: /* char *s, *t; */ 958: /* t=in;s=out; */ 959: /* while ((*in != *chain) && (*in != '\0')){ */ 960: /* *out++ = *in++; */ 961: /* } */ 962: 963: /* /\* *in matches *chain *\/ */ 964: /* while ((*in++ == *chain++) && (*in != '\0')){ */ 965: /* printf("*in = %c, *out= %c *chain= %c \n", *in, *out, *chain); */ 966: /* } */ 967: /* in--; chain--; */ 968: /* while ( (*in != '\0')){ */ 969: /* printf("Bef *in = %c, *out= %c *chain= %c \n", *in, *out, *chain); */ 970: /* *out++ = *in++; */ 971: /* printf("Aft *in = %c, *out= %c *chain= %c \n", *in, *out, *chain); */ 972: /* } */ 973: /* *out='\0'; */ 974: /* out=s; */ 975: /* return out; */ 976: /* } */ 977: char *substrchaine(char *out, char *in, char *chain) 978: { 979: /* Substract chain 'chain' from 'in', return and output 'out' */ 980: /* in="V1+V1*age+age*age+V2", chain="age*age" */ 981: 982: char *strloc; 983: 984: strcpy (out, in); 985: strloc = strstr(out, chain); /* strloc points to out at age*age+V2 */ 986: printf("Bef strloc=%s chain=%s out=%s \n", strloc, chain, out); 987: if(strloc != NULL){ 988: /* will affect out */ /* strloc+strlenc(chain)=+V2 */ /* Will also work in Unicode */ 989: memmove(strloc,strloc+strlen(chain), strlen(strloc+strlen(chain))+1); 990: /* strcpy (strloc, strloc +strlen(chain));*/ 991: } 992: printf("Aft strloc=%s chain=%s in=%s out=%s \n", strloc, chain, in, out); 993: return out; 994: } 995: 996: 997: char *cutl(char *blocc, char *alocc, char *in, char occ) 998: { 999: /* cuts string in into blocc and alocc where blocc ends before FIRST occurence of char 'occ' 1000: and alocc starts after first occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2') 1001: gives blocc="abcdef" and alocc="ghi2j". 1002: If occ is not found blocc is null and alocc is equal to in. Returns blocc 1003: */ 1004: char *s, *t; 1005: t=in;s=in; 1006: while ((*in != occ) && (*in != '\0')){ 1007: *alocc++ = *in++; 1008: } 1009: if( *in == occ){ 1010: *(alocc)='\0'; 1011: s=++in; 1012: } 1013: 1014: if (s == t) {/* occ not found */ 1015: *(alocc-(in-s))='\0'; 1016: in=s; 1017: } 1018: while ( *in != '\0'){ 1019: *blocc++ = *in++; 1020: } 1021: 1022: *blocc='\0'; 1023: return t; 1024: } 1025: char *cutv(char *blocc, char *alocc, char *in, char occ) 1026: { 1027: /* cuts string in into blocc and alocc where blocc ends before LAST occurence of char 'occ' 1028: and alocc starts after last occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2') 1029: gives blocc="abcdef2ghi" and alocc="j". 1030: If occ is not found blocc is null and alocc is equal to in. Returns alocc 1031: */ 1032: char *s, *t; 1033: t=in;s=in; 1034: while (*in != '\0'){ 1035: while( *in == occ){ 1036: *blocc++ = *in++; 1037: s=in; 1038: } 1039: *blocc++ = *in++; 1040: } 1041: if (s == t) /* occ not found */ 1042: *(blocc-(in-s))='\0'; 1043: else 1044: *(blocc-(in-s)-1)='\0'; 1045: in=s; 1046: while ( *in != '\0'){ 1047: *alocc++ = *in++; 1048: } 1049: 1050: *alocc='\0'; 1051: return s; 1052: } 1053: 1054: int nbocc(char *s, char occ) 1055: { 1056: int i,j=0; 1057: int lg=20; 1058: i=0; 1059: lg=strlen(s); 1060: for(i=0; i<= lg; i++) { 1061: if (s[i] == occ ) j++; 1062: } 1063: return j; 1064: } 1065: 1066: /* void cutv(char *u,char *v, char*t, char occ) */ 1067: /* { */ 1068: /* /\* cuts string t into u and v where u ends before last occurence of char 'occ' */ 1069: /* and v starts after last occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2') */ 1070: /* gives u="abcdef2ghi" and v="j" *\/ */ 1071: /* int i,lg,j,p=0; */ 1072: /* i=0; */ 1073: /* lg=strlen(t); */ 1074: /* for(j=0; j<=lg-1; j++) { */ 1075: /* if((t[j]!= occ) && (t[j+1]== occ)) p=j+1; */ 1076: /* } */ 1077: 1078: /* for(j=0; j<p; j++) { */ 1079: /* (u[j] = t[j]); */ 1080: /* } */ 1081: /* u[p]='\0'; */ 1082: 1083: /* for(j=0; j<= lg; j++) { */ 1084: /* if (j>=(p+1))(v[j-p-1] = t[j]); */ 1085: /* } */ 1086: /* } */ 1087: 1088: #ifdef _WIN32 1089: char * strsep(char **pp, const char *delim) 1090: { 1091: char *p, *q; 1092: 1093: if ((p = *pp) == NULL) 1094: return 0; 1095: if ((q = strpbrk (p, delim)) != NULL) 1096: { 1097: *pp = q + 1; 1098: *q = '\0'; 1099: } 1100: else 1101: *pp = 0; 1102: return p; 1103: } 1104: #endif 1105: 1106: /********************** nrerror ********************/ 1107: 1108: void nrerror(char error_text[]) 1109: { 1110: fprintf(stderr,"ERREUR ...\n"); 1111: fprintf(stderr,"%s\n",error_text); 1112: exit(EXIT_FAILURE); 1113: } 1114: /*********************** vector *******************/ 1115: double *vector(int nl, int nh) 1116: { 1117: double *v; 1118: v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double))); 1119: if (!v) nrerror("allocation failure in vector"); 1120: return v-nl+NR_END; 1121: } 1122: 1123: /************************ free vector ******************/ 1124: void free_vector(double*v, int nl, int nh) 1125: { 1126: free((FREE_ARG)(v+nl-NR_END)); 1127: } 1128: 1129: /************************ivector *******************************/ 1130: int *ivector(long nl,long nh) 1131: { 1132: int *v; 1133: v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int))); 1134: if (!v) nrerror("allocation failure in ivector"); 1135: return v-nl+NR_END; 1136: } 1137: 1138: /******************free ivector **************************/ 1139: void free_ivector(int *v, long nl, long nh) 1140: { 1141: free((FREE_ARG)(v+nl-NR_END)); 1142: } 1143: 1144: /************************lvector *******************************/ 1145: long *lvector(long nl,long nh) 1146: { 1147: long *v; 1148: v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long))); 1149: if (!v) nrerror("allocation failure in ivector"); 1150: return v-nl+NR_END; 1151: } 1152: 1153: /******************free lvector **************************/ 1154: void free_lvector(long *v, long nl, long nh) 1155: { 1156: free((FREE_ARG)(v+nl-NR_END)); 1157: } 1158: 1159: /******************* imatrix *******************************/ 1160: int **imatrix(long nrl, long nrh, long ncl, long nch) 1161: /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 1162: { 1163: long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 1164: int **m; 1165: 1166: /* allocate pointers to rows */ 1167: m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 1168: if (!m) nrerror("allocation failure 1 in matrix()"); 1169: m += NR_END; 1170: m -= nrl; 1171: 1172: 1173: /* allocate rows and set pointers to them */ 1174: m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 1175: if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 1176: m[nrl] += NR_END; 1177: m[nrl] -= ncl; 1178: 1179: for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 1180: 1181: /* return pointer to array of pointers to rows */ 1182: return m; 1183: } 1184: 1185: /****************** free_imatrix *************************/ 1186: void free_imatrix(m,nrl,nrh,ncl,nch) 1187: int **m; 1188: long nch,ncl,nrh,nrl; 1189: /* free an int matrix allocated by imatrix() */ 1190: { 1191: free((FREE_ARG) (m[nrl]+ncl-NR_END)); 1192: free((FREE_ARG) (m+nrl-NR_END)); 1193: } 1194: 1195: /******************* matrix *******************************/ 1196: double **matrix(long nrl, long nrh, long ncl, long nch) 1197: { 1198: long i, nrow=nrh-nrl+1, ncol=nch-ncl+1; 1199: double **m; 1200: 1201: m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*))); 1202: if (!m) nrerror("allocation failure 1 in matrix()"); 1203: m += NR_END; 1204: m -= nrl; 1205: 1206: m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double))); 1207: if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 1208: m[nrl] += NR_END; 1209: m[nrl] -= ncl; 1210: 1211: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol; 1212: return m; 1213: /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) or &(m[1][0]) 1214: m[i] = address of ith row of the table. &(m[i]) is its value which is another adress 1215: that of m[i][0]. In order to get the value p m[i][0] but it is unitialized. 1216: */ 1217: } 1218: 1219: /*************************free matrix ************************/ 1220: void free_matrix(double **m, long nrl, long nrh, long ncl, long nch) 1221: { 1222: free((FREE_ARG)(m[nrl]+ncl-NR_END)); 1223: free((FREE_ARG)(m+nrl-NR_END)); 1224: } 1225: 1226: /******************* ma3x *******************************/ 1227: double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh) 1228: { 1229: long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1; 1230: double ***m; 1231: 1232: m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*))); 1233: if (!m) nrerror("allocation failure 1 in matrix()"); 1234: m += NR_END; 1235: m -= nrl; 1236: 1237: m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double))); 1238: if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 1239: m[nrl] += NR_END; 1240: m[nrl] -= ncl; 1241: 1242: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol; 1243: 1244: m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double))); 1245: if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()"); 1246: m[nrl][ncl] += NR_END; 1247: m[nrl][ncl] -= nll; 1248: for (j=ncl+1; j<=nch; j++) 1249: m[nrl][j]=m[nrl][j-1]+nlay; 1250: 1251: for (i=nrl+1; i<=nrh; i++) { 1252: m[i][ncl]=m[i-1l][ncl]+ncol*nlay; 1253: for (j=ncl+1; j<=nch; j++) 1254: m[i][j]=m[i][j-1]+nlay; 1255: } 1256: return m; 1257: /* gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1]) 1258: &(m[i][j][k]) <=> *((*(m+i) + j)+k) 1259: */ 1260: } 1261: 1262: /*************************free ma3x ************************/ 1263: void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh) 1264: { 1265: free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END)); 1266: free((FREE_ARG)(m[nrl]+ncl-NR_END)); 1267: free((FREE_ARG)(m+nrl-NR_END)); 1268: } 1269: 1270: /*************** function subdirf ***********/ 1271: char *subdirf(char fileres[]) 1272: { 1273: /* Caution optionfilefiname is hidden */ 1274: strcpy(tmpout,optionfilefiname); 1275: strcat(tmpout,"/"); /* Add to the right */ 1276: strcat(tmpout,fileres); 1277: return tmpout; 1278: } 1279: 1280: /*************** function subdirf2 ***********/ 1281: char *subdirf2(char fileres[], char *preop) 1282: { 1283: 1284: /* Caution optionfilefiname is hidden */ 1285: strcpy(tmpout,optionfilefiname); 1286: strcat(tmpout,"/"); 1287: strcat(tmpout,preop); 1288: strcat(tmpout,fileres); 1289: return tmpout; 1290: } 1291: 1292: /*************** function subdirf3 ***********/ 1293: char *subdirf3(char fileres[], char *preop, char *preop2) 1294: { 1295: 1296: /* Caution optionfilefiname is hidden */ 1297: strcpy(tmpout,optionfilefiname); 1298: strcat(tmpout,"/"); 1299: strcat(tmpout,preop); 1300: strcat(tmpout,preop2); 1301: strcat(tmpout,fileres); 1302: return tmpout; 1303: } 1304: 1305: char *asc_diff_time(long time_sec, char ascdiff[]) 1306: { 1307: long sec_left, days, hours, minutes; 1308: days = (time_sec) / (60*60*24); 1309: sec_left = (time_sec) % (60*60*24); 1310: hours = (sec_left) / (60*60) ; 1311: sec_left = (sec_left) %(60*60); 1312: minutes = (sec_left) /60; 1313: sec_left = (sec_left) % (60); 1314: sprintf(ascdiff,"%ld day(s) %ld hour(s) %ld minute(s) %ld second(s)",days, hours, minutes, sec_left); 1315: return ascdiff; 1316: } 1317: 1318: /***************** f1dim *************************/ 1319: extern int ncom; 1320: extern double *pcom,*xicom; 1321: extern double (*nrfunc)(double []); 1322: 1323: double f1dim(double x) 1324: { 1325: int j; 1326: double f; 1327: double *xt; 1328: 1329: xt=vector(1,ncom); 1330: for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 1331: f=(*nrfunc)(xt); 1332: free_vector(xt,1,ncom); 1333: return f; 1334: } 1335: 1336: /*****************brent *************************/ 1337: double brent(double ax, double bx, double cx, double (*f)(double), double tol, double *xmin) 1338: { 1339: /* Given a function f, and given a bracketing triplet of abscissas ax, bx, cx (such that bx is 1340: * between ax and cx, and f(bx) is less than both f(ax) and f(cx) ), this routine isolates 1341: * the minimum to a fractional precision of about tol using Brent’s method. The abscissa of 1342: * the minimum is returned as xmin, and the minimum function value is returned as brent , the 1343: * returned function value. 1344: */ 1345: int iter; 1346: double a,b,d,etemp; 1347: double fu=0,fv,fw,fx; 1348: double ftemp=0.; 1349: double p,q,r,tol1,tol2,u,v,w,x,xm; 1350: double e=0.0; 1351: 1352: a=(ax < cx ? ax : cx); 1353: b=(ax > cx ? ax : cx); 1354: x=w=v=bx; 1355: fw=fv=fx=(*f)(x); 1356: for (iter=1;iter<=ITMAX;iter++) { 1357: xm=0.5*(a+b); 1358: tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 1359: /* if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/ 1360: printf(".");fflush(stdout); 1361: fprintf(ficlog,".");fflush(ficlog); 1362: #ifdef DEBUGBRENT 1363: 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); 1364: 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); 1365: /* if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */ 1366: #endif 1367: if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 1368: *xmin=x; 1369: return fx; 1370: } 1371: ftemp=fu; 1372: if (fabs(e) > tol1) { 1373: r=(x-w)*(fx-fv); 1374: q=(x-v)*(fx-fw); 1375: p=(x-v)*q-(x-w)*r; 1376: q=2.0*(q-r); 1377: if (q > 0.0) p = -p; 1378: q=fabs(q); 1379: etemp=e; 1380: e=d; 1381: if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 1382: d=CGOLD*(e=(x >= xm ? a-x : b-x)); 1383: else { 1384: d=p/q; 1385: u=x+d; 1386: if (u-a < tol2 || b-u < tol2) 1387: d=SIGN(tol1,xm-x); 1388: } 1389: } else { 1390: d=CGOLD*(e=(x >= xm ? a-x : b-x)); 1391: } 1392: u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 1393: fu=(*f)(u); 1394: if (fu <= fx) { 1395: if (u >= x) a=x; else b=x; 1396: SHFT(v,w,x,u) 1397: SHFT(fv,fw,fx,fu) 1398: } else { 1399: if (u < x) a=u; else b=u; 1400: if (fu <= fw || w == x) { 1401: v=w; 1402: w=u; 1403: fv=fw; 1404: fw=fu; 1405: } else if (fu <= fv || v == x || v == w) { 1406: v=u; 1407: fv=fu; 1408: } 1409: } 1410: } 1411: nrerror("Too many iterations in brent"); 1412: *xmin=x; 1413: return fx; 1414: } 1415: 1416: /****************** mnbrak ***********************/ 1417: 1418: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 1419: double (*func)(double)) 1420: { /* Given a function func , and given distinct initial points ax and bx , this routine searches in 1421: the downhill direction (defined by the function as evaluated at the initial points) and returns 1422: new points ax , bx , cx that bracket a minimum of the function. Also returned are the function 1423: values at the three points, fa, fb , and fc such that fa > fb and fb < fc. 1424: */ 1425: double ulim,u,r,q, dum; 1426: double fu; 1427: 1428: double scale=10.; 1429: int iterscale=0; 1430: 1431: *fa=(*func)(*ax); /* xta[j]=pcom[j]+(*ax)*xicom[j]; fa=f(xta[j])*/ 1432: *fb=(*func)(*bx); /* xtb[j]=pcom[j]+(*bx)*xicom[j]; fb=f(xtb[j]) */ 1433: 1434: 1435: /* while(*fb != *fb){ /\* *ax should be ok, reducing distance to *ax *\/ */ 1436: /* printf("Warning mnbrak *fb = %lf, *bx=%lf *ax=%lf *fa==%lf iter=%d\n",*fb, *bx, *ax, *fa, iterscale++); */ 1437: /* *bx = *ax - (*ax - *bx)/scale; */ 1438: /* *fb=(*func)(*bx); /\* xtb[j]=pcom[j]+(*bx)*xicom[j]; fb=f(xtb[j]) *\/ */ 1439: /* } */ 1440: 1441: if (*fb > *fa) { 1442: SHFT(dum,*ax,*bx,dum) 1443: SHFT(dum,*fb,*fa,dum) 1444: } 1445: *cx=(*bx)+GOLD*(*bx-*ax); 1446: *fc=(*func)(*cx); 1447: #ifdef DEBUG 1448: printf("mnbrak0 *fb=%.12e *fc=%.12e\n",*fb,*fc); 1449: fprintf(ficlog,"mnbrak0 *fb=%.12e *fc=%.12e\n",*fb,*fc); 1450: #endif 1451: while (*fb > *fc) { /* Declining a,b,c with fa> fb > fc */ 1452: r=(*bx-*ax)*(*fb-*fc); 1453: q=(*bx-*cx)*(*fb-*fa); 1454: u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 1455: (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); /* Minimum abscissa of a parabolic estimated from (a,fa), (b,fb) and (c,fc). */ 1456: ulim=(*bx)+GLIMIT*(*cx-*bx); /* Maximum abscissa where function should be evaluated */ 1457: if ((*bx-u)*(u-*cx) > 0.0) { /* if u_p is between b and c */ 1458: fu=(*func)(u); 1459: #ifdef DEBUG 1460: /* f(x)=A(x-u)**2+f(u) */ 1461: double A, fparabu; 1462: A= (*fb - *fa)/(*bx-*ax)/(*bx+*ax-2*u); 1463: fparabu= *fa - A*(*ax-u)*(*ax-u); 1464: printf("mnbrak (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf), (*u=%.12f, fu=%.12lf, fparabu=%.12f)\n",*ax,*fa,*bx,*fb,*cx,*fc,u,fu, fparabu); 1465: fprintf(ficlog, "mnbrak (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf), (*u=%.12f, fu=%.12lf, fparabu=%.12f)\n",*ax,*fa,*bx,*fb,*cx,*fc,u,fu, fparabu); 1466: /* And thus,it can be that fu > *fc even if fparabu < *fc */ 1467: /* mnbrak (*ax=7.666299858533, *fa=299039.693133272231), (*bx=8.595447774979, *fb=298976.598289369489), 1468: (*cx=10.098840694817, *fc=298946.631474258087), (*u=9.852501168332, fu=298948.773013752128, fparabu=298945.434711494134) */ 1469: /* In that case, there is no bracket in the output! Routine is wrong with many consequences.*/ 1470: #endif 1471: #ifdef MNBRAKORIGINAL 1472: #else 1473: /* if (fu > *fc) { */ 1474: /* #ifdef DEBUG */ 1475: /* printf("mnbrak4 fu > fc \n"); */ 1476: /* fprintf(ficlog, "mnbrak4 fu > fc\n"); */ 1477: /* #endif */ 1478: /* /\* SHFT(u,*cx,*cx,u) /\\* ie a=c, c=u and u=c; in that case, next SHFT(a,b,c,u) will give a=b=b, b=c=u, c=u=c and *\\/ *\/ */ 1479: /* /\* SHFT(*fa,*fc,fu,*fc) /\\* (b, u, c) is a bracket while test fb > fc will be fu > fc will exit *\\/ *\/ */ 1480: /* dum=u; /\* Shifting c and u *\/ */ 1481: /* u = *cx; */ 1482: /* *cx = dum; */ 1483: /* dum = fu; */ 1484: /* fu = *fc; */ 1485: /* *fc =dum; */ 1486: /* } else { /\* end *\/ */ 1487: /* #ifdef DEBUG */ 1488: /* printf("mnbrak3 fu < fc \n"); */ 1489: /* fprintf(ficlog, "mnbrak3 fu < fc\n"); */ 1490: /* #endif */ 1491: /* dum=u; /\* Shifting c and u *\/ */ 1492: /* u = *cx; */ 1493: /* *cx = dum; */ 1494: /* dum = fu; */ 1495: /* fu = *fc; */ 1496: /* *fc =dum; */ 1497: /* } */ 1498: #ifdef DEBUG 1499: printf("mnbrak34 fu < or >= fc \n"); 1500: fprintf(ficlog, "mnbrak34 fu < fc\n"); 1501: #endif 1502: dum=u; /* Shifting c and u */ 1503: u = *cx; 1504: *cx = dum; 1505: dum = fu; 1506: fu = *fc; 1507: *fc =dum; 1508: #endif 1509: } else if ((*cx-u)*(u-ulim) > 0.0) { /* u is after c but before ulim */ 1510: #ifdef DEBUG 1511: printf("mnbrak2 u after c but before ulim\n"); 1512: fprintf(ficlog, "mnbrak2 u after c but before ulim\n"); 1513: #endif 1514: fu=(*func)(u); 1515: if (fu < *fc) { 1516: #ifdef DEBUG 1517: printf("mnbrak2 u after c but before ulim AND fu < fc\n"); 1518: fprintf(ficlog, "mnbrak2 u after c but before ulim AND fu <fc \n"); 1519: #endif 1520: SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 1521: SHFT(*fb,*fc,fu,(*func)(u)) 1522: } 1523: } else if ((u-ulim)*(ulim-*cx) >= 0.0) { /* u outside ulim (verifying that ulim is beyond c) */ 1524: #ifdef DEBUG 1525: printf("mnbrak2 u outside ulim (verifying that ulim is beyond c)\n"); 1526: fprintf(ficlog, "mnbrak2 u outside ulim (verifying that ulim is beyond c)\n"); 1527: #endif 1528: u=ulim; 1529: fu=(*func)(u); 1530: } else { /* u could be left to b (if r > q parabola has a maximum) */ 1531: #ifdef DEBUG 1532: printf("mnbrak2 u could be left to b (if r > q parabola has a maximum)\n"); 1533: fprintf(ficlog, "mnbrak2 u could be left to b (if r > q parabola has a maximum)\n"); 1534: #endif 1535: u=(*cx)+GOLD*(*cx-*bx); 1536: fu=(*func)(u); 1537: } /* end tests */ 1538: SHFT(*ax,*bx,*cx,u) 1539: SHFT(*fa,*fb,*fc,fu) 1540: #ifdef DEBUG 1541: printf("mnbrak2 (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf), (*u=%.12f, fu=%.12lf)\n",*ax,*fa,*bx,*fb,*cx,*fc,u,fu); 1542: fprintf(ficlog, "mnbrak2 (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf), (*u=%.12f, fu=%.12lf)\n",*ax,*fa,*bx,*fb,*cx,*fc,u,fu); 1543: #endif 1544: } /* end while; ie return (a, b, c, fa, fb, fc) such that a f(b) and fb < f(c) */ 1545: } 1546: 1547: /*************** linmin ************************/ 1548: /* Given an n -dimensional point p[1..n] and an n -dimensional direction xi[1..n] , moves and 1549: resets p to where the function func(p) takes on a minimum along the direction xi from p , 1550: and replaces xi by the actual vector displacement that p was moved. Also returns as fret 1551: the value of func at the returned location p . This is actually all accomplished by calling the 1552: routines mnbrak and brent .*/ 1553: int ncom; 1554: double *pcom,*xicom; 1555: double (*nrfunc)(double []); 1556: 1557: void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 1558: { 1559: double brent(double ax, double bx, double cx, 1560: double (*f)(double), double tol, double *xmin); 1561: double f1dim(double x); 1562: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 1563: double *fc, double (*func)(double)); 1564: int j; 1565: double xx,xmin,bx,ax; 1566: double fx,fb,fa; 1567: 1568: double scale=10., axs, xxs, xxss; /* Scale added for infinity */ 1569: 1570: ncom=n; 1571: pcom=vector(1,n); 1572: xicom=vector(1,n); 1573: nrfunc=func; 1574: for (j=1;j<=n;j++) { 1575: pcom[j]=p[j]; 1576: xicom[j]=xi[j]; 1577: } 1578: 1579: /* axs=0.0; */ 1580: /* xxss=1; /\* 1 and using scale *\/ */ 1581: xxs=1; 1582: /* do{ */ 1583: ax=0.; 1584: xx= xxs; 1585: mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); /* Outputs: xtx[j]=pcom[j]+(*xx)*xicom[j]; fx=f(xtx[j]) */ 1586: /* brackets with inputs ax=0 and xx=1, but points, pcom=p, and directions values, xicom=xi, are sent via f1dim(x) */ 1587: /* xt[x,j]=pcom[j]+x*xicom[j] f(ax) = f(xt(a,j=1,n)) = f(p(j) + 0 * xi(j)) and f(xx) = f(xt(x, j=1,n)) = f(p(j) + 1 * xi(j)) */ 1588: /* Outputs: fa=f(p(j)) and fx=f(p(j) + xxs * xi(j) ) and f(bx)= f(p(j)+ bx* xi(j)) */ 1589: /* Given input ax=axs and xx=xxs, xx might be too far from ax to get a finite f(xx) */ 1590: /* Searches on line, outputs (ax, xx, bx) such that fx < min(fa and fb) */ 1591: /* Find a bracket a,x,b in direction n=xi ie xicom, order may change. Scale is [0:xxs*xi[j]] et non plus [0:xi[j]]*/ 1592: /* if (fx != fx){ */ 1593: /* xxs=xxs/scale; /\* Trying a smaller xx, closer to initial ax=0 *\/ */ 1594: /* printf("\nLinmin NAN : input [axs=%lf:xxs=%lf], mnbrak outputs fx=%lf <(fb=%lf and fa=%lf) with xx=%lf in [ax=%lf:bx=%lf] \n", axs, xxs, fx,fb, fa, xx, ax, bx); */ 1595: /* } */ 1596: /* }while(fx != fx); */ 1597: 1598: #ifdef DEBUGLINMIN 1599: printf("\nLinmin after mnbrak: ax=%12.7f xx=%12.7f bx=%12.7f fa=%12.2f fx=%12.2f fb=%12.2f\n", ax,xx,bx,fa,fx,fb); 1600: #endif 1601: *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); /* Giving a bracketting triplet (ax, xx, bx), find a minimum, xmin, according to f1dim, *fret(xmin),*/ 1602: /* fa = f(p[j] + ax * xi[j]), fx = f(p[j] + xx * xi[j]), fb = f(p[j] + bx * xi[j]) */ 1603: /* fmin = f(p[j] + xmin * xi[j]) */ 1604: /* P+lambda n in that direction (lambdamin), with TOL between abscisses */ 1605: /* f1dim(xmin): for (j=1;j<=ncom;j++) xt[j]=pcom[j]+xmin*xicom[j]; */ 1606: #ifdef DEBUG 1607: printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin); 1608: fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin); 1609: #endif 1610: #ifdef DEBUGLINMIN 1611: printf("linmin end "); 1612: #endif 1613: for (j=1;j<=n;j++) { 1614: /* printf(" before xi[%d]=%12.8f", j,xi[j]); */ 1615: xi[j] *= xmin; /* xi rescaled by xmin: if xmin=-1.237 and xi=(1,0,...,0) xi=(-1.237,0,...,0) */ 1616: /* if(xxs <1.0) */ 1617: /* printf(" after xi[%d]=%12.8f, xmin=%12.8f, ax=%12.8f, xx=%12.8f, bx=%12.8f, xxs=%12.8f", j,xi[j], xmin, ax, xx, bx,xxs ); */ 1618: p[j] += xi[j]; /* Parameters values are updated accordingly */ 1619: } 1620: /* printf("\n"); */ 1621: #ifdef DEBUGLINMIN 1622: printf("Comparing last *frec(xmin=%12.8f)=%12.8f from Brent and frec(0.)=%12.8f \n", xmin, *fret, (*func)(p)); 1623: for (j=1;j<=n;j++) { 1624: printf(" xi[%d]= %12.7f p[%d]= %12.7f",j,xi[j],j,p[j]); 1625: if(j % ncovmodel == 0) 1626: printf("\n"); 1627: } 1628: #endif 1629: free_vector(xicom,1,n); 1630: free_vector(pcom,1,n); 1631: } 1632: 1633: 1634: /*************** powell ************************/ 1635: /* 1636: Minimization of a function func of n variables. Input consists of an initial starting point 1637: p[1..n] ; an initial matrix xi[1..n][1..n] , whose columns contain the initial set of di- 1638: rections (usually the n unit vectors); and ftol , the fractional tolerance in the function value 1639: such that failure to decrease by more than this amount on one iteration signals doneness. On 1640: output, p is set to the best point found, xi is the then-current direction set, fret is the returned 1641: function value at p , and iter is the number of iterations taken. The routine linmin is used. 1642: */ 1643: void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 1644: double (*func)(double [])) 1645: { 1646: void linmin(double p[], double xi[], int n, double *fret, 1647: double (*func)(double [])); 1648: int i,ibig,j; 1649: double del,t,*pt,*ptt,*xit; 1650: double directest; 1651: double fp,fptt; 1652: double *xits; 1653: int niterf, itmp; 1654: 1655: pt=vector(1,n); 1656: ptt=vector(1,n); 1657: xit=vector(1,n); 1658: xits=vector(1,n); 1659: *fret=(*func)(p); 1660: for (j=1;j<=n;j++) pt[j]=p[j]; 1661: rcurr_time = time(NULL); 1662: for (*iter=1;;++(*iter)) { 1663: fp=(*fret); /* From former iteration or initial value */ 1664: ibig=0; 1665: del=0.0; 1666: rlast_time=rcurr_time; 1667: /* (void) gettimeofday(&curr_time,&tzp); */ 1668: rcurr_time = time(NULL); 1669: curr_time = *localtime(&rcurr_time); 1670: printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, rcurr_time-rlast_time, rcurr_time-rstart_time);fflush(stdout); 1671: fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret,rcurr_time-rlast_time, rcurr_time-rstart_time); fflush(ficlog); 1672: /* fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tm_sec-start_time.tm_sec); */ 1673: for (i=1;i<=n;i++) { 1674: printf(" %d %.12f",i, p[i]); 1675: fprintf(ficlog," %d %.12lf",i, p[i]); 1676: fprintf(ficrespow," %.12lf", p[i]); 1677: } 1678: printf("\n"); 1679: fprintf(ficlog,"\n"); 1680: fprintf(ficrespow,"\n");fflush(ficrespow); 1681: if(*iter <=3){ 1682: tml = *localtime(&rcurr_time); 1683: strcpy(strcurr,asctime(&tml)); 1684: rforecast_time=rcurr_time; 1685: itmp = strlen(strcurr); 1686: if(strcurr[itmp-1]=='\n') /* Windows outputs with a new line */ 1687: strcurr[itmp-1]='\0'; 1688: printf("\nConsidering the time needed for the last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time); 1689: fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time); 1690: for(niterf=10;niterf<=30;niterf+=10){ 1691: rforecast_time=rcurr_time+(niterf-*iter)*(rcurr_time-rlast_time); 1692: forecast_time = *localtime(&rforecast_time); 1693: strcpy(strfor,asctime(&forecast_time)); 1694: itmp = strlen(strfor); 1695: if(strfor[itmp-1]=='\n') 1696: strfor[itmp-1]='\0'; 1697: 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); 1698: 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); 1699: } 1700: } 1701: for (i=1;i<=n;i++) { /* For each direction i */ 1702: for (j=1;j<=n;j++) xit[j]=xi[j][i]; /* Directions stored from previous iteration with previous scales */ 1703: fptt=(*fret); 1704: #ifdef DEBUG 1705: printf("fret=%lf, %lf, %lf \n", *fret, *fret, *fret); 1706: fprintf(ficlog, "fret=%lf, %lf, %lf \n", *fret, *fret, *fret); 1707: #endif 1708: printf("%d",i);fflush(stdout); /* print direction (parameter) i */ 1709: fprintf(ficlog,"%d",i);fflush(ficlog); 1710: linmin(p,xit,n,fret,func); /* Point p[n]. xit[n] has been loaded for direction i as input.*/ 1711: /* Outputs are fret(new point p) p is updated and xit rescaled */ 1712: if (fabs(fptt-(*fret)) > del) { /* We are keeping the max gain on each of the n directions */ 1713: /* because that direction will be replaced unless the gain del is small */ 1714: /* in comparison with the 'probable' gain, mu^2, with the last average direction. */ 1715: /* Unless the n directions are conjugate some gain in the determinant may be obtained */ 1716: /* with the new direction. */ 1717: del=fabs(fptt-(*fret)); 1718: ibig=i; 1719: } 1720: #ifdef DEBUG 1721: printf("%d %.12e",i,(*fret)); 1722: fprintf(ficlog,"%d %.12e",i,(*fret)); 1723: for (j=1;j<=n;j++) { 1724: xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5); 1725: printf(" x(%d)=%.12e",j,xit[j]); 1726: fprintf(ficlog," x(%d)=%.12e",j,xit[j]); 1727: } 1728: for(j=1;j<=n;j++) { 1729: printf(" p(%d)=%.12e",j,p[j]); 1730: fprintf(ficlog," p(%d)=%.12e",j,p[j]); 1731: } 1732: printf("\n"); 1733: fprintf(ficlog,"\n"); 1734: #endif 1735: } /* end loop on each direction i */ 1736: /* Convergence test will use last linmin estimation (fret) and compare former iteration (fp) */ 1737: /* But p and xit have been updated at the end of linmin, *fret corresponds to new p, xit */ 1738: /* New value of last point Pn is not computed, P(n-1) */ 1739: if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) { /* Did we reach enough precision? */ 1740: /* We could compare with a chi^2. chisquare(0.95,ddl=1)=3.84 */ 1741: /* By adding age*age in a model, the new -2LL should be lower and the difference follows a */ 1742: /* a chisquare statistics with 1 degree. To be significant at the 95% level, it should have */ 1743: /* decreased of more than 3.84 */ 1744: /* By adding age*age and V1*age the gain (-2LL) should be more than 5.99 (ddl=2) */ 1745: /* By using V1+V2+V3, the gain should be 7.82, compared with basic 1+age. */ 1746: /* By adding 10 parameters more the gain should be 18.31 */ 1747: 1748: /* Starting the program with initial values given by a former maximization will simply change */ 1749: /* the scales of the directions and the directions, because the are reset to canonical directions */ 1750: /* Thus the first calls to linmin will give new points and better maximizations until fp-(*fret) is */ 1751: /* under the tolerance value. If the tolerance is very small 1.e-9, it could last long. */ 1752: #ifdef DEBUG 1753: int k[2],l; 1754: k[0]=1; 1755: k[1]=-1; 1756: printf("Max: %.12e",(*func)(p)); 1757: fprintf(ficlog,"Max: %.12e",(*func)(p)); 1758: for (j=1;j<=n;j++) { 1759: printf(" %.12e",p[j]); 1760: fprintf(ficlog," %.12e",p[j]); 1761: } 1762: printf("\n"); 1763: fprintf(ficlog,"\n"); 1764: for(l=0;l<=1;l++) { 1765: for (j=1;j<=n;j++) { 1766: ptt[j]=p[j]+(p[j]-pt[j])*k[l]; 1767: printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]); 1768: fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]); 1769: } 1770: printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p))); 1771: fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p))); 1772: } 1773: #endif 1774: 1775: 1776: free_vector(xit,1,n); 1777: free_vector(xits,1,n); 1778: free_vector(ptt,1,n); 1779: free_vector(pt,1,n); 1780: return; 1781: } /* enough precision */ 1782: if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 1783: for (j=1;j<=n;j++) { /* Computes the extrapolated point P_0 + 2 (P_n-P_0) */ 1784: ptt[j]=2.0*p[j]-pt[j]; 1785: xit[j]=p[j]-pt[j]; 1786: pt[j]=p[j]; 1787: } 1788: fptt=(*func)(ptt); /* f_3 */ 1789: #ifdef POWELLF1F3 1790: #else 1791: if (fptt < fp) { /* If extrapolated point is better, decide if we keep that new direction or not */ 1792: #endif 1793: /* (x1 f1=fp), (x2 f2=*fret), (x3 f3=fptt), (xm fm) */ 1794: /* From x1 (P0) distance of x2 is at h and x3 is 2h */ 1795: /* Let f"(x2) be the 2nd derivative equal everywhere. */ 1796: /* Then the parabolic through (x1,f1), (x2,f2) and (x3,f3) */ 1797: /* will reach at f3 = fm + h^2/2 f"m ; f" = (f1 -2f2 +f3 ) / h**2 */ 1798: /* Conditional for using this new direction is that mu^2 = (f1-2f2+f3)^2 /2 < del */ 1799: /* t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); */ 1800: #ifdef NRCORIGINAL 1801: t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)- del*SQR(fp-fptt); /* Original Numerical Recipes in C*/ 1802: #else 1803: t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del); /* Intel compiler doesn't work on one line; bug reported */ 1804: t= t- del*SQR(fp-fptt); 1805: #endif 1806: directest = fp-2.0*(*fret)+fptt - 2.0 * del; /* If del was big enough we change it for a new direction */ 1807: #ifdef DEBUG 1808: printf("t1= %.12lf, t2= %.12lf, t=%.12lf directest=%.12lf\n", 2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del),del*SQR(fp-fptt),t,directest); 1809: fprintf(ficlog,"t1= %.12lf, t2= %.12lf, t=%.12lf directest=%.12lf\n", 2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del),del*SQR(fp-fptt),t,directest); 1810: printf("t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt), 1811: (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt)); 1812: fprintf(ficlog,"t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt), 1813: (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt)); 1814: 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); 1815: 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); 1816: #endif 1817: #ifdef POWELLORIGINAL 1818: if (t < 0.0) { /* Then we use it for new direction */ 1819: #else 1820: if (directest*t < 0.0) { /* Contradiction between both tests */ 1821: printf("directest= %.12lf, t= %.12lf, f1= %.12lf,f2= %.12lf,f3= %.12lf, del= %.12lf\n",directest, t, fp,(*fret),fptt,del); 1822: printf("f1-2f2+f3= %.12lf, f1-f2-del= %.12lf, f1-f3= %.12lf\n",fp-2.0*(*fret)+fptt, fp -(*fret) -del, fp-fptt); 1823: fprintf(ficlog,"directest= %.12lf, t= %.12lf, f1= %.12lf,f2= %.12lf,f3= %.12lf, del= %.12lf\n",directest, t, fp,(*fret),fptt, del); 1824: fprintf(ficlog,"f1-2f2+f3= %.12lf, f1-f2-del= %.12lf, f1-f3= %.12lf\n",fp-2.0*(*fret)+fptt, fp -(*fret) -del, fp-fptt); 1825: } 1826: if (directest < 0.0) { /* Then we use it for new direction */ 1827: #endif 1828: #ifdef DEBUGLINMIN 1829: printf("Before linmin in direction P%d-P0\n",n); 1830: for (j=1;j<=n;j++) { 1831: printf("Before xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]); 1832: if(j % ncovmodel == 0) 1833: printf("\n"); 1834: } 1835: #endif 1836: linmin(p,xit,n,fret,func); /* computes minimum on the extrapolated direction: changes p and rescales xit.*/ 1837: #ifdef DEBUGLINMIN 1838: for (j=1;j<=n;j++) { 1839: printf("After xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]); 1840: if(j % ncovmodel == 0) 1841: printf("\n"); 1842: } 1843: #endif 1844: for (j=1;j<=n;j++) { 1845: xi[j][ibig]=xi[j][n]; /* Replace direction with biggest decrease by last direction n */ 1846: xi[j][n]=xit[j]; /* and this nth direction by the by the average p_0 p_n */ 1847: } 1848: printf("Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig); 1849: fprintf(ficlog,"Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig); 1850: 1851: #ifdef DEBUG 1852: printf("Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig); 1853: fprintf(ficlog,"Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig); 1854: for(j=1;j<=n;j++){ 1855: printf(" %.12e",xit[j]); 1856: fprintf(ficlog," %.12e",xit[j]); 1857: } 1858: printf("\n"); 1859: fprintf(ficlog,"\n"); 1860: #endif 1861: } /* end of t or directest negative */ 1862: #ifdef POWELLF1F3 1863: #else 1864: } /* end if (fptt < fp) */ 1865: #endif 1866: } /* loop iteration */ 1867: } 1868: 1869: /**** Prevalence limit (stable or period prevalence) ****************/ 1870: 1871: double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij) 1872: { 1873: /* Computes the prevalence limit in each live state at age x by left multiplying the unit 1874: matrix by transitions matrix until convergence is reached */ 1875: 1876: int i, ii,j,k; 1877: double min, max, maxmin, maxmax,sumnew=0.; 1878: /* double **matprod2(); */ /* test */ 1879: double **out, cov[NCOVMAX+1], **pmij(); 1880: double **newm; 1881: double agefin, delaymax=50 ; /* Max number of years to converge */ 1882: 1883: for (ii=1;ii<=nlstate+ndeath;ii++) 1884: for (j=1;j<=nlstate+ndeath;j++){ 1885: oldm[ii][j]=(ii==j ? 1.0 : 0.0); 1886: } 1887: 1888: cov[1]=1.; 1889: 1890: /* Even if hstepm = 1, at least one multiplication by the unit matrix */ 1891: for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){ 1892: newm=savm; 1893: /* Covariates have to be included here again */ 1894: cov[2]=agefin; 1895: if(nagesqr==1) 1896: cov[3]= agefin*agefin;; 1897: for (k=1; k<=cptcovn;k++) { 1898: cov[2+nagesqr+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]]; 1899: /*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]]);*/ 1900: } 1901: /*wrong? for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */ 1902: for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]]*cov[2]; 1903: for (k=1; k<=cptcovprod;k++) /* Useless */ 1904: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]] * nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]]; 1905: 1906: /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/ 1907: /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/ 1908: /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/ 1909: /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */ 1910: /* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind *\/ */ 1911: out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /* Bug Valgrind */ 1912: 1913: savm=oldm; 1914: oldm=newm; 1915: maxmax=0.; 1916: for(j=1;j<=nlstate;j++){ 1917: min=1.; 1918: max=0.; 1919: for(i=1; i<=nlstate; i++) { 1920: sumnew=0; 1921: for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k]; 1922: prlim[i][j]= newm[i][j]/(1-sumnew); 1923: /*printf(" prevalim i=%d, j=%d, prmlim[%d][%d]=%f, agefin=%d \n", i, j, i, j, prlim[i][j],(int)agefin);*/ 1924: max=FMAX(max,prlim[i][j]); 1925: min=FMIN(min,prlim[i][j]); 1926: } 1927: maxmin=max-min; 1928: maxmax=FMAX(maxmax,maxmin); 1929: } /* j loop */ 1930: if(maxmax < ftolpl){ 1931: return prlim; 1932: } 1933: } /* age loop */ 1934: return prlim; /* should not reach here */ 1935: } 1936: 1937: /*************** transition probabilities ***************/ 1938: 1939: double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate ) 1940: { 1941: /* According to parameters values stored in x and the covariate's values stored in cov, 1942: computes the probability to be observed in state j being in state i by appying the 1943: model to the ncovmodel covariates (including constant and age). 1944: lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc] 1945: and, according on how parameters are entered, the position of the coefficient xij(nc) of the 1946: ncth covariate in the global vector x is given by the formula: 1947: j=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel 1949: Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation, 1950: sums on j different of i to get 1-pii/pii, deduces pii, and then all pij. 1951: Outputs ps[i][j] the probability to be observed in j being in j according to 1952: the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij] 1953: */ 1954: double s1, lnpijopii; 1955: /*double t34;*/ 1956: int i,j, nc, ii, jj; 1957: 1958: for(i=1; i<= nlstate; i++){ 1959: for(j=1; j<i;j++){ 1960: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){ 1961: /*lnpijopii += param[i][j][nc]*cov[nc];*/ 1962: lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc]; 1963: /* printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */ 1964: } 1965: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */ 1966: /* printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */ 1967: } 1968: for(j=i+1; j<=nlstate+ndeath;j++){ 1969: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){ 1970: /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/ 1971: lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc]; 1972: /* printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */ 1973: } 1974: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */ 1975: } 1976: } 1977: 1978: for(i=1; i<= nlstate; i++){ 1979: s1=0; 1980: for(j=1; j<i; j++){ 1981: s1+=exp(ps[i][j]); /* In fact sums pij/pii */ 1982: /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */ 1983: } 1984: for(j=i+1; j<=nlstate+ndeath; j++){ 1985: s1+=exp(ps[i][j]); /* In fact sums pij/pii */ 1986: /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */ 1987: } 1988: /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */ 1989: ps[i][i]=1./(s1+1.); 1990: /* Computing other pijs */ 1991: for(j=1; j<i; j++) 1992: ps[i][j]= exp(ps[i][j])*ps[i][i]; 1993: for(j=i+1; j<=nlstate+ndeath; j++) 1994: ps[i][j]= exp(ps[i][j])*ps[i][i]; 1995: /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */ 1996: } /* end i */ 1997: 1998: for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){ 1999: for(jj=1; jj<= nlstate+ndeath; jj++){ 2000: ps[ii][jj]=0; 2001: ps[ii][ii]=1; 2002: } 2003: } 2004: 2005: 2006: /* for(ii=1; ii<= nlstate+ndeath; ii++){ */ 2007: /* for(jj=1; jj<= nlstate+ndeath; jj++){ */ 2008: /* printf(" pmij ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */ 2009: /* } */ 2010: /* printf("\n "); */ 2011: /* } */ 2012: /* printf("\n ");printf("%lf ",cov[2]);*/ 2013: /* 2014: for(i=1; i<= npar; i++) printf("%f ",x[i]); 2015: goto end;*/ 2016: return ps; 2017: } 2018: 2019: /**************** Product of 2 matrices ******************/ 2020: 2021: double **matprod2(double **out, double **in,int nrl, int nrh, int ncl, int nch, int ncolol, int ncoloh, double **b) 2022: { 2023: /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times 2024: b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */ 2025: /* in, b, out are matrice of pointers which should have been initialized 2026: before: only the contents of out is modified. The function returns 2027: a pointer to pointers identical to out */ 2028: int i, j, k; 2029: for(i=nrl; i<= nrh; i++) 2030: for(k=ncolol; k<=ncoloh; k++){ 2031: out[i][k]=0.; 2032: for(j=ncl; j<=nch; j++) 2033: out[i][k] +=in[i][j]*b[j][k]; 2034: } 2035: return out; 2036: } 2037: 2038: 2039: /************* Higher Matrix Product ***************/ 2040: 2041: double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij ) 2042: { 2043: /* Computes the transition matrix starting at age 'age' over 2044: 'nhstepm*hstepm*stepm' months (i.e. until 2045: age (in years) age+nhstepm*hstepm*stepm/12) by multiplying 2046: nhstepm*hstepm matrices. 2047: Output is stored in matrix po[i][j][h] for h every 'hstepm' step 2048: (typically every 2 years instead of every month which is too big 2049: for the memory). 2050: Model is determined by parameters x and covariates have to be 2051: included manually here. 2052: 2053: */ 2054: 2055: int i, j, d, h, k; 2056: double **out, cov[NCOVMAX+1]; 2057: double **newm; 2058: double agexact; 2059: 2060: /* Hstepm could be zero and should return the unit matrix */ 2061: for (i=1;i<=nlstate+ndeath;i++) 2062: for (j=1;j<=nlstate+ndeath;j++){ 2063: oldm[i][j]=(i==j ? 1.0 : 0.0); 2064: po[i][j][0]=(i==j ? 1.0 : 0.0); 2065: } 2066: /* Even if hstepm = 1, at least one multiplication by the unit matrix */ 2067: for(h=1; h <=nhstepm; h++){ 2068: for(d=1; d <=hstepm; d++){ 2069: newm=savm; 2070: /* Covariates have to be included here again */ 2071: cov[1]=1.; 2072: agexact=age+((h-1)*hstepm + (d-1))*stepm/YEARM; 2073: cov[2]=agexact; 2074: if(nagesqr==1) 2075: cov[3]= agexact*agexact; 2076: for (k=1; k<=cptcovn;k++) 2077: cov[2+nagesqr+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]]; 2078: for (k=1; k<=cptcovage;k++) /* Should start at cptcovn+1 */ 2079: /* cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */ 2080: cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtab[ij][Tvar[Tage[k]]]]*cov[2]; 2081: for (k=1; k<=cptcovprod;k++) /* Useless because included in cptcovn */ 2082: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]]; 2083: 2084: 2085: /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/ 2086: /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/ 2087: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 2088: pmij(pmmij,cov,ncovmodel,x,nlstate)); 2089: savm=oldm; 2090: oldm=newm; 2091: } 2092: for(i=1; i<=nlstate+ndeath; i++) 2093: for(j=1;j<=nlstate+ndeath;j++) { 2094: po[i][j][h]=newm[i][j]; 2095: /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/ 2096: } 2097: /*printf("h=%d ",h);*/ 2098: } /* end h */ 2099: /* printf("\n H=%d \n",h); */ 2100: return po; 2101: } 2102: 2103: #ifdef NLOPT 2104: double myfunc(unsigned n, const double *p1, double *grad, void *pd){ 2105: double fret; 2106: double *xt; 2107: int j; 2108: myfunc_data *d2 = (myfunc_data *) pd; 2109: /* xt = (p1-1); */ 2110: xt=vector(1,n); 2111: for (j=1;j<=n;j++) xt[j]=p1[j-1]; /* xt[1]=p1[0] */ 2112: 2113: fret=(d2->function)(xt); /* p xt[1]@8 is fine */ 2114: /* fret=(*func)(xt); /\* p xt[1]@8 is fine *\/ */ 2115: printf("Function = %.12lf ",fret); 2116: for (j=1;j<=n;j++) printf(" %d %.8lf", j, xt[j]); 2117: printf("\n"); 2118: free_vector(xt,1,n); 2119: return fret; 2120: } 2121: #endif 2122: 2123: /*************** log-likelihood *************/ 2124: double func( double *x) 2125: { 2126: int i, ii, j, k, mi, d, kk; 2127: double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1]; 2128: double **out; 2129: double sw; /* Sum of weights */ 2130: double lli; /* Individual log likelihood */ 2131: int s1, s2; 2132: double bbh, survp; 2133: long ipmx; 2134: double agexact; 2135: /*extern weight */ 2136: /* We are differentiating ll according to initial status */ 2137: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/ 2138: /*for(i=1;i<imx;i++) 2139: printf(" %d\n",s[4][i]); 2140: */ 2141: 2142: ++countcallfunc; 2143: 2144: cov[1]=1.; 2145: 2146: for(k=1; k<=nlstate; k++) ll[k]=0.; 2147: 2148: if(mle==1){ 2149: for (i=1,ipmx=0, sw=0.; i<=imx; i++){ 2150: /* Computes the values of the ncovmodel covariates of the model 2151: depending if the covariates are fixed or variying (age dependent) and stores them in cov[] 2152: Then computes with function pmij which return a matrix p[i][j] giving the elementary probability 2153: to be observed in j being in i according to the model. 2154: */ 2155: for (k=1; k<=cptcovn;k++){ /* Simple and product covariates without age* products */ 2156: cov[2+nagesqr+k]=covar[Tvar[k]][i]; 2157: } 2158: /* In model V2+V1*V4+age*V3+V3*V2 Tvar[1] is V2, Tvar[2=V1*V4] 2159: is 6, Tvar[3=age*V3] should not be computed because of age Tvar[4=V3*V2] 2160: has been calculated etc */ 2161: for(mi=1; mi<= wav[i]-1; mi++){ 2162: for (ii=1;ii<=nlstate+ndeath;ii++) 2163: for (j=1;j<=nlstate+ndeath;j++){ 2164: oldm[ii][j]=(ii==j ? 1.0 : 0.0); 2165: savm[ii][j]=(ii==j ? 1.0 : 0.0); 2166: } 2167: for(d=0; d<dh[mi][i]; d++){ 2168: newm=savm; 2169: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM; 2170: cov[2]=agexact; 2171: if(nagesqr==1) 2172: cov[3]= agexact*agexact; 2173: for (kk=1; kk<=cptcovage;kk++) { 2174: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact; /* Tage[kk] gives the data-covariate associated with age */ 2175: } 2176: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, 2177: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); 2178: savm=oldm; 2179: oldm=newm; 2180: } /* end mult */ 2181: 2182: /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */ 2183: /* But now since version 0.9 we anticipate for bias at large stepm. 2184: * If stepm is larger than one month (smallest stepm) and if the exact delay 2185: * (in months) between two waves is not a multiple of stepm, we rounded to 2186: * the nearest (and in case of equal distance, to the lowest) interval but now 2187: * we keep into memory the bias bh[mi][i] and also the previous matrix product 2188: * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the 2189: * probability in order to take into account the bias as a fraction of the way 2190: * from savm to out if bh is negative or even beyond if bh is positive. bh varies 2191: * -stepm/2 to stepm/2 . 2192: * For stepm=1 the results are the same as for previous versions of Imach. 2193: * For stepm > 1 the results are less biased than in previous versions. 2194: */ 2195: s1=s[mw[mi][i]][i]; 2196: s2=s[mw[mi+1][i]][i]; 2197: bbh=(double)bh[mi][i]/(double)stepm; 2198: /* bias bh is positive if real duration 2199: * is higher than the multiple of stepm and negative otherwise. 2200: */ 2201: /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/ 2202: if( s2 > nlstate){ 2203: /* i.e. if s2 is a death state and if the date of death is known 2204: then the contribution to the likelihood is the probability to 2205: die between last step unit time and current step unit time, 2206: which is also equal to probability to die before dh 2207: minus probability to die before dh-stepm . 2208: In version up to 0.92 likelihood was computed 2209: as if date of death was unknown. Death was treated as any other 2210: health state: the date of the interview describes the actual state 2211: and not the date of a change in health state. The former idea was 2212: to consider that at each interview the state was recorded 2213: (healthy, disable or death) and IMaCh was corrected; but when we 2214: introduced the exact date of death then we should have modified 2215: the contribution of an exact death to the likelihood. This new 2216: contribution is smaller and very dependent of the step unit 2217: stepm. It is no more the probability to die between last interview 2218: and month of death but the probability to survive from last 2219: interview up to one month before death multiplied by the 2220: probability to die within a month. Thanks to Chris 2221: Jackson for correcting this bug. Former versions increased 2222: mortality artificially. The bad side is that we add another loop 2223: which slows down the processing. The difference can be up to 10% 2224: lower mortality. 2225: */ 2226: /* If, at the beginning of the maximization mostly, the 2227: cumulative probability or probability to be dead is 2228: constant (ie = 1) over time d, the difference is equal to 2229: 0. out[s1][3] = savm[s1][3]: probability, being at state 2230: s1 at precedent wave, to be dead a month before current 2231: wave is equal to probability, being at state s1 at 2232: precedent wave, to be dead at mont of the current 2233: wave. Then the observed probability (that this person died) 2234: is null according to current estimated parameter. In fact, 2235: it should be very low but not zero otherwise the log go to 2236: infinity. 2237: */ 2238: /* #ifdef INFINITYORIGINAL */ 2239: /* lli=log(out[s1][s2] - savm[s1][s2]); */ 2240: /* #else */ 2241: /* if ((out[s1][s2] - savm[s1][s2]) < mytinydouble) */ 2242: /* lli=log(mytinydouble); */ 2243: /* else */ 2244: /* lli=log(out[s1][s2] - savm[s1][s2]); */ 2245: /* #endif */ 2246: lli=log(out[s1][s2] - savm[s1][s2]); 2247: 2248: } else if (s2==-2) { 2249: for (j=1,survp=0. ; j<=nlstate; j++) 2250: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j]; 2251: /*survp += out[s1][j]; */ 2252: lli= log(survp); 2253: } 2254: 2255: else if (s2==-4) { 2256: for (j=3,survp=0. ; j<=nlstate; j++) 2257: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j]; 2258: lli= log(survp); 2259: } 2260: 2261: else if (s2==-5) { 2262: for (j=1,survp=0. ; j<=2; j++) 2263: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j]; 2264: lli= log(survp); 2265: } 2266: 2267: else{ 2268: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */ 2269: /* 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 */ 2270: } 2271: /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/ 2272: /*if(lli ==000.0)*/ 2273: /*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); */ 2274: ipmx +=1; 2275: sw += weight[i]; 2276: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli; 2277: /* if (lli < log(mytinydouble)){ */ 2278: /* printf("Close to inf lli = %.10lf < %.10lf i= %d mi= %d, s[%d][i]=%d s1=%d s2=%d\n", lli,log(mytinydouble), i, mi,mw[mi][i], s[mw[mi][i]][i], s1,s2); */ 2279: /* fprintf(ficlog,"Close to inf lli = %.10lf i= %d mi= %d, s[mw[mi][i]][i]=%d\n", lli, i, mi,s[mw[mi][i]][i]); */ 2280: /* } */ 2281: } /* end of wave */ 2282: } /* end of individual */ 2283: } else if(mle==2){ 2284: for (i=1,ipmx=0, sw=0.; i<=imx; i++){ 2285: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i]; 2286: for(mi=1; mi<= wav[i]-1; mi++){ 2287: for (ii=1;ii<=nlstate+ndeath;ii++) 2288: for (j=1;j<=nlstate+ndeath;j++){ 2289: oldm[ii][j]=(ii==j ? 1.0 : 0.0); 2290: savm[ii][j]=(ii==j ? 1.0 : 0.0); 2291: } 2292: for(d=0; d<=dh[mi][i]; d++){ 2293: newm=savm; 2294: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM; 2295: cov[2]=agexact; 2296: if(nagesqr==1) 2297: cov[3]= agexact*agexact; 2298: for (kk=1; kk<=cptcovage;kk++) { 2299: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact; 2300: } 2301: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, 2302: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); 2303: savm=oldm; 2304: oldm=newm; 2305: } /* end mult */ 2306: 2307: s1=s[mw[mi][i]][i]; 2308: s2=s[mw[mi+1][i]][i]; 2309: bbh=(double)bh[mi][i]/(double)stepm; 2310: 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 */ 2311: ipmx +=1; 2312: sw += weight[i]; 2313: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli; 2314: } /* end of wave */ 2315: } /* end of individual */ 2316: } else if(mle==3){ /* exponential inter-extrapolation */ 2317: for (i=1,ipmx=0, sw=0.; i<=imx; i++){ 2318: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i]; 2319: for(mi=1; mi<= wav[i]-1; mi++){ 2320: for (ii=1;ii<=nlstate+ndeath;ii++) 2321: for (j=1;j<=nlstate+ndeath;j++){ 2322: oldm[ii][j]=(ii==j ? 1.0 : 0.0); 2323: savm[ii][j]=(ii==j ? 1.0 : 0.0); 2324: } 2325: for(d=0; d<dh[mi][i]; d++){ 2326: newm=savm; 2327: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM; 2328: cov[2]=agexact; 2329: if(nagesqr==1) 2330: cov[3]= agexact*agexact; 2331: for (kk=1; kk<=cptcovage;kk++) { 2332: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact; 2333: } 2334: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, 2335: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); 2336: savm=oldm; 2337: oldm=newm; 2338: } /* end mult */ 2339: 2340: s1=s[mw[mi][i]][i]; 2341: s2=s[mw[mi+1][i]][i]; 2342: bbh=(double)bh[mi][i]/(double)stepm; 2343: 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 */ 2344: ipmx +=1; 2345: sw += weight[i]; 2346: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli; 2347: } /* end of wave */ 2348: } /* end of individual */ 2349: }else if (mle==4){ /* ml=4 no inter-extrapolation */ 2350: for (i=1,ipmx=0, sw=0.; i<=imx; i++){ 2351: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i]; 2352: for(mi=1; mi<= wav[i]-1; mi++){ 2353: for (ii=1;ii<=nlstate+ndeath;ii++) 2354: for (j=1;j<=nlstate+ndeath;j++){ 2355: oldm[ii][j]=(ii==j ? 1.0 : 0.0); 2356: savm[ii][j]=(ii==j ? 1.0 : 0.0); 2357: } 2358: for(d=0; d<dh[mi][i]; d++){ 2359: newm=savm; 2360: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM; 2361: cov[2]=agexact; 2362: if(nagesqr==1) 2363: cov[3]= agexact*agexact; 2364: for (kk=1; kk<=cptcovage;kk++) { 2365: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact; 2366: } 2367: 2368: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, 2369: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); 2370: savm=oldm; 2371: oldm=newm; 2372: } /* end mult */ 2373: 2374: s1=s[mw[mi][i]][i]; 2375: s2=s[mw[mi+1][i]][i]; 2376: if( s2 > nlstate){ 2377: lli=log(out[s1][s2] - savm[s1][s2]); 2378: }else{ 2379: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */ 2380: } 2381: ipmx +=1; 2382: sw += weight[i]; 2383: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli; 2384: /* 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]); */ 2385: } /* end of wave */ 2386: } /* end of individual */ 2387: }else{ /* ml=5 no inter-extrapolation no jackson =0.8a */ 2388: for (i=1,ipmx=0, sw=0.; i<=imx; i++){ 2389: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i]; 2390: for(mi=1; mi<= wav[i]-1; mi++){ 2391: for (ii=1;ii<=nlstate+ndeath;ii++) 2392: for (j=1;j<=nlstate+ndeath;j++){ 2393: oldm[ii][j]=(ii==j ? 1.0 : 0.0); 2394: savm[ii][j]=(ii==j ? 1.0 : 0.0); 2395: } 2396: for(d=0; d<dh[mi][i]; d++){ 2397: newm=savm; 2398: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM; 2399: cov[2]=agexact; 2400: if(nagesqr==1) 2401: cov[3]= agexact*agexact; 2402: for (kk=1; kk<=cptcovage;kk++) { 2403: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact; 2404: } 2405: 2406: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, 2407: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); 2408: savm=oldm; 2409: oldm=newm; 2410: } /* end mult */ 2411: 2412: s1=s[mw[mi][i]][i]; 2413: s2=s[mw[mi+1][i]][i]; 2414: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */ 2415: ipmx +=1; 2416: sw += weight[i]; 2417: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli; 2418: /*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]);*/ 2419: } /* end of wave */ 2420: } /* end of individual */ 2421: } /* End of if */ 2422: for(k=1,l=0.; k<=nlstate; k++) l += ll[k]; 2423: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */ 2424: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */ 2425: return -l; 2426: } 2427: 2428: /*************** log-likelihood *************/ 2429: double funcone( double *x) 2430: { 2431: /* Same as likeli but slower because of a lot of printf and if */ 2432: int i, ii, j, k, mi, d, kk; 2433: double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1]; 2434: double **out; 2435: double lli; /* Individual log likelihood */ 2436: double llt; 2437: int s1, s2; 2438: double bbh, survp; 2439: double agexact; 2440: /*extern weight */ 2441: /* We are differentiating ll according to initial status */ 2442: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/ 2443: /*for(i=1;i<imx;i++) 2444: printf(" %d\n",s[4][i]); 2445: */ 2446: cov[1]=1.; 2447: 2448: for(k=1; k<=nlstate; k++) ll[k]=0.; 2449: 2450: for (i=1,ipmx=0, sw=0.; i<=imx; i++){ 2451: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i]; 2452: for(mi=1; mi<= wav[i]-1; mi++){ 2453: for (ii=1;ii<=nlstate+ndeath;ii++) 2454: for (j=1;j<=nlstate+ndeath;j++){ 2455: oldm[ii][j]=(ii==j ? 1.0 : 0.0); 2456: savm[ii][j]=(ii==j ? 1.0 : 0.0); 2457: } 2458: for(d=0; d<dh[mi][i]; d++){ 2459: newm=savm; 2460: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM; 2461: cov[2]=agexact; 2462: if(nagesqr==1) 2463: cov[3]= agexact*agexact; 2464: for (kk=1; kk<=cptcovage;kk++) { 2465: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact; 2466: } 2467: 2468: /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */ 2469: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, 2470: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); 2471: /* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, */ 2472: /* 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); */ 2473: savm=oldm; 2474: oldm=newm; 2475: } /* end mult */ 2476: 2477: s1=s[mw[mi][i]][i]; 2478: s2=s[mw[mi+1][i]][i]; 2479: bbh=(double)bh[mi][i]/(double)stepm; 2480: /* bias is positive if real duration 2481: * is higher than the multiple of stepm and negative otherwise. 2482: */ 2483: if( s2 > nlstate && (mle <5) ){ /* Jackson */ 2484: lli=log(out[s1][s2] - savm[s1][s2]); 2485: } else if (s2==-2) { 2486: for (j=1,survp=0. ; j<=nlstate; j++) 2487: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j]; 2488: lli= log(survp); 2489: }else if (mle==1){ 2490: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */ 2491: } else if(mle==2){ 2492: 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 */ 2493: } else if(mle==3){ /* exponential inter-extrapolation */ 2494: 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 */ 2495: } else if (mle==4){ /* mle=4 no inter-extrapolation */ 2496: lli=log(out[s1][s2]); /* Original formula */ 2497: } else{ /* mle=0 back to 1 */ 2498: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */ 2499: /*lli=log(out[s1][s2]); */ /* Original formula */ 2500: } /* End of if */ 2501: ipmx +=1; 2502: sw += weight[i]; 2503: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli; 2504: /*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]); */ 2505: if(globpr){ 2506: fprintf(ficresilk,"%9ld %6d %2d %2d %1d %1d %3d %11.6f %8.4f\ 2507: %11.6f %11.6f %11.6f ", \ 2508: num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i], 2509: 2*weight[i]*lli,out[s1][s2],savm[s1][s2]); 2510: for(k=1,llt=0.,l=0.; k<=nlstate; k++){ 2511: llt +=ll[k]*gipmx/gsw; 2512: fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw); 2513: } 2514: fprintf(ficresilk," %10.6f\n", -llt); 2515: } 2516: } /* end of wave */ 2517: } /* end of individual */ 2518: for(k=1,l=0.; k<=nlstate; k++) l += ll[k]; 2519: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */ 2520: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */ 2521: if(globpr==0){ /* First time we count the contributions and weights */ 2522: gipmx=ipmx; 2523: gsw=sw; 2524: } 2525: return -l; 2526: } 2527: 2528: 2529: /*************** function likelione ***********/ 2530: void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double [])) 2531: { 2532: /* This routine should help understanding what is done with 2533: the selection of individuals/waves and 2534: to check the exact contribution to the likelihood. 2535: Plotting could be done. 2536: */ 2537: int k; 2538: 2539: if(*globpri !=0){ /* Just counts and sums, no printings */ 2540: strcpy(fileresilk,"ilk"); 2541: strcat(fileresilk,fileres); 2542: if((ficresilk=fopen(fileresilk,"w"))==NULL) { 2543: printf("Problem with resultfile: %s\n", fileresilk); 2544: fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk); 2545: } 2546: 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"); 2547: fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav "); 2548: /* i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */ 2549: for(k=1; k<=nlstate; k++) 2550: fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k); 2551: fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n"); 2552: } 2553: 2554: *fretone=(*funcone)(p); 2555: if(*globpri !=0){ 2556: fclose(ficresilk); 2557: fprintf(fichtm,"\n File of contributions to the likelihood: <a href=\"%s\">%s</a> \n",subdirf(fileresilk),subdirf(fileresilk)); 2558: fflush(fichtm); 2559: } 2560: return; 2561: } 2562: 2563: 2564: /*********** Maximum Likelihood Estimation ***************/ 2565: 2566: void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double [])) 2567: { 2568: int i,j, iter=0; 2569: double **xi; 2570: double fret; 2571: double fretone; /* Only one call to likelihood */ 2572: /* char filerespow[FILENAMELENGTH];*/ 2573: 2574: #ifdef NLOPT 2575: int creturn; 2576: nlopt_opt opt; 2577: /* double lb[9] = { -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL }; /\* lower bounds *\/ */ 2578: double *lb; 2579: double minf; /* the minimum objective value, upon return */ 2580: double * p1; /* Shifted parameters from 0 instead of 1 */ 2581: myfunc_data dinst, *d = &dinst; 2582: #endif 2583: 2584: 2585: xi=matrix(1,npar,1,npar); 2586: for (i=1;i<=npar;i++) 2587: for (j=1;j<=npar;j++) 2588: xi[i][j]=(i==j ? 1.0 : 0.0); 2589: printf("Powell\n"); fprintf(ficlog,"Powell\n"); 2590: strcpy(filerespow,"pow"); 2591: strcat(filerespow,fileres); 2592: if((ficrespow=fopen(filerespow,"w"))==NULL) { 2593: printf("Problem with resultfile: %s\n", filerespow); 2594: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow); 2595: } 2596: fprintf(ficrespow,"# Powell\n# iter -2*LL"); 2597: for (i=1;i<=nlstate;i++) 2598: for(j=1;j<=nlstate+ndeath;j++) 2599: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j); 2600: fprintf(ficrespow,"\n"); 2601: #ifdef POWELL 2602: powell(p,xi,npar,ftol,&iter,&fret,func); 2603: #endif 2604: 2605: #ifdef NLOPT 2606: #ifdef NEWUOA 2607: opt = nlopt_create(NLOPT_LN_NEWUOA,npar); 2608: #else 2609: opt = nlopt_create(NLOPT_LN_BOBYQA,npar); 2610: #endif 2611: lb=vector(0,npar-1); 2612: for (i=0;i<npar;i++) lb[i]= -HUGE_VAL; 2613: nlopt_set_lower_bounds(opt, lb); 2614: nlopt_set_initial_step1(opt, 0.1); 2615: 2616: p1= (p+1); /* p *(p+1)@8 and p *(p1)@8 are equal p1[0]=p[1] */ 2617: d->function = func; 2618: printf(" Func %.12lf \n",myfunc(npar,p1,NULL,d)); 2619: nlopt_set_min_objective(opt, myfunc, d); 2620: nlopt_set_xtol_rel(opt, ftol); 2621: if ((creturn=nlopt_optimize(opt, p1, &minf)) < 0) { 2622: printf("nlopt failed! %d\n",creturn); 2623: } 2624: else { 2625: printf("found minimum after %d evaluations (NLOPT=%d)\n", countcallfunc ,NLOPT); 2626: printf("found minimum at f(%g,%g) = %0.10g\n", p[0], p[1], minf); 2627: iter=1; /* not equal */ 2628: } 2629: nlopt_destroy(opt); 2630: #endif 2631: free_matrix(xi,1,npar,1,npar); 2632: fclose(ficrespow); 2633: printf("#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p)); 2634: fprintf(ficlog,"#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p)); 2635: fprintf(ficres,"#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p)); 2636: 2637: } 2638: 2639: /**** Computes Hessian and covariance matrix ***/ 2640: void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double [])) 2641: { 2642: double **a,**y,*x,pd; 2643: double **hess; 2644: int i, j; 2645: int *indx; 2646: 2647: double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar); 2648: double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar); 2649: void lubksb(double **a, int npar, int *indx, double b[]) ; 2650: void ludcmp(double **a, int npar, int *indx, double *d) ; 2651: double gompertz(double p[]); 2652: hess=matrix(1,npar,1,npar); 2653: 2654: printf("\nCalculation of the hessian matrix. Wait...\n"); 2655: fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n"); 2656: for (i=1;i<=npar;i++){ 2657: printf("%d",i);fflush(stdout); 2658: fprintf(ficlog,"%d",i);fflush(ficlog); 2659: 2660: hess[i][i]=hessii(p,ftolhess,i,delti,func,npar); 2661: 2662: /* printf(" %f ",p[i]); 2663: printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/ 2664: } 2665: 2666: for (i=1;i<=npar;i++) { 2667: for (j=1;j<=npar;j++) { 2668: if (j>i) { 2669: printf(".%d%d",i,j);fflush(stdout); 2670: fprintf(ficlog,".%d%d",i,j);fflush(ficlog); 2671: hess[i][j]=hessij(p,delti,i,j,func,npar); 2672: 2673: hess[j][i]=hess[i][j]; 2674: /*printf(" %lf ",hess[i][j]);*/ 2675: } 2676: } 2677: } 2678: printf("\n"); 2679: fprintf(ficlog,"\n"); 2680: 2681: printf("\nInverting the hessian to get the covariance matrix. Wait...\n"); 2682: fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n"); 2683: 2684: a=matrix(1,npar,1,npar); 2685: y=matrix(1,npar,1,npar); 2686: x=vector(1,npar); 2687: indx=ivector(1,npar); 2688: for (i=1;i<=npar;i++) 2689: for (j=1;j<=npar;j++) a[i][j]=hess[i][j]; 2690: ludcmp(a,npar,indx,&pd); 2691: 2692: for (j=1;j<=npar;j++) { 2693: for (i=1;i<=npar;i++) x[i]=0; 2694: x[j]=1; 2695: lubksb(a,npar,indx,x); 2696: for (i=1;i<=npar;i++){ 2697: matcov[i][j]=x[i]; 2698: } 2699: } 2700: 2701: printf("\n#Hessian matrix#\n"); 2702: fprintf(ficlog,"\n#Hessian matrix#\n"); 2703: for (i=1;i<=npar;i++) { 2704: for (j=1;j<=npar;j++) { 2705: printf("%.3e ",hess[i][j]); 2706: fprintf(ficlog,"%.3e ",hess[i][j]); 2707: } 2708: printf("\n"); 2709: fprintf(ficlog,"\n"); 2710: } 2711: 2712: /* Recompute Inverse */ 2713: for (i=1;i<=npar;i++) 2714: for (j=1;j<=npar;j++) a[i][j]=matcov[i][j]; 2715: ludcmp(a,npar,indx,&pd); 2716: 2717: /* printf("\n#Hessian matrix recomputed#\n"); 2718: 2719: for (j=1;j<=npar;j++) { 2720: for (i=1;i<=npar;i++) x[i]=0; 2721: x[j]=1; 2722: lubksb(a,npar,indx,x); 2723: for (i=1;i<=npar;i++){ 2724: y[i][j]=x[i]; 2725: printf("%.3e ",y[i][j]); 2726: fprintf(ficlog,"%.3e ",y[i][j]); 2727: } 2728: printf("\n"); 2729: fprintf(ficlog,"\n"); 2730: } 2731: */ 2732: 2733: free_matrix(a,1,npar,1,npar); 2734: free_matrix(y,1,npar,1,npar); 2735: free_vector(x,1,npar); 2736: free_ivector(indx,1,npar); 2737: free_matrix(hess,1,npar,1,npar); 2738: 2739: 2740: } 2741: 2742: /*************** hessian matrix ****************/ 2743: double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar) 2744: { 2745: int i; 2746: int l=1, lmax=20; 2747: double k1,k2; 2748: double p2[MAXPARM+1]; /* identical to x */ 2749: double res; 2750: double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4; 2751: double fx; 2752: int k=0,kmax=10; 2753: double l1; 2754: 2755: fx=func(x); 2756: for (i=1;i<=npar;i++) p2[i]=x[i]; 2757: for(l=0 ; l <=lmax; l++){ /* Enlarging the zone around the Maximum */ 2758: l1=pow(10,l); 2759: delts=delt; 2760: for(k=1 ; k <kmax; k=k+1){ 2761: delt = delta*(l1*k); 2762: p2[theta]=x[theta] +delt; 2763: k1=func(p2)-fx; /* Might be negative if too close to the theoretical maximum */ 2764: p2[theta]=x[theta]-delt; 2765: k2=func(p2)-fx; 2766: /*res= (k1-2.0*fx+k2)/delt/delt; */ 2767: res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */ 2768: 2769: #ifdef DEBUGHESS 2770: 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); 2771: 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); 2772: #endif 2773: /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */ 2774: if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){ 2775: k=kmax; 2776: } 2777: else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */ 2778: k=kmax; l=lmax*10; 2779: } 2780: else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 2781: delts=delt; 2782: } 2783: } 2784: } 2785: delti[theta]=delts; 2786: return res; 2787: 2788: } 2789: 2790: double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar) 2791: { 2792: int i; 2793: int l=1, lmax=20; 2794: double k1,k2,k3,k4,res,fx; 2795: double p2[MAXPARM+1]; 2796: int k; 2797: 2798: fx=func(x); 2799: for (k=1; k<=2; k++) { 2800: for (i=1;i<=npar;i++) p2[i]=x[i]; 2801: p2[thetai]=x[thetai]+delti[thetai]/k; 2802: p2[thetaj]=x[thetaj]+delti[thetaj]/k; 2803: k1=func(p2)-fx; 2804: 2805: p2[thetai]=x[thetai]+delti[thetai]/k; 2806: p2[thetaj]=x[thetaj]-delti[thetaj]/k; 2807: k2=func(p2)-fx; 2808: 2809: p2[thetai]=x[thetai]-delti[thetai]/k; 2810: p2[thetaj]=x[thetaj]+delti[thetaj]/k; 2811: k3=func(p2)-fx; 2812: 2813: p2[thetai]=x[thetai]-delti[thetai]/k; 2814: p2[thetaj]=x[thetaj]-delti[thetaj]/k; 2815: k4=func(p2)-fx; 2816: res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */ 2817: #ifdef DEBUG 2818: 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); 2819: 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); 2820: #endif 2821: } 2822: return res; 2823: } 2824: 2825: /************** Inverse of matrix **************/ 2826: void ludcmp(double **a, int n, int *indx, double *d) 2827: { 2828: int i,imax,j,k; 2829: double big,dum,sum,temp; 2830: double *vv; 2831: 2832: vv=vector(1,n); 2833: *d=1.0; 2834: for (i=1;i<=n;i++) { 2835: big=0.0; 2836: for (j=1;j<=n;j++) 2837: if ((temp=fabs(a[i][j])) > big) big=temp; 2838: if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 2839: vv[i]=1.0/big; 2840: } 2841: for (j=1;j<=n;j++) { 2842: for (i=1;i<j;i++) { 2843: sum=a[i][j]; 2844: for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 2845: a[i][j]=sum; 2846: } 2847: big=0.0; 2848: for (i=j;i<=n;i++) { 2849: sum=a[i][j]; 2850: for (k=1;k<j;k++) 2851: sum -= a[i][k]*a[k][j]; 2852: a[i][j]=sum; 2853: if ( (dum=vv[i]*fabs(sum)) >= big) { 2854: big=dum; 2855: imax=i; 2856: } 2857: } 2858: if (j != imax) { 2859: for (k=1;k<=n;k++) { 2860: dum=a[imax][k]; 2861: a[imax][k]=a[j][k]; 2862: a[j][k]=dum; 2863: } 2864: *d = -(*d); 2865: vv[imax]=vv[j]; 2866: } 2867: indx[j]=imax; 2868: if (a[j][j] == 0.0) a[j][j]=TINY; 2869: if (j != n) { 2870: dum=1.0/(a[j][j]); 2871: for (i=j+1;i<=n;i++) a[i][j] *= dum; 2872: } 2873: } 2874: free_vector(vv,1,n); /* Doesn't work */ 2875: ; 2876: } 2877: 2878: void lubksb(double **a, int n, int *indx, double b[]) 2879: { 2880: int i,ii=0,ip,j; 2881: double sum; 2882: 2883: for (i=1;i<=n;i++) { 2884: ip=indx[i]; 2885: sum=b[ip]; 2886: b[ip]=b[i]; 2887: if (ii) 2888: for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 2889: else if (sum) ii=i; 2890: b[i]=sum; 2891: } 2892: for (i=n;i>=1;i--) { 2893: sum=b[i]; 2894: for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 2895: b[i]=sum/a[i][i]; 2896: } 2897: } 2898: 2899: void pstamp(FILE *fichier) 2900: { 2901: fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart); 2902: } 2903: 2904: /************ Frequencies ********************/ 2905: 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[]) 2906: { /* Some frequencies */ 2907: 2908: int i, m, jk, j1, bool, z1,j; 2909: int first; 2910: double ***freq; /* Frequencies */ 2911: double *pp, **prop; 2912: double pos,posprop, k2, dateintsum=0,k2cpt=0; 2913: char fileresp[FILENAMELENGTH]; 2914: 2915: pp=vector(1,nlstate); 2916: prop=matrix(1,nlstate,iagemin,iagemax+3); 2917: strcpy(fileresp,"p"); 2918: strcat(fileresp,fileres); 2919: if((ficresp=fopen(fileresp,"w"))==NULL) { 2920: printf("Problem with prevalence resultfile: %s\n", fileresp); 2921: fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp); 2922: exit(0); 2923: } 2924: freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3); 2925: j1=0; 2926: 2927: j=cptcoveff; 2928: if (cptcovn<1) {j=1;ncodemax[1]=1;} 2929: 2930: first=1; 2931: 2932: /* for(k1=1; k1<=j ; k1++){ */ /* Loop on covariates */ 2933: /* for(i1=1; i1<=ncodemax[k1];i1++){ */ /* Now it is 2 */ 2934: /* j1++; */ 2935: for (j1 = 1; j1 <= (int) pow(2,cptcoveff); j1++){ 2936: /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]); 2937: scanf("%d", i);*/ 2938: for (i=-5; i<=nlstate+ndeath; i++) 2939: for (jk=-5; jk<=nlstate+ndeath; jk++) 2940: for(m=iagemin; m <= iagemax+3; m++) 2941: freq[i][jk][m]=0; 2942: 2943: for (i=1; i<=nlstate; i++) 2944: for(m=iagemin; m <= iagemax+3; m++) 2945: prop[i][m]=0; 2946: 2947: dateintsum=0; 2948: k2cpt=0; 2949: for (i=1; i<=imx; i++) { 2950: bool=1; 2951: if (cptcovn>0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */ 2952: for (z1=1; z1<=cptcoveff; z1++) 2953: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]){ 2954: /* Tests if the value of each of the covariates of i is equal to filter j1 */ 2955: bool=0; 2956: /* 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", 2957: bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtab[j1][z1], 2958: j1,z1,nbcode[Tvaraff[z1]][codtab[j1][z1]],j1);*/ 2959: /* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtab[7][3]=1 and nbcde[3][?]=1*/ 2960: } 2961: } 2962: 2963: if (bool==1){ 2964: for(m=firstpass; m<=lastpass; m++){ 2965: k2=anint[m][i]+(mint[m][i]/12.); 2966: /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/ 2967: if(agev[m][i]==0) agev[m][i]=iagemax+1; 2968: if(agev[m][i]==1) agev[m][i]=iagemax+2; 2969: if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i]; 2970: if (m<lastpass) { 2971: freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i]; 2972: freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i]; 2973: } 2974: 2975: if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) { 2976: dateintsum=dateintsum+k2; 2977: k2cpt++; 2978: } 2979: /*}*/ 2980: } 2981: } 2982: } /* end i */ 2983: 2984: /* fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/ 2985: pstamp(ficresp); 2986: if (cptcovn>0) { 2987: fprintf(ficresp, "\n#********** Variable "); 2988: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]); 2989: fprintf(ficresp, "**********\n#"); 2990: fprintf(ficlog, "\n#********** Variable "); 2991: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficlog, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]); 2992: fprintf(ficlog, "**********\n#"); 2993: } 2994: for(i=1; i<=nlstate;i++) 2995: fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i); 2996: fprintf(ficresp, "\n"); 2997: 2998: for(i=iagemin; i <= iagemax+3; i++){ 2999: if(i==iagemax+3){ 3000: fprintf(ficlog,"Total"); 3001: }else{ 3002: if(first==1){ 3003: first=0; 3004: printf("See log file for details...\n"); 3005: } 3006: fprintf(ficlog,"Age %d", i); 3007: } 3008: for(jk=1; jk <=nlstate ; jk++){ 3009: for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++) 3010: pp[jk] += freq[jk][m][i]; 3011: } 3012: for(jk=1; jk <=nlstate ; jk++){ 3013: for(m=-1, pos=0; m <=0 ; m++) 3014: pos += freq[jk][m][i]; 3015: if(pp[jk]>=1.e-10){ 3016: if(first==1){ 3017: printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]); 3018: } 3019: fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]); 3020: }else{ 3021: if(first==1) 3022: printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk); 3023: fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk); 3024: } 3025: } 3026: 3027: for(jk=1; jk <=nlstate ; jk++){ 3028: for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++) 3029: pp[jk] += freq[jk][m][i]; 3030: } 3031: for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){ 3032: pos += pp[jk]; 3033: posprop += prop[jk][i]; 3034: } 3035: for(jk=1; jk <=nlstate ; jk++){ 3036: if(pos>=1.e-5){ 3037: if(first==1) 3038: printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos); 3039: fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos); 3040: }else{ 3041: if(first==1) 3042: printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk); 3043: fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk); 3044: } 3045: if( i <= iagemax){ 3046: if(pos>=1.e-5){ 3047: fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop); 3048: /*probs[i][jk][j1]= pp[jk]/pos;*/ 3049: /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/ 3050: } 3051: else 3052: fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop); 3053: } 3054: } 3055: 3056: for(jk=-1; jk <=nlstate+ndeath; jk++) 3057: for(m=-1; m <=nlstate+ndeath; m++) 3058: if(freq[jk][m][i] !=0 ) { 3059: if(first==1) 3060: printf(" %d%d=%.0f",jk,m,freq[jk][m][i]); 3061: fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]); 3062: } 3063: if(i <= iagemax) 3064: fprintf(ficresp,"\n"); 3065: if(first==1) 3066: printf("Others in log...\n"); 3067: fprintf(ficlog,"\n"); 3068: } 3069: /*}*/ 3070: } 3071: dateintmean=dateintsum/k2cpt; 3072: 3073: fclose(ficresp); 3074: free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3); 3075: free_vector(pp,1,nlstate); 3076: free_matrix(prop,1,nlstate,iagemin, iagemax+3); 3077: /* End of Freq */ 3078: } 3079: 3080: /************ Prevalence ********************/ 3081: 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) 3082: { 3083: /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people 3084: in each health status at the date of interview (if between dateprev1 and dateprev2). 3085: We still use firstpass and lastpass as another selection. 3086: */ 3087: 3088: int i, m, jk, j1, bool, z1,j; 3089: 3090: double **prop; 3091: double posprop; 3092: double y2; /* in fractional years */ 3093: int iagemin, iagemax; 3094: int first; /** to stop verbosity which is redirected to log file */ 3095: 3096: iagemin= (int) agemin; 3097: iagemax= (int) agemax; 3098: /*pp=vector(1,nlstate);*/ 3099: prop=matrix(1,nlstate,iagemin,iagemax+3); 3100: /* freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/ 3101: j1=0; 3102: 3103: /*j=cptcoveff;*/ 3104: if (cptcovn<1) {j=1;ncodemax[1]=1;} 3105: 3106: first=1; 3107: for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){ 3108: /*for(i1=1; i1<=ncodemax[k1];i1++){ 3109: j1++;*/ 3110: 3111: for (i=1; i<=nlstate; i++) 3112: for(m=iagemin; m <= iagemax+3; m++) 3113: prop[i][m]=0.0; 3114: 3115: for (i=1; i<=imx; i++) { /* Each individual */ 3116: bool=1; 3117: if (cptcovn>0) { 3118: for (z1=1; z1<=cptcoveff; z1++) 3119: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 3120: bool=0; 3121: } 3122: if (bool==1) { 3123: for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/ 3124: y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */ 3125: if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */ 3126: if(agev[m][i]==0) agev[m][i]=iagemax+1; 3127: if(agev[m][i]==1) agev[m][i]=iagemax+2; 3128: 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); 3129: if (s[m][i]>0 && s[m][i]<=nlstate) { 3130: /*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]]);*/ 3131: prop[s[m][i]][(int)agev[m][i]] += weight[i]; 3132: prop[s[m][i]][iagemax+3] += weight[i]; 3133: } 3134: } 3135: } /* end selection of waves */ 3136: } 3137: } 3138: for(i=iagemin; i <= iagemax+3; i++){ 3139: for(jk=1,posprop=0; jk <=nlstate ; jk++) { 3140: posprop += prop[jk][i]; 3141: } 3142: 3143: for(jk=1; jk <=nlstate ; jk++){ 3144: if( i <= iagemax){ 3145: if(posprop>=1.e-5){ 3146: probs[i][jk][j1]= prop[jk][i]/posprop; 3147: } else{ 3148: if(first==1){ 3149: first=0; 3150: 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]); 3151: } 3152: } 3153: } 3154: }/* end jk */ 3155: }/* end i */ 3156: /*} *//* end i1 */ 3157: } /* end j1 */ 3158: 3159: /* free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/ 3160: /*free_vector(pp,1,nlstate);*/ 3161: free_matrix(prop,1,nlstate, iagemin,iagemax+3); 3162: } /* End of prevalence */ 3163: 3164: /************* Waves Concatenation ***************/ 3165: 3166: 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) 3167: { 3168: /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i. 3169: Death is a valid wave (if date is known). 3170: mw[mi][i] is the mi (mi=1 to wav[i]) effective wave of individual i 3171: dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i] 3172: and mw[mi+1][i]. dh depends on stepm. 3173: */ 3174: 3175: int i, mi, m; 3176: /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1; 3177: double sum=0., jmean=0.;*/ 3178: int first; 3179: int j, k=0,jk, ju, jl; 3180: double sum=0.; 3181: first=0; 3182: jmin=100000; 3183: jmax=-1; 3184: jmean=0.; 3185: for(i=1; i<=imx; i++){ 3186: mi=0; 3187: m=firstpass; 3188: while(s[m][i] <= nlstate){ 3189: if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5) 3190: mw[++mi][i]=m; 3191: if(m >=lastpass) 3192: break; 3193: else 3194: m++; 3195: }/* end while */ 3196: if (s[m][i] > nlstate){ 3197: mi++; /* Death is another wave */ 3198: /* if(mi==0) never been interviewed correctly before death */ 3199: /* Only death is a correct wave */ 3200: mw[mi][i]=m; 3201: } 3202: 3203: wav[i]=mi; 3204: if(mi==0){ 3205: nbwarn++; 3206: if(first==0){ 3207: printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i); 3208: first=1; 3209: } 3210: if(first==1){ 3211: fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i); 3212: } 3213: } /* end mi==0 */ 3214: } /* End individuals */ 3215: 3216: for(i=1; i<=imx; i++){ 3217: for(mi=1; mi<wav[i];mi++){ 3218: if (stepm <=0) 3219: dh[mi][i]=1; 3220: else{ 3221: if (s[mw[mi+1][i]][i] > nlstate) { /* A death */ 3222: if (agedc[i] < 2*AGESUP) { 3223: j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 3224: if(j==0) j=1; /* Survives at least one month after exam */ 3225: else if(j<0){ 3226: nberr++; 3227: 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]); 3228: j=1; /* Temporary Dangerous patch */ 3229: 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); 3230: 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]); 3231: 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); 3232: } 3233: k=k+1; 3234: if (j >= jmax){ 3235: jmax=j; 3236: ijmax=i; 3237: } 3238: if (j <= jmin){ 3239: jmin=j; 3240: ijmin=i; 3241: } 3242: sum=sum+j; 3243: /*if (j<0) printf("j=%d num=%d \n",j,i);*/ 3244: /* printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/ 3245: } 3246: } 3247: else{ 3248: j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12)); 3249: /* 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]); */ 3250: 3251: k=k+1; 3252: if (j >= jmax) { 3253: jmax=j; 3254: ijmax=i; 3255: } 3256: else if (j <= jmin){ 3257: jmin=j; 3258: ijmin=i; 3259: } 3260: /* if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */ 3261: /*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]);*/ 3262: if(j<0){ 3263: nberr++; 3264: 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]); 3265: 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]); 3266: } 3267: sum=sum+j; 3268: } 3269: jk= j/stepm; 3270: jl= j -jk*stepm; 3271: ju= j -(jk+1)*stepm; 3272: if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */ 3273: if(jl==0){ 3274: dh[mi][i]=jk; 3275: bh[mi][i]=0; 3276: }else{ /* We want a negative bias in order to only have interpolation ie 3277: * to avoid the price of an extra matrix product in likelihood */ 3278: dh[mi][i]=jk+1; 3279: bh[mi][i]=ju; 3280: } 3281: }else{ 3282: if(jl <= -ju){ 3283: dh[mi][i]=jk; 3284: bh[mi][i]=jl; /* bias is positive if real duration 3285: * is higher than the multiple of stepm and negative otherwise. 3286: */ 3287: } 3288: else{ 3289: dh[mi][i]=jk+1; 3290: bh[mi][i]=ju; 3291: } 3292: if(dh[mi][i]==0){ 3293: dh[mi][i]=1; /* At least one step */ 3294: bh[mi][i]=ju; /* At least one step */ 3295: /* 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);*/ 3296: } 3297: } /* end if mle */ 3298: } 3299: } /* end wave */ 3300: } 3301: jmean=sum/k; 3302: 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); 3303: 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); 3304: } 3305: 3306: /*********** Tricode ****************************/ 3307: void tricode(int *Tvar, int **nbcode, int imx, int *Ndum) 3308: { 3309: /**< Uses cptcovn+2*cptcovprod as the number of covariates */ 3310: /* Tvar[i]=atoi(stre); find 'n' in Vn and stores in Tvar. If model=V2+V1 Tvar[1]=2 and Tvar[2]=1 3311: * Boring subroutine which should only output nbcode[Tvar[j]][k] 3312: * Tvar[5] in V2+V1+V3*age+V2*V4 is 2 (V2) 3313: * nbcode[Tvar[j]][1]= 3314: */ 3315: 3316: int ij=1, k=0, j=0, i=0, maxncov=NCOVMAX; 3317: int modmaxcovj=0; /* Modality max of covariates j */ 3318: int cptcode=0; /* Modality max of covariates j */ 3319: int modmincovj=0; /* Modality min of covariates j */ 3320: 3321: 3322: cptcoveff=0; 3323: 3324: for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */ 3325: 3326: /* Loop on covariates without age and products */ 3327: for (j=1; j<=(cptcovs); j++) { /* From model V1 + V2*age+ V3 + V3*V4 keeps V1 + V3 = 2 only */ 3328: for (k=-1; k < maxncov; k++) Ndum[k]=0; 3329: for (i=1; i<=imx; i++) { /* Loop on individuals: reads the data file to get the maximum value of the 3330: modality of this covariate Vj*/ 3331: ij=(int)(covar[Tvar[j]][i]); /* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i 3332: * If product of Vn*Vm, still boolean *: 3333: * If it was coded 1, 2, 3, 4 should be splitted into 3 boolean variables 3334: * 1 => 0 0 0, 2 => 0 0 1, 3 => 0 1 1, 4=1 0 0 */ 3335: /* Finds for covariate j, n=Tvar[j] of Vn . ij is the 3336: modality of the nth covariate of individual i. */ 3337: if (ij > modmaxcovj) 3338: modmaxcovj=ij; 3339: else if (ij < modmincovj) 3340: modmincovj=ij; 3341: if ((ij < -1) && (ij > NCOVMAX)){ 3342: printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX ); 3343: exit(1); 3344: }else 3345: Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/ 3346: /* If coded 1, 2, 3 , counts the number of 1 Ndum[1], number of 2, Ndum[2], etc */ 3347: /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/ 3348: /* getting the maximum value of the modality of the covariate 3349: (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and 3350: female is 1, then modmaxcovj=1.*/ 3351: } /* end for loop on individuals i */ 3352: printf(" Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", j, Tvar[j], modmincovj, modmaxcovj); 3353: fprintf(ficlog," Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", j, Tvar[j], modmincovj, modmaxcovj); 3354: cptcode=modmaxcovj; 3355: /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */ 3356: /*for (i=0; i<=cptcode; i++) {*/ 3357: for (k=modmincovj; k<=modmaxcovj; k++) { /* k=-1 ? 0 and 1*//* For each value k of the modality of model-cov j */ 3358: printf("Frequencies of covariates %d ie V%d with value %d: %d\n", j, Tvar[j], k, Ndum[k]); 3359: fprintf(ficlog, "Frequencies of covariates %d ie V%d with value %d: %d\n", j, Tvar[j], k, Ndum[k]); 3360: if( Ndum[k] != 0 ){ /* Counts if nobody answered modality k ie empty modality, we skip it and reorder */ 3361: if( k != -1){ 3362: ncodemax[j]++; /* ncodemax[j]= Number of modalities of the j th 3363: covariate for which somebody answered excluding 3364: undefined. Usually 2: 0 and 1. */ 3365: } 3366: ncodemaxwundef[j]++; /* ncodemax[j]= Number of modalities of the j th 3367: covariate for which somebody answered including 3368: undefined. Usually 3: -1, 0 and 1. */ 3369: } 3370: /* In fact ncodemax[j]=2 (dichotom. variables only) but it could be more for 3371: historical reasons: 3 if coded 1, 2, 3 and 4 and Ndum[2]=0 */ 3372: } /* Ndum[-1] number of undefined modalities */ 3373: 3374: /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */ 3375: /* For covariate j, modalities could be 1, 2, 3, 4, 5, 6, 7. 3376: If Ndum[1]=0, Ndum[2]=0, Ndum[3]= 635, Ndum[4]=0, Ndum[5]=0, Ndum[6]=27, Ndum[7]=125; 3377: modmincovj=3; modmaxcovj = 7; 3378: There are only 3 modalities non empty 3, 6, 7 (or 2 if 27 is too few) : ncodemax[j]=3; 3379: which will be coded 0, 1, 2 which in binary on 2=3-1 digits are 0=00 1=01, 2=10; 3380: defining two dummy variables: variables V1_1 and V1_2. 3381: nbcode[Tvar[j]][ij]=k; 3382: nbcode[Tvar[j]][1]=0; 3383: nbcode[Tvar[j]][2]=1; 3384: nbcode[Tvar[j]][3]=2; 3385: */ 3386: ij=0; /* ij is similar to i but can jumps over null modalities */ 3387: for (i=modmincovj; i<=modmaxcovj; i++) { /* i= 1 to 2 for dichotomous, or from 1 to 3 or from -1 to 1*/ 3388: if (Ndum[i] == 0) { /* If at least one individual responded to this modality k */ 3389: break; 3390: } 3391: ij++; 3392: nbcode[Tvar[j]][ij]=i; /* stores the original modality i in an array nbcode, ij modality from 1 to last non-nul modality.*/ 3393: cptcode = ij; /* New max modality for covar j */ 3394: } /* end of loop on modality i=-1 to 1 or more */ 3395: 3396: /* for (k=0; k<= cptcode; k++) { /\* k=-1 ? k=0 to 1 *\//\* Could be 1 to 4 *\//\* cptcode=modmaxcovj *\/ */ 3397: /* /\*recode from 0 *\/ */ 3398: /* k is a modality. If we have model=V1+V1*sex */ 3399: /* then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */ 3400: /* But if some modality were not used, it is recoded from 0 to a newer modmaxcovj=cptcode *\/ */ 3401: /* } */ 3402: /* /\* cptcode = ij; *\/ /\* New max modality for covar j *\/ */ 3403: /* if (ij > ncodemax[j]) { */ 3404: /* printf( " Error ij=%d > ncodemax[%d]=%d\n", ij, j, ncodemax[j]); */ 3405: /* fprintf(ficlog, " Error ij=%d > ncodemax[%d]=%d\n", ij, j, ncodemax[j]); */ 3406: /* break; */ 3407: /* } */ 3408: /* } /\* end of loop on modality k *\/ */ 3409: } /* end of loop on model-covariate j. nbcode[Tvarj][1]=0 and nbcode[Tvarj][2]=1 sets the value of covariate j*/ 3410: 3411: for (k=-1; k< maxncov; k++) Ndum[k]=0; 3412: 3413: for (i=1; i<=ncovmodel-2-nagesqr; i++) { /* -2, cste and age and eventually age*age */ 3414: /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/ 3415: ij=Tvar[i]; /* Tvar might be -1 if status was unknown */ 3416: Ndum[ij]++; /* Might be supersed V1 + V1*age */ 3417: } 3418: 3419: ij=0; 3420: for (i=0; i<= maxncov-1; i++) { /* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) */ 3421: /*printf("Ndum[%d]=%d\n",i, Ndum[i]);*/ 3422: if((Ndum[i]!=0) && (i<=ncovcol)){ 3423: ij++; 3424: /*printf("diff Ndum[%d]=%d\n",i, Ndum[i]);*/ 3425: Tvaraff[ij]=i; /*For printing (unclear) */ 3426: }else{ 3427: /* Tvaraff[ij]=0; */ 3428: } 3429: } 3430: /* ij--; */ 3431: cptcoveff=ij; /*Number of total covariates*/ 3432: 3433: } 3434: 3435: 3436: /*********** Health Expectancies ****************/ 3437: 3438: void evsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,char strstart[] ) 3439: 3440: { 3441: /* Health expectancies, no variances */ 3442: int i, j, nhstepm, hstepm, h, nstepm; 3443: int nhstepma, nstepma; /* Decreasing with age */ 3444: double age, agelim, hf; 3445: double ***p3mat; 3446: double eip; 3447: 3448: pstamp(ficreseij); 3449: fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n"); 3450: fprintf(ficreseij,"# Age"); 3451: for(i=1; i<=nlstate;i++){ 3452: for(j=1; j<=nlstate;j++){ 3453: fprintf(ficreseij," e%1d%1d ",i,j); 3454: } 3455: fprintf(ficreseij," e%1d. ",i); 3456: } 3457: fprintf(ficreseij,"\n"); 3458: 3459: 3460: if(estepm < stepm){ 3461: printf ("Problem %d lower than %d\n",estepm, stepm); 3462: } 3463: else hstepm=estepm; 3464: /* We compute the life expectancy from trapezoids spaced every estepm months 3465: * This is mainly to measure the difference between two models: for example 3466: * if stepm=24 months pijx are given only every 2 years and by summing them 3467: * we are calculating an estimate of the Life Expectancy assuming a linear 3468: * progression in between and thus overestimating or underestimating according 3469: * to the curvature of the survival function. If, for the same date, we 3470: * estimate the model with stepm=1 month, we can keep estepm to 24 months 3471: * to compare the new estimate of Life expectancy with the same linear 3472: * hypothesis. A more precise result, taking into account a more precise 3473: * curvature will be obtained if estepm is as small as stepm. */ 3474: 3475: /* For example we decided to compute the life expectancy with the smallest unit */ 3476: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 3477: nhstepm is the number of hstepm from age to agelim 3478: nstepm is the number of stepm from age to agelin. 3479: Look at hpijx to understand the reason of that which relies in memory size 3480: and note for a fixed period like estepm months */ 3481: /* We decided (b) to get a life expectancy respecting the most precise curvature of the 3482: survival function given by stepm (the optimization length). Unfortunately it 3483: means that if the survival funtion is printed only each two years of age and if 3484: you sum them up and add 1 year (area under the trapezoids) you won't get the same 3485: results. So we changed our mind and took the option of the best precision. 3486: */ 3487: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 3488: 3489: agelim=AGESUP; 3490: /* If stepm=6 months */ 3491: /* Computed by stepm unit matrices, product of hstepm matrices, stored 3492: in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */ 3493: 3494: /* nhstepm age range expressed in number of stepm */ 3495: nstepm=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */ 3496: /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 3497: /* if (stepm >= YEARM) hstepm=1;*/ 3498: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */ 3499: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); 3500: 3501: for (age=bage; age<=fage; age ++){ 3502: nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */ 3503: /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 3504: /* if (stepm >= YEARM) hstepm=1;*/ 3505: nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */ 3506: 3507: /* If stepm=6 months */ 3508: /* Computed by stepm unit matrices, product of hstepma matrices, stored 3509: in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */ 3510: 3511: hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij); 3512: 3513: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */ 3514: 3515: printf("%d|",(int)age);fflush(stdout); 3516: fprintf(ficlog,"%d|",(int)age);fflush(ficlog); 3517: 3518: /* Computing expectancies */ 3519: for(i=1; i<=nlstate;i++) 3520: for(j=1; j<=nlstate;j++) 3521: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){ 3522: eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf; 3523: 3524: /* 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]);*/ 3525: 3526: } 3527: 3528: fprintf(ficreseij,"%3.0f",age ); 3529: for(i=1; i<=nlstate;i++){ 3530: eip=0; 3531: for(j=1; j<=nlstate;j++){ 3532: eip +=eij[i][j][(int)age]; 3533: fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] ); 3534: } 3535: fprintf(ficreseij,"%9.4f", eip ); 3536: } 3537: fprintf(ficreseij,"\n"); 3538: 3539: } 3540: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); 3541: printf("\n"); 3542: fprintf(ficlog,"\n"); 3543: 3544: } 3545: 3546: 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[] ) 3547: 3548: { 3549: /* Covariances of health expectancies eij and of total life expectancies according 3550: to initial status i, ei. . 3551: */ 3552: int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji; 3553: int nhstepma, nstepma; /* Decreasing with age */ 3554: double age, agelim, hf; 3555: double ***p3matp, ***p3matm, ***varhe; 3556: double **dnewm,**doldm; 3557: double *xp, *xm; 3558: double **gp, **gm; 3559: double ***gradg, ***trgradg; 3560: int theta; 3561: 3562: double eip, vip; 3563: 3564: varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage); 3565: xp=vector(1,npar); 3566: xm=vector(1,npar); 3567: dnewm=matrix(1,nlstate*nlstate,1,npar); 3568: doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate); 3569: 3570: pstamp(ficresstdeij); 3571: fprintf(ficresstdeij,"# Health expectancies with standard errors\n"); 3572: fprintf(ficresstdeij,"# Age"); 3573: for(i=1; i<=nlstate;i++){ 3574: for(j=1; j<=nlstate;j++) 3575: fprintf(ficresstdeij," e%1d%1d (SE)",i,j); 3576: fprintf(ficresstdeij," e%1d. ",i); 3577: } 3578: fprintf(ficresstdeij,"\n"); 3579: 3580: pstamp(ficrescveij); 3581: fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n"); 3582: fprintf(ficrescveij,"# Age"); 3583: for(i=1; i<=nlstate;i++) 3584: for(j=1; j<=nlstate;j++){ 3585: cptj= (j-1)*nlstate+i; 3586: for(i2=1; i2<=nlstate;i2++) 3587: for(j2=1; j2<=nlstate;j2++){ 3588: cptj2= (j2-1)*nlstate+i2; 3589: if(cptj2 <= cptj) 3590: fprintf(ficrescveij," %1d%1d,%1d%1d",i,j,i2,j2); 3591: } 3592: } 3593: fprintf(ficrescveij,"\n"); 3594: 3595: if(estepm < stepm){ 3596: printf ("Problem %d lower than %d\n",estepm, stepm); 3597: } 3598: else hstepm=estepm; 3599: /* We compute the life expectancy from trapezoids spaced every estepm months 3600: * This is mainly to measure the difference between two models: for example 3601: * if stepm=24 months pijx are given only every 2 years and by summing them 3602: * we are calculating an estimate of the Life Expectancy assuming a linear 3603: * progression in between and thus overestimating or underestimating according 3604: * to the curvature of the survival function. If, for the same date, we 3605: * estimate the model with stepm=1 month, we can keep estepm to 24 months 3606: * to compare the new estimate of Life expectancy with the same linear 3607: * hypothesis. A more precise result, taking into account a more precise 3608: * curvature will be obtained if estepm is as small as stepm. */ 3609: 3610: /* For example we decided to compute the life expectancy with the smallest unit */ 3611: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 3612: nhstepm is the number of hstepm from age to agelim 3613: nstepm is the number of stepm from age to agelin. 3614: Look at hpijx to understand the reason of that which relies in memory size 3615: and note for a fixed period like estepm months */ 3616: /* We decided (b) to get a life expectancy respecting the most precise curvature of the 3617: survival function given by stepm (the optimization length). Unfortunately it 3618: means that if the survival funtion is printed only each two years of age and if 3619: you sum them up and add 1 year (area under the trapezoids) you won't get the same 3620: results. So we changed our mind and took the option of the best precision. 3621: */ 3622: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 3623: 3624: /* If stepm=6 months */ 3625: /* nhstepm age range expressed in number of stepm */ 3626: agelim=AGESUP; 3627: nstepm=(int) rint((agelim-bage)*YEARM/stepm); 3628: /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 3629: /* if (stepm >= YEARM) hstepm=1;*/ 3630: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */ 3631: 3632: p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); 3633: p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); 3634: gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate); 3635: trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar); 3636: gp=matrix(0,nhstepm,1,nlstate*nlstate); 3637: gm=matrix(0,nhstepm,1,nlstate*nlstate); 3638: 3639: for (age=bage; age<=fage; age ++){ 3640: nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */ 3641: /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 3642: /* if (stepm >= YEARM) hstepm=1;*/ 3643: nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */ 3644: 3645: /* If stepm=6 months */ 3646: /* Computed by stepm unit matrices, product of hstepma matrices, stored 3647: in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */ 3648: 3649: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */ 3650: 3651: /* Computing Variances of health expectancies */ 3652: /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to 3653: decrease memory allocation */ 3654: for(theta=1; theta <=npar; theta++){ 3655: for(i=1; i<=npar; i++){ 3656: xp[i] = x[i] + (i==theta ?delti[theta]:0); 3657: xm[i] = x[i] - (i==theta ?delti[theta]:0); 3658: } 3659: hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij); 3660: hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij); 3661: 3662: for(j=1; j<= nlstate; j++){ 3663: for(i=1; i<=nlstate; i++){ 3664: for(h=0; h<=nhstepm-1; h++){ 3665: gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.; 3666: gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.; 3667: } 3668: } 3669: } 3670: 3671: for(ij=1; ij<= nlstate*nlstate; ij++) 3672: for(h=0; h<=nhstepm-1; h++){ 3673: gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta]; 3674: } 3675: }/* End theta */ 3676: 3677: 3678: for(h=0; h<=nhstepm-1; h++) 3679: for(j=1; j<=nlstate*nlstate;j++) 3680: for(theta=1; theta <=npar; theta++) 3681: trgradg[h][j][theta]=gradg[h][theta][j]; 3682: 3683: 3684: for(ij=1;ij<=nlstate*nlstate;ij++) 3685: for(ji=1;ji<=nlstate*nlstate;ji++) 3686: varhe[ij][ji][(int)age] =0.; 3687: 3688: printf("%d|",(int)age);fflush(stdout); 3689: fprintf(ficlog,"%d|",(int)age);fflush(ficlog); 3690: for(h=0;h<=nhstepm-1;h++){ 3691: for(k=0;k<=nhstepm-1;k++){ 3692: matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov); 3693: matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]); 3694: for(ij=1;ij<=nlstate*nlstate;ij++) 3695: for(ji=1;ji<=nlstate*nlstate;ji++) 3696: varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf; 3697: } 3698: } 3699: 3700: /* Computing expectancies */ 3701: hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij); 3702: for(i=1; i<=nlstate;i++) 3703: for(j=1; j<=nlstate;j++) 3704: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){ 3705: eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf; 3706: 3707: /* 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]);*/ 3708: 3709: } 3710: 3711: fprintf(ficresstdeij,"%3.0f",age ); 3712: for(i=1; i<=nlstate;i++){ 3713: eip=0.; 3714: vip=0.; 3715: for(j=1; j<=nlstate;j++){ 3716: eip += eij[i][j][(int)age]; 3717: for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */ 3718: vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age]; 3719: fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) ); 3720: } 3721: fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip)); 3722: } 3723: fprintf(ficresstdeij,"\n"); 3724: 3725: fprintf(ficrescveij,"%3.0f",age ); 3726: for(i=1; i<=nlstate;i++) 3727: for(j=1; j<=nlstate;j++){ 3728: cptj= (j-1)*nlstate+i; 3729: for(i2=1; i2<=nlstate;i2++) 3730: for(j2=1; j2<=nlstate;j2++){ 3731: cptj2= (j2-1)*nlstate+i2; 3732: if(cptj2 <= cptj) 3733: fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]); 3734: } 3735: } 3736: fprintf(ficrescveij,"\n"); 3737: 3738: } 3739: free_matrix(gm,0,nhstepm,1,nlstate*nlstate); 3740: free_matrix(gp,0,nhstepm,1,nlstate*nlstate); 3741: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate); 3742: free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar); 3743: free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); 3744: free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); 3745: printf("\n"); 3746: fprintf(ficlog,"\n"); 3747: 3748: free_vector(xm,1,npar); 3749: free_vector(xp,1,npar); 3750: free_matrix(dnewm,1,nlstate*nlstate,1,npar); 3751: free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate); 3752: free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage); 3753: } 3754: 3755: /************ Variance ******************/ 3756: 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[]) 3757: { 3758: /* Variance of health expectancies */ 3759: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/ 3760: /* double **newm;*/ 3761: /* int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav)*/ 3762: 3763: int movingaverage(); 3764: double **dnewm,**doldm; 3765: double **dnewmp,**doldmp; 3766: int i, j, nhstepm, hstepm, h, nstepm ; 3767: int k; 3768: double *xp; 3769: double **gp, **gm; /* for var eij */ 3770: double ***gradg, ***trgradg; /*for var eij */ 3771: double **gradgp, **trgradgp; /* for var p point j */ 3772: double *gpp, *gmp; /* for var p point j */ 3773: double **varppt; /* for var p point j nlstate to nlstate+ndeath */ 3774: double ***p3mat; 3775: double age,agelim, hf; 3776: double ***mobaverage; 3777: int theta; 3778: char digit[4]; 3779: char digitp[25]; 3780: 3781: char fileresprobmorprev[FILENAMELENGTH]; 3782: 3783: if(popbased==1){ 3784: if(mobilav!=0) 3785: strcpy(digitp,"-populbased-mobilav-"); 3786: else strcpy(digitp,"-populbased-nomobil-"); 3787: } 3788: else 3789: strcpy(digitp,"-stablbased-"); 3790: 3791: if (mobilav!=0) { 3792: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); 3793: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){ 3794: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav); 3795: printf(" Error in movingaverage mobilav=%d\n",mobilav); 3796: } 3797: } 3798: 3799: strcpy(fileresprobmorprev,"prmorprev"); 3800: sprintf(digit,"%-d",ij); 3801: /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/ 3802: strcat(fileresprobmorprev,digit); /* Tvar to be done */ 3803: strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */ 3804: strcat(fileresprobmorprev,fileres); 3805: if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) { 3806: printf("Problem with resultfile: %s\n", fileresprobmorprev); 3807: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev); 3808: } 3809: printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev); 3810: 3811: fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev); 3812: pstamp(ficresprobmorprev); 3813: 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); 3814: fprintf(ficresprobmorprev,"# Age cov=%-d",ij); 3815: for(j=nlstate+1; j<=(nlstate+ndeath);j++){ 3816: fprintf(ficresprobmorprev," p.%-d SE",j); 3817: for(i=1; i<=nlstate;i++) 3818: fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j); 3819: } 3820: fprintf(ficresprobmorprev,"\n"); 3821: fprintf(ficgp,"\n# Routine varevsij"); 3822: /* fprintf(fichtm, "#Local time at start: %s", strstart);*/ 3823: 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"); 3824: fprintf(fichtm,"\n %s \n",digitp); 3825: /* } */ 3826: varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath); 3827: pstamp(ficresvij); 3828: fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n# (weighted average of eij where weights are "); 3829: if(popbased==1) 3830: 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); 3831: else 3832: fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n"); 3833: fprintf(ficresvij,"# Age"); 3834: for(i=1; i<=nlstate;i++) 3835: for(j=1; j<=nlstate;j++) 3836: fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j); 3837: fprintf(ficresvij,"\n"); 3838: 3839: xp=vector(1,npar); 3840: dnewm=matrix(1,nlstate,1,npar); 3841: doldm=matrix(1,nlstate,1,nlstate); 3842: dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar); 3843: doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath); 3844: 3845: gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath); 3846: gpp=vector(nlstate+1,nlstate+ndeath); 3847: gmp=vector(nlstate+1,nlstate+ndeath); 3848: trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/ 3849: 3850: if(estepm < stepm){ 3851: printf ("Problem %d lower than %d\n",estepm, stepm); 3852: } 3853: else hstepm=estepm; 3854: /* For example we decided to compute the life expectancy with the smallest unit */ 3855: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 3856: nhstepm is the number of hstepm from age to agelim 3857: nstepm is the number of stepm from age to agelin. 3858: Look at function hpijx to understand why (it is linked to memory size questions) */ 3859: /* We decided (b) to get a life expectancy respecting the most precise curvature of the 3860: survival function given by stepm (the optimization length). Unfortunately it 3861: means that if the survival funtion is printed every two years of age and if 3862: you sum them up and add 1 year (area under the trapezoids) you won't get the same 3863: results. So we changed our mind and took the option of the best precision. 3864: */ 3865: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 3866: agelim = AGESUP; 3867: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */ 3868: nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 3869: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */ 3870: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); 3871: gradg=ma3x(0,nhstepm,1,npar,1,nlstate); 3872: gp=matrix(0,nhstepm,1,nlstate); 3873: gm=matrix(0,nhstepm,1,nlstate); 3874: 3875: 3876: for(theta=1; theta <=npar; theta++){ 3877: for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/ 3878: xp[i] = x[i] + (i==theta ?delti[theta]:0); 3879: } 3880: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij); 3881: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij); 3882: 3883: if (popbased==1) { 3884: if(mobilav ==0){ 3885: for(i=1; i<=nlstate;i++) 3886: prlim[i][i]=probs[(int)age][i][ij]; 3887: }else{ /* mobilav */ 3888: for(i=1; i<=nlstate;i++) 3889: prlim[i][i]=mobaverage[(int)age][i][ij]; 3890: } 3891: } 3892: 3893: for(j=1; j<= nlstate; j++){ 3894: for(h=0; h<=nhstepm; h++){ 3895: for(i=1, gp[h][j]=0.;i<=nlstate;i++) 3896: gp[h][j] += prlim[i][i]*p3mat[i][j][h]; 3897: } 3898: } 3899: /* This for computing probability of death (h=1 means 3900: computed over hstepm matrices product = hstepm*stepm months) 3901: as a weighted average of prlim. 3902: */ 3903: for(j=nlstate+1;j<=nlstate+ndeath;j++){ 3904: for(i=1,gpp[j]=0.; i<= nlstate; i++) 3905: gpp[j] += prlim[i][i]*p3mat[i][j][1]; 3906: } 3907: /* end probability of death */ 3908: 3909: for(i=1; i<=npar; i++) /* Computes gradient x - delta */ 3910: xp[i] = x[i] - (i==theta ?delti[theta]:0); 3911: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij); 3912: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij); 3913: 3914: if (popbased==1) { 3915: if(mobilav ==0){ 3916: for(i=1; i<=nlstate;i++) 3917: prlim[i][i]=probs[(int)age][i][ij]; 3918: }else{ /* mobilav */ 3919: for(i=1; i<=nlstate;i++) 3920: prlim[i][i]=mobaverage[(int)age][i][ij]; 3921: } 3922: } 3923: 3924: for(j=1; j<= nlstate; j++){ /* Sum of wi * eij = e.j */ 3925: for(h=0; h<=nhstepm; h++){ 3926: for(i=1, gm[h][j]=0.;i<=nlstate;i++) 3927: gm[h][j] += prlim[i][i]*p3mat[i][j][h]; 3928: } 3929: } 3930: /* This for computing probability of death (h=1 means 3931: computed over hstepm matrices product = hstepm*stepm months) 3932: as a weighted average of prlim. 3933: */ 3934: for(j=nlstate+1;j<=nlstate+ndeath;j++){ 3935: for(i=1,gmp[j]=0.; i<= nlstate; i++) 3936: gmp[j] += prlim[i][i]*p3mat[i][j][1]; 3937: } 3938: /* end probability of death */ 3939: 3940: for(j=1; j<= nlstate; j++) /* vareij */ 3941: for(h=0; h<=nhstepm; h++){ 3942: gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta]; 3943: } 3944: 3945: for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */ 3946: gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta]; 3947: } 3948: 3949: } /* End theta */ 3950: 3951: trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */ 3952: 3953: for(h=0; h<=nhstepm; h++) /* veij */ 3954: for(j=1; j<=nlstate;j++) 3955: for(theta=1; theta <=npar; theta++) 3956: trgradg[h][j][theta]=gradg[h][theta][j]; 3957: 3958: for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */ 3959: for(theta=1; theta <=npar; theta++) 3960: trgradgp[j][theta]=gradgp[theta][j]; 3961: 3962: 3963: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */ 3964: for(i=1;i<=nlstate;i++) 3965: for(j=1;j<=nlstate;j++) 3966: vareij[i][j][(int)age] =0.; 3967: 3968: for(h=0;h<=nhstepm;h++){ 3969: for(k=0;k<=nhstepm;k++){ 3970: matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov); 3971: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]); 3972: for(i=1;i<=nlstate;i++) 3973: for(j=1;j<=nlstate;j++) 3974: vareij[i][j][(int)age] += doldm[i][j]*hf*hf; 3975: } 3976: } 3977: 3978: /* pptj */ 3979: matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov); 3980: matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp); 3981: for(j=nlstate+1;j<=nlstate+ndeath;j++) 3982: for(i=nlstate+1;i<=nlstate+ndeath;i++) 3983: varppt[j][i]=doldmp[j][i]; 3984: /* end ppptj */ 3985: /* x centered again */ 3986: hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij); 3987: prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij); 3988: 3989: if (popbased==1) { 3990: if(mobilav ==0){ 3991: for(i=1; i<=nlstate;i++) 3992: prlim[i][i]=probs[(int)age][i][ij]; 3993: }else{ /* mobilav */ 3994: for(i=1; i<=nlstate;i++) 3995: prlim[i][i]=mobaverage[(int)age][i][ij]; 3996: } 3997: } 3998: 3999: /* This for computing probability of death (h=1 means 4000: computed over hstepm (estepm) matrices product = hstepm*stepm months) 4001: as a weighted average of prlim. 4002: */ 4003: for(j=nlstate+1;j<=nlstate+ndeath;j++){ 4004: for(i=1,gmp[j]=0.;i<= nlstate; i++) 4005: gmp[j] += prlim[i][i]*p3mat[i][j][1]; 4006: } 4007: /* end probability of death */ 4008: 4009: fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij); 4010: for(j=nlstate+1; j<=(nlstate+ndeath);j++){ 4011: fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j])); 4012: for(i=1; i<=nlstate;i++){ 4013: fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]); 4014: } 4015: } 4016: fprintf(ficresprobmorprev,"\n"); 4017: 4018: fprintf(ficresvij,"%.0f ",age ); 4019: for(i=1; i<=nlstate;i++) 4020: for(j=1; j<=nlstate;j++){ 4021: fprintf(ficresvij," %.4f", vareij[i][j][(int)age]); 4022: } 4023: fprintf(ficresvij,"\n"); 4024: free_matrix(gp,0,nhstepm,1,nlstate); 4025: free_matrix(gm,0,nhstepm,1,nlstate); 4026: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate); 4027: free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar); 4028: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); 4029: } /* End age */ 4030: free_vector(gpp,nlstate+1,nlstate+ndeath); 4031: free_vector(gmp,nlstate+1,nlstate+ndeath); 4032: free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath); 4033: free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/ 4034: fprintf(ficgp,"\nunset parametric;unset label; set ter png small size 320, 240"); 4035: /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */ 4036: fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";"); 4037: /* fprintf(ficgp,"\n plot \"%s\" u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */ 4038: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */ 4039: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */ 4040: fprintf(ficgp,"\n plot \"%s\" u 1:($3) not w l lt 1 ",subdirf(fileresprobmorprev)); 4041: fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)) t \"95%% interval\" w l lt 2 ",subdirf(fileresprobmorprev)); 4042: fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)) not w l lt 2 ",subdirf(fileresprobmorprev)); 4043: fprintf(fichtm,"\n File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev)); 4044: fprintf(fichtm,"\n Probability is computed over estepm=%d months. <img src=\"%s%s.png\"> \n", estepm,subdirf3(optionfilefiname,"varmuptjgr",digitp),digit); 4045: /* fprintf(fichtm,"\n 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 <img src=\"varmuptjgr%s%s.png\"> \n", stepm,YEARM,digitp,digit); 4046: */ 4047: /* fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */ 4048: fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit); 4049: 4050: free_vector(xp,1,npar); 4051: free_matrix(doldm,1,nlstate,1,nlstate); 4052: free_matrix(dnewm,1,nlstate,1,npar); 4053: free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath); 4054: free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar); 4055: free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath); 4056: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); 4057: fclose(ficresprobmorprev); 4058: fflush(ficgp); 4059: fflush(fichtm); 4060: } /* end varevsij */ 4061: 4062: /************ Variance of prevlim ******************/ 4063: 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[]) 4064: { 4065: /* Variance of prevalence limit */ 4066: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/ 4067: 4068: double **dnewm,**doldm; 4069: int i, j, nhstepm, hstepm; 4070: double *xp; 4071: double *gp, *gm; 4072: double **gradg, **trgradg; 4073: double age,agelim; 4074: int theta; 4075: 4076: pstamp(ficresvpl); 4077: fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n"); 4078: fprintf(ficresvpl,"# Age"); 4079: for(i=1; i<=nlstate;i++) 4080: fprintf(ficresvpl," %1d-%1d",i,i); 4081: fprintf(ficresvpl,"\n"); 4082: 4083: xp=vector(1,npar); 4084: dnewm=matrix(1,nlstate,1,npar); 4085: doldm=matrix(1,nlstate,1,nlstate); 4086: 4087: hstepm=1*YEARM; /* Every year of age */ 4088: hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 4089: agelim = AGESUP; 4090: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */ 4091: nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 4092: if (stepm >= YEARM) hstepm=1; 4093: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */ 4094: gradg=matrix(1,npar,1,nlstate); 4095: gp=vector(1,nlstate); 4096: gm=vector(1,nlstate); 4097: 4098: for(theta=1; theta <=npar; theta++){ 4099: for(i=1; i<=npar; i++){ /* Computes gradient */ 4100: xp[i] = x[i] + (i==theta ?delti[theta]:0); 4101: } 4102: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij); 4103: for(i=1;i<=nlstate;i++) 4104: gp[i] = prlim[i][i]; 4105: 4106: for(i=1; i<=npar; i++) /* Computes gradient */ 4107: xp[i] = x[i] - (i==theta ?delti[theta]:0); 4108: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij); 4109: for(i=1;i<=nlstate;i++) 4110: gm[i] = prlim[i][i]; 4111: 4112: for(i=1;i<=nlstate;i++) 4113: gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta]; 4114: } /* End theta */ 4115: 4116: trgradg =matrix(1,nlstate,1,npar); 4117: 4118: for(j=1; j<=nlstate;j++) 4119: for(theta=1; theta <=npar; theta++) 4120: trgradg[j][theta]=gradg[theta][j]; 4121: 4122: for(i=1;i<=nlstate;i++) 4123: varpl[i][(int)age] =0.; 4124: matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov); 4125: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg); 4126: for(i=1;i<=nlstate;i++) 4127: varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */ 4128: 4129: fprintf(ficresvpl,"%.0f ",age ); 4130: for(i=1; i<=nlstate;i++) 4131: fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age])); 4132: fprintf(ficresvpl,"\n"); 4133: free_vector(gp,1,nlstate); 4134: free_vector(gm,1,nlstate); 4135: free_matrix(gradg,1,npar,1,nlstate); 4136: free_matrix(trgradg,1,nlstate,1,npar); 4137: } /* End age */ 4138: 4139: free_vector(xp,1,npar); 4140: free_matrix(doldm,1,nlstate,1,npar); 4141: free_matrix(dnewm,1,nlstate,1,nlstate); 4142: 4143: } 4144: 4145: /************ Variance of one-step probabilities ******************/ 4146: 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[]) 4147: { 4148: int i, j=0, k1, l1, tj; 4149: int k2, l2, j1, z1; 4150: int k=0, l; 4151: int first=1, first1, first2; 4152: double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp; 4153: double **dnewm,**doldm; 4154: double *xp; 4155: double *gp, *gm; 4156: double **gradg, **trgradg; 4157: double **mu; 4158: double age, cov[NCOVMAX+1]; 4159: double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */ 4160: int theta; 4161: char fileresprob[FILENAMELENGTH]; 4162: char fileresprobcov[FILENAMELENGTH]; 4163: char fileresprobcor[FILENAMELENGTH]; 4164: double ***varpij; 4165: 4166: strcpy(fileresprob,"prob"); 4167: strcat(fileresprob,fileres); 4168: if((ficresprob=fopen(fileresprob,"w"))==NULL) { 4169: printf("Problem with resultfile: %s\n", fileresprob); 4170: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob); 4171: } 4172: strcpy(fileresprobcov,"probcov"); 4173: strcat(fileresprobcov,fileres); 4174: if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) { 4175: printf("Problem with resultfile: %s\n", fileresprobcov); 4176: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov); 4177: } 4178: strcpy(fileresprobcor,"probcor"); 4179: strcat(fileresprobcor,fileres); 4180: if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) { 4181: printf("Problem with resultfile: %s\n", fileresprobcor); 4182: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor); 4183: } 4184: printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob); 4185: fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob); 4186: printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov); 4187: fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov); 4188: printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor); 4189: fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor); 4190: pstamp(ficresprob); 4191: fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n"); 4192: fprintf(ficresprob,"# Age"); 4193: pstamp(ficresprobcov); 4194: fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n"); 4195: fprintf(ficresprobcov,"# Age"); 4196: pstamp(ficresprobcor); 4197: fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n"); 4198: fprintf(ficresprobcor,"# Age"); 4199: 4200: 4201: for(i=1; i<=nlstate;i++) 4202: for(j=1; j<=(nlstate+ndeath);j++){ 4203: fprintf(ficresprob," p%1d-%1d (SE)",i,j); 4204: fprintf(ficresprobcov," p%1d-%1d ",i,j); 4205: fprintf(ficresprobcor," p%1d-%1d ",i,j); 4206: } 4207: /* fprintf(ficresprob,"\n"); 4208: fprintf(ficresprobcov,"\n"); 4209: fprintf(ficresprobcor,"\n"); 4210: */ 4211: xp=vector(1,npar); 4212: dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar); 4213: doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath)); 4214: mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage); 4215: varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage); 4216: first=1; 4217: fprintf(ficgp,"\n# Routine varprob"); 4218: fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n"); 4219: fprintf(fichtm,"\n"); 4220: 4221: fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov); 4222: fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\ 4223: file %s \n",optionfilehtmcov); 4224: fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\ 4225: and drawn. It helps understanding how is the covariance between two incidences.\ 4226: They are expressed in year-1 in order to be less dependent of stepm. \n"); 4227: fprintf(fichtmcov,"\n Contour plot corresponding to x'cov-1x = 4 (where x is the column vector (pij,pkl)) are drawn. \ 4228: It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \ 4229: would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \ 4230: standard deviations wide on each axis. \ 4231: Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\ 4232: and made the appropriate rotation to look at the uncorrelated principal directions. \ 4233: To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one. \n"); 4234: 4235: cov[1]=1; 4236: /* tj=cptcoveff; */ 4237: tj = (int) pow(2,cptcoveff); 4238: if (cptcovn<1) {tj=1;ncodemax[1]=1;} 4239: j1=0; 4240: for(j1=1; j1<=tj;j1++){ 4241: /*for(i1=1; i1<=ncodemax[t];i1++){ */ 4242: /*j1++;*/ 4243: if (cptcovn>0) { 4244: fprintf(ficresprob, "\n#********** Variable "); 4245: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]); 4246: fprintf(ficresprob, "**********\n#\n"); 4247: fprintf(ficresprobcov, "\n#********** Variable "); 4248: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]); 4249: fprintf(ficresprobcov, "**********\n#\n"); 4250: 4251: fprintf(ficgp, "\n#********** Variable "); 4252: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]); 4253: fprintf(ficgp, "**********\n#\n"); 4254: 4255: 4256: fprintf(fichtmcov, "\n<hr size=\"2\" color=\"#EC5E5E\">********** Variable "); 4257: for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]); 4258: fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">"); 4259: 4260: fprintf(ficresprobcor, "\n#********** Variable "); 4261: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]); 4262: fprintf(ficresprobcor, "**********\n#"); 4263: } 4264: 4265: gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath)); 4266: trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar); 4267: gp=vector(1,(nlstate)*(nlstate+ndeath)); 4268: gm=vector(1,(nlstate)*(nlstate+ndeath)); 4269: for (age=bage; age<=fage; age ++){ 4270: cov[2]=age; 4271: if(nagesqr==1) 4272: cov[3]= age*age; 4273: for (k=1; k<=cptcovn;k++) { 4274: cov[2+nagesqr+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];/* j1 1 2 3 4 4275: * 1 1 1 1 1 4276: * 2 2 1 1 1 4277: * 3 1 2 1 1 4278: */ 4279: /* nbcode[1][1]=0 nbcode[1][2]=1;*/ 4280: } 4281: /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */ 4282: for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtab[ij][Tvar[Tage[k]]]]*cov[2]; 4283: for (k=1; k<=cptcovprod;k++) 4284: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]]; 4285: 4286: 4287: for(theta=1; theta <=npar; theta++){ 4288: for(i=1; i<=npar; i++) 4289: xp[i] = x[i] + (i==theta ?delti[theta]:(double)0); 4290: 4291: pmij(pmmij,cov,ncovmodel,xp,nlstate); 4292: 4293: k=0; 4294: for(i=1; i<= (nlstate); i++){ 4295: for(j=1; j<=(nlstate+ndeath);j++){ 4296: k=k+1; 4297: gp[k]=pmmij[i][j]; 4298: } 4299: } 4300: 4301: for(i=1; i<=npar; i++) 4302: xp[i] = x[i] - (i==theta ?delti[theta]:(double)0); 4303: 4304: pmij(pmmij,cov,ncovmodel,xp,nlstate); 4305: k=0; 4306: for(i=1; i<=(nlstate); i++){ 4307: for(j=1; j<=(nlstate+ndeath);j++){ 4308: k=k+1; 4309: gm[k]=pmmij[i][j]; 4310: } 4311: } 4312: 4313: for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) 4314: gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta]; 4315: } 4316: 4317: for(j=1; j<=(nlstate)*(nlstate+ndeath);j++) 4318: for(theta=1; theta <=npar; theta++) 4319: trgradg[j][theta]=gradg[theta][j]; 4320: 4321: matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov); 4322: matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg); 4323: 4324: pmij(pmmij,cov,ncovmodel,x,nlstate); 4325: 4326: k=0; 4327: for(i=1; i<=(nlstate); i++){ 4328: for(j=1; j<=(nlstate+ndeath);j++){ 4329: k=k+1; 4330: mu[k][(int) age]=pmmij[i][j]; 4331: } 4332: } 4333: for(i=1;i<=(nlstate)*(nlstate+ndeath);i++) 4334: for(j=1;j<=(nlstate)*(nlstate+ndeath);j++) 4335: varpij[i][j][(int)age] = doldm[i][j]; 4336: 4337: /*printf("\n%d ",(int)age); 4338: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){ 4339: printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i])); 4340: fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i])); 4341: }*/ 4342: 4343: fprintf(ficresprob,"\n%d ",(int)age); 4344: fprintf(ficresprobcov,"\n%d ",(int)age); 4345: fprintf(ficresprobcor,"\n%d ",(int)age); 4346: 4347: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++) 4348: fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age])); 4349: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){ 4350: fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]); 4351: fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]); 4352: } 4353: i=0; 4354: for (k=1; k<=(nlstate);k++){ 4355: for (l=1; l<=(nlstate+ndeath);l++){ 4356: i++; 4357: fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l); 4358: fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l); 4359: for (j=1; j<=i;j++){ 4360: /* printf(" k=%d l=%d i=%d j=%d\n",k,l,i,j);fflush(stdout); */ 4361: fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]); 4362: fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age])); 4363: } 4364: } 4365: }/* end of loop for state */ 4366: } /* end of loop for age */ 4367: free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath)); 4368: free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath)); 4369: free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar); 4370: free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar); 4371: 4372: /* Confidence intervalle of pij */ 4373: /* 4374: fprintf(ficgp,"\nunset parametric;unset label"); 4375: fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\""); 4376: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65"); 4377: fprintf(fichtm,"\n Probability with confidence intervals expressed in year-1 :<a href=\"pijgr%s.png\">pijgr%s.png</A>, ",optionfilefiname,optionfilefiname); 4378: fprintf(fichtm,"\n <img src=\"pijgr%s.png\"> ",optionfilefiname); 4379: fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname); 4380: fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob); 4381: */ 4382: 4383: /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/ 4384: first1=1;first2=2; 4385: for (k2=1; k2<=(nlstate);k2++){ 4386: for (l2=1; l2<=(nlstate+ndeath);l2++){ 4387: if(l2==k2) continue; 4388: j=(k2-1)*(nlstate+ndeath)+l2; 4389: for (k1=1; k1<=(nlstate);k1++){ 4390: for (l1=1; l1<=(nlstate+ndeath);l1++){ 4391: if(l1==k1) continue; 4392: i=(k1-1)*(nlstate+ndeath)+l1; 4393: if(i<=j) continue; 4394: for (age=bage; age<=fage; age ++){ 4395: if ((int)age %5==0){ 4396: v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM; 4397: v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM; 4398: cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM; 4399: mu1=mu[i][(int) age]/stepm*YEARM ; 4400: mu2=mu[j][(int) age]/stepm*YEARM; 4401: c12=cv12/sqrt(v1*v2); 4402: /* Computing eigen value of matrix of covariance */ 4403: lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.; 4404: lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.; 4405: if ((lc2 <0) || (lc1 <0) ){ 4406: if(first2==1){ 4407: first1=0; 4408: 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); 4409: } 4410: 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); 4411: /* lc1=fabs(lc1); */ /* If we want to have them positive */ 4412: /* lc2=fabs(lc2); */ 4413: } 4414: 4415: /* Eigen vectors */ 4416: v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12)); 4417: /*v21=sqrt(1.-v11*v11); *//* error */ 4418: v21=(lc1-v1)/cv12*v11; 4419: v12=-v21; 4420: v22=v11; 4421: tnalp=v21/v11; 4422: if(first1==1){ 4423: first1=0; 4424: 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); 4425: } 4426: 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); 4427: /*printf(fignu*/ 4428: /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */ 4429: /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */ 4430: if(first==1){ 4431: first=0; 4432: fprintf(ficgp,"\nset parametric;unset label"); 4433: 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); 4434: fprintf(ficgp,"\nset ter png small size 320, 240"); 4435: fprintf(fichtmcov,"\n Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year-1\ 4436: :<a href=\"%s%d%1d%1d-%1d%1d.png\">\ 4437: %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\ 4438: subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\ 4439: subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2); 4440: fprintf(fichtmcov,"\n <img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2); 4441: fprintf(fichtmcov,"\n Correlation at age %d (%.3f),",(int) age, c12); 4442: fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2); 4443: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2); 4444: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2); 4445: 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",\ 4446: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\ 4447: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2)); 4448: }else{ 4449: first=0; 4450: fprintf(fichtmcov," %d (%.3f),",(int) age, c12); 4451: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2); 4452: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2); 4453: 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",\ 4454: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\ 4455: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2)); 4456: }/* if first */ 4457: } /* age mod 5 */ 4458: } /* end loop age */ 4459: fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2); 4460: first=1; 4461: } /*l12 */ 4462: } /* k12 */ 4463: } /*l1 */ 4464: }/* k1 */ 4465: /* } */ /* loop covariates */ 4466: } 4467: free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage); 4468: free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage); 4469: free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath)); 4470: free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar); 4471: free_vector(xp,1,npar); 4472: fclose(ficresprob); 4473: fclose(ficresprobcov); 4474: fclose(ficresprobcor); 4475: fflush(ficgp); 4476: fflush(fichtmcov); 4477: } 4478: 4479: 4480: /******************* Printing html file ***********/ 4481: void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \ 4482: int lastpass, int stepm, int weightopt, char model[],\ 4483: int imx,int jmin, int jmax, double jmeanint,char rfileres[],\ 4484: int popforecast, int estepm ,\ 4485: double jprev1, double mprev1,double anprev1, \ 4486: double jprev2, double mprev2,double anprev2){ 4487: int jj1, k1, i1, cpt; 4488: 4489: fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \ 4490: <li><a href='#secondorder'>Result files (second order (variance)</a>\n \ 4491: </ul>"); 4492: fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \ 4493: - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> \n ", 4494: jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p")); 4495: fprintf(fichtm,"\ 4496: - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a> \n ", 4497: stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij")); 4498: fprintf(fichtm,"\ 4499: - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> \n", 4500: subdirf2(fileres,"pl"),subdirf2(fileres,"pl")); 4501: fprintf(fichtm,"\ 4502: - (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): \ 4503: <a href=\"%s\">%s</a> \n", 4504: estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e")); 4505: fprintf(fichtm,"\ 4506: - Population projections by age and states: \ 4507: <a href=\"%s\">%s</a> \n</li>", subdirf2(fileres,"f"),subdirf2(fileres,"f")); 4508: 4509: fprintf(fichtm," \n<ul><li>Graphs</li>"); 4510: 4511: m=pow(2,cptcoveff); 4512: if (cptcovn < 1) {m=1;ncodemax[1]=1;} 4513: 4514: jj1=0; 4515: for(k1=1; k1<=m;k1++){ 4516: /* for(i1=1; i1<=ncodemax[k1];i1++){ */ 4517: jj1++; 4518: if (cptcovn > 0) { 4519: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates"); 4520: for (cpt=1; cpt<=cptcoveff;cpt++){ 4521: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]); 4522: printf(" V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);fflush(stdout); 4523: } 4524: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">"); 4525: } 4526: /* Pij */ 4527: fprintf(fichtm," - 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> \ 4528: <img src=\"%s%d_1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1); 4529: /* Quasi-incidences */ 4530: fprintf(fichtm," - Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\ 4531: 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> \ 4532: <img src=\"%s%d_2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1); 4533: /* Period (stable) prevalence in each health state */ 4534: for(cpt=1; cpt<=nlstate;cpt++){ 4535: fprintf(fichtm," - Convergence to period (stable) prevalence in state %d. Or probability to be in state %d being in state (1 to %d) at different ages. <a href=\"%s%d_%d.png\">%s%d_%d.png</a> \ 4536: <img src=\"%s%d_%d.png\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1); 4537: } 4538: for(cpt=1; cpt<=nlstate;cpt++) { 4539: fprintf(fichtm,"\n - 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> \ 4540: <img src=\"%s%d%d.png\">",cpt,nlstate,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1); 4541: } 4542: /* } /\* end i1 *\/ */ 4543: }/* End k1 */ 4544: fprintf(fichtm,"</ul>"); 4545: 4546: fprintf(fichtm,"\ 4547: \n <li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\ 4548: - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> \ 4549: - 95%% confidence intervals and T statistics are in the log file. \n", rfileres,rfileres); 4550: 4551: fprintf(fichtm," - Standard deviation of one-step probabilities: <a href=\"%s\">%s</a> \n", 4552: subdirf2(fileres,"prob"),subdirf2(fileres,"prob")); 4553: fprintf(fichtm,"\ 4554: - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> \n", 4555: subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov")); 4556: 4557: fprintf(fichtm,"\ 4558: - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> \n", 4559: subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor")); 4560: fprintf(fichtm,"\ 4561: - Variances and covariances of health expectancies by age and initial health status (cov(eij,ekl)(estepm=%2d months): \ 4562: <a href=\"%s\">%s</a> \n</li>", 4563: estepm,subdirf2(fileres,"cve"),subdirf2(fileres,"cve")); 4564: fprintf(fichtm,"\ 4565: - (a) Health expectancies by health status at initial age (eij) and standard errors (in parentheses) (b) life expectancies and standard errors (ei.=ei1+ei2+...)(estepm=%2d months): \ 4566: <a href=\"%s\">%s</a> \n</li>", 4567: estepm,subdirf2(fileres,"stde"),subdirf2(fileres,"stde")); 4568: fprintf(fichtm,"\ 4569: - Variances and covariances of health expectancies by age. Status (i) based health expectancies (in state j), eij 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> \n", 4570: estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v")); 4571: fprintf(fichtm,"\ 4572: - Total life expectancy and total health expectancies to be spent in each health state e.j 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> \n", 4573: estepm, subdirf2(fileres,"t"),subdirf2(fileres,"t")); 4574: fprintf(fichtm,"\ 4575: - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> \n",\ 4576: subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl")); 4577: 4578: /* if(popforecast==1) fprintf(fichtm,"\n */ 4579: /* - Prevalences forecasting: <a href=\"f%s\">f%s</a> \n */ 4580: /* - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> \n */ 4581: /* ",fileres,fileres,fileres,fileres); */ 4582: /* else */ 4583: /* fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .) </li>\n",popforecast, stepm, model); */ 4584: fflush(fichtm); 4585: fprintf(fichtm," <ul><li>Graphs</li>"); 4586: 4587: m=pow(2,cptcoveff); 4588: if (cptcovn < 1) {m=1;ncodemax[1]=1;} 4589: 4590: jj1=0; 4591: for(k1=1; k1<=m;k1++){ 4592: /* for(i1=1; i1<=ncodemax[k1];i1++){ */ 4593: jj1++; 4594: if (cptcovn > 0) { 4595: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates"); 4596: for (cpt=1; cpt<=cptcoveff;cpt++) 4597: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]); 4598: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">"); 4599: } 4600: for(cpt=1; cpt<=nlstate;cpt++) { 4601: fprintf(fichtm," - Observed (cross-sectional) and period (incidence based) \ 4602: prevalence (with 95%% confidence interval) in state (%d): %s%d_%d.png \ 4603: <img src=\"%s%d_%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1); 4604: } 4605: fprintf(fichtm,"\n - Total life expectancy by age and \ 4606: health expectancies in states (1) and (2). If popbased=1 the smooth (due to the model) \ 4607: true period expectancies (those weighted with period prevalences are also\ 4608: drawn in addition to the population based expectancies computed using\ 4609: observed and cahotic prevalences: %s%d.png \ 4610: <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1); 4611: /* } /\* end i1 *\/ */ 4612: }/* End k1 */ 4613: fprintf(fichtm,"</ul>"); 4614: fflush(fichtm); 4615: } 4616: 4617: /******************* Gnuplot file **************/ 4618: void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){ 4619: 4620: char dirfileres[132],optfileres[132]; 4621: int cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,ij=0,l=0; 4622: int ng=0; 4623: /* if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */ 4624: /* printf("Problem with file %s",optionfilegnuplot); */ 4625: /* fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */ 4626: /* } */ 4627: 4628: /*#ifdef windows */ 4629: fprintf(ficgp,"cd \"%s\" \n",pathc); 4630: /*#endif */ 4631: m=pow(2,cptcoveff); 4632: 4633: strcpy(dirfileres,optionfilefiname); 4634: strcpy(optfileres,"vpl"); 4635: /* 1eme*/ 4636: fprintf(ficgp,"\n# 1st: Period (stable) prevalence with CI: 'vpl' files\n"); 4637: for (cpt=1; cpt<= nlstate ; cpt ++) { 4638: for (k1=1; k1<= m ; k1 ++) { /* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */ 4639: fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1); 4640: fprintf(ficgp,"\n#set out \"v%s%d_%d.png\" \n",optionfilefiname,cpt,k1); 4641: fprintf(ficgp,"set xlabel \"Age\" \n\ 4642: set ylabel \"Probability\" \n\ 4643: set ter png small size 320, 240\n\ 4644: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1); 4645: 4646: for (i=1; i<= nlstate ; i ++) { 4647: if (i==cpt) fprintf(ficgp," %%lf (%%lf)"); 4648: else fprintf(ficgp," %%*lf (%%*lf)"); 4649: } 4650: 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); 4651: for (i=1; i<= nlstate ; i ++) { 4652: if (i==cpt) fprintf(ficgp," %%lf (%%lf)"); 4653: else fprintf(ficgp," %%*lf (%%*lf)"); 4654: } 4655: fprintf(ficgp,"\" t\"95%% CI\" w l lt 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1); 4656: for (i=1; i<= nlstate ; i ++) { 4657: if (i==cpt) fprintf(ficgp," %%lf (%%lf)"); 4658: else fprintf(ficgp," %%*lf (%%*lf)"); 4659: } 4660: fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l lt 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1)); 4661: } 4662: } 4663: /*2 eme*/ 4664: fprintf(ficgp,"\n# 2nd: Total life expectancy with CI: 't' files\n"); 4665: for (k1=1; k1<= m ; k1 ++) { 4666: fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1); 4667: fprintf(ficgp,"set ylabel \"Years\" \nset ter png small size 320, 240\nplot [%.f:%.f] ",ageminpar,fage); 4668: 4669: for (i=1; i<= nlstate+1 ; i ++) { 4670: k=2*i; 4671: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"%%lf",subdirf2(fileres,"t"),k1-1,k1-1); 4672: for (j=1; j<= nlstate+1 ; j ++) { 4673: if (j==i) fprintf(ficgp," %%lf (%%lf)"); 4674: else fprintf(ficgp," %%*lf (%%*lf)"); 4675: } 4676: if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,"); 4677: else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1); 4678: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"%%lf",subdirf2(fileres,"t"),k1-1,k1-1); 4679: for (j=1; j<= nlstate+1 ; j ++) { 4680: if (j==i) fprintf(ficgp," %%lf (%%lf)"); 4681: else fprintf(ficgp," %%*lf (%%*lf)"); 4682: } 4683: fprintf(ficgp,"\" t\"\" w l lt 0,"); 4684: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"%%lf",subdirf2(fileres,"t"),k1-1,k1-1); 4685: for (j=1; j<= nlstate+1 ; j ++) { 4686: if (j==i) fprintf(ficgp," %%lf (%%lf)"); 4687: else fprintf(ficgp," %%*lf (%%*lf)"); 4688: } 4689: if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l lt 0"); 4690: else fprintf(ficgp,"\" t\"\" w l lt 0,"); 4691: } 4692: } 4693: 4694: /*3eme*/ 4695: 4696: for (k1=1; k1<= m ; k1 ++) { 4697: for (cpt=1; cpt<= nlstate ; cpt ++) { 4698: /* k=2+nlstate*(2*cpt-2); */ 4699: k=2+(nlstate+1)*(cpt-1); 4700: fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1); 4701: fprintf(ficgp,"set ter png small size 320, 240\n\ 4702: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt); 4703: /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1); 4704: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) "); 4705: fprintf(ficgp,"\" t \"e%d1\" w l",cpt); 4706: fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1); 4707: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) "); 4708: fprintf(ficgp,"\" t \"e%d1\" w l",cpt); 4709: 4710: */ 4711: for (i=1; i< nlstate ; i ++) { 4712: 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); 4713: /* 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);*/ 4714: 4715: } 4716: fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+nlstate,cpt); 4717: } 4718: } 4719: 4720: /* CV preval stable (period) */ 4721: for (k1=1; k1<= m ; k1 ++) { /* For each multivariate if any */ 4722: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */ 4723: k=3; 4724: fprintf(ficgp,"\n#\n#\n#CV preval stable (period): 'pij' files, cov=%d state=%d",k1, cpt); 4725: fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1); 4726: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\ 4727: set ter png small size 320, 240\n\ 4728: unset log y\n\ 4729: plot [%.f:%.f] ", ageminpar, agemaxpar); 4730: for (i=1; i<= nlstate ; i ++){ 4731: if(i==1) 4732: fprintf(ficgp,"\"%s\"",subdirf2(fileres,"pij")); 4733: else 4734: fprintf(ficgp,", '' "); 4735: l=(nlstate+ndeath)*(i-1)+1; 4736: fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l); 4737: for (j=1; j<= (nlstate-1) ; j ++) 4738: fprintf(ficgp,"+$%d",k+l+j); 4739: fprintf(ficgp,")) t \"prev(%d,%d)\" w l",i,cpt); 4740: } /* nlstate */ 4741: fprintf(ficgp,"\n"); 4742: } /* end cpt state*/ 4743: } /* end covariate */ 4744: 4745: /* proba elementaires */ 4746: fprintf(ficgp,"\n##############\n#MLE estimated parameters\n#############\n"); 4747: for(i=1,jk=1; i <=nlstate; i++){ 4748: fprintf(ficgp,"# initial state %d\n",i); 4749: for(k=1; k <=(nlstate+ndeath); k++){ 4750: if (k != i) { 4751: fprintf(ficgp,"# current state %d\n",k); 4752: for(j=1; j <=ncovmodel; j++){ 4753: fprintf(ficgp,"p%d=%f; ",jk,p[jk]); 4754: jk++; 4755: } 4756: fprintf(ficgp,"\n"); 4757: } 4758: } 4759: } 4760: fprintf(ficgp,"##############\n#\n"); 4761: 4762: /*goto avoid;*/ 4763: fprintf(ficgp,"\n##############\n#Graphics of of probabilities or incidences\n#############\n"); 4764: fprintf(ficgp,"# logi(p12/p11)=a12+b12*age+c12age*age+d12*V1+e12*V1*age\n"); 4765: fprintf(ficgp,"# logi(p12/p11)=p1 +p2*age +p3*age*age+ p4*V1+ p5*V1*age\n"); 4766: fprintf(ficgp,"# logi(p13/p11)=a13+b13*age+c13age*age+d13*V1+e13*V1*age\n"); 4767: fprintf(ficgp,"# logi(p13/p11)=p6 +p7*age +p8*age*age+ p9*V1+ p10*V1*age\n"); 4768: fprintf(ficgp,"# p12+p13+p14+p11=1=p11(1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n"); 4769: fprintf(ficgp,"# +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age)+...)\n"); 4770: fprintf(ficgp,"# p11=1/(1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n"); 4771: fprintf(ficgp,"# +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age)+...)\n"); 4772: fprintf(ficgp,"# p12=exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)/\n"); 4773: fprintf(ficgp,"# (1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n"); 4774: fprintf(ficgp,"# +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age))\n"); 4775: fprintf(ficgp,"# +exp(a14+b14*age+c14age*age+d14*V1+e14*V1*age)+...)\n"); 4776: fprintf(ficgp,"#\n"); 4777: for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/ 4778: fprintf(ficgp,"# ng=%d\n",ng); 4779: fprintf(ficgp,"# jk=1 to 2^%d=%d\n",cptcoveff,m); 4780: for(jk=1; jk <=m; jk++) { 4781: fprintf(ficgp,"# jk=%d\n",jk); 4782: fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng); 4783: if (ng==2) 4784: fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n"); 4785: else 4786: fprintf(ficgp,"\nset title \"Probability\"\n"); 4787: fprintf(ficgp,"\nset ter png small size 320, 240\nset log y\nplot [%.f:%.f] ",ageminpar,agemaxpar); 4788: i=1; 4789: for(k2=1; k2<=nlstate; k2++) { 4790: k3=i; 4791: for(k=1; k<=(nlstate+ndeath); k++) { 4792: if (k != k2){ 4793: if(ng==2) 4794: if(nagesqr==0) 4795: fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1); 4796: else /* nagesqr =1 */ 4797: fprintf(ficgp," %f*exp(p%d+p%d*x+p%d*x*x",YEARM/stepm,i,i+1,i+1+nagesqr); 4798: else 4799: if(nagesqr==0) 4800: fprintf(ficgp," exp(p%d+p%d*x",i,i+1); 4801: else /* nagesqr =1 */ 4802: fprintf(ficgp," exp(p%d+p%d*x+p%d*x*x",i,i+1,i+1+nagesqr); 4803: ij=1;/* To be checked else nbcode[0][0] wrong */ 4804: for(j=3; j <=ncovmodel-nagesqr; j++) { 4805: if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) { /* Bug valgrind */ 4806: fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]); 4807: ij++; 4808: } 4809: else 4810: fprintf(ficgp,"+p%d*%d",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]); 4811: } 4812: fprintf(ficgp,")/(1"); 4813: 4814: for(k1=1; k1 <=nlstate; k1++){ 4815: if(nagesqr==0) 4816: fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1); 4817: else /* nagesqr =1 */ 4818: fprintf(ficgp,"+exp(p%d+p%d*x+p%d*x*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1,k3+(k1-1)*ncovmodel+1+nagesqr); 4819: 4820: ij=1; 4821: for(j=3; j <=ncovmodel-nagesqr; j++){ 4822: if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) { 4823: fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]); 4824: ij++; 4825: } 4826: else 4827: fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtab[jk][j-2]]); 4828: } 4829: fprintf(ficgp,")"); 4830: } 4831: fprintf(ficgp,") t \"p%d%d\" ", k2,k); 4832: if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,","); 4833: i=i+ncovmodel; 4834: } 4835: } /* end k */ 4836: } /* end k2 */ 4837: } /* end jk */ 4838: } /* end ng */ 4839: /* avoid: */ 4840: fflush(ficgp); 4841: } /* end gnuplot */ 4842: 4843: 4844: /*************** Moving average **************/ 4845: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){ 4846: 4847: int i, cpt, cptcod; 4848: int modcovmax =1; 4849: int mobilavrange, mob; 4850: double age; 4851: 4852: modcovmax=2*cptcoveff;/* Max number of modalities. We suppose 4853: a covariate has 2 modalities */ 4854: if (cptcovn<1) modcovmax=1; /* At least 1 pass */ 4855: 4856: if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){ 4857: if(mobilav==1) mobilavrange=5; /* default */ 4858: else mobilavrange=mobilav; 4859: for (age=bage; age<=fage; age++) 4860: for (i=1; i<=nlstate;i++) 4861: for (cptcod=1;cptcod<=modcovmax;cptcod++) 4862: mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod]; 4863: /* We keep the original values on the extreme ages bage, fage and for 4864: fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2 4865: we use a 5 terms etc. until the borders are no more concerned. 4866: */ 4867: for (mob=3;mob <=mobilavrange;mob=mob+2){ 4868: for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){ 4869: for (i=1; i<=nlstate;i++){ 4870: for (cptcod=1;cptcod<=modcovmax;cptcod++){ 4871: mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod]; 4872: for (cpt=1;cpt<=(mob-1)/2;cpt++){ 4873: mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod]; 4874: mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod]; 4875: } 4876: mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob; 4877: } 4878: } 4879: }/* end age */ 4880: }/* end mob */ 4881: }else return -1; 4882: return 0; 4883: }/* End movingaverage */ 4884: 4885: 4886: /************** Forecasting ******************/ 4887: void prevforecast(char fileres[], double anproj1, double mproj1, double jproj1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double anproj2, double p[], int cptcoveff){ 4888: /* proj1, year, month, day of starting projection 4889: agemin, agemax range of age 4890: dateprev1 dateprev2 range of dates during which prevalence is computed 4891: anproj2 year of en of projection (same day and month as proj1). 4892: */ 4893: int yearp, stepsize, hstepm, nhstepm, j, k, cptcod, i, h, i1; 4894: double agec; /* generic age */ 4895: double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean; 4896: double *popeffectif,*popcount; 4897: double ***p3mat; 4898: double ***mobaverage; 4899: char fileresf[FILENAMELENGTH]; 4900: 4901: agelim=AGESUP; 4902: prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass); 4903: 4904: strcpy(fileresf,"f"); 4905: strcat(fileresf,fileres); 4906: if((ficresf=fopen(fileresf,"w"))==NULL) { 4907: printf("Problem with forecast resultfile: %s\n", fileresf); 4908: fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf); 4909: } 4910: printf("Computing forecasting: result on file '%s' \n", fileresf); 4911: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf); 4912: 4913: if (cptcoveff==0) ncodemax[cptcoveff]=1; 4914: 4915: if (mobilav!=0) { 4916: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); 4917: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){ 4918: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav); 4919: printf(" Error in movingaverage mobilav=%d\n",mobilav); 4920: } 4921: } 4922: 4923: stepsize=(int) (stepm+YEARM-1)/YEARM; 4924: if (stepm<=12) stepsize=1; 4925: if(estepm < stepm){ 4926: printf ("Problem %d lower than %d\n",estepm, stepm); 4927: } 4928: else hstepm=estepm; 4929: 4930: hstepm=hstepm/stepm; 4931: yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp and 4932: fractional in yp1 */ 4933: anprojmean=yp; 4934: yp2=modf((yp1*12),&yp); 4935: mprojmean=yp; 4936: yp1=modf((yp2*30.5),&yp); 4937: jprojmean=yp; 4938: if(jprojmean==0) jprojmean=1; 4939: if(mprojmean==0) jprojmean=1; 4940: 4941: i1=cptcoveff; 4942: if (cptcovn < 1){i1=1;} 4943: 4944: fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2); 4945: 4946: fprintf(ficresf,"#****** Routine prevforecast **\n"); 4947: 4948: /* if (h==(int)(YEARM*yearp)){ */ 4949: for(cptcov=1, k=0;cptcov<=i1;cptcov++){ 4950: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){ 4951: k=k+1; 4952: fprintf(ficresf,"\n#******"); 4953: for(j=1;j<=cptcoveff;j++) { 4954: 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]]); 4955: } 4956: fprintf(ficresf,"******\n"); 4957: fprintf(ficresf,"# Covariate valuofcovar yearproj age"); 4958: for(j=1; j<=nlstate+ndeath;j++){ 4959: for(i=1; i<=nlstate;i++) 4960: fprintf(ficresf," p%d%d",i,j); 4961: fprintf(ficresf," p.%d",j); 4962: } 4963: for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) { 4964: fprintf(ficresf,"\n"); 4965: fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp); 4966: 4967: for (agec=fage; agec>=(ageminpar-1); agec--){ 4968: nhstepm=(int) rint((agelim-agec)*YEARM/stepm); 4969: nhstepm = nhstepm/hstepm; 4970: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); 4971: oldm=oldms;savm=savms; 4972: hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k); 4973: 4974: for (h=0; h<=nhstepm; h++){ 4975: if (h*hstepm/YEARM*stepm ==yearp) { 4976: fprintf(ficresf,"\n"); 4977: for(j=1;j<=cptcoveff;j++) 4978: fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]); 4979: fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm); 4980: } 4981: for(j=1; j<=nlstate+ndeath;j++) { 4982: ppij=0.; 4983: for(i=1; i<=nlstate;i++) { 4984: if (mobilav==1) 4985: ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod]; 4986: else { 4987: ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod]; 4988: } 4989: if (h*hstepm/YEARM*stepm== yearp) { 4990: fprintf(ficresf," %.3f", p3mat[i][j][h]); 4991: } 4992: } /* end i */ 4993: if (h*hstepm/YEARM*stepm==yearp) { 4994: fprintf(ficresf," %.3f", ppij); 4995: } 4996: }/* end j */ 4997: } /* end h */ 4998: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); 4999: } /* end agec */ 5000: } /* end yearp */ 5001: } /* end cptcod */ 5002: } /* end cptcov */ 5003: 5004: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); 5005: 5006: fclose(ficresf); 5007: } 5008: 5009: /************** Forecasting *****not tested NB*************/ 5010: void populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){ 5011: 5012: int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h; 5013: int *popage; 5014: double calagedatem, agelim, kk1, kk2; 5015: double *popeffectif,*popcount; 5016: double ***p3mat,***tabpop,***tabpopprev; 5017: double ***mobaverage; 5018: char filerespop[FILENAMELENGTH]; 5019: 5020: tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); 5021: tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); 5022: agelim=AGESUP; 5023: calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM; 5024: 5025: prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass); 5026: 5027: 5028: strcpy(filerespop,"pop"); 5029: strcat(filerespop,fileres); 5030: if((ficrespop=fopen(filerespop,"w"))==NULL) { 5031: printf("Problem with forecast resultfile: %s\n", filerespop); 5032: fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop); 5033: } 5034: printf("Computing forecasting: result on file '%s' \n", filerespop); 5035: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop); 5036: 5037: if (cptcoveff==0) ncodemax[cptcoveff]=1; 5038: 5039: if (mobilav!=0) { 5040: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); 5041: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){ 5042: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav); 5043: printf(" Error in movingaverage mobilav=%d\n",mobilav); 5044: } 5045: } 5046: 5047: stepsize=(int) (stepm+YEARM-1)/YEARM; 5048: if (stepm<=12) stepsize=1; 5049: 5050: agelim=AGESUP; 5051: 5052: hstepm=1; 5053: hstepm=hstepm/stepm; 5054: 5055: if (popforecast==1) { 5056: if((ficpop=fopen(popfile,"r"))==NULL) { 5057: printf("Problem with population file : %s\n",popfile);exit(0); 5058: fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0); 5059: } 5060: popage=ivector(0,AGESUP); 5061: popeffectif=vector(0,AGESUP); 5062: popcount=vector(0,AGESUP); 5063: 5064: i=1; 5065: while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1; 5066: 5067: imx=i; 5068: for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i]; 5069: } 5070: 5071: for(cptcov=1,k=0;cptcov<=i2;cptcov++){ 5072: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){ 5073: k=k+1; 5074: fprintf(ficrespop,"\n#******"); 5075: for(j=1;j<=cptcoveff;j++) { 5076: fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]); 5077: } 5078: fprintf(ficrespop,"******\n"); 5079: fprintf(ficrespop,"# Age"); 5080: for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j); 5081: if (popforecast==1) fprintf(ficrespop," [Population]"); 5082: 5083: for (cpt=0; cpt<=0;cpt++) { 5084: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt); 5085: 5086: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 5087: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 5088: nhstepm = nhstepm/hstepm; 5089: 5090: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); 5091: oldm=oldms;savm=savms; 5092: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k); 5093: 5094: for (h=0; h<=nhstepm; h++){ 5095: if (h==(int) (calagedatem+YEARM*cpt)) { 5096: fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm); 5097: } 5098: for(j=1; j<=nlstate+ndeath;j++) { 5099: kk1=0.;kk2=0; 5100: for(i=1; i<=nlstate;i++) { 5101: if (mobilav==1) 5102: kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod]; 5103: else { 5104: kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod]; 5105: } 5106: } 5107: if (h==(int)(calagedatem+12*cpt)){ 5108: tabpop[(int)(agedeb)][j][cptcod]=kk1; 5109: /*fprintf(ficrespop," %.3f", kk1); 5110: if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/ 5111: } 5112: } 5113: for(i=1; i<=nlstate;i++){ 5114: kk1=0.; 5115: for(j=1; j<=nlstate;j++){ 5116: kk1= kk1+tabpop[(int)(agedeb)][j][cptcod]; 5117: } 5118: tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)]; 5119: } 5120: 5121: if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++) 5122: fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]); 5123: } 5124: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); 5125: } 5126: } 5127: 5128: /******/ 5129: 5130: for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) { 5131: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt); 5132: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 5133: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 5134: nhstepm = nhstepm/hstepm; 5135: 5136: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); 5137: oldm=oldms;savm=savms; 5138: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k); 5139: for (h=0; h<=nhstepm; h++){ 5140: if (h==(int) (calagedatem+YEARM*cpt)) { 5141: fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm); 5142: } 5143: for(j=1; j<=nlstate+ndeath;j++) { 5144: kk1=0.;kk2=0; 5145: for(i=1; i<=nlstate;i++) { 5146: kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod]; 5147: } 5148: if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1); 5149: } 5150: } 5151: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); 5152: } 5153: } 5154: } 5155: } 5156: 5157: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); 5158: 5159: if (popforecast==1) { 5160: free_ivector(popage,0,AGESUP); 5161: free_vector(popeffectif,0,AGESUP); 5162: free_vector(popcount,0,AGESUP); 5163: } 5164: free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); 5165: free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); 5166: fclose(ficrespop); 5167: } /* End of popforecast */ 5168: 5169: int fileappend(FILE *fichier, char *optionfich) 5170: { 5171: if((fichier=fopen(optionfich,"a"))==NULL) { 5172: printf("Problem with file: %s\n", optionfich); 5173: fprintf(ficlog,"Problem with file: %s\n", optionfich); 5174: return (0); 5175: } 5176: fflush(fichier); 5177: return (1); 5178: } 5179: 5180: 5181: /**************** function prwizard **********************/ 5182: void prwizard(int ncovmodel, int nlstate, int ndeath, char model[], FILE *ficparo) 5183: { 5184: 5185: /* Wizard to print covariance matrix template */ 5186: 5187: char ca[32], cb[32]; 5188: int i,j, k, li, lj, lk, ll, jj, npar, itimes; 5189: int numlinepar; 5190: 5191: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n"); 5192: fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n"); 5193: for(i=1; i <=nlstate; i++){ 5194: jj=0; 5195: for(j=1; j <=nlstate+ndeath; j++){ 5196: if(j==i) continue; 5197: jj++; 5198: /*ca[0]= k+'a'-1;ca[1]='\0';*/ 5199: printf("%1d%1d",i,j); 5200: fprintf(ficparo,"%1d%1d",i,j); 5201: for(k=1; k<=ncovmodel;k++){ 5202: /* printf(" %lf",param[i][j][k]); */ 5203: /* fprintf(ficparo," %lf",param[i][j][k]); */ 5204: printf(" 0."); 5205: fprintf(ficparo," 0."); 5206: } 5207: printf("\n"); 5208: fprintf(ficparo,"\n"); 5209: } 5210: } 5211: printf("# Scales (for hessian or gradient estimation)\n"); 5212: fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n"); 5213: npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/ 5214: for(i=1; i <=nlstate; i++){ 5215: jj=0; 5216: for(j=1; j <=nlstate+ndeath; j++){ 5217: if(j==i) continue; 5218: jj++; 5219: fprintf(ficparo,"%1d%1d",i,j); 5220: printf("%1d%1d",i,j); 5221: fflush(stdout); 5222: for(k=1; k<=ncovmodel;k++){ 5223: /* printf(" %le",delti3[i][j][k]); */ 5224: /* fprintf(ficparo," %le",delti3[i][j][k]); */ 5225: printf(" 0."); 5226: fprintf(ficparo," 0."); 5227: } 5228: numlinepar++; 5229: printf("\n"); 5230: fprintf(ficparo,"\n"); 5231: } 5232: } 5233: printf("# Covariance matrix\n"); 5234: /* # 121 Var(a12)\n\ */ 5235: /* # 122 Cov(b12,a12) Var(b12)\n\ */ 5236: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */ 5237: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */ 5238: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */ 5239: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */ 5240: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */ 5241: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */ 5242: fflush(stdout); 5243: fprintf(ficparo,"# Covariance matrix\n"); 5244: /* # 121 Var(a12)\n\ */ 5245: /* # 122 Cov(b12,a12) Var(b12)\n\ */ 5246: /* # ...\n\ */ 5247: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */ 5248: 5249: for(itimes=1;itimes<=2;itimes++){ 5250: jj=0; 5251: for(i=1; i <=nlstate; i++){ 5252: for(j=1; j <=nlstate+ndeath; j++){ 5253: if(j==i) continue; 5254: for(k=1; k<=ncovmodel;k++){ 5255: jj++; 5256: ca[0]= k+'a'-1;ca[1]='\0'; 5257: if(itimes==1){ 5258: printf("#%1d%1d%d",i,j,k); 5259: fprintf(ficparo,"#%1d%1d%d",i,j,k); 5260: }else{ 5261: printf("%1d%1d%d",i,j,k); 5262: fprintf(ficparo,"%1d%1d%d",i,j,k); 5263: /* printf(" %.5le",matcov[i][j]); */ 5264: } 5265: ll=0; 5266: for(li=1;li <=nlstate; li++){ 5267: for(lj=1;lj <=nlstate+ndeath; lj++){ 5268: if(lj==li) continue; 5269: for(lk=1;lk<=ncovmodel;lk++){ 5270: ll++; 5271: if(ll<=jj){ 5272: cb[0]= lk +'a'-1;cb[1]='\0'; 5273: if(ll<jj){ 5274: if(itimes==1){ 5275: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj); 5276: fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj); 5277: }else{ 5278: printf(" 0."); 5279: fprintf(ficparo," 0."); 5280: } 5281: }else{ 5282: if(itimes==1){ 5283: printf(" Var(%s%1d%1d)",ca,i,j); 5284: fprintf(ficparo," Var(%s%1d%1d)",ca,i,j); 5285: }else{ 5286: printf(" 0."); 5287: fprintf(ficparo," 0."); 5288: } 5289: } 5290: } 5291: } /* end lk */ 5292: } /* end lj */ 5293: } /* end li */ 5294: printf("\n"); 5295: fprintf(ficparo,"\n"); 5296: numlinepar++; 5297: } /* end k*/ 5298: } /*end j */ 5299: } /* end i */ 5300: } /* end itimes */ 5301: 5302: } /* end of prwizard */ 5303: /******************* Gompertz Likelihood ******************************/ 5304: double gompertz(double x[]) 5305: { 5306: double A,B,L=0.0,sump=0.,num=0.; 5307: int i,n=0; /* n is the size of the sample */ 5308: 5309: for (i=0;i<=imx-1 ; i++) { 5310: sump=sump+weight[i]; 5311: /* sump=sump+1;*/ 5312: num=num+1; 5313: } 5314: 5315: 5316: /* for (i=0; i<=imx; i++) 5317: 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]);*/ 5318: 5319: for (i=1;i<=imx ; i++) 5320: { 5321: if (cens[i] == 1 && wav[i]>1) 5322: A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp))); 5323: 5324: if (cens[i] == 0 && wav[i]>1) 5325: A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp))) 5326: +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM); 5327: 5328: /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */ 5329: if (wav[i] > 1 ) { /* ??? */ 5330: L=L+A*weight[i]; 5331: /* 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]);*/ 5332: } 5333: } 5334: 5335: /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/ 5336: 5337: return -2*L*num/sump; 5338: } 5339: 5340: #ifdef GSL 5341: /******************* Gompertz_f Likelihood ******************************/ 5342: double gompertz_f(const gsl_vector *v, void *params) 5343: { 5344: double A,B,LL=0.0,sump=0.,num=0.; 5345: double *x= (double *) v->data; 5346: int i,n=0; /* n is the size of the sample */ 5347: 5348: for (i=0;i<=imx-1 ; i++) { 5349: sump=sump+weight[i]; 5350: /* sump=sump+1;*/ 5351: num=num+1; 5352: } 5353: 5354: 5355: /* for (i=0; i<=imx; i++) 5356: 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]);*/ 5357: printf("x[0]=%lf x[1]=%lf\n",x[0],x[1]); 5358: for (i=1;i<=imx ; i++) 5359: { 5360: if (cens[i] == 1 && wav[i]>1) 5361: A=-x[0]/(x[1])*(exp(x[1]*(agecens[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp))); 5362: 5363: if (cens[i] == 0 && wav[i]>1) 5364: A=-x[0]/(x[1])*(exp(x[1]*(agedc[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp))) 5365: +log(x[0]/YEARM)+x[1]*(agedc[i]-agegomp)+log(YEARM); 5366: 5367: /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */ 5368: if (wav[i] > 1 ) { /* ??? */ 5369: LL=LL+A*weight[i]; 5370: /* 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]);*/ 5371: } 5372: } 5373: 5374: /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/ 5375: printf("x[0]=%lf x[1]=%lf -2*LL*num/sump=%lf\n",x[0],x[1],-2*LL*num/sump); 5376: 5377: return -2*LL*num/sump; 5378: } 5379: #endif 5380: 5381: /******************* Printing html file ***********/ 5382: void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \ 5383: int lastpass, int stepm, int weightopt, char model[],\ 5384: int imx, double p[],double **matcov,double agemortsup){ 5385: int i,k; 5386: 5387: fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets): "); 5388: fprintf(fichtm," mu(age) =%lf*exp(%lf*(age-%d)) per year ",p[1],p[2],agegomp); 5389: for (i=1;i<=2;i++) 5390: fprintf(fichtm," p[%d] = %lf [%f ; %f] \n",i,p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i])); 5391: fprintf(fichtm," <img src=\"graphmort.png\">"); 5392: fprintf(fichtm,"</ul>"); 5393: 5394: fprintf(fichtm,"<ul><li><h4>Life table</h4>\n "); 5395: 5396: 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> "); 5397: 5398: for (k=agegomp;k<(agemortsup-2);k++) 5399: fprintf(fichtm,"%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]); 5400: 5401: 5402: fflush(fichtm); 5403: } 5404: 5405: /******************* Gnuplot file **************/ 5406: void printinggnuplotmort(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){ 5407: 5408: char dirfileres[132],optfileres[132]; 5409: 5410: int ng; 5411: 5412: 5413: /*#ifdef windows */ 5414: fprintf(ficgp,"cd \"%s\" \n",pathc); 5415: /*#endif */ 5416: 5417: 5418: strcpy(dirfileres,optionfilefiname); 5419: strcpy(optfileres,"vpl"); 5420: fprintf(ficgp,"set out \"graphmort.png\"\n "); 5421: fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n "); 5422: fprintf(ficgp, "set ter png small size 320, 240\n set log y\n"); 5423: /* fprintf(ficgp, "set size 0.65,0.65\n"); */ 5424: fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp); 5425: 5426: } 5427: 5428: int readdata(char datafile[], int firstobs, int lastobs, int *imax) 5429: { 5430: 5431: /*-------- data file ----------*/ 5432: FILE *fic; 5433: char dummy[]=" "; 5434: int i=0, j=0, n=0; 5435: int linei, month, year,iout; 5436: char line[MAXLINE], linetmp[MAXLINE]; 5437: char stra[MAXLINE], strb[MAXLINE]; 5438: char *stratrunc; 5439: int lstra; 5440: 5441: 5442: if((fic=fopen(datafile,"r"))==NULL) { 5443: printf("Problem while opening datafile: %s\n", datafile);return 1; 5444: fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);return 1; 5445: } 5446: 5447: i=1; 5448: linei=0; 5449: while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) { 5450: linei=linei+1; 5451: for(j=strlen(line); j>=0;j--){ /* Untabifies line */ 5452: if(line[j] == '\t') 5453: line[j] = ' '; 5454: } 5455: for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){ 5456: ; 5457: }; 5458: line[j+1]=0; /* Trims blanks at end of line */ 5459: if(line[0]=='#'){ 5460: fprintf(ficlog,"Comment line\n%s\n",line); 5461: printf("Comment line\n%s\n",line); 5462: continue; 5463: } 5464: trimbb(linetmp,line); /* Trims multiple blanks in line */ 5465: strcpy(line, linetmp); 5466: 5467: 5468: for (j=maxwav;j>=1;j--){ 5469: cutv(stra, strb, line, ' '); 5470: if(strb[0]=='.') { /* Missing status */ 5471: lval=-1; 5472: }else{ 5473: errno=0; 5474: lval=strtol(strb,&endptr,10); 5475: /* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/ 5476: if( strb[0]=='\0' || (*endptr != '\0')){ 5477: 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); 5478: 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); 5479: return 1; 5480: } 5481: } 5482: s[j][i]=lval; 5483: 5484: strcpy(line,stra); 5485: cutv(stra, strb,line,' '); 5486: if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){ 5487: } 5488: else if( (iout=sscanf(strb,"%s.",dummy)) != 0){ 5489: month=99; 5490: year=9999; 5491: }else{ 5492: 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); 5493: 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); 5494: return 1; 5495: } 5496: anint[j][i]= (double) year; 5497: mint[j][i]= (double)month; 5498: strcpy(line,stra); 5499: } /* ENd Waves */ 5500: 5501: cutv(stra, strb,line,' '); 5502: if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){ 5503: } 5504: else if( (iout=sscanf(strb,"%s.",dummy)) != 0){ 5505: month=99; 5506: year=9999; 5507: }else{ 5508: 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); 5509: 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); 5510: return 1; 5511: } 5512: andc[i]=(double) year; 5513: moisdc[i]=(double) month; 5514: strcpy(line,stra); 5515: 5516: cutv(stra, strb,line,' '); 5517: if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){ 5518: } 5519: else if( (iout=sscanf(strb,"%s.", dummy)) != 0){ 5520: month=99; 5521: year=9999; 5522: }else{ 5523: 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); 5524: 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); 5525: return 1; 5526: } 5527: if (year==9999) { 5528: 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); 5529: 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); 5530: return 1; 5531: 5532: } 5533: annais[i]=(double)(year); 5534: moisnais[i]=(double)(month); 5535: strcpy(line,stra); 5536: 5537: cutv(stra, strb,line,' '); 5538: errno=0; 5539: dval=strtod(strb,&endptr); 5540: if( strb[0]=='\0' || (*endptr != '\0')){ 5541: printf("Error reading data around '%f' at line number %d, \"%s\" for individual %d\nShould be a weight. Exiting.\n",dval, i,line,linei); 5542: 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); 5543: fflush(ficlog); 5544: return 1; 5545: } 5546: weight[i]=dval; 5547: strcpy(line,stra); 5548: 5549: for (j=ncovcol;j>=1;j--){ 5550: cutv(stra, strb,line,' '); 5551: if(strb[0]=='.') { /* Missing status */ 5552: lval=-1; 5553: }else{ 5554: errno=0; 5555: lval=strtol(strb,&endptr,10); 5556: if( strb[0]=='\0' || (*endptr != '\0')){ 5557: 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); 5558: 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); 5559: return 1; 5560: } 5561: } 5562: if(lval <-1 || lval >1){ 5563: printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\n \ 5564: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \ 5565: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \ 5566: For example, for multinomial values like 1, 2 and 3,\n \ 5567: build V1=0 V2=0 for the reference value (1),\n \ 5568: V1=1 V2=0 for (2) \n \ 5569: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \ 5570: output of IMaCh is often meaningless.\n \ 5571: Exiting.\n",lval,linei, i,line,j); 5572: fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\n \ 5573: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \ 5574: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \ 5575: For example, for multinomial values like 1, 2 and 3,\n \ 5576: build V1=0 V2=0 for the reference value (1),\n \ 5577: V1=1 V2=0 for (2) \n \ 5578: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \ 5579: output of IMaCh is often meaningless.\n \ 5580: Exiting.\n",lval,linei, i,line,j);fflush(ficlog); 5581: return 1; 5582: } 5583: covar[j][i]=(double)(lval); 5584: strcpy(line,stra); 5585: } 5586: lstra=strlen(stra); 5587: 5588: if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */ 5589: stratrunc = &(stra[lstra-9]); 5590: num[i]=atol(stratrunc); 5591: } 5592: else 5593: num[i]=atol(stra); 5594: /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){ 5595: 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;}*/ 5596: 5597: i=i+1; 5598: } /* End loop reading data */ 5599: 5600: *imax=i-1; /* Number of individuals */ 5601: fclose(fic); 5602: 5603: return (0); 5604: /* endread: */ 5605: printf("Exiting readdata: "); 5606: fclose(fic); 5607: return (1); 5608: 5609: 5610: 5611: } 5612: void removespace(char *str) { 5613: char *p1 = str, *p2 = str; 5614: do 5615: while (*p2 == ' ') 5616: p2++; 5617: while (*p1++ == *p2++); 5618: } 5619: 5620: int decodemodel ( char model[], int lastobs) /**< This routine decode the model and returns: 5621: * Model V1+V2+V3+V8+V7*V8+V5*V6+V8*age+V3*age+age*age 5622: * - nagesqr = 1 if age*age in the model, otherwise 0. 5623: * - cptcovt total number of covariates of the model nbocc(+)+1 = 8 excepting constant and age and age*age 5624: * - cptcovn or number of covariates k of the models excluding age*products =6 and age*age 5625: * - cptcovage number of covariates with age*products =2 5626: * - cptcovs number of simple covariates 5627: * - 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 5628: * which is a new column after the 9 (ncovcol) variables. 5629: * - if k is a product Vn*Vm covar[k][i] is filled with correct values for each individual 5630: * - Tprod[l] gives the kth covariates of the product Vn*Vm l=1 to cptcovprod-cptcovage 5631: * Tprod[1]@2 {5, 6}: position of first product V7*V8 is 5, and second V5*V6 is 6. 5632: * - Tvard[k] p Tvard[1][1]@4 {7, 8, 5, 6} for V7*V8 and V5*V6 . 5633: */ 5634: { 5635: int i, j, k, ks; 5636: int j1, k1, k2; 5637: char modelsav[80]; 5638: char stra[80], strb[80], strc[80], strd[80],stre[80]; 5639: char *strpt; 5640: 5641: /*removespace(model);*/ 5642: if (strlen(model) >1){ /* If there is at least 1 covariate */ 5643: j=0, j1=0, k1=0, k2=-1, ks=0, cptcovn=0; 5644: if (strstr(model,"AGE") !=0){ 5645: printf("Error. AGE must be in lower case 'age' model=1+age+%s. ",model); 5646: fprintf(ficlog,"Error. AGE must be in lower case model=1+age+%s. ",model);fflush(ficlog); 5647: return 1; 5648: } 5649: if (strstr(model,"v") !=0){ 5650: printf("Error. 'v' must be in upper case 'V' model=%s ",model); 5651: fprintf(ficlog,"Error. 'v' must be in upper case model=%s ",model);fflush(ficlog); 5652: return 1; 5653: } 5654: strcpy(modelsav,model); 5655: if ((strpt=strstr(model,"age*age")) !=0){ 5656: printf(" strpt=%s, model=%s\n",strpt, model); 5657: if(strpt != model){ 5658: printf("Error in model: 'model=%s'; 'age*age' should in first place before other covariates\n \ 5659: 'model=1+age+age*age+V1.' or 'model=1+age+age*age+V1+V1*age.', please swap as well as \n \ 5660: corresponding column of parameters.\n",model); 5661: fprintf(ficlog,"Error in model: 'model=%s'; 'age*age' should in first place before other covariates\n \ 5662: 'model=1+age+age*age+V1.' or 'model=1+age+age*age+V1+V1*age.', please swap as well as \n \ 5663: corresponding column of parameters.\n",model); fflush(ficlog); 5664: return 1; 5665: } 5666: 5667: nagesqr=1; 5668: if (strstr(model,"+age*age") !=0) 5669: substrchaine(modelsav, model, "+age*age"); 5670: else if (strstr(model,"age*age+") !=0) 5671: substrchaine(modelsav, model, "age*age+"); 5672: else 5673: substrchaine(modelsav, model, "age*age"); 5674: }else 5675: nagesqr=0; 5676: if (strlen(modelsav) >1){ 5677: j=nbocc(modelsav,'+'); /**< j=Number of '+' */ 5678: j1=nbocc(modelsav,'*'); /**< j1=Number of '*' */ 5679: cptcovs=j+1-j1; /**< Number of simple covariates V1+V1*age+V3 +V3*V4+age*age=> V1 + V3 =2 */ 5680: cptcovt= j+1; /* Number of total covariates in the model, not including 5681: * cst, age and age*age 5682: * V1+V1*age+ V3 + V3*V4+age*age=> 4*/ 5683: /* including age products which are counted in cptcovage. 5684: * but the covariates which are products must be treated 5685: * separately: ncovn=4- 2=2 (V1+V3). */ 5686: cptcovprod=j1; /**< Number of products V1*V2 +v3*age = 2 */ 5687: cptcovprodnoage=0; /**< Number of covariate products without age: V3*V4 =1 */ 5688: 5689: 5690: /* Design 5691: * V1 V2 V3 V4 V5 V6 V7 V8 V9 Weight 5692: * < ncovcol=8 > 5693: * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8 5694: * k= 1 2 3 4 5 6 7 8 5695: * cptcovn number of covariates (not including constant and age ) = # of + plus 1 = 7+1=8 5696: * covar[k,i], value of kth covariate if not including age for individual i: 5697: * covar[1][i]= (V2), covar[4][i]=(V3), covar[8][i]=(V8) 5698: * Tvar[k] # of the kth covariate: Tvar[1]=2 Tvar[4]=3 Tvar[8]=8 5699: * if multiplied by age: V3*age Tvar[3=V3*age]=3 (V3) Tvar[7]=8 and 5700: * Tage[++cptcovage]=k 5701: * if products, new covar are created after ncovcol with k1 5702: * Tvar[k]=ncovcol+k1; # of the kth covariate product: Tvar[5]=ncovcol+1=10 Tvar[6]=ncovcol+1=11 5703: * Tprod[k1]=k; Tprod[1]=5 Tprod[2]= 6; gives the position of the k1th product 5704: * 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 5705: * Tvar[cptcovn+k2]=Tvard[k1][1];Tvar[cptcovn+k2+1]=Tvard[k1][2]; 5706: * Tvar[8+1]=5;Tvar[8+2]=6;Tvar[8+3]=7;Tvar[8+4]=8 inverted 5707: * V1 V2 V3 V4 V5 V6 V7 V8 V9 V10 V11 5708: * < ncovcol=8 > 5709: * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8 d1 d1 d2 d2 5710: * k= 1 2 3 4 5 6 7 8 9 10 11 12 5711: * Tvar[k]= 2 1 3 3 10 11 8 8 5 6 7 8 5712: * p Tvar[1]@12={2, 1, 3, 3, 11, 10, 8, 8, 7, 8, 5, 6} 5713: * p Tprod[1]@2={ 6, 5} 5714: *p Tvard[1][1]@4= {7, 8, 5, 6} 5715: * covar[k][i]= V2 V1 ? V3 V5*V6? V7*V8? ? V8 5716: * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; 5717: *How to reorganize? 5718: * Model V1 + V2 + V3 + V8 + V5*V6 + V7*V8 + V3*age + V8*age 5719: * Tvars {2, 1, 3, 3, 11, 10, 8, 8, 7, 8, 5, 6} 5720: * {2, 1, 4, 8, 5, 6, 3, 7} 5721: * Struct [] 5722: */ 5723: 5724: /* This loop fills the array Tvar from the string 'model'.*/ 5725: /* j is the number of + signs in the model V1+V2+V3 j=2 i=3 to 1 */ 5726: /* modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4 */ 5727: /* k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tage[cptcovage=1]=4 */ 5728: /* k=3 V4 Tvar[k=3]= 4 (from V4) */ 5729: /* k=2 V1 Tvar[k=2]= 1 (from V1) */ 5730: /* k=1 Tvar[1]=2 (from V2) */ 5731: /* k=5 Tvar[5] */ 5732: /* for (k=1; k<=cptcovn;k++) { */ 5733: /* cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]]; */ 5734: /* } */ 5735: /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtab[ij][Tvar[Tage[k]]]]*cov[2]; */ 5736: /* 5737: * Treating invertedly V2+V1+V3*age+V2*V4 is as if written V2*V4 +V3*age + V1 + V2 */ 5738: for(k=cptcovt; k>=1;k--) /**< Number of covariates */ 5739: Tvar[k]=0; 5740: cptcovage=0; 5741: for(k=1; k<=cptcovt;k++){ /* Loop on total covariates of the model */ 5742: cutl(stra,strb,modelsav,'+'); /* keeps in strb after the first '+' 5743: modelsav==V2+V1+V4+V3*age strb=V3*age stra=V2+V1+V4 */ 5744: if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */ 5745: /* printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/ 5746: /*scanf("%d",i);*/ 5747: if (strchr(strb,'*')) { /**< Model includes a product V2+V1+V4+V3*age strb=V3*age */ 5748: cutl(strc,strd,strb,'*'); /**< strd*strc Vm*Vn: strb=V3*age(input) strc=age strd=V3 ; V3*V2 strc=V2, strd=V3 */ 5749: if (strcmp(strc,"age")==0) { /**< Model includes age: Vn*age */ 5750: /* covar is not filled and then is empty */ 5751: cptcovprod--; 5752: cutl(stre,strb,strd,'V'); /* strd=V3(input): stre="3" */ 5753: Tvar[k]=atoi(stre); /* V2+V1+V4+V3*age Tvar[4]=3 ; V1+V2*age Tvar[2]=2; V1+V1*age Tvar[2]=1 */ 5754: cptcovage++; /* Sums the number of covariates which include age as a product */ 5755: Tage[cptcovage]=k; /* Tvar[4]=3, Tage[1] = 4 or V1+V1*age Tvar[2]=1, Tage[1]=2 */ 5756: /*printf("stre=%s ", stre);*/ 5757: } else if (strcmp(strd,"age")==0) { /* or age*Vn */ 5758: cptcovprod--; 5759: cutl(stre,strb,strc,'V'); 5760: Tvar[k]=atoi(stre); 5761: cptcovage++; 5762: Tage[cptcovage]=k; 5763: } else { /* Age is not in the model product V2+V1+V1*V4+V3*age+V3*V2 strb=V3*V2*/ 5764: /* loops on k1=1 (V3*V2) and k1=2 V4*V3 */ 5765: cptcovn++; 5766: cptcovprodnoage++;k1++; 5767: cutl(stre,strb,strc,'V'); /* strc= Vn, stre is n; strb=V3*V2 stre=3 strc=*/ 5768: Tvar[k]=ncovcol+k1; /* For model-covariate k tells which data-covariate to use but 5769: because this model-covariate is a construction we invent a new column 5770: ncovcol + k1 5771: If already ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2 5772: Tvar[3=V1*V4]=4+1 Tvar[5=V3*V2]=4 + 2= 6, etc */ 5773: cutl(strc,strb,strd,'V'); /* strd was Vm, strc is m */ 5774: Tprod[k1]=k; /* Tprod[1]=3(=V1*V4) for V2+V1+V1*V4+age*V3+V3*V2 */ 5775: Tvard[k1][1] =atoi(strc); /* m 1 for V1*/ 5776: Tvard[k1][2] =atoi(stre); /* n 4 for V4*/ 5777: k2=k2+2; 5778: Tvar[cptcovt+k2]=Tvard[k1][1]; /* Tvar[(cptcovt=4+k2=1)=5]= 1 (V1) */ 5779: Tvar[cptcovt+k2+1]=Tvard[k1][2]; /* Tvar[(cptcovt=4+(k2=1)+1)=6]= 4 (V4) */ 5780: for (i=1; i<=lastobs;i++){ 5781: /* Computes the new covariate which is a product of 5782: covar[n][i]* covar[m][i] and stores it at ncovol+k1 May not be defined */ 5783: covar[ncovcol+k1][i]=covar[atoi(stre)][i]*covar[atoi(strc)][i]; 5784: } 5785: } /* End age is not in the model */ 5786: } /* End if model includes a product */ 5787: else { /* no more sum */ 5788: /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/ 5789: /* scanf("%d",i);*/ 5790: cutl(strd,strc,strb,'V'); 5791: ks++; /**< Number of simple covariates */ 5792: cptcovn++; 5793: Tvar[k]=atoi(strd); 5794: } 5795: strcpy(modelsav,stra); /* modelsav=V2+V1+V4 stra=V2+V1+V4 */ 5796: /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav); 5797: scanf("%d",i);*/ 5798: } /* end of loop + on total covariates */ 5799: } /* end if strlen(modelsave == 0) age*age might exist */ 5800: } /* end if strlen(model == 0) */ 5801: 5802: /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products. 5803: If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/ 5804: 5805: /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]); 5806: printf("cptcovprod=%d ", cptcovprod); 5807: fprintf(ficlog,"cptcovprod=%d ", cptcovprod); 5808: 5809: scanf("%d ",i);*/ 5810: 5811: 5812: return (0); /* with covar[new additional covariate if product] and Tage if age */ 5813: /*endread:*/ 5814: printf("Exiting decodemodel: "); 5815: return (1); 5816: } 5817: 5818: int calandcheckages(int imx, int maxwav, double *agemin, double *agemax, int *nberr, int *nbwarn ) 5819: { 5820: int i, m; 5821: 5822: for (i=1; i<=imx; i++) { 5823: for(m=2; (m<= maxwav); m++) { 5824: if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){ 5825: anint[m][i]=9999; 5826: s[m][i]=-1; 5827: } 5828: if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){ 5829: *nberr = *nberr + 1; 5830: printf("Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased (%d)\n",(int)moisdc[i],(int)andc[i],num[i],i, *nberr); 5831: fprintf(ficlog,"Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased (%d)\n",(int)moisdc[i],(int)andc[i],num[i],i, *nberr); 5832: s[m][i]=-1; 5833: } 5834: if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){ 5835: (*nberr)++; 5836: 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]); 5837: 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]); 5838: s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */ 5839: } 5840: } 5841: } 5842: 5843: for (i=1; i<=imx; i++) { 5844: agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]); 5845: for(m=firstpass; (m<= lastpass); m++){ 5846: if(s[m][i] >0 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){ 5847: if (s[m][i] >= nlstate+1) { 5848: if(agedc[i]>0){ 5849: if((int)moisdc[i]!=99 && (int)andc[i]!=9999){ 5850: agev[m][i]=agedc[i]; 5851: /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/ 5852: }else { 5853: if ((int)andc[i]!=9999){ 5854: nbwarn++; 5855: printf("Warning negative age at death: %ld line:%d\n",num[i],i); 5856: fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i); 5857: agev[m][i]=-1; 5858: } 5859: } 5860: } /* agedc > 0 */ 5861: } 5862: else if(s[m][i] !=9){ /* Standard case, age in fractional 5863: years but with the precision of a month */ 5864: agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]); 5865: if((int)mint[m][i]==99 || (int)anint[m][i]==9999) 5866: agev[m][i]=1; 5867: else if(agev[m][i] < *agemin){ 5868: *agemin=agev[m][i]; 5869: printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], *agemin); 5870: } 5871: else if(agev[m][i] >*agemax){ 5872: *agemax=agev[m][i]; 5873: /* printf(" Max anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.2f\n",m,i,anint[m][i], i,annais[i], *agemax);*/ 5874: } 5875: /*agev[m][i]=anint[m][i]-annais[i];*/ 5876: /* agev[m][i] = age[i]+2*m;*/ 5877: } 5878: else { /* =9 */ 5879: agev[m][i]=1; 5880: s[m][i]=-1; 5881: } 5882: } 5883: else /*= 0 Unknown */ 5884: agev[m][i]=1; 5885: } 5886: 5887: } 5888: for (i=1; i<=imx; i++) { 5889: for(m=firstpass; (m<=lastpass); m++){ 5890: if (s[m][i] > (nlstate+ndeath)) { 5891: (*nberr)++; 5892: 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); 5893: 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); 5894: return 1; 5895: } 5896: } 5897: } 5898: 5899: /*for (i=1; i<=imx; i++){ 5900: for (m=firstpass; (m<lastpass); m++){ 5901: printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]); 5902: } 5903: 5904: }*/ 5905: 5906: 5907: printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax); 5908: fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax); 5909: 5910: return (0); 5911: /* endread:*/ 5912: printf("Exiting calandcheckages: "); 5913: return (1); 5914: } 5915: 5916: #if defined(_MSC_VER) 5917: /*printf("Visual C++ compiler: %s \n;", _MSC_FULL_VER);*/ 5918: /*fprintf(ficlog, "Visual C++ compiler: %s \n;", _MSC_FULL_VER);*/ 5919: //#include "stdafx.h" 5920: //#include <stdio.h> 5921: //#include <tchar.h> 5922: //#include <windows.h> 5923: //#include <iostream> 5924: typedef BOOL(WINAPI *LPFN_ISWOW64PROCESS) (HANDLE, PBOOL); 5925: 5926: LPFN_ISWOW64PROCESS fnIsWow64Process; 5927: 5928: BOOL IsWow64() 5929: { 5930: BOOL bIsWow64 = FALSE; 5931: 5932: //typedef BOOL (APIENTRY *LPFN_ISWOW64PROCESS) 5933: // (HANDLE, PBOOL); 5934: 5935: //LPFN_ISWOW64PROCESS fnIsWow64Process; 5936: 5937: HMODULE module = GetModuleHandle(_T("kernel32")); 5938: const char funcName[] = "IsWow64Process"; 5939: fnIsWow64Process = (LPFN_ISWOW64PROCESS) 5940: GetProcAddress(module, funcName); 5941: 5942: if (NULL != fnIsWow64Process) 5943: { 5944: if (!fnIsWow64Process(GetCurrentProcess(), 5945: &bIsWow64)) 5946: //throw std::exception("Unknown error"); 5947: printf("Unknown error\n"); 5948: } 5949: return bIsWow64 != FALSE; 5950: } 5951: #endif 5952: 5953: void syscompilerinfo(int logged) 5954: { 5955: /* #include "syscompilerinfo.h"*/ 5956: /* command line Intel compiler 32bit windows, XP compatible:*/ 5957: /* /GS /W3 /Gy 5958: /Zc:wchar_t /Zi /O2 /Fd"Release\vc120.pdb" /D "WIN32" /D "NDEBUG" /D 5959: "_CONSOLE" /D "_LIB" /D "_USING_V110_SDK71_" /D "_UNICODE" /D 5960: "UNICODE" /Qipo /Zc:forScope /Gd /Oi /MT /Fa"Release\" /EHsc /nologo 5961: /Fo"Release\" /Qprof-dir "Release\" /Fp"Release\IMaCh.pch" 5962: */ 5963: /* 64 bits */ 5964: /* 5965: /GS /W3 /Gy 5966: /Zc:wchar_t /Zi /O2 /Fd"x64\Release\vc120.pdb" /D "WIN32" /D "NDEBUG" 5967: /D "_CONSOLE" /D "_LIB" /D "_UNICODE" /D "UNICODE" /Qipo /Zc:forScope 5968: /Oi /MD /Fa"x64\Release\" /EHsc /nologo /Fo"x64\Release\" /Qprof-dir 5969: "x64\Release\" /Fp"x64\Release\IMaCh.pch" */ 5970: /* Optimization are useless and O3 is slower than O2 */ 5971: /* 5972: /GS /W3 /Gy /Zc:wchar_t /Zi /O3 /Fd"x64\Release\vc120.pdb" /D "WIN32" 5973: /D "NDEBUG" /D "_CONSOLE" /D "_LIB" /D "_UNICODE" /D "UNICODE" /Qipo 5974: /Zc:forScope /Oi /MD /Fa"x64\Release\" /EHsc /nologo /Qparallel 5975: /Fo"x64\Release\" /Qprof-dir "x64\Release\" /Fp"x64\Release\IMaCh.pch" 5976: */ 5977: /* Link is */ /* /OUT:"visual studio 5978: 2013\Projects\IMaCh\Release\IMaCh.exe" /MANIFEST /NXCOMPAT 5979: /PDB:"visual studio 5980: 2013\Projects\IMaCh\Release\IMaCh.pdb" /DYNAMICBASE 5981: "kernel32.lib" "user32.lib" "gdi32.lib" "winspool.lib" 5982: "comdlg32.lib" "advapi32.lib" "shell32.lib" "ole32.lib" 5983: "oleaut32.lib" "uuid.lib" "odbc32.lib" "odbccp32.lib" 5984: /MACHINE:X86 /OPT:REF /SAFESEH /INCREMENTAL:NO 5985: /SUBSYSTEM:CONSOLE",5.01" /MANIFESTUAC:"level='asInvoker' 5986: uiAccess='false'" 5987: /ManifestFile:"Release\IMaCh.exe.intermediate.manifest" /OPT:ICF 5988: /NOLOGO /TLBID:1 5989: */ 5990: #if defined __INTEL_COMPILER 5991: #if defined(__GNUC__) 5992: struct utsname sysInfo; /* For Intel on Linux and OS/X */ 5993: #endif 5994: #elif defined(__GNUC__) 5995: #ifndef __APPLE__ 5996: #include <gnu/libc-version.h> /* Only on gnu */ 5997: #endif 5998: struct utsname sysInfo; 5999: int cross = CROSS; 6000: if (cross){ 6001: printf("Cross-"); 6002: if(logged) fprintf(ficlog, "Cross-"); 6003: } 6004: #endif 6005: 6006: #include <stdint.h> 6007: 6008: printf("Compiled with:");if(logged)fprintf(ficlog,"Compiled with:"); 6009: #if defined(__clang__) 6010: printf(" Clang/LLVM");if(logged)fprintf(ficlog," Clang/LLVM"); /* Clang/LLVM. ---------------------------------------------- */ 6011: #endif 6012: #if defined(__ICC) || defined(__INTEL_COMPILER) 6013: printf(" Intel ICC/ICPC");if(logged)fprintf(ficlog," Intel ICC/ICPC");/* Intel ICC/ICPC. ------------------------------------------ */ 6014: #endif 6015: #if defined(__GNUC__) || defined(__GNUG__) 6016: printf(" GNU GCC/G++");if(logged)fprintf(ficlog," GNU GCC/G++");/* GNU GCC/G++. --------------------------------------------- */ 6017: #endif 6018: #if defined(__HP_cc) || defined(__HP_aCC) 6019: printf(" Hewlett-Packard C/aC++");if(logged)fprintf(fcilog," Hewlett-Packard C/aC++"); /* Hewlett-Packard C/aC++. ---------------------------------- */ 6020: #endif 6021: #if defined(__IBMC__) || defined(__IBMCPP__) 6022: printf(" IBM XL C/C++"); if(logged) fprintf(ficlog," IBM XL C/C++");/* IBM XL C/C++. -------------------------------------------- */ 6023: #endif 6024: #if defined(_MSC_VER) 6025: printf(" Microsoft Visual Studio");if(logged)fprintf(ficlog," Microsoft Visual Studio");/* Microsoft Visual Studio. --------------------------------- */ 6026: #endif 6027: #if defined(__PGI) 6028: printf(" Portland Group PGCC/PGCPP");if(logged) fprintf(ficlog," Portland Group PGCC/PGCPP");/* Portland Group PGCC/PGCPP. ------------------------------- */ 6029: #endif 6030: #if defined(__SUNPRO_C) || defined(__SUNPRO_CC) 6031: printf(" Oracle Solaris Studio");if(logged)fprintf(ficlog," Oracle Solaris Studio\n");/* Oracle Solaris Studio. ----------------------------------- */ 6032: #endif 6033: printf(" for "); if (logged) fprintf(ficlog, " for "); 6034: 6035: // http://stackoverflow.com/questions/4605842/how-to-identify-platform-compiler-from-preprocessor-macros 6036: #ifdef _WIN32 // note the underscore: without it, it's not msdn official! 6037: // Windows (x64 and x86) 6038: printf("Windows (x64 and x86) ");if(logged) fprintf(ficlog,"Windows (x64 and x86) "); 6039: #elif __unix__ // all unices, not all compilers 6040: // Unix 6041: printf("Unix ");if(logged) fprintf(ficlog,"Unix "); 6042: #elif __linux__ 6043: // linux 6044: printf("linux ");if(logged) fprintf(ficlog,"linux "); 6045: #elif __APPLE__ 6046: // Mac OS, not sure if this is covered by __posix__ and/or __unix__ though.. 6047: printf("Mac OS ");if(logged) fprintf(ficlog,"Mac OS "); 6048: #endif 6049: 6050: /* __MINGW32__ */ 6051: /* __CYGWIN__ */ 6052: /* __MINGW64__ */ 6053: // http://msdn.microsoft.com/en-us/library/b0084kay.aspx 6054: /* _MSC_VER //the Visual C++ compiler is 17.00.51106.1, the _MSC_VER macro evaluates to 1700. Type cl /? */ 6055: /* _MSC_FULL_VER //the Visual C++ compiler is 15.00.20706.01, the _MSC_FULL_VER macro evaluates to 150020706 */ 6056: /* _WIN64 // Defined for applications for Win64. */ 6057: /* _M_X64 // Defined for compilations that target x64 processors. */ 6058: /* _DEBUG // Defined when you compile with /LDd, /MDd, and /MTd. */ 6059: 6060: #if UINTPTR_MAX == 0xffffffff 6061: printf(" 32-bit"); if(logged) fprintf(ficlog," 32-bit");/* 32-bit */ 6062: #elif UINTPTR_MAX == 0xffffffffffffffff 6063: printf(" 64-bit"); if(logged) fprintf(ficlog," 64-bit");/* 64-bit */ 6064: #else 6065: printf(" wtf-bit"); if(logged) fprintf(ficlog," wtf-bit");/* wtf */ 6066: #endif 6067: 6068: #if defined(__GNUC__) 6069: # if defined(__GNUC_PATCHLEVEL__) 6070: # define __GNUC_VERSION__ (__GNUC__ * 10000 \ 6071: + __GNUC_MINOR__ * 100 \ 6072: + __GNUC_PATCHLEVEL__) 6073: # else 6074: # define __GNUC_VERSION__ (__GNUC__ * 10000 \ 6075: + __GNUC_MINOR__ * 100) 6076: # endif 6077: printf(" using GNU C version %d.\n", __GNUC_VERSION__); 6078: if(logged) fprintf(ficlog, " using GNU C version %d.\n", __GNUC_VERSION__); 6079: 6080: if (uname(&sysInfo) != -1) { 6081: printf("Running on: %s %s %s %s %s\n",sysInfo.sysname, sysInfo.nodename, sysInfo.release, sysInfo.version, sysInfo.machine); 6082: if(logged) fprintf(ficlog,"Running on: %s %s %s %s %s\n ",sysInfo.sysname, sysInfo.nodename, sysInfo.release, sysInfo.version, sysInfo.machine); 6083: } 6084: else 6085: perror("uname() error"); 6086: //#ifndef __INTEL_COMPILER 6087: #if !defined (__INTEL_COMPILER) && !defined(__APPLE__) 6088: printf("GNU libc version: %s\n", gnu_get_libc_version()); 6089: if(logged) fprintf(ficlog,"GNU libc version: %s\n", gnu_get_libc_version()); 6090: #endif 6091: #endif 6092: 6093: // void main() 6094: // { 6095: #if defined(_MSC_VER) 6096: if (IsWow64()){ 6097: printf("\nThe program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n"); 6098: if (logged) fprintf(ficlog, "\nThe program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n"); 6099: } 6100: else{ 6101: printf("\nThe program is not running under WOW64 (i.e probably on a 64bit Windows).\n"); 6102: if (logged) fprintf(ficlog, "\nThe programm is not running under WOW64 (i.e probably on a 64bit Windows).\n"); 6103: } 6104: // printf("\nPress Enter to continue..."); 6105: // getchar(); 6106: // } 6107: 6108: #endif 6109: 6110: 6111: } 6112: 6113: int prevalence_limit(double *p, double **prlim, double ageminpar, double agemaxpar){ 6114: /*--------------- Prevalence limit (period or stable prevalence) --------------*/ 6115: int i, j, k, i1 ; 6116: double ftolpl = 1.e-10; 6117: double age, agebase, agelim; 6118: 6119: strcpy(filerespl,"pl"); 6120: strcat(filerespl,fileres); 6121: if((ficrespl=fopen(filerespl,"w"))==NULL) { 6122: printf("Problem with period (stable) prevalence resultfile: %s\n", filerespl);return 1; 6123: fprintf(ficlog,"Problem with period (stable) prevalence resultfile: %s\n", filerespl);return 1; 6124: } 6125: printf("Computing period (stable) prevalence: result on file '%s' \n", filerespl); 6126: fprintf(ficlog,"Computing period (stable) prevalence: result on file '%s' \n", filerespl); 6127: pstamp(ficrespl); 6128: fprintf(ficrespl,"# Period (stable) prevalence \n"); 6129: fprintf(ficrespl,"#Age "); 6130: for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i); 6131: fprintf(ficrespl,"\n"); 6132: 6133: /* prlim=matrix(1,nlstate,1,nlstate);*/ /* back in main */ 6134: 6135: agebase=ageminpar; 6136: agelim=agemaxpar; 6137: 6138: i1=pow(2,cptcoveff); 6139: if (cptcovn < 1){i1=1;} 6140: 6141: for(cptcov=1,k=0;cptcov<=i1;cptcov++){ 6142: /* for(cptcov=1,k=0;cptcov<=1;cptcov++){ */ 6143: //for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){ 6144: k=k+1; 6145: /* to clean */ 6146: //printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtab[cptcod][cptcov]); 6147: fprintf(ficrespl,"\n#******"); 6148: printf("\n#******"); 6149: fprintf(ficlog,"\n#******"); 6150: for(j=1;j<=cptcoveff;j++) { 6151: fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]); 6152: printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]); 6153: fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]); 6154: } 6155: fprintf(ficrespl,"******\n"); 6156: printf("******\n"); 6157: fprintf(ficlog,"******\n"); 6158: 6159: fprintf(ficrespl,"#Age "); 6160: for(j=1;j<=cptcoveff;j++) { 6161: fprintf(ficrespl,"V%d %d",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]); 6162: } 6163: for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i); 6164: fprintf(ficrespl,"\n"); 6165: 6166: for (age=agebase; age<=agelim; age++){ 6167: /* for (age=agebase; age<=agebase; age++){ */ 6168: prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k); 6169: fprintf(ficrespl,"%.0f ",age ); 6170: for(j=1;j<=cptcoveff;j++) 6171: fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]); 6172: for(i=1; i<=nlstate;i++) 6173: fprintf(ficrespl," %.5f", prlim[i][i]); 6174: fprintf(ficrespl,"\n"); 6175: } /* Age */ 6176: /* was end of cptcod */ 6177: } /* cptcov */ 6178: return 0; 6179: } 6180: 6181: int hPijx(double *p, int bage, int fage){ 6182: /*------------- h Pij x at various ages ------------*/ 6183: 6184: int stepsize; 6185: int agelim; 6186: int hstepm; 6187: int nhstepm; 6188: int h, i, i1, j, k; 6189: 6190: double agedeb; 6191: double ***p3mat; 6192: 6193: strcpy(filerespij,"pij"); strcat(filerespij,fileres); 6194: if((ficrespij=fopen(filerespij,"w"))==NULL) { 6195: printf("Problem with Pij resultfile: %s\n", filerespij); return 1; 6196: fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij); return 1; 6197: } 6198: printf("Computing pij: result on file '%s' \n", filerespij); 6199: fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij); 6200: 6201: stepsize=(int) (stepm+YEARM-1)/YEARM; 6202: /*if (stepm<=24) stepsize=2;*/ 6203: 6204: agelim=AGESUP; 6205: hstepm=stepsize*YEARM; /* Every year of age */ 6206: hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */ 6207: 6208: /* hstepm=1; aff par mois*/ 6209: pstamp(ficrespij); 6210: fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x "); 6211: i1= pow(2,cptcoveff); 6212: /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */ 6213: /* /\*for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*\/ */ 6214: /* k=k+1; */ 6215: for (k=1; k <= (int) pow(2,cptcoveff); k++){ 6216: fprintf(ficrespij,"\n#****** "); 6217: for(j=1;j<=cptcoveff;j++) 6218: fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]); 6219: fprintf(ficrespij,"******\n"); 6220: 6221: for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */ 6222: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 6223: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */ 6224: 6225: /* nhstepm=nhstepm*YEARM; aff par mois*/ 6226: 6227: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); 6228: oldm=oldms;savm=savms; 6229: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k); 6230: fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j="); 6231: for(i=1; i<=nlstate;i++) 6232: for(j=1; j<=nlstate+ndeath;j++) 6233: fprintf(ficrespij," %1d-%1d",i,j); 6234: fprintf(ficrespij,"\n"); 6235: for (h=0; h<=nhstepm; h++){ 6236: /*agedebphstep = agedeb + h*hstepm/YEARM*stepm;*/ 6237: fprintf(ficrespij,"%d %3.f %3.f",k, agedeb, agedeb + h*hstepm/YEARM*stepm ); 6238: for(i=1; i<=nlstate;i++) 6239: for(j=1; j<=nlstate+ndeath;j++) 6240: fprintf(ficrespij," %.5f", p3mat[i][j][h]); 6241: fprintf(ficrespij,"\n"); 6242: } 6243: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); 6244: fprintf(ficrespij,"\n"); 6245: } 6246: /*}*/ 6247: } 6248: return 0; 6249: } 6250: 6251: 6252: /***********************************************/ 6253: /**************** Main Program *****************/ 6254: /***********************************************/ 6255: 6256: int main(int argc, char *argv[]) 6257: { 6258: #ifdef GSL 6259: const gsl_multimin_fminimizer_type *T; 6260: size_t iteri = 0, it; 6261: int rval = GSL_CONTINUE; 6262: int status = GSL_SUCCESS; 6263: double ssval; 6264: #endif 6265: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav); 6266: int i,j, k, n=MAXN,iter=0,m,size=100, cptcod; 6267: 6268: int jj, ll, li, lj, lk; 6269: int numlinepar=0; /* Current linenumber of parameter file */ 6270: int itimes; 6271: int NDIM=2; 6272: int vpopbased=0; 6273: 6274: char ca[32], cb[32]; 6275: /* FILE *fichtm; *//* Html File */ 6276: /* FILE *ficgp;*/ /*Gnuplot File */ 6277: struct stat info; 6278: double agedeb=0.; 6279: 6280: double ageminpar=AGEOVERFLOW,agemin=AGEOVERFLOW, agemaxpar=-AGEOVERFLOW, agemax=-AGEOVERFLOW; 6281: 6282: double fret; 6283: double dum=0.; /* Dummy variable */ 6284: double ***p3mat; 6285: double ***mobaverage; 6286: 6287: char line[MAXLINE]; 6288: char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE]; 6289: char pathr[MAXLINE], pathimach[MAXLINE]; 6290: char *tok, *val; /* pathtot */ 6291: int firstobs=1, lastobs=10; 6292: int c, h , cpt; 6293: int jl=0; 6294: int i1, j1, jk, stepsize=0; 6295: int count=0; 6296: 6297: int *tab; 6298: int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */ 6299: int mobilav=0,popforecast=0; 6300: int hstepm=0, nhstepm=0; 6301: int agemortsup; 6302: float sumlpop=0.; 6303: double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000; 6304: double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000; 6305: 6306: double bage=0, fage=110., age, agelim=0., agebase=0.; 6307: double ftolpl=FTOL; 6308: double **prlim; 6309: double ***param; /* Matrix of parameters */ 6310: double *p; 6311: double **matcov; /* Matrix of covariance */ 6312: double ***delti3; /* Scale */ 6313: double *delti; /* Scale */ 6314: double ***eij, ***vareij; 6315: double **varpl; /* Variances of prevalence limits by age */ 6316: double *epj, vepp; 6317: 6318: double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000; 6319: double **ximort; 6320: char *alph[]={"a","a","b","c","d","e"}, str[4]="1234"; 6321: int *dcwave; 6322: 6323: char z[1]="c"; 6324: 6325: /*char *strt;*/ 6326: char strtend[80]; 6327: 6328: 6329: /* setlocale (LC_ALL, ""); */ 6330: /* bindtextdomain (PACKAGE, LOCALEDIR); */ 6331: /* textdomain (PACKAGE); */ 6332: /* setlocale (LC_CTYPE, ""); */ 6333: /* setlocale (LC_MESSAGES, ""); */ 6334: 6335: /* gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */ 6336: rstart_time = time(NULL); 6337: /* (void) gettimeofday(&start_time,&tzp);*/ 6338: start_time = *localtime(&rstart_time); 6339: curr_time=start_time; 6340: /*tml = *localtime(&start_time.tm_sec);*/ 6341: /* strcpy(strstart,asctime(&tml)); */ 6342: strcpy(strstart,asctime(&start_time)); 6343: 6344: /* printf("Localtime (at start)=%s",strstart); */ 6345: /* tp.tm_sec = tp.tm_sec +86400; */ 6346: /* tm = *localtime(&start_time.tm_sec); */ 6347: /* tmg.tm_year=tmg.tm_year +dsign*dyear; */ 6348: /* tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */ 6349: /* tmg.tm_hour=tmg.tm_hour + 1; */ 6350: /* tp.tm_sec = mktime(&tmg); */ 6351: /* strt=asctime(&tmg); */ 6352: /* printf("Time(after) =%s",strstart); */ 6353: /* (void) time (&time_value); 6354: * printf("time=%d,t-=%d\n",time_value,time_value-86400); 6355: * tm = *localtime(&time_value); 6356: * strstart=asctime(&tm); 6357: * printf("tim_value=%d,asctime=%s\n",time_value,strstart); 6358: */ 6359: 6360: nberr=0; /* Number of errors and warnings */ 6361: nbwarn=0; 6362: #ifdef WIN32 6363: _getcwd(pathcd, size); 6364: #else 6365: getcwd(pathcd, size); 6366: #endif 6367: syscompilerinfo(0); 6368: printf("\n%s\n%s",version,fullversion); 6369: if(argc <=1){ 6370: printf("\nEnter the parameter file name: "); 6371: fgets(pathr,FILENAMELENGTH,stdin); 6372: i=strlen(pathr); 6373: if(pathr[i-1]=='\n') 6374: pathr[i-1]='\0'; 6375: i=strlen(pathr); 6376: if(pathr[i-1]==' ') /* This may happen when dragging on oS/X! */ 6377: pathr[i-1]='\0'; 6378: for (tok = pathr; tok != NULL; ){ 6379: printf("Pathr |%s|\n",pathr); 6380: while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0'); 6381: printf("val= |%s| pathr=%s\n",val,pathr); 6382: strcpy (pathtot, val); 6383: if(pathr[0] == '\0') break; /* Dirty */ 6384: } 6385: } 6386: else{ 6387: strcpy(pathtot,argv[1]); 6388: } 6389: /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/ 6390: /*cygwin_split_path(pathtot,path,optionfile); 6391: printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/ 6392: /* cutv(path,optionfile,pathtot,'\\');*/ 6393: 6394: /* Split argv[0], imach program to get pathimach */ 6395: printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]); 6396: split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname); 6397: printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname); 6398: /* strcpy(pathimach,argv[0]); */ 6399: /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */ 6400: split(pathtot,path,optionfile,optionfilext,optionfilefiname); 6401: printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname); 6402: #ifdef WIN32 6403: _chdir(path); /* Can be a relative path */ 6404: if(_getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */ 6405: #else 6406: chdir(path); /* Can be a relative path */ 6407: if (getcwd(pathcd, MAXLINE) > 0) /* So pathcd is the full path */ 6408: #endif 6409: printf("Current directory %s!\n",pathcd); 6410: strcpy(command,"mkdir "); 6411: strcat(command,optionfilefiname); 6412: if((outcmd=system(command)) != 0){ 6413: printf("Directory already exists (or can't create it) %s%s, err=%d\n",path,optionfilefiname,outcmd); 6414: /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */ 6415: /* fclose(ficlog); */ 6416: /* exit(1); */ 6417: } 6418: /* if((imk=mkdir(optionfilefiname))<0){ */ 6419: /* perror("mkdir"); */ 6420: /* } */ 6421: 6422: /*-------- arguments in the command line --------*/ 6423: 6424: /* Main Log file */ 6425: strcat(filelog, optionfilefiname); 6426: strcat(filelog,".log"); /* */ 6427: if((ficlog=fopen(filelog,"w"))==NULL) { 6428: printf("Problem with logfile %s\n",filelog); 6429: goto end; 6430: } 6431: fprintf(ficlog,"Log filename:%s\n",filelog); 6432: fprintf(ficlog,"\n%s\n%s",version,fullversion); 6433: fprintf(ficlog,"\nEnter the parameter file name: \n"); 6434: fprintf(ficlog,"pathimach=%s\npathtot=%s\n\ 6435: path=%s \n\ 6436: optionfile=%s\n\ 6437: optionfilext=%s\n\ 6438: optionfilefiname='%s'\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname); 6439: 6440: syscompilerinfo(0); 6441: 6442: printf("Local time (at start):%s",strstart); 6443: fprintf(ficlog,"Local time (at start): %s",strstart); 6444: fflush(ficlog); 6445: /* (void) gettimeofday(&curr_time,&tzp); */ 6446: /* printf("Elapsed time %d\n", asc_diff_time(curr_time.tm_sec-start_time.tm_sec,tmpout)); */ 6447: 6448: /* */ 6449: strcpy(fileres,"r"); 6450: strcat(fileres, optionfilefiname); 6451: strcat(fileres,".txt"); /* Other files have txt extension */ 6452: 6453: /* Main ---------arguments file --------*/ 6454: 6455: if((ficpar=fopen(optionfile,"r"))==NULL) { 6456: printf("Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno)); 6457: fprintf(ficlog,"Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno)); 6458: fflush(ficlog); 6459: /* goto end; */ 6460: exit(70); 6461: } 6462: 6463: 6464: 6465: strcpy(filereso,"o"); 6466: strcat(filereso,fileres); 6467: if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */ 6468: printf("Problem with Output resultfile: %s\n", filereso); 6469: fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso); 6470: fflush(ficlog); 6471: goto end; 6472: } 6473: 6474: /* Reads comments: lines beginning with '#' */ 6475: numlinepar=0; 6476: while((c=getc(ficpar))=='#' && c!= EOF){ 6477: ungetc(c,ficpar); 6478: fgets(line, MAXLINE, ficpar); 6479: numlinepar++; 6480: fputs(line,stdout); 6481: fputs(line,ficparo); 6482: fputs(line,ficlog); 6483: } 6484: ungetc(c,ficpar); 6485: 6486: 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=1+age+%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model); 6487: numlinepar=numlinepar+3; /* In general */ 6488: 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=1+age+%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model); 6489: if(model[strlen(model)-1]=='.') /* Suppressing leading dot in the model */ 6490: model[strlen(model)-1]='\0'; 6491: 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=1+age+%s.\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model); 6492: 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=1+age+%s.\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model); 6493: fflush(ficlog); 6494: /* if(model[0]=='#'|| model[0]== '\0'){ */ 6495: if(model[0]=='#'){ 6496: printf("Error in 'model' line: model should start with 'model=1+age+' and end with '.' \n \ 6497: 'model=1+age+.' or 'model=1+age+V1.' or 'model=1+age+age*age+V1+V1*age.' or \n \ 6498: 'model=1+age+V1+V2.' or 'model=1+age+V1+V2+V1*V2.' etc. \n"); \ 6499: if(mle != -1){ 6500: printf("Fix the model line and run imach with mle=-1 to get a correct template of the parameter file.\n"); 6501: exit(1); 6502: } 6503: } 6504: while((c=getc(ficpar))=='#' && c!= EOF){ 6505: ungetc(c,ficpar); 6506: fgets(line, MAXLINE, ficpar); 6507: numlinepar++; 6508: fputs(line, stdout); 6509: //puts(line); 6510: fputs(line,ficparo); 6511: fputs(line,ficlog); 6512: } 6513: ungetc(c,ficpar); 6514: 6515: 6516: covar=matrix(0,NCOVMAX,1,n); /**< used in readdata */ 6517: cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement plus one, indepently of n in Vn*/ 6518: /* v1+v2+v3+v2*v4+v5*age makes cptcovn = 5 6519: v1+v2*age+v2*v3 makes cptcovn = 3 6520: */ 6521: if (strlen(model)>1) 6522: 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,age*age makes 3*/ 6523: else 6524: ncovmodel=2; /* Constant and age */ 6525: nforce= (nlstate+ndeath-1)*nlstate; /* Number of forces ij from state i to j */ 6526: npar= nforce*ncovmodel; /* Number of parameters like aij*/ 6527: if(npar >MAXPARM || nlstate >NLSTATEMAX || ndeath >NDEATHMAX || ncovmodel>NCOVMAX){ 6528: 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); 6529: 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); 6530: fflush(stdout); 6531: fclose (ficlog); 6532: goto end; 6533: } 6534: delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); 6535: delti=delti3[1][1]; 6536: /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/ 6537: if(mle==-1){ /* Print a wizard for help writing covariance matrix */ 6538: prwizard(ncovmodel, nlstate, ndeath, model, ficparo); 6539: printf(" You chose mle=-1, look at file %s for a template of covariance matrix \n",filereso); 6540: fprintf(ficlog," You chose mle=-1, look at file %s for a template of covariance matrix \n",filereso); 6541: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 6542: fclose (ficparo); 6543: fclose (ficlog); 6544: goto end; 6545: exit(0); 6546: } 6547: else if(mle==-3) { /* Main Wizard */ 6548: prwizard(ncovmodel, nlstate, ndeath, model, ficparo); 6549: printf(" You chose mle=-3, look at file %s for a template of covariance matrix \n",filereso); 6550: fprintf(ficlog," You chose mle=-3, look at file %s for a template of covariance matrix \n",filereso); 6551: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); 6552: matcov=matrix(1,npar,1,npar); 6553: } 6554: else{ 6555: /* Read guessed parameters */ 6556: /* Reads comments: lines beginning with '#' */ 6557: while((c=getc(ficpar))=='#' && c!= EOF){ 6558: ungetc(c,ficpar); 6559: fgets(line, MAXLINE, ficpar); 6560: numlinepar++; 6561: fputs(line,stdout); 6562: fputs(line,ficparo); 6563: fputs(line,ficlog); 6564: } 6565: ungetc(c,ficpar); 6566: 6567: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); 6568: for(i=1; i <=nlstate; i++){ 6569: j=0; 6570: for(jj=1; jj <=nlstate+ndeath; jj++){ 6571: if(jj==i) continue; 6572: j++; 6573: fscanf(ficpar,"%1d%1d",&i1,&j1); 6574: if ((i1 != i) || (j1 != jj)){ 6575: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \ 6576: It might be a problem of design; if ncovcol and the model are correct\n \ 6577: run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1); 6578: exit(1); 6579: } 6580: fprintf(ficparo,"%1d%1d",i1,j1); 6581: if(mle==1) 6582: printf("%1d%1d",i,jj); 6583: fprintf(ficlog,"%1d%1d",i,jj); 6584: for(k=1; k<=ncovmodel;k++){ 6585: fscanf(ficpar," %lf",&param[i][j][k]); 6586: if(mle==1){ 6587: printf(" %lf",param[i][j][k]); 6588: fprintf(ficlog," %lf",param[i][j][k]); 6589: } 6590: else 6591: fprintf(ficlog," %lf",param[i][j][k]); 6592: fprintf(ficparo," %lf",param[i][j][k]); 6593: } 6594: fscanf(ficpar,"\n"); 6595: numlinepar++; 6596: if(mle==1) 6597: printf("\n"); 6598: fprintf(ficlog,"\n"); 6599: fprintf(ficparo,"\n"); 6600: } 6601: } 6602: fflush(ficlog); 6603: 6604: /* Reads scales values */ 6605: p=param[1][1]; 6606: 6607: /* Reads comments: lines beginning with '#' */ 6608: while((c=getc(ficpar))=='#' && c!= EOF){ 6609: ungetc(c,ficpar); 6610: fgets(line, MAXLINE, ficpar); 6611: numlinepar++; 6612: fputs(line,stdout); 6613: fputs(line,ficparo); 6614: fputs(line,ficlog); 6615: } 6616: ungetc(c,ficpar); 6617: 6618: for(i=1; i <=nlstate; i++){ 6619: for(j=1; j <=nlstate+ndeath-1; j++){ 6620: fscanf(ficpar,"%1d%1d",&i1,&j1); 6621: if ( (i1-i) * (j1-j) != 0){ 6622: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1); 6623: exit(1); 6624: } 6625: printf("%1d%1d",i,j); 6626: fprintf(ficparo,"%1d%1d",i1,j1); 6627: fprintf(ficlog,"%1d%1d",i1,j1); 6628: for(k=1; k<=ncovmodel;k++){ 6629: fscanf(ficpar,"%le",&delti3[i][j][k]); 6630: printf(" %le",delti3[i][j][k]); 6631: fprintf(ficparo," %le",delti3[i][j][k]); 6632: fprintf(ficlog," %le",delti3[i][j][k]); 6633: } 6634: fscanf(ficpar,"\n"); 6635: numlinepar++; 6636: printf("\n"); 6637: fprintf(ficparo,"\n"); 6638: fprintf(ficlog,"\n"); 6639: } 6640: } 6641: fflush(ficlog); 6642: 6643: /* Reads covariance matrix */ 6644: delti=delti3[1][1]; 6645: 6646: 6647: /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */ 6648: 6649: /* Reads comments: lines beginning with '#' */ 6650: while((c=getc(ficpar))=='#' && c!= EOF){ 6651: ungetc(c,ficpar); 6652: fgets(line, MAXLINE, ficpar); 6653: numlinepar++; 6654: fputs(line,stdout); 6655: fputs(line,ficparo); 6656: fputs(line,ficlog); 6657: } 6658: ungetc(c,ficpar); 6659: 6660: matcov=matrix(1,npar,1,npar); 6661: for(i=1; i <=npar; i++) 6662: for(j=1; j <=npar; j++) matcov[i][j]=0.; 6663: 6664: /* Scans npar lines */ 6665: for(i=1; i <=npar; i++){ 6666: count=fscanf(ficpar,"%1d%1d%1d",&i1,&j1,&jk); 6667: if(count != 3){ 6668: printf("Error! Error in parameter file %s at line %d after line starting with %1d%1d%1d\n\ 6669: This is probably because your covariance matrix doesn't \n contain exactly %d lines corresponding to your model line '1+age+%s'.\n\ 6670: Please run with mle=-1 to get a correct covariance matrix.\n",optionfile,numlinepar, i1,j1,jk, npar, model); 6671: fprintf(ficlog,"Error! Error in parameter file %s at line %d after line starting with %1d%1d%1d\n\ 6672: This is probably because your covariance matrix doesn't \n contain exactly %d lines corresponding to your model line '1+age+%s'.\n\ 6673: Please run with mle=-1 to get a correct covariance matrix.\n",optionfile,numlinepar, i1,j1,jk, npar, model); 6674: exit(1); 6675: }else 6676: if(mle==1) 6677: printf("%1d%1d%1d",i1,j1,jk); 6678: fprintf(ficlog,"%1d%1d%1d",i1,j1,jk); 6679: fprintf(ficparo,"%1d%1d%1d",i1,j1,jk); 6680: for(j=1; j <=i; j++){ 6681: fscanf(ficpar," %le",&matcov[i][j]); 6682: if(mle==1){ 6683: printf(" %.5le",matcov[i][j]); 6684: } 6685: fprintf(ficlog," %.5le",matcov[i][j]); 6686: fprintf(ficparo," %.5le",matcov[i][j]); 6687: } 6688: fscanf(ficpar,"\n"); 6689: numlinepar++; 6690: if(mle==1) 6691: printf("\n"); 6692: fprintf(ficlog,"\n"); 6693: fprintf(ficparo,"\n"); 6694: } 6695: /* End of read covariance matrix npar lines */ 6696: for(i=1; i <=npar; i++) 6697: for(j=i+1;j<=npar;j++) 6698: matcov[i][j]=matcov[j][i]; 6699: 6700: if(mle==1) 6701: printf("\n"); 6702: fprintf(ficlog,"\n"); 6703: 6704: fflush(ficlog); 6705: 6706: /*-------- Rewriting parameter file ----------*/ 6707: strcpy(rfileres,"r"); /* "Rparameterfile */ 6708: strcat(rfileres,optionfilefiname); /* Parameter file first name*/ 6709: strcat(rfileres,"."); /* */ 6710: strcat(rfileres,optionfilext); /* Other files have txt extension */ 6711: if((ficres =fopen(rfileres,"w"))==NULL) { 6712: printf("Problem writing new parameter file: %s\n", fileres);goto end; 6713: fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end; 6714: } 6715: fprintf(ficres,"#%s\n",version); 6716: } /* End of mle != -3 */ 6717: 6718: /* Main data 6719: */ 6720: n= lastobs; 6721: num=lvector(1,n); 6722: moisnais=vector(1,n); 6723: annais=vector(1,n); 6724: moisdc=vector(1,n); 6725: andc=vector(1,n); 6726: agedc=vector(1,n); 6727: cod=ivector(1,n); 6728: weight=vector(1,n); 6729: for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */ 6730: mint=matrix(1,maxwav,1,n); 6731: anint=matrix(1,maxwav,1,n); 6732: s=imatrix(1,maxwav+1,1,n); /* s[i][j] health state for wave i and individual j */ 6733: tab=ivector(1,NCOVMAX); 6734: ncodemax=ivector(1,NCOVMAX); /* Number of code per covariate; if O and 1 only, 2**ncov; V1+V2+V3+V4=>16 */ 6735: ncodemaxwundef=ivector(1,NCOVMAX); /* Number of code per covariate; if - 1 O and 1 only, 2**ncov; V1+V2+V3+V4=>16 */ 6736: 6737: /* Reads data from file datafile */ 6738: if (readdata(datafile, firstobs, lastobs, &imx)==1) 6739: goto end; 6740: 6741: /* Calculation of the number of parameters from char model */ 6742: /* modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4 6743: k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tag[cptcovage=1]=4 6744: k=3 V4 Tvar[k=3]= 4 (from V4) 6745: k=2 V1 Tvar[k=2]= 1 (from V1) 6746: k=1 Tvar[1]=2 (from V2) 6747: */ 6748: Tvar=ivector(1,NCOVMAX); /* Was 15 changed to NCOVMAX. */ 6749: /* V2+V1+V4+age*V3 is a model with 4 covariates (3 plus signs). 6750: For each model-covariate stores the data-covariate id. Tvar[1]=2, Tvar[2]=1, Tvar[3]=4, 6751: Tvar[4=age*V3] is 3 and 'age' is recorded in Tage. 6752: */ 6753: /* For model-covariate k tells which data-covariate to use but 6754: because this model-covariate is a construction we invent a new column 6755: ncovcol + k1 6756: If already ncovcol=4 and model=V2+V1+V1*V4+age*V3 6757: Tvar[3=V1*V4]=4+1 etc */ 6758: Tprod=ivector(1,NCOVMAX); /* Gives the position of a product */ 6759: /* Tprod[k1=1]=3(=V1*V4) for V2+V1+V1*V4+age*V3 6760: if V2+V1+V1*V4+age*V3+V3*V2 TProd[k1=2]=5 (V3*V2) 6761: */ 6762: Tvaraff=ivector(1,NCOVMAX); /* Unclear */ 6763: 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 6764: * For V3*V2 (in V2+V1+V1*V4+age*V3+V3*V2), V3*V2 position is 2nd. 6765: * Tvard[k1=2][1]=3 (V3) Tvard[k1=2][2]=2(V2) */ 6766: Tage=ivector(1,NCOVMAX); /* Gives the covariate id of covariates associated with age: V2 + V1 + age*V4 + V3*age 6767: 4 covariates (3 plus signs) 6768: Tage[1=V3*age]= 4; Tage[2=age*V4] = 3 6769: */ 6770: 6771: /* Main decodemodel */ 6772: 6773: 6774: if(decodemodel(model, lastobs) == 1) 6775: goto end; 6776: 6777: if((double)(lastobs-imx)/(double)imx > 1.10){ 6778: nbwarn++; 6779: 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); 6780: 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); 6781: } 6782: /* if(mle==1){*/ 6783: if (weightopt != 1) { /* Maximisation without weights. We can have weights different from 1 but want no weight*/ 6784: for(i=1;i<=imx;i++) weight[i]=1.0; /* changed to imx */ 6785: } 6786: 6787: /*-calculation of age at interview from date of interview and age at death -*/ 6788: agev=matrix(1,maxwav,1,imx); 6789: 6790: if(calandcheckages(imx, maxwav, &agemin, &agemax, &nberr, &nbwarn) == 1) 6791: goto end; 6792: 6793: 6794: agegomp=(int)agemin; 6795: free_vector(moisnais,1,n); 6796: free_vector(annais,1,n); 6797: /* free_matrix(mint,1,maxwav,1,n); 6798: free_matrix(anint,1,maxwav,1,n);*/ 6799: free_vector(moisdc,1,n); 6800: free_vector(andc,1,n); 6801: /* */ 6802: 6803: wav=ivector(1,imx); 6804: dh=imatrix(1,lastpass-firstpass+1,1,imx); 6805: bh=imatrix(1,lastpass-firstpass+1,1,imx); 6806: mw=imatrix(1,lastpass-firstpass+1,1,imx); 6807: 6808: /* Concatenates waves */ 6809: concatwav(wav, dh, bh, mw, s, agedc, agev, firstpass, lastpass, imx, nlstate, stepm); 6810: /* */ 6811: 6812: /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */ 6813: 6814: nbcode=imatrix(0,NCOVMAX,0,NCOVMAX); 6815: ncodemax[1]=1; 6816: Ndum =ivector(-1,NCOVMAX); 6817: if (ncovmodel-nagesqr > 2 ) /* That is if covariate other than cst, age and age*age */ 6818: tricode(Tvar,nbcode,imx, Ndum); /**< Fills nbcode[Tvar[j]][l]; */ 6819: /* Nbcode gives the value of the lth modality of jth covariate, in 6820: V2+V1*age, there are 3 covariates Tvar[2]=1 (V1).*/ 6821: /* 1 to ncodemax[j] is the maximum value of this jth covariate */ 6822: 6823: codtab=imatrix(1,100,1,10); /* codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) */ 6824: /*printf(" codtab[1,1],codtab[100,10]=%d,%d\n", codtab[1][1],codtab[100][10]);*/ 6825: /* codtab gives the value 1 or 2 of the hth combination of k covariates (1 or 2).*/ 6826: h=0; 6827: 6828: 6829: /*if (cptcovn > 0) */ 6830: 6831: 6832: m=pow(2,cptcoveff); 6833: 6834: for(k=1;k<=cptcoveff; k++){ /* scans any effective covariate */ 6835: 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 */ 6836: for(j=1; j <= ncodemax[k]; j++){ /* For each modality of this covariate ncodemax=2*/ 6837: for(cpt=1; cpt <=pow(2,k-1); cpt++){ /* cpt=1 to 8/2**(3+1-1 or 3+1-3) =1 or 4 */ 6838: h++; 6839: if (h>m) 6840: h=1; 6841: /**< codtab(h,k) k = codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) + 1 6842: * For k=4 covariates, h goes from 1 to 2**k 6843: * codtabm(h,k)= 1 & (h-1) >> (k-1) ; 6844: * h\k 1 2 3 4 6845: *______________________________ 6846: * 1 i=1 1 i=1 1 i=1 1 i=1 1 6847: * 2 2 1 1 1 6848: * 3 i=2 1 2 1 1 6849: * 4 2 2 1 1 6850: * 5 i=3 1 i=2 1 2 1 6851: * 6 2 1 2 1 6852: * 7 i=4 1 2 2 1 6853: * 8 2 2 2 1 6854: * 9 i=5 1 i=3 1 i=2 1 1 6855: * 10 2 1 1 1 6856: * 11 i=6 1 2 1 1 6857: * 12 2 2 1 1 6858: * 13 i=7 1 i=4 1 2 1 6859: * 14 2 1 2 1 6860: * 15 i=8 1 2 2 1 6861: * 16 2 2 2 1 6862: */ 6863: codtab[h][k]=j; 6864: /* codtab[12][3]=1; */ 6865: /*codtab[h][Tvar[k]]=j;*/ 6866: 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]]); 6867: } 6868: } 6869: } 6870: } 6871: /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]); 6872: codtab[1][2]=1;codtab[2][2]=2; */ 6873: /* for(i=1; i <=m ;i++){ 6874: for(k=1; k <=cptcovn; k++){ 6875: printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff); 6876: } 6877: printf("\n"); 6878: } 6879: scanf("%d",i);*/ 6880: 6881: free_ivector(Ndum,-1,NCOVMAX); 6882: 6883: 6884: 6885: /* Initialisation of ----------- gnuplot -------------*/ 6886: strcpy(optionfilegnuplot,optionfilefiname); 6887: if(mle==-3) 6888: strcat(optionfilegnuplot,"-mort"); 6889: strcat(optionfilegnuplot,".gp"); 6890: 6891: if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) { 6892: printf("Problem with file %s",optionfilegnuplot); 6893: } 6894: else{ 6895: fprintf(ficgp,"\n# %s\n", version); 6896: fprintf(ficgp,"# %s\n", optionfilegnuplot); 6897: //fprintf(ficgp,"set missing 'NaNq'\n"); 6898: fprintf(ficgp,"set datafile missing 'NaNq'\n"); 6899: } 6900: /* fclose(ficgp);*/ 6901: 6902: 6903: /* Initialisation of --------- index.htm --------*/ 6904: 6905: strcpy(optionfilehtm,optionfilefiname); /* Main html file */ 6906: if(mle==-3) 6907: strcat(optionfilehtm,"-mort"); 6908: strcat(optionfilehtm,".htm"); 6909: if((fichtm=fopen(optionfilehtm,"w"))==NULL) { 6910: printf("Problem with %s \n",optionfilehtm); 6911: exit(0); 6912: } 6913: 6914: strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */ 6915: strcat(optionfilehtmcov,"-cov.htm"); 6916: if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL) { 6917: printf("Problem with %s \n",optionfilehtmcov), exit(0); 6918: } 6919: else{ 6920: fprintf(fichtmcov,"<html><head>\n<title>IMaCh Cov %s</title></head>\n <body>%s %s \ 6921: <hr size=\"2\" color=\"#EC5E5E\"> \n\ 6922: Title=%s Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s \n",\ 6923: optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model); 6924: } 6925: 6926: fprintf(fichtm,"<html><head>\n<title>IMaCh %s</title></head>\n <body>%s %s \ 6927: <hr size=\"2\" color=\"#EC5E5E\"> \n\ 6928: Title=%s Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s \n\ 6929: \n\ 6930: <hr size=\"2\" color=\"#EC5E5E\">\ 6931: <ul><li><h4>Parameter files</h4>\n\ 6932: - Parameter file: <a href=\"%s.%s\">%s.%s</a> \n\ 6933: - Copy of the parameter file: <a href=\"o%s\">o%s</a> \n\ 6934: - Log file of the run: <a href=\"%s\">%s</a> \n\ 6935: - Gnuplot file name: <a href=\"%s\">%s</a> \n\ 6936: - Date and time at start: %s</ul>\n",\ 6937: optionfilehtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\ 6938: optionfilefiname,optionfilext,optionfilefiname,optionfilext,\ 6939: fileres,fileres,\ 6940: filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart); 6941: fflush(fichtm); 6942: 6943: strcpy(pathr,path); 6944: strcat(pathr,optionfilefiname); 6945: #ifdef WIN32 6946: _chdir(optionfilefiname); /* Move to directory named optionfile */ 6947: #else 6948: chdir(optionfilefiname); /* Move to directory named optionfile */ 6949: #endif 6950: 6951: 6952: /* Calculates basic frequencies. Computes observed prevalence at single age 6953: and prints on file fileres'p'. */ 6954: freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart); 6955: 6956: fprintf(fichtm,"\n"); 6957: fprintf(fichtm," Total number of observations=%d \n\ 6958: Youngest age at first (selected) pass %.2f, oldest age %.2f \n\ 6959: Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf \n",\ 6960: imx,agemin,agemax,jmin,jmax,jmean); 6961: pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */ 6962: oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */ 6963: newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */ 6964: savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */ 6965: oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */ 6966: 6967: 6968: /* For Powell, parameters are in a vector p[] starting at p[1] 6969: so we point p on param[1][1] so that p[1] maps on param[1][1][1] */ 6970: p=param[1][1]; /* *(*(*(param +1)+1)+0) */ 6971: 6972: globpr=0; /* To get the number ipmx of contributions and the sum of weights*/ 6973: /* For mortality only */ 6974: if (mle==-3){ 6975: ximort=matrix(1,NDIM,1,NDIM); 6976: /* ximort=gsl_matrix_alloc(1,NDIM,1,NDIM); */ 6977: cens=ivector(1,n); 6978: ageexmed=vector(1,n); 6979: agecens=vector(1,n); 6980: dcwave=ivector(1,n); 6981: 6982: for (i=1; i<=imx; i++){ 6983: dcwave[i]=-1; 6984: for (m=firstpass; m<=lastpass; m++) 6985: if (s[m][i]>nlstate) { 6986: dcwave[i]=m; 6987: /* printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/ 6988: break; 6989: } 6990: } 6991: 6992: for (i=1; i<=imx; i++) { 6993: if (wav[i]>0){ 6994: ageexmed[i]=agev[mw[1][i]][i]; 6995: j=wav[i]; 6996: agecens[i]=1.; 6997: 6998: if (ageexmed[i]> 1 && wav[i] > 0){ 6999: agecens[i]=agev[mw[j][i]][i]; 7000: cens[i]= 1; 7001: }else if (ageexmed[i]< 1) 7002: cens[i]= -1; 7003: if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass) 7004: cens[i]=0 ; 7005: } 7006: else cens[i]=-1; 7007: } 7008: 7009: for (i=1;i<=NDIM;i++) { 7010: for (j=1;j<=NDIM;j++) 7011: ximort[i][j]=(i == j ? 1.0 : 0.0); 7012: } 7013: 7014: /*p[1]=0.0268; p[NDIM]=0.083;*/ 7015: /*printf("%lf %lf", p[1], p[2]);*/ 7016: 7017: 7018: #ifdef GSL 7019: printf("GSL optimization\n"); fprintf(ficlog,"Powell\n"); 7020: #else 7021: printf("Powell\n"); fprintf(ficlog,"Powell\n"); 7022: #endif 7023: strcpy(filerespow,"pow-mort"); 7024: strcat(filerespow,fileres); 7025: if((ficrespow=fopen(filerespow,"w"))==NULL) { 7026: printf("Problem with resultfile: %s\n", filerespow); 7027: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow); 7028: } 7029: #ifdef GSL 7030: fprintf(ficrespow,"# GSL optimization\n# iter -2*LL"); 7031: #else 7032: fprintf(ficrespow,"# Powell\n# iter -2*LL"); 7033: #endif 7034: /* for (i=1;i<=nlstate;i++) 7035: for(j=1;j<=nlstate+ndeath;j++) 7036: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j); 7037: */ 7038: fprintf(ficrespow,"\n"); 7039: #ifdef GSL 7040: /* gsl starts here */ 7041: T = gsl_multimin_fminimizer_nmsimplex; 7042: gsl_multimin_fminimizer *sfm = NULL; 7043: gsl_vector *ss, *x; 7044: gsl_multimin_function minex_func; 7045: 7046: /* Initial vertex size vector */ 7047: ss = gsl_vector_alloc (NDIM); 7048: 7049: if (ss == NULL){ 7050: GSL_ERROR_VAL ("failed to allocate space for ss", GSL_ENOMEM, 0); 7051: } 7052: /* Set all step sizes to 1 */ 7053: gsl_vector_set_all (ss, 0.001); 7054: 7055: /* Starting point */ 7056: 7057: x = gsl_vector_alloc (NDIM); 7058: 7059: if (x == NULL){ 7060: gsl_vector_free(ss); 7061: GSL_ERROR_VAL ("failed to allocate space for x", GSL_ENOMEM, 0); 7062: } 7063: 7064: /* Initialize method and iterate */ 7065: /* p[1]=0.0268; p[NDIM]=0.083; */ 7066: /* gsl_vector_set(x, 0, 0.0268); */ 7067: /* gsl_vector_set(x, 1, 0.083); */ 7068: gsl_vector_set(x, 0, p[1]); 7069: gsl_vector_set(x, 1, p[2]); 7070: 7071: minex_func.f = &gompertz_f; 7072: minex_func.n = NDIM; 7073: minex_func.params = (void *)&p; /* ??? */ 7074: 7075: sfm = gsl_multimin_fminimizer_alloc (T, NDIM); 7076: gsl_multimin_fminimizer_set (sfm, &minex_func, x, ss); 7077: 7078: printf("Iterations beginning .....\n\n"); 7079: printf("Iter. # Intercept Slope -Log Likelihood Simplex size\n"); 7080: 7081: iteri=0; 7082: while (rval == GSL_CONTINUE){ 7083: iteri++; 7084: status = gsl_multimin_fminimizer_iterate(sfm); 7085: 7086: if (status) printf("error: %s\n", gsl_strerror (status)); 7087: fflush(0); 7088: 7089: if (status) 7090: break; 7091: 7092: rval = gsl_multimin_test_size (gsl_multimin_fminimizer_size (sfm), 1e-6); 7093: ssval = gsl_multimin_fminimizer_size (sfm); 7094: 7095: if (rval == GSL_SUCCESS) 7096: printf ("converged to a local maximum at\n"); 7097: 7098: printf("%5d ", iteri); 7099: for (it = 0; it < NDIM; it++){ 7100: printf ("%10.5f ", gsl_vector_get (sfm->x, it)); 7101: } 7102: printf("f() = %-10.5f ssize = %.7f\n", sfm->fval, ssval); 7103: } 7104: 7105: printf("\n\n Please note: Program should be run many times with varying starting points to detemine global maximum\n\n"); 7106: 7107: gsl_vector_free(x); /* initial values */ 7108: gsl_vector_free(ss); /* inital step size */ 7109: for (it=0; it<NDIM; it++){ 7110: p[it+1]=gsl_vector_get(sfm->x,it); 7111: fprintf(ficrespow," %.12lf", p[it]); 7112: } 7113: gsl_multimin_fminimizer_free (sfm); /* p *(sfm.x.data) et p *(sfm.x.data+1) */ 7114: #endif 7115: #ifdef POWELL 7116: powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz); 7117: #endif 7118: fclose(ficrespow); 7119: 7120: hesscov(matcov, p, NDIM, delti, 1e-4, gompertz); 7121: 7122: for(i=1; i <=NDIM; i++) 7123: for(j=i+1;j<=NDIM;j++) 7124: matcov[i][j]=matcov[j][i]; 7125: 7126: printf("\nCovariance matrix\n "); 7127: for(i=1; i <=NDIM; i++) { 7128: for(j=1;j<=NDIM;j++){ 7129: printf("%f ",matcov[i][j]); 7130: } 7131: printf("\n "); 7132: } 7133: 7134: printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp); 7135: for (i=1;i<=NDIM;i++) { 7136: printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i])); 7137: fprintf(ficlog,"%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i])); 7138: } 7139: lsurv=vector(1,AGESUP); 7140: lpop=vector(1,AGESUP); 7141: tpop=vector(1,AGESUP); 7142: lsurv[agegomp]=100000; 7143: 7144: for (k=agegomp;k<=AGESUP;k++) { 7145: agemortsup=k; 7146: if (p[1]*exp(p[2]*(k-agegomp))>1) break; 7147: } 7148: 7149: for (k=agegomp;k<agemortsup;k++) 7150: lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp))); 7151: 7152: for (k=agegomp;k<agemortsup;k++){ 7153: lpop[k]=(lsurv[k]+lsurv[k+1])/2.; 7154: sumlpop=sumlpop+lpop[k]; 7155: } 7156: 7157: tpop[agegomp]=sumlpop; 7158: for (k=agegomp;k<(agemortsup-3);k++){ 7159: /* tpop[k+1]=2;*/ 7160: tpop[k+1]=tpop[k]-lpop[k]; 7161: } 7162: 7163: 7164: printf("\nAge lx qx dx Lx Tx e(x)\n"); 7165: for (k=agegomp;k<(agemortsup-2);k++) 7166: 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]); 7167: 7168: 7169: replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */ 7170: if(ageminpar == AGEOVERFLOW ||agemaxpar == AGEOVERFLOW){ 7171: printf("Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\ 7172: This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\ 7173: Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar); 7174: fprintf(ficlog,"Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\ 7175: This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\ 7176: Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar); 7177: }else 7178: printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p); 7179: printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \ 7180: stepm, weightopt,\ 7181: model,imx,p,matcov,agemortsup); 7182: 7183: free_vector(lsurv,1,AGESUP); 7184: free_vector(lpop,1,AGESUP); 7185: free_vector(tpop,1,AGESUP); 7186: #ifdef GSL 7187: free_ivector(cens,1,n); 7188: free_vector(agecens,1,n); 7189: free_ivector(dcwave,1,n); 7190: free_matrix(ximort,1,NDIM,1,NDIM); 7191: #endif 7192: } /* Endof if mle==-3 mortality only */ 7193: /* Standard maximisation */ 7194: else{ /* For mle >=1 */ 7195: globpr=0;/* debug */ 7196: /* Computes likelihood for initial parameters */ 7197: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */ 7198: printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw); 7199: for (k=1; k<=npar;k++) 7200: printf(" %d %8.5f",k,p[k]); 7201: printf("\n"); 7202: globpr=1; /* again, to print the contributions */ 7203: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */ 7204: printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw); 7205: for (k=1; k<=npar;k++) 7206: printf(" %d %8.5f",k,p[k]); 7207: printf("\n"); 7208: if(mle>=1){ /* Could be 1 or 2, Real Maximisation */ 7209: mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func); 7210: } 7211: 7212: /*--------- results files --------------*/ 7213: 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=1+age+%s.\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate, ndeath, maxwav, weightopt,model); 7214: 7215: 7216: fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n"); 7217: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n"); 7218: fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n"); 7219: for(i=1,jk=1; i <=nlstate; i++){ 7220: for(k=1; k <=(nlstate+ndeath); k++){ 7221: if (k != i) { 7222: printf("%d%d ",i,k); 7223: fprintf(ficlog,"%d%d ",i,k); 7224: fprintf(ficres,"%1d%1d ",i,k); 7225: for(j=1; j <=ncovmodel; j++){ 7226: printf("%12.7f ",p[jk]); 7227: fprintf(ficlog,"%12.7f ",p[jk]); 7228: fprintf(ficres,"%12.7f ",p[jk]); 7229: jk++; 7230: } 7231: printf("\n"); 7232: fprintf(ficlog,"\n"); 7233: fprintf(ficres,"\n"); 7234: } 7235: } 7236: } 7237: if(mle!=0){ 7238: /* Computing hessian and covariance matrix */ 7239: ftolhess=ftol; /* Usually correct */ 7240: hesscov(matcov, p, npar, delti, ftolhess, func); 7241: } 7242: printf("Parameters and 95%% confidence intervals\n"); 7243: fprintf(ficlog, "Parameters, T and confidence intervals\n"); 7244: for(i=1,jk=1; i <=nlstate; i++){ 7245: for(k=1; k <=(nlstate+ndeath); k++){ 7246: if (k != i) { 7247: printf("%d%d ",i,k); 7248: fprintf(ficlog,"%d%d ",i,k); 7249: for(j=1; j <=ncovmodel; j++){ 7250: printf("%12.7f T=%8.3f CI=[%12.7f ; %12.7f] ",p[jk], p[jk]/sqrt(matcov[jk][jk]), p[jk]-2*sqrt(matcov[jk][jk]),p[jk]+2*sqrt(matcov[jk][jk])); 7251: fprintf(ficlog,"%12.7f T=%8.3f CI=[%12.7f ; %12.7f] ",p[jk], p[jk]/sqrt(matcov[jk][jk]), p[jk]-2*sqrt(matcov[jk][jk]),p[jk]+2*sqrt(matcov[jk][jk])); 7252: jk++; 7253: } 7254: printf("\n"); 7255: fprintf(ficlog,"\n"); 7256: } 7257: } 7258: } 7259: 7260: fprintf(ficres,"# Scales (for hessian or gradient estimation)\n"); 7261: printf("# Scales (for hessian or gradient estimation)\n"); 7262: fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n"); 7263: for(i=1,jk=1; i <=nlstate; i++){ 7264: for(j=1; j <=nlstate+ndeath; j++){ 7265: if (j!=i) { 7266: fprintf(ficres,"%1d%1d",i,j); 7267: printf("%1d%1d",i,j); 7268: fprintf(ficlog,"%1d%1d",i,j); 7269: for(k=1; k<=ncovmodel;k++){ 7270: printf(" %.5e",delti[jk]); 7271: fprintf(ficlog," %.5e",delti[jk]); 7272: fprintf(ficres," %.5e",delti[jk]); 7273: jk++; 7274: } 7275: printf("\n"); 7276: fprintf(ficlog,"\n"); 7277: fprintf(ficres,"\n"); 7278: } 7279: } 7280: } 7281: 7282: 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"); 7283: if(mle>=1) 7284: 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"); 7285: 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"); 7286: /* # 121 Var(a12)\n\ */ 7287: /* # 122 Cov(b12,a12) Var(b12)\n\ */ 7288: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */ 7289: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */ 7290: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */ 7291: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */ 7292: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */ 7293: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */ 7294: 7295: 7296: /* Just to have a covariance matrix which will be more understandable 7297: even is we still don't want to manage dictionary of variables 7298: */ 7299: for(itimes=1;itimes<=2;itimes++){ 7300: jj=0; 7301: for(i=1; i <=nlstate; i++){ 7302: for(j=1; j <=nlstate+ndeath; j++){ 7303: if(j==i) continue; 7304: for(k=1; k<=ncovmodel;k++){ 7305: jj++; 7306: ca[0]= k+'a'-1;ca[1]='\0'; 7307: if(itimes==1){ 7308: if(mle>=1) 7309: printf("#%1d%1d%d",i,j,k); 7310: fprintf(ficlog,"#%1d%1d%d",i,j,k); 7311: fprintf(ficres,"#%1d%1d%d",i,j,k); 7312: }else{ 7313: if(mle>=1) 7314: printf("%1d%1d%d",i,j,k); 7315: fprintf(ficlog,"%1d%1d%d",i,j,k); 7316: fprintf(ficres,"%1d%1d%d",i,j,k); 7317: } 7318: ll=0; 7319: for(li=1;li <=nlstate; li++){ 7320: for(lj=1;lj <=nlstate+ndeath; lj++){ 7321: if(lj==li) continue; 7322: for(lk=1;lk<=ncovmodel;lk++){ 7323: ll++; 7324: if(ll<=jj){ 7325: cb[0]= lk +'a'-1;cb[1]='\0'; 7326: if(ll<jj){ 7327: if(itimes==1){ 7328: if(mle>=1) 7329: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj); 7330: fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj); 7331: fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj); 7332: }else{ 7333: if(mle>=1) 7334: printf(" %.5e",matcov[jj][ll]); 7335: fprintf(ficlog," %.5e",matcov[jj][ll]); 7336: fprintf(ficres," %.5e",matcov[jj][ll]); 7337: } 7338: }else{ 7339: if(itimes==1){ 7340: if(mle>=1) 7341: printf(" Var(%s%1d%1d)",ca,i,j); 7342: fprintf(ficlog," Var(%s%1d%1d)",ca,i,j); 7343: fprintf(ficres," Var(%s%1d%1d)",ca,i,j); 7344: }else{ 7345: if(mle>=1) 7346: printf(" %.5e",matcov[jj][ll]); 7347: fprintf(ficlog," %.5e",matcov[jj][ll]); 7348: fprintf(ficres," %.5e",matcov[jj][ll]); 7349: } 7350: } 7351: } 7352: } /* end lk */ 7353: } /* end lj */ 7354: } /* end li */ 7355: if(mle>=1) 7356: printf("\n"); 7357: fprintf(ficlog,"\n"); 7358: fprintf(ficres,"\n"); 7359: numlinepar++; 7360: } /* end k*/ 7361: } /*end j */ 7362: } /* end i */ 7363: } /* end itimes */ 7364: 7365: fflush(ficlog); 7366: fflush(ficres); 7367: 7368: while((c=getc(ficpar))=='#' && c!= EOF){ 7369: ungetc(c,ficpar); 7370: fgets(line, MAXLINE, ficpar); 7371: fputs(line,stdout); 7372: fputs(line,ficparo); 7373: } 7374: ungetc(c,ficpar); 7375: 7376: estepm=0; 7377: fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm); 7378: if (estepm==0 || estepm < stepm) estepm=stepm; 7379: if (fage <= 2) { 7380: bage = ageminpar; 7381: fage = agemaxpar; 7382: } 7383: 7384: fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n"); 7385: fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm); 7386: fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm); 7387: 7388: /* Other stuffs, more or less useful */ 7389: while((c=getc(ficpar))=='#' && c!= EOF){ 7390: ungetc(c,ficpar); 7391: fgets(line, MAXLINE, ficpar); 7392: fputs(line,stdout); 7393: fputs(line,ficparo); 7394: } 7395: ungetc(c,ficpar); 7396: 7397: 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); 7398: 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); 7399: 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); 7400: printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav); 7401: 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); 7402: 7403: while((c=getc(ficpar))=='#' && c!= EOF){ 7404: ungetc(c,ficpar); 7405: fgets(line, MAXLINE, ficpar); 7406: fputs(line,stdout); 7407: fputs(line,ficparo); 7408: } 7409: ungetc(c,ficpar); 7410: 7411: 7412: dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.; 7413: dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.; 7414: 7415: fscanf(ficpar,"pop_based=%d\n",&popbased); 7416: fprintf(ficlog,"pop_based=%d\n",popbased); 7417: fprintf(ficparo,"pop_based=%d\n",popbased); 7418: fprintf(ficres,"pop_based=%d\n",popbased); 7419: 7420: while((c=getc(ficpar))=='#' && c!= EOF){ 7421: ungetc(c,ficpar); 7422: fgets(line, MAXLINE, ficpar); 7423: fputs(line,stdout); 7424: fputs(line,ficparo); 7425: } 7426: ungetc(c,ficpar); 7427: 7428: 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); 7429: 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); 7430: 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); 7431: 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); 7432: 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); 7433: /* day and month of proj2 are not used but only year anproj2.*/ 7434: 7435: 7436: 7437: /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint); */ 7438: /* ,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2); */ 7439: 7440: replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */ 7441: if(ageminpar == AGEOVERFLOW ||agemaxpar == -AGEOVERFLOW){ 7442: printf("Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\ 7443: This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\ 7444: Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar); 7445: fprintf(ficlog,"Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\ 7446: This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\ 7447: Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar); 7448: }else 7449: printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p); 7450: 7451: printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\ 7452: model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\ 7453: jprev1,mprev1,anprev1,jprev2,mprev2,anprev2); 7454: 7455: /*------------ free_vector -------------*/ 7456: /* chdir(path); */ 7457: 7458: free_ivector(wav,1,imx); 7459: free_imatrix(dh,1,lastpass-firstpass+1,1,imx); 7460: free_imatrix(bh,1,lastpass-firstpass+1,1,imx); 7461: free_imatrix(mw,1,lastpass-firstpass+1,1,imx); 7462: free_lvector(num,1,n); 7463: free_vector(agedc,1,n); 7464: /*free_matrix(covar,0,NCOVMAX,1,n);*/ 7465: /*free_matrix(covar,1,NCOVMAX,1,n);*/ 7466: fclose(ficparo); 7467: fclose(ficres); 7468: 7469: 7470: /* Other results (useful)*/ 7471: 7472: 7473: /*--------------- Prevalence limit (period or stable prevalence) --------------*/ 7474: /*#include "prevlim.h"*/ /* Use ficrespl, ficlog */ 7475: prlim=matrix(1,nlstate,1,nlstate); 7476: prevalence_limit(p, prlim, ageminpar, agemaxpar); 7477: fclose(ficrespl); 7478: 7479: #ifdef FREEEXIT2 7480: #include "freeexit2.h" 7481: #endif 7482: 7483: /*------------- h Pij x at various ages ------------*/ 7484: /*#include "hpijx.h"*/ 7485: hPijx(p, bage, fage); 7486: fclose(ficrespij); 7487: 7488: /*-------------- Variance of one-step probabilities---*/ 7489: k=1; 7490: varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart); 7491: 7492: 7493: probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX); 7494: for(i=1;i<=AGESUP;i++) 7495: for(j=1;j<=NCOVMAX;j++) 7496: for(k=1;k<=NCOVMAX;k++) 7497: probs[i][j][k]=0.; 7498: 7499: /*---------- Forecasting ------------------*/ 7500: /*if((stepm == 1) && (strcmp(model,".")==0)){*/ 7501: if(prevfcast==1){ 7502: /* if(stepm ==1){*/ 7503: prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff); 7504: /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/ 7505: /* } */ 7506: /* else{ */ 7507: /* erreur=108; */ 7508: /* 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); */ 7509: /* 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); */ 7510: /* } */ 7511: } 7512: 7513: /* ------ Other prevalence ratios------------ */ 7514: 7515: /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */ 7516: 7517: prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass); 7518: /* 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",\ 7519: ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass); 7520: */ 7521: 7522: if (mobilav!=0) { 7523: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); 7524: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){ 7525: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav); 7526: printf(" Error in movingaverage mobilav=%d\n",mobilav); 7527: } 7528: } 7529: 7530: 7531: /*---------- Health expectancies, no variances ------------*/ 7532: 7533: strcpy(filerese,"e"); 7534: strcat(filerese,fileres); 7535: if((ficreseij=fopen(filerese,"w"))==NULL) { 7536: printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0); 7537: fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0); 7538: } 7539: printf("Computing Health Expectancies: result on file '%s' \n", filerese); 7540: fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese); 7541: /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){ 7542: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/ 7543: 7544: for (k=1; k <= (int) pow(2,cptcoveff); k++){ 7545: fprintf(ficreseij,"\n#****** "); 7546: for(j=1;j<=cptcoveff;j++) { 7547: fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]); 7548: } 7549: fprintf(ficreseij,"******\n"); 7550: 7551: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage); 7552: oldm=oldms;savm=savms; 7553: evsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart); 7554: 7555: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage); 7556: /*}*/ 7557: } 7558: fclose(ficreseij); 7559: 7560: 7561: /*---------- Health expectancies and variances ------------*/ 7562: 7563: 7564: strcpy(filerest,"t"); 7565: strcat(filerest,fileres); 7566: if((ficrest=fopen(filerest,"w"))==NULL) { 7567: printf("Problem with total LE resultfile: %s\n", filerest);goto end; 7568: fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end; 7569: } 7570: printf("Computing Total Life expectancies with their standard errors: file '%s' \n", filerest); 7571: fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' \n", filerest); 7572: 7573: 7574: strcpy(fileresstde,"stde"); 7575: strcat(fileresstde,fileres); 7576: if((ficresstdeij=fopen(fileresstde,"w"))==NULL) { 7577: printf("Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0); 7578: fprintf(ficlog,"Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0); 7579: } 7580: printf("Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde); 7581: fprintf(ficlog,"Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde); 7582: 7583: strcpy(filerescve,"cve"); 7584: strcat(filerescve,fileres); 7585: if((ficrescveij=fopen(filerescve,"w"))==NULL) { 7586: printf("Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0); 7587: fprintf(ficlog,"Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0); 7588: } 7589: printf("Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve); 7590: fprintf(ficlog,"Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve); 7591: 7592: strcpy(fileresv,"v"); 7593: strcat(fileresv,fileres); 7594: if((ficresvij=fopen(fileresv,"w"))==NULL) { 7595: printf("Problem with variance resultfile: %s\n", fileresv);exit(0); 7596: fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0); 7597: } 7598: printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv); 7599: fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv); 7600: 7601: /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){ 7602: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/ 7603: 7604: for (k=1; k <= (int) pow(2,cptcoveff); k++){ 7605: fprintf(ficrest,"\n#****** "); 7606: for(j=1;j<=cptcoveff;j++) 7607: fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]); 7608: fprintf(ficrest,"******\n"); 7609: 7610: fprintf(ficresstdeij,"\n#****** "); 7611: fprintf(ficrescveij,"\n#****** "); 7612: for(j=1;j<=cptcoveff;j++) { 7613: fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]); 7614: fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]); 7615: } 7616: fprintf(ficresstdeij,"******\n"); 7617: fprintf(ficrescveij,"******\n"); 7618: 7619: fprintf(ficresvij,"\n#****** "); 7620: for(j=1;j<=cptcoveff;j++) 7621: fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]); 7622: fprintf(ficresvij,"******\n"); 7623: 7624: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage); 7625: oldm=oldms;savm=savms; 7626: cvevsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart); 7627: /* 7628: */ 7629: /* goto endfree; */ 7630: 7631: vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage); 7632: pstamp(ficrest); 7633: 7634: 7635: for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/ 7636: oldm=oldms;savm=savms; /* Segmentation fault */ 7637: cptcod= 0; /* To be deleted */ 7638: 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 */ 7639: 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 "); 7640: if(vpopbased==1) 7641: 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); 7642: else 7643: fprintf(ficrest,"the age specific period (stable) prevalences in each health state \n"); 7644: fprintf(ficrest,"# Age e.. (std) "); 7645: for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i); 7646: fprintf(ficrest,"\n"); 7647: 7648: epj=vector(1,nlstate+1); 7649: for(age=bage; age <=fage ;age++){ 7650: prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k); 7651: if (vpopbased==1) { 7652: if(mobilav ==0){ 7653: for(i=1; i<=nlstate;i++) 7654: prlim[i][i]=probs[(int)age][i][k]; 7655: }else{ /* mobilav */ 7656: for(i=1; i<=nlstate;i++) 7657: prlim[i][i]=mobaverage[(int)age][i][k]; 7658: } 7659: } 7660: 7661: fprintf(ficrest," %4.0f",age); 7662: for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){ 7663: for(i=1, epj[j]=0.;i <=nlstate;i++) { 7664: epj[j] += prlim[i][i]*eij[i][j][(int)age]; 7665: /* printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/ 7666: } 7667: epj[nlstate+1] +=epj[j]; 7668: } 7669: 7670: for(i=1, vepp=0.;i <=nlstate;i++) 7671: for(j=1;j <=nlstate;j++) 7672: vepp += vareij[i][j][(int)age]; 7673: fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp)); 7674: for(j=1;j <=nlstate;j++){ 7675: fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age])); 7676: } 7677: fprintf(ficrest,"\n"); 7678: } 7679: } 7680: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage); 7681: free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage); 7682: free_vector(epj,1,nlstate+1); 7683: /*}*/ 7684: } 7685: free_vector(weight,1,n); 7686: free_imatrix(Tvard,1,NCOVMAX,1,2); 7687: free_imatrix(s,1,maxwav+1,1,n); 7688: free_matrix(anint,1,maxwav,1,n); 7689: free_matrix(mint,1,maxwav,1,n); 7690: free_ivector(cod,1,n); 7691: free_ivector(tab,1,NCOVMAX); 7692: fclose(ficresstdeij); 7693: fclose(ficrescveij); 7694: fclose(ficresvij); 7695: fclose(ficrest); 7696: fclose(ficpar); 7697: 7698: /*------- Variance of period (stable) prevalence------*/ 7699: 7700: strcpy(fileresvpl,"vpl"); 7701: strcat(fileresvpl,fileres); 7702: if((ficresvpl=fopen(fileresvpl,"w"))==NULL) { 7703: printf("Problem with variance of period (stable) prevalence resultfile: %s\n", fileresvpl); 7704: exit(0); 7705: } 7706: printf("Computing Variance-covariance of period (stable) prevalence: file '%s' \n", fileresvpl); 7707: 7708: /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){ 7709: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/ 7710: 7711: for (k=1; k <= (int) pow(2,cptcoveff); k++){ 7712: fprintf(ficresvpl,"\n#****** "); 7713: for(j=1;j<=cptcoveff;j++) 7714: fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]); 7715: fprintf(ficresvpl,"******\n"); 7716: 7717: varpl=matrix(1,nlstate,(int) bage, (int) fage); 7718: oldm=oldms;savm=savms; 7719: varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k,strstart); 7720: free_matrix(varpl,1,nlstate,(int) bage, (int)fage); 7721: /*}*/ 7722: } 7723: 7724: fclose(ficresvpl); 7725: 7726: /*---------- End : free ----------------*/ 7727: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); 7728: free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX); 7729: } /* mle==-3 arrives here for freeing */ 7730: /* endfree:*/ 7731: free_matrix(prlim,1,nlstate,1,nlstate); /*here or after loop ? */ 7732: free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath); 7733: free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath); 7734: free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath); 7735: free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath); 7736: free_matrix(covar,0,NCOVMAX,1,n); 7737: free_matrix(matcov,1,npar,1,npar); 7738: /*free_vector(delti,1,npar);*/ 7739: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 7740: free_matrix(agev,1,maxwav,1,imx); 7741: free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 7742: 7743: free_ivector(ncodemax,1,NCOVMAX); 7744: free_ivector(ncodemaxwundef,1,NCOVMAX); 7745: free_ivector(Tvar,1,NCOVMAX); 7746: free_ivector(Tprod,1,NCOVMAX); 7747: free_ivector(Tvaraff,1,NCOVMAX); 7748: free_ivector(Tage,1,NCOVMAX); 7749: 7750: free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX); 7751: free_imatrix(codtab,1,100,1,10); 7752: fflush(fichtm); 7753: fflush(ficgp); 7754: 7755: 7756: if((nberr >0) || (nbwarn>0)){ 7757: printf("End of Imach with %d errors and/or %d warnings\n",nberr,nbwarn); 7758: fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn); 7759: }else{ 7760: printf("End of Imach\n"); 7761: fprintf(ficlog,"End of Imach\n"); 7762: } 7763: printf("See log file on %s\n",filelog); 7764: /* gettimeofday(&end_time, (struct timezone*)0);*/ /* after time */ 7765: /*(void) gettimeofday(&end_time,&tzp);*/ 7766: rend_time = time(NULL); 7767: end_time = *localtime(&rend_time); 7768: /* tml = *localtime(&end_time.tm_sec); */ 7769: strcpy(strtend,asctime(&end_time)); 7770: printf("Local time at start %s\nLocal time at end %s",strstart, strtend); 7771: fprintf(ficlog,"Local time at start %s\nLocal time at end %s\n",strstart, strtend); 7772: printf("Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout)); 7773: 7774: printf("Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time)); 7775: fprintf(ficlog,"Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout)); 7776: fprintf(ficlog,"Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time)); 7777: /* printf("Total time was %d uSec.\n", total_usecs);*/ 7778: /* if(fileappend(fichtm,optionfilehtm)){ */ 7779: fprintf(fichtm," Local time at start %s Local time at end %s \n</body></html>",strstart, strtend); 7780: fclose(fichtm); 7781: fprintf(fichtmcov," Local time at start %s Local time at end %s \n</body></html>",strstart, strtend); 7782: fclose(fichtmcov); 7783: fclose(ficgp); 7784: fclose(ficlog); 7785: /*------ End -----------*/ 7786: 7787: 7788: printf("Before Current directory %s!\n",pathcd); 7789: #ifdef WIN32 7790: if (_chdir(pathcd) != 0) 7791: printf("Can't move to directory %s!\n",path); 7792: if(_getcwd(pathcd,MAXLINE) > 0) 7793: #else 7794: if(chdir(pathcd) != 0) 7795: printf("Can't move to directory %s!\n", path); 7796: if (getcwd(pathcd, MAXLINE) > 0) 7797: #endif 7798: printf("Current directory %s!\n",pathcd); 7799: /*strcat(plotcmd,CHARSEPARATOR);*/ 7800: sprintf(plotcmd,"gnuplot"); 7801: #ifdef _WIN32 7802: sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach); 7803: #endif 7804: if(!stat(plotcmd,&info)){ 7805: printf("Error or gnuplot program not found: '%s'\n",plotcmd);fflush(stdout); 7806: if(!stat(getenv("GNUPLOTBIN"),&info)){ 7807: printf("Error or gnuplot program not found: '%s' Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout); 7808: }else 7809: strcpy(pplotcmd,plotcmd); 7810: #ifdef __unix 7811: strcpy(plotcmd,GNUPLOTPROGRAM); 7812: if(!stat(plotcmd,&info)){ 7813: printf("Error gnuplot program not found: '%s'\n",plotcmd);fflush(stdout); 7814: }else 7815: strcpy(pplotcmd,plotcmd); 7816: #endif 7817: }else 7818: strcpy(pplotcmd,plotcmd); 7819: 7820: sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot); 7821: printf("Starting graphs with: '%s'\n",plotcmd);fflush(stdout); 7822: 7823: if((outcmd=system(plotcmd)) != 0){ 7824: printf("gnuplot command might not be in your path: '%s', err=%d\n", plotcmd, outcmd); 7825: printf("\n Trying if gnuplot resides on the same directory that IMaCh\n"); 7826: sprintf(plotcmd,"%sgnuplot %s", pathimach, optionfilegnuplot); 7827: if((outcmd=system(plotcmd)) != 0) 7828: printf("\n Still a problem with gnuplot command %s, err=%d\n", plotcmd, outcmd); 7829: } 7830: printf(" Successful, please wait..."); 7831: while (z[0] != 'q') { 7832: /* chdir(path); */ 7833: printf("\nType e to edit results with your browser, g to graph again and q for exit: "); 7834: scanf("%s",z); 7835: /* if (z[0] == 'c') system("./imach"); */ 7836: if (z[0] == 'e') { 7837: #ifdef __APPLE__ 7838: sprintf(pplotcmd, "open %s", optionfilehtm); 7839: #elif __linux 7840: sprintf(pplotcmd, "xdg-open %s", optionfilehtm); 7841: #else 7842: sprintf(pplotcmd, "%s", optionfilehtm); 7843: #endif 7844: printf("Starting browser with: %s",pplotcmd);fflush(stdout); 7845: system(pplotcmd); 7846: } 7847: else if (z[0] == 'g') system(plotcmd); 7848: else if (z[0] == 'q') exit(0); 7849: } 7850: end: 7851: while (z[0] != 'q') { 7852: printf("\nType q for exiting: "); 7853: scanf("%s",z); 7854: } 7855: }