imach/src/imach.c - view

File: [Local Repository] / imach / src / imach.c
Revision 1.192: download - view: text, annotated - select for diffs
Thu Jul 16 16:49:02 2015 UTC (8 years, 11 months ago) by brouard
Branches: MAIN
CVS tags: HEAD

Summary: Fixing some outputs

1: /* $Id: imach.c,v 1.192 2015/07/16 16:49:02 brouard Exp $ 2: $State: Exp $ 3: $Log: imach.c,v $ 4: Revision 1.192 2015/07/16 16:49:02 brouard 5: Summary: Fixing some outputs 6: 7: Revision 1.191 2015/07/14 10:00:33 brouard 8: Summary: Some fixes 9: 10: Revision 1.190 2015/05/05 08:51:13 brouard 11: Summary: Adding digits in output parameters (7 digits instead of 6) 12: 13: Fix 1+age+. 14: 15: Revision 1.189 2015/04/30 14:45:16 brouard 16: Summary: 0.98q2 17: 18: Revision 1.188 2015/04/30 08:27:53 brouard 19: *** empty log message *** 20: 21: Revision 1.187 2015/04/29 09:11:15 brouard 22: *** empty log message *** 23: 24: Revision 1.186 2015/04/23 12:01:52 brouard 25: Summary: V1*age is working now, version 0.98q1 26: 27: Some codes had been disabled in order to simplify and Vn*age was 28: working in the optimization phase, ie, giving correct MLE parameters, 29: but, as usual, outputs were not correct and program core dumped. 30: 31: Revision 1.185 2015/03/11 13:26:42 brouard 32: Summary: Inclusion of compile and links command line for Intel Compiler 33: 34: Revision 1.184 2015/03/11 11:52:39 brouard 35: Summary: Back from Windows 8. Intel Compiler 36: 37: Revision 1.183 2015/03/10 20:34:32 brouard 38: Summary: 0.98q0, trying with directest, mnbrak fixed 39: 40: We use directest instead of original Powell test; probably no 41: incidence on the results, but better justifications; 42: We fixed Numerical Recipes mnbrak routine which was wrong and gave 43: wrong results. 44: 45: Revision 1.182 2015/02/12 08:19:57 brouard 46: Summary: Trying to keep directest which seems simpler and more general 47: Author: Nicolas Brouard 48: 49: Revision 1.181 2015/02/11 23:22:24 brouard 50: Summary: Comments on Powell added 51: 52: Author: 53: 54: Revision 1.180 2015/02/11 17:33:45 brouard 55: Summary: Finishing move from main to function (hpijx and prevalence_limit) 56: 57: Revision 1.179 2015/01/04 09:57:06 brouard 58: Summary: back to OS/X 59: 60: Revision 1.178 2015/01/04 09:35:48 brouard 61: *** empty log message *** 62: 63: Revision 1.177 2015/01/03 18:40:56 brouard 64: Summary: Still testing ilc32 on OSX 65: 66: Revision 1.176 2015/01/03 16:45:04 brouard 67: *** empty log message *** 68: 69: Revision 1.175 2015/01/03 16:33:42 brouard 70: *** empty log message *** 71: 72: Revision 1.174 2015/01/03 16:15:49 brouard 73: Summary: Still in cross-compilation 74: 75: Revision 1.173 2015/01/03 12:06:26 brouard 76: Summary: trying to detect cross-compilation 77: 78: Revision 1.172 2014/12/27 12:07:47 brouard 79: Summary: Back from Visual Studio and Intel, options for compiling for Windows XP 80: 81: Revision 1.171 2014/12/23 13:26:59 brouard 82: Summary: Back from Visual C 83: 84: Still problem with utsname.h on Windows 85: 86: Revision 1.170 2014/12/23 11:17:12 brouard 87: Summary: Cleaning some \%% back to %% 88: 89: The escape was mandatory for a specific compiler (which one?), but too many warnings. 90: 91: Revision 1.169 2014/12/22 23:08:31 brouard 92: Summary: 0.98p 93: 94: Outputs some informations on compiler used, OS etc. Testing on different platforms. 95: 96: Revision 1.168 2014/12/22 15:17:42 brouard 97: Summary: update 98: 99: Revision 1.167 2014/12/22 13:50:56 brouard 100: Summary: Testing uname and compiler version and if compiled 32 or 64 101: 102: Testing on Linux 64 103: 104: Revision 1.166 2014/12/22 11:40:47 brouard 105: *** empty log message *** 106: 107: Revision 1.165 2014/12/16 11:20:36 brouard 108: Summary: After compiling on Visual C 109: 110: * imach.c (Module): Merging 1.61 to 1.162 111: 112: Revision 1.164 2014/12/16 10:52:11 brouard 113: Summary: Merging with Visual C after suppressing some warnings for unused variables. Also fixing Saito's bug 0.98Xn 114: 115: * imach.c (Module): Merging 1.61 to 1.162 116: 117: Revision 1.163 2014/12/16 10:30:11 brouard 118: * imach.c (Module): Merging 1.61 to 1.162 119: 120: Revision 1.162 2014/09/25 11:43:39 brouard 121: Summary: temporary backup 0.99! 122: 123: Revision 1.1 2014/09/16 11:06:58 brouard 124: Summary: With some code (wrong) for nlopt 125: 126: Author: 127: 128: Revision 1.161 2014/09/15 20:41:41 brouard 129: Summary: Problem with macro SQR on Intel compiler 130: 131: Revision 1.160 2014/09/02 09:24:05 brouard 132: *** empty log message *** 133: 134: Revision 1.159 2014/09/01 10:34:10 brouard 135: Summary: WIN32 136: Author: Brouard 137: 138: Revision 1.158 2014/08/27 17:11:51 brouard 139: *** empty log message *** 140: 141: Revision 1.157 2014/08/27 16:26:55 brouard 142: Summary: Preparing windows Visual studio version 143: Author: Brouard 144: 145: In order to compile on Visual studio, time.h is now correct and time_t 146: and tm struct should be used. difftime should be used but sometimes I 147: just make the differences in raw time format (time(&now). 148: Trying to suppress #ifdef LINUX 149: Add xdg-open for __linux in order to open default browser. 150: 151: Revision 1.156 2014/08/25 20:10:10 brouard 152: *** empty log message *** 153: 154: Revision 1.155 2014/08/25 18:32:34 brouard 155: Summary: New compile, minor changes 156: Author: Brouard 157: 158: Revision 1.154 2014/06/20 17:32:08 brouard 159: Summary: Outputs now all graphs of convergence to period prevalence 160: 161: Revision 1.153 2014/06/20 16:45:46 brouard 162: Summary: If 3 live state, convergence to period prevalence on same graph 163: Author: Brouard 164: 165: Revision 1.152 2014/06/18 17:54:09 brouard 166: Summary: open browser, use gnuplot on same dir than imach if not found in the path 167: 168: Revision 1.151 2014/06/18 16:43:30 brouard 169: *** empty log message *** 170: 171: Revision 1.150 2014/06/18 16:42:35 brouard 172: Summary: If gnuplot is not in the path try on same directory than imach binary (OSX) 173: Author: brouard 174: 175: Revision 1.149 2014/06/18 15:51:14 brouard 176: Summary: Some fixes in parameter files errors 177: Author: Nicolas Brouard 178: 179: Revision 1.148 2014/06/17 17:38:48 brouard 180: Summary: Nothing new 181: Author: Brouard 182: 183: Just a new packaging for OS/X version 0.98nS 184: 185: Revision 1.147 2014/06/16 10:33:11 brouard 186: *** empty log message *** 187: 188: Revision 1.146 2014/06/16 10:20:28 brouard 189: Summary: Merge 190: Author: Brouard 191: 192: Merge, before building revised version. 193: 194: Revision 1.145 2014/06/10 21:23:15 brouard 195: Summary: Debugging with valgrind 196: Author: Nicolas Brouard 197: 198: Lot of changes in order to output the results with some covariates 199: After the Edimburgh REVES conference 2014, it seems mandatory to 200: improve the code. 201: No more memory valgrind error but a lot has to be done in order to 202: continue the work of splitting the code into subroutines. 203: Also, decodemodel has been improved. Tricode is still not 204: optimal. nbcode should be improved. Documentation has been added in 205: the source code. 206: 207: Revision 1.143 2014/01/26 09:45:38 brouard 208: Summary: Version 0.98nR (to be improved, but gives same optimization results as 0.98k. Nice, promising 209: 210: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested... 211: (Module): Version 0.98nR Running ok, but output format still only works for three covariates. 212: 213: Revision 1.142 2014/01/26 03:57:36 brouard 214: Summary: gnuplot changed plot w l 1 has to be changed to plot w l lt 2 215: 216: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested... 217: 218: Revision 1.141 2014/01/26 02:42:01 brouard 219: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested... 220: 221: Revision 1.140 2011/09/02 10:37:54 brouard 222: Summary: times.h is ok with mingw32 now. 223: 224: Revision 1.139 2010/06/14 07:50:17 brouard 225: After the theft of my laptop, I probably lost some lines of codes which were not uploaded to the CVS tree. 226: I remember having already fixed agemin agemax which are pointers now but not cvs saved. 227: 228: Revision 1.138 2010/04/30 18:19:40 brouard 229: *** empty log message *** 230: 231: Revision 1.137 2010/04/29 18:11:38 brouard 232: (Module): Checking covariates for more complex models 233: than V1+V2. A lot of change to be done. Unstable. 234: 235: Revision 1.136 2010/04/26 20:30:53 brouard 236: (Module): merging some libgsl code. Fixing computation 237: of likelione (using inter/intrapolation if mle = 0) in order to 238: get same likelihood as if mle=1. 239: Some cleaning of code and comments added. 240: 241: Revision 1.135 2009/10/29 15:33:14 brouard 242: (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code. 243: 244: Revision 1.134 2009/10/29 13:18:53 brouard 245: (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code. 246: 247: Revision 1.133 2009/07/06 10:21:25 brouard 248: just nforces 249: 250: Revision 1.132 2009/07/06 08:22:05 brouard 251: Many tings 252: 253: Revision 1.131 2009/06/20 16:22:47 brouard 254: Some dimensions resccaled 255: 256: Revision 1.130 2009/05/26 06:44:34 brouard 257: (Module): Max Covariate is now set to 20 instead of 8. A 258: lot of cleaning with variables initialized to 0. Trying to make 259: V2+V3*age+V1+V4 strb=V3*age+V1+V4 working better. 260: 261: Revision 1.129 2007/08/31 13:49:27 lievre 262: Modification of the way of exiting when the covariate is not binary in order to see on the window the error message before exiting 263: 264: Revision 1.128 2006/06/30 13:02:05 brouard 265: (Module): Clarifications on computing e.j 266: 267: Revision 1.127 2006/04/28 18:11:50 brouard 268: (Module): Yes the sum of survivors was wrong since 269: imach-114 because nhstepm was no more computed in the age 270: loop. Now we define nhstepma in the age loop. 271: (Module): In order to speed up (in case of numerous covariates) we 272: compute health expectancies (without variances) in a first step 273: and then all the health expectancies with variances or standard 274: deviation (needs data from the Hessian matrices) which slows the 275: computation. 276: In the future we should be able to stop the program is only health 277: expectancies and graph are needed without standard deviations. 278: 279: Revision 1.126 2006/04/28 17:23:28 brouard 280: (Module): Yes the sum of survivors was wrong since 281: imach-114 because nhstepm was no more computed in the age 282: loop. Now we define nhstepma in the age loop. 283: Version 0.98h 284: 285: Revision 1.125 2006/04/04 15:20:31 lievre 286: Errors in calculation of health expectancies. Age was not initialized. 287: Forecasting file added. 288: 289: Revision 1.124 2006/03/22 17:13:53 lievre 290: Parameters are printed with %lf instead of %f (more numbers after the comma). 291: The log-likelihood is printed in the log file 292: 293: Revision 1.123 2006/03/20 10:52:43 brouard 294: * imach.c (Module): <title> changed, corresponds to .htm file 295: name. <head> headers where missing. 296: 297: * imach.c (Module): Weights can have a decimal point as for 298: English (a comma might work with a correct LC_NUMERIC environment, 299: otherwise the weight is truncated). 300: Modification of warning when the covariates values are not 0 or 301: 1. 302: Version 0.98g 303: 304: Revision 1.122 2006/03/20 09:45:41 brouard 305: (Module): Weights can have a decimal point as for 306: English (a comma might work with a correct LC_NUMERIC environment, 307: otherwise the weight is truncated). 308: Modification of warning when the covariates values are not 0 or 309: 1. 310: Version 0.98g 311: 312: Revision 1.121 2006/03/16 17:45:01 lievre 313: * imach.c (Module): Comments concerning covariates added 314: 315: * imach.c (Module): refinements in the computation of lli if 316: status=-2 in order to have more reliable computation if stepm is 317: not 1 month. Version 0.98f 318: 319: Revision 1.120 2006/03/16 15:10:38 lievre 320: (Module): refinements in the computation of lli if 321: status=-2 in order to have more reliable computation if stepm is 322: not 1 month. Version 0.98f 323: 324: Revision 1.119 2006/03/15 17:42:26 brouard 325: (Module): Bug if status = -2, the loglikelihood was 326: computed as likelihood omitting the logarithm. Version O.98e 327: 328: Revision 1.118 2006/03/14 18:20:07 brouard 329: (Module): varevsij Comments added explaining the second 330: table of variances if popbased=1 . 331: (Module): Covariances of eij, ekl added, graphs fixed, new html link. 332: (Module): Function pstamp added 333: (Module): Version 0.98d 334: 335: Revision 1.117 2006/03/14 17:16:22 brouard 336: (Module): varevsij Comments added explaining the second 337: table of variances if popbased=1 . 338: (Module): Covariances of eij, ekl added, graphs fixed, new html link. 339: (Module): Function pstamp added 340: (Module): Version 0.98d 341: 342: Revision 1.116 2006/03/06 10:29:27 brouard 343: (Module): Variance-covariance wrong links and 344: varian-covariance of ej. is needed (Saito). 345: 346: Revision 1.115 2006/02/27 12:17:45 brouard 347: (Module): One freematrix added in mlikeli! 0.98c 348: 349: Revision 1.114 2006/02/26 12:57:58 brouard 350: (Module): Some improvements in processing parameter 351: filename with strsep. 352: 353: Revision 1.113 2006/02/24 14:20:24 brouard 354: (Module): Memory leaks checks with valgrind and: 355: datafile was not closed, some imatrix were not freed and on matrix 356: allocation too. 357: 358: Revision 1.112 2006/01/30 09:55:26 brouard 359: (Module): Back to gnuplot.exe instead of wgnuplot.exe 360: 361: Revision 1.111 2006/01/25 20:38:18 brouard 362: (Module): Lots of cleaning and bugs added (Gompertz) 363: (Module): Comments can be added in data file. Missing date values 364: can be a simple dot '.'. 365: 366: Revision 1.110 2006/01/25 00:51:50 brouard 367: (Module): Lots of cleaning and bugs added (Gompertz) 368: 369: Revision 1.109 2006/01/24 19:37:15 brouard 370: (Module): Comments (lines starting with a #) are allowed in data. 371: 372: Revision 1.108 2006/01/19 18:05:42 lievre 373: Gnuplot problem appeared... 374: To be fixed 375: 376: Revision 1.107 2006/01/19 16:20:37 brouard 377: Test existence of gnuplot in imach path 378: 379: Revision 1.106 2006/01/19 13:24:36 brouard 380: Some cleaning and links added in html output 381: 382: Revision 1.105 2006/01/05 20:23:19 lievre 383: *** empty log message *** 384: 385: Revision 1.104 2005/09/30 16:11:43 lievre 386: (Module): sump fixed, loop imx fixed, and simplifications. 387: (Module): If the status is missing at the last wave but we know 388: that the person is alive, then we can code his/her status as -2 389: (instead of missing=-1 in earlier versions) and his/her 390: contributions to the likelihood is 1 - Prob of dying from last 391: health status (= 1-p13= p11+p12 in the easiest case of somebody in 392: the healthy state at last known wave). Version is 0.98 393: 394: Revision 1.103 2005/09/30 15:54:49 lievre 395: (Module): sump fixed, loop imx fixed, and simplifications. 396: 397: Revision 1.102 2004/09/15 17:31:30 brouard 398: Add the possibility to read data file including tab characters. 399: 400: Revision 1.101 2004/09/15 10:38:38 brouard 401: Fix on curr_time 402: 403: Revision 1.100 2004/07/12 18:29:06 brouard 404: Add version for Mac OS X. Just define UNIX in Makefile 405: 406: Revision 1.99 2004/06/05 08:57:40 brouard 407: *** empty log message *** 408: 409: Revision 1.98 2004/05/16 15:05:56 brouard 410: New version 0.97 . First attempt to estimate force of mortality 411: directly from the data i.e. without the need of knowing the health 412: state at each age, but using a Gompertz model: log u =a + b*age . 413: This is the basic analysis of mortality and should be done before any 414: other analysis, in order to test if the mortality estimated from the 415: cross-longitudinal survey is different from the mortality estimated 416: from other sources like vital statistic data. 417: 418: The same imach parameter file can be used but the option for mle should be -3. 419: 420: Agnès, who wrote this part of the code, tried to keep most of the 421: former routines in order to include the new code within the former code. 422: 423: The output is very simple: only an estimate of the intercept and of 424: the slope with 95% confident intervals. 425: 426: Current limitations: 427: A) Even if you enter covariates, i.e. with the 428: model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates. 429: B) There is no computation of Life Expectancy nor Life Table. 430: 431: Revision 1.97 2004/02/20 13:25:42 lievre 432: Version 0.96d. Population forecasting command line is (temporarily) 433: suppressed. 434: 435: Revision 1.96 2003/07/15 15:38:55 brouard 436: * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is 437: rewritten within the same printf. Workaround: many printfs. 438: 439: Revision 1.95 2003/07/08 07:54:34 brouard 440: * imach.c (Repository): 441: (Repository): Using imachwizard code to output a more meaningful covariance 442: matrix (cov(a12,c31) instead of numbers. 443: 444: Revision 1.94 2003/06/27 13:00:02 brouard 445: Just cleaning 446: 447: Revision 1.93 2003/06/25 16:33:55 brouard 448: (Module): On windows (cygwin) function asctime_r doesn't 449: exist so I changed back to asctime which exists. 450: (Module): Version 0.96b 451: 452: Revision 1.92 2003/06/25 16:30:45 brouard 453: (Module): On windows (cygwin) function asctime_r doesn't 454: exist so I changed back to asctime which exists. 455: 456: Revision 1.91 2003/06/25 15:30:29 brouard 457: * imach.c (Repository): Duplicated warning errors corrected. 458: (Repository): Elapsed time after each iteration is now output. It 459: helps to forecast when convergence will be reached. Elapsed time 460: is stamped in powell. We created a new html file for the graphs 461: concerning matrix of covariance. It has extension -cov.htm. 462: 463: Revision 1.90 2003/06/24 12:34:15 brouard 464: (Module): Some bugs corrected for windows. Also, when 465: mle=-1 a template is output in file "or"mypar.txt with the design 466: of the covariance matrix to be input. 467: 468: Revision 1.89 2003/06/24 12:30:52 brouard 469: (Module): Some bugs corrected for windows. Also, when 470: mle=-1 a template is output in file "or"mypar.txt with the design 471: of the covariance matrix to be input. 472: 473: Revision 1.88 2003/06/23 17:54:56 brouard 474: * 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. 475: 476: Revision 1.87 2003/06/18 12:26:01 brouard 477: Version 0.96 478: 479: Revision 1.86 2003/06/17 20:04:08 brouard 480: (Module): Change position of html and gnuplot routines and added 481: routine fileappend. 482: 483: Revision 1.85 2003/06/17 13:12:43 brouard 484: * imach.c (Repository): Check when date of death was earlier that 485: current date of interview. It may happen when the death was just 486: prior to the death. In this case, dh was negative and likelihood 487: was wrong (infinity). We still send an "Error" but patch by 488: assuming that the date of death was just one stepm after the 489: interview. 490: (Repository): Because some people have very long ID (first column) 491: we changed int to long in num[] and we added a new lvector for 492: memory allocation. But we also truncated to 8 characters (left 493: truncation) 494: (Repository): No more line truncation errors. 495: 496: Revision 1.84 2003/06/13 21:44:43 brouard 497: * imach.c (Repository): Replace "freqsummary" at a correct 498: place. It differs from routine "prevalence" which may be called 499: many times. Probs is memory consuming and must be used with 500: parcimony. 501: Version 0.95a3 (should output exactly the same maximization than 0.8a2) 502: 503: Revision 1.83 2003/06/10 13:39:11 lievre 504: *** empty log message *** 505: 506: Revision 1.82 2003/06/05 15:57:20 brouard 507: Add log in imach.c and fullversion number is now printed. 508: 509: */ 510: /* 511: Interpolated Markov Chain 512: 513: Short summary of the programme: 514: 515: This program computes Healthy Life Expectancies from 516: cross-longitudinal data. Cross-longitudinal data consist in: -1- a 517: first survey ("cross") where individuals from different ages are 518: interviewed on their health status or degree of disability (in the 519: case of a health survey which is our main interest) -2- at least a 520: second wave of interviews ("longitudinal") which measure each change 521: (if any) in individual health status. Health expectancies are 522: computed from the time spent in each health state according to a 523: model. More health states you consider, more time is necessary to reach the 524: Maximum Likelihood of the parameters involved in the model. The 525: simplest model is the multinomial logistic model where pij is the 526: probability to be observed in state j at the second wave 527: conditional to be observed in state i at the first wave. Therefore 528: the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where 529: 'age' is age and 'sex' is a covariate. If you want to have a more 530: complex model than "constant and age", you should modify the program 531: where the markup *Covariates have to be included here again* invites 532: you to do it. More covariates you add, slower the 533: convergence. 534: 535: The advantage of this computer programme, compared to a simple 536: multinomial logistic model, is clear when the delay between waves is not 537: identical for each individual. Also, if a individual missed an 538: intermediate interview, the information is lost, but taken into 539: account using an interpolation or extrapolation. 540: 541: hPijx is the probability to be observed in state i at age x+h 542: conditional to the observed state i at age x. The delay 'h' can be 543: split into an exact number (nh*stepm) of unobserved intermediate 544: states. This elementary transition (by month, quarter, 545: semester or year) is modelled as a multinomial logistic. The hPx 546: matrix is simply the matrix product of nh*stepm elementary matrices 547: and the contribution of each individual to the likelihood is simply 548: hPijx. 549: 550: Also this programme outputs the covariance matrix of the parameters but also 551: of the life expectancies. It also computes the period (stable) prevalence. 552: 553: Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr). 554: Institut national d'études démographiques, Paris. 555: This software have been partly granted by Euro-REVES, a concerted action 556: from the European Union. 557: It is copyrighted identically to a GNU software product, ie programme and 558: software can be distributed freely for non commercial use. Latest version 559: can be accessed at http://euroreves.ined.fr/imach . 560: 561: Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach 562: or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so 563: 564: **********************************************************************/ 565: /* 566: main 567: read parameterfile 568: read datafile 569: concatwav 570: freqsummary 571: if (mle >= 1) 572: mlikeli 573: print results files 574: if mle==1 575: computes hessian 576: read end of parameter file: agemin, agemax, bage, fage, estepm 577: begin-prev-date,... 578: open gnuplot file 579: open html file 580: period (stable) prevalence | pl_nom 1-1 2-2 etc by covariate 581: for age prevalim() | #****** V1=0 V2=1 V3=1 V4=0 ****** 582: | 65 1 0 2 1 3 1 4 0 0.96326 0.03674 583: freexexit2 possible for memory heap. 584: 585: h Pij x | pij_nom ficrestpij 586: # Cov Agex agex+h hpijx with i,j= 1-1 1-2 1-3 2-1 2-2 2-3 587: 1 85 85 1.00000 0.00000 0.00000 0.00000 1.00000 0.00000 588: 1 85 86 0.68299 0.22291 0.09410 0.71093 0.00000 0.28907 589: 590: 1 65 99 0.00364 0.00322 0.99314 0.00350 0.00310 0.99340 591: 1 65 100 0.00214 0.00204 0.99581 0.00206 0.00196 0.99597 592: variance of p one-step probabilities varprob | prob_nom ficresprob #One-step probabilities and stand. devi in () 593: Standard deviation of one-step probabilities | probcor_nom ficresprobcor #One-step probabilities and correlation matrix 594: Matrix of variance covariance of one-step probabilities | probcov_nom ficresprobcov #One-step probabilities and covariance matrix 595: 596: forecasting if prevfcast==1 prevforecast call prevalence() 597: health expectancies 598: Variance-covariance of DFLE 599: prevalence() 600: movingaverage() 601: varevsij() 602: if popbased==1 varevsij(,popbased) 603: total life expectancies 604: Variance of period (stable) prevalence 605: end 606: */ 607: 608: /* #define DEBUG */ 609: /* #define DEBUGBRENT */ 610: #define POWELL /* Instead of NLOPT */ 611: #define POWELLF1F3 /* Skip test */ 612: /* #define POWELLORIGINAL /\* Don't use Directest to decide new direction but original Powell test *\/ */ 613: /* #define MNBRAKORIGINAL /\* Don't use mnbrak fix *\/ */ 614: 615: #include <math.h> 616: #include <stdio.h> 617: #include <stdlib.h> 618: #include <string.h> 619: 620: #ifdef _WIN32 621: #include <io.h> 622: #include <windows.h> 623: #include <tchar.h> 624: #else 625: #include <unistd.h> 626: #endif 627: 628: #include <limits.h> 629: #include <sys/types.h> 630: 631: #if defined(__GNUC__) 632: #include <sys/utsname.h> /* Doesn't work on Windows */ 633: #endif 634: 635: #include <sys/stat.h> 636: #include <errno.h> 637: /* extern int errno; */ 638: 639: /* #ifdef LINUX */ 640: /* #include <time.h> */ 641: /* #include "timeval.h" */ 642: /* #else */ 643: /* #include <sys/time.h> */ 644: /* #endif */ 645: 646: #include <time.h> 647: 648: #ifdef GSL 649: #include <gsl/gsl_errno.h> 650: #include <gsl/gsl_multimin.h> 651: #endif 652: 653: 654: #ifdef NLOPT 655: #include <nlopt.h> 656: typedef struct { 657: double (* function)(double [] ); 658: } myfunc_data ; 659: #endif 660: 661: /* #include <libintl.h> */ 662: /* #define _(String) gettext (String) */ 663: 664: #define MAXLINE 1024 /* Was 256. Overflow with 312 with 2 states and 4 covariates. Should be ok */ 665: 666: #define GNUPLOTPROGRAM "gnuplot" 667: /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/ 668: #define FILENAMELENGTH 132 669: 670: #define GLOCK_ERROR_NOPATH -1 /* empty path */ 671: #define GLOCK_ERROR_GETCWD -2 /* cannot get cwd */ 672: 673: #define MAXPARM 128 /**< Maximum number of parameters for the optimization */ 674: #define NPARMAX 64 /**< (nlstate+ndeath-1)*nlstate*ncovmodel */ 675: 676: #define NINTERVMAX 8 677: #define NLSTATEMAX 8 /**< Maximum number of live states (for func) */ 678: #define NDEATHMAX 8 /**< Maximum number of dead states (for func) */ 679: #define NCOVMAX 20 /**< Maximum number of covariates, including generated covariates V1*V2 */ 680: #define codtabm(h,k) 1 & (h-1) >> (k-1) ; 681: #define MAXN 20000 682: #define YEARM 12. /**< Number of months per year */ 683: #define AGESUP 130 684: #define AGEBASE 40 685: #define AGEGOMP 10 /**< Minimal age for Gompertz adjustment */ 686: #ifdef _WIN32 687: #define DIRSEPARATOR '\\' 688: #define CHARSEPARATOR "\\" 689: #define ODIRSEPARATOR '/' 690: #else 691: #define DIRSEPARATOR '/' 692: #define CHARSEPARATOR "/" 693: #define ODIRSEPARATOR '\\' 694: #endif 695: 696: /* $Id: imach.c,v 1.192 2015/07/16 16:49:02 brouard Exp $ */ 697: /* $State: Exp $ */ 698: 699: char version[]="Imach version 0.98q3, July 2015,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121), Intel Software 2015"; 700: char fullversion[]="$Revision: 1.192 $ $Date: 2015/07/16 16:49:02 $"; 701: char strstart[80]; 702: char optionfilext[10], optionfilefiname[FILENAMELENGTH]; 703: int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings */ 704: int nagesqr=0, nforce=0; /* nagesqr=1 if model is including age*age, number of forces */ 705: /* Number of covariates model=V2+V1+ V3*age+V2*V4 */ 706: int cptcovn=0; /**< cptcovn number of covariates added in the model (excepting constant and age and age*product) */ 707: int cptcovt=0; /**< cptcovt number of covariates added in the model (excepting constant and age) */ 708: int cptcovs=0; /**< cptcovs number of simple covariates V2+V1 =2 */ 709: int cptcovage=0; /**< Number of covariates with age: V3*age only =1 */ 710: int cptcovprodnoage=0; /**< Number of covariate products without age */ 711: int cptcoveff=0; /* Total number of covariates to vary for printing results */ 712: int cptcov=0; /* Working variable */ 713: int npar=NPARMAX; 714: int nlstate=2; /* Number of live states */ 715: int ndeath=1; /* Number of dead states */ 716: int ncovmodel=0, ncovcol=0; /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */ 717: int popbased=0; 718: 719: int *wav; /* Number of waves for this individuual 0 is possible */ 720: int maxwav=0; /* Maxim number of waves */ 721: int jmin=0, jmax=0; /* min, max spacing between 2 waves */ 722: int ijmin=0, ijmax=0; /* Individuals having jmin and jmax */ 723: int gipmx=0, gsw=0; /* Global variables on the number of contributions 724: to the likelihood and the sum of weights (done by funcone)*/ 725: int mle=1, weightopt=0; 726: int **mw; /* mw[mi][i] is number of the mi wave for this individual */ 727: int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */ 728: int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between 729: * wave mi and wave mi+1 is not an exact multiple of stepm. */ 730: int countcallfunc=0; /* Count the number of calls to func */ 731: double jmean=1; /* Mean space between 2 waves */ 732: double **matprod2(); /* test */ 733: double **oldm, **newm, **savm; /* Working pointers to matrices */ 734: double **oldms, **newms, **savms; /* Fixed working pointers to matrices */ 735: /*FILE *fic ; */ /* Used in readdata only */ 736: FILE *ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop; 737: FILE *ficlog, *ficrespow; 738: int globpr=0; /* Global variable for printing or not */ 739: double fretone; /* Only one call to likelihood */ 740: long ipmx=0; /* Number of contributions */ 741: double sw; /* Sum of weights */ 742: char filerespow[FILENAMELENGTH]; 743: char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */ 744: FILE *ficresilk; 745: FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor; 746: FILE *ficresprobmorprev; 747: FILE *fichtm, *fichtmcov; /* Html File */ 748: FILE *ficreseij; 749: char filerese[FILENAMELENGTH]; 750: FILE *ficresstdeij; 751: char fileresstde[FILENAMELENGTH]; 752: FILE *ficrescveij; 753: char filerescve[FILENAMELENGTH]; 754: FILE *ficresvij; 755: char fileresv[FILENAMELENGTH]; 756: FILE *ficresvpl; 757: char fileresvpl[FILENAMELENGTH]; 758: char title[MAXLINE]; 759: char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH], filerespl[FILENAMELENGTH]; 760: char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH]; 761: char tmpout[FILENAMELENGTH], tmpout2[FILENAMELENGTH]; 762: char command[FILENAMELENGTH]; 763: int outcmd=0; 764: 765: char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH]; 766: 767: char filelog[FILENAMELENGTH]; /* Log file */ 768: char filerest[FILENAMELENGTH]; 769: char fileregp[FILENAMELENGTH]; 770: char popfile[FILENAMELENGTH]; 771: 772: char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ; 773: 774: /* struct timeval start_time, end_time, curr_time, last_time, forecast_time; */ 775: /* struct timezone tzp; */ 776: /* extern int gettimeofday(); */ 777: struct tm tml, *gmtime(), *localtime(); 778: 779: extern time_t time(); 780: 781: struct tm start_time, end_time, curr_time, last_time, forecast_time; 782: time_t rstart_time, rend_time, rcurr_time, rlast_time, rforecast_time; /* raw time */ 783: struct tm tm; 784: 785: char strcurr[80], strfor[80]; 786: 787: char *endptr; 788: long lval; 789: double dval; 790: 791: #define NR_END 1 792: #define FREE_ARG char* 793: #define FTOL 1.0e-10 794: 795: #define NRANSI 796: #define ITMAX 200 797: 798: #define TOL 2.0e-4 799: 800: #define CGOLD 0.3819660 801: #define ZEPS 1.0e-10 802: #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 803: 804: #define GOLD 1.618034 805: #define GLIMIT 100.0 806: #define TINY 1.0e-20 807: 808: static double maxarg1,maxarg2; 809: #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2)) 810: #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2)) 811: 812: #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a)) 813: #define rint(a) floor(a+0.5) 814: /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/myutils_8h-source.html */ 815: #define mytinydouble 1.0e-16 816: /* #define DEQUAL(a,b) (fabs((a)-(b))<mytinydouble) */ 817: /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/mynrutils_8h-source.html */ 818: /* static double dsqrarg; */ 819: /* #define DSQR(a) (DEQUAL((dsqrarg=(a)),0.0) ? 0.0 : dsqrarg*dsqrarg) */ 820: static double sqrarg; 821: #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg) 822: #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 823: int agegomp= AGEGOMP; 824: 825: int imx; 826: int stepm=1; 827: /* Stepm, step in month: minimum step interpolation*/ 828: 829: int estepm; 830: /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/ 831: 832: int m,nb; 833: long *num; 834: int firstpass=0, lastpass=4,*cod, *Tage,*cens; 835: int *ncodemax; /* ncodemax[j]= Number of modalities of the j th 836: covariate for which somebody answered excluding 837: undefined. Usually 2: 0 and 1. */ 838: int *ncodemaxwundef; /* ncodemax[j]= Number of modalities of the j th 839: covariate for which somebody answered including 840: undefined. Usually 3: -1, 0 and 1. */ 841: double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint; 842: double **pmmij, ***probs; 843: double *ageexmed,*agecens; 844: double dateintmean=0; 845: 846: double *weight; 847: int **s; /* Status */ 848: double *agedc; 849: double **covar; /**< covar[j,i], value of jth covariate for individual i, 850: * covar=matrix(0,NCOVMAX,1,n); 851: * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*age; */ 852: double idx; 853: int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */ 854: int *Ndum; /** Freq of modality (tricode */ 855: int **codtab; /**< codtab=imatrix(1,100,1,10); */ 856: int **Tvard, *Tprod, cptcovprod, *Tvaraff; 857: double *lsurv, *lpop, *tpop; 858: 859: double ftol=FTOL; /**< Tolerance for computing Max Likelihood */ 860: double ftolhess; /**< Tolerance for computing hessian */ 861: 862: /**************** split *************************/ 863: static int split( char *path, char *dirc, char *name, char *ext, char *finame ) 864: { 865: /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc) 866: the name of the file (name), its extension only (ext) and its first part of the name (finame) 867: */ 868: char *ss; /* pointer */ 869: int l1=0, l2=0; /* length counters */ 870: 871: l1 = strlen(path ); /* length of path */ 872: if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH ); 873: ss= strrchr( path, DIRSEPARATOR ); /* find last / */ 874: if ( ss == NULL ) { /* no directory, so determine current directory */ 875: strcpy( name, path ); /* we got the fullname name because no directory */ 876: /*if(strrchr(path, ODIRSEPARATOR )==NULL) 877: printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/ 878: /* get current working directory */ 879: /* extern char* getcwd ( char *buf , int len);*/ 880: #ifdef WIN32 881: if (_getcwd( dirc, FILENAME_MAX ) == NULL ) { 882: #else 883: if (getcwd(dirc, FILENAME_MAX) == NULL) { 884: #endif 885: return( GLOCK_ERROR_GETCWD ); 886: } 887: /* got dirc from getcwd*/ 888: printf(" DIRC = %s \n",dirc); 889: } else { /* strip direcotry from path */ 890: ss++; /* after this, the filename */ 891: l2 = strlen( ss ); /* length of filename */ 892: if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH ); 893: strcpy( name, ss ); /* save file name */ 894: strncpy( dirc, path, l1 - l2 ); /* now the directory */ 895: dirc[l1-l2] = '\0'; /* add zero */ 896: printf(" DIRC2 = %s \n",dirc); 897: } 898: /* We add a separator at the end of dirc if not exists */ 899: l1 = strlen( dirc ); /* length of directory */ 900: if( dirc[l1-1] != DIRSEPARATOR ){ 901: dirc[l1] = DIRSEPARATOR; 902: dirc[l1+1] = 0; 903: printf(" DIRC3 = %s \n",dirc); 904: } 905: ss = strrchr( name, '.' ); /* find last / */ 906: if (ss >0){ 907: ss++; 908: strcpy(ext,ss); /* save extension */ 909: l1= strlen( name); 910: l2= strlen(ss)+1; 911: strncpy( finame, name, l1-l2); 912: finame[l1-l2]= 0; 913: } 914: 915: return( 0 ); /* we're done */ 916: } 917: 918: 919: /******************************************/ 920: 921: void replace_back_to_slash(char *s, char*t) 922: { 923: int i; 924: int lg=0; 925: i=0; 926: lg=strlen(t); 927: for(i=0; i<= lg; i++) { 928: (s[i] = t[i]); 929: if (t[i]== '\\') s[i]='/'; 930: } 931: } 932: 933: char *trimbb(char *out, char *in) 934: { /* Trim multiple blanks in line but keeps first blanks if line starts with blanks */ 935: char *s; 936: s=out; 937: while (*in != '\0'){ 938: while( *in == ' ' && *(in+1) == ' '){ /* && *(in+1) != '\0'){*/ 939: in++; 940: } 941: *out++ = *in++; 942: } 943: *out='\0'; 944: return s; 945: } 946: 947: /* char *substrchaine(char *out, char *in, char *chain) */ 948: /* { */ 949: /* /\* Substract chain 'chain' from 'in', return and output 'out' *\/ */ 950: /* char *s, *t; */ 951: /* t=in;s=out; */ 952: /* while ((*in != *chain) && (*in != '\0')){ */ 953: /* *out++ = *in++; */ 954: /* } */ 955: 956: /* /\* *in matches *chain *\/ */ 957: /* while ((*in++ == *chain++) && (*in != '\0')){ */ 958: /* printf("*in = %c, *out= %c *chain= %c \n", *in, *out, *chain); */ 959: /* } */ 960: /* in--; chain--; */ 961: /* while ( (*in != '\0')){ */ 962: /* printf("Bef *in = %c, *out= %c *chain= %c \n", *in, *out, *chain); */ 963: /* *out++ = *in++; */ 964: /* printf("Aft *in = %c, *out= %c *chain= %c \n", *in, *out, *chain); */ 965: /* } */ 966: /* *out='\0'; */ 967: /* out=s; */ 968: /* return out; */ 969: /* } */ 970: char *substrchaine(char *out, char *in, char *chain) 971: { 972: /* Substract chain 'chain' from 'in', return and output 'out' */ 973: /* in="V1+V1*age+age*age+V2", chain="age*age" */ 974: 975: char *strloc; 976: 977: strcpy (out, in); 978: strloc = strstr(out, chain); /* strloc points to out at age*age+V2 */ 979: printf("Bef strloc=%s chain=%s out=%s \n", strloc, chain, out); 980: if(strloc != NULL){ 981: /* will affect out */ /* strloc+strlenc(chain)=+V2 */ /* Will also work in Unicode */ 982: memmove(strloc,strloc+strlen(chain), strlen(strloc+strlen(chain))+1); 983: /* strcpy (strloc, strloc +strlen(chain));*/ 984: } 985: printf("Aft strloc=%s chain=%s in=%s out=%s \n", strloc, chain, in, out); 986: return out; 987: } 988: 989: 990: char *cutl(char *blocc, char *alocc, char *in, char occ) 991: { 992: /* cuts string in into blocc and alocc where blocc ends before FIRST occurence of char 'occ' 993: and alocc starts after first occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2') 994: gives blocc="abcdef" and alocc="ghi2j". 995: If occ is not found blocc is null and alocc is equal to in. Returns blocc 996: */ 997: char *s, *t; 998: t=in;s=in; 999: while ((*in != occ) && (*in != '\0')){ 1000: *alocc++ = *in++; 1001: } 1002: if( *in == occ){ 1003: *(alocc)='\0'; 1004: s=++in; 1005: } 1006: 1007: if (s == t) {/* occ not found */ 1008: *(alocc-(in-s))='\0'; 1009: in=s; 1010: } 1011: while ( *in != '\0'){ 1012: *blocc++ = *in++; 1013: } 1014: 1015: *blocc='\0'; 1016: return t; 1017: } 1018: char *cutv(char *blocc, char *alocc, char *in, char occ) 1019: { 1020: /* cuts string in into blocc and alocc where blocc ends before LAST occurence of char 'occ' 1021: and alocc starts after last occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2') 1022: gives blocc="abcdef2ghi" and alocc="j". 1023: If occ is not found blocc is null and alocc is equal to in. Returns alocc 1024: */ 1025: char *s, *t; 1026: t=in;s=in; 1027: while (*in != '\0'){ 1028: while( *in == occ){ 1029: *blocc++ = *in++; 1030: s=in; 1031: } 1032: *blocc++ = *in++; 1033: } 1034: if (s == t) /* occ not found */ 1035: *(blocc-(in-s))='\0'; 1036: else 1037: *(blocc-(in-s)-1)='\0'; 1038: in=s; 1039: while ( *in != '\0'){ 1040: *alocc++ = *in++; 1041: } 1042: 1043: *alocc='\0'; 1044: return s; 1045: } 1046: 1047: int nbocc(char *s, char occ) 1048: { 1049: int i,j=0; 1050: int lg=20; 1051: i=0; 1052: lg=strlen(s); 1053: for(i=0; i<= lg; i++) { 1054: if (s[i] == occ ) j++; 1055: } 1056: return j; 1057: } 1058: 1059: /* void cutv(char *u,char *v, char*t, char occ) */ 1060: /* { */ 1061: /* /\* cuts string t into u and v where u ends before last occurence of char 'occ' */ 1062: /* and v starts after last occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2') */ 1063: /* gives u="abcdef2ghi" and v="j" *\/ */ 1064: /* int i,lg,j,p=0; */ 1065: /* i=0; */ 1066: /* lg=strlen(t); */ 1067: /* for(j=0; j<=lg-1; j++) { */ 1068: /* if((t[j]!= occ) && (t[j+1]== occ)) p=j+1; */ 1069: /* } */ 1070: 1071: /* for(j=0; j<p; j++) { */ 1072: /* (u[j] = t[j]); */ 1073: /* } */ 1074: /* u[p]='\0'; */ 1075: 1076: /* for(j=0; j<= lg; j++) { */ 1077: /* if (j>=(p+1))(v[j-p-1] = t[j]); */ 1078: /* } */ 1079: /* } */ 1080: 1081: #ifdef _WIN32 1082: char * strsep(char **pp, const char *delim) 1083: { 1084: char *p, *q; 1085: 1086: if ((p = *pp) == NULL) 1087: return 0; 1088: if ((q = strpbrk (p, delim)) != NULL) 1089: { 1090: *pp = q + 1; 1091: *q = '\0'; 1092: } 1093: else 1094: *pp = 0; 1095: return p; 1096: } 1097: #endif 1098: 1099: /********************** nrerror ********************/ 1100: 1101: void nrerror(char error_text[]) 1102: { 1103: fprintf(stderr,"ERREUR ...\n"); 1104: fprintf(stderr,"%s\n",error_text); 1105: exit(EXIT_FAILURE); 1106: } 1107: /*********************** vector *******************/ 1108: double *vector(int nl, int nh) 1109: { 1110: double *v; 1111: v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double))); 1112: if (!v) nrerror("allocation failure in vector"); 1113: return v-nl+NR_END; 1114: } 1115: 1116: /************************ free vector ******************/ 1117: void free_vector(double*v, int nl, int nh) 1118: { 1119: free((FREE_ARG)(v+nl-NR_END)); 1120: } 1121: 1122: /************************ivector *******************************/ 1123: int *ivector(long nl,long nh) 1124: { 1125: int *v; 1126: v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int))); 1127: if (!v) nrerror("allocation failure in ivector"); 1128: return v-nl+NR_END; 1129: } 1130: 1131: /******************free ivector **************************/ 1132: void free_ivector(int *v, long nl, long nh) 1133: { 1134: free((FREE_ARG)(v+nl-NR_END)); 1135: } 1136: 1137: /************************lvector *******************************/ 1138: long *lvector(long nl,long nh) 1139: { 1140: long *v; 1141: v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long))); 1142: if (!v) nrerror("allocation failure in ivector"); 1143: return v-nl+NR_END; 1144: } 1145: 1146: /******************free lvector **************************/ 1147: void free_lvector(long *v, long nl, long nh) 1148: { 1149: free((FREE_ARG)(v+nl-NR_END)); 1150: } 1151: 1152: /******************* imatrix *******************************/ 1153: int **imatrix(long nrl, long nrh, long ncl, long nch) 1154: /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 1155: { 1156: long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 1157: int **m; 1158: 1159: /* allocate pointers to rows */ 1160: m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 1161: if (!m) nrerror("allocation failure 1 in matrix()"); 1162: m += NR_END; 1163: m -= nrl; 1164: 1165: 1166: /* allocate rows and set pointers to them */ 1167: m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 1168: if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 1169: m[nrl] += NR_END; 1170: m[nrl] -= ncl; 1171: 1172: for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 1173: 1174: /* return pointer to array of pointers to rows */ 1175: return m; 1176: } 1177: 1178: /****************** free_imatrix *************************/ 1179: void free_imatrix(m,nrl,nrh,ncl,nch) 1180: int **m; 1181: long nch,ncl,nrh,nrl; 1182: /* free an int matrix allocated by imatrix() */ 1183: { 1184: free((FREE_ARG) (m[nrl]+ncl-NR_END)); 1185: free((FREE_ARG) (m+nrl-NR_END)); 1186: } 1187: 1188: /******************* matrix *******************************/ 1189: double **matrix(long nrl, long nrh, long ncl, long nch) 1190: { 1191: long i, nrow=nrh-nrl+1, ncol=nch-ncl+1; 1192: double **m; 1193: 1194: m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*))); 1195: if (!m) nrerror("allocation failure 1 in matrix()"); 1196: m += NR_END; 1197: m -= nrl; 1198: 1199: m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double))); 1200: if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 1201: m[nrl] += NR_END; 1202: m[nrl] -= ncl; 1203: 1204: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol; 1205: return m; 1206: /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) or &(m[1][0]) 1207: m[i] = address of ith row of the table. &(m[i]) is its value which is another adress 1208: that of m[i][0]. In order to get the value p m[i][0] but it is unitialized. 1209: */ 1210: } 1211: 1212: /*************************free matrix ************************/ 1213: void free_matrix(double **m, long nrl, long nrh, long ncl, long nch) 1214: { 1215: free((FREE_ARG)(m[nrl]+ncl-NR_END)); 1216: free((FREE_ARG)(m+nrl-NR_END)); 1217: } 1218: 1219: /******************* ma3x *******************************/ 1220: double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh) 1221: { 1222: long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1; 1223: double ***m; 1224: 1225: m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*))); 1226: if (!m) nrerror("allocation failure 1 in matrix()"); 1227: m += NR_END; 1228: m -= nrl; 1229: 1230: m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double))); 1231: if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 1232: m[nrl] += NR_END; 1233: m[nrl] -= ncl; 1234: 1235: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol; 1236: 1237: m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double))); 1238: if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()"); 1239: m[nrl][ncl] += NR_END; 1240: m[nrl][ncl] -= nll; 1241: for (j=ncl+1; j<=nch; j++) 1242: m[nrl][j]=m[nrl][j-1]+nlay; 1243: 1244: for (i=nrl+1; i<=nrh; i++) { 1245: m[i][ncl]=m[i-1l][ncl]+ncol*nlay; 1246: for (j=ncl+1; j<=nch; j++) 1247: m[i][j]=m[i][j-1]+nlay; 1248: } 1249: return m; 1250: /* gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1]) 1251: &(m[i][j][k]) <=> *((*(m+i) + j)+k) 1252: */ 1253: } 1254: 1255: /*************************free ma3x ************************/ 1256: void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh) 1257: { 1258: free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END)); 1259: free((FREE_ARG)(m[nrl]+ncl-NR_END)); 1260: free((FREE_ARG)(m+nrl-NR_END)); 1261: } 1262: 1263: /*************** function subdirf ***********/ 1264: char *subdirf(char fileres[]) 1265: { 1266: /* Caution optionfilefiname is hidden */ 1267: strcpy(tmpout,optionfilefiname); 1268: strcat(tmpout,"/"); /* Add to the right */ 1269: strcat(tmpout,fileres); 1270: return tmpout; 1271: } 1272: 1273: /*************** function subdirf2 ***********/ 1274: char *subdirf2(char fileres[], char *preop) 1275: { 1276: 1277: /* Caution optionfilefiname is hidden */ 1278: strcpy(tmpout,optionfilefiname); 1279: strcat(tmpout,"/"); 1280: strcat(tmpout,preop); 1281: strcat(tmpout,fileres); 1282: return tmpout; 1283: } 1284: 1285: /*************** function subdirf3 ***********/ 1286: char *subdirf3(char fileres[], char *preop, char *preop2) 1287: { 1288: 1289: /* Caution optionfilefiname is hidden */ 1290: strcpy(tmpout,optionfilefiname); 1291: strcat(tmpout,"/"); 1292: strcat(tmpout,preop); 1293: strcat(tmpout,preop2); 1294: strcat(tmpout,fileres); 1295: return tmpout; 1296: } 1297: 1298: char *asc_diff_time(long time_sec, char ascdiff[]) 1299: { 1300: long sec_left, days, hours, minutes; 1301: days = (time_sec) / (60*60*24); 1302: sec_left = (time_sec) % (60*60*24); 1303: hours = (sec_left) / (60*60) ; 1304: sec_left = (sec_left) %(60*60); 1305: minutes = (sec_left) /60; 1306: sec_left = (sec_left) % (60); 1307: sprintf(ascdiff,"%ld day(s) %ld hour(s) %ld minute(s) %ld second(s)",days, hours, minutes, sec_left); 1308: return ascdiff; 1309: } 1310: 1311: /***************** f1dim *************************/ 1312: extern int ncom; 1313: extern double *pcom,*xicom; 1314: extern double (*nrfunc)(double []); 1315: 1316: double f1dim(double x) 1317: { 1318: int j; 1319: double f; 1320: double *xt; 1321: 1322: xt=vector(1,ncom); 1323: for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 1324: f=(*nrfunc)(xt); 1325: free_vector(xt,1,ncom); 1326: return f; 1327: } 1328: 1329: /*****************brent *************************/ 1330: double brent(double ax, double bx, double cx, double (*f)(double), double tol, double *xmin) 1331: { 1332: /* Given a function f, and given a bracketing triplet of abscissas ax, bx, cx (such that bx is 1333: * between ax and cx, and f(bx) is less than both f(ax) and f(cx) ), this routine isolates 1334: * the minimum to a fractional precision of about tol using Brent’s method. The abscissa of 1335: * the minimum is returned as xmin, and the minimum function value is returned as brent , the 1336: * returned function value. 1337: */ 1338: int iter; 1339: double a,b,d,etemp; 1340: double fu=0,fv,fw,fx; 1341: double ftemp=0.; 1342: double p,q,r,tol1,tol2,u,v,w,x,xm; 1343: double e=0.0; 1344: 1345: a=(ax < cx ? ax : cx); 1346: b=(ax > cx ? ax : cx); 1347: x=w=v=bx; 1348: fw=fv=fx=(*f)(x); 1349: for (iter=1;iter<=ITMAX;iter++) { 1350: xm=0.5*(a+b); 1351: tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 1352: /* if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/ 1353: printf(".");fflush(stdout); 1354: fprintf(ficlog,".");fflush(ficlog); 1355: #ifdef DEBUGBRENT 1356: 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); 1357: 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); 1358: /* if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */ 1359: #endif 1360: if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 1361: *xmin=x; 1362: return fx; 1363: } 1364: ftemp=fu; 1365: if (fabs(e) > tol1) { 1366: r=(x-w)*(fx-fv); 1367: q=(x-v)*(fx-fw); 1368: p=(x-v)*q-(x-w)*r; 1369: q=2.0*(q-r); 1370: if (q > 0.0) p = -p; 1371: q=fabs(q); 1372: etemp=e; 1373: e=d; 1374: if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 1375: d=CGOLD*(e=(x >= xm ? a-x : b-x)); 1376: else { 1377: d=p/q; 1378: u=x+d; 1379: if (u-a < tol2 || b-u < tol2) 1380: d=SIGN(tol1,xm-x); 1381: } 1382: } else { 1383: d=CGOLD*(e=(x >= xm ? a-x : b-x)); 1384: } 1385: u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 1386: fu=(*f)(u); 1387: if (fu <= fx) { 1388: if (u >= x) a=x; else b=x; 1389: SHFT(v,w,x,u) 1390: SHFT(fv,fw,fx,fu) 1391: } else { 1392: if (u < x) a=u; else b=u; 1393: if (fu <= fw || w == x) { 1394: v=w; 1395: w=u; 1396: fv=fw; 1397: fw=fu; 1398: } else if (fu <= fv || v == x || v == w) { 1399: v=u; 1400: fv=fu; 1401: } 1402: } 1403: } 1404: nrerror("Too many iterations in brent"); 1405: *xmin=x; 1406: return fx; 1407: } 1408: 1409: /****************** mnbrak ***********************/ 1410: 1411: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 1412: double (*func)(double)) 1413: { /* Given a function func , and given distinct initial points ax and bx , this routine searches in 1414: the downhill direction (defined by the function as evaluated at the initial points) and returns 1415: new points ax , bx , cx that bracket a minimum of the function. Also returned are the function 1416: values at the three points, fa, fb , and fc such that fa > fb and fb < fc. 1417: */ 1418: double ulim,u,r,q, dum; 1419: double fu; 1420: 1421: double scale=10.; 1422: int iterscale=0; 1423: 1424: *fa=(*func)(*ax); /* xta[j]=pcom[j]+(*ax)*xicom[j]; fa=f(xta[j])*/ 1425: *fb=(*func)(*bx); /* xtb[j]=pcom[j]+(*bx)*xicom[j]; fb=f(xtb[j]) */ 1426: 1427: 1428: /* while(*fb != *fb){ /\* *ax should be ok, reducing distance to *ax *\/ */ 1429: /* printf("Warning mnbrak *fb = %lf, *bx=%lf *ax=%lf *fa==%lf iter=%d\n",*fb, *bx, *ax, *fa, iterscale++); */ 1430: /* *bx = *ax - (*ax - *bx)/scale; */ 1431: /* *fb=(*func)(*bx); /\* xtb[j]=pcom[j]+(*bx)*xicom[j]; fb=f(xtb[j]) *\/ */ 1432: /* } */ 1433: 1434: if (*fb > *fa) { 1435: SHFT(dum,*ax,*bx,dum) 1436: SHFT(dum,*fb,*fa,dum) 1437: } 1438: *cx=(*bx)+GOLD*(*bx-*ax); 1439: *fc=(*func)(*cx); 1440: #ifdef DEBUG 1441: printf("mnbrak0 *fb=%.12e *fc=%.12e\n",*fb,*fc); 1442: fprintf(ficlog,"mnbrak0 *fb=%.12e *fc=%.12e\n",*fb,*fc); 1443: #endif 1444: while (*fb > *fc) { /* Declining a,b,c with fa> fb > fc */ 1445: r=(*bx-*ax)*(*fb-*fc); 1446: q=(*bx-*cx)*(*fb-*fa); 1447: u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 1448: (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); /* Minimum abscissa of a parabolic estimated from (a,fa), (b,fb) and (c,fc). */ 1449: ulim=(*bx)+GLIMIT*(*cx-*bx); /* Maximum abscissa where function should be evaluated */ 1450: if ((*bx-u)*(u-*cx) > 0.0) { /* if u_p is between b and c */ 1451: fu=(*func)(u); 1452: #ifdef DEBUG 1453: /* f(x)=A(x-u)**2+f(u) */ 1454: double A, fparabu; 1455: A= (*fb - *fa)/(*bx-*ax)/(*bx+*ax-2*u); 1456: fparabu= *fa - A*(*ax-u)*(*ax-u); 1457: 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); 1458: 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); 1459: /* And thus,it can be that fu > *fc even if fparabu < *fc */ 1460: /* mnbrak (*ax=7.666299858533, *fa=299039.693133272231), (*bx=8.595447774979, *fb=298976.598289369489), 1461: (*cx=10.098840694817, *fc=298946.631474258087), (*u=9.852501168332, fu=298948.773013752128, fparabu=298945.434711494134) */ 1462: /* In that case, there is no bracket in the output! Routine is wrong with many consequences.*/ 1463: #endif 1464: #ifdef MNBRAKORIGINAL 1465: #else 1466: /* if (fu > *fc) { */ 1467: /* #ifdef DEBUG */ 1468: /* printf("mnbrak4 fu > fc \n"); */ 1469: /* fprintf(ficlog, "mnbrak4 fu > fc\n"); */ 1470: /* #endif */ 1471: /* /\* 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 *\\/ *\/ */ 1472: /* /\* SHFT(*fa,*fc,fu,*fc) /\\* (b, u, c) is a bracket while test fb > fc will be fu > fc will exit *\\/ *\/ */ 1473: /* dum=u; /\* Shifting c and u *\/ */ 1474: /* u = *cx; */ 1475: /* *cx = dum; */ 1476: /* dum = fu; */ 1477: /* fu = *fc; */ 1478: /* *fc =dum; */ 1479: /* } else { /\* end *\/ */ 1480: /* #ifdef DEBUG */ 1481: /* printf("mnbrak3 fu < fc \n"); */ 1482: /* fprintf(ficlog, "mnbrak3 fu < fc\n"); */ 1483: /* #endif */ 1484: /* dum=u; /\* Shifting c and u *\/ */ 1485: /* u = *cx; */ 1486: /* *cx = dum; */ 1487: /* dum = fu; */ 1488: /* fu = *fc; */ 1489: /* *fc =dum; */ 1490: /* } */ 1491: #ifdef DEBUG 1492: printf("mnbrak34 fu < or >= fc \n"); 1493: fprintf(ficlog, "mnbrak34 fu < fc\n"); 1494: #endif 1495: dum=u; /* Shifting c and u */ 1496: u = *cx; 1497: *cx = dum; 1498: dum = fu; 1499: fu = *fc; 1500: *fc =dum; 1501: #endif 1502: } else if ((*cx-u)*(u-ulim) > 0.0) { /* u is after c but before ulim */ 1503: #ifdef DEBUG 1504: printf("mnbrak2 u after c but before ulim\n"); 1505: fprintf(ficlog, "mnbrak2 u after c but before ulim\n"); 1506: #endif 1507: fu=(*func)(u); 1508: if (fu < *fc) { 1509: #ifdef DEBUG 1510: printf("mnbrak2 u after c but before ulim AND fu < fc\n"); 1511: fprintf(ficlog, "mnbrak2 u after c but before ulim AND fu <fc \n"); 1512: #endif 1513: SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 1514: SHFT(*fb,*fc,fu,(*func)(u)) 1515: } 1516: } else if ((u-ulim)*(ulim-*cx) >= 0.0) { /* u outside ulim (verifying that ulim is beyond c) */ 1517: #ifdef DEBUG 1518: printf("mnbrak2 u outside ulim (verifying that ulim is beyond c)\n"); 1519: fprintf(ficlog, "mnbrak2 u outside ulim (verifying that ulim is beyond c)\n"); 1520: #endif 1521: u=ulim; 1522: fu=(*func)(u); 1523: } else { /* u could be left to b (if r > q parabola has a maximum) */ 1524: #ifdef DEBUG 1525: printf("mnbrak2 u could be left to b (if r > q parabola has a maximum)\n"); 1526: fprintf(ficlog, "mnbrak2 u could be left to b (if r > q parabola has a maximum)\n"); 1527: #endif 1528: u=(*cx)+GOLD*(*cx-*bx); 1529: fu=(*func)(u); 1530: } /* end tests */ 1531: SHFT(*ax,*bx,*cx,u) 1532: SHFT(*fa,*fb,*fc,fu) 1533: #ifdef DEBUG 1534: 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); 1535: 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); 1536: #endif 1537: } /* end while; ie return (a, b, c, fa, fb, fc) such that a f(b) and fb < f(c) */ 1538: } 1539: 1540: /*************** linmin ************************/ 1541: /* Given an n -dimensional point p[1..n] and an n -dimensional direction xi[1..n] , moves and 1542: resets p to where the function func(p) takes on a minimum along the direction xi from p , 1543: and replaces xi by the actual vector displacement that p was moved. Also returns as fret 1544: the value of func at the returned location p . This is actually all accomplished by calling the 1545: routines mnbrak and brent .*/ 1546: int ncom; 1547: double *pcom,*xicom; 1548: double (*nrfunc)(double []); 1549: 1550: void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 1551: { 1552: double brent(double ax, double bx, double cx, 1553: double (*f)(double), double tol, double *xmin); 1554: double f1dim(double x); 1555: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 1556: double *fc, double (*func)(double)); 1557: int j; 1558: double xx,xmin,bx,ax; 1559: double fx,fb,fa; 1560: 1561: double scale=10., axs, xxs, xxss; /* Scale added for infinity */ 1562: 1563: ncom=n; 1564: pcom=vector(1,n); 1565: xicom=vector(1,n); 1566: nrfunc=func; 1567: for (j=1;j<=n;j++) { 1568: pcom[j]=p[j]; 1569: xicom[j]=xi[j]; 1570: } 1571: 1572: /* axs=0.0; */ 1573: /* xxss=1; /\* 1 and using scale *\/ */ 1574: xxs=1; 1575: /* do{ */ 1576: ax=0.; 1577: xx= xxs; 1578: mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); /* Outputs: xtx[j]=pcom[j]+(*xx)*xicom[j]; fx=f(xtx[j]) */ 1579: /* brackets with inputs ax=0 and xx=1, but points, pcom=p, and directions values, xicom=xi, are sent via f1dim(x) */ 1580: /* 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)) */ 1581: /* Outputs: fa=f(p(j)) and fx=f(p(j) + xxs * xi(j) ) and f(bx)= f(p(j)+ bx* xi(j)) */ 1582: /* Given input ax=axs and xx=xxs, xx might be too far from ax to get a finite f(xx) */ 1583: /* Searches on line, outputs (ax, xx, bx) such that fx < min(fa and fb) */ 1584: /* 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]]*/ 1585: /* if (fx != fx){ */ 1586: /* xxs=xxs/scale; /\* Trying a smaller xx, closer to initial ax=0 *\/ */ 1587: /* 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); */ 1588: /* } */ 1589: /* }while(fx != fx); */ 1590: 1591: #ifdef DEBUGLINMIN 1592: 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); 1593: #endif 1594: *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); /* Giving a bracketting triplet (ax, xx, bx), find a minimum, xmin, according to f1dim, *fret(xmin),*/ 1595: /* fa = f(p[j] + ax * xi[j]), fx = f(p[j] + xx * xi[j]), fb = f(p[j] + bx * xi[j]) */ 1596: /* fmin = f(p[j] + xmin * xi[j]) */ 1597: /* P+lambda n in that direction (lambdamin), with TOL between abscisses */ 1598: /* f1dim(xmin): for (j=1;j<=ncom;j++) xt[j]=pcom[j]+xmin*xicom[j]; */ 1599: #ifdef DEBUG 1600: printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin); 1601: fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin); 1602: #endif 1603: #ifdef DEBUGLINMIN 1604: printf("linmin end "); 1605: #endif 1606: for (j=1;j<=n;j++) { 1607: /* printf(" before xi[%d]=%12.8f", j,xi[j]); */ 1608: xi[j] *= xmin; /* xi rescaled by xmin: if xmin=-1.237 and xi=(1,0,...,0) xi=(-1.237,0,...,0) */ 1609: /* if(xxs <1.0) */ 1610: /* 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 ); */ 1611: p[j] += xi[j]; /* Parameters values are updated accordingly */ 1612: } 1613: /* printf("\n"); */ 1614: #ifdef DEBUGLINMIN 1615: printf("Comparing last *frec(xmin=%12.8f)=%12.8f from Brent and frec(0.)=%12.8f \n", xmin, *fret, (*func)(p)); 1616: for (j=1;j<=n;j++) { 1617: printf(" xi[%d]= %12.7f p[%d]= %12.7f",j,xi[j],j,p[j]); 1618: if(j % ncovmodel == 0) 1619: printf("\n"); 1620: } 1621: #endif 1622: free_vector(xicom,1,n); 1623: free_vector(pcom,1,n); 1624: } 1625: 1626: 1627: /*************** powell ************************/ 1628: /* 1629: Minimization of a function func of n variables. Input consists of an initial starting point 1630: p[1..n] ; an initial matrix xi[1..n][1..n] , whose columns contain the initial set of di- 1631: rections (usually the n unit vectors); and ftol , the fractional tolerance in the function value 1632: such that failure to decrease by more than this amount on one iteration signals doneness. On 1633: output, p is set to the best point found, xi is the then-current direction set, fret is the returned 1634: function value at p , and iter is the number of iterations taken. The routine linmin is used. 1635: */ 1636: void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 1637: double (*func)(double [])) 1638: { 1639: void linmin(double p[], double xi[], int n, double *fret, 1640: double (*func)(double [])); 1641: int i,ibig,j; 1642: double del,t,*pt,*ptt,*xit; 1643: double directest; 1644: double fp,fptt; 1645: double *xits; 1646: int niterf, itmp; 1647: 1648: pt=vector(1,n); 1649: ptt=vector(1,n); 1650: xit=vector(1,n); 1651: xits=vector(1,n); 1652: *fret=(*func)(p); 1653: for (j=1;j<=n;j++) pt[j]=p[j]; 1654: rcurr_time = time(NULL); 1655: for (*iter=1;;++(*iter)) { 1656: fp=(*fret); /* From former iteration or initial value */ 1657: ibig=0; 1658: del=0.0; 1659: rlast_time=rcurr_time; 1660: /* (void) gettimeofday(&curr_time,&tzp); */ 1661: rcurr_time = time(NULL); 1662: curr_time = *localtime(&rcurr_time); 1663: printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, rcurr_time-rlast_time, rcurr_time-rstart_time);fflush(stdout); 1664: fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret,rcurr_time-rlast_time, rcurr_time-rstart_time); fflush(ficlog); 1665: /* fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tm_sec-start_time.tm_sec); */ 1666: for (i=1;i<=n;i++) { 1667: printf(" %d %.12f",i, p[i]); 1668: fprintf(ficlog," %d %.12lf",i, p[i]); 1669: fprintf(ficrespow," %.12lf", p[i]); 1670: } 1671: printf("\n"); 1672: fprintf(ficlog,"\n"); 1673: fprintf(ficrespow,"\n");fflush(ficrespow); 1674: if(*iter <=3){ 1675: tml = *localtime(&rcurr_time); 1676: strcpy(strcurr,asctime(&tml)); 1677: rforecast_time=rcurr_time; 1678: itmp = strlen(strcurr); 1679: if(strcurr[itmp-1]=='\n') /* Windows outputs with a new line */ 1680: strcurr[itmp-1]='\0'; 1681: printf("\nConsidering the time needed for the last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time); 1682: fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time); 1683: for(niterf=10;niterf<=30;niterf+=10){ 1684: rforecast_time=rcurr_time+(niterf-*iter)*(rcurr_time-rlast_time); 1685: forecast_time = *localtime(&rforecast_time); 1686: strcpy(strfor,asctime(&forecast_time)); 1687: itmp = strlen(strfor); 1688: if(strfor[itmp-1]=='\n') 1689: strfor[itmp-1]='\0'; 1690: 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); 1691: 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); 1692: } 1693: } 1694: for (i=1;i<=n;i++) { /* For each direction i */ 1695: for (j=1;j<=n;j++) xit[j]=xi[j][i]; /* Directions stored from previous iteration with previous scales */ 1696: fptt=(*fret); 1697: #ifdef DEBUG 1698: printf("fret=%lf, %lf, %lf \n", *fret, *fret, *fret); 1699: fprintf(ficlog, "fret=%lf, %lf, %lf \n", *fret, *fret, *fret); 1700: #endif 1701: printf("%d",i);fflush(stdout); /* print direction (parameter) i */ 1702: fprintf(ficlog,"%d",i);fflush(ficlog); 1703: linmin(p,xit,n,fret,func); /* Point p[n]. xit[n] has been loaded for direction i as input.*/ 1704: /* Outputs are fret(new point p) p is updated and xit rescaled */ 1705: if (fabs(fptt-(*fret)) > del) { /* We are keeping the max gain on each of the n directions */ 1706: /* because that direction will be replaced unless the gain del is small */ 1707: /* in comparison with the 'probable' gain, mu^2, with the last average direction. */ 1708: /* Unless the n directions are conjugate some gain in the determinant may be obtained */ 1709: /* with the new direction. */ 1710: del=fabs(fptt-(*fret)); 1711: ibig=i; 1712: } 1713: #ifdef DEBUG 1714: printf("%d %.12e",i,(*fret)); 1715: fprintf(ficlog,"%d %.12e",i,(*fret)); 1716: for (j=1;j<=n;j++) { 1717: xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5); 1718: printf(" x(%d)=%.12e",j,xit[j]); 1719: fprintf(ficlog," x(%d)=%.12e",j,xit[j]); 1720: } 1721: for(j=1;j<=n;j++) { 1722: printf(" p(%d)=%.12e",j,p[j]); 1723: fprintf(ficlog," p(%d)=%.12e",j,p[j]); 1724: } 1725: printf("\n"); 1726: fprintf(ficlog,"\n"); 1727: #endif 1728: } /* end loop on each direction i */ 1729: /* Convergence test will use last linmin estimation (fret) and compare former iteration (fp) */ 1730: /* But p and xit have been updated at the end of linmin, *fret corresponds to new p, xit */ 1731: /* New value of last point Pn is not computed, P(n-1) */ 1732: if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) { /* Did we reach enough precision? */ 1733: /* We could compare with a chi^2. chisquare(0.95,ddl=1)=3.84 */ 1734: /* By adding age*age in a model, the new -2LL should be lower and the difference follows a */ 1735: /* a chisquare statistics with 1 degree. To be significant at the 95% level, it should have */ 1736: /* decreased of more than 3.84 */ 1737: /* By adding age*age and V1*age the gain (-2LL) should be more than 5.99 (ddl=2) */ 1738: /* By using V1+V2+V3, the gain should be 7.82, compared with basic 1+age. */ 1739: /* By adding 10 parameters more the gain should be 18.31 */ 1740: 1741: /* Starting the program with initial values given by a former maximization will simply change */ 1742: /* the scales of the directions and the directions, because the are reset to canonical directions */ 1743: /* Thus the first calls to linmin will give new points and better maximizations until fp-(*fret) is */ 1744: /* under the tolerance value. If the tolerance is very small 1.e-9, it could last long. */ 1745: #ifdef DEBUG 1746: int k[2],l; 1747: k[0]=1; 1748: k[1]=-1; 1749: printf("Max: %.12e",(*func)(p)); 1750: fprintf(ficlog,"Max: %.12e",(*func)(p)); 1751: for (j=1;j<=n;j++) { 1752: printf(" %.12e",p[j]); 1753: fprintf(ficlog," %.12e",p[j]); 1754: } 1755: printf("\n"); 1756: fprintf(ficlog,"\n"); 1757: for(l=0;l<=1;l++) { 1758: for (j=1;j<=n;j++) { 1759: ptt[j]=p[j]+(p[j]-pt[j])*k[l]; 1760: printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]); 1761: fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]); 1762: } 1763: printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p))); 1764: fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p))); 1765: } 1766: #endif 1767: 1768: 1769: free_vector(xit,1,n); 1770: free_vector(xits,1,n); 1771: free_vector(ptt,1,n); 1772: free_vector(pt,1,n); 1773: return; 1774: } /* enough precision */ 1775: if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 1776: for (j=1;j<=n;j++) { /* Computes the extrapolated point P_0 + 2 (P_n-P_0) */ 1777: ptt[j]=2.0*p[j]-pt[j]; 1778: xit[j]=p[j]-pt[j]; 1779: pt[j]=p[j]; 1780: } 1781: fptt=(*func)(ptt); /* f_3 */ 1782: #ifdef POWELLF1F3 1783: #else 1784: if (fptt < fp) { /* If extrapolated point is better, decide if we keep that new direction or not */ 1785: #endif 1786: /* (x1 f1=fp), (x2 f2=*fret), (x3 f3=fptt), (xm fm) */ 1787: /* From x1 (P0) distance of x2 is at h and x3 is 2h */ 1788: /* Let f"(x2) be the 2nd derivative equal everywhere. */ 1789: /* Then the parabolic through (x1,f1), (x2,f2) and (x3,f3) */ 1790: /* will reach at f3 = fm + h^2/2 f"m ; f" = (f1 -2f2 +f3 ) / h**2 */ 1791: /* Conditional for using this new direction is that mu^2 = (f1-2f2+f3)^2 /2 < del */ 1792: /* t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); */ 1793: #ifdef NRCORIGINAL 1794: t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)- del*SQR(fp-fptt); /* Original Numerical Recipes in C*/ 1795: #else 1796: t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del); /* Intel compiler doesn't work on one line; bug reported */ 1797: t= t- del*SQR(fp-fptt); 1798: #endif 1799: directest = fp-2.0*(*fret)+fptt - 2.0 * del; /* If del was big enough we change it for a new direction */ 1800: #ifdef DEBUG 1801: 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); 1802: 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); 1803: printf("t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt), 1804: (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt)); 1805: fprintf(ficlog,"t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt), 1806: (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt)); 1807: 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); 1808: 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); 1809: #endif 1810: #ifdef POWELLORIGINAL 1811: if (t < 0.0) { /* Then we use it for new direction */ 1812: #else 1813: if (directest*t < 0.0) { /* Contradiction between both tests */ 1814: printf("directest= %.12lf, t= %.12lf, f1= %.12lf,f2= %.12lf,f3= %.12lf, del= %.12lf\n",directest, t, fp,(*fret),fptt,del); 1815: printf("f1-2f2+f3= %.12lf, f1-f2-del= %.12lf, f1-f3= %.12lf\n",fp-2.0*(*fret)+fptt, fp -(*fret) -del, fp-fptt); 1816: fprintf(ficlog,"directest= %.12lf, t= %.12lf, f1= %.12lf,f2= %.12lf,f3= %.12lf, del= %.12lf\n",directest, t, fp,(*fret),fptt, del); 1817: fprintf(ficlog,"f1-2f2+f3= %.12lf, f1-f2-del= %.12lf, f1-f3= %.12lf\n",fp-2.0*(*fret)+fptt, fp -(*fret) -del, fp-fptt); 1818: } 1819: if (directest < 0.0) { /* Then we use it for new direction */ 1820: #endif 1821: #ifdef DEBUGLINMIN 1822: printf("Before linmin in direction P%d-P0\n",n); 1823: for (j=1;j<=n;j++) { 1824: printf("Before xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]); 1825: if(j % ncovmodel == 0) 1826: printf("\n"); 1827: } 1828: #endif 1829: linmin(p,xit,n,fret,func); /* computes minimum on the extrapolated direction: changes p and rescales xit.*/ 1830: #ifdef DEBUGLINMIN 1831: for (j=1;j<=n;j++) { 1832: printf("After xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]); 1833: if(j % ncovmodel == 0) 1834: printf("\n"); 1835: } 1836: #endif 1837: for (j=1;j<=n;j++) { 1838: xi[j][ibig]=xi[j][n]; /* Replace direction with biggest decrease by last direction n */ 1839: xi[j][n]=xit[j]; /* and this nth direction by the by the average p_0 p_n */ 1840: } 1841: printf("Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig); 1842: fprintf(ficlog,"Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig); 1843: 1844: #ifdef DEBUG 1845: printf("Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig); 1846: fprintf(ficlog,"Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig); 1847: for(j=1;j<=n;j++){ 1848: printf(" %.12e",xit[j]); 1849: fprintf(ficlog," %.12e",xit[j]); 1850: } 1851: printf("\n"); 1852: fprintf(ficlog,"\n"); 1853: #endif 1854: } /* end of t or directest negative */ 1855: #ifdef POWELLF1F3 1856: #else 1857: } /* end if (fptt < fp) */ 1858: #endif 1859: } /* loop iteration */ 1860: } 1861: 1862: /**** Prevalence limit (stable or period prevalence) ****************/ 1863: 1864: double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij) 1865: { 1866: /* Computes the prevalence limit in each live state at age x by left multiplying the unit 1867: matrix by transitions matrix until convergence is reached */ 1868: 1869: int i, ii,j,k; 1870: double min, max, maxmin, maxmax,sumnew=0.; 1871: /* double **matprod2(); */ /* test */ 1872: double **out, cov[NCOVMAX+1], **pmij(); 1873: double **newm; 1874: double agefin, delaymax=50 ; /* Max number of years to converge */ 1875: 1876: for (ii=1;ii<=nlstate+ndeath;ii++) 1877: for (j=1;j<=nlstate+ndeath;j++){ 1878: oldm[ii][j]=(ii==j ? 1.0 : 0.0); 1879: } 1880: 1881: cov[1]=1.; 1882: 1883: /* Even if hstepm = 1, at least one multiplication by the unit matrix */ 1884: for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){ 1885: newm=savm; 1886: /* Covariates have to be included here again */ 1887: cov[2]=agefin; 1888: if(nagesqr==1) 1889: cov[3]= agefin*agefin;; 1890: for (k=1; k<=cptcovn;k++) { 1891: cov[2+nagesqr+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]]; 1892: /*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]]);*/ 1893: } 1894: /*wrong? for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */ 1895: for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]]*cov[2]; 1896: for (k=1; k<=cptcovprod;k++) /* Useless */ 1897: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]] * nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]]; 1898: 1899: /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/ 1900: /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/ 1901: /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/ 1902: /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */ 1903: /* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind *\/ */ 1904: out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /* Bug Valgrind */ 1905: 1906: savm=oldm; 1907: oldm=newm; 1908: maxmax=0.; 1909: for(j=1;j<=nlstate;j++){ 1910: min=1.; 1911: max=0.; 1912: for(i=1; i<=nlstate; i++) { 1913: sumnew=0; 1914: for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k]; 1915: prlim[i][j]= newm[i][j]/(1-sumnew); 1916: /*printf(" prevalim i=%d, j=%d, prmlim[%d][%d]=%f, agefin=%d \n", i, j, i, j, prlim[i][j],(int)agefin);*/ 1917: max=FMAX(max,prlim[i][j]); 1918: min=FMIN(min,prlim[i][j]); 1919: } 1920: maxmin=max-min; 1921: maxmax=FMAX(maxmax,maxmin); 1922: } /* j loop */ 1923: if(maxmax < ftolpl){ 1924: return prlim; 1925: } 1926: } /* age loop */ 1927: return prlim; /* should not reach here */ 1928: } 1929: 1930: /*************** transition probabilities ***************/ 1931: 1932: double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate ) 1933: { 1934: /* According to parameters values stored in x and the covariate's values stored in cov, 1935: computes the probability to be observed in state j being in state i by appying the 1936: model to the ncovmodel covariates (including constant and age). 1937: lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc] 1938: and, according on how parameters are entered, the position of the coefficient xij(nc) of the 1939: ncth covariate in the global vector x is given by the formula: 1940: j=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel 1942: Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation, 1943: sums on j different of i to get 1-pii/pii, deduces pii, and then all pij. 1944: Outputs ps[i][j] the probability to be observed in j being in j according to 1945: the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij] 1946: */ 1947: double s1, lnpijopii; 1948: /*double t34;*/ 1949: int i,j, nc, ii, jj; 1950: 1951: for(i=1; i<= nlstate; i++){ 1952: for(j=1; j<i;j++){ 1953: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){ 1954: /*lnpijopii += param[i][j][nc]*cov[nc];*/ 1955: lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc]; 1956: /* printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */ 1957: } 1958: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */ 1959: /* printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */ 1960: } 1961: for(j=i+1; j<=nlstate+ndeath;j++){ 1962: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){ 1963: /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/ 1964: lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc]; 1965: /* printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */ 1966: } 1967: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */ 1968: } 1969: } 1970: 1971: for(i=1; i<= nlstate; i++){ 1972: s1=0; 1973: for(j=1; j<i; j++){ 1974: s1+=exp(ps[i][j]); /* In fact sums pij/pii */ 1975: /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */ 1976: } 1977: for(j=i+1; j<=nlstate+ndeath; j++){ 1978: s1+=exp(ps[i][j]); /* In fact sums pij/pii */ 1979: /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */ 1980: } 1981: /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */ 1982: ps[i][i]=1./(s1+1.); 1983: /* Computing other pijs */ 1984: for(j=1; j<i; j++) 1985: ps[i][j]= exp(ps[i][j])*ps[i][i]; 1986: for(j=i+1; j<=nlstate+ndeath; j++) 1987: ps[i][j]= exp(ps[i][j])*ps[i][i]; 1988: /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */ 1989: } /* end i */ 1990: 1991: for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){ 1992: for(jj=1; jj<= nlstate+ndeath; jj++){ 1993: ps[ii][jj]=0; 1994: ps[ii][ii]=1; 1995: } 1996: } 1997: 1998: 1999: /* for(ii=1; ii<= nlstate+ndeath; ii++){ */ 2000: /* for(jj=1; jj<= nlstate+ndeath; jj++){ */ 2001: /* printf(" pmij ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */ 2002: /* } */ 2003: /* printf("\n "); */ 2004: /* } */ 2005: /* printf("\n ");printf("%lf ",cov[2]);*/ 2006: /* 2007: for(i=1; i<= npar; i++) printf("%f ",x[i]); 2008: goto end;*/ 2009: return ps; 2010: } 2011: 2012: /**************** Product of 2 matrices ******************/ 2013: 2014: double **matprod2(double **out, double **in,int nrl, int nrh, int ncl, int nch, int ncolol, int ncoloh, double **b) 2015: { 2016: /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times 2017: b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */ 2018: /* in, b, out are matrice of pointers which should have been initialized 2019: before: only the contents of out is modified. The function returns 2020: a pointer to pointers identical to out */ 2021: int i, j, k; 2022: for(i=nrl; i<= nrh; i++) 2023: for(k=ncolol; k<=ncoloh; k++){ 2024: out[i][k]=0.; 2025: for(j=ncl; j<=nch; j++) 2026: out[i][k] +=in[i][j]*b[j][k]; 2027: } 2028: return out; 2029: } 2030: 2031: 2032: /************* Higher Matrix Product ***************/ 2033: 2034: double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij ) 2035: { 2036: /* Computes the transition matrix starting at age 'age' over 2037: 'nhstepm*hstepm*stepm' months (i.e. until 2038: age (in years) age+nhstepm*hstepm*stepm/12) by multiplying 2039: nhstepm*hstepm matrices. 2040: Output is stored in matrix po[i][j][h] for h every 'hstepm' step 2041: (typically every 2 years instead of every month which is too big 2042: for the memory). 2043: Model is determined by parameters x and covariates have to be 2044: included manually here. 2045: 2046: */ 2047: 2048: int i, j, d, h, k; 2049: double **out, cov[NCOVMAX+1]; 2050: double **newm; 2051: double agexact; 2052: 2053: /* Hstepm could be zero and should return the unit matrix */ 2054: for (i=1;i<=nlstate+ndeath;i++) 2055: for (j=1;j<=nlstate+ndeath;j++){ 2056: oldm[i][j]=(i==j ? 1.0 : 0.0); 2057: po[i][j][0]=(i==j ? 1.0 : 0.0); 2058: } 2059: /* Even if hstepm = 1, at least one multiplication by the unit matrix */ 2060: for(h=1; h <=nhstepm; h++){ 2061: for(d=1; d <=hstepm; d++){ 2062: newm=savm; 2063: /* Covariates have to be included here again */ 2064: cov[1]=1.; 2065: agexact=age+((h-1)*hstepm + (d-1))*stepm/YEARM; 2066: cov[2]=agexact; 2067: if(nagesqr==1) 2068: cov[3]= agexact*agexact; 2069: for (k=1; k<=cptcovn;k++) 2070: cov[2+nagesqr+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]]; 2071: for (k=1; k<=cptcovage;k++) /* Should start at cptcovn+1 */ 2072: /* cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */ 2073: cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtab[ij][Tvar[Tage[k]]]]*cov[2]; 2074: for (k=1; k<=cptcovprod;k++) /* Useless because included in cptcovn */ 2075: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]]; 2076: 2077: 2078: /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/ 2079: /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/ 2080: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 2081: pmij(pmmij,cov,ncovmodel,x,nlstate)); 2082: savm=oldm; 2083: oldm=newm; 2084: } 2085: for(i=1; i<=nlstate+ndeath; i++) 2086: for(j=1;j<=nlstate+ndeath;j++) { 2087: po[i][j][h]=newm[i][j]; 2088: /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/ 2089: } 2090: /*printf("h=%d ",h);*/ 2091: } /* end h */ 2092: /* printf("\n H=%d \n",h); */ 2093: return po; 2094: } 2095: 2096: #ifdef NLOPT 2097: double myfunc(unsigned n, const double *p1, double *grad, void *pd){ 2098: double fret; 2099: double *xt; 2100: int j; 2101: myfunc_data *d2 = (myfunc_data *) pd; 2102: /* xt = (p1-1); */ 2103: xt=vector(1,n); 2104: for (j=1;j<=n;j++) xt[j]=p1[j-1]; /* xt[1]=p1[0] */ 2105: 2106: fret=(d2->function)(xt); /* p xt[1]@8 is fine */ 2107: /* fret=(*func)(xt); /\* p xt[1]@8 is fine *\/ */ 2108: printf("Function = %.12lf ",fret); 2109: for (j=1;j<=n;j++) printf(" %d %.8lf", j, xt[j]); 2110: printf("\n"); 2111: free_vector(xt,1,n); 2112: return fret; 2113: } 2114: #endif 2115: 2116: /*************** log-likelihood *************/ 2117: double func( double *x) 2118: { 2119: int i, ii, j, k, mi, d, kk; 2120: double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1]; 2121: double **out; 2122: double sw; /* Sum of weights */ 2123: double lli; /* Individual log likelihood */ 2124: int s1, s2; 2125: double bbh, survp; 2126: long ipmx; 2127: double agexact; 2128: /*extern weight */ 2129: /* We are differentiating ll according to initial status */ 2130: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/ 2131: /*for(i=1;i<imx;i++) 2132: printf(" %d\n",s[4][i]); 2133: */ 2134: 2135: ++countcallfunc; 2136: 2137: cov[1]=1.; 2138: 2139: for(k=1; k<=nlstate; k++) ll[k]=0.; 2140: 2141: if(mle==1){ 2142: for (i=1,ipmx=0, sw=0.; i<=imx; i++){ 2143: /* Computes the values of the ncovmodel covariates of the model 2144: depending if the covariates are fixed or variying (age dependent) and stores them in cov[] 2145: Then computes with function pmij which return a matrix p[i][j] giving the elementary probability 2146: to be observed in j being in i according to the model. 2147: */ 2148: for (k=1; k<=cptcovn;k++){ /* Simple and product covariates without age* products */ 2149: cov[2+nagesqr+k]=covar[Tvar[k]][i]; 2150: } 2151: /* In model V2+V1*V4+age*V3+V3*V2 Tvar[1] is V2, Tvar[2=V1*V4] 2152: is 6, Tvar[3=age*V3] should not be computed because of age Tvar[4=V3*V2] 2153: has been calculated etc */ 2154: for(mi=1; mi<= wav[i]-1; mi++){ 2155: for (ii=1;ii<=nlstate+ndeath;ii++) 2156: for (j=1;j<=nlstate+ndeath;j++){ 2157: oldm[ii][j]=(ii==j ? 1.0 : 0.0); 2158: savm[ii][j]=(ii==j ? 1.0 : 0.0); 2159: } 2160: for(d=0; d<dh[mi][i]; d++){ 2161: newm=savm; 2162: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM; 2163: cov[2]=agexact; 2164: if(nagesqr==1) 2165: cov[3]= agexact*agexact; 2166: for (kk=1; kk<=cptcovage;kk++) { 2167: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact; /* Tage[kk] gives the data-covariate associated with age */ 2168: } 2169: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, 2170: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); 2171: savm=oldm; 2172: oldm=newm; 2173: } /* end mult */ 2174: 2175: /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */ 2176: /* But now since version 0.9 we anticipate for bias at large stepm. 2177: * If stepm is larger than one month (smallest stepm) and if the exact delay 2178: * (in months) between two waves is not a multiple of stepm, we rounded to 2179: * the nearest (and in case of equal distance, to the lowest) interval but now 2180: * we keep into memory the bias bh[mi][i] and also the previous matrix product 2181: * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the 2182: * probability in order to take into account the bias as a fraction of the way 2183: * from savm to out if bh is negative or even beyond if bh is positive. bh varies 2184: * -stepm/2 to stepm/2 . 2185: * For stepm=1 the results are the same as for previous versions of Imach. 2186: * For stepm > 1 the results are less biased than in previous versions. 2187: */ 2188: s1=s[mw[mi][i]][i]; 2189: s2=s[mw[mi+1][i]][i]; 2190: bbh=(double)bh[mi][i]/(double)stepm; 2191: /* bias bh is positive if real duration 2192: * is higher than the multiple of stepm and negative otherwise. 2193: */ 2194: /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/ 2195: if( s2 > nlstate){ 2196: /* i.e. if s2 is a death state and if the date of death is known 2197: then the contribution to the likelihood is the probability to 2198: die between last step unit time and current step unit time, 2199: which is also equal to probability to die before dh 2200: minus probability to die before dh-stepm . 2201: In version up to 0.92 likelihood was computed 2202: as if date of death was unknown. Death was treated as any other 2203: health state: the date of the interview describes the actual state 2204: and not the date of a change in health state. The former idea was 2205: to consider that at each interview the state was recorded 2206: (healthy, disable or death) and IMaCh was corrected; but when we 2207: introduced the exact date of death then we should have modified 2208: the contribution of an exact death to the likelihood. This new 2209: contribution is smaller and very dependent of the step unit 2210: stepm. It is no more the probability to die between last interview 2211: and month of death but the probability to survive from last 2212: interview up to one month before death multiplied by the 2213: probability to die within a month. Thanks to Chris 2214: Jackson for correcting this bug. Former versions increased 2215: mortality artificially. The bad side is that we add another loop 2216: which slows down the processing. The difference can be up to 10% 2217: lower mortality. 2218: */ 2219: /* If, at the beginning of the maximization mostly, the 2220: cumulative probability or probability to be dead is 2221: constant (ie = 1) over time d, the difference is equal to 2222: 0. out[s1][3] = savm[s1][3]: probability, being at state 2223: s1 at precedent wave, to be dead a month before current 2224: wave is equal to probability, being at state s1 at 2225: precedent wave, to be dead at mont of the current 2226: wave. Then the observed probability (that this person died) 2227: is null according to current estimated parameter. In fact, 2228: it should be very low but not zero otherwise the log go to 2229: infinity. 2230: */ 2231: /* #ifdef INFINITYORIGINAL */ 2232: /* lli=log(out[s1][s2] - savm[s1][s2]); */ 2233: /* #else */ 2234: /* if ((out[s1][s2] - savm[s1][s2]) < mytinydouble) */ 2235: /* lli=log(mytinydouble); */ 2236: /* else */ 2237: /* lli=log(out[s1][s2] - savm[s1][s2]); */ 2238: /* #endif */ 2239: lli=log(out[s1][s2] - savm[s1][s2]); 2240: 2241: } else if (s2==-2) { 2242: for (j=1,survp=0. ; j<=nlstate; j++) 2243: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j]; 2244: /*survp += out[s1][j]; */ 2245: lli= log(survp); 2246: } 2247: 2248: else if (s2==-4) { 2249: for (j=3,survp=0. ; j<=nlstate; j++) 2250: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j]; 2251: lli= log(survp); 2252: } 2253: 2254: else if (s2==-5) { 2255: for (j=1,survp=0. ; j<=2; j++) 2256: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j]; 2257: lli= log(survp); 2258: } 2259: 2260: else{ 2261: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */ 2262: /* 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 */ 2263: } 2264: /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/ 2265: /*if(lli ==000.0)*/ 2266: /*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); */ 2267: ipmx +=1; 2268: sw += weight[i]; 2269: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli; 2270: /* if (lli < log(mytinydouble)){ */ 2271: /* 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); */ 2272: /* 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]); */ 2273: /* } */ 2274: } /* end of wave */ 2275: } /* end of individual */ 2276: } else if(mle==2){ 2277: for (i=1,ipmx=0, sw=0.; i<=imx; i++){ 2278: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i]; 2279: for(mi=1; mi<= wav[i]-1; mi++){ 2280: for (ii=1;ii<=nlstate+ndeath;ii++) 2281: for (j=1;j<=nlstate+ndeath;j++){ 2282: oldm[ii][j]=(ii==j ? 1.0 : 0.0); 2283: savm[ii][j]=(ii==j ? 1.0 : 0.0); 2284: } 2285: for(d=0; d<=dh[mi][i]; d++){ 2286: newm=savm; 2287: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM; 2288: cov[2]=agexact; 2289: if(nagesqr==1) 2290: cov[3]= agexact*agexact; 2291: for (kk=1; kk<=cptcovage;kk++) { 2292: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact; 2293: } 2294: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, 2295: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); 2296: savm=oldm; 2297: oldm=newm; 2298: } /* end mult */ 2299: 2300: s1=s[mw[mi][i]][i]; 2301: s2=s[mw[mi+1][i]][i]; 2302: bbh=(double)bh[mi][i]/(double)stepm; 2303: 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 */ 2304: ipmx +=1; 2305: sw += weight[i]; 2306: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli; 2307: } /* end of wave */ 2308: } /* end of individual */ 2309: } else if(mle==3){ /* exponential inter-extrapolation */ 2310: for (i=1,ipmx=0, sw=0.; i<=imx; i++){ 2311: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i]; 2312: for(mi=1; mi<= wav[i]-1; mi++){ 2313: for (ii=1;ii<=nlstate+ndeath;ii++) 2314: for (j=1;j<=nlstate+ndeath;j++){ 2315: oldm[ii][j]=(ii==j ? 1.0 : 0.0); 2316: savm[ii][j]=(ii==j ? 1.0 : 0.0); 2317: } 2318: for(d=0; d<dh[mi][i]; d++){ 2319: newm=savm; 2320: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM; 2321: cov[2]=agexact; 2322: if(nagesqr==1) 2323: cov[3]= agexact*agexact; 2324: for (kk=1; kk<=cptcovage;kk++) { 2325: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact; 2326: } 2327: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, 2328: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); 2329: savm=oldm; 2330: oldm=newm; 2331: } /* end mult */ 2332: 2333: s1=s[mw[mi][i]][i]; 2334: s2=s[mw[mi+1][i]][i]; 2335: bbh=(double)bh[mi][i]/(double)stepm; 2336: 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 */ 2337: ipmx +=1; 2338: sw += weight[i]; 2339: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli; 2340: } /* end of wave */ 2341: } /* end of individual */ 2342: }else if (mle==4){ /* ml=4 no inter-extrapolation */ 2343: for (i=1,ipmx=0, sw=0.; i<=imx; i++){ 2344: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i]; 2345: for(mi=1; mi<= wav[i]-1; mi++){ 2346: for (ii=1;ii<=nlstate+ndeath;ii++) 2347: for (j=1;j<=nlstate+ndeath;j++){ 2348: oldm[ii][j]=(ii==j ? 1.0 : 0.0); 2349: savm[ii][j]=(ii==j ? 1.0 : 0.0); 2350: } 2351: for(d=0; d<dh[mi][i]; d++){ 2352: newm=savm; 2353: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM; 2354: cov[2]=agexact; 2355: if(nagesqr==1) 2356: cov[3]= agexact*agexact; 2357: for (kk=1; kk<=cptcovage;kk++) { 2358: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact; 2359: } 2360: 2361: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, 2362: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); 2363: savm=oldm; 2364: oldm=newm; 2365: } /* end mult */ 2366: 2367: s1=s[mw[mi][i]][i]; 2368: s2=s[mw[mi+1][i]][i]; 2369: if( s2 > nlstate){ 2370: lli=log(out[s1][s2] - savm[s1][s2]); 2371: }else{ 2372: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */ 2373: } 2374: ipmx +=1; 2375: sw += weight[i]; 2376: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli; 2377: /* 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]); */ 2378: } /* end of wave */ 2379: } /* end of individual */ 2380: }else{ /* ml=5 no inter-extrapolation no jackson =0.8a */ 2381: for (i=1,ipmx=0, sw=0.; i<=imx; i++){ 2382: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i]; 2383: for(mi=1; mi<= wav[i]-1; mi++){ 2384: for (ii=1;ii<=nlstate+ndeath;ii++) 2385: for (j=1;j<=nlstate+ndeath;j++){ 2386: oldm[ii][j]=(ii==j ? 1.0 : 0.0); 2387: savm[ii][j]=(ii==j ? 1.0 : 0.0); 2388: } 2389: for(d=0; d<dh[mi][i]; d++){ 2390: newm=savm; 2391: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM; 2392: cov[2]=agexact; 2393: if(nagesqr==1) 2394: cov[3]= agexact*agexact; 2395: for (kk=1; kk<=cptcovage;kk++) { 2396: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact; 2397: } 2398: 2399: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, 2400: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); 2401: savm=oldm; 2402: oldm=newm; 2403: } /* end mult */ 2404: 2405: s1=s[mw[mi][i]][i]; 2406: s2=s[mw[mi+1][i]][i]; 2407: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */ 2408: ipmx +=1; 2409: sw += weight[i]; 2410: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli; 2411: /*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]);*/ 2412: } /* end of wave */ 2413: } /* end of individual */ 2414: } /* End of if */ 2415: for(k=1,l=0.; k<=nlstate; k++) l += ll[k]; 2416: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */ 2417: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */ 2418: return -l; 2419: } 2420: 2421: /*************** log-likelihood *************/ 2422: double funcone( double *x) 2423: { 2424: /* Same as likeli but slower because of a lot of printf and if */ 2425: int i, ii, j, k, mi, d, kk; 2426: double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1]; 2427: double **out; 2428: double lli; /* Individual log likelihood */ 2429: double llt; 2430: int s1, s2; 2431: double bbh, survp; 2432: double agexact; 2433: /*extern weight */ 2434: /* We are differentiating ll according to initial status */ 2435: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/ 2436: /*for(i=1;i<imx;i++) 2437: printf(" %d\n",s[4][i]); 2438: */ 2439: cov[1]=1.; 2440: 2441: for(k=1; k<=nlstate; k++) ll[k]=0.; 2442: 2443: for (i=1,ipmx=0, sw=0.; i<=imx; i++){ 2444: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i]; 2445: for(mi=1; mi<= wav[i]-1; mi++){ 2446: for (ii=1;ii<=nlstate+ndeath;ii++) 2447: for (j=1;j<=nlstate+ndeath;j++){ 2448: oldm[ii][j]=(ii==j ? 1.0 : 0.0); 2449: savm[ii][j]=(ii==j ? 1.0 : 0.0); 2450: } 2451: for(d=0; d<dh[mi][i]; d++){ 2452: newm=savm; 2453: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM; 2454: cov[2]=agexact; 2455: if(nagesqr==1) 2456: cov[3]= agexact*agexact; 2457: for (kk=1; kk<=cptcovage;kk++) { 2458: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact; 2459: } 2460: 2461: /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */ 2462: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, 2463: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); 2464: /* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, */ 2465: /* 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); */ 2466: savm=oldm; 2467: oldm=newm; 2468: } /* end mult */ 2469: 2470: s1=s[mw[mi][i]][i]; 2471: s2=s[mw[mi+1][i]][i]; 2472: bbh=(double)bh[mi][i]/(double)stepm; 2473: /* bias is positive if real duration 2474: * is higher than the multiple of stepm and negative otherwise. 2475: */ 2476: if( s2 > nlstate && (mle <5) ){ /* Jackson */ 2477: lli=log(out[s1][s2] - savm[s1][s2]); 2478: } else if (s2==-2) { 2479: for (j=1,survp=0. ; j<=nlstate; j++) 2480: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j]; 2481: lli= log(survp); 2482: }else if (mle==1){ 2483: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */ 2484: } else if(mle==2){ 2485: 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 */ 2486: } else if(mle==3){ /* exponential inter-extrapolation */ 2487: 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 */ 2488: } else if (mle==4){ /* mle=4 no inter-extrapolation */ 2489: lli=log(out[s1][s2]); /* Original formula */ 2490: } else{ /* mle=0 back to 1 */ 2491: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */ 2492: /*lli=log(out[s1][s2]); */ /* Original formula */ 2493: } /* End of if */ 2494: ipmx +=1; 2495: sw += weight[i]; 2496: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli; 2497: /*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]); */ 2498: if(globpr){ 2499: fprintf(ficresilk,"%9ld %6d %2d %2d %1d %1d %3d %11.6f %8.4f\ 2500: %11.6f %11.6f %11.6f ", \ 2501: num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i], 2502: 2*weight[i]*lli,out[s1][s2],savm[s1][s2]); 2503: for(k=1,llt=0.,l=0.; k<=nlstate; k++){ 2504: llt +=ll[k]*gipmx/gsw; 2505: fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw); 2506: } 2507: fprintf(ficresilk," %10.6f\n", -llt); 2508: } 2509: } /* end of wave */ 2510: } /* end of individual */ 2511: for(k=1,l=0.; k<=nlstate; k++) l += ll[k]; 2512: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */ 2513: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */ 2514: if(globpr==0){ /* First time we count the contributions and weights */ 2515: gipmx=ipmx; 2516: gsw=sw; 2517: } 2518: return -l; 2519: } 2520: 2521: 2522: /*************** function likelione ***********/ 2523: void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double [])) 2524: { 2525: /* This routine should help understanding what is done with 2526: the selection of individuals/waves and 2527: to check the exact contribution to the likelihood. 2528: Plotting could be done. 2529: */ 2530: int k; 2531: 2532: if(*globpri !=0){ /* Just counts and sums, no printings */ 2533: strcpy(fileresilk,"ilk"); 2534: strcat(fileresilk,fileres); 2535: if((ficresilk=fopen(fileresilk,"w"))==NULL) { 2536: printf("Problem with resultfile: %s\n", fileresilk); 2537: fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk); 2538: } 2539: 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"); 2540: fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav "); 2541: /* i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */ 2542: for(k=1; k<=nlstate; k++) 2543: fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k); 2544: fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n"); 2545: } 2546: 2547: *fretone=(*funcone)(p); 2548: if(*globpri !=0){ 2549: fclose(ficresilk); 2550: fprintf(fichtm,"\n File of contributions to the likelihood: <a href=\"%s\">%s</a> \n",subdirf(fileresilk),subdirf(fileresilk)); 2551: fflush(fichtm); 2552: } 2553: return; 2554: } 2555: 2556: 2557: /*********** Maximum Likelihood Estimation ***************/ 2558: 2559: void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double [])) 2560: { 2561: int i,j, iter=0; 2562: double **xi; 2563: double fret; 2564: double fretone; /* Only one call to likelihood */ 2565: /* char filerespow[FILENAMELENGTH];*/ 2566: 2567: #ifdef NLOPT 2568: int creturn; 2569: nlopt_opt opt; 2570: /* double lb[9] = { -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL }; /\* lower bounds *\/ */ 2571: double *lb; 2572: double minf; /* the minimum objective value, upon return */ 2573: double * p1; /* Shifted parameters from 0 instead of 1 */ 2574: myfunc_data dinst, *d = &dinst; 2575: #endif 2576: 2577: 2578: xi=matrix(1,npar,1,npar); 2579: for (i=1;i<=npar;i++) 2580: for (j=1;j<=npar;j++) 2581: xi[i][j]=(i==j ? 1.0 : 0.0); 2582: printf("Powell\n"); fprintf(ficlog,"Powell\n"); 2583: strcpy(filerespow,"pow"); 2584: strcat(filerespow,fileres); 2585: if((ficrespow=fopen(filerespow,"w"))==NULL) { 2586: printf("Problem with resultfile: %s\n", filerespow); 2587: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow); 2588: } 2589: fprintf(ficrespow,"# Powell\n# iter -2*LL"); 2590: for (i=1;i<=nlstate;i++) 2591: for(j=1;j<=nlstate+ndeath;j++) 2592: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j); 2593: fprintf(ficrespow,"\n"); 2594: #ifdef POWELL 2595: powell(p,xi,npar,ftol,&iter,&fret,func); 2596: #endif 2597: 2598: #ifdef NLOPT 2599: #ifdef NEWUOA 2600: opt = nlopt_create(NLOPT_LN_NEWUOA,npar); 2601: #else 2602: opt = nlopt_create(NLOPT_LN_BOBYQA,npar); 2603: #endif 2604: lb=vector(0,npar-1); 2605: for (i=0;i<npar;i++) lb[i]= -HUGE_VAL; 2606: nlopt_set_lower_bounds(opt, lb); 2607: nlopt_set_initial_step1(opt, 0.1); 2608: 2609: p1= (p+1); /* p *(p+1)@8 and p *(p1)@8 are equal p1[0]=p[1] */ 2610: d->function = func; 2611: printf(" Func %.12lf \n",myfunc(npar,p1,NULL,d)); 2612: nlopt_set_min_objective(opt, myfunc, d); 2613: nlopt_set_xtol_rel(opt, ftol); 2614: if ((creturn=nlopt_optimize(opt, p1, &minf)) < 0) { 2615: printf("nlopt failed! %d\n",creturn); 2616: } 2617: else { 2618: printf("found minimum after %d evaluations (NLOPT=%d)\n", countcallfunc ,NLOPT); 2619: printf("found minimum at f(%g,%g) = %0.10g\n", p[0], p[1], minf); 2620: iter=1; /* not equal */ 2621: } 2622: nlopt_destroy(opt); 2623: #endif 2624: free_matrix(xi,1,npar,1,npar); 2625: fclose(ficrespow); 2626: printf("#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p)); 2627: fprintf(ficlog,"#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p)); 2628: fprintf(ficres,"#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p)); 2629: 2630: } 2631: 2632: /**** Computes Hessian and covariance matrix ***/ 2633: void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double [])) 2634: { 2635: double **a,**y,*x,pd; 2636: double **hess; 2637: int i, j; 2638: int *indx; 2639: 2640: double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar); 2641: double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar); 2642: void lubksb(double **a, int npar, int *indx, double b[]) ; 2643: void ludcmp(double **a, int npar, int *indx, double *d) ; 2644: double gompertz(double p[]); 2645: hess=matrix(1,npar,1,npar); 2646: 2647: printf("\nCalculation of the hessian matrix. Wait...\n"); 2648: fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n"); 2649: for (i=1;i<=npar;i++){ 2650: printf("%d",i);fflush(stdout); 2651: fprintf(ficlog,"%d",i);fflush(ficlog); 2652: 2653: hess[i][i]=hessii(p,ftolhess,i,delti,func,npar); 2654: 2655: /* printf(" %f ",p[i]); 2656: printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/ 2657: } 2658: 2659: for (i=1;i<=npar;i++) { 2660: for (j=1;j<=npar;j++) { 2661: if (j>i) { 2662: printf(".%d%d",i,j);fflush(stdout); 2663: fprintf(ficlog,".%d%d",i,j);fflush(ficlog); 2664: hess[i][j]=hessij(p,delti,i,j,func,npar); 2665: 2666: hess[j][i]=hess[i][j]; 2667: /*printf(" %lf ",hess[i][j]);*/ 2668: } 2669: } 2670: } 2671: printf("\n"); 2672: fprintf(ficlog,"\n"); 2673: 2674: printf("\nInverting the hessian to get the covariance matrix. Wait...\n"); 2675: fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n"); 2676: 2677: a=matrix(1,npar,1,npar); 2678: y=matrix(1,npar,1,npar); 2679: x=vector(1,npar); 2680: indx=ivector(1,npar); 2681: for (i=1;i<=npar;i++) 2682: for (j=1;j<=npar;j++) a[i][j]=hess[i][j]; 2683: ludcmp(a,npar,indx,&pd); 2684: 2685: for (j=1;j<=npar;j++) { 2686: for (i=1;i<=npar;i++) x[i]=0; 2687: x[j]=1; 2688: lubksb(a,npar,indx,x); 2689: for (i=1;i<=npar;i++){ 2690: matcov[i][j]=x[i]; 2691: } 2692: } 2693: 2694: printf("\n#Hessian matrix#\n"); 2695: fprintf(ficlog,"\n#Hessian matrix#\n"); 2696: for (i=1;i<=npar;i++) { 2697: for (j=1;j<=npar;j++) { 2698: printf("%.3e ",hess[i][j]); 2699: fprintf(ficlog,"%.3e ",hess[i][j]); 2700: } 2701: printf("\n"); 2702: fprintf(ficlog,"\n"); 2703: } 2704: 2705: /* Recompute Inverse */ 2706: for (i=1;i<=npar;i++) 2707: for (j=1;j<=npar;j++) a[i][j]=matcov[i][j]; 2708: ludcmp(a,npar,indx,&pd); 2709: 2710: /* printf("\n#Hessian matrix recomputed#\n"); 2711: 2712: for (j=1;j<=npar;j++) { 2713: for (i=1;i<=npar;i++) x[i]=0; 2714: x[j]=1; 2715: lubksb(a,npar,indx,x); 2716: for (i=1;i<=npar;i++){ 2717: y[i][j]=x[i]; 2718: printf("%.3e ",y[i][j]); 2719: fprintf(ficlog,"%.3e ",y[i][j]); 2720: } 2721: printf("\n"); 2722: fprintf(ficlog,"\n"); 2723: } 2724: */ 2725: 2726: free_matrix(a,1,npar,1,npar); 2727: free_matrix(y,1,npar,1,npar); 2728: free_vector(x,1,npar); 2729: free_ivector(indx,1,npar); 2730: free_matrix(hess,1,npar,1,npar); 2731: 2732: 2733: } 2734: 2735: /*************** hessian matrix ****************/ 2736: double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar) 2737: { 2738: int i; 2739: int l=1, lmax=20; 2740: double k1,k2; 2741: double p2[MAXPARM+1]; /* identical to x */ 2742: double res; 2743: double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4; 2744: double fx; 2745: int k=0,kmax=10; 2746: double l1; 2747: 2748: fx=func(x); 2749: for (i=1;i<=npar;i++) p2[i]=x[i]; 2750: for(l=0 ; l <=lmax; l++){ /* Enlarging the zone around the Maximum */ 2751: l1=pow(10,l); 2752: delts=delt; 2753: for(k=1 ; k <kmax; k=k+1){ 2754: delt = delta*(l1*k); 2755: p2[theta]=x[theta] +delt; 2756: k1=func(p2)-fx; /* Might be negative if too close to the theoretical maximum */ 2757: p2[theta]=x[theta]-delt; 2758: k2=func(p2)-fx; 2759: /*res= (k1-2.0*fx+k2)/delt/delt; */ 2760: res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */ 2761: 2762: #ifdef DEBUGHESS 2763: 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); 2764: 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); 2765: #endif 2766: /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */ 2767: if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){ 2768: k=kmax; 2769: } 2770: else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */ 2771: k=kmax; l=lmax*10; 2772: } 2773: else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 2774: delts=delt; 2775: } 2776: } 2777: } 2778: delti[theta]=delts; 2779: return res; 2780: 2781: } 2782: 2783: double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar) 2784: { 2785: int i; 2786: int l=1, lmax=20; 2787: double k1,k2,k3,k4,res,fx; 2788: double p2[MAXPARM+1]; 2789: int k; 2790: 2791: fx=func(x); 2792: for (k=1; k<=2; k++) { 2793: for (i=1;i<=npar;i++) p2[i]=x[i]; 2794: p2[thetai]=x[thetai]+delti[thetai]/k; 2795: p2[thetaj]=x[thetaj]+delti[thetaj]/k; 2796: k1=func(p2)-fx; 2797: 2798: p2[thetai]=x[thetai]+delti[thetai]/k; 2799: p2[thetaj]=x[thetaj]-delti[thetaj]/k; 2800: k2=func(p2)-fx; 2801: 2802: p2[thetai]=x[thetai]-delti[thetai]/k; 2803: p2[thetaj]=x[thetaj]+delti[thetaj]/k; 2804: k3=func(p2)-fx; 2805: 2806: p2[thetai]=x[thetai]-delti[thetai]/k; 2807: p2[thetaj]=x[thetaj]-delti[thetaj]/k; 2808: k4=func(p2)-fx; 2809: res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */ 2810: #ifdef DEBUG 2811: 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); 2812: 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); 2813: #endif 2814: } 2815: return res; 2816: } 2817: 2818: /************** Inverse of matrix **************/ 2819: void ludcmp(double **a, int n, int *indx, double *d) 2820: { 2821: int i,imax,j,k; 2822: double big,dum,sum,temp; 2823: double *vv; 2824: 2825: vv=vector(1,n); 2826: *d=1.0; 2827: for (i=1;i<=n;i++) { 2828: big=0.0; 2829: for (j=1;j<=n;j++) 2830: if ((temp=fabs(a[i][j])) > big) big=temp; 2831: if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 2832: vv[i]=1.0/big; 2833: } 2834: for (j=1;j<=n;j++) { 2835: for (i=1;i<j;i++) { 2836: sum=a[i][j]; 2837: for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 2838: a[i][j]=sum; 2839: } 2840: big=0.0; 2841: for (i=j;i<=n;i++) { 2842: sum=a[i][j]; 2843: for (k=1;k<j;k++) 2844: sum -= a[i][k]*a[k][j]; 2845: a[i][j]=sum; 2846: if ( (dum=vv[i]*fabs(sum)) >= big) { 2847: big=dum; 2848: imax=i; 2849: } 2850: } 2851: if (j != imax) { 2852: for (k=1;k<=n;k++) { 2853: dum=a[imax][k]; 2854: a[imax][k]=a[j][k]; 2855: a[j][k]=dum; 2856: } 2857: *d = -(*d); 2858: vv[imax]=vv[j]; 2859: } 2860: indx[j]=imax; 2861: if (a[j][j] == 0.0) a[j][j]=TINY; 2862: if (j != n) { 2863: dum=1.0/(a[j][j]); 2864: for (i=j+1;i<=n;i++) a[i][j] *= dum; 2865: } 2866: } 2867: free_vector(vv,1,n); /* Doesn't work */ 2868: ; 2869: } 2870: 2871: void lubksb(double **a, int n, int *indx, double b[]) 2872: { 2873: int i,ii=0,ip,j; 2874: double sum; 2875: 2876: for (i=1;i<=n;i++) { 2877: ip=indx[i]; 2878: sum=b[ip]; 2879: b[ip]=b[i]; 2880: if (ii) 2881: for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 2882: else if (sum) ii=i; 2883: b[i]=sum; 2884: } 2885: for (i=n;i>=1;i--) { 2886: sum=b[i]; 2887: for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 2888: b[i]=sum/a[i][i]; 2889: } 2890: } 2891: 2892: void pstamp(FILE *fichier) 2893: { 2894: fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart); 2895: } 2896: 2897: /************ Frequencies ********************/ 2898: 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[]) 2899: { /* Some frequencies */ 2900: 2901: int i, m, jk, j1, bool, z1,j; 2902: int first; 2903: double ***freq; /* Frequencies */ 2904: double *pp, **prop; 2905: double pos,posprop, k2, dateintsum=0,k2cpt=0; 2906: char fileresp[FILENAMELENGTH]; 2907: 2908: pp=vector(1,nlstate); 2909: prop=matrix(1,nlstate,iagemin,iagemax+3); 2910: strcpy(fileresp,"p"); 2911: strcat(fileresp,fileres); 2912: if((ficresp=fopen(fileresp,"w"))==NULL) { 2913: printf("Problem with prevalence resultfile: %s\n", fileresp); 2914: fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp); 2915: exit(0); 2916: } 2917: freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3); 2918: j1=0; 2919: 2920: j=cptcoveff; 2921: if (cptcovn<1) {j=1;ncodemax[1]=1;} 2922: 2923: first=1; 2924: 2925: /* for(k1=1; k1<=j ; k1++){ */ /* Loop on covariates */ 2926: /* for(i1=1; i1<=ncodemax[k1];i1++){ */ /* Now it is 2 */ 2927: /* j1++; */ 2928: for (j1 = 1; j1 <= (int) pow(2,cptcoveff); j1++){ 2929: /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]); 2930: scanf("%d", i);*/ 2931: for (i=-5; i<=nlstate+ndeath; i++) 2932: for (jk=-5; jk<=nlstate+ndeath; jk++) 2933: for(m=iagemin; m <= iagemax+3; m++) 2934: freq[i][jk][m]=0; 2935: 2936: for (i=1; i<=nlstate; i++) 2937: for(m=iagemin; m <= iagemax+3; m++) 2938: prop[i][m]=0; 2939: 2940: dateintsum=0; 2941: k2cpt=0; 2942: for (i=1; i<=imx; i++) { 2943: bool=1; 2944: if (cptcovn>0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */ 2945: for (z1=1; z1<=cptcoveff; z1++) 2946: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]){ 2947: /* Tests if the value of each of the covariates of i is equal to filter j1 */ 2948: bool=0; 2949: /* 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", 2950: bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtab[j1][z1], 2951: j1,z1,nbcode[Tvaraff[z1]][codtab[j1][z1]],j1);*/ 2952: /* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtab[7][3]=1 and nbcde[3][?]=1*/ 2953: } 2954: } 2955: 2956: if (bool==1){ 2957: for(m=firstpass; m<=lastpass; m++){ 2958: k2=anint[m][i]+(mint[m][i]/12.); 2959: /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/ 2960: if(agev[m][i]==0) agev[m][i]=iagemax+1; 2961: if(agev[m][i]==1) agev[m][i]=iagemax+2; 2962: if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i]; 2963: if (m<lastpass) { 2964: freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i]; 2965: freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i]; 2966: } 2967: 2968: if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) { 2969: dateintsum=dateintsum+k2; 2970: k2cpt++; 2971: } 2972: /*}*/ 2973: } 2974: } 2975: } /* end i */ 2976: 2977: /* fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/ 2978: pstamp(ficresp); 2979: if (cptcovn>0) { 2980: fprintf(ficresp, "\n#********** Variable "); 2981: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]); 2982: fprintf(ficresp, "**********\n#"); 2983: fprintf(ficlog, "\n#********** Variable "); 2984: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficlog, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]); 2985: fprintf(ficlog, "**********\n#"); 2986: } 2987: for(i=1; i<=nlstate;i++) 2988: fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i); 2989: fprintf(ficresp, "\n"); 2990: 2991: for(i=iagemin; i <= iagemax+3; i++){ 2992: if(i==iagemax+3){ 2993: fprintf(ficlog,"Total"); 2994: }else{ 2995: if(first==1){ 2996: first=0; 2997: printf("See log file for details...\n"); 2998: } 2999: fprintf(ficlog,"Age %d", i); 3000: } 3001: for(jk=1; jk <=nlstate ; jk++){ 3002: for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++) 3003: pp[jk] += freq[jk][m][i]; 3004: } 3005: for(jk=1; jk <=nlstate ; jk++){ 3006: for(m=-1, pos=0; m <=0 ; m++) 3007: pos += freq[jk][m][i]; 3008: if(pp[jk]>=1.e-10){ 3009: if(first==1){ 3010: printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]); 3011: } 3012: fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]); 3013: }else{ 3014: if(first==1) 3015: printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk); 3016: fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk); 3017: } 3018: } 3019: 3020: for(jk=1; jk <=nlstate ; jk++){ 3021: for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++) 3022: pp[jk] += freq[jk][m][i]; 3023: } 3024: for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){ 3025: pos += pp[jk]; 3026: posprop += prop[jk][i]; 3027: } 3028: for(jk=1; jk <=nlstate ; jk++){ 3029: if(pos>=1.e-5){ 3030: if(first==1) 3031: printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos); 3032: fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos); 3033: }else{ 3034: if(first==1) 3035: printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk); 3036: fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk); 3037: } 3038: if( i <= iagemax){ 3039: if(pos>=1.e-5){ 3040: fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop); 3041: /*probs[i][jk][j1]= pp[jk]/pos;*/ 3042: /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/ 3043: } 3044: else 3045: fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop); 3046: } 3047: } 3048: 3049: for(jk=-1; jk <=nlstate+ndeath; jk++) 3050: for(m=-1; m <=nlstate+ndeath; m++) 3051: if(freq[jk][m][i] !=0 ) { 3052: if(first==1) 3053: printf(" %d%d=%.0f",jk,m,freq[jk][m][i]); 3054: fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]); 3055: } 3056: if(i <= iagemax) 3057: fprintf(ficresp,"\n"); 3058: if(first==1) 3059: printf("Others in log...\n"); 3060: fprintf(ficlog,"\n"); 3061: } 3062: /*}*/ 3063: } 3064: dateintmean=dateintsum/k2cpt; 3065: 3066: fclose(ficresp); 3067: free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3); 3068: free_vector(pp,1,nlstate); 3069: free_matrix(prop,1,nlstate,iagemin, iagemax+3); 3070: /* End of Freq */ 3071: } 3072: 3073: /************ Prevalence ********************/ 3074: 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) 3075: { 3076: /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people 3077: in each health status at the date of interview (if between dateprev1 and dateprev2). 3078: We still use firstpass and lastpass as another selection. 3079: */ 3080: 3081: int i, m, jk, j1, bool, z1,j; 3082: 3083: double **prop; 3084: double posprop; 3085: double y2; /* in fractional years */ 3086: int iagemin, iagemax; 3087: int first; /** to stop verbosity which is redirected to log file */ 3088: 3089: iagemin= (int) agemin; 3090: iagemax= (int) agemax; 3091: /*pp=vector(1,nlstate);*/ 3092: prop=matrix(1,nlstate,iagemin,iagemax+3); 3093: /* freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/ 3094: j1=0; 3095: 3096: /*j=cptcoveff;*/ 3097: if (cptcovn<1) {j=1;ncodemax[1]=1;} 3098: 3099: first=1; 3100: for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){ 3101: /*for(i1=1; i1<=ncodemax[k1];i1++){ 3102: j1++;*/ 3103: 3104: for (i=1; i<=nlstate; i++) 3105: for(m=iagemin; m <= iagemax+3; m++) 3106: prop[i][m]=0.0; 3107: 3108: for (i=1; i<=imx; i++) { /* Each individual */ 3109: bool=1; 3110: if (cptcovn>0) { 3111: for (z1=1; z1<=cptcoveff; z1++) 3112: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 3113: bool=0; 3114: } 3115: if (bool==1) { 3116: for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/ 3117: y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */ 3118: if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */ 3119: if(agev[m][i]==0) agev[m][i]=iagemax+1; 3120: if(agev[m][i]==1) agev[m][i]=iagemax+2; 3121: 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); 3122: if (s[m][i]>0 && s[m][i]<=nlstate) { 3123: /*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]]);*/ 3124: prop[s[m][i]][(int)agev[m][i]] += weight[i]; 3125: prop[s[m][i]][iagemax+3] += weight[i]; 3126: } 3127: } 3128: } /* end selection of waves */ 3129: } 3130: } 3131: for(i=iagemin; i <= iagemax+3; i++){ 3132: for(jk=1,posprop=0; jk <=nlstate ; jk++) { 3133: posprop += prop[jk][i]; 3134: } 3135: 3136: for(jk=1; jk <=nlstate ; jk++){ 3137: if( i <= iagemax){ 3138: if(posprop>=1.e-5){ 3139: probs[i][jk][j1]= prop[jk][i]/posprop; 3140: } else{ 3141: if(first==1){ 3142: first=0; 3143: 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]); 3144: } 3145: } 3146: } 3147: }/* end jk */ 3148: }/* end i */ 3149: /*} *//* end i1 */ 3150: } /* end j1 */ 3151: 3152: /* free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/ 3153: /*free_vector(pp,1,nlstate);*/ 3154: free_matrix(prop,1,nlstate, iagemin,iagemax+3); 3155: } /* End of prevalence */ 3156: 3157: /************* Waves Concatenation ***************/ 3158: 3159: 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) 3160: { 3161: /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i. 3162: Death is a valid wave (if date is known). 3163: mw[mi][i] is the mi (mi=1 to wav[i]) effective wave of individual i 3164: dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i] 3165: and mw[mi+1][i]. dh depends on stepm. 3166: */ 3167: 3168: int i, mi, m; 3169: /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1; 3170: double sum=0., jmean=0.;*/ 3171: int first; 3172: int j, k=0,jk, ju, jl; 3173: double sum=0.; 3174: first=0; 3175: jmin=100000; 3176: jmax=-1; 3177: jmean=0.; 3178: for(i=1; i<=imx; i++){ 3179: mi=0; 3180: m=firstpass; 3181: while(s[m][i] <= nlstate){ 3182: if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5) 3183: mw[++mi][i]=m; 3184: if(m >=lastpass) 3185: break; 3186: else 3187: m++; 3188: }/* end while */ 3189: if (s[m][i] > nlstate){ 3190: mi++; /* Death is another wave */ 3191: /* if(mi==0) never been interviewed correctly before death */ 3192: /* Only death is a correct wave */ 3193: mw[mi][i]=m; 3194: } 3195: 3196: wav[i]=mi; 3197: if(mi==0){ 3198: nbwarn++; 3199: if(first==0){ 3200: printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i); 3201: first=1; 3202: } 3203: if(first==1){ 3204: fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i); 3205: } 3206: } /* end mi==0 */ 3207: } /* End individuals */ 3208: 3209: for(i=1; i<=imx; i++){ 3210: for(mi=1; mi<wav[i];mi++){ 3211: if (stepm <=0) 3212: dh[mi][i]=1; 3213: else{ 3214: if (s[mw[mi+1][i]][i] > nlstate) { /* A death */ 3215: if (agedc[i] < 2*AGESUP) { 3216: j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 3217: if(j==0) j=1; /* Survives at least one month after exam */ 3218: else if(j<0){ 3219: nberr++; 3220: 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]); 3221: j=1; /* Temporary Dangerous patch */ 3222: 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); 3223: 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]); 3224: 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); 3225: } 3226: k=k+1; 3227: if (j >= jmax){ 3228: jmax=j; 3229: ijmax=i; 3230: } 3231: if (j <= jmin){ 3232: jmin=j; 3233: ijmin=i; 3234: } 3235: sum=sum+j; 3236: /*if (j<0) printf("j=%d num=%d \n",j,i);*/ 3237: /* printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/ 3238: } 3239: } 3240: else{ 3241: j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12)); 3242: /* 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]); */ 3243: 3244: k=k+1; 3245: if (j >= jmax) { 3246: jmax=j; 3247: ijmax=i; 3248: } 3249: else if (j <= jmin){ 3250: jmin=j; 3251: ijmin=i; 3252: } 3253: /* if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */ 3254: /*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]);*/ 3255: if(j<0){ 3256: nberr++; 3257: 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]); 3258: 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]); 3259: } 3260: sum=sum+j; 3261: } 3262: jk= j/stepm; 3263: jl= j -jk*stepm; 3264: ju= j -(jk+1)*stepm; 3265: if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */ 3266: if(jl==0){ 3267: dh[mi][i]=jk; 3268: bh[mi][i]=0; 3269: }else{ /* We want a negative bias in order to only have interpolation ie 3270: * to avoid the price of an extra matrix product in likelihood */ 3271: dh[mi][i]=jk+1; 3272: bh[mi][i]=ju; 3273: } 3274: }else{ 3275: if(jl <= -ju){ 3276: dh[mi][i]=jk; 3277: bh[mi][i]=jl; /* bias is positive if real duration 3278: * is higher than the multiple of stepm and negative otherwise. 3279: */ 3280: } 3281: else{ 3282: dh[mi][i]=jk+1; 3283: bh[mi][i]=ju; 3284: } 3285: if(dh[mi][i]==0){ 3286: dh[mi][i]=1; /* At least one step */ 3287: bh[mi][i]=ju; /* At least one step */ 3288: /* 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);*/ 3289: } 3290: } /* end if mle */ 3291: } 3292: } /* end wave */ 3293: } 3294: jmean=sum/k; 3295: 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); 3296: 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); 3297: } 3298: 3299: /*********** Tricode ****************************/ 3300: void tricode(int *Tvar, int **nbcode, int imx, int *Ndum) 3301: { 3302: /**< Uses cptcovn+2*cptcovprod as the number of covariates */ 3303: /* Tvar[i]=atoi(stre); find 'n' in Vn and stores in Tvar. If model=V2+V1 Tvar[1]=2 and Tvar[2]=1 3304: * Boring subroutine which should only output nbcode[Tvar[j]][k] 3305: * Tvar[5] in V2+V1+V3*age+V2*V4 is 2 (V2) 3306: * nbcode[Tvar[j]][1]= 3307: */ 3308: 3309: int ij=1, k=0, j=0, i=0, maxncov=NCOVMAX; 3310: int modmaxcovj=0; /* Modality max of covariates j */ 3311: int cptcode=0; /* Modality max of covariates j */ 3312: int modmincovj=0; /* Modality min of covariates j */ 3313: 3314: 3315: cptcoveff=0; 3316: 3317: for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */ 3318: 3319: /* Loop on covariates without age and products */ 3320: for (j=1; j<=(cptcovs); j++) { /* From model V1 + V2*age+ V3 + V3*V4 keeps V1 + V3 = 2 only */ 3321: for (k=-1; k < maxncov; k++) Ndum[k]=0; 3322: for (i=1; i<=imx; i++) { /* Loop on individuals: reads the data file to get the maximum value of the 3323: modality of this covariate Vj*/ 3324: ij=(int)(covar[Tvar[j]][i]); /* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i 3325: * If product of Vn*Vm, still boolean *: 3326: * If it was coded 1, 2, 3, 4 should be splitted into 3 boolean variables 3327: * 1 => 0 0 0, 2 => 0 0 1, 3 => 0 1 1, 4=1 0 0 */ 3328: /* Finds for covariate j, n=Tvar[j] of Vn . ij is the 3329: modality of the nth covariate of individual i. */ 3330: if (ij > modmaxcovj) 3331: modmaxcovj=ij; 3332: else if (ij < modmincovj) 3333: modmincovj=ij; 3334: if ((ij < -1) && (ij > NCOVMAX)){ 3335: printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX ); 3336: exit(1); 3337: }else 3338: Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/ 3339: /* If coded 1, 2, 3 , counts the number of 1 Ndum[1], number of 2, Ndum[2], etc */ 3340: /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/ 3341: /* getting the maximum value of the modality of the covariate 3342: (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and 3343: female is 1, then modmaxcovj=1.*/ 3344: } /* end for loop on individuals i */ 3345: printf(" Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", j, Tvar[j], modmincovj, modmaxcovj); 3346: fprintf(ficlog," Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", j, Tvar[j], modmincovj, modmaxcovj); 3347: cptcode=modmaxcovj; 3348: /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */ 3349: /*for (i=0; i<=cptcode; i++) {*/ 3350: for (k=modmincovj; k<=modmaxcovj; k++) { /* k=-1 ? 0 and 1*//* For each value k of the modality of model-cov j */ 3351: printf("Frequencies of covariates %d ie V%d with value %d: %d\n", j, Tvar[j], k, Ndum[k]); 3352: fprintf(ficlog, "Frequencies of covariates %d ie V%d with value %d: %d\n", j, Tvar[j], k, Ndum[k]); 3353: if( Ndum[k] != 0 ){ /* Counts if nobody answered modality k ie empty modality, we skip it and reorder */ 3354: if( k != -1){ 3355: ncodemax[j]++; /* ncodemax[j]= Number of modalities of the j th 3356: covariate for which somebody answered excluding 3357: undefined. Usually 2: 0 and 1. */ 3358: } 3359: ncodemaxwundef[j]++; /* ncodemax[j]= Number of modalities of the j th 3360: covariate for which somebody answered including 3361: undefined. Usually 3: -1, 0 and 1. */ 3362: } 3363: /* In fact ncodemax[j]=2 (dichotom. variables only) but it could be more for 3364: historical reasons: 3 if coded 1, 2, 3 and 4 and Ndum[2]=0 */ 3365: } /* Ndum[-1] number of undefined modalities */ 3366: 3367: /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */ 3368: /* For covariate j, modalities could be 1, 2, 3, 4, 5, 6, 7. 3369: If Ndum[1]=0, Ndum[2]=0, Ndum[3]= 635, Ndum[4]=0, Ndum[5]=0, Ndum[6]=27, Ndum[7]=125; 3370: modmincovj=3; modmaxcovj = 7; 3371: There are only 3 modalities non empty 3, 6, 7 (or 2 if 27 is too few) : ncodemax[j]=3; 3372: which will be coded 0, 1, 2 which in binary on 2=3-1 digits are 0=00 1=01, 2=10; 3373: defining two dummy variables: variables V1_1 and V1_2. 3374: nbcode[Tvar[j]][ij]=k; 3375: nbcode[Tvar[j]][1]=0; 3376: nbcode[Tvar[j]][2]=1; 3377: nbcode[Tvar[j]][3]=2; 3378: */ 3379: ij=0; /* ij is similar to i but can jumps over null modalities */ 3380: for (i=modmincovj; i<=modmaxcovj; i++) { /* i= 1 to 2 for dichotomous, or from 1 to 3 or from -1 to 1*/ 3381: if (Ndum[i] == 0) { /* If at least one individual responded to this modality k */ 3382: break; 3383: } 3384: ij++; 3385: nbcode[Tvar[j]][ij]=i; /* stores the original modality i in an array nbcode, ij modality from 1 to last non-nul modality.*/ 3386: cptcode = ij; /* New max modality for covar j */ 3387: } /* end of loop on modality i=-1 to 1 or more */ 3388: 3389: /* for (k=0; k<= cptcode; k++) { /\* k=-1 ? k=0 to 1 *\//\* Could be 1 to 4 *\//\* cptcode=modmaxcovj *\/ */ 3390: /* /\*recode from 0 *\/ */ 3391: /* k is a modality. If we have model=V1+V1*sex */ 3392: /* then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */ 3393: /* But if some modality were not used, it is recoded from 0 to a newer modmaxcovj=cptcode *\/ */ 3394: /* } */ 3395: /* /\* cptcode = ij; *\/ /\* New max modality for covar j *\/ */ 3396: /* if (ij > ncodemax[j]) { */ 3397: /* printf( " Error ij=%d > ncodemax[%d]=%d\n", ij, j, ncodemax[j]); */ 3398: /* fprintf(ficlog, " Error ij=%d > ncodemax[%d]=%d\n", ij, j, ncodemax[j]); */ 3399: /* break; */ 3400: /* } */ 3401: /* } /\* end of loop on modality k *\/ */ 3402: } /* end of loop on model-covariate j. nbcode[Tvarj][1]=0 and nbcode[Tvarj][2]=1 sets the value of covariate j*/ 3403: 3404: for (k=-1; k< maxncov; k++) Ndum[k]=0; 3405: 3406: for (i=1; i<=ncovmodel-2-nagesqr; i++) { /* -2, cste and age and eventually age*age */ 3407: /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/ 3408: ij=Tvar[i]; /* Tvar might be -1 if status was unknown */ 3409: Ndum[ij]++; /* Might be supersed V1 + V1*age */ 3410: } 3411: 3412: ij=0; 3413: for (i=0; i<= maxncov-1; i++) { /* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) */ 3414: /*printf("Ndum[%d]=%d\n",i, Ndum[i]);*/ 3415: if((Ndum[i]!=0) && (i<=ncovcol)){ 3416: ij++; 3417: /*printf("diff Ndum[%d]=%d\n",i, Ndum[i]);*/ 3418: Tvaraff[ij]=i; /*For printing (unclear) */ 3419: }else{ 3420: /* Tvaraff[ij]=0; */ 3421: } 3422: } 3423: /* ij--; */ 3424: cptcoveff=ij; /*Number of total covariates*/ 3425: 3426: } 3427: 3428: 3429: /*********** Health Expectancies ****************/ 3430: 3431: void evsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,char strstart[] ) 3432: 3433: { 3434: /* Health expectancies, no variances */ 3435: int i, j, nhstepm, hstepm, h, nstepm; 3436: int nhstepma, nstepma; /* Decreasing with age */ 3437: double age, agelim, hf; 3438: double ***p3mat; 3439: double eip; 3440: 3441: pstamp(ficreseij); 3442: fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n"); 3443: fprintf(ficreseij,"# Age"); 3444: for(i=1; i<=nlstate;i++){ 3445: for(j=1; j<=nlstate;j++){ 3446: fprintf(ficreseij," e%1d%1d ",i,j); 3447: } 3448: fprintf(ficreseij," e%1d. ",i); 3449: } 3450: fprintf(ficreseij,"\n"); 3451: 3452: 3453: if(estepm < stepm){ 3454: printf ("Problem %d lower than %d\n",estepm, stepm); 3455: } 3456: else hstepm=estepm; 3457: /* We compute the life expectancy from trapezoids spaced every estepm months 3458: * This is mainly to measure the difference between two models: for example 3459: * if stepm=24 months pijx are given only every 2 years and by summing them 3460: * we are calculating an estimate of the Life Expectancy assuming a linear 3461: * progression in between and thus overestimating or underestimating according 3462: * to the curvature of the survival function. If, for the same date, we 3463: * estimate the model with stepm=1 month, we can keep estepm to 24 months 3464: * to compare the new estimate of Life expectancy with the same linear 3465: * hypothesis. A more precise result, taking into account a more precise 3466: * curvature will be obtained if estepm is as small as stepm. */ 3467: 3468: /* For example we decided to compute the life expectancy with the smallest unit */ 3469: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 3470: nhstepm is the number of hstepm from age to agelim 3471: nstepm is the number of stepm from age to agelin. 3472: Look at hpijx to understand the reason of that which relies in memory size 3473: and note for a fixed period like estepm months */ 3474: /* We decided (b) to get a life expectancy respecting the most precise curvature of the 3475: survival function given by stepm (the optimization length). Unfortunately it 3476: means that if the survival funtion is printed only each two years of age and if 3477: you sum them up and add 1 year (area under the trapezoids) you won't get the same 3478: results. So we changed our mind and took the option of the best precision. 3479: */ 3480: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 3481: 3482: agelim=AGESUP; 3483: /* If stepm=6 months */ 3484: /* Computed by stepm unit matrices, product of hstepm matrices, stored 3485: in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */ 3486: 3487: /* nhstepm age range expressed in number of stepm */ 3488: nstepm=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */ 3489: /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 3490: /* if (stepm >= YEARM) hstepm=1;*/ 3491: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */ 3492: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); 3493: 3494: for (age=bage; age<=fage; age ++){ 3495: nstepma=(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: nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */ 3499: 3500: /* If stepm=6 months */ 3501: /* Computed by stepm unit matrices, product of hstepma matrices, stored 3502: in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */ 3503: 3504: hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij); 3505: 3506: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */ 3507: 3508: printf("%d|",(int)age);fflush(stdout); 3509: fprintf(ficlog,"%d|",(int)age);fflush(ficlog); 3510: 3511: /* Computing expectancies */ 3512: for(i=1; i<=nlstate;i++) 3513: for(j=1; j<=nlstate;j++) 3514: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){ 3515: eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf; 3516: 3517: /* 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]);*/ 3518: 3519: } 3520: 3521: fprintf(ficreseij,"%3.0f",age ); 3522: for(i=1; i<=nlstate;i++){ 3523: eip=0; 3524: for(j=1; j<=nlstate;j++){ 3525: eip +=eij[i][j][(int)age]; 3526: fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] ); 3527: } 3528: fprintf(ficreseij,"%9.4f", eip ); 3529: } 3530: fprintf(ficreseij,"\n"); 3531: 3532: } 3533: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); 3534: printf("\n"); 3535: fprintf(ficlog,"\n"); 3536: 3537: } 3538: 3539: 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[] ) 3540: 3541: { 3542: /* Covariances of health expectancies eij and of total life expectancies according 3543: to initial status i, ei. . 3544: */ 3545: int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji; 3546: int nhstepma, nstepma; /* Decreasing with age */ 3547: double age, agelim, hf; 3548: double ***p3matp, ***p3matm, ***varhe; 3549: double **dnewm,**doldm; 3550: double *xp, *xm; 3551: double **gp, **gm; 3552: double ***gradg, ***trgradg; 3553: int theta; 3554: 3555: double eip, vip; 3556: 3557: varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage); 3558: xp=vector(1,npar); 3559: xm=vector(1,npar); 3560: dnewm=matrix(1,nlstate*nlstate,1,npar); 3561: doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate); 3562: 3563: pstamp(ficresstdeij); 3564: fprintf(ficresstdeij,"# Health expectancies with standard errors\n"); 3565: fprintf(ficresstdeij,"# Age"); 3566: for(i=1; i<=nlstate;i++){ 3567: for(j=1; j<=nlstate;j++) 3568: fprintf(ficresstdeij," e%1d%1d (SE)",i,j); 3569: fprintf(ficresstdeij," e%1d. ",i); 3570: } 3571: fprintf(ficresstdeij,"\n"); 3572: 3573: pstamp(ficrescveij); 3574: fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n"); 3575: fprintf(ficrescveij,"# Age"); 3576: for(i=1; i<=nlstate;i++) 3577: for(j=1; j<=nlstate;j++){ 3578: cptj= (j-1)*nlstate+i; 3579: for(i2=1; i2<=nlstate;i2++) 3580: for(j2=1; j2<=nlstate;j2++){ 3581: cptj2= (j2-1)*nlstate+i2; 3582: if(cptj2 <= cptj) 3583: fprintf(ficrescveij," %1d%1d,%1d%1d",i,j,i2,j2); 3584: } 3585: } 3586: fprintf(ficrescveij,"\n"); 3587: 3588: if(estepm < stepm){ 3589: printf ("Problem %d lower than %d\n",estepm, stepm); 3590: } 3591: else hstepm=estepm; 3592: /* We compute the life expectancy from trapezoids spaced every estepm months 3593: * This is mainly to measure the difference between two models: for example 3594: * if stepm=24 months pijx are given only every 2 years and by summing them 3595: * we are calculating an estimate of the Life Expectancy assuming a linear 3596: * progression in between and thus overestimating or underestimating according 3597: * to the curvature of the survival function. If, for the same date, we 3598: * estimate the model with stepm=1 month, we can keep estepm to 24 months 3599: * to compare the new estimate of Life expectancy with the same linear 3600: * hypothesis. A more precise result, taking into account a more precise 3601: * curvature will be obtained if estepm is as small as stepm. */ 3602: 3603: /* For example we decided to compute the life expectancy with the smallest unit */ 3604: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 3605: nhstepm is the number of hstepm from age to agelim 3606: nstepm is the number of stepm from age to agelin. 3607: Look at hpijx to understand the reason of that which relies in memory size 3608: and note for a fixed period like estepm months */ 3609: /* We decided (b) to get a life expectancy respecting the most precise curvature of the 3610: survival function given by stepm (the optimization length). Unfortunately it 3611: means that if the survival funtion is printed only each two years of age and if 3612: you sum them up and add 1 year (area under the trapezoids) you won't get the same 3613: results. So we changed our mind and took the option of the best precision. 3614: */ 3615: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 3616: 3617: /* If stepm=6 months */ 3618: /* nhstepm age range expressed in number of stepm */ 3619: agelim=AGESUP; 3620: nstepm=(int) rint((agelim-bage)*YEARM/stepm); 3621: /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 3622: /* if (stepm >= YEARM) hstepm=1;*/ 3623: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */ 3624: 3625: p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); 3626: p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); 3627: gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate); 3628: trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar); 3629: gp=matrix(0,nhstepm,1,nlstate*nlstate); 3630: gm=matrix(0,nhstepm,1,nlstate*nlstate); 3631: 3632: for (age=bage; age<=fage; age ++){ 3633: nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */ 3634: /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 3635: /* if (stepm >= YEARM) hstepm=1;*/ 3636: nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */ 3637: 3638: /* If stepm=6 months */ 3639: /* Computed by stepm unit matrices, product of hstepma matrices, stored 3640: in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */ 3641: 3642: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */ 3643: 3644: /* Computing Variances of health expectancies */ 3645: /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to 3646: decrease memory allocation */ 3647: for(theta=1; theta <=npar; theta++){ 3648: for(i=1; i<=npar; i++){ 3649: xp[i] = x[i] + (i==theta ?delti[theta]:0); 3650: xm[i] = x[i] - (i==theta ?delti[theta]:0); 3651: } 3652: hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij); 3653: hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij); 3654: 3655: for(j=1; j<= nlstate; j++){ 3656: for(i=1; i<=nlstate; i++){ 3657: for(h=0; h<=nhstepm-1; h++){ 3658: gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.; 3659: gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.; 3660: } 3661: } 3662: } 3663: 3664: for(ij=1; ij<= nlstate*nlstate; ij++) 3665: for(h=0; h<=nhstepm-1; h++){ 3666: gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta]; 3667: } 3668: }/* End theta */ 3669: 3670: 3671: for(h=0; h<=nhstepm-1; h++) 3672: for(j=1; j<=nlstate*nlstate;j++) 3673: for(theta=1; theta <=npar; theta++) 3674: trgradg[h][j][theta]=gradg[h][theta][j]; 3675: 3676: 3677: for(ij=1;ij<=nlstate*nlstate;ij++) 3678: for(ji=1;ji<=nlstate*nlstate;ji++) 3679: varhe[ij][ji][(int)age] =0.; 3680: 3681: printf("%d|",(int)age);fflush(stdout); 3682: fprintf(ficlog,"%d|",(int)age);fflush(ficlog); 3683: for(h=0;h<=nhstepm-1;h++){ 3684: for(k=0;k<=nhstepm-1;k++){ 3685: matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov); 3686: matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]); 3687: for(ij=1;ij<=nlstate*nlstate;ij++) 3688: for(ji=1;ji<=nlstate*nlstate;ji++) 3689: varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf; 3690: } 3691: } 3692: 3693: /* Computing expectancies */ 3694: hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij); 3695: for(i=1; i<=nlstate;i++) 3696: for(j=1; j<=nlstate;j++) 3697: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){ 3698: eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf; 3699: 3700: /* 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]);*/ 3701: 3702: } 3703: 3704: fprintf(ficresstdeij,"%3.0f",age ); 3705: for(i=1; i<=nlstate;i++){ 3706: eip=0.; 3707: vip=0.; 3708: for(j=1; j<=nlstate;j++){ 3709: eip += eij[i][j][(int)age]; 3710: for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */ 3711: vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age]; 3712: fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) ); 3713: } 3714: fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip)); 3715: } 3716: fprintf(ficresstdeij,"\n"); 3717: 3718: fprintf(ficrescveij,"%3.0f",age ); 3719: for(i=1; i<=nlstate;i++) 3720: for(j=1; j<=nlstate;j++){ 3721: cptj= (j-1)*nlstate+i; 3722: for(i2=1; i2<=nlstate;i2++) 3723: for(j2=1; j2<=nlstate;j2++){ 3724: cptj2= (j2-1)*nlstate+i2; 3725: if(cptj2 <= cptj) 3726: fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]); 3727: } 3728: } 3729: fprintf(ficrescveij,"\n"); 3730: 3731: } 3732: free_matrix(gm,0,nhstepm,1,nlstate*nlstate); 3733: free_matrix(gp,0,nhstepm,1,nlstate*nlstate); 3734: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate); 3735: free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar); 3736: free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); 3737: free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); 3738: printf("\n"); 3739: fprintf(ficlog,"\n"); 3740: 3741: free_vector(xm,1,npar); 3742: free_vector(xp,1,npar); 3743: free_matrix(dnewm,1,nlstate*nlstate,1,npar); 3744: free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate); 3745: free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage); 3746: } 3747: 3748: /************ Variance ******************/ 3749: 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[]) 3750: { 3751: /* Variance of health expectancies */ 3752: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/ 3753: /* double **newm;*/ 3754: /* int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav)*/ 3755: 3756: int movingaverage(); 3757: double **dnewm,**doldm; 3758: double **dnewmp,**doldmp; 3759: int i, j, nhstepm, hstepm, h, nstepm ; 3760: int k; 3761: double *xp; 3762: double **gp, **gm; /* for var eij */ 3763: double ***gradg, ***trgradg; /*for var eij */ 3764: double **gradgp, **trgradgp; /* for var p point j */ 3765: double *gpp, *gmp; /* for var p point j */ 3766: double **varppt; /* for var p point j nlstate to nlstate+ndeath */ 3767: double ***p3mat; 3768: double age,agelim, hf; 3769: double ***mobaverage; 3770: int theta; 3771: char digit[4]; 3772: char digitp[25]; 3773: 3774: char fileresprobmorprev[FILENAMELENGTH]; 3775: 3776: if(popbased==1){ 3777: if(mobilav!=0) 3778: strcpy(digitp,"-populbased-mobilav-"); 3779: else strcpy(digitp,"-populbased-nomobil-"); 3780: } 3781: else 3782: strcpy(digitp,"-stablbased-"); 3783: 3784: if (mobilav!=0) { 3785: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); 3786: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){ 3787: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav); 3788: printf(" Error in movingaverage mobilav=%d\n",mobilav); 3789: } 3790: } 3791: 3792: strcpy(fileresprobmorprev,"prmorprev"); 3793: sprintf(digit,"%-d",ij); 3794: /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/ 3795: strcat(fileresprobmorprev,digit); /* Tvar to be done */ 3796: strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */ 3797: strcat(fileresprobmorprev,fileres); 3798: if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) { 3799: printf("Problem with resultfile: %s\n", fileresprobmorprev); 3800: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev); 3801: } 3802: printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev); 3803: 3804: fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev); 3805: pstamp(ficresprobmorprev); 3806: 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); 3807: fprintf(ficresprobmorprev,"# Age cov=%-d",ij); 3808: for(j=nlstate+1; j<=(nlstate+ndeath);j++){ 3809: fprintf(ficresprobmorprev," p.%-d SE",j); 3810: for(i=1; i<=nlstate;i++) 3811: fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j); 3812: } 3813: fprintf(ficresprobmorprev,"\n"); 3814: fprintf(ficgp,"\n# Routine varevsij"); 3815: /* fprintf(fichtm, "#Local time at start: %s", strstart);*/ 3816: 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"); 3817: fprintf(fichtm,"\n %s \n",digitp); 3818: /* } */ 3819: varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath); 3820: pstamp(ficresvij); 3821: fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n# (weighted average of eij where weights are "); 3822: if(popbased==1) 3823: 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); 3824: else 3825: fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n"); 3826: fprintf(ficresvij,"# Age"); 3827: for(i=1; i<=nlstate;i++) 3828: for(j=1; j<=nlstate;j++) 3829: fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j); 3830: fprintf(ficresvij,"\n"); 3831: 3832: xp=vector(1,npar); 3833: dnewm=matrix(1,nlstate,1,npar); 3834: doldm=matrix(1,nlstate,1,nlstate); 3835: dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar); 3836: doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath); 3837: 3838: gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath); 3839: gpp=vector(nlstate+1,nlstate+ndeath); 3840: gmp=vector(nlstate+1,nlstate+ndeath); 3841: trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/ 3842: 3843: if(estepm < stepm){ 3844: printf ("Problem %d lower than %d\n",estepm, stepm); 3845: } 3846: else hstepm=estepm; 3847: /* For example we decided to compute the life expectancy with the smallest unit */ 3848: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 3849: nhstepm is the number of hstepm from age to agelim 3850: nstepm is the number of stepm from age to agelin. 3851: Look at function hpijx to understand why (it is linked to memory size questions) */ 3852: /* We decided (b) to get a life expectancy respecting the most precise curvature of the 3853: survival function given by stepm (the optimization length). Unfortunately it 3854: means that if the survival funtion is printed every two years of age and if 3855: you sum them up and add 1 year (area under the trapezoids) you won't get the same 3856: results. So we changed our mind and took the option of the best precision. 3857: */ 3858: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 3859: agelim = AGESUP; 3860: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */ 3861: nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 3862: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */ 3863: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); 3864: gradg=ma3x(0,nhstepm,1,npar,1,nlstate); 3865: gp=matrix(0,nhstepm,1,nlstate); 3866: gm=matrix(0,nhstepm,1,nlstate); 3867: 3868: 3869: for(theta=1; theta <=npar; theta++){ 3870: for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/ 3871: xp[i] = x[i] + (i==theta ?delti[theta]:0); 3872: } 3873: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij); 3874: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij); 3875: 3876: if (popbased==1) { 3877: if(mobilav ==0){ 3878: for(i=1; i<=nlstate;i++) 3879: prlim[i][i]=probs[(int)age][i][ij]; 3880: }else{ /* mobilav */ 3881: for(i=1; i<=nlstate;i++) 3882: prlim[i][i]=mobaverage[(int)age][i][ij]; 3883: } 3884: } 3885: 3886: for(j=1; j<= nlstate; j++){ 3887: for(h=0; h<=nhstepm; h++){ 3888: for(i=1, gp[h][j]=0.;i<=nlstate;i++) 3889: gp[h][j] += prlim[i][i]*p3mat[i][j][h]; 3890: } 3891: } 3892: /* This for computing probability of death (h=1 means 3893: computed over hstepm matrices product = hstepm*stepm months) 3894: as a weighted average of prlim. 3895: */ 3896: for(j=nlstate+1;j<=nlstate+ndeath;j++){ 3897: for(i=1,gpp[j]=0.; i<= nlstate; i++) 3898: gpp[j] += prlim[i][i]*p3mat[i][j][1]; 3899: } 3900: /* end probability of death */ 3901: 3902: for(i=1; i<=npar; i++) /* Computes gradient x - delta */ 3903: xp[i] = x[i] - (i==theta ?delti[theta]:0); 3904: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij); 3905: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij); 3906: 3907: if (popbased==1) { 3908: if(mobilav ==0){ 3909: for(i=1; i<=nlstate;i++) 3910: prlim[i][i]=probs[(int)age][i][ij]; 3911: }else{ /* mobilav */ 3912: for(i=1; i<=nlstate;i++) 3913: prlim[i][i]=mobaverage[(int)age][i][ij]; 3914: } 3915: } 3916: 3917: for(j=1; j<= nlstate; j++){ /* Sum of wi * eij = e.j */ 3918: for(h=0; h<=nhstepm; h++){ 3919: for(i=1, gm[h][j]=0.;i<=nlstate;i++) 3920: gm[h][j] += prlim[i][i]*p3mat[i][j][h]; 3921: } 3922: } 3923: /* This for computing probability of death (h=1 means 3924: computed over hstepm matrices product = hstepm*stepm months) 3925: as a weighted average of prlim. 3926: */ 3927: for(j=nlstate+1;j<=nlstate+ndeath;j++){ 3928: for(i=1,gmp[j]=0.; i<= nlstate; i++) 3929: gmp[j] += prlim[i][i]*p3mat[i][j][1]; 3930: } 3931: /* end probability of death */ 3932: 3933: for(j=1; j<= nlstate; j++) /* vareij */ 3934: for(h=0; h<=nhstepm; h++){ 3935: gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta]; 3936: } 3937: 3938: for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */ 3939: gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta]; 3940: } 3941: 3942: } /* End theta */ 3943: 3944: trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */ 3945: 3946: for(h=0; h<=nhstepm; h++) /* veij */ 3947: for(j=1; j<=nlstate;j++) 3948: for(theta=1; theta <=npar; theta++) 3949: trgradg[h][j][theta]=gradg[h][theta][j]; 3950: 3951: for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */ 3952: for(theta=1; theta <=npar; theta++) 3953: trgradgp[j][theta]=gradgp[theta][j]; 3954: 3955: 3956: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */ 3957: for(i=1;i<=nlstate;i++) 3958: for(j=1;j<=nlstate;j++) 3959: vareij[i][j][(int)age] =0.; 3960: 3961: for(h=0;h<=nhstepm;h++){ 3962: for(k=0;k<=nhstepm;k++){ 3963: matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov); 3964: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]); 3965: for(i=1;i<=nlstate;i++) 3966: for(j=1;j<=nlstate;j++) 3967: vareij[i][j][(int)age] += doldm[i][j]*hf*hf; 3968: } 3969: } 3970: 3971: /* pptj */ 3972: matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov); 3973: matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp); 3974: for(j=nlstate+1;j<=nlstate+ndeath;j++) 3975: for(i=nlstate+1;i<=nlstate+ndeath;i++) 3976: varppt[j][i]=doldmp[j][i]; 3977: /* end ppptj */ 3978: /* x centered again */ 3979: hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij); 3980: prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij); 3981: 3982: if (popbased==1) { 3983: if(mobilav ==0){ 3984: for(i=1; i<=nlstate;i++) 3985: prlim[i][i]=probs[(int)age][i][ij]; 3986: }else{ /* mobilav */ 3987: for(i=1; i<=nlstate;i++) 3988: prlim[i][i]=mobaverage[(int)age][i][ij]; 3989: } 3990: } 3991: 3992: /* This for computing probability of death (h=1 means 3993: computed over hstepm (estepm) matrices product = hstepm*stepm months) 3994: as a weighted average of prlim. 3995: */ 3996: for(j=nlstate+1;j<=nlstate+ndeath;j++){ 3997: for(i=1,gmp[j]=0.;i<= nlstate; i++) 3998: gmp[j] += prlim[i][i]*p3mat[i][j][1]; 3999: } 4000: /* end probability of death */ 4001: 4002: fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij); 4003: for(j=nlstate+1; j<=(nlstate+ndeath);j++){ 4004: fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j])); 4005: for(i=1; i<=nlstate;i++){ 4006: fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]); 4007: } 4008: } 4009: fprintf(ficresprobmorprev,"\n"); 4010: 4011: fprintf(ficresvij,"%.0f ",age ); 4012: for(i=1; i<=nlstate;i++) 4013: for(j=1; j<=nlstate;j++){ 4014: fprintf(ficresvij," %.4f", vareij[i][j][(int)age]); 4015: } 4016: fprintf(ficresvij,"\n"); 4017: free_matrix(gp,0,nhstepm,1,nlstate); 4018: free_matrix(gm,0,nhstepm,1,nlstate); 4019: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate); 4020: free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar); 4021: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); 4022: } /* End age */ 4023: free_vector(gpp,nlstate+1,nlstate+ndeath); 4024: free_vector(gmp,nlstate+1,nlstate+ndeath); 4025: free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath); 4026: free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/ 4027: fprintf(ficgp,"\nunset parametric;unset label; set ter png small size 320, 240"); 4028: /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */ 4029: fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";"); 4030: /* fprintf(ficgp,"\n plot \"%s\" u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */ 4031: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */ 4032: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */ 4033: fprintf(ficgp,"\n plot \"%s\" u 1:($3) not w l lt 1 ",subdirf(fileresprobmorprev)); 4034: fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)) t \"95%% interval\" w l lt 2 ",subdirf(fileresprobmorprev)); 4035: fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)) not w l lt 2 ",subdirf(fileresprobmorprev)); 4036: fprintf(fichtm,"\n File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev)); 4037: fprintf(fichtm,"\n Probability is computed over estepm=%d months. <img src=\"%s%s.png\"> \n", estepm,subdirf3(optionfilefiname,"varmuptjgr",digitp),digit); 4038: /* 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); 4039: */ 4040: /* fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */ 4041: fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit); 4042: 4043: free_vector(xp,1,npar); 4044: free_matrix(doldm,1,nlstate,1,nlstate); 4045: free_matrix(dnewm,1,nlstate,1,npar); 4046: free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath); 4047: free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar); 4048: free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath); 4049: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); 4050: fclose(ficresprobmorprev); 4051: fflush(ficgp); 4052: fflush(fichtm); 4053: } /* end varevsij */ 4054: 4055: /************ Variance of prevlim ******************/ 4056: 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[]) 4057: { 4058: /* Variance of prevalence limit */ 4059: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/ 4060: 4061: double **dnewm,**doldm; 4062: int i, j, nhstepm, hstepm; 4063: double *xp; 4064: double *gp, *gm; 4065: double **gradg, **trgradg; 4066: double age,agelim; 4067: int theta; 4068: 4069: pstamp(ficresvpl); 4070: fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n"); 4071: fprintf(ficresvpl,"# Age"); 4072: for(i=1; i<=nlstate;i++) 4073: fprintf(ficresvpl," %1d-%1d",i,i); 4074: fprintf(ficresvpl,"\n"); 4075: 4076: xp=vector(1,npar); 4077: dnewm=matrix(1,nlstate,1,npar); 4078: doldm=matrix(1,nlstate,1,nlstate); 4079: 4080: hstepm=1*YEARM; /* Every year of age */ 4081: hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 4082: agelim = AGESUP; 4083: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */ 4084: nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 4085: if (stepm >= YEARM) hstepm=1; 4086: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */ 4087: gradg=matrix(1,npar,1,nlstate); 4088: gp=vector(1,nlstate); 4089: gm=vector(1,nlstate); 4090: 4091: for(theta=1; theta <=npar; theta++){ 4092: for(i=1; i<=npar; i++){ /* Computes gradient */ 4093: xp[i] = x[i] + (i==theta ?delti[theta]:0); 4094: } 4095: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij); 4096: for(i=1;i<=nlstate;i++) 4097: gp[i] = prlim[i][i]; 4098: 4099: for(i=1; i<=npar; i++) /* Computes gradient */ 4100: xp[i] = x[i] - (i==theta ?delti[theta]:0); 4101: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij); 4102: for(i=1;i<=nlstate;i++) 4103: gm[i] = prlim[i][i]; 4104: 4105: for(i=1;i<=nlstate;i++) 4106: gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta]; 4107: } /* End theta */ 4108: 4109: trgradg =matrix(1,nlstate,1,npar); 4110: 4111: for(j=1; j<=nlstate;j++) 4112: for(theta=1; theta <=npar; theta++) 4113: trgradg[j][theta]=gradg[theta][j]; 4114: 4115: for(i=1;i<=nlstate;i++) 4116: varpl[i][(int)age] =0.; 4117: matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov); 4118: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg); 4119: for(i=1;i<=nlstate;i++) 4120: varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */ 4121: 4122: fprintf(ficresvpl,"%.0f ",age ); 4123: for(i=1; i<=nlstate;i++) 4124: fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age])); 4125: fprintf(ficresvpl,"\n"); 4126: free_vector(gp,1,nlstate); 4127: free_vector(gm,1,nlstate); 4128: free_matrix(gradg,1,npar,1,nlstate); 4129: free_matrix(trgradg,1,nlstate,1,npar); 4130: } /* End age */ 4131: 4132: free_vector(xp,1,npar); 4133: free_matrix(doldm,1,nlstate,1,npar); 4134: free_matrix(dnewm,1,nlstate,1,nlstate); 4135: 4136: } 4137: 4138: /************ Variance of one-step probabilities ******************/ 4139: 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[]) 4140: { 4141: int i, j=0, k1, l1, tj; 4142: int k2, l2, j1, z1; 4143: int k=0, l; 4144: int first=1, first1, first2; 4145: double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp; 4146: double **dnewm,**doldm; 4147: double *xp; 4148: double *gp, *gm; 4149: double **gradg, **trgradg; 4150: double **mu; 4151: double age, cov[NCOVMAX+1]; 4152: double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */ 4153: int theta; 4154: char fileresprob[FILENAMELENGTH]; 4155: char fileresprobcov[FILENAMELENGTH]; 4156: char fileresprobcor[FILENAMELENGTH]; 4157: double ***varpij; 4158: 4159: strcpy(fileresprob,"prob"); 4160: strcat(fileresprob,fileres); 4161: if((ficresprob=fopen(fileresprob,"w"))==NULL) { 4162: printf("Problem with resultfile: %s\n", fileresprob); 4163: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob); 4164: } 4165: strcpy(fileresprobcov,"probcov"); 4166: strcat(fileresprobcov,fileres); 4167: if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) { 4168: printf("Problem with resultfile: %s\n", fileresprobcov); 4169: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov); 4170: } 4171: strcpy(fileresprobcor,"probcor"); 4172: strcat(fileresprobcor,fileres); 4173: if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) { 4174: printf("Problem with resultfile: %s\n", fileresprobcor); 4175: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor); 4176: } 4177: printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob); 4178: fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob); 4179: printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov); 4180: fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov); 4181: printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor); 4182: fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor); 4183: pstamp(ficresprob); 4184: fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n"); 4185: fprintf(ficresprob,"# Age"); 4186: pstamp(ficresprobcov); 4187: fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n"); 4188: fprintf(ficresprobcov,"# Age"); 4189: pstamp(ficresprobcor); 4190: fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n"); 4191: fprintf(ficresprobcor,"# Age"); 4192: 4193: 4194: for(i=1; i<=nlstate;i++) 4195: for(j=1; j<=(nlstate+ndeath);j++){ 4196: fprintf(ficresprob," p%1d-%1d (SE)",i,j); 4197: fprintf(ficresprobcov," p%1d-%1d ",i,j); 4198: fprintf(ficresprobcor," p%1d-%1d ",i,j); 4199: } 4200: /* fprintf(ficresprob,"\n"); 4201: fprintf(ficresprobcov,"\n"); 4202: fprintf(ficresprobcor,"\n"); 4203: */ 4204: xp=vector(1,npar); 4205: dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar); 4206: doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath)); 4207: mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage); 4208: varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage); 4209: first=1; 4210: fprintf(ficgp,"\n# Routine varprob"); 4211: fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n"); 4212: fprintf(fichtm,"\n"); 4213: 4214: fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov); 4215: fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\ 4216: file %s \n",optionfilehtmcov); 4217: fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\ 4218: and drawn. It helps understanding how is the covariance between two incidences.\ 4219: They are expressed in year-1 in order to be less dependent of stepm. \n"); 4220: fprintf(fichtmcov,"\n Contour plot corresponding to x'cov-1x = 4 (where x is the column vector (pij,pkl)) are drawn. \ 4221: It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \ 4222: would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \ 4223: standard deviations wide on each axis. \ 4224: Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\ 4225: and made the appropriate rotation to look at the uncorrelated principal directions. \ 4226: To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one. \n"); 4227: 4228: cov[1]=1; 4229: /* tj=cptcoveff; */ 4230: tj = (int) pow(2,cptcoveff); 4231: if (cptcovn<1) {tj=1;ncodemax[1]=1;} 4232: j1=0; 4233: for(j1=1; j1<=tj;j1++){ 4234: /*for(i1=1; i1<=ncodemax[t];i1++){ */ 4235: /*j1++;*/ 4236: if (cptcovn>0) { 4237: fprintf(ficresprob, "\n#********** Variable "); 4238: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]); 4239: fprintf(ficresprob, "**********\n#\n"); 4240: fprintf(ficresprobcov, "\n#********** Variable "); 4241: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]); 4242: fprintf(ficresprobcov, "**********\n#\n"); 4243: 4244: fprintf(ficgp, "\n#********** Variable "); 4245: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]); 4246: fprintf(ficgp, "**********\n#\n"); 4247: 4248: 4249: fprintf(fichtmcov, "\n<hr size=\"2\" color=\"#EC5E5E\">********** Variable "); 4250: for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]); 4251: fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">"); 4252: 4253: fprintf(ficresprobcor, "\n#********** Variable "); 4254: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]); 4255: fprintf(ficresprobcor, "**********\n#"); 4256: } 4257: 4258: gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath)); 4259: trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar); 4260: gp=vector(1,(nlstate)*(nlstate+ndeath)); 4261: gm=vector(1,(nlstate)*(nlstate+ndeath)); 4262: for (age=bage; age<=fage; age ++){ 4263: cov[2]=age; 4264: if(nagesqr==1) 4265: cov[3]= age*age; 4266: for (k=1; k<=cptcovn;k++) { 4267: cov[2+nagesqr+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];/* j1 1 2 3 4 4268: * 1 1 1 1 1 4269: * 2 2 1 1 1 4270: * 3 1 2 1 1 4271: */ 4272: /* nbcode[1][1]=0 nbcode[1][2]=1;*/ 4273: } 4274: /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */ 4275: for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtab[ij][Tvar[Tage[k]]]]*cov[2]; 4276: for (k=1; k<=cptcovprod;k++) 4277: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]]; 4278: 4279: 4280: for(theta=1; theta <=npar; theta++){ 4281: for(i=1; i<=npar; i++) 4282: xp[i] = x[i] + (i==theta ?delti[theta]:(double)0); 4283: 4284: pmij(pmmij,cov,ncovmodel,xp,nlstate); 4285: 4286: k=0; 4287: for(i=1; i<= (nlstate); i++){ 4288: for(j=1; j<=(nlstate+ndeath);j++){ 4289: k=k+1; 4290: gp[k]=pmmij[i][j]; 4291: } 4292: } 4293: 4294: for(i=1; i<=npar; i++) 4295: xp[i] = x[i] - (i==theta ?delti[theta]:(double)0); 4296: 4297: pmij(pmmij,cov,ncovmodel,xp,nlstate); 4298: k=0; 4299: for(i=1; i<=(nlstate); i++){ 4300: for(j=1; j<=(nlstate+ndeath);j++){ 4301: k=k+1; 4302: gm[k]=pmmij[i][j]; 4303: } 4304: } 4305: 4306: for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) 4307: gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta]; 4308: } 4309: 4310: for(j=1; j<=(nlstate)*(nlstate+ndeath);j++) 4311: for(theta=1; theta <=npar; theta++) 4312: trgradg[j][theta]=gradg[theta][j]; 4313: 4314: matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov); 4315: matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg); 4316: 4317: pmij(pmmij,cov,ncovmodel,x,nlstate); 4318: 4319: k=0; 4320: for(i=1; i<=(nlstate); i++){ 4321: for(j=1; j<=(nlstate+ndeath);j++){ 4322: k=k+1; 4323: mu[k][(int) age]=pmmij[i][j]; 4324: } 4325: } 4326: for(i=1;i<=(nlstate)*(nlstate+ndeath);i++) 4327: for(j=1;j<=(nlstate)*(nlstate+ndeath);j++) 4328: varpij[i][j][(int)age] = doldm[i][j]; 4329: 4330: /*printf("\n%d ",(int)age); 4331: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){ 4332: printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i])); 4333: fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i])); 4334: }*/ 4335: 4336: fprintf(ficresprob,"\n%d ",(int)age); 4337: fprintf(ficresprobcov,"\n%d ",(int)age); 4338: fprintf(ficresprobcor,"\n%d ",(int)age); 4339: 4340: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++) 4341: fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age])); 4342: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){ 4343: fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]); 4344: fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]); 4345: } 4346: i=0; 4347: for (k=1; k<=(nlstate);k++){ 4348: for (l=1; l<=(nlstate+ndeath);l++){ 4349: i++; 4350: fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l); 4351: fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l); 4352: for (j=1; j<=i;j++){ 4353: /* printf(" k=%d l=%d i=%d j=%d\n",k,l,i,j);fflush(stdout); */ 4354: fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]); 4355: fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age])); 4356: } 4357: } 4358: }/* end of loop for state */ 4359: } /* end of loop for age */ 4360: free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath)); 4361: free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath)); 4362: free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar); 4363: free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar); 4364: 4365: /* Confidence intervalle of pij */ 4366: /* 4367: fprintf(ficgp,"\nunset parametric;unset label"); 4368: fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\""); 4369: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65"); 4370: fprintf(fichtm,"\n Probability with confidence intervals expressed in year-1 :<a href=\"pijgr%s.png\">pijgr%s.png</A>, ",optionfilefiname,optionfilefiname); 4371: fprintf(fichtm,"\n <img src=\"pijgr%s.png\"> ",optionfilefiname); 4372: fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname); 4373: fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob); 4374: */ 4375: 4376: /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/ 4377: first1=1;first2=2; 4378: for (k2=1; k2<=(nlstate);k2++){ 4379: for (l2=1; l2<=(nlstate+ndeath);l2++){ 4380: if(l2==k2) continue; 4381: j=(k2-1)*(nlstate+ndeath)+l2; 4382: for (k1=1; k1<=(nlstate);k1++){ 4383: for (l1=1; l1<=(nlstate+ndeath);l1++){ 4384: if(l1==k1) continue; 4385: i=(k1-1)*(nlstate+ndeath)+l1; 4386: if(i<=j) continue; 4387: for (age=bage; age<=fage; age ++){ 4388: if ((int)age %5==0){ 4389: v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM; 4390: v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM; 4391: cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM; 4392: mu1=mu[i][(int) age]/stepm*YEARM ; 4393: mu2=mu[j][(int) age]/stepm*YEARM; 4394: c12=cv12/sqrt(v1*v2); 4395: /* Computing eigen value of matrix of covariance */ 4396: lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.; 4397: lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.; 4398: if ((lc2 <0) || (lc1 <0) ){ 4399: if(first2==1){ 4400: first1=0; 4401: 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); 4402: } 4403: 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); 4404: /* lc1=fabs(lc1); */ /* If we want to have them positive */ 4405: /* lc2=fabs(lc2); */ 4406: } 4407: 4408: /* Eigen vectors */ 4409: v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12)); 4410: /*v21=sqrt(1.-v11*v11); *//* error */ 4411: v21=(lc1-v1)/cv12*v11; 4412: v12=-v21; 4413: v22=v11; 4414: tnalp=v21/v11; 4415: if(first1==1){ 4416: first1=0; 4417: 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); 4418: } 4419: 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); 4420: /*printf(fignu*/ 4421: /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */ 4422: /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */ 4423: if(first==1){ 4424: first=0; 4425: fprintf(ficgp,"\nset parametric;unset label"); 4426: 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); 4427: fprintf(ficgp,"\nset ter png small size 320, 240"); 4428: fprintf(fichtmcov,"\n Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year-1\ 4429: :<a href=\"%s%d%1d%1d-%1d%1d.png\">\ 4430: %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\ 4431: subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\ 4432: subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2); 4433: fprintf(fichtmcov,"\n <img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2); 4434: fprintf(fichtmcov,"\n Correlation at age %d (%.3f),",(int) age, c12); 4435: fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2); 4436: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2); 4437: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2); 4438: 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",\ 4439: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\ 4440: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2)); 4441: }else{ 4442: first=0; 4443: fprintf(fichtmcov," %d (%.3f),",(int) age, c12); 4444: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2); 4445: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2); 4446: 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",\ 4447: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\ 4448: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2)); 4449: }/* if first */ 4450: } /* age mod 5 */ 4451: } /* end loop age */ 4452: fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2); 4453: first=1; 4454: } /*l12 */ 4455: } /* k12 */ 4456: } /*l1 */ 4457: }/* k1 */ 4458: /* } */ /* loop covariates */ 4459: } 4460: free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage); 4461: free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage); 4462: free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath)); 4463: free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar); 4464: free_vector(xp,1,npar); 4465: fclose(ficresprob); 4466: fclose(ficresprobcov); 4467: fclose(ficresprobcor); 4468: fflush(ficgp); 4469: fflush(fichtmcov); 4470: } 4471: 4472: 4473: /******************* Printing html file ***********/ 4474: void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \ 4475: int lastpass, int stepm, int weightopt, char model[],\ 4476: int imx,int jmin, int jmax, double jmeanint,char rfileres[],\ 4477: int popforecast, int estepm ,\ 4478: double jprev1, double mprev1,double anprev1, \ 4479: double jprev2, double mprev2,double anprev2){ 4480: int jj1, k1, i1, cpt; 4481: 4482: fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \ 4483: <li><a href='#secondorder'>Result files (second order (variance)</a>\n \ 4484: </ul>"); 4485: fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \ 4486: - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> \n ", 4487: jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p")); 4488: fprintf(fichtm,"\ 4489: - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a> \n ", 4490: stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij")); 4491: fprintf(fichtm,"\ 4492: - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> \n", 4493: subdirf2(fileres,"pl"),subdirf2(fileres,"pl")); 4494: fprintf(fichtm,"\ 4495: - (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): \ 4496: <a href=\"%s\">%s</a> \n", 4497: estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e")); 4498: fprintf(fichtm,"\ 4499: - Population projections by age and states: \ 4500: <a href=\"%s\">%s</a> \n</li>", subdirf2(fileres,"f"),subdirf2(fileres,"f")); 4501: 4502: fprintf(fichtm," \n<ul><li>Graphs</li>"); 4503: 4504: m=pow(2,cptcoveff); 4505: if (cptcovn < 1) {m=1;ncodemax[1]=1;} 4506: 4507: jj1=0; 4508: for(k1=1; k1<=m;k1++){ 4509: /* for(i1=1; i1<=ncodemax[k1];i1++){ */ 4510: jj1++; 4511: if (cptcovn > 0) { 4512: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates"); 4513: for (cpt=1; cpt<=cptcoveff;cpt++){ 4514: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]); 4515: printf(" V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);fflush(stdout); 4516: } 4517: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">"); 4518: } 4519: /* Pij */ 4520: 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> \ 4521: <img src=\"%s%d_1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1); 4522: /* Quasi-incidences */ 4523: fprintf(fichtm," - Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\ 4524: 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> \ 4525: <img src=\"%s%d_2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1); 4526: /* Period (stable) prevalence in each health state */ 4527: for(cpt=1; cpt<=nlstate;cpt++){ 4528: 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> \ 4529: <img src=\"%s%d_%d.png\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1); 4530: } 4531: for(cpt=1; cpt<=nlstate;cpt++) { 4532: 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> \ 4533: <img src=\"%s%d%d.png\">",cpt,nlstate,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1); 4534: } 4535: /* } /\* end i1 *\/ */ 4536: }/* End k1 */ 4537: fprintf(fichtm,"</ul>"); 4538: 4539: 4540: fprintf(fichtm,"\ 4541: \n <li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\ 4542: - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> \n", rfileres,rfileres); 4543: 4544: fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> \n", 4545: subdirf2(fileres,"prob"),subdirf2(fileres,"prob")); 4546: fprintf(fichtm,"\ 4547: - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> \n", 4548: subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov")); 4549: 4550: fprintf(fichtm,"\ 4551: - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> \n", 4552: subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor")); 4553: fprintf(fichtm,"\ 4554: - Variances and covariances of health expectancies by age and initial health status (cov(eij,ekl)(estepm=%2d months): \ 4555: <a href=\"%s\">%s</a> \n</li>", 4556: estepm,subdirf2(fileres,"cve"),subdirf2(fileres,"cve")); 4557: fprintf(fichtm,"\ 4558: - (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): \ 4559: <a href=\"%s\">%s</a> \n</li>", 4560: estepm,subdirf2(fileres,"stde"),subdirf2(fileres,"stde")); 4561: fprintf(fichtm,"\ 4562: - 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", 4563: estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v")); 4564: fprintf(fichtm,"\ 4565: - 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", 4566: estepm, subdirf2(fileres,"t"),subdirf2(fileres,"t")); 4567: fprintf(fichtm,"\ 4568: - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> \n",\ 4569: subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl")); 4570: 4571: /* if(popforecast==1) fprintf(fichtm,"\n */ 4572: /* - Prevalences forecasting: <a href=\"f%s\">f%s</a> \n */ 4573: /* - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> \n */ 4574: /* ",fileres,fileres,fileres,fileres); */ 4575: /* else */ 4576: /* 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); */ 4577: fflush(fichtm); 4578: fprintf(fichtm," <ul><li>Graphs</li>"); 4579: 4580: m=pow(2,cptcoveff); 4581: if (cptcovn < 1) {m=1;ncodemax[1]=1;} 4582: 4583: jj1=0; 4584: for(k1=1; k1<=m;k1++){ 4585: /* for(i1=1; i1<=ncodemax[k1];i1++){ */ 4586: jj1++; 4587: if (cptcovn > 0) { 4588: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates"); 4589: for (cpt=1; cpt<=cptcoveff;cpt++) 4590: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]); 4591: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">"); 4592: } 4593: for(cpt=1; cpt<=nlstate;cpt++) { 4594: fprintf(fichtm," - Observed (cross-sectional) and period (incidence based) \ 4595: prevalence (with 95%% confidence interval) in state (%d): %s%d_%d.png \ 4596: <img src=\"%s%d_%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1); 4597: } 4598: fprintf(fichtm,"\n - Total life expectancy by age and \ 4599: health expectancies in states (1) and (2). If popbased=1 the smooth (due to the model) \ 4600: true period expectancies (those weighted with period prevalences are also\ 4601: drawn in addition to the population based expectancies computed using\ 4602: observed and cahotic prevalences: %s%d.png \ 4603: <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1); 4604: /* } /\* end i1 *\/ */ 4605: }/* End k1 */ 4606: fprintf(fichtm,"</ul>"); 4607: fflush(fichtm); 4608: } 4609: 4610: /******************* Gnuplot file **************/ 4611: void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){ 4612: 4613: char dirfileres[132],optfileres[132]; 4614: int cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,ij=0,l=0; 4615: int ng=0; 4616: /* if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */ 4617: /* printf("Problem with file %s",optionfilegnuplot); */ 4618: /* fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */ 4619: /* } */ 4620: 4621: /*#ifdef windows */ 4622: fprintf(ficgp,"cd \"%s\" \n",pathc); 4623: /*#endif */ 4624: m=pow(2,cptcoveff); 4625: 4626: strcpy(dirfileres,optionfilefiname); 4627: strcpy(optfileres,"vpl"); 4628: /* 1eme*/ 4629: fprintf(ficgp,"\n# 1st: Period (stable) prevalence with CI: 'vpl' files\n"); 4630: for (cpt=1; cpt<= nlstate ; cpt ++) { 4631: for (k1=1; k1<= m ; k1 ++) { /* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */ 4632: fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1); 4633: fprintf(ficgp,"\n#set out \"v%s%d_%d.png\" \n",optionfilefiname,cpt,k1); 4634: fprintf(ficgp,"set xlabel \"Age\" \n\ 4635: set ylabel \"Probability\" \n\ 4636: set ter png small size 320, 240\n\ 4637: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1); 4638: 4639: for (i=1; i<= nlstate ; i ++) { 4640: if (i==cpt) fprintf(ficgp," %%lf (%%lf)"); 4641: else fprintf(ficgp," %%*lf (%%*lf)"); 4642: } 4643: 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); 4644: for (i=1; i<= nlstate ; i ++) { 4645: if (i==cpt) fprintf(ficgp," %%lf (%%lf)"); 4646: else fprintf(ficgp," %%*lf (%%*lf)"); 4647: } 4648: fprintf(ficgp,"\" t\"95%% CI\" w l lt 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1); 4649: for (i=1; i<= nlstate ; i ++) { 4650: if (i==cpt) fprintf(ficgp," %%lf (%%lf)"); 4651: else fprintf(ficgp," %%*lf (%%*lf)"); 4652: } 4653: fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l lt 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1)); 4654: } 4655: } 4656: /*2 eme*/ 4657: fprintf(ficgp,"\n# 2nd: Total life expectancy with CI: 't' files\n"); 4658: for (k1=1; k1<= m ; k1 ++) { 4659: fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1); 4660: fprintf(ficgp,"set ylabel \"Years\" \nset ter png small size 320, 240\nplot [%.f:%.f] ",ageminpar,fage); 4661: 4662: for (i=1; i<= nlstate+1 ; i ++) { 4663: k=2*i; 4664: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"%%lf",subdirf2(fileres,"t"),k1-1,k1-1); 4665: for (j=1; j<= nlstate+1 ; j ++) { 4666: if (j==i) fprintf(ficgp," %%lf (%%lf)"); 4667: else fprintf(ficgp," %%*lf (%%*lf)"); 4668: } 4669: if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,"); 4670: else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1); 4671: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*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: fprintf(ficgp,"\" t\"\" w l lt 0,"); 4677: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"%%lf",subdirf2(fileres,"t"),k1-1,k1-1); 4678: for (j=1; j<= nlstate+1 ; j ++) { 4679: if (j==i) fprintf(ficgp," %%lf (%%lf)"); 4680: else fprintf(ficgp," %%*lf (%%*lf)"); 4681: } 4682: if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l lt 0"); 4683: else fprintf(ficgp,"\" t\"\" w l lt 0,"); 4684: } 4685: } 4686: 4687: /*3eme*/ 4688: 4689: for (k1=1; k1<= m ; k1 ++) { 4690: for (cpt=1; cpt<= nlstate ; cpt ++) { 4691: /* k=2+nlstate*(2*cpt-2); */ 4692: k=2+(nlstate+1)*(cpt-1); 4693: fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1); 4694: fprintf(ficgp,"set ter png small size 320, 240\n\ 4695: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt); 4696: /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1); 4697: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) "); 4698: fprintf(ficgp,"\" t \"e%d1\" w l",cpt); 4699: fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1); 4700: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) "); 4701: fprintf(ficgp,"\" t \"e%d1\" w l",cpt); 4702: 4703: */ 4704: for (i=1; i< nlstate ; i ++) { 4705: 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); 4706: /* 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);*/ 4707: 4708: } 4709: fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+nlstate,cpt); 4710: } 4711: } 4712: 4713: /* CV preval stable (period) */ 4714: for (k1=1; k1<= m ; k1 ++) { /* For each multivariate if any */ 4715: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */ 4716: k=3; 4717: fprintf(ficgp,"\n#\n#\n#CV preval stable (period): 'pij' files, cov=%d state=%d",k1, cpt); 4718: fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1); 4719: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\ 4720: set ter png small size 320, 240\n\ 4721: unset log y\n\ 4722: plot [%.f:%.f] ", ageminpar, agemaxpar); 4723: for (i=1; i<= nlstate ; i ++){ 4724: if(i==1) 4725: fprintf(ficgp,"\"%s\"",subdirf2(fileres,"pij")); 4726: else 4727: fprintf(ficgp,", '' "); 4728: l=(nlstate+ndeath)*(i-1)+1; 4729: fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l); 4730: for (j=1; j<= (nlstate-1) ; j ++) 4731: fprintf(ficgp,"+$%d",k+l+j); 4732: fprintf(ficgp,")) t \"prev(%d,%d)\" w l",i,cpt); 4733: } /* nlstate */ 4734: fprintf(ficgp,"\n"); 4735: } /* end cpt state*/ 4736: } /* end covariate */ 4737: 4738: /* proba elementaires */ 4739: fprintf(ficgp,"\n##############\n#MLE estimated parameters\n#############\n"); 4740: for(i=1,jk=1; i <=nlstate; i++){ 4741: fprintf(ficgp,"# initial state %d\n",i); 4742: for(k=1; k <=(nlstate+ndeath); k++){ 4743: if (k != i) { 4744: fprintf(ficgp,"# current state %d\n",k); 4745: for(j=1; j <=ncovmodel; j++){ 4746: fprintf(ficgp,"p%d=%f; ",jk,p[jk]); 4747: jk++; 4748: } 4749: fprintf(ficgp,"\n"); 4750: } 4751: } 4752: } 4753: fprintf(ficgp,"##############\n#\n"); 4754: 4755: /*goto avoid;*/ 4756: fprintf(ficgp,"\n##############\n#Graphics of of probabilities or incidences\n#############\n"); 4757: fprintf(ficgp,"# logi(p12/p11)=a12+b12*age+c12age*age+d12*V1+e12*V1*age\n"); 4758: fprintf(ficgp,"# logi(p12/p11)=p1 +p2*age +p3*age*age+ p4*V1+ p5*V1*age\n"); 4759: fprintf(ficgp,"# logi(p13/p11)=a13+b13*age+c13age*age+d13*V1+e13*V1*age\n"); 4760: fprintf(ficgp,"# logi(p13/p11)=p6 +p7*age +p8*age*age+ p9*V1+ p10*V1*age\n"); 4761: fprintf(ficgp,"# p12+p13+p14+p11=1=p11(1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n"); 4762: fprintf(ficgp,"# +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age)+...)\n"); 4763: fprintf(ficgp,"# p11=1/(1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n"); 4764: fprintf(ficgp,"# +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age)+...)\n"); 4765: fprintf(ficgp,"# p12=exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)/\n"); 4766: fprintf(ficgp,"# (1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n"); 4767: fprintf(ficgp,"# +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age))\n"); 4768: fprintf(ficgp,"# +exp(a14+b14*age+c14age*age+d14*V1+e14*V1*age)+...)\n"); 4769: fprintf(ficgp,"#\n"); 4770: for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/ 4771: fprintf(ficgp,"# ng=%d\n",ng); 4772: fprintf(ficgp,"# jk=1 to 2^%d=%d\n",cptcoveff,m); 4773: for(jk=1; jk <=m; jk++) { 4774: fprintf(ficgp,"# jk=%d\n",jk); 4775: fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng); 4776: if (ng==2) 4777: fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n"); 4778: else 4779: fprintf(ficgp,"\nset title \"Probability\"\n"); 4780: fprintf(ficgp,"\nset ter png small size 320, 240\nset log y\nplot [%.f:%.f] ",ageminpar,agemaxpar); 4781: i=1; 4782: for(k2=1; k2<=nlstate; k2++) { 4783: k3=i; 4784: for(k=1; k<=(nlstate+ndeath); k++) { 4785: if (k != k2){ 4786: if(ng==2) 4787: if(nagesqr==0) 4788: fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1); 4789: else /* nagesqr =1 */ 4790: fprintf(ficgp," %f*exp(p%d+p%d*x+p%d*x*x",YEARM/stepm,i,i+1,i+1+nagesqr); 4791: else 4792: if(nagesqr==0) 4793: fprintf(ficgp," exp(p%d+p%d*x",i,i+1); 4794: else /* nagesqr =1 */ 4795: fprintf(ficgp," exp(p%d+p%d*x+p%d*x*x",i,i+1,i+1+nagesqr); 4796: ij=1;/* To be checked else nbcode[0][0] wrong */ 4797: for(j=3; j <=ncovmodel-nagesqr; j++) { 4798: if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) { /* Bug valgrind */ 4799: fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]); 4800: ij++; 4801: } 4802: else 4803: fprintf(ficgp,"+p%d*%d",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]); 4804: } 4805: fprintf(ficgp,")/(1"); 4806: 4807: for(k1=1; k1 <=nlstate; k1++){ 4808: if(nagesqr==0) 4809: fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1); 4810: else /* nagesqr =1 */ 4811: 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); 4812: 4813: ij=1; 4814: for(j=3; j <=ncovmodel-nagesqr; j++){ 4815: if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) { 4816: fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]); 4817: ij++; 4818: } 4819: else 4820: fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtab[jk][j-2]]); 4821: } 4822: fprintf(ficgp,")"); 4823: } 4824: fprintf(ficgp,") t \"p%d%d\" ", k2,k); 4825: if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,","); 4826: i=i+ncovmodel; 4827: } 4828: } /* end k */ 4829: } /* end k2 */ 4830: } /* end jk */ 4831: } /* end ng */ 4832: /* avoid: */ 4833: fflush(ficgp); 4834: } /* end gnuplot */ 4835: 4836: 4837: /*************** Moving average **************/ 4838: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){ 4839: 4840: int i, cpt, cptcod; 4841: int modcovmax =1; 4842: int mobilavrange, mob; 4843: double age; 4844: 4845: modcovmax=2*cptcoveff;/* Max number of modalities. We suppose 4846: a covariate has 2 modalities */ 4847: if (cptcovn<1) modcovmax=1; /* At least 1 pass */ 4848: 4849: if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){ 4850: if(mobilav==1) mobilavrange=5; /* default */ 4851: else mobilavrange=mobilav; 4852: for (age=bage; age<=fage; age++) 4853: for (i=1; i<=nlstate;i++) 4854: for (cptcod=1;cptcod<=modcovmax;cptcod++) 4855: mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod]; 4856: /* We keep the original values on the extreme ages bage, fage and for 4857: fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2 4858: we use a 5 terms etc. until the borders are no more concerned. 4859: */ 4860: for (mob=3;mob <=mobilavrange;mob=mob+2){ 4861: for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){ 4862: for (i=1; i<=nlstate;i++){ 4863: for (cptcod=1;cptcod<=modcovmax;cptcod++){ 4864: mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod]; 4865: for (cpt=1;cpt<=(mob-1)/2;cpt++){ 4866: mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod]; 4867: mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod]; 4868: } 4869: mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob; 4870: } 4871: } 4872: }/* end age */ 4873: }/* end mob */ 4874: }else return -1; 4875: return 0; 4876: }/* End movingaverage */ 4877: 4878: 4879: /************** Forecasting ******************/ 4880: 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){ 4881: /* proj1, year, month, day of starting projection 4882: agemin, agemax range of age 4883: dateprev1 dateprev2 range of dates during which prevalence is computed 4884: anproj2 year of en of projection (same day and month as proj1). 4885: */ 4886: int yearp, stepsize, hstepm, nhstepm, j, k, cptcod, i, h, i1; 4887: double agec; /* generic age */ 4888: double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean; 4889: double *popeffectif,*popcount; 4890: double ***p3mat; 4891: double ***mobaverage; 4892: char fileresf[FILENAMELENGTH]; 4893: 4894: agelim=AGESUP; 4895: prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass); 4896: 4897: strcpy(fileresf,"f"); 4898: strcat(fileresf,fileres); 4899: if((ficresf=fopen(fileresf,"w"))==NULL) { 4900: printf("Problem with forecast resultfile: %s\n", fileresf); 4901: fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf); 4902: } 4903: printf("Computing forecasting: result on file '%s' \n", fileresf); 4904: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf); 4905: 4906: if (cptcoveff==0) ncodemax[cptcoveff]=1; 4907: 4908: if (mobilav!=0) { 4909: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); 4910: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){ 4911: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav); 4912: printf(" Error in movingaverage mobilav=%d\n",mobilav); 4913: } 4914: } 4915: 4916: stepsize=(int) (stepm+YEARM-1)/YEARM; 4917: if (stepm<=12) stepsize=1; 4918: if(estepm < stepm){ 4919: printf ("Problem %d lower than %d\n",estepm, stepm); 4920: } 4921: else hstepm=estepm; 4922: 4923: hstepm=hstepm/stepm; 4924: yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp and 4925: fractional in yp1 */ 4926: anprojmean=yp; 4927: yp2=modf((yp1*12),&yp); 4928: mprojmean=yp; 4929: yp1=modf((yp2*30.5),&yp); 4930: jprojmean=yp; 4931: if(jprojmean==0) jprojmean=1; 4932: if(mprojmean==0) jprojmean=1; 4933: 4934: i1=cptcoveff; 4935: if (cptcovn < 1){i1=1;} 4936: 4937: fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2); 4938: 4939: fprintf(ficresf,"#****** Routine prevforecast **\n"); 4940: 4941: /* if (h==(int)(YEARM*yearp)){ */ 4942: for(cptcov=1, k=0;cptcov<=i1;cptcov++){ 4943: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){ 4944: k=k+1; 4945: fprintf(ficresf,"\n#******"); 4946: for(j=1;j<=cptcoveff;j++) { 4947: 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]]); 4948: } 4949: fprintf(ficresf,"******\n"); 4950: fprintf(ficresf,"# Covariate valuofcovar yearproj age"); 4951: for(j=1; j<=nlstate+ndeath;j++){ 4952: for(i=1; i<=nlstate;i++) 4953: fprintf(ficresf," p%d%d",i,j); 4954: fprintf(ficresf," p.%d",j); 4955: } 4956: for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) { 4957: fprintf(ficresf,"\n"); 4958: fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp); 4959: 4960: for (agec=fage; agec>=(ageminpar-1); agec--){ 4961: nhstepm=(int) rint((agelim-agec)*YEARM/stepm); 4962: nhstepm = nhstepm/hstepm; 4963: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); 4964: oldm=oldms;savm=savms; 4965: hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k); 4966: 4967: for (h=0; h<=nhstepm; h++){ 4968: if (h*hstepm/YEARM*stepm ==yearp) { 4969: fprintf(ficresf,"\n"); 4970: for(j=1;j<=cptcoveff;j++) 4971: fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]); 4972: fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm); 4973: } 4974: for(j=1; j<=nlstate+ndeath;j++) { 4975: ppij=0.; 4976: for(i=1; i<=nlstate;i++) { 4977: if (mobilav==1) 4978: ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod]; 4979: else { 4980: ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod]; 4981: } 4982: if (h*hstepm/YEARM*stepm== yearp) { 4983: fprintf(ficresf," %.3f", p3mat[i][j][h]); 4984: } 4985: } /* end i */ 4986: if (h*hstepm/YEARM*stepm==yearp) { 4987: fprintf(ficresf," %.3f", ppij); 4988: } 4989: }/* end j */ 4990: } /* end h */ 4991: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); 4992: } /* end agec */ 4993: } /* end yearp */ 4994: } /* end cptcod */ 4995: } /* end cptcov */ 4996: 4997: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); 4998: 4999: fclose(ficresf); 5000: } 5001: 5002: /************** Forecasting *****not tested NB*************/ 5003: 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){ 5004: 5005: int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h; 5006: int *popage; 5007: double calagedatem, agelim, kk1, kk2; 5008: double *popeffectif,*popcount; 5009: double ***p3mat,***tabpop,***tabpopprev; 5010: double ***mobaverage; 5011: char filerespop[FILENAMELENGTH]; 5012: 5013: tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); 5014: tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); 5015: agelim=AGESUP; 5016: calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM; 5017: 5018: prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass); 5019: 5020: 5021: strcpy(filerespop,"pop"); 5022: strcat(filerespop,fileres); 5023: if((ficrespop=fopen(filerespop,"w"))==NULL) { 5024: printf("Problem with forecast resultfile: %s\n", filerespop); 5025: fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop); 5026: } 5027: printf("Computing forecasting: result on file '%s' \n", filerespop); 5028: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop); 5029: 5030: if (cptcoveff==0) ncodemax[cptcoveff]=1; 5031: 5032: if (mobilav!=0) { 5033: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); 5034: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){ 5035: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav); 5036: printf(" Error in movingaverage mobilav=%d\n",mobilav); 5037: } 5038: } 5039: 5040: stepsize=(int) (stepm+YEARM-1)/YEARM; 5041: if (stepm<=12) stepsize=1; 5042: 5043: agelim=AGESUP; 5044: 5045: hstepm=1; 5046: hstepm=hstepm/stepm; 5047: 5048: if (popforecast==1) { 5049: if((ficpop=fopen(popfile,"r"))==NULL) { 5050: printf("Problem with population file : %s\n",popfile);exit(0); 5051: fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0); 5052: } 5053: popage=ivector(0,AGESUP); 5054: popeffectif=vector(0,AGESUP); 5055: popcount=vector(0,AGESUP); 5056: 5057: i=1; 5058: while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1; 5059: 5060: imx=i; 5061: for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i]; 5062: } 5063: 5064: for(cptcov=1,k=0;cptcov<=i2;cptcov++){ 5065: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){ 5066: k=k+1; 5067: fprintf(ficrespop,"\n#******"); 5068: for(j=1;j<=cptcoveff;j++) { 5069: fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]); 5070: } 5071: fprintf(ficrespop,"******\n"); 5072: fprintf(ficrespop,"# Age"); 5073: for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j); 5074: if (popforecast==1) fprintf(ficrespop," [Population]"); 5075: 5076: for (cpt=0; cpt<=0;cpt++) { 5077: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt); 5078: 5079: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 5080: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 5081: nhstepm = nhstepm/hstepm; 5082: 5083: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); 5084: oldm=oldms;savm=savms; 5085: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k); 5086: 5087: for (h=0; h<=nhstepm; h++){ 5088: if (h==(int) (calagedatem+YEARM*cpt)) { 5089: fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm); 5090: } 5091: for(j=1; j<=nlstate+ndeath;j++) { 5092: kk1=0.;kk2=0; 5093: for(i=1; i<=nlstate;i++) { 5094: if (mobilav==1) 5095: kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod]; 5096: else { 5097: kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod]; 5098: } 5099: } 5100: if (h==(int)(calagedatem+12*cpt)){ 5101: tabpop[(int)(agedeb)][j][cptcod]=kk1; 5102: /*fprintf(ficrespop," %.3f", kk1); 5103: if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/ 5104: } 5105: } 5106: for(i=1; i<=nlstate;i++){ 5107: kk1=0.; 5108: for(j=1; j<=nlstate;j++){ 5109: kk1= kk1+tabpop[(int)(agedeb)][j][cptcod]; 5110: } 5111: tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)]; 5112: } 5113: 5114: if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++) 5115: fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]); 5116: } 5117: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); 5118: } 5119: } 5120: 5121: /******/ 5122: 5123: for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) { 5124: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt); 5125: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 5126: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 5127: nhstepm = nhstepm/hstepm; 5128: 5129: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); 5130: oldm=oldms;savm=savms; 5131: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k); 5132: for (h=0; h<=nhstepm; h++){ 5133: if (h==(int) (calagedatem+YEARM*cpt)) { 5134: fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm); 5135: } 5136: for(j=1; j<=nlstate+ndeath;j++) { 5137: kk1=0.;kk2=0; 5138: for(i=1; i<=nlstate;i++) { 5139: kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod]; 5140: } 5141: if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1); 5142: } 5143: } 5144: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); 5145: } 5146: } 5147: } 5148: } 5149: 5150: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); 5151: 5152: if (popforecast==1) { 5153: free_ivector(popage,0,AGESUP); 5154: free_vector(popeffectif,0,AGESUP); 5155: free_vector(popcount,0,AGESUP); 5156: } 5157: free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); 5158: free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); 5159: fclose(ficrespop); 5160: } /* End of popforecast */ 5161: 5162: int fileappend(FILE *fichier, char *optionfich) 5163: { 5164: if((fichier=fopen(optionfich,"a"))==NULL) { 5165: printf("Problem with file: %s\n", optionfich); 5166: fprintf(ficlog,"Problem with file: %s\n", optionfich); 5167: return (0); 5168: } 5169: fflush(fichier); 5170: return (1); 5171: } 5172: 5173: 5174: /**************** function prwizard **********************/ 5175: void prwizard(int ncovmodel, int nlstate, int ndeath, char model[], FILE *ficparo) 5176: { 5177: 5178: /* Wizard to print covariance matrix template */ 5179: 5180: char ca[32], cb[32]; 5181: int i,j, k, li, lj, lk, ll, jj, npar, itimes; 5182: int numlinepar; 5183: 5184: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n"); 5185: fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n"); 5186: for(i=1; i <=nlstate; i++){ 5187: jj=0; 5188: for(j=1; j <=nlstate+ndeath; j++){ 5189: if(j==i) continue; 5190: jj++; 5191: /*ca[0]= k+'a'-1;ca[1]='\0';*/ 5192: printf("%1d%1d",i,j); 5193: fprintf(ficparo,"%1d%1d",i,j); 5194: for(k=1; k<=ncovmodel;k++){ 5195: /* printf(" %lf",param[i][j][k]); */ 5196: /* fprintf(ficparo," %lf",param[i][j][k]); */ 5197: printf(" 0."); 5198: fprintf(ficparo," 0."); 5199: } 5200: printf("\n"); 5201: fprintf(ficparo,"\n"); 5202: } 5203: } 5204: printf("# Scales (for hessian or gradient estimation)\n"); 5205: fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n"); 5206: npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/ 5207: for(i=1; i <=nlstate; i++){ 5208: jj=0; 5209: for(j=1; j <=nlstate+ndeath; j++){ 5210: if(j==i) continue; 5211: jj++; 5212: fprintf(ficparo,"%1d%1d",i,j); 5213: printf("%1d%1d",i,j); 5214: fflush(stdout); 5215: for(k=1; k<=ncovmodel;k++){ 5216: /* printf(" %le",delti3[i][j][k]); */ 5217: /* fprintf(ficparo," %le",delti3[i][j][k]); */ 5218: printf(" 0."); 5219: fprintf(ficparo," 0."); 5220: } 5221: numlinepar++; 5222: printf("\n"); 5223: fprintf(ficparo,"\n"); 5224: } 5225: } 5226: printf("# Covariance matrix\n"); 5227: /* # 121 Var(a12)\n\ */ 5228: /* # 122 Cov(b12,a12) Var(b12)\n\ */ 5229: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */ 5230: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */ 5231: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */ 5232: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */ 5233: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */ 5234: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */ 5235: fflush(stdout); 5236: fprintf(ficparo,"# Covariance matrix\n"); 5237: /* # 121 Var(a12)\n\ */ 5238: /* # 122 Cov(b12,a12) Var(b12)\n\ */ 5239: /* # ...\n\ */ 5240: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */ 5241: 5242: for(itimes=1;itimes<=2;itimes++){ 5243: jj=0; 5244: for(i=1; i <=nlstate; i++){ 5245: for(j=1; j <=nlstate+ndeath; j++){ 5246: if(j==i) continue; 5247: for(k=1; k<=ncovmodel;k++){ 5248: jj++; 5249: ca[0]= k+'a'-1;ca[1]='\0'; 5250: if(itimes==1){ 5251: printf("#%1d%1d%d",i,j,k); 5252: fprintf(ficparo,"#%1d%1d%d",i,j,k); 5253: }else{ 5254: printf("%1d%1d%d",i,j,k); 5255: fprintf(ficparo,"%1d%1d%d",i,j,k); 5256: /* printf(" %.5le",matcov[i][j]); */ 5257: } 5258: ll=0; 5259: for(li=1;li <=nlstate; li++){ 5260: for(lj=1;lj <=nlstate+ndeath; lj++){ 5261: if(lj==li) continue; 5262: for(lk=1;lk<=ncovmodel;lk++){ 5263: ll++; 5264: if(ll<=jj){ 5265: cb[0]= lk +'a'-1;cb[1]='\0'; 5266: if(ll<jj){ 5267: if(itimes==1){ 5268: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj); 5269: fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj); 5270: }else{ 5271: printf(" 0."); 5272: fprintf(ficparo," 0."); 5273: } 5274: }else{ 5275: if(itimes==1){ 5276: printf(" Var(%s%1d%1d)",ca,i,j); 5277: fprintf(ficparo," Var(%s%1d%1d)",ca,i,j); 5278: }else{ 5279: printf(" 0."); 5280: fprintf(ficparo," 0."); 5281: } 5282: } 5283: } 5284: } /* end lk */ 5285: } /* end lj */ 5286: } /* end li */ 5287: printf("\n"); 5288: fprintf(ficparo,"\n"); 5289: numlinepar++; 5290: } /* end k*/ 5291: } /*end j */ 5292: } /* end i */ 5293: } /* end itimes */ 5294: 5295: } /* end of prwizard */ 5296: /******************* Gompertz Likelihood ******************************/ 5297: double gompertz(double x[]) 5298: { 5299: double A,B,L=0.0,sump=0.,num=0.; 5300: int i,n=0; /* n is the size of the sample */ 5301: 5302: for (i=0;i<=imx-1 ; i++) { 5303: sump=sump+weight[i]; 5304: /* sump=sump+1;*/ 5305: num=num+1; 5306: } 5307: 5308: 5309: /* for (i=0; i<=imx; i++) 5310: 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]);*/ 5311: 5312: for (i=1;i<=imx ; i++) 5313: { 5314: if (cens[i] == 1 && wav[i]>1) 5315: A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp))); 5316: 5317: if (cens[i] == 0 && wav[i]>1) 5318: A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp))) 5319: +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM); 5320: 5321: /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */ 5322: if (wav[i] > 1 ) { /* ??? */ 5323: L=L+A*weight[i]; 5324: /* 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]);*/ 5325: } 5326: } 5327: 5328: /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/ 5329: 5330: return -2*L*num/sump; 5331: } 5332: 5333: #ifdef GSL 5334: /******************* Gompertz_f Likelihood ******************************/ 5335: double gompertz_f(const gsl_vector *v, void *params) 5336: { 5337: double A,B,LL=0.0,sump=0.,num=0.; 5338: double *x= (double *) v->data; 5339: int i,n=0; /* n is the size of the sample */ 5340: 5341: for (i=0;i<=imx-1 ; i++) { 5342: sump=sump+weight[i]; 5343: /* sump=sump+1;*/ 5344: num=num+1; 5345: } 5346: 5347: 5348: /* for (i=0; i<=imx; i++) 5349: 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]);*/ 5350: printf("x[0]=%lf x[1]=%lf\n",x[0],x[1]); 5351: for (i=1;i<=imx ; i++) 5352: { 5353: if (cens[i] == 1 && wav[i]>1) 5354: A=-x[0]/(x[1])*(exp(x[1]*(agecens[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp))); 5355: 5356: if (cens[i] == 0 && wav[i]>1) 5357: A=-x[0]/(x[1])*(exp(x[1]*(agedc[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp))) 5358: +log(x[0]/YEARM)+x[1]*(agedc[i]-agegomp)+log(YEARM); 5359: 5360: /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */ 5361: if (wav[i] > 1 ) { /* ??? */ 5362: LL=LL+A*weight[i]; 5363: /* 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]);*/ 5364: } 5365: } 5366: 5367: /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/ 5368: printf("x[0]=%lf x[1]=%lf -2*LL*num/sump=%lf\n",x[0],x[1],-2*LL*num/sump); 5369: 5370: return -2*LL*num/sump; 5371: } 5372: #endif 5373: 5374: /******************* Printing html file ***********/ 5375: void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \ 5376: int lastpass, int stepm, int weightopt, char model[],\ 5377: int imx, double p[],double **matcov,double agemortsup){ 5378: int i,k; 5379: 5380: fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets): "); 5381: fprintf(fichtm," mu(age) =%lf*exp(%lf*(age-%d)) per year ",p[1],p[2],agegomp); 5382: for (i=1;i<=2;i++) 5383: 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])); 5384: fprintf(fichtm," <img src=\"graphmort.png\">"); 5385: fprintf(fichtm,"</ul>"); 5386: 5387: fprintf(fichtm,"<ul><li><h4>Life table</h4>\n "); 5388: 5389: 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> "); 5390: 5391: for (k=agegomp;k<(agemortsup-2);k++) 5392: 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]); 5393: 5394: 5395: fflush(fichtm); 5396: } 5397: 5398: /******************* Gnuplot file **************/ 5399: void printinggnuplotmort(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){ 5400: 5401: char dirfileres[132],optfileres[132]; 5402: 5403: int ng; 5404: 5405: 5406: /*#ifdef windows */ 5407: fprintf(ficgp,"cd \"%s\" \n",pathc); 5408: /*#endif */ 5409: 5410: 5411: strcpy(dirfileres,optionfilefiname); 5412: strcpy(optfileres,"vpl"); 5413: fprintf(ficgp,"set out \"graphmort.png\"\n "); 5414: fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n "); 5415: fprintf(ficgp, "set ter png small size 320, 240\n set log y\n"); 5416: /* fprintf(ficgp, "set size 0.65,0.65\n"); */ 5417: fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp); 5418: 5419: } 5420: 5421: int readdata(char datafile[], int firstobs, int lastobs, int *imax) 5422: { 5423: 5424: /*-------- data file ----------*/ 5425: FILE *fic; 5426: char dummy[]=" "; 5427: int i=0, j=0, n=0; 5428: int linei, month, year,iout; 5429: char line[MAXLINE], linetmp[MAXLINE]; 5430: char stra[MAXLINE], strb[MAXLINE]; 5431: char *stratrunc; 5432: int lstra; 5433: 5434: 5435: if((fic=fopen(datafile,"r"))==NULL) { 5436: printf("Problem while opening datafile: %s\n", datafile);return 1; 5437: fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);return 1; 5438: } 5439: 5440: i=1; 5441: linei=0; 5442: while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) { 5443: linei=linei+1; 5444: for(j=strlen(line); j>=0;j--){ /* Untabifies line */ 5445: if(line[j] == '\t') 5446: line[j] = ' '; 5447: } 5448: for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){ 5449: ; 5450: }; 5451: line[j+1]=0; /* Trims blanks at end of line */ 5452: if(line[0]=='#'){ 5453: fprintf(ficlog,"Comment line\n%s\n",line); 5454: printf("Comment line\n%s\n",line); 5455: continue; 5456: } 5457: trimbb(linetmp,line); /* Trims multiple blanks in line */ 5458: strcpy(line, linetmp); 5459: 5460: 5461: for (j=maxwav;j>=1;j--){ 5462: cutv(stra, strb, line, ' '); 5463: if(strb[0]=='.') { /* Missing status */ 5464: lval=-1; 5465: }else{ 5466: errno=0; 5467: lval=strtol(strb,&endptr,10); 5468: /* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/ 5469: if( strb[0]=='\0' || (*endptr != '\0')){ 5470: 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); 5471: 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); 5472: return 1; 5473: } 5474: } 5475: s[j][i]=lval; 5476: 5477: strcpy(line,stra); 5478: cutv(stra, strb,line,' '); 5479: if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){ 5480: } 5481: else if( (iout=sscanf(strb,"%s.",dummy)) != 0){ 5482: month=99; 5483: year=9999; 5484: }else{ 5485: 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); 5486: 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); 5487: return 1; 5488: } 5489: anint[j][i]= (double) year; 5490: mint[j][i]= (double)month; 5491: strcpy(line,stra); 5492: } /* ENd Waves */ 5493: 5494: cutv(stra, strb,line,' '); 5495: if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){ 5496: } 5497: else if( (iout=sscanf(strb,"%s.",dummy)) != 0){ 5498: month=99; 5499: year=9999; 5500: }else{ 5501: 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); 5502: 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); 5503: return 1; 5504: } 5505: andc[i]=(double) year; 5506: moisdc[i]=(double) month; 5507: strcpy(line,stra); 5508: 5509: cutv(stra, strb,line,' '); 5510: if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){ 5511: } 5512: else if( (iout=sscanf(strb,"%s.", dummy)) != 0){ 5513: month=99; 5514: year=9999; 5515: }else{ 5516: 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); 5517: 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); 5518: return 1; 5519: } 5520: if (year==9999) { 5521: 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); 5522: 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); 5523: return 1; 5524: 5525: } 5526: annais[i]=(double)(year); 5527: moisnais[i]=(double)(month); 5528: strcpy(line,stra); 5529: 5530: cutv(stra, strb,line,' '); 5531: errno=0; 5532: dval=strtod(strb,&endptr); 5533: if( strb[0]=='\0' || (*endptr != '\0')){ 5534: printf("Error reading data around '%f' at line number %d, \"%s\" for individual %d\nShould be a weight. Exiting.\n",dval, i,line,linei); 5535: 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); 5536: fflush(ficlog); 5537: return 1; 5538: } 5539: weight[i]=dval; 5540: strcpy(line,stra); 5541: 5542: for (j=ncovcol;j>=1;j--){ 5543: cutv(stra, strb,line,' '); 5544: if(strb[0]=='.') { /* Missing status */ 5545: lval=-1; 5546: }else{ 5547: errno=0; 5548: lval=strtol(strb,&endptr,10); 5549: if( strb[0]=='\0' || (*endptr != '\0')){ 5550: 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); 5551: 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); 5552: return 1; 5553: } 5554: } 5555: if(lval <-1 || lval >1){ 5556: printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\n \ 5557: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \ 5558: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \ 5559: For example, for multinomial values like 1, 2 and 3,\n \ 5560: build V1=0 V2=0 for the reference value (1),\n \ 5561: V1=1 V2=0 for (2) \n \ 5562: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \ 5563: output of IMaCh is often meaningless.\n \ 5564: Exiting.\n",lval,linei, i,line,j); 5565: fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\n \ 5566: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \ 5567: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \ 5568: For example, for multinomial values like 1, 2 and 3,\n \ 5569: build V1=0 V2=0 for the reference value (1),\n \ 5570: V1=1 V2=0 for (2) \n \ 5571: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \ 5572: output of IMaCh is often meaningless.\n \ 5573: Exiting.\n",lval,linei, i,line,j);fflush(ficlog); 5574: return 1; 5575: } 5576: covar[j][i]=(double)(lval); 5577: strcpy(line,stra); 5578: } 5579: lstra=strlen(stra); 5580: 5581: if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */ 5582: stratrunc = &(stra[lstra-9]); 5583: num[i]=atol(stratrunc); 5584: } 5585: else 5586: num[i]=atol(stra); 5587: /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){ 5588: 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;}*/ 5589: 5590: i=i+1; 5591: } /* End loop reading data */ 5592: 5593: *imax=i-1; /* Number of individuals */ 5594: fclose(fic); 5595: 5596: return (0); 5597: /* endread: */ 5598: printf("Exiting readdata: "); 5599: fclose(fic); 5600: return (1); 5601: 5602: 5603: 5604: } 5605: void removespace(char *str) { 5606: char *p1 = str, *p2 = str; 5607: do 5608: while (*p2 == ' ') 5609: p2++; 5610: while (*p1++ == *p2++); 5611: } 5612: 5613: int decodemodel ( char model[], int lastobs) /**< This routine decode the model and returns: 5614: * Model V1+V2+V3+V8+V7*V8+V5*V6+V8*age+V3*age+age*age 5615: * - nagesqr = 1 if age*age in the model, otherwise 0. 5616: * - cptcovt total number of covariates of the model nbocc(+)+1 = 8 excepting constant and age and age*age 5617: * - cptcovn or number of covariates k of the models excluding age*products =6 and age*age 5618: * - cptcovage number of covariates with age*products =2 5619: * - cptcovs number of simple covariates 5620: * - 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 5621: * which is a new column after the 9 (ncovcol) variables. 5622: * - if k is a product Vn*Vm covar[k][i] is filled with correct values for each individual 5623: * - Tprod[l] gives the kth covariates of the product Vn*Vm l=1 to cptcovprod-cptcovage 5624: * Tprod[1]@2 {5, 6}: position of first product V7*V8 is 5, and second V5*V6 is 6. 5625: * - Tvard[k] p Tvard[1][1]@4 {7, 8, 5, 6} for V7*V8 and V5*V6 . 5626: */ 5627: { 5628: int i, j, k, ks; 5629: int j1, k1, k2; 5630: char modelsav[80]; 5631: char stra[80], strb[80], strc[80], strd[80],stre[80]; 5632: char *strpt; 5633: 5634: /*removespace(model);*/ 5635: if (strlen(model) >1){ /* If there is at least 1 covariate */ 5636: j=0, j1=0, k1=0, k2=-1, ks=0, cptcovn=0; 5637: if (strstr(model,"AGE") !=0){ 5638: printf("Error. AGE must be in lower case 'age' model=1+age+%s. ",model); 5639: fprintf(ficlog,"Error. AGE must be in lower case model=1+age+%s. ",model);fflush(ficlog); 5640: return 1; 5641: } 5642: if (strstr(model,"v") !=0){ 5643: printf("Error. 'v' must be in upper case 'V' model=%s ",model); 5644: fprintf(ficlog,"Error. 'v' must be in upper case model=%s ",model);fflush(ficlog); 5645: return 1; 5646: } 5647: strcpy(modelsav,model); 5648: if ((strpt=strstr(model,"age*age")) !=0){ 5649: printf(" strpt=%s, model=%s\n",strpt, model); 5650: if(strpt != model){ 5651: printf("Error in model: 'model=%s'; 'age*age' should in first place before other covariates\n \ 5652: 'model=1+age+age*age+V1.' or 'model=1+age+age*age+V1+V1*age.', please swap as well as \n \ 5653: corresponding column of parameters.\n",model); 5654: fprintf(ficlog,"Error in model: 'model=%s'; 'age*age' should in first place before other covariates\n \ 5655: 'model=1+age+age*age+V1.' or 'model=1+age+age*age+V1+V1*age.', please swap as well as \n \ 5656: corresponding column of parameters.\n",model); fflush(ficlog); 5657: return 1; 5658: } 5659: 5660: nagesqr=1; 5661: if (strstr(model,"+age*age") !=0) 5662: substrchaine(modelsav, model, "+age*age"); 5663: else if (strstr(model,"age*age+") !=0) 5664: substrchaine(modelsav, model, "age*age+"); 5665: else 5666: substrchaine(modelsav, model, "age*age"); 5667: }else 5668: nagesqr=0; 5669: if (strlen(modelsav) >1){ 5670: j=nbocc(modelsav,'+'); /**< j=Number of '+' */ 5671: j1=nbocc(modelsav,'*'); /**< j1=Number of '*' */ 5672: cptcovs=j+1-j1; /**< Number of simple covariates V1+V1*age+V3 +V3*V4+age*age=> V1 + V3 =2 */ 5673: cptcovt= j+1; /* Number of total covariates in the model, not including 5674: * cst, age and age*age 5675: * V1+V1*age+ V3 + V3*V4+age*age=> 4*/ 5676: /* including age products which are counted in cptcovage. 5677: * but the covariates which are products must be treated 5678: * separately: ncovn=4- 2=2 (V1+V3). */ 5679: cptcovprod=j1; /**< Number of products V1*V2 +v3*age = 2 */ 5680: cptcovprodnoage=0; /**< Number of covariate products without age: V3*V4 =1 */ 5681: 5682: 5683: /* Design 5684: * V1 V2 V3 V4 V5 V6 V7 V8 V9 Weight 5685: * < ncovcol=8 > 5686: * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8 5687: * k= 1 2 3 4 5 6 7 8 5688: * cptcovn number of covariates (not including constant and age ) = # of + plus 1 = 7+1=8 5689: * covar[k,i], value of kth covariate if not including age for individual i: 5690: * covar[1][i]= (V2), covar[4][i]=(V3), covar[8][i]=(V8) 5691: * Tvar[k] # of the kth covariate: Tvar[1]=2 Tvar[4]=3 Tvar[8]=8 5692: * if multiplied by age: V3*age Tvar[3=V3*age]=3 (V3) Tvar[7]=8 and 5693: * Tage[++cptcovage]=k 5694: * if products, new covar are created after ncovcol with k1 5695: * Tvar[k]=ncovcol+k1; # of the kth covariate product: Tvar[5]=ncovcol+1=10 Tvar[6]=ncovcol+1=11 5696: * Tprod[k1]=k; Tprod[1]=5 Tprod[2]= 6; gives the position of the k1th product 5697: * 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 5698: * Tvar[cptcovn+k2]=Tvard[k1][1];Tvar[cptcovn+k2+1]=Tvard[k1][2]; 5699: * Tvar[8+1]=5;Tvar[8+2]=6;Tvar[8+3]=7;Tvar[8+4]=8 inverted 5700: * V1 V2 V3 V4 V5 V6 V7 V8 V9 V10 V11 5701: * < ncovcol=8 > 5702: * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8 d1 d1 d2 d2 5703: * k= 1 2 3 4 5 6 7 8 9 10 11 12 5704: * Tvar[k]= 2 1 3 3 10 11 8 8 5 6 7 8 5705: * p Tvar[1]@12={2, 1, 3, 3, 11, 10, 8, 8, 7, 8, 5, 6} 5706: * p Tprod[1]@2={ 6, 5} 5707: *p Tvard[1][1]@4= {7, 8, 5, 6} 5708: * covar[k][i]= V2 V1 ? V3 V5*V6? V7*V8? ? V8 5709: * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; 5710: *How to reorganize? 5711: * Model V1 + V2 + V3 + V8 + V5*V6 + V7*V8 + V3*age + V8*age 5712: * Tvars {2, 1, 3, 3, 11, 10, 8, 8, 7, 8, 5, 6} 5713: * {2, 1, 4, 8, 5, 6, 3, 7} 5714: * Struct [] 5715: */ 5716: 5717: /* This loop fills the array Tvar from the string 'model'.*/ 5718: /* j is the number of + signs in the model V1+V2+V3 j=2 i=3 to 1 */ 5719: /* modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4 */ 5720: /* k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tage[cptcovage=1]=4 */ 5721: /* k=3 V4 Tvar[k=3]= 4 (from V4) */ 5722: /* k=2 V1 Tvar[k=2]= 1 (from V1) */ 5723: /* k=1 Tvar[1]=2 (from V2) */ 5724: /* k=5 Tvar[5] */ 5725: /* for (k=1; k<=cptcovn;k++) { */ 5726: /* cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]]; */ 5727: /* } */ 5728: /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtab[ij][Tvar[Tage[k]]]]*cov[2]; */ 5729: /* 5730: * Treating invertedly V2+V1+V3*age+V2*V4 is as if written V2*V4 +V3*age + V1 + V2 */ 5731: for(k=cptcovt; k>=1;k--) /**< Number of covariates */ 5732: Tvar[k]=0; 5733: cptcovage=0; 5734: for(k=1; k<=cptcovt;k++){ /* Loop on total covariates of the model */ 5735: cutl(stra,strb,modelsav,'+'); /* keeps in strb after the first '+' 5736: modelsav==V2+V1+V4+V3*age strb=V3*age stra=V2+V1+V4 */ 5737: if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */ 5738: /* printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/ 5739: /*scanf("%d",i);*/ 5740: if (strchr(strb,'*')) { /**< Model includes a product V2+V1+V4+V3*age strb=V3*age */ 5741: cutl(strc,strd,strb,'*'); /**< strd*strc Vm*Vn: strb=V3*age(input) strc=age strd=V3 ; V3*V2 strc=V2, strd=V3 */ 5742: if (strcmp(strc,"age")==0) { /**< Model includes age: Vn*age */ 5743: /* covar is not filled and then is empty */ 5744: cptcovprod--; 5745: cutl(stre,strb,strd,'V'); /* strd=V3(input): stre="3" */ 5746: Tvar[k]=atoi(stre); /* V2+V1+V4+V3*age Tvar[4]=3 ; V1+V2*age Tvar[2]=2; V1+V1*age Tvar[2]=1 */ 5747: cptcovage++; /* Sums the number of covariates which include age as a product */ 5748: Tage[cptcovage]=k; /* Tvar[4]=3, Tage[1] = 4 or V1+V1*age Tvar[2]=1, Tage[1]=2 */ 5749: /*printf("stre=%s ", stre);*/ 5750: } else if (strcmp(strd,"age")==0) { /* or age*Vn */ 5751: cptcovprod--; 5752: cutl(stre,strb,strc,'V'); 5753: Tvar[k]=atoi(stre); 5754: cptcovage++; 5755: Tage[cptcovage]=k; 5756: } else { /* Age is not in the model product V2+V1+V1*V4+V3*age+V3*V2 strb=V3*V2*/ 5757: /* loops on k1=1 (V3*V2) and k1=2 V4*V3 */ 5758: cptcovn++; 5759: cptcovprodnoage++;k1++; 5760: cutl(stre,strb,strc,'V'); /* strc= Vn, stre is n; strb=V3*V2 stre=3 strc=*/ 5761: Tvar[k]=ncovcol+k1; /* For model-covariate k tells which data-covariate to use but 5762: because this model-covariate is a construction we invent a new column 5763: ncovcol + k1 5764: If already ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2 5765: Tvar[3=V1*V4]=4+1 Tvar[5=V3*V2]=4 + 2= 6, etc */ 5766: cutl(strc,strb,strd,'V'); /* strd was Vm, strc is m */ 5767: Tprod[k1]=k; /* Tprod[1]=3(=V1*V4) for V2+V1+V1*V4+age*V3+V3*V2 */ 5768: Tvard[k1][1] =atoi(strc); /* m 1 for V1*/ 5769: Tvard[k1][2] =atoi(stre); /* n 4 for V4*/ 5770: k2=k2+2; 5771: Tvar[cptcovt+k2]=Tvard[k1][1]; /* Tvar[(cptcovt=4+k2=1)=5]= 1 (V1) */ 5772: Tvar[cptcovt+k2+1]=Tvard[k1][2]; /* Tvar[(cptcovt=4+(k2=1)+1)=6]= 4 (V4) */ 5773: for (i=1; i<=lastobs;i++){ 5774: /* Computes the new covariate which is a product of 5775: covar[n][i]* covar[m][i] and stores it at ncovol+k1 May not be defined */ 5776: covar[ncovcol+k1][i]=covar[atoi(stre)][i]*covar[atoi(strc)][i]; 5777: } 5778: } /* End age is not in the model */ 5779: } /* End if model includes a product */ 5780: else { /* no more sum */ 5781: /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/ 5782: /* scanf("%d",i);*/ 5783: cutl(strd,strc,strb,'V'); 5784: ks++; /**< Number of simple covariates */ 5785: cptcovn++; 5786: Tvar[k]=atoi(strd); 5787: } 5788: strcpy(modelsav,stra); /* modelsav=V2+V1+V4 stra=V2+V1+V4 */ 5789: /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav); 5790: scanf("%d",i);*/ 5791: } /* end of loop + on total covariates */ 5792: } /* end if strlen(modelsave == 0) age*age might exist */ 5793: } /* end if strlen(model == 0) */ 5794: 5795: /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products. 5796: If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/ 5797: 5798: /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]); 5799: printf("cptcovprod=%d ", cptcovprod); 5800: fprintf(ficlog,"cptcovprod=%d ", cptcovprod); 5801: 5802: scanf("%d ",i);*/ 5803: 5804: 5805: return (0); /* with covar[new additional covariate if product] and Tage if age */ 5806: /*endread:*/ 5807: printf("Exiting decodemodel: "); 5808: return (1); 5809: } 5810: 5811: int calandcheckages(int imx, int maxwav, double *agemin, double *agemax, int *nberr, int *nbwarn ) 5812: { 5813: int i, m; 5814: 5815: for (i=1; i<=imx; i++) { 5816: for(m=2; (m<= maxwav); m++) { 5817: if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){ 5818: anint[m][i]=9999; 5819: s[m][i]=-1; 5820: } 5821: if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){ 5822: *nberr = *nberr + 1; 5823: 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); 5824: 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); 5825: s[m][i]=-1; 5826: } 5827: if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){ 5828: (*nberr)++; 5829: 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]); 5830: 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]); 5831: s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */ 5832: } 5833: } 5834: } 5835: 5836: for (i=1; i<=imx; i++) { 5837: agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]); 5838: for(m=firstpass; (m<= lastpass); m++){ 5839: if(s[m][i] >0 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){ 5840: if (s[m][i] >= nlstate+1) { 5841: if(agedc[i]>0){ 5842: if((int)moisdc[i]!=99 && (int)andc[i]!=9999){ 5843: agev[m][i]=agedc[i]; 5844: /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/ 5845: }else { 5846: if ((int)andc[i]!=9999){ 5847: nbwarn++; 5848: printf("Warning negative age at death: %ld line:%d\n",num[i],i); 5849: fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i); 5850: agev[m][i]=-1; 5851: } 5852: } 5853: } /* agedc > 0 */ 5854: } 5855: else if(s[m][i] !=9){ /* Standard case, age in fractional 5856: years but with the precision of a month */ 5857: agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]); 5858: if((int)mint[m][i]==99 || (int)anint[m][i]==9999) 5859: agev[m][i]=1; 5860: else if(agev[m][i] < *agemin){ 5861: *agemin=agev[m][i]; 5862: printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], *agemin); 5863: } 5864: else if(agev[m][i] >*agemax){ 5865: *agemax=agev[m][i]; 5866: /* printf(" Max anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.2f\n",m,i,anint[m][i], i,annais[i], *agemax);*/ 5867: } 5868: /*agev[m][i]=anint[m][i]-annais[i];*/ 5869: /* agev[m][i] = age[i]+2*m;*/ 5870: } 5871: else { /* =9 */ 5872: agev[m][i]=1; 5873: s[m][i]=-1; 5874: } 5875: } 5876: else /*= 0 Unknown */ 5877: agev[m][i]=1; 5878: } 5879: 5880: } 5881: for (i=1; i<=imx; i++) { 5882: for(m=firstpass; (m<=lastpass); m++){ 5883: if (s[m][i] > (nlstate+ndeath)) { 5884: (*nberr)++; 5885: 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); 5886: 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); 5887: return 1; 5888: } 5889: } 5890: } 5891: 5892: /*for (i=1; i<=imx; i++){ 5893: for (m=firstpass; (m<lastpass); m++){ 5894: printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]); 5895: } 5896: 5897: }*/ 5898: 5899: 5900: printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax); 5901: fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax); 5902: 5903: return (0); 5904: /* endread:*/ 5905: printf("Exiting calandcheckages: "); 5906: return (1); 5907: } 5908: 5909: #if defined(_MSC_VER) 5910: /*printf("Visual C++ compiler: %s \n;", _MSC_FULL_VER);*/ 5911: /*fprintf(ficlog, "Visual C++ compiler: %s \n;", _MSC_FULL_VER);*/ 5912: //#include "stdafx.h" 5913: //#include <stdio.h> 5914: //#include <tchar.h> 5915: //#include <windows.h> 5916: //#include <iostream> 5917: typedef BOOL(WINAPI *LPFN_ISWOW64PROCESS) (HANDLE, PBOOL); 5918: 5919: LPFN_ISWOW64PROCESS fnIsWow64Process; 5920: 5921: BOOL IsWow64() 5922: { 5923: BOOL bIsWow64 = FALSE; 5924: 5925: //typedef BOOL (APIENTRY *LPFN_ISWOW64PROCESS) 5926: // (HANDLE, PBOOL); 5927: 5928: //LPFN_ISWOW64PROCESS fnIsWow64Process; 5929: 5930: HMODULE module = GetModuleHandle(_T("kernel32")); 5931: const char funcName[] = "IsWow64Process"; 5932: fnIsWow64Process = (LPFN_ISWOW64PROCESS) 5933: GetProcAddress(module, funcName); 5934: 5935: if (NULL != fnIsWow64Process) 5936: { 5937: if (!fnIsWow64Process(GetCurrentProcess(), 5938: &bIsWow64)) 5939: //throw std::exception("Unknown error"); 5940: printf("Unknown error\n"); 5941: } 5942: return bIsWow64 != FALSE; 5943: } 5944: #endif 5945: 5946: void syscompilerinfo(int logged) 5947: { 5948: /* #include "syscompilerinfo.h"*/ 5949: /* command line Intel compiler 32bit windows, XP compatible:*/ 5950: /* /GS /W3 /Gy 5951: /Zc:wchar_t /Zi /O2 /Fd"Release\vc120.pdb" /D "WIN32" /D "NDEBUG" /D 5952: "_CONSOLE" /D "_LIB" /D "_USING_V110_SDK71_" /D "_UNICODE" /D 5953: "UNICODE" /Qipo /Zc:forScope /Gd /Oi /MT /Fa"Release\" /EHsc /nologo 5954: /Fo"Release\" /Qprof-dir "Release\" /Fp"Release\IMaCh.pch" 5955: */ 5956: /* 64 bits */ 5957: /* 5958: /GS /W3 /Gy 5959: /Zc:wchar_t /Zi /O2 /Fd"x64\Release\vc120.pdb" /D "WIN32" /D "NDEBUG" 5960: /D "_CONSOLE" /D "_LIB" /D "_UNICODE" /D "UNICODE" /Qipo /Zc:forScope 5961: /Oi /MD /Fa"x64\Release\" /EHsc /nologo /Fo"x64\Release\" /Qprof-dir 5962: "x64\Release\" /Fp"x64\Release\IMaCh.pch" */ 5963: /* Optimization are useless and O3 is slower than O2 */ 5964: /* 5965: /GS /W3 /Gy /Zc:wchar_t /Zi /O3 /Fd"x64\Release\vc120.pdb" /D "WIN32" 5966: /D "NDEBUG" /D "_CONSOLE" /D "_LIB" /D "_UNICODE" /D "UNICODE" /Qipo 5967: /Zc:forScope /Oi /MD /Fa"x64\Release\" /EHsc /nologo /Qparallel 5968: /Fo"x64\Release\" /Qprof-dir "x64\Release\" /Fp"x64\Release\IMaCh.pch" 5969: */ 5970: /* Link is */ /* /OUT:"visual studio 5971: 2013\Projects\IMaCh\Release\IMaCh.exe" /MANIFEST /NXCOMPAT 5972: /PDB:"visual studio 5973: 2013\Projects\IMaCh\Release\IMaCh.pdb" /DYNAMICBASE 5974: "kernel32.lib" "user32.lib" "gdi32.lib" "winspool.lib" 5975: "comdlg32.lib" "advapi32.lib" "shell32.lib" "ole32.lib" 5976: "oleaut32.lib" "uuid.lib" "odbc32.lib" "odbccp32.lib" 5977: /MACHINE:X86 /OPT:REF /SAFESEH /INCREMENTAL:NO 5978: /SUBSYSTEM:CONSOLE",5.01" /MANIFESTUAC:"level='asInvoker' 5979: uiAccess='false'" 5980: /ManifestFile:"Release\IMaCh.exe.intermediate.manifest" /OPT:ICF 5981: /NOLOGO /TLBID:1 5982: */ 5983: #if defined __INTEL_COMPILER 5984: #if defined(__GNUC__) 5985: struct utsname sysInfo; /* For Intel on Linux and OS/X */ 5986: #endif 5987: #elif defined(__GNUC__) 5988: #ifndef __APPLE__ 5989: #include <gnu/libc-version.h> /* Only on gnu */ 5990: #endif 5991: struct utsname sysInfo; 5992: int cross = CROSS; 5993: if (cross){ 5994: printf("Cross-"); 5995: if(logged) fprintf(ficlog, "Cross-"); 5996: } 5997: #endif 5998: 5999: #include <stdint.h> 6000: 6001: printf("Compiled with:");if(logged)fprintf(ficlog,"Compiled with:"); 6002: #if defined(__clang__) 6003: printf(" Clang/LLVM");if(logged)fprintf(ficlog," Clang/LLVM"); /* Clang/LLVM. ---------------------------------------------- */ 6004: #endif 6005: #if defined(__ICC) || defined(__INTEL_COMPILER) 6006: printf(" Intel ICC/ICPC");if(logged)fprintf(ficlog," Intel ICC/ICPC");/* Intel ICC/ICPC. ------------------------------------------ */ 6007: #endif 6008: #if defined(__GNUC__) || defined(__GNUG__) 6009: printf(" GNU GCC/G++");if(logged)fprintf(ficlog," GNU GCC/G++");/* GNU GCC/G++. --------------------------------------------- */ 6010: #endif 6011: #if defined(__HP_cc) || defined(__HP_aCC) 6012: printf(" Hewlett-Packard C/aC++");if(logged)fprintf(fcilog," Hewlett-Packard C/aC++"); /* Hewlett-Packard C/aC++. ---------------------------------- */ 6013: #endif 6014: #if defined(__IBMC__) || defined(__IBMCPP__) 6015: printf(" IBM XL C/C++"); if(logged) fprintf(ficlog," IBM XL C/C++");/* IBM XL C/C++. -------------------------------------------- */ 6016: #endif 6017: #if defined(_MSC_VER) 6018: printf(" Microsoft Visual Studio");if(logged)fprintf(ficlog," Microsoft Visual Studio");/* Microsoft Visual Studio. --------------------------------- */ 6019: #endif 6020: #if defined(__PGI) 6021: printf(" Portland Group PGCC/PGCPP");if(logged) fprintf(ficlog," Portland Group PGCC/PGCPP");/* Portland Group PGCC/PGCPP. ------------------------------- */ 6022: #endif 6023: #if defined(__SUNPRO_C) || defined(__SUNPRO_CC) 6024: printf(" Oracle Solaris Studio");if(logged)fprintf(ficlog," Oracle Solaris Studio\n");/* Oracle Solaris Studio. ----------------------------------- */ 6025: #endif 6026: printf(" for "); if (logged) fprintf(ficlog, " for "); 6027: 6028: // http://stackoverflow.com/questions/4605842/how-to-identify-platform-compiler-from-preprocessor-macros 6029: #ifdef _WIN32 // note the underscore: without it, it's not msdn official! 6030: // Windows (x64 and x86) 6031: printf("Windows (x64 and x86) ");if(logged) fprintf(ficlog,"Windows (x64 and x86) "); 6032: #elif __unix__ // all unices, not all compilers 6033: // Unix 6034: printf("Unix ");if(logged) fprintf(ficlog,"Unix "); 6035: #elif __linux__ 6036: // linux 6037: printf("linux ");if(logged) fprintf(ficlog,"linux "); 6038: #elif __APPLE__ 6039: // Mac OS, not sure if this is covered by __posix__ and/or __unix__ though.. 6040: printf("Mac OS ");if(logged) fprintf(ficlog,"Mac OS "); 6041: #endif 6042: 6043: /* __MINGW32__ */ 6044: /* __CYGWIN__ */ 6045: /* __MINGW64__ */ 6046: // http://msdn.microsoft.com/en-us/library/b0084kay.aspx 6047: /* _MSC_VER //the Visual C++ compiler is 17.00.51106.1, the _MSC_VER macro evaluates to 1700. Type cl /? */ 6048: /* _MSC_FULL_VER //the Visual C++ compiler is 15.00.20706.01, the _MSC_FULL_VER macro evaluates to 150020706 */ 6049: /* _WIN64 // Defined for applications for Win64. */ 6050: /* _M_X64 // Defined for compilations that target x64 processors. */ 6051: /* _DEBUG // Defined when you compile with /LDd, /MDd, and /MTd. */ 6052: 6053: #if UINTPTR_MAX == 0xffffffff 6054: printf(" 32-bit"); if(logged) fprintf(ficlog," 32-bit");/* 32-bit */ 6055: #elif UINTPTR_MAX == 0xffffffffffffffff 6056: printf(" 64-bit"); if(logged) fprintf(ficlog," 64-bit");/* 64-bit */ 6057: #else 6058: printf(" wtf-bit"); if(logged) fprintf(ficlog," wtf-bit");/* wtf */ 6059: #endif 6060: 6061: #if defined(__GNUC__) 6062: # if defined(__GNUC_PATCHLEVEL__) 6063: # define __GNUC_VERSION__ (__GNUC__ * 10000 \ 6064: + __GNUC_MINOR__ * 100 \ 6065: + __GNUC_PATCHLEVEL__) 6066: # else 6067: # define __GNUC_VERSION__ (__GNUC__ * 10000 \ 6068: + __GNUC_MINOR__ * 100) 6069: # endif 6070: printf(" using GNU C version %d.\n", __GNUC_VERSION__); 6071: if(logged) fprintf(ficlog, " using GNU C version %d.\n", __GNUC_VERSION__); 6072: 6073: if (uname(&sysInfo) != -1) { 6074: printf("Running on: %s %s %s %s %s\n",sysInfo.sysname, sysInfo.nodename, sysInfo.release, sysInfo.version, sysInfo.machine); 6075: if(logged) fprintf(ficlog,"Running on: %s %s %s %s %s\n ",sysInfo.sysname, sysInfo.nodename, sysInfo.release, sysInfo.version, sysInfo.machine); 6076: } 6077: else 6078: perror("uname() error"); 6079: //#ifndef __INTEL_COMPILER 6080: #if !defined (__INTEL_COMPILER) && !defined(__APPLE__) 6081: printf("GNU libc version: %s\n", gnu_get_libc_version()); 6082: if(logged) fprintf(ficlog,"GNU libc version: %s\n", gnu_get_libc_version()); 6083: #endif 6084: #endif 6085: 6086: // void main() 6087: // { 6088: #if defined(_MSC_VER) 6089: if (IsWow64()){ 6090: printf("\nThe program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n"); 6091: if (logged) fprintf(ficlog, "\nThe program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n"); 6092: } 6093: else{ 6094: printf("\nThe program is not running under WOW64 (i.e probably on a 64bit Windows).\n"); 6095: if (logged) fprintf(ficlog, "\nThe programm is not running under WOW64 (i.e probably on a 64bit Windows).\n"); 6096: } 6097: // printf("\nPress Enter to continue..."); 6098: // getchar(); 6099: // } 6100: 6101: #endif 6102: 6103: 6104: } 6105: 6106: int prevalence_limit(double *p, double **prlim, double ageminpar, double agemaxpar){ 6107: /*--------------- Prevalence limit (period or stable prevalence) --------------*/ 6108: int i, j, k, i1 ; 6109: double ftolpl = 1.e-10; 6110: double age, agebase, agelim; 6111: 6112: strcpy(filerespl,"pl"); 6113: strcat(filerespl,fileres); 6114: if((ficrespl=fopen(filerespl,"w"))==NULL) { 6115: printf("Problem with period (stable) prevalence resultfile: %s\n", filerespl);return 1; 6116: fprintf(ficlog,"Problem with period (stable) prevalence resultfile: %s\n", filerespl);return 1; 6117: } 6118: printf("Computing period (stable) prevalence: result on file '%s' \n", filerespl); 6119: fprintf(ficlog,"Computing period (stable) prevalence: result on file '%s' \n", filerespl); 6120: pstamp(ficrespl); 6121: fprintf(ficrespl,"# Period (stable) prevalence \n"); 6122: fprintf(ficrespl,"#Age "); 6123: for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i); 6124: fprintf(ficrespl,"\n"); 6125: 6126: /* prlim=matrix(1,nlstate,1,nlstate);*/ /* back in main */ 6127: 6128: agebase=ageminpar; 6129: agelim=agemaxpar; 6130: 6131: i1=pow(2,cptcoveff); 6132: if (cptcovn < 1){i1=1;} 6133: 6134: for(cptcov=1,k=0;cptcov<=i1;cptcov++){ 6135: /* for(cptcov=1,k=0;cptcov<=1;cptcov++){ */ 6136: //for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){ 6137: k=k+1; 6138: /* to clean */ 6139: //printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtab[cptcod][cptcov]); 6140: fprintf(ficrespl,"\n#******"); 6141: printf("\n#******"); 6142: fprintf(ficlog,"\n#******"); 6143: for(j=1;j<=cptcoveff;j++) { 6144: fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]); 6145: printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]); 6146: fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]); 6147: } 6148: fprintf(ficrespl,"******\n"); 6149: printf("******\n"); 6150: fprintf(ficlog,"******\n"); 6151: 6152: fprintf(ficrespl,"#Age "); 6153: for(j=1;j<=cptcoveff;j++) { 6154: fprintf(ficrespl,"V%d %d",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]); 6155: } 6156: for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i); 6157: fprintf(ficrespl,"\n"); 6158: 6159: for (age=agebase; age<=agelim; age++){ 6160: /* for (age=agebase; age<=agebase; age++){ */ 6161: prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k); 6162: fprintf(ficrespl,"%.0f ",age ); 6163: for(j=1;j<=cptcoveff;j++) 6164: fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]); 6165: for(i=1; i<=nlstate;i++) 6166: fprintf(ficrespl," %.5f", prlim[i][i]); 6167: fprintf(ficrespl,"\n"); 6168: } /* Age */ 6169: /* was end of cptcod */ 6170: } /* cptcov */ 6171: return 0; 6172: } 6173: 6174: int hPijx(double *p, int bage, int fage){ 6175: /*------------- h Pij x at various ages ------------*/ 6176: 6177: int stepsize; 6178: int agelim; 6179: int hstepm; 6180: int nhstepm; 6181: int h, i, i1, j, k; 6182: 6183: double agedeb; 6184: double ***p3mat; 6185: 6186: strcpy(filerespij,"pij"); strcat(filerespij,fileres); 6187: if((ficrespij=fopen(filerespij,"w"))==NULL) { 6188: printf("Problem with Pij resultfile: %s\n", filerespij); return 1; 6189: fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij); return 1; 6190: } 6191: printf("Computing pij: result on file '%s' \n", filerespij); 6192: fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij); 6193: 6194: stepsize=(int) (stepm+YEARM-1)/YEARM; 6195: /*if (stepm<=24) stepsize=2;*/ 6196: 6197: agelim=AGESUP; 6198: hstepm=stepsize*YEARM; /* Every year of age */ 6199: hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */ 6200: 6201: /* hstepm=1; aff par mois*/ 6202: pstamp(ficrespij); 6203: fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x "); 6204: i1= pow(2,cptcoveff); 6205: /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */ 6206: /* /\*for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*\/ */ 6207: /* k=k+1; */ 6208: for (k=1; k <= (int) pow(2,cptcoveff); k++){ 6209: fprintf(ficrespij,"\n#****** "); 6210: for(j=1;j<=cptcoveff;j++) 6211: fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]); 6212: fprintf(ficrespij,"******\n"); 6213: 6214: for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */ 6215: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 6216: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */ 6217: 6218: /* nhstepm=nhstepm*YEARM; aff par mois*/ 6219: 6220: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); 6221: oldm=oldms;savm=savms; 6222: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k); 6223: fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j="); 6224: for(i=1; i<=nlstate;i++) 6225: for(j=1; j<=nlstate+ndeath;j++) 6226: fprintf(ficrespij," %1d-%1d",i,j); 6227: fprintf(ficrespij,"\n"); 6228: for (h=0; h<=nhstepm; h++){ 6229: /*agedebphstep = agedeb + h*hstepm/YEARM*stepm;*/ 6230: fprintf(ficrespij,"%d %3.f %3.f",k, agedeb, agedeb + h*hstepm/YEARM*stepm ); 6231: for(i=1; i<=nlstate;i++) 6232: for(j=1; j<=nlstate+ndeath;j++) 6233: fprintf(ficrespij," %.5f", p3mat[i][j][h]); 6234: fprintf(ficrespij,"\n"); 6235: } 6236: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); 6237: fprintf(ficrespij,"\n"); 6238: } 6239: /*}*/ 6240: } 6241: return 0; 6242: } 6243: 6244: 6245: /***********************************************/ 6246: /**************** Main Program *****************/ 6247: /***********************************************/ 6248: 6249: int main(int argc, char *argv[]) 6250: { 6251: #ifdef GSL 6252: const gsl_multimin_fminimizer_type *T; 6253: size_t iteri = 0, it; 6254: int rval = GSL_CONTINUE; 6255: int status = GSL_SUCCESS; 6256: double ssval; 6257: #endif 6258: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav); 6259: int i,j, k, n=MAXN,iter=0,m,size=100, cptcod; 6260: 6261: int jj, ll, li, lj, lk; 6262: int numlinepar=0; /* Current linenumber of parameter file */ 6263: int itimes; 6264: int NDIM=2; 6265: int vpopbased=0; 6266: 6267: char ca[32], cb[32]; 6268: /* FILE *fichtm; *//* Html File */ 6269: /* FILE *ficgp;*/ /*Gnuplot File */ 6270: struct stat info; 6271: double agedeb=0.; 6272: double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20; 6273: 6274: double fret; 6275: double dum=0.; /* Dummy variable */ 6276: double ***p3mat; 6277: double ***mobaverage; 6278: 6279: char line[MAXLINE]; 6280: char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE]; 6281: char pathr[MAXLINE], pathimach[MAXLINE]; 6282: char *tok, *val; /* pathtot */ 6283: int firstobs=1, lastobs=10; 6284: int c, h , cpt; 6285: int jl=0; 6286: int i1, j1, jk, stepsize=0; 6287: int *tab; 6288: int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */ 6289: int mobilav=0,popforecast=0; 6290: int hstepm=0, nhstepm=0; 6291: int agemortsup; 6292: float sumlpop=0.; 6293: double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000; 6294: double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000; 6295: 6296: double bage=0, fage=110., age, agelim=0., agebase=0.; 6297: double ftolpl=FTOL; 6298: double **prlim; 6299: double ***param; /* Matrix of parameters */ 6300: double *p; 6301: double **matcov; /* Matrix of covariance */ 6302: double ***delti3; /* Scale */ 6303: double *delti; /* Scale */ 6304: double ***eij, ***vareij; 6305: double **varpl; /* Variances of prevalence limits by age */ 6306: double *epj, vepp; 6307: 6308: double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000; 6309: double **ximort; 6310: char *alph[]={"a","a","b","c","d","e"}, str[4]="1234"; 6311: int *dcwave; 6312: 6313: char z[1]="c"; 6314: 6315: /*char *strt;*/ 6316: char strtend[80]; 6317: 6318: 6319: /* setlocale (LC_ALL, ""); */ 6320: /* bindtextdomain (PACKAGE, LOCALEDIR); */ 6321: /* textdomain (PACKAGE); */ 6322: /* setlocale (LC_CTYPE, ""); */ 6323: /* setlocale (LC_MESSAGES, ""); */ 6324: 6325: /* gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */ 6326: rstart_time = time(NULL); 6327: /* (void) gettimeofday(&start_time,&tzp);*/ 6328: start_time = *localtime(&rstart_time); 6329: curr_time=start_time; 6330: /*tml = *localtime(&start_time.tm_sec);*/ 6331: /* strcpy(strstart,asctime(&tml)); */ 6332: strcpy(strstart,asctime(&start_time)); 6333: 6334: /* printf("Localtime (at start)=%s",strstart); */ 6335: /* tp.tm_sec = tp.tm_sec +86400; */ 6336: /* tm = *localtime(&start_time.tm_sec); */ 6337: /* tmg.tm_year=tmg.tm_year +dsign*dyear; */ 6338: /* tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */ 6339: /* tmg.tm_hour=tmg.tm_hour + 1; */ 6340: /* tp.tm_sec = mktime(&tmg); */ 6341: /* strt=asctime(&tmg); */ 6342: /* printf("Time(after) =%s",strstart); */ 6343: /* (void) time (&time_value); 6344: * printf("time=%d,t-=%d\n",time_value,time_value-86400); 6345: * tm = *localtime(&time_value); 6346: * strstart=asctime(&tm); 6347: * printf("tim_value=%d,asctime=%s\n",time_value,strstart); 6348: */ 6349: 6350: nberr=0; /* Number of errors and warnings */ 6351: nbwarn=0; 6352: #ifdef WIN32 6353: _getcwd(pathcd, size); 6354: #else 6355: getcwd(pathcd, size); 6356: #endif 6357: syscompilerinfo(0); 6358: printf("\n%s\n%s",version,fullversion); 6359: if(argc <=1){ 6360: printf("\nEnter the parameter file name: "); 6361: fgets(pathr,FILENAMELENGTH,stdin); 6362: i=strlen(pathr); 6363: if(pathr[i-1]=='\n') 6364: pathr[i-1]='\0'; 6365: i=strlen(pathr); 6366: if(pathr[i-1]==' ') /* This may happen when dragging on oS/X! */ 6367: pathr[i-1]='\0'; 6368: for (tok = pathr; tok != NULL; ){ 6369: printf("Pathr |%s|\n",pathr); 6370: while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0'); 6371: printf("val= |%s| pathr=%s\n",val,pathr); 6372: strcpy (pathtot, val); 6373: if(pathr[0] == '\0') break; /* Dirty */ 6374: } 6375: } 6376: else{ 6377: strcpy(pathtot,argv[1]); 6378: } 6379: /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/ 6380: /*cygwin_split_path(pathtot,path,optionfile); 6381: printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/ 6382: /* cutv(path,optionfile,pathtot,'\\');*/ 6383: 6384: /* Split argv[0], imach program to get pathimach */ 6385: printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]); 6386: split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname); 6387: printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname); 6388: /* strcpy(pathimach,argv[0]); */ 6389: /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */ 6390: split(pathtot,path,optionfile,optionfilext,optionfilefiname); 6391: printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname); 6392: #ifdef WIN32 6393: _chdir(path); /* Can be a relative path */ 6394: if(_getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */ 6395: #else 6396: chdir(path); /* Can be a relative path */ 6397: if (getcwd(pathcd, MAXLINE) > 0) /* So pathcd is the full path */ 6398: #endif 6399: printf("Current directory %s!\n",pathcd); 6400: strcpy(command,"mkdir "); 6401: strcat(command,optionfilefiname); 6402: if((outcmd=system(command)) != 0){ 6403: printf("Directory already exists (or can't create it) %s%s, err=%d\n",path,optionfilefiname,outcmd); 6404: /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */ 6405: /* fclose(ficlog); */ 6406: /* exit(1); */ 6407: } 6408: /* if((imk=mkdir(optionfilefiname))<0){ */ 6409: /* perror("mkdir"); */ 6410: /* } */ 6411: 6412: /*-------- arguments in the command line --------*/ 6413: 6414: /* Main Log file */ 6415: strcat(filelog, optionfilefiname); 6416: strcat(filelog,".log"); /* */ 6417: if((ficlog=fopen(filelog,"w"))==NULL) { 6418: printf("Problem with logfile %s\n",filelog); 6419: goto end; 6420: } 6421: fprintf(ficlog,"Log filename:%s\n",filelog); 6422: fprintf(ficlog,"\n%s\n%s",version,fullversion); 6423: fprintf(ficlog,"\nEnter the parameter file name: \n"); 6424: fprintf(ficlog,"pathimach=%s\npathtot=%s\n\ 6425: path=%s \n\ 6426: optionfile=%s\n\ 6427: optionfilext=%s\n\ 6428: optionfilefiname='%s'\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname); 6429: 6430: syscompilerinfo(0); 6431: 6432: printf("Local time (at start):%s",strstart); 6433: fprintf(ficlog,"Local time (at start): %s",strstart); 6434: fflush(ficlog); 6435: /* (void) gettimeofday(&curr_time,&tzp); */ 6436: /* printf("Elapsed time %d\n", asc_diff_time(curr_time.tm_sec-start_time.tm_sec,tmpout)); */ 6437: 6438: /* */ 6439: strcpy(fileres,"r"); 6440: strcat(fileres, optionfilefiname); 6441: strcat(fileres,".txt"); /* Other files have txt extension */ 6442: 6443: /* Main ---------arguments file --------*/ 6444: 6445: if((ficpar=fopen(optionfile,"r"))==NULL) { 6446: printf("Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno)); 6447: fprintf(ficlog,"Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno)); 6448: fflush(ficlog); 6449: /* goto end; */ 6450: exit(70); 6451: } 6452: 6453: 6454: 6455: strcpy(filereso,"o"); 6456: strcat(filereso,fileres); 6457: if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */ 6458: printf("Problem with Output resultfile: %s\n", filereso); 6459: fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso); 6460: fflush(ficlog); 6461: goto end; 6462: } 6463: 6464: /* Reads comments: lines beginning with '#' */ 6465: numlinepar=0; 6466: while((c=getc(ficpar))=='#' && c!= EOF){ 6467: ungetc(c,ficpar); 6468: fgets(line, MAXLINE, ficpar); 6469: numlinepar++; 6470: fputs(line,stdout); 6471: fputs(line,ficparo); 6472: fputs(line,ficlog); 6473: } 6474: ungetc(c,ficpar); 6475: 6476: 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); 6477: numlinepar++; 6478: 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); 6479: if(model[strlen(model)-1]=='.') /* Suppressing leading dot in the model */ 6480: model[strlen(model)-1]='\0'; 6481: 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); 6482: 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); 6483: fflush(ficlog); 6484: /* if(model[0]=='#'|| model[0]== '\0'){ */ 6485: if(model[0]=='#'){ 6486: printf("Error in 'model' line: model should start with 'model=1+age+' and end with '.' \n \ 6487: 'model=1+age+.' or 'model=1+age+V1.' or 'model=1+age+age*age+V1+V1*age.' or \n \ 6488: 'model=1+age+V1+V2.' or 'model=1+age+V1+V2+V1*V2.' etc. \n"); \ 6489: if(mle != -1){ 6490: printf("Fix the model line and run imach with mle=-1 to get a correct template of the parameter file.\n"); 6491: exit(1); 6492: } 6493: } 6494: while((c=getc(ficpar))=='#' && c!= EOF){ 6495: ungetc(c,ficpar); 6496: fgets(line, MAXLINE, ficpar); 6497: numlinepar++; 6498: fputs(line, stdout); 6499: //puts(line); 6500: fputs(line,ficparo); 6501: fputs(line,ficlog); 6502: } 6503: ungetc(c,ficpar); 6504: 6505: 6506: covar=matrix(0,NCOVMAX,1,n); /**< used in readdata */ 6507: cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement plus one, indepently of n in Vn*/ 6508: /* v1+v2+v3+v2*v4+v5*age makes cptcovn = 5 6509: v1+v2*age+v2*v3 makes cptcovn = 3 6510: */ 6511: if (strlen(model)>1) 6512: 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*/ 6513: else 6514: ncovmodel=2; /* Constant and age */ 6515: nforce= (nlstate+ndeath-1)*nlstate; /* Number of forces ij from state i to j */ 6516: npar= nforce*ncovmodel; /* Number of parameters like aij*/ 6517: if(npar >MAXPARM || nlstate >NLSTATEMAX || ndeath >NDEATHMAX || ncovmodel>NCOVMAX){ 6518: 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); 6519: 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); 6520: fflush(stdout); 6521: fclose (ficlog); 6522: goto end; 6523: } 6524: delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); 6525: delti=delti3[1][1]; 6526: /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/ 6527: if(mle==-1){ /* Print a wizard for help writing covariance matrix */ 6528: prwizard(ncovmodel, nlstate, ndeath, model, ficparo); 6529: printf(" You chose mle=-1, look at file %s for a template of covariance matrix \n",filereso); 6530: fprintf(ficlog," You chose mle=-1, look at file %s for a template of covariance matrix \n",filereso); 6531: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 6532: fclose (ficparo); 6533: fclose (ficlog); 6534: goto end; 6535: exit(0); 6536: } 6537: else if(mle==-3) { /* Main Wizard */ 6538: prwizard(ncovmodel, nlstate, ndeath, model, ficparo); 6539: printf(" You chose mle=-3, look at file %s for a template of covariance matrix \n",filereso); 6540: fprintf(ficlog," You chose mle=-3, look at file %s for a template of covariance matrix \n",filereso); 6541: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); 6542: matcov=matrix(1,npar,1,npar); 6543: } 6544: else{ 6545: /* Read guessed parameters */ 6546: /* Reads comments: lines beginning with '#' */ 6547: while((c=getc(ficpar))=='#' && c!= EOF){ 6548: ungetc(c,ficpar); 6549: fgets(line, MAXLINE, ficpar); 6550: numlinepar++; 6551: fputs(line,stdout); 6552: fputs(line,ficparo); 6553: fputs(line,ficlog); 6554: } 6555: ungetc(c,ficpar); 6556: 6557: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); 6558: for(i=1; i <=nlstate; i++){ 6559: j=0; 6560: for(jj=1; jj <=nlstate+ndeath; jj++){ 6561: if(jj==i) continue; 6562: j++; 6563: fscanf(ficpar,"%1d%1d",&i1,&j1); 6564: if ((i1 != i) && (j1 != j)){ 6565: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \ 6566: It might be a problem of design; if ncovcol and the model are correct\n \ 6567: run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1); 6568: exit(1); 6569: } 6570: fprintf(ficparo,"%1d%1d",i1,j1); 6571: if(mle==1) 6572: printf("%1d%1d",i,j); 6573: fprintf(ficlog,"%1d%1d",i,j); 6574: for(k=1; k<=ncovmodel;k++){ 6575: fscanf(ficpar," %lf",&param[i][j][k]); 6576: if(mle==1){ 6577: printf(" %lf",param[i][j][k]); 6578: fprintf(ficlog," %lf",param[i][j][k]); 6579: } 6580: else 6581: fprintf(ficlog," %lf",param[i][j][k]); 6582: fprintf(ficparo," %lf",param[i][j][k]); 6583: } 6584: fscanf(ficpar,"\n"); 6585: numlinepar++; 6586: if(mle==1) 6587: printf("\n"); 6588: fprintf(ficlog,"\n"); 6589: fprintf(ficparo,"\n"); 6590: } 6591: } 6592: fflush(ficlog); 6593: 6594: /* Reads scales values */ 6595: p=param[1][1]; 6596: 6597: /* Reads comments: lines beginning with '#' */ 6598: while((c=getc(ficpar))=='#' && c!= EOF){ 6599: ungetc(c,ficpar); 6600: fgets(line, MAXLINE, ficpar); 6601: numlinepar++; 6602: fputs(line,stdout); 6603: fputs(line,ficparo); 6604: fputs(line,ficlog); 6605: } 6606: ungetc(c,ficpar); 6607: 6608: for(i=1; i <=nlstate; i++){ 6609: for(j=1; j <=nlstate+ndeath-1; j++){ 6610: fscanf(ficpar,"%1d%1d",&i1,&j1); 6611: if ( (i1-i) * (j1-j) != 0){ 6612: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1); 6613: exit(1); 6614: } 6615: printf("%1d%1d",i,j); 6616: fprintf(ficparo,"%1d%1d",i1,j1); 6617: fprintf(ficlog,"%1d%1d",i1,j1); 6618: for(k=1; k<=ncovmodel;k++){ 6619: fscanf(ficpar,"%le",&delti3[i][j][k]); 6620: printf(" %le",delti3[i][j][k]); 6621: fprintf(ficparo," %le",delti3[i][j][k]); 6622: fprintf(ficlog," %le",delti3[i][j][k]); 6623: } 6624: fscanf(ficpar,"\n"); 6625: numlinepar++; 6626: printf("\n"); 6627: fprintf(ficparo,"\n"); 6628: fprintf(ficlog,"\n"); 6629: } 6630: } 6631: fflush(ficlog); 6632: 6633: /* Reads covariance matrix */ 6634: delti=delti3[1][1]; 6635: 6636: 6637: /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */ 6638: 6639: /* Reads comments: lines beginning with '#' */ 6640: while((c=getc(ficpar))=='#' && c!= EOF){ 6641: ungetc(c,ficpar); 6642: fgets(line, MAXLINE, ficpar); 6643: numlinepar++; 6644: fputs(line,stdout); 6645: fputs(line,ficparo); 6646: fputs(line,ficlog); 6647: } 6648: ungetc(c,ficpar); 6649: 6650: matcov=matrix(1,npar,1,npar); 6651: for(i=1; i <=npar; i++) 6652: for(j=1; j <=npar; j++) matcov[i][j]=0.; 6653: 6654: for(i=1; i <=npar; i++){ 6655: fscanf(ficpar,"%s",str); 6656: if(mle==1) 6657: printf("%s",str); 6658: fprintf(ficlog,"%s",str); 6659: fprintf(ficparo,"%s",str); 6660: for(j=1; j <=i; j++){ 6661: fscanf(ficpar," %le",&matcov[i][j]); 6662: if(mle==1){ 6663: printf(" %.5le",matcov[i][j]); 6664: } 6665: fprintf(ficlog," %.5le",matcov[i][j]); 6666: fprintf(ficparo," %.5le",matcov[i][j]); 6667: } 6668: fscanf(ficpar,"\n"); 6669: numlinepar++; 6670: if(mle==1) 6671: printf("\n"); 6672: fprintf(ficlog,"\n"); 6673: fprintf(ficparo,"\n"); 6674: } 6675: for(i=1; i <=npar; i++) 6676: for(j=i+1;j<=npar;j++) 6677: matcov[i][j]=matcov[j][i]; 6678: 6679: if(mle==1) 6680: printf("\n"); 6681: fprintf(ficlog,"\n"); 6682: 6683: fflush(ficlog); 6684: 6685: /*-------- Rewriting parameter file ----------*/ 6686: strcpy(rfileres,"r"); /* "Rparameterfile */ 6687: strcat(rfileres,optionfilefiname); /* Parameter file first name*/ 6688: strcat(rfileres,"."); /* */ 6689: strcat(rfileres,optionfilext); /* Other files have txt extension */ 6690: if((ficres =fopen(rfileres,"w"))==NULL) { 6691: printf("Problem writing new parameter file: %s\n", fileres);goto end; 6692: fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end; 6693: } 6694: fprintf(ficres,"#%s\n",version); 6695: } /* End of mle != -3 */ 6696: 6697: /* Main data 6698: */ 6699: n= lastobs; 6700: num=lvector(1,n); 6701: moisnais=vector(1,n); 6702: annais=vector(1,n); 6703: moisdc=vector(1,n); 6704: andc=vector(1,n); 6705: agedc=vector(1,n); 6706: cod=ivector(1,n); 6707: weight=vector(1,n); 6708: for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */ 6709: mint=matrix(1,maxwav,1,n); 6710: anint=matrix(1,maxwav,1,n); 6711: s=imatrix(1,maxwav+1,1,n); /* s[i][j] health state for wave i and individual j */ 6712: tab=ivector(1,NCOVMAX); 6713: ncodemax=ivector(1,NCOVMAX); /* Number of code per covariate; if O and 1 only, 2**ncov; V1+V2+V3+V4=>16 */ 6714: ncodemaxwundef=ivector(1,NCOVMAX); /* Number of code per covariate; if - 1 O and 1 only, 2**ncov; V1+V2+V3+V4=>16 */ 6715: 6716: /* Reads data from file datafile */ 6717: if (readdata(datafile, firstobs, lastobs, &imx)==1) 6718: goto end; 6719: 6720: /* Calculation of the number of parameters from char model */ 6721: /* modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4 6722: k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tag[cptcovage=1]=4 6723: k=3 V4 Tvar[k=3]= 4 (from V4) 6724: k=2 V1 Tvar[k=2]= 1 (from V1) 6725: k=1 Tvar[1]=2 (from V2) 6726: */ 6727: Tvar=ivector(1,NCOVMAX); /* Was 15 changed to NCOVMAX. */ 6728: /* V2+V1+V4+age*V3 is a model with 4 covariates (3 plus signs). 6729: For each model-covariate stores the data-covariate id. Tvar[1]=2, Tvar[2]=1, Tvar[3]=4, 6730: Tvar[4=age*V3] is 3 and 'age' is recorded in Tage. 6731: */ 6732: /* For model-covariate k tells which data-covariate to use but 6733: because this model-covariate is a construction we invent a new column 6734: ncovcol + k1 6735: If already ncovcol=4 and model=V2+V1+V1*V4+age*V3 6736: Tvar[3=V1*V4]=4+1 etc */ 6737: Tprod=ivector(1,NCOVMAX); /* Gives the position of a product */ 6738: /* Tprod[k1=1]=3(=V1*V4) for V2+V1+V1*V4+age*V3 6739: if V2+V1+V1*V4+age*V3+V3*V2 TProd[k1=2]=5 (V3*V2) 6740: */ 6741: Tvaraff=ivector(1,NCOVMAX); /* Unclear */ 6742: 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 6743: * For V3*V2 (in V2+V1+V1*V4+age*V3+V3*V2), V3*V2 position is 2nd. 6744: * Tvard[k1=2][1]=3 (V3) Tvard[k1=2][2]=2(V2) */ 6745: Tage=ivector(1,NCOVMAX); /* Gives the covariate id of covariates associated with age: V2 + V1 + age*V4 + V3*age 6746: 4 covariates (3 plus signs) 6747: Tage[1=V3*age]= 4; Tage[2=age*V4] = 3 6748: */ 6749: 6750: /* Main decodemodel */ 6751: 6752: 6753: if(decodemodel(model, lastobs) == 1) 6754: goto end; 6755: 6756: if((double)(lastobs-imx)/(double)imx > 1.10){ 6757: nbwarn++; 6758: 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); 6759: 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); 6760: } 6761: /* if(mle==1){*/ 6762: if (weightopt != 1) { /* Maximisation without weights. We can have weights different from 1 but want no weight*/ 6763: for(i=1;i<=imx;i++) weight[i]=1.0; /* changed to imx */ 6764: } 6765: 6766: /*-calculation of age at interview from date of interview and age at death -*/ 6767: agev=matrix(1,maxwav,1,imx); 6768: 6769: if(calandcheckages(imx, maxwav, &agemin, &agemax, &nberr, &nbwarn) == 1) 6770: goto end; 6771: 6772: 6773: agegomp=(int)agemin; 6774: free_vector(moisnais,1,n); 6775: free_vector(annais,1,n); 6776: /* free_matrix(mint,1,maxwav,1,n); 6777: free_matrix(anint,1,maxwav,1,n);*/ 6778: free_vector(moisdc,1,n); 6779: free_vector(andc,1,n); 6780: /* */ 6781: 6782: wav=ivector(1,imx); 6783: dh=imatrix(1,lastpass-firstpass+1,1,imx); 6784: bh=imatrix(1,lastpass-firstpass+1,1,imx); 6785: mw=imatrix(1,lastpass-firstpass+1,1,imx); 6786: 6787: /* Concatenates waves */ 6788: concatwav(wav, dh, bh, mw, s, agedc, agev, firstpass, lastpass, imx, nlstate, stepm); 6789: /* */ 6790: 6791: /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */ 6792: 6793: nbcode=imatrix(0,NCOVMAX,0,NCOVMAX); 6794: ncodemax[1]=1; 6795: Ndum =ivector(-1,NCOVMAX); 6796: if (ncovmodel-nagesqr > 2 ) /* That is if covariate other than cst, age and age*age */ 6797: tricode(Tvar,nbcode,imx, Ndum); /**< Fills nbcode[Tvar[j]][l]; */ 6798: /* Nbcode gives the value of the lth modality of jth covariate, in 6799: V2+V1*age, there are 3 covariates Tvar[2]=1 (V1).*/ 6800: /* 1 to ncodemax[j] is the maximum value of this jth covariate */ 6801: 6802: codtab=imatrix(1,100,1,10); /* codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) */ 6803: /*printf(" codtab[1,1],codtab[100,10]=%d,%d\n", codtab[1][1],codtab[100][10]);*/ 6804: /* codtab gives the value 1 or 2 of the hth combination of k covariates (1 or 2).*/ 6805: h=0; 6806: 6807: 6808: /*if (cptcovn > 0) */ 6809: 6810: 6811: m=pow(2,cptcoveff); 6812: 6813: for(k=1;k<=cptcoveff; k++){ /* scans any effective covariate */ 6814: 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 */ 6815: for(j=1; j <= ncodemax[k]; j++){ /* For each modality of this covariate ncodemax=2*/ 6816: for(cpt=1; cpt <=pow(2,k-1); cpt++){ /* cpt=1 to 8/2**(3+1-1 or 3+1-3) =1 or 4 */ 6817: h++; 6818: if (h>m) 6819: h=1; 6820: /**< codtab(h,k) k = codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) + 1 6821: * For k=4 covariates, h goes from 1 to 2**k 6822: * codtabm(h,k)= 1 & (h-1) >> (k-1) ; 6823: * h\k 1 2 3 4 6824: *______________________________ 6825: * 1 i=1 1 i=1 1 i=1 1 i=1 1 6826: * 2 2 1 1 1 6827: * 3 i=2 1 2 1 1 6828: * 4 2 2 1 1 6829: * 5 i=3 1 i=2 1 2 1 6830: * 6 2 1 2 1 6831: * 7 i=4 1 2 2 1 6832: * 8 2 2 2 1 6833: * 9 i=5 1 i=3 1 i=2 1 1 6834: * 10 2 1 1 1 6835: * 11 i=6 1 2 1 1 6836: * 12 2 2 1 1 6837: * 13 i=7 1 i=4 1 2 1 6838: * 14 2 1 2 1 6839: * 15 i=8 1 2 2 1 6840: * 16 2 2 2 1 6841: */ 6842: codtab[h][k]=j; 6843: /* codtab[12][3]=1; */ 6844: /*codtab[h][Tvar[k]]=j;*/ 6845: 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]]); 6846: } 6847: } 6848: } 6849: } 6850: /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]); 6851: codtab[1][2]=1;codtab[2][2]=2; */ 6852: /* for(i=1; i <=m ;i++){ 6853: for(k=1; k <=cptcovn; k++){ 6854: printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff); 6855: } 6856: printf("\n"); 6857: } 6858: scanf("%d",i);*/ 6859: 6860: free_ivector(Ndum,-1,NCOVMAX); 6861: 6862: 6863: 6864: /* Initialisation of ----------- gnuplot -------------*/ 6865: strcpy(optionfilegnuplot,optionfilefiname); 6866: if(mle==-3) 6867: strcat(optionfilegnuplot,"-mort"); 6868: strcat(optionfilegnuplot,".gp"); 6869: 6870: if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) { 6871: printf("Problem with file %s",optionfilegnuplot); 6872: } 6873: else{ 6874: fprintf(ficgp,"\n# %s\n", version); 6875: fprintf(ficgp,"# %s\n", optionfilegnuplot); 6876: //fprintf(ficgp,"set missing 'NaNq'\n"); 6877: fprintf(ficgp,"set datafile missing 'NaNq'\n"); 6878: } 6879: /* fclose(ficgp);*/ 6880: 6881: 6882: /* Initialisation of --------- index.htm --------*/ 6883: 6884: strcpy(optionfilehtm,optionfilefiname); /* Main html file */ 6885: if(mle==-3) 6886: strcat(optionfilehtm,"-mort"); 6887: strcat(optionfilehtm,".htm"); 6888: if((fichtm=fopen(optionfilehtm,"w"))==NULL) { 6889: printf("Problem with %s \n",optionfilehtm); 6890: exit(0); 6891: } 6892: 6893: strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */ 6894: strcat(optionfilehtmcov,"-cov.htm"); 6895: if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL) { 6896: printf("Problem with %s \n",optionfilehtmcov), exit(0); 6897: } 6898: else{ 6899: fprintf(fichtmcov,"<html><head>\n<title>IMaCh Cov %s</title></head>\n <body>%s %s \ 6900: <hr size=\"2\" color=\"#EC5E5E\"> \n\ 6901: Title=%s Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s \n",\ 6902: optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model); 6903: } 6904: 6905: fprintf(fichtm,"<html><head>\n<title>IMaCh %s</title></head>\n <body>%s %s \ 6906: <hr size=\"2\" color=\"#EC5E5E\"> \n\ 6907: Title=%s Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s \n\ 6908: \n\ 6909: <hr size=\"2\" color=\"#EC5E5E\">\ 6910: <ul><li><h4>Parameter files</h4>\n\ 6911: - Parameter file: <a href=\"%s.%s\">%s.%s</a> \n\ 6912: - Copy of the parameter file: <a href=\"o%s\">o%s</a> \n\ 6913: - Log file of the run: <a href=\"%s\">%s</a> \n\ 6914: - Gnuplot file name: <a href=\"%s\">%s</a> \n\ 6915: - Date and time at start: %s</ul>\n",\ 6916: optionfilehtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\ 6917: optionfilefiname,optionfilext,optionfilefiname,optionfilext,\ 6918: fileres,fileres,\ 6919: filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart); 6920: fflush(fichtm); 6921: 6922: strcpy(pathr,path); 6923: strcat(pathr,optionfilefiname); 6924: #ifdef WIN32 6925: _chdir(optionfilefiname); /* Move to directory named optionfile */ 6926: #else 6927: chdir(optionfilefiname); /* Move to directory named optionfile */ 6928: #endif 6929: 6930: 6931: /* Calculates basic frequencies. Computes observed prevalence at single age 6932: and prints on file fileres'p'. */ 6933: freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart); 6934: 6935: fprintf(fichtm,"\n"); 6936: fprintf(fichtm," Total number of observations=%d \n\ 6937: Youngest age at first (selected) pass %.2f, oldest age %.2f \n\ 6938: Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf \n",\ 6939: imx,agemin,agemax,jmin,jmax,jmean); 6940: pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */ 6941: oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */ 6942: newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */ 6943: savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */ 6944: oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */ 6945: 6946: 6947: /* For Powell, parameters are in a vector p[] starting at p[1] 6948: so we point p on param[1][1] so that p[1] maps on param[1][1][1] */ 6949: p=param[1][1]; /* *(*(*(param +1)+1)+0) */ 6950: 6951: globpr=0; /* To get the number ipmx of contributions and the sum of weights*/ 6952: /* For mortality only */ 6953: if (mle==-3){ 6954: ximort=matrix(1,NDIM,1,NDIM); 6955: /* ximort=gsl_matrix_alloc(1,NDIM,1,NDIM); */ 6956: cens=ivector(1,n); 6957: ageexmed=vector(1,n); 6958: agecens=vector(1,n); 6959: dcwave=ivector(1,n); 6960: 6961: for (i=1; i<=imx; i++){ 6962: dcwave[i]=-1; 6963: for (m=firstpass; m<=lastpass; m++) 6964: if (s[m][i]>nlstate) { 6965: dcwave[i]=m; 6966: /* printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/ 6967: break; 6968: } 6969: } 6970: 6971: for (i=1; i<=imx; i++) { 6972: if (wav[i]>0){ 6973: ageexmed[i]=agev[mw[1][i]][i]; 6974: j=wav[i]; 6975: agecens[i]=1.; 6976: 6977: if (ageexmed[i]> 1 && wav[i] > 0){ 6978: agecens[i]=agev[mw[j][i]][i]; 6979: cens[i]= 1; 6980: }else if (ageexmed[i]< 1) 6981: cens[i]= -1; 6982: if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass) 6983: cens[i]=0 ; 6984: } 6985: else cens[i]=-1; 6986: } 6987: 6988: for (i=1;i<=NDIM;i++) { 6989: for (j=1;j<=NDIM;j++) 6990: ximort[i][j]=(i == j ? 1.0 : 0.0); 6991: } 6992: 6993: /*p[1]=0.0268; p[NDIM]=0.083;*/ 6994: /*printf("%lf %lf", p[1], p[2]);*/ 6995: 6996: 6997: #ifdef GSL 6998: printf("GSL optimization\n"); fprintf(ficlog,"Powell\n"); 6999: #else 7000: printf("Powell\n"); fprintf(ficlog,"Powell\n"); 7001: #endif 7002: strcpy(filerespow,"pow-mort"); 7003: strcat(filerespow,fileres); 7004: if((ficrespow=fopen(filerespow,"w"))==NULL) { 7005: printf("Problem with resultfile: %s\n", filerespow); 7006: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow); 7007: } 7008: #ifdef GSL 7009: fprintf(ficrespow,"# GSL optimization\n# iter -2*LL"); 7010: #else 7011: fprintf(ficrespow,"# Powell\n# iter -2*LL"); 7012: #endif 7013: /* for (i=1;i<=nlstate;i++) 7014: for(j=1;j<=nlstate+ndeath;j++) 7015: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j); 7016: */ 7017: fprintf(ficrespow,"\n"); 7018: #ifdef GSL 7019: /* gsl starts here */ 7020: T = gsl_multimin_fminimizer_nmsimplex; 7021: gsl_multimin_fminimizer *sfm = NULL; 7022: gsl_vector *ss, *x; 7023: gsl_multimin_function minex_func; 7024: 7025: /* Initial vertex size vector */ 7026: ss = gsl_vector_alloc (NDIM); 7027: 7028: if (ss == NULL){ 7029: GSL_ERROR_VAL ("failed to allocate space for ss", GSL_ENOMEM, 0); 7030: } 7031: /* Set all step sizes to 1 */ 7032: gsl_vector_set_all (ss, 0.001); 7033: 7034: /* Starting point */ 7035: 7036: x = gsl_vector_alloc (NDIM); 7037: 7038: if (x == NULL){ 7039: gsl_vector_free(ss); 7040: GSL_ERROR_VAL ("failed to allocate space for x", GSL_ENOMEM, 0); 7041: } 7042: 7043: /* Initialize method and iterate */ 7044: /* p[1]=0.0268; p[NDIM]=0.083; */ 7045: /* gsl_vector_set(x, 0, 0.0268); */ 7046: /* gsl_vector_set(x, 1, 0.083); */ 7047: gsl_vector_set(x, 0, p[1]); 7048: gsl_vector_set(x, 1, p[2]); 7049: 7050: minex_func.f = &gompertz_f; 7051: minex_func.n = NDIM; 7052: minex_func.params = (void *)&p; /* ??? */ 7053: 7054: sfm = gsl_multimin_fminimizer_alloc (T, NDIM); 7055: gsl_multimin_fminimizer_set (sfm, &minex_func, x, ss); 7056: 7057: printf("Iterations beginning .....\n\n"); 7058: printf("Iter. # Intercept Slope -Log Likelihood Simplex size\n"); 7059: 7060: iteri=0; 7061: while (rval == GSL_CONTINUE){ 7062: iteri++; 7063: status = gsl_multimin_fminimizer_iterate(sfm); 7064: 7065: if (status) printf("error: %s\n", gsl_strerror (status)); 7066: fflush(0); 7067: 7068: if (status) 7069: break; 7070: 7071: rval = gsl_multimin_test_size (gsl_multimin_fminimizer_size (sfm), 1e-6); 7072: ssval = gsl_multimin_fminimizer_size (sfm); 7073: 7074: if (rval == GSL_SUCCESS) 7075: printf ("converged to a local maximum at\n"); 7076: 7077: printf("%5d ", iteri); 7078: for (it = 0; it < NDIM; it++){ 7079: printf ("%10.5f ", gsl_vector_get (sfm->x, it)); 7080: } 7081: printf("f() = %-10.5f ssize = %.7f\n", sfm->fval, ssval); 7082: } 7083: 7084: printf("\n\n Please note: Program should be run many times with varying starting points to detemine global maximum\n\n"); 7085: 7086: gsl_vector_free(x); /* initial values */ 7087: gsl_vector_free(ss); /* inital step size */ 7088: for (it=0; it<NDIM; it++){ 7089: p[it+1]=gsl_vector_get(sfm->x,it); 7090: fprintf(ficrespow," %.12lf", p[it]); 7091: } 7092: gsl_multimin_fminimizer_free (sfm); /* p *(sfm.x.data) et p *(sfm.x.data+1) */ 7093: #endif 7094: #ifdef POWELL 7095: powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz); 7096: #endif 7097: fclose(ficrespow); 7098: 7099: hesscov(matcov, p, NDIM, delti, 1e-4, gompertz); 7100: 7101: for(i=1; i <=NDIM; i++) 7102: for(j=i+1;j<=NDIM;j++) 7103: matcov[i][j]=matcov[j][i]; 7104: 7105: printf("\nCovariance matrix\n "); 7106: for(i=1; i <=NDIM; i++) { 7107: for(j=1;j<=NDIM;j++){ 7108: printf("%f ",matcov[i][j]); 7109: } 7110: printf("\n "); 7111: } 7112: 7113: printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp); 7114: for (i=1;i<=NDIM;i++) 7115: printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i])); 7116: 7117: lsurv=vector(1,AGESUP); 7118: lpop=vector(1,AGESUP); 7119: tpop=vector(1,AGESUP); 7120: lsurv[agegomp]=100000; 7121: 7122: for (k=agegomp;k<=AGESUP;k++) { 7123: agemortsup=k; 7124: if (p[1]*exp(p[2]*(k-agegomp))>1) break; 7125: } 7126: 7127: for (k=agegomp;k<agemortsup;k++) 7128: lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp))); 7129: 7130: for (k=agegomp;k<agemortsup;k++){ 7131: lpop[k]=(lsurv[k]+lsurv[k+1])/2.; 7132: sumlpop=sumlpop+lpop[k]; 7133: } 7134: 7135: tpop[agegomp]=sumlpop; 7136: for (k=agegomp;k<(agemortsup-3);k++){ 7137: /* tpop[k+1]=2;*/ 7138: tpop[k+1]=tpop[k]-lpop[k]; 7139: } 7140: 7141: 7142: printf("\nAge lx qx dx Lx Tx e(x)\n"); 7143: for (k=agegomp;k<(agemortsup-2);k++) 7144: 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]); 7145: 7146: 7147: replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */ 7148: printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p); 7149: 7150: printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \ 7151: stepm, weightopt,\ 7152: model,imx,p,matcov,agemortsup); 7153: 7154: free_vector(lsurv,1,AGESUP); 7155: free_vector(lpop,1,AGESUP); 7156: free_vector(tpop,1,AGESUP); 7157: #ifdef GSL 7158: free_ivector(cens,1,n); 7159: free_vector(agecens,1,n); 7160: free_ivector(dcwave,1,n); 7161: free_matrix(ximort,1,NDIM,1,NDIM); 7162: #endif 7163: } /* Endof if mle==-3 mortality only */ 7164: /* Standard maximisation */ 7165: else{ /* For mle >=1 */ 7166: globpr=0;/* debug */ 7167: /* Computes likelihood for initial parameters */ 7168: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */ 7169: printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw); 7170: for (k=1; k<=npar;k++) 7171: printf(" %d %8.5f",k,p[k]); 7172: printf("\n"); 7173: globpr=1; /* again, to print the contributions */ 7174: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */ 7175: printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw); 7176: for (k=1; k<=npar;k++) 7177: printf(" %d %8.5f",k,p[k]); 7178: printf("\n"); 7179: if(mle>=1){ /* Could be 1 or 2, Real Maximisation */ 7180: mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func); 7181: } 7182: 7183: /*--------- results files --------------*/ 7184: 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); 7185: 7186: 7187: fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n"); 7188: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n"); 7189: fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n"); 7190: for(i=1,jk=1; i <=nlstate; i++){ 7191: for(k=1; k <=(nlstate+ndeath); k++){ 7192: if (k != i) { 7193: printf("%d%d ",i,k); 7194: fprintf(ficlog,"%d%d ",i,k); 7195: fprintf(ficres,"%1d%1d ",i,k); 7196: for(j=1; j <=ncovmodel; j++){ 7197: printf("%12.7f ",p[jk]); 7198: fprintf(ficlog,"%12.7f ",p[jk]); 7199: fprintf(ficres,"%12.7f ",p[jk]); 7200: jk++; 7201: } 7202: printf("\n"); 7203: fprintf(ficlog,"\n"); 7204: fprintf(ficres,"\n"); 7205: } 7206: } 7207: } 7208: if(mle!=0){ 7209: /* Computing hessian and covariance matrix */ 7210: ftolhess=ftol; /* Usually correct */ 7211: hesscov(matcov, p, npar, delti, ftolhess, func); 7212: } 7213: fprintf(ficres,"# Scales (for hessian or gradient estimation)\n"); 7214: printf("# Scales (for hessian or gradient estimation)\n"); 7215: fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n"); 7216: for(i=1,jk=1; i <=nlstate; i++){ 7217: for(j=1; j <=nlstate+ndeath; j++){ 7218: if (j!=i) { 7219: fprintf(ficres,"%1d%1d",i,j); 7220: printf("%1d%1d",i,j); 7221: fprintf(ficlog,"%1d%1d",i,j); 7222: for(k=1; k<=ncovmodel;k++){ 7223: printf(" %.5e",delti[jk]); 7224: fprintf(ficlog," %.5e",delti[jk]); 7225: fprintf(ficres," %.5e",delti[jk]); 7226: jk++; 7227: } 7228: printf("\n"); 7229: fprintf(ficlog,"\n"); 7230: fprintf(ficres,"\n"); 7231: } 7232: } 7233: } 7234: 7235: 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"); 7236: if(mle>=1) 7237: 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"); 7238: 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"); 7239: /* # 121 Var(a12)\n\ */ 7240: /* # 122 Cov(b12,a12) Var(b12)\n\ */ 7241: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */ 7242: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */ 7243: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */ 7244: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */ 7245: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */ 7246: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */ 7247: 7248: 7249: /* Just to have a covariance matrix which will be more understandable 7250: even is we still don't want to manage dictionary of variables 7251: */ 7252: for(itimes=1;itimes<=2;itimes++){ 7253: jj=0; 7254: for(i=1; i <=nlstate; i++){ 7255: for(j=1; j <=nlstate+ndeath; j++){ 7256: if(j==i) continue; 7257: for(k=1; k<=ncovmodel;k++){ 7258: jj++; 7259: ca[0]= k+'a'-1;ca[1]='\0'; 7260: if(itimes==1){ 7261: if(mle>=1) 7262: printf("#%1d%1d%d",i,j,k); 7263: fprintf(ficlog,"#%1d%1d%d",i,j,k); 7264: fprintf(ficres,"#%1d%1d%d",i,j,k); 7265: }else{ 7266: if(mle>=1) 7267: printf("%1d%1d%d",i,j,k); 7268: fprintf(ficlog,"%1d%1d%d",i,j,k); 7269: fprintf(ficres,"%1d%1d%d",i,j,k); 7270: } 7271: ll=0; 7272: for(li=1;li <=nlstate; li++){ 7273: for(lj=1;lj <=nlstate+ndeath; lj++){ 7274: if(lj==li) continue; 7275: for(lk=1;lk<=ncovmodel;lk++){ 7276: ll++; 7277: if(ll<=jj){ 7278: cb[0]= lk +'a'-1;cb[1]='\0'; 7279: if(ll<jj){ 7280: if(itimes==1){ 7281: if(mle>=1) 7282: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj); 7283: fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj); 7284: fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj); 7285: }else{ 7286: if(mle>=1) 7287: printf(" %.5e",matcov[jj][ll]); 7288: fprintf(ficlog," %.5e",matcov[jj][ll]); 7289: fprintf(ficres," %.5e",matcov[jj][ll]); 7290: } 7291: }else{ 7292: if(itimes==1){ 7293: if(mle>=1) 7294: printf(" Var(%s%1d%1d)",ca,i,j); 7295: fprintf(ficlog," Var(%s%1d%1d)",ca,i,j); 7296: fprintf(ficres," Var(%s%1d%1d)",ca,i,j); 7297: }else{ 7298: if(mle>=1) 7299: printf(" %.5e",matcov[jj][ll]); 7300: fprintf(ficlog," %.5e",matcov[jj][ll]); 7301: fprintf(ficres," %.5e",matcov[jj][ll]); 7302: } 7303: } 7304: } 7305: } /* end lk */ 7306: } /* end lj */ 7307: } /* end li */ 7308: if(mle>=1) 7309: printf("\n"); 7310: fprintf(ficlog,"\n"); 7311: fprintf(ficres,"\n"); 7312: numlinepar++; 7313: } /* end k*/ 7314: } /*end j */ 7315: } /* end i */ 7316: } /* end itimes */ 7317: 7318: fflush(ficlog); 7319: fflush(ficres); 7320: 7321: while((c=getc(ficpar))=='#' && c!= EOF){ 7322: ungetc(c,ficpar); 7323: fgets(line, MAXLINE, ficpar); 7324: fputs(line,stdout); 7325: fputs(line,ficparo); 7326: } 7327: ungetc(c,ficpar); 7328: 7329: estepm=0; 7330: fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm); 7331: if (estepm==0 || estepm < stepm) estepm=stepm; 7332: if (fage <= 2) { 7333: bage = ageminpar; 7334: fage = agemaxpar; 7335: } 7336: 7337: fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n"); 7338: fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm); 7339: fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm); 7340: 7341: /* Other stuffs, more or less useful */ 7342: while((c=getc(ficpar))=='#' && c!= EOF){ 7343: ungetc(c,ficpar); 7344: fgets(line, MAXLINE, ficpar); 7345: fputs(line,stdout); 7346: fputs(line,ficparo); 7347: } 7348: ungetc(c,ficpar); 7349: 7350: 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); 7351: 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); 7352: 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); 7353: printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav); 7354: 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); 7355: 7356: while((c=getc(ficpar))=='#' && c!= EOF){ 7357: ungetc(c,ficpar); 7358: fgets(line, MAXLINE, ficpar); 7359: fputs(line,stdout); 7360: fputs(line,ficparo); 7361: } 7362: ungetc(c,ficpar); 7363: 7364: 7365: dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.; 7366: dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.; 7367: 7368: fscanf(ficpar,"pop_based=%d\n",&popbased); 7369: fprintf(ficparo,"pop_based=%d\n",popbased); 7370: fprintf(ficres,"pop_based=%d\n",popbased); 7371: 7372: while((c=getc(ficpar))=='#' && c!= EOF){ 7373: ungetc(c,ficpar); 7374: fgets(line, MAXLINE, ficpar); 7375: fputs(line,stdout); 7376: fputs(line,ficparo); 7377: } 7378: ungetc(c,ficpar); 7379: 7380: 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); 7381: 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); 7382: 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); 7383: 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); 7384: 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); 7385: /* day and month of proj2 are not used but only year anproj2.*/ 7386: 7387: 7388: 7389: /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint); */ 7390: /* ,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2); */ 7391: 7392: replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */ 7393: printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p); 7394: 7395: printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\ 7396: model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\ 7397: jprev1,mprev1,anprev1,jprev2,mprev2,anprev2); 7398: 7399: /*------------ free_vector -------------*/ 7400: /* chdir(path); */ 7401: 7402: free_ivector(wav,1,imx); 7403: free_imatrix(dh,1,lastpass-firstpass+1,1,imx); 7404: free_imatrix(bh,1,lastpass-firstpass+1,1,imx); 7405: free_imatrix(mw,1,lastpass-firstpass+1,1,imx); 7406: free_lvector(num,1,n); 7407: free_vector(agedc,1,n); 7408: /*free_matrix(covar,0,NCOVMAX,1,n);*/ 7409: /*free_matrix(covar,1,NCOVMAX,1,n);*/ 7410: fclose(ficparo); 7411: fclose(ficres); 7412: 7413: 7414: /* Other results (useful)*/ 7415: 7416: 7417: /*--------------- Prevalence limit (period or stable prevalence) --------------*/ 7418: /*#include "prevlim.h"*/ /* Use ficrespl, ficlog */ 7419: prlim=matrix(1,nlstate,1,nlstate); 7420: prevalence_limit(p, prlim, ageminpar, agemaxpar); 7421: fclose(ficrespl); 7422: 7423: #ifdef FREEEXIT2 7424: #include "freeexit2.h" 7425: #endif 7426: 7427: /*------------- h Pij x at various ages ------------*/ 7428: /*#include "hpijx.h"*/ 7429: hPijx(p, bage, fage); 7430: fclose(ficrespij); 7431: 7432: /*-------------- Variance of one-step probabilities---*/ 7433: k=1; 7434: varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart); 7435: 7436: 7437: probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX); 7438: for(i=1;i<=AGESUP;i++) 7439: for(j=1;j<=NCOVMAX;j++) 7440: for(k=1;k<=NCOVMAX;k++) 7441: probs[i][j][k]=0.; 7442: 7443: /*---------- Forecasting ------------------*/ 7444: /*if((stepm == 1) && (strcmp(model,".")==0)){*/ 7445: if(prevfcast==1){ 7446: /* if(stepm ==1){*/ 7447: prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff); 7448: /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/ 7449: /* } */ 7450: /* else{ */ 7451: /* erreur=108; */ 7452: /* 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); */ 7453: /* 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); */ 7454: /* } */ 7455: } 7456: 7457: /* ------ Other prevalence ratios------------ */ 7458: 7459: /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */ 7460: 7461: prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass); 7462: /* 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",\ 7463: ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass); 7464: */ 7465: 7466: if (mobilav!=0) { 7467: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); 7468: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){ 7469: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav); 7470: printf(" Error in movingaverage mobilav=%d\n",mobilav); 7471: } 7472: } 7473: 7474: 7475: /*---------- Health expectancies, no variances ------------*/ 7476: 7477: strcpy(filerese,"e"); 7478: strcat(filerese,fileres); 7479: if((ficreseij=fopen(filerese,"w"))==NULL) { 7480: printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0); 7481: fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0); 7482: } 7483: printf("Computing Health Expectancies: result on file '%s' \n", filerese); 7484: fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese); 7485: /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){ 7486: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/ 7487: 7488: for (k=1; k <= (int) pow(2,cptcoveff); k++){ 7489: fprintf(ficreseij,"\n#****** "); 7490: for(j=1;j<=cptcoveff;j++) { 7491: fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]); 7492: } 7493: fprintf(ficreseij,"******\n"); 7494: 7495: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage); 7496: oldm=oldms;savm=savms; 7497: evsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart); 7498: 7499: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage); 7500: /*}*/ 7501: } 7502: fclose(ficreseij); 7503: 7504: 7505: /*---------- Health expectancies and variances ------------*/ 7506: 7507: 7508: strcpy(filerest,"t"); 7509: strcat(filerest,fileres); 7510: if((ficrest=fopen(filerest,"w"))==NULL) { 7511: printf("Problem with total LE resultfile: %s\n", filerest);goto end; 7512: fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end; 7513: } 7514: printf("Computing Total Life expectancies with their standard errors: file '%s' \n", filerest); 7515: fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' \n", filerest); 7516: 7517: 7518: strcpy(fileresstde,"stde"); 7519: strcat(fileresstde,fileres); 7520: if((ficresstdeij=fopen(fileresstde,"w"))==NULL) { 7521: printf("Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0); 7522: fprintf(ficlog,"Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0); 7523: } 7524: printf("Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde); 7525: fprintf(ficlog,"Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde); 7526: 7527: strcpy(filerescve,"cve"); 7528: strcat(filerescve,fileres); 7529: if((ficrescveij=fopen(filerescve,"w"))==NULL) { 7530: printf("Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0); 7531: fprintf(ficlog,"Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0); 7532: } 7533: printf("Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve); 7534: fprintf(ficlog,"Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve); 7535: 7536: strcpy(fileresv,"v"); 7537: strcat(fileresv,fileres); 7538: if((ficresvij=fopen(fileresv,"w"))==NULL) { 7539: printf("Problem with variance resultfile: %s\n", fileresv);exit(0); 7540: fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0); 7541: } 7542: printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv); 7543: fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv); 7544: 7545: /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){ 7546: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/ 7547: 7548: for (k=1; k <= (int) pow(2,cptcoveff); k++){ 7549: fprintf(ficrest,"\n#****** "); 7550: for(j=1;j<=cptcoveff;j++) 7551: fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]); 7552: fprintf(ficrest,"******\n"); 7553: 7554: fprintf(ficresstdeij,"\n#****** "); 7555: fprintf(ficrescveij,"\n#****** "); 7556: for(j=1;j<=cptcoveff;j++) { 7557: fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]); 7558: fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]); 7559: } 7560: fprintf(ficresstdeij,"******\n"); 7561: fprintf(ficrescveij,"******\n"); 7562: 7563: fprintf(ficresvij,"\n#****** "); 7564: for(j=1;j<=cptcoveff;j++) 7565: fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]); 7566: fprintf(ficresvij,"******\n"); 7567: 7568: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage); 7569: oldm=oldms;savm=savms; 7570: cvevsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart); 7571: /* 7572: */ 7573: /* goto endfree; */ 7574: 7575: vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage); 7576: pstamp(ficrest); 7577: 7578: 7579: for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/ 7580: oldm=oldms;savm=savms; /* Segmentation fault */ 7581: cptcod= 0; /* To be deleted */ 7582: 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 */ 7583: 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 "); 7584: if(vpopbased==1) 7585: 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); 7586: else 7587: fprintf(ficrest,"the age specific period (stable) prevalences in each health state \n"); 7588: fprintf(ficrest,"# Age e.. (std) "); 7589: for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i); 7590: fprintf(ficrest,"\n"); 7591: 7592: epj=vector(1,nlstate+1); 7593: for(age=bage; age <=fage ;age++){ 7594: prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k); 7595: if (vpopbased==1) { 7596: if(mobilav ==0){ 7597: for(i=1; i<=nlstate;i++) 7598: prlim[i][i]=probs[(int)age][i][k]; 7599: }else{ /* mobilav */ 7600: for(i=1; i<=nlstate;i++) 7601: prlim[i][i]=mobaverage[(int)age][i][k]; 7602: } 7603: } 7604: 7605: fprintf(ficrest," %4.0f",age); 7606: for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){ 7607: for(i=1, epj[j]=0.;i <=nlstate;i++) { 7608: epj[j] += prlim[i][i]*eij[i][j][(int)age]; 7609: /* printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/ 7610: } 7611: epj[nlstate+1] +=epj[j]; 7612: } 7613: 7614: for(i=1, vepp=0.;i <=nlstate;i++) 7615: for(j=1;j <=nlstate;j++) 7616: vepp += vareij[i][j][(int)age]; 7617: fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp)); 7618: for(j=1;j <=nlstate;j++){ 7619: fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age])); 7620: } 7621: fprintf(ficrest,"\n"); 7622: } 7623: } 7624: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage); 7625: free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage); 7626: free_vector(epj,1,nlstate+1); 7627: /*}*/ 7628: } 7629: free_vector(weight,1,n); 7630: free_imatrix(Tvard,1,NCOVMAX,1,2); 7631: free_imatrix(s,1,maxwav+1,1,n); 7632: free_matrix(anint,1,maxwav,1,n); 7633: free_matrix(mint,1,maxwav,1,n); 7634: free_ivector(cod,1,n); 7635: free_ivector(tab,1,NCOVMAX); 7636: fclose(ficresstdeij); 7637: fclose(ficrescveij); 7638: fclose(ficresvij); 7639: fclose(ficrest); 7640: fclose(ficpar); 7641: 7642: /*------- Variance of period (stable) prevalence------*/ 7643: 7644: strcpy(fileresvpl,"vpl"); 7645: strcat(fileresvpl,fileres); 7646: if((ficresvpl=fopen(fileresvpl,"w"))==NULL) { 7647: printf("Problem with variance of period (stable) prevalence resultfile: %s\n", fileresvpl); 7648: exit(0); 7649: } 7650: printf("Computing Variance-covariance of period (stable) prevalence: file '%s' \n", fileresvpl); 7651: 7652: /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){ 7653: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/ 7654: 7655: for (k=1; k <= (int) pow(2,cptcoveff); k++){ 7656: fprintf(ficresvpl,"\n#****** "); 7657: for(j=1;j<=cptcoveff;j++) 7658: fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]); 7659: fprintf(ficresvpl,"******\n"); 7660: 7661: varpl=matrix(1,nlstate,(int) bage, (int) fage); 7662: oldm=oldms;savm=savms; 7663: varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k,strstart); 7664: free_matrix(varpl,1,nlstate,(int) bage, (int)fage); 7665: /*}*/ 7666: } 7667: 7668: fclose(ficresvpl); 7669: 7670: /*---------- End : free ----------------*/ 7671: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); 7672: free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX); 7673: } /* mle==-3 arrives here for freeing */ 7674: /* endfree:*/ 7675: free_matrix(prlim,1,nlstate,1,nlstate); /*here or after loop ? */ 7676: free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath); 7677: free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath); 7678: free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath); 7679: free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath); 7680: free_matrix(covar,0,NCOVMAX,1,n); 7681: free_matrix(matcov,1,npar,1,npar); 7682: /*free_vector(delti,1,npar);*/ 7683: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 7684: free_matrix(agev,1,maxwav,1,imx); 7685: free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 7686: 7687: free_ivector(ncodemax,1,NCOVMAX); 7688: free_ivector(ncodemaxwundef,1,NCOVMAX); 7689: free_ivector(Tvar,1,NCOVMAX); 7690: free_ivector(Tprod,1,NCOVMAX); 7691: free_ivector(Tvaraff,1,NCOVMAX); 7692: free_ivector(Tage,1,NCOVMAX); 7693: 7694: free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX); 7695: free_imatrix(codtab,1,100,1,10); 7696: fflush(fichtm); 7697: fflush(ficgp); 7698: 7699: 7700: if((nberr >0) || (nbwarn>0)){ 7701: printf("End of Imach with %d errors and/or %d warnings\n",nberr,nbwarn); 7702: fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn); 7703: }else{ 7704: printf("End of Imach\n"); 7705: fprintf(ficlog,"End of Imach\n"); 7706: } 7707: printf("See log file on %s\n",filelog); 7708: /* gettimeofday(&end_time, (struct timezone*)0);*/ /* after time */ 7709: /*(void) gettimeofday(&end_time,&tzp);*/ 7710: rend_time = time(NULL); 7711: end_time = *localtime(&rend_time); 7712: /* tml = *localtime(&end_time.tm_sec); */ 7713: strcpy(strtend,asctime(&end_time)); 7714: printf("Local time at start %s\nLocal time at end %s",strstart, strtend); 7715: fprintf(ficlog,"Local time at start %s\nLocal time at end %s\n",strstart, strtend); 7716: printf("Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout)); 7717: 7718: printf("Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time)); 7719: fprintf(ficlog,"Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout)); 7720: fprintf(ficlog,"Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time)); 7721: /* printf("Total time was %d uSec.\n", total_usecs);*/ 7722: /* if(fileappend(fichtm,optionfilehtm)){ */ 7723: fprintf(fichtm," Local time at start %s Local time at end %s \n</body></html>",strstart, strtend); 7724: fclose(fichtm); 7725: fprintf(fichtmcov," Local time at start %s Local time at end %s \n</body></html>",strstart, strtend); 7726: fclose(fichtmcov); 7727: fclose(ficgp); 7728: fclose(ficlog); 7729: /*------ End -----------*/ 7730: 7731: 7732: printf("Before Current directory %s!\n",pathcd); 7733: #ifdef WIN32 7734: if (_chdir(pathcd) != 0) 7735: printf("Can't move to directory %s!\n",path); 7736: if(_getcwd(pathcd,MAXLINE) > 0) 7737: #else 7738: if(chdir(pathcd) != 0) 7739: printf("Can't move to directory %s!\n", path); 7740: if (getcwd(pathcd, MAXLINE) > 0) 7741: #endif 7742: printf("Current directory %s!\n",pathcd); 7743: /*strcat(plotcmd,CHARSEPARATOR);*/ 7744: sprintf(plotcmd,"gnuplot"); 7745: #ifdef _WIN32 7746: sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach); 7747: #endif 7748: if(!stat(plotcmd,&info)){ 7749: printf("Error or gnuplot program not found: '%s'\n",plotcmd);fflush(stdout); 7750: if(!stat(getenv("GNUPLOTBIN"),&info)){ 7751: printf("Error or gnuplot program not found: '%s' Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout); 7752: }else 7753: strcpy(pplotcmd,plotcmd); 7754: #ifdef __unix 7755: strcpy(plotcmd,GNUPLOTPROGRAM); 7756: if(!stat(plotcmd,&info)){ 7757: printf("Error gnuplot program not found: '%s'\n",plotcmd);fflush(stdout); 7758: }else 7759: strcpy(pplotcmd,plotcmd); 7760: #endif 7761: }else 7762: strcpy(pplotcmd,plotcmd); 7763: 7764: sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot); 7765: printf("Starting graphs with: '%s'\n",plotcmd);fflush(stdout); 7766: 7767: if((outcmd=system(plotcmd)) != 0){ 7768: printf("gnuplot command might not be in your path: '%s', err=%d\n", plotcmd, outcmd); 7769: printf("\n Trying if gnuplot resides on the same directory that IMaCh\n"); 7770: sprintf(plotcmd,"%sgnuplot %s", pathimach, optionfilegnuplot); 7771: if((outcmd=system(plotcmd)) != 0) 7772: printf("\n Still a problem with gnuplot command %s, err=%d\n", plotcmd, outcmd); 7773: } 7774: printf(" Successful, please wait..."); 7775: while (z[0] != 'q') { 7776: /* chdir(path); */ 7777: printf("\nType e to edit results with your browser, g to graph again and q for exit: "); 7778: scanf("%s",z); 7779: /* if (z[0] == 'c') system("./imach"); */ 7780: if (z[0] == 'e') { 7781: #ifdef __APPLE__ 7782: sprintf(pplotcmd, "open %s", optionfilehtm); 7783: #elif __linux 7784: sprintf(pplotcmd, "xdg-open %s", optionfilehtm); 7785: #else 7786: sprintf(pplotcmd, "%s", optionfilehtm); 7787: #endif 7788: printf("Starting browser with: %s",pplotcmd);fflush(stdout); 7789: system(pplotcmd); 7790: } 7791: else if (z[0] == 'g') system(plotcmd); 7792: else if (z[0] == 'q') exit(0); 7793: } 7794: end: 7795: while (z[0] != 'q') { 7796: printf("\nType q for exiting: "); 7797: scanf("%s",z); 7798: } 7799: }