--- imach/src/imach.c 2014/06/10 21:23:15 1.145 +++ imach/src/imach.c 2017/04/26 16:22:11 1.265 @@ -1,6 +1,439 @@ -/* $Id: imach.c,v 1.145 2014/06/10 21:23:15 brouard Exp $ +/* $Id: imach.c,v 1.265 2017/04/26 16:22:11 brouard Exp $ $State: Exp $ $Log: imach.c,v $ + Revision 1.265 2017/04/26 16:22:11 brouard + Summary: imach 0.99r13 Some bugs fixed + + Revision 1.264 2017/04/26 06:01:29 brouard + Summary: Labels in graphs + + Revision 1.263 2017/04/24 15:23:15 brouard + Summary: to save + + Revision 1.262 2017/04/18 16:48:12 brouard + *** empty log message *** + + Revision 1.261 2017/04/05 10:14:09 brouard + Summary: Bug in E_ as well as in T_ fixed nres-1 vs k1-1 + + Revision 1.260 2017/04/04 17:46:59 brouard + Summary: Gnuplot indexations fixed (humm) + + Revision 1.259 2017/04/04 13:01:16 brouard + Summary: Some errors to warnings only if date of death is unknown but status is death we could set to pi3 + + Revision 1.258 2017/04/03 10:17:47 brouard + Summary: Version 0.99r12 + + Some cleanings, conformed with updated documentation. + + Revision 1.257 2017/03/29 16:53:30 brouard + Summary: Temp + + Revision 1.256 2017/03/27 05:50:23 brouard + Summary: Temporary + + Revision 1.255 2017/03/08 16:02:28 brouard + Summary: IMaCh version 0.99r10 bugs in gnuplot fixed + + Revision 1.254 2017/03/08 07:13:00 brouard + Summary: Fixing data parameter line + + Revision 1.253 2016/12/15 11:59:41 brouard + Summary: 0.99 in progress + + Revision 1.252 2016/09/15 21:15:37 brouard + *** empty log message *** + + Revision 1.251 2016/09/15 15:01:13 brouard + Summary: not working + + Revision 1.250 2016/09/08 16:07:27 brouard + Summary: continue + + Revision 1.249 2016/09/07 17:14:18 brouard + Summary: Starting values from frequencies + + Revision 1.248 2016/09/07 14:10:18 brouard + *** empty log message *** + + Revision 1.247 2016/09/02 11:11:21 brouard + *** empty log message *** + + Revision 1.246 2016/09/02 08:49:22 brouard + *** empty log message *** + + Revision 1.245 2016/09/02 07:25:01 brouard + *** empty log message *** + + Revision 1.244 2016/09/02 07:17:34 brouard + *** empty log message *** + + Revision 1.243 2016/09/02 06:45:35 brouard + *** empty log message *** + + Revision 1.242 2016/08/30 15:01:20 brouard + Summary: Fixing a lots + + Revision 1.241 2016/08/29 17:17:25 brouard + Summary: gnuplot problem in Back projection to fix + + Revision 1.240 2016/08/29 07:53:18 brouard + Summary: Better + + Revision 1.239 2016/08/26 15:51:03 brouard + Summary: Improvement in Powell output in order to copy and paste + + Author: + + Revision 1.238 2016/08/26 14:23:35 brouard + Summary: Starting tests of 0.99 + + Revision 1.237 2016/08/26 09:20:19 brouard + Summary: to valgrind + + Revision 1.236 2016/08/25 10:50:18 brouard + *** empty log message *** + + Revision 1.235 2016/08/25 06:59:23 brouard + *** empty log message *** + + Revision 1.234 2016/08/23 16:51:20 brouard + *** empty log message *** + + Revision 1.233 2016/08/23 07:40:50 brouard + Summary: not working + + Revision 1.232 2016/08/22 14:20:21 brouard + Summary: not working + + Revision 1.231 2016/08/22 07:17:15 brouard + Summary: not working + + Revision 1.230 2016/08/22 06:55:53 brouard + Summary: Not working + + Revision 1.229 2016/07/23 09:45:53 brouard + Summary: Completing for func too + + Revision 1.228 2016/07/22 17:45:30 brouard + Summary: Fixing some arrays, still debugging + + Revision 1.226 2016/07/12 18:42:34 brouard + Summary: temp + + Revision 1.225 2016/07/12 08:40:03 brouard + Summary: saving but not running + + Revision 1.224 2016/07/01 13:16:01 brouard + Summary: Fixes + + Revision 1.223 2016/02/19 09:23:35 brouard + Summary: temporary + + Revision 1.222 2016/02/17 08:14:50 brouard + Summary: Probably last 0.98 stable version 0.98r6 + + Revision 1.221 2016/02/15 23:35:36 brouard + Summary: minor bug + + Revision 1.219 2016/02/15 00:48:12 brouard + *** empty log message *** + + Revision 1.218 2016/02/12 11:29:23 brouard + Summary: 0.99 Back projections + + Revision 1.217 2015/12/23 17:18:31 brouard + Summary: Experimental backcast + + Revision 1.216 2015/12/18 17:32:11 brouard + Summary: 0.98r4 Warning and status=-2 + + Version 0.98r4 is now: + - displaying an error when status is -1, date of interview unknown and date of death known; + - permitting a status -2 when the vital status is unknown at a known date of right truncation. + Older changes concerning s=-2, dating from 2005 have been supersed. + + Revision 1.215 2015/12/16 08:52:24 brouard + Summary: 0.98r4 working + + Revision 1.214 2015/12/16 06:57:54 brouard + Summary: temporary not working + + Revision 1.213 2015/12/11 18:22:17 brouard + Summary: 0.98r4 + + Revision 1.212 2015/11/21 12:47:24 brouard + Summary: minor typo + + Revision 1.211 2015/11/21 12:41:11 brouard + Summary: 0.98r3 with some graph of projected cross-sectional + + Author: Nicolas Brouard + + Revision 1.210 2015/11/18 17:41:20 brouard + Summary: Start working on projected prevalences Revision 1.209 2015/11/17 22:12:03 brouard + Summary: Adding ftolpl parameter + Author: N Brouard + + We had difficulties to get smoothed confidence intervals. It was due + to the period prevalence which wasn't computed accurately. The inner + parameter ftolpl is now an outer parameter of the .imach parameter + file after estepm. If ftolpl is small 1.e-4 and estepm too, + computation are long. + + Revision 1.208 2015/11/17 14:31:57 brouard + Summary: temporary + + Revision 1.207 2015/10/27 17:36:57 brouard + *** empty log message *** + + Revision 1.206 2015/10/24 07:14:11 brouard + *** empty log message *** + + Revision 1.205 2015/10/23 15:50:53 brouard + Summary: 0.98r3 some clarification for graphs on likelihood contributions + + Revision 1.204 2015/10/01 16:20:26 brouard + Summary: Some new graphs of contribution to likelihood + + Revision 1.203 2015/09/30 17:45:14 brouard + Summary: looking at better estimation of the hessian + + Also a better criteria for convergence to the period prevalence And + therefore adding the number of years needed to converge. (The + prevalence in any alive state shold sum to one + + Revision 1.202 2015/09/22 19:45:16 brouard + Summary: Adding some overall graph on contribution to likelihood. Might change + + Revision 1.201 2015/09/15 17:34:58 brouard + Summary: 0.98r0 + + - Some new graphs like suvival functions + - Some bugs fixed like model=1+age+V2. + + Revision 1.200 2015/09/09 16:53:55 brouard + Summary: Big bug thanks to Flavia + + Even model=1+age+V2. did not work anymore + + Revision 1.199 2015/09/07 14:09:23 brouard + Summary: 0.98q6 changing default small png format for graph to vectorized svg. + + Revision 1.198 2015/09/03 07:14:39 brouard + Summary: 0.98q5 Flavia + + Revision 1.197 2015/09/01 18:24:39 brouard + *** empty log message *** + + Revision 1.196 2015/08/18 23:17:52 brouard + Summary: 0.98q5 + + Revision 1.195 2015/08/18 16:28:39 brouard + Summary: Adding a hack for testing purpose + + After reading the title, ftol and model lines, if the comment line has + a q, starting with #q, the answer at the end of the run is quit. It + permits to run test files in batch with ctest. The former workaround was + $ echo q | imach foo.imach + + Revision 1.194 2015/08/18 13:32:00 brouard + Summary: Adding error when the covariance matrix doesn't contain the exact number of lines required by the model line. + + Revision 1.193 2015/08/04 07:17:42 brouard + Summary: 0.98q4 + + Revision 1.192 2015/07/16 16:49:02 brouard + Summary: Fixing some outputs + + Revision 1.191 2015/07/14 10:00:33 brouard + Summary: Some fixes + + Revision 1.190 2015/05/05 08:51:13 brouard + Summary: Adding digits in output parameters (7 digits instead of 6) + + Fix 1+age+. + + Revision 1.189 2015/04/30 14:45:16 brouard + Summary: 0.98q2 + + Revision 1.188 2015/04/30 08:27:53 brouard + *** empty log message *** + + Revision 1.187 2015/04/29 09:11:15 brouard + *** empty log message *** + + Revision 1.186 2015/04/23 12:01:52 brouard + Summary: V1*age is working now, version 0.98q1 + + Some codes had been disabled in order to simplify and Vn*age was + working in the optimization phase, ie, giving correct MLE parameters, + but, as usual, outputs were not correct and program core dumped. + + Revision 1.185 2015/03/11 13:26:42 brouard + Summary: Inclusion of compile and links command line for Intel Compiler + + Revision 1.184 2015/03/11 11:52:39 brouard + Summary: Back from Windows 8. Intel Compiler + + Revision 1.183 2015/03/10 20:34:32 brouard + Summary: 0.98q0, trying with directest, mnbrak fixed + + We use directest instead of original Powell test; probably no + incidence on the results, but better justifications; + We fixed Numerical Recipes mnbrak routine which was wrong and gave + wrong results. + + Revision 1.182 2015/02/12 08:19:57 brouard + Summary: Trying to keep directest which seems simpler and more general + Author: Nicolas Brouard + + Revision 1.181 2015/02/11 23:22:24 brouard + Summary: Comments on Powell added + + Author: + + Revision 1.180 2015/02/11 17:33:45 brouard + Summary: Finishing move from main to function (hpijx and prevalence_limit) + + Revision 1.179 2015/01/04 09:57:06 brouard + Summary: back to OS/X + + Revision 1.178 2015/01/04 09:35:48 brouard + *** empty log message *** + + Revision 1.177 2015/01/03 18:40:56 brouard + Summary: Still testing ilc32 on OSX + + Revision 1.176 2015/01/03 16:45:04 brouard + *** empty log message *** + + Revision 1.175 2015/01/03 16:33:42 brouard + *** empty log message *** + + Revision 1.174 2015/01/03 16:15:49 brouard + Summary: Still in cross-compilation + + Revision 1.173 2015/01/03 12:06:26 brouard + Summary: trying to detect cross-compilation + + Revision 1.172 2014/12/27 12:07:47 brouard + Summary: Back from Visual Studio and Intel, options for compiling for Windows XP + + Revision 1.171 2014/12/23 13:26:59 brouard + Summary: Back from Visual C + + Still problem with utsname.h on Windows + + Revision 1.170 2014/12/23 11:17:12 brouard + Summary: Cleaning some \%% back to %% + + The escape was mandatory for a specific compiler (which one?), but too many warnings. + + Revision 1.169 2014/12/22 23:08:31 brouard + Summary: 0.98p + + Outputs some informations on compiler used, OS etc. Testing on different platforms. + + Revision 1.168 2014/12/22 15:17:42 brouard + Summary: update + + Revision 1.167 2014/12/22 13:50:56 brouard + Summary: Testing uname and compiler version and if compiled 32 or 64 + + Testing on Linux 64 + + Revision 1.166 2014/12/22 11:40:47 brouard + *** empty log message *** + + Revision 1.165 2014/12/16 11:20:36 brouard + Summary: After compiling on Visual C + + * imach.c (Module): Merging 1.61 to 1.162 + + Revision 1.164 2014/12/16 10:52:11 brouard + Summary: Merging with Visual C after suppressing some warnings for unused variables. Also fixing Saito's bug 0.98Xn + + * imach.c (Module): Merging 1.61 to 1.162 + + Revision 1.163 2014/12/16 10:30:11 brouard + * imach.c (Module): Merging 1.61 to 1.162 + + Revision 1.162 2014/09/25 11:43:39 brouard + Summary: temporary backup 0.99! + + Revision 1.1 2014/09/16 11:06:58 brouard + Summary: With some code (wrong) for nlopt + + Author: + + Revision 1.161 2014/09/15 20:41:41 brouard + Summary: Problem with macro SQR on Intel compiler + + Revision 1.160 2014/09/02 09:24:05 brouard + *** empty log message *** + + Revision 1.159 2014/09/01 10:34:10 brouard + Summary: WIN32 + Author: Brouard + + Revision 1.158 2014/08/27 17:11:51 brouard + *** empty log message *** + + Revision 1.157 2014/08/27 16:26:55 brouard + Summary: Preparing windows Visual studio version + Author: Brouard + + In order to compile on Visual studio, time.h is now correct and time_t + and tm struct should be used. difftime should be used but sometimes I + just make the differences in raw time format (time(&now). + Trying to suppress #ifdef LINUX + Add xdg-open for __linux in order to open default browser. + + Revision 1.156 2014/08/25 20:10:10 brouard + *** empty log message *** + + Revision 1.155 2014/08/25 18:32:34 brouard + Summary: New compile, minor changes + Author: Brouard + + Revision 1.154 2014/06/20 17:32:08 brouard + Summary: Outputs now all graphs of convergence to period prevalence + + Revision 1.153 2014/06/20 16:45:46 brouard + Summary: If 3 live state, convergence to period prevalence on same graph + Author: Brouard + + Revision 1.152 2014/06/18 17:54:09 brouard + Summary: open browser, use gnuplot on same dir than imach if not found in the path + + Revision 1.151 2014/06/18 16:43:30 brouard + *** empty log message *** + + Revision 1.150 2014/06/18 16:42:35 brouard + Summary: If gnuplot is not in the path try on same directory than imach binary (OSX) + Author: brouard + + Revision 1.149 2014/06/18 15:51:14 brouard + Summary: Some fixes in parameter files errors + Author: Nicolas Brouard + + Revision 1.148 2014/06/17 17:38:48 brouard + Summary: Nothing new + Author: Brouard + + Just a new packaging for OS/X version 0.98nS + + Revision 1.147 2014/06/16 10:33:11 brouard + *** empty log message *** + + Revision 1.146 2014/06/16 10:20:28 brouard + Summary: Merge + Author: Brouard + + Merge, before building revised version. + Revision 1.145 2014/06/10 21:23:15 brouard Summary: Debugging with valgrind Author: Nicolas Brouard @@ -322,24 +755,27 @@ Short summary of the programme: - This program computes Healthy Life Expectancies from - cross-longitudinal data. Cross-longitudinal data consist in: -1- a - first survey ("cross") where individuals from different ages are - interviewed on their health status or degree of disability (in the - case of a health survey which is our main interest) -2- at least a - second wave of interviews ("longitudinal") which measure each change - (if any) in individual health status. Health expectancies are - computed from the time spent in each health state according to a - model. More health states you consider, more time is necessary to reach the - Maximum Likelihood of the parameters involved in the model. The - simplest model is the multinomial logistic model where pij is the - probability to be observed in state j at the second wave - conditional to be observed in state i at the first wave. Therefore - the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where - 'age' is age and 'sex' is a covariate. If you want to have a more - complex model than "constant and age", you should modify the program - where the markup *Covariates have to be included here again* invites - you to do it. More covariates you add, slower the + This program computes Healthy Life Expectancies or State-specific + (if states aren't health statuses) Expectancies from + cross-longitudinal data. Cross-longitudinal data consist in: + + -1- a first survey ("cross") where individuals from different ages + are interviewed on their health status or degree of disability (in + the case of a health survey which is our main interest) + + -2- at least a second wave of interviews ("longitudinal") which + measure each change (if any) in individual health status. Health + expectancies are computed from the time spent in each health state + according to a model. More health states you consider, more time is + necessary to reach the Maximum Likelihood of the parameters involved + in the model. The simplest model is the multinomial logistic model + where pij is the probability to be observed in state j at the second + wave conditional to be observed in state i at the first + wave. Therefore the model is: log(pij/pii)= aij + bij*age+ cij*sex + + etc , where 'age' is age and 'sex' is a covariate. If you want to + have a more complex model than "constant and age", you should modify + the program where the markup *Covariates have to be included here + again* invites you to do it. More covariates you add, slower the convergence. The advantage of this computer programme, compared to a simple @@ -358,7 +794,55 @@ hPijx. Also this programme outputs the covariance matrix of the parameters but also - of the life expectancies. It also computes the period (stable) prevalence. + of the life expectancies. It also computes the period (stable) prevalence. + +Back prevalence and projections: + + - back_prevalence_limit(double *p, double **bprlim, double ageminpar, + double agemaxpar, double ftolpl, int *ncvyearp, double + dateprev1,double dateprev2, int firstpass, int lastpass, int + mobilavproj) + + Computes the back prevalence limit for any combination of + covariate values k at any age between ageminpar and agemaxpar and + returns it in **bprlim. In the loops, + + - **bprevalim(**bprlim, ***mobaverage, nlstate, *p, age, **oldm, + **savm, **dnewm, **doldm, **dsavm, ftolpl, ncvyearp, k); + + - hBijx Back Probability to be in state i at age x-h being in j at x + Computes for any combination of covariates k and any age between bage and fage + p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); + oldm=oldms;savm=savms; + + - hbxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k); + Computes the transition matrix starting at age 'age' over + 'nhstepm*hstepm*stepm' months (i.e. until + age (in years) age+nhstepm*hstepm*stepm/12) by multiplying + nhstepm*hstepm matrices. + + Returns p3mat[i][j][h] after calling + p3mat[i][j][h]=matprod2(newm, + bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent, dnewm, doldm, + dsavm,ij),\ 1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, + oldm); + +Important routines + +- func (or funcone), computes logit (pij) distinguishing + o fixed variables (single or product dummies or quantitative); + o varying variables by: + (1) wave (single, product dummies, quantitative), + (2) by age (can be month) age (done), age*age (done), age*Vn where Vn can be: + % fixed dummy (treated) or quantitative (not done because time-consuming); + % varying dummy (not done) or quantitative (not done); +- Tricode which tests the modality of dummy variables (in order to warn with wrong or empty modalities) + and returns the number of efficient covariates cptcoveff and modalities nbcode[Tvar[k]][1]= 0 and nbcode[Tvar[k]][2]= 1 usually. +- printinghtml which outputs results like life expectancy in and from a state for a combination of modalities of dummy variables + o There are 2*cptcoveff combinations of (0,1) for cptcoveff variables. Outputting only combinations with people, éliminating 1 1 if + race White (0 0), Black vs White (1 0), Hispanic (0 1) and 1 1 being meaningless. + + Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr). Institut national d'études démographiques, Paris. @@ -415,37 +899,68 @@ end */ +/* #define DEBUG */ +/* #define DEBUGBRENT */ +/* #define DEBUGLINMIN */ +/* #define DEBUGHESS */ +#define DEBUGHESSIJ +/* #define LINMINORIGINAL /\* Don't use loop on scale in linmin (accepting nan) *\/ */ +#define POWELL /* Instead of NLOPT */ +#define POWELLNOF3INFF1TEST /* Skip test */ +/* #define POWELLORIGINAL /\* Don't use Directest to decide new direction but original Powell test *\/ */ +/* #define MNBRAKORIGINAL /\* Don't use mnbrak fix *\/ */ - - #include #include #include #include +#include + +#ifdef _WIN32 +#include +#include +#include +#else #include +#endif #include #include + +#if defined(__GNUC__) +#include /* Doesn't work on Windows */ +#endif + #include #include -extern int errno; +/* extern int errno; */ + +/* #ifdef LINUX */ +/* #include */ +/* #include "timeval.h" */ +/* #else */ +/* #include */ +/* #endif */ -#ifdef LINUX #include -#include "timeval.h" -#else -#include -#endif #ifdef GSL #include #include #endif + +#ifdef NLOPT +#include +typedef struct { + double (* function)(double [] ); +} myfunc_data ; +#endif + /* #include */ /* #define _(String) gettext (String) */ -#define MAXLINE 1024 /* Was 256. Overflow with 312 with 2 states and 4 covariates. Should be ok */ +#define MAXLINE 2048 /* Was 256 and 1024. Overflow with 312 with 2 states and 4 covariates. Should be ok */ #define GNUPLOTPROGRAM "gnuplot" /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/ @@ -461,43 +976,61 @@ extern int errno; #define NLSTATEMAX 8 /**< Maximum number of live states (for func) */ #define NDEATHMAX 8 /**< Maximum number of dead states (for func) */ #define NCOVMAX 20 /**< Maximum number of covariates, including generated covariates V1*V2 */ -#define codtabm(h,k) 1 & (h-1) >> (k-1) ; +#define codtabm(h,k) (1 & (h-1) >> (k-1))+1 +/*#define decodtabm(h,k,cptcoveff)= (h <= (1<> (k-1)) & 1) +1 : -1)*/ +#define decodtabm(h,k,cptcoveff) (((h-1) >> (k-1)) & 1) +1 #define MAXN 20000 #define YEARM 12. /**< Number of months per year */ -#define AGESUP 130 +/* #define AGESUP 130 */ +#define AGESUP 150 +#define AGEMARGE 25 /* Marge for agemin and agemax for(iage=agemin-AGEMARGE; iage <= agemax+3+AGEMARGE; iage++) */ #define AGEBASE 40 -#define AGEGOMP 10. /**< Minimal age for Gompertz adjustment */ -#ifdef UNIX -#define DIRSEPARATOR '/' -#define CHARSEPARATOR "/" -#define ODIRSEPARATOR '\\' -#else +#define AGEOVERFLOW 1.e20 +#define AGEGOMP 10 /**< Minimal age for Gompertz adjustment */ +#ifdef _WIN32 #define DIRSEPARATOR '\\' #define CHARSEPARATOR "\\" #define ODIRSEPARATOR '/' +#else +#define DIRSEPARATOR '/' +#define CHARSEPARATOR "/" +#define ODIRSEPARATOR '\\' #endif -/* $Id: imach.c,v 1.145 2014/06/10 21:23:15 brouard Exp $ */ +/* $Id: imach.c,v 1.265 2017/04/26 16:22:11 brouard Exp $ */ /* $State: Exp $ */ - -char version[]="Imach version 0.98nR2, January 2014,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121)"; -char fullversion[]="$Revision: 1.145 $ $Date: 2014/06/10 21:23:15 $"; +#include "version.h" +char version[]=__IMACH_VERSION__; +char copyright[]="February 2016,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121), Intel Software 2015-2018"; +char fullversion[]="$Revision: 1.265 $ $Date: 2017/04/26 16:22:11 $"; char strstart[80]; char optionfilext[10], optionfilefiname[FILENAMELENGTH]; int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings */ -int nvar=0, nforce=0; /* Number of variables, number of forces */ +int nagesqr=0, nforce=0; /* nagesqr=1 if model is including age*age, number of forces */ /* Number of covariates model=V2+V1+ V3*age+V2*V4 */ int cptcovn=0; /**< cptcovn number of covariates added in the model (excepting constant and age and age*product) */ int cptcovt=0; /**< cptcovt number of covariates added in the model (excepting constant and age) */ -int cptcovs=0; /**< cptcovs number of simple covariates V2+V1 =2 */ +int cptcovs=0; /**< cptcovs number of simple covariates in the model V2+V1 =2 */ +int cptcovsnq=0; /**< cptcovsnq number of simple covariates in the model but non quantitative V2+V1 =2 */ int cptcovage=0; /**< Number of covariates with age: V3*age only =1 */ int cptcovprodnoage=0; /**< Number of covariate products without age */ int cptcoveff=0; /* Total number of covariates to vary for printing results */ +int ncovf=0; /* Total number of effective fixed covariates (dummy or quantitative) in the model */ +int ncovv=0; /* Total number of effective (wave) varying covariates (dummy or quantitative) in the model */ +int ncova=0; /* Total number of effective (wave and stepm) varying with age covariates (dummy of quantitative) in the model */ +int nsd=0; /**< Total number of single dummy variables (output) */ +int nsq=0; /**< Total number of single quantitative variables (output) */ +int ncoveff=0; /* Total number of effective fixed dummy covariates in the model */ +int nqfveff=0; /**< nqfveff Number of Quantitative Fixed Variables Effective */ +int ntveff=0; /**< ntveff number of effective time varying variables */ +int nqtveff=0; /**< ntqveff number of effective time varying quantitative variables */ int cptcov=0; /* Working variable */ +int ncovcombmax=NCOVMAX; /* Maximum calculated number of covariate combination = pow(2, cptcoveff) */ int npar=NPARMAX; int nlstate=2; /* Number of live states */ int ndeath=1; /* Number of dead states */ int ncovmodel=0, ncovcol=0; /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */ +int nqv=0, ntv=0, nqtv=0; /* Total number of quantitative variables, time variable (dummy), quantitative and time variable */ int popbased=0; int *wav; /* Number of waves for this individuual 0 is possible */ @@ -511,12 +1044,17 @@ int **mw; /* mw[mi][i] is number of the int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */ int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between * wave mi and wave mi+1 is not an exact multiple of stepm. */ +int countcallfunc=0; /* Count the number of calls to func */ +int selected(int kvar); /* Is covariate kvar selected for printing results */ + double jmean=1; /* Mean space between 2 waves */ double **matprod2(); /* test */ double **oldm, **newm, **savm; /* Working pointers to matrices */ double **oldms, **newms, **savms; /* Fixed working pointers to matrices */ +double **ddnewms, **ddoldms, **ddsavms; /* for freeing later */ + /*FILE *fic ; */ /* Used in readdata only */ -FILE *ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop; +FILE *ficpar, *ficparo,*ficres, *ficresp, *ficresphtm, *ficresphtmfr, *ficrespl, *ficresplb,*ficrespij, *ficrespijb, *ficrest,*ficresf, *ficresfb,*ficrespop; FILE *ficlog, *ficrespow; int globpr=0; /* Global variable for printing or not */ double fretone; /* Only one call to likelihood */ @@ -539,14 +1077,15 @@ char fileresv[FILENAMELENGTH]; FILE *ficresvpl; char fileresvpl[FILENAMELENGTH]; char title[MAXLINE]; -char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH], filerespl[FILENAMELENGTH]; +char model[MAXLINE]; /**< The model line */ +char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH], filerespl[FILENAMELENGTH], fileresplb[FILENAMELENGTH]; char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH]; char tmpout[FILENAMELENGTH], tmpout2[FILENAMELENGTH]; char command[FILENAMELENGTH]; int outcmd=0; -char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH]; - +char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filerespijb[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH]; +char fileresu[FILENAMELENGTH]; /* fileres without r in front */ char filelog[FILENAMELENGTH]; /* Log file */ char filerest[FILENAMELENGTH]; char fileregp[FILENAMELENGTH]; @@ -554,12 +1093,17 @@ char popfile[FILENAMELENGTH]; char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ; -struct timeval start_time, end_time, curr_time, last_time, forecast_time; -struct timezone tzp; -extern int gettimeofday(); -struct tm tmg, tm, tmf, *gmtime(), *localtime(); -long time_value; -extern long time(); +/* struct timeval start_time, end_time, curr_time, last_time, forecast_time; */ +/* struct timezone tzp; */ +/* extern int gettimeofday(); */ +struct tm tml, *gmtime(), *localtime(); + +extern time_t time(); + +struct tm start_time, end_time, curr_time, last_time, forecast_time; +time_t rstart_time, rend_time, rcurr_time, rlast_time, rforecast_time; /* raw time */ +struct tm tm; + char strcurr[80], strfor[80]; char *endptr; @@ -571,7 +1115,8 @@ double dval; #define FTOL 1.0e-10 #define NRANSI -#define ITMAX 200 +#define ITMAX 200 +#define ITPOWMAX 20 /* This is now multiplied by the number of parameters */ #define TOL 2.0e-4 @@ -589,7 +1134,12 @@ static double maxarg1,maxarg2; #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a)) #define rint(a) floor(a+0.5) - +/* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/myutils_8h-source.html */ +#define mytinydouble 1.0e-16 +/* #define DEQUAL(a,b) (fabs((a)-(b)) Tvar[1]= 2 */ +/* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ +/*k 1 2 3 4 5 6 7 8 9 */ +/*Tvar[k]= 5 4 3 6 5 2 7 1 1 */ +/* Tndvar[k] 1 2 3 4 5 */ +/*TDvar 4 3 6 7 1 */ /* For outputs only; combination of dummies fixed or varying */ +/* Tns[k] 1 2 2 4 5 */ /* Number of single cova */ +/* TvarsD[k] 1 2 3 */ /* Number of single dummy cova */ +/* TvarsDind 2 3 9 */ /* position K of single dummy cova */ +/* TvarsQ[k] 1 2 */ /* Number of single quantitative cova */ +/* TvarsQind 1 6 */ /* position K of single quantitative cova */ +/* Tprod[i]=k 4 7 */ +/* Tage[i]=k 5 8 */ +/* */ +/* Type */ +/* V 1 2 3 4 5 */ +/* F F V V V */ +/* D Q D D Q */ +/* */ +int *TvarsD; +int *TvarsDind; +int *TvarsQ; +int *TvarsQind; + +#define MAXRESULTLINES 10 +int nresult=0; +int parameterline=0; /* # of the parameter (type) line */ +int TKresult[MAXRESULTLINES]; +int Tresult[MAXRESULTLINES][NCOVMAX];/* For dummy variable , value (output) */ +int Tinvresult[MAXRESULTLINES][NCOVMAX];/* For dummy variable , value (output) */ +int Tvresult[MAXRESULTLINES][NCOVMAX]; /* For dummy variable , variable # (output) */ +double Tqresult[MAXRESULTLINES][NCOVMAX]; /* For quantitative variable , value (output) */ +double Tqinvresult[MAXRESULTLINES][NCOVMAX]; /* For quantitative variable , value (output) */ +int Tvqresult[MAXRESULTLINES][NCOVMAX]; /* For quantitative variable , variable # (output) */ + +/* int *TDvar; /\**< TDvar[1]=4, TDvarF[2]=3, TDvar[3]=6 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 *\/ */ +int *TvarF; /**< TvarF[1]=Tvar[6]=2, TvarF[2]=Tvar[7]=7, TvarF[3]=Tvar[9]=1 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ +int *TvarFind; /**< TvarFind[1]=6, TvarFind[2]=7, Tvarind[3]=9 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ +int *TvarV; /**< TvarV[1]=Tvar[1]=5, TvarV[2]=Tvar[2]=4 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ +int *TvarVind; /**< TvarVind[1]=1, TvarVind[2]=2 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ +int *TvarA; /**< TvarA[1]=Tvar[5]=5, TvarA[2]=Tvar[8]=1 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ +int *TvarAind; /**< TvarindA[1]=5, TvarAind[2]=8 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ +int *TvarFD; /**< TvarFD[1]=V1 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ +int *TvarFDind; /* TvarFDind[1]=9 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ +int *TvarFQ; /* TvarFQ[1]=V2 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple fixed quantitative variable */ +int *TvarFQind; /* TvarFQind[1]=6 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple fixed quantitative variable */ +int *TvarVD; /* TvarVD[1]=V5 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple fixed quantitative variable */ +int *TvarVDind; /* TvarVDind[1]=1 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple fixed quantitative variable */ +int *TvarVQ; /* TvarVQ[1]=V5 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple time varying quantitative variable */ +int *TvarVQind; /* TvarVQind[1]=1 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple time varying quantitative variable */ + +int *Tvarsel; /**< Selected covariates for output */ +double *Tvalsel; /**< Selected modality value of covariate for output */ +int *Typevar; /**< 0 for simple covariate (dummy, quantitative, fixed or varying), 1 for age product, 2 for product */ +int *Fixed; /** Fixed[k] 0=fixed, 1 varying, 2 fixed with age product, 3 varying with age product */ +int *Dummy; /** Dummy[k] 0=dummy (0 1), 1 quantitative (single or product without age), 2 dummy with age product, 3 quant with age product */ +int *DummyV; /** Dummy[v] 0=dummy (0 1), 1 quantitative */ +int *FixedV; /** FixedV[v] 0 fixed, 1 varying */ +int *Tage; +int anyvaryingduminmodel=0; /**< Any varying dummy in Model=1 yes, 0 no, to avoid a loop on waves in freq */ +int *Tmodelind; /** Tmodelind[Tvaraff[3]]=9 for V1 position,Tvaraff[1]@9={4, 3, 1, 0, 0, 0, 0, 0, 0}, model=V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1*/ +int *TmodelInvind; /** Tmodelind[Tvaraff[3]]=9 for V1 position,Tvaraff[1]@9={4, 3, 1, 0, 0, 0, 0, 0, 0}, model=V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1*/ +int *TmodelInvQind; /** Tmodelqind[1]=1 for V5(quantitative varying) position,Tvaraff[1]@9={4, 3, 1, 0, 0, 0, 0, 0, 0}, model=V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ int *Ndum; /** Freq of modality (tricode */ -int **codtab; /**< codtab=imatrix(1,100,1,10); */ -int **Tvard, *Tprod, cptcovprod, *Tvaraff; +/* int **codtab;*/ /**< codtab=imatrix(1,100,1,10); */ +int **Tvard; +int *Tprod;/**< Gives the k position of the k1 product */ +/* Tprod[k1=1]=3(=V1*V4) for V2+V1+V1*V4+age*V3 */ +int *Tposprod; /**< Gives the k1 product from the k position */ + /* if V2+V1+V1*V4+age*V3+V3*V2 TProd[k1=2]=5 (V3*V2) */ + /* Tposprod[k]=k1 , Tposprod[3]=1, Tposprod[5(V3*V2)]=2 (2nd product without age) */ +int cptcovprod, *Tvaraff, *invalidvarcomb; double *lsurv, *lpop, *tpop; +#define FD 1; /* Fixed dummy covariate */ +#define FQ 2; /* Fixed quantitative covariate */ +#define FP 3; /* Fixed product covariate */ +#define FPDD 7; /* Fixed product dummy*dummy covariate */ +#define FPDQ 8; /* Fixed product dummy*quantitative covariate */ +#define FPQQ 9; /* Fixed product quantitative*quantitative covariate */ +#define VD 10; /* Varying dummy covariate */ +#define VQ 11; /* Varying quantitative covariate */ +#define VP 12; /* Varying product covariate */ +#define VPDD 13; /* Varying product dummy*dummy covariate */ +#define VPDQ 14; /* Varying product dummy*quantitative covariate */ +#define VPQQ 15; /* Varying product quantitative*quantitative covariate */ +#define APFD 16; /* Age product * fixed dummy covariate */ +#define APFQ 17; /* Age product * fixed quantitative covariate */ +#define APVD 18; /* Age product * varying dummy covariate */ +#define APVQ 19; /* Age product * varying quantitative covariate */ + +#define FTYPE 1; /* Fixed covariate */ +#define VTYPE 2; /* Varying covariate (loop in wave) */ +#define ATYPE 2; /* Age product covariate (loop in dh within wave)*/ + +struct kmodel{ + int maintype; /* main type */ + int subtype; /* subtype */ +}; +struct kmodel modell[NCOVMAX]; + double ftol=FTOL; /**< Tolerance for computing Max Likelihood */ double ftolhess; /**< Tolerance for computing hessian */ @@ -633,7 +1288,7 @@ static int split( char *path, char *dirc the name of the file (name), its extension only (ext) and its first part of the name (finame) */ char *ss; /* pointer */ - int l1, l2; /* length counters */ + int l1=0, l2=0; /* length counters */ l1 = strlen(path ); /* length of path */ if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH ); @@ -644,18 +1299,22 @@ static int split( char *path, char *dirc printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/ /* get current working directory */ /* extern char* getcwd ( char *buf , int len);*/ - if ( getcwd( dirc, FILENAME_MAX ) == NULL ) { +#ifdef WIN32 + if (_getcwd( dirc, FILENAME_MAX ) == NULL ) { +#else + if (getcwd(dirc, FILENAME_MAX) == NULL) { +#endif return( GLOCK_ERROR_GETCWD ); } /* got dirc from getcwd*/ printf(" DIRC = %s \n",dirc); - } else { /* strip direcotry from path */ + } else { /* strip directory from path */ ss++; /* after this, the filename */ l2 = strlen( ss ); /* length of filename */ if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH ); strcpy( name, ss ); /* save file name */ strncpy( dirc, path, l1 - l2 ); /* now the directory */ - dirc[l1-l2] = 0; /* add zero */ + dirc[l1-l2] = '\0'; /* add zero */ printf(" DIRC2 = %s \n",dirc); } /* We add a separator at the end of dirc if not exists */ @@ -707,14 +1366,57 @@ char *trimbb(char *out, char *in) return s; } +/* char *substrchaine(char *out, char *in, char *chain) */ +/* { */ +/* /\* Substract chain 'chain' from 'in', return and output 'out' *\/ */ +/* char *s, *t; */ +/* t=in;s=out; */ +/* while ((*in != *chain) && (*in != '\0')){ */ +/* *out++ = *in++; */ +/* } */ + +/* /\* *in matches *chain *\/ */ +/* while ((*in++ == *chain++) && (*in != '\0')){ */ +/* printf("*in = %c, *out= %c *chain= %c \n", *in, *out, *chain); */ +/* } */ +/* in--; chain--; */ +/* while ( (*in != '\0')){ */ +/* printf("Bef *in = %c, *out= %c *chain= %c \n", *in, *out, *chain); */ +/* *out++ = *in++; */ +/* printf("Aft *in = %c, *out= %c *chain= %c \n", *in, *out, *chain); */ +/* } */ +/* *out='\0'; */ +/* out=s; */ +/* return out; */ +/* } */ +char *substrchaine(char *out, char *in, char *chain) +{ + /* Substract chain 'chain' from 'in', return and output 'out' */ + /* in="V1+V1*age+age*age+V2", chain="age*age" */ + + char *strloc; + + strcpy (out, in); + strloc = strstr(out, chain); /* strloc points to out at age*age+V2 */ + printf("Bef strloc=%s chain=%s out=%s \n", strloc, chain, out); + if(strloc != NULL){ + /* will affect out */ /* strloc+strlenc(chain)=+V2 */ /* Will also work in Unicode */ + memmove(strloc,strloc+strlen(chain), strlen(strloc+strlen(chain))+1); + /* strcpy (strloc, strloc +strlen(chain));*/ + } + printf("Aft strloc=%s chain=%s in=%s out=%s \n", strloc, chain, in, out); + return out; +} + + char *cutl(char *blocc, char *alocc, char *in, char occ) { - /* cuts string in into blocc and alocc where blocc ends before first occurence of char 'occ' + /* cuts string in into blocc and alocc where blocc ends before FIRST occurence of char 'occ' and alocc starts after first occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2') - gives blocc="abcdef2ghi" and alocc="j". + gives blocc="abcdef" and alocc="ghi2j". If occ is not found blocc is null and alocc is equal to in. Returns blocc */ - char *s, *t, *bl; + char *s, *t; t=in;s=in; while ((*in != occ) && (*in != '\0')){ *alocc++ = *in++; @@ -737,7 +1439,7 @@ char *cutl(char *blocc, char *alocc, cha } char *cutv(char *blocc, char *alocc, char *in, char occ) { - /* cuts string in into blocc and alocc where blocc ends before last occurence of char 'occ' + /* cuts string in into blocc and alocc where blocc ends before LAST occurence of char 'occ' and alocc starts after last occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2') gives blocc="abcdef2ghi" and alocc="j". If occ is not found blocc is null and alocc is equal to in. Returns alocc @@ -771,7 +1473,7 @@ int nbocc(char *s, char occ) i=0; lg=strlen(s); for(i=0; i<= lg; i++) { - if (s[i] == occ ) j++; + if (s[i] == occ ) j++; } return j; } @@ -798,6 +1500,24 @@ int nbocc(char *s, char occ) /* } */ /* } */ +#ifdef _WIN32 +char * strsep(char **pp, const char *delim) +{ + char *p, *q; + + if ((p = *pp) == NULL) + return 0; + if ((q = strpbrk (p, delim)) != NULL) + { + *pp = q + 1; + *q = '\0'; + } + else + *pp = 0; + return p; +} +#endif + /********************** nrerror ********************/ void nrerror(char error_text[]) @@ -996,32 +1716,74 @@ char *subdirf3(char fileres[], char *pre strcat(tmpout,fileres); return tmpout; } - -/***************** f1dim *************************/ -extern int ncom; -extern double *pcom,*xicom; -extern double (*nrfunc)(double []); - -double f1dim(double x) -{ - int j; - double f; - double *xt; - xt=vector(1,ncom); - for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; - f=(*nrfunc)(xt); - free_vector(xt,1,ncom); - return f; -} +/*************** function subdirfext ***********/ +char *subdirfext(char fileres[], char *preop, char *postop) +{ + + strcpy(tmpout,preop); + strcat(tmpout,fileres); + strcat(tmpout,postop); + return tmpout; +} -/*****************brent *************************/ -double brent(double ax, double bx, double cx, double (*f)(double), double tol, double *xmin) +/*************** function subdirfext3 ***********/ +char *subdirfext3(char fileres[], char *preop, char *postop) +{ + + /* Caution optionfilefiname is hidden */ + strcpy(tmpout,optionfilefiname); + strcat(tmpout,"/"); + strcat(tmpout,preop); + strcat(tmpout,fileres); + strcat(tmpout,postop); + return tmpout; +} + +char *asc_diff_time(long time_sec, char ascdiff[]) +{ + long sec_left, days, hours, minutes; + days = (time_sec) / (60*60*24); + sec_left = (time_sec) % (60*60*24); + hours = (sec_left) / (60*60) ; + sec_left = (sec_left) %(60*60); + minutes = (sec_left) /60; + sec_left = (sec_left) % (60); + sprintf(ascdiff,"%ld day(s) %ld hour(s) %ld minute(s) %ld second(s)",days, hours, minutes, sec_left); + return ascdiff; +} + +/***************** f1dim *************************/ +extern int ncom; +extern double *pcom,*xicom; +extern double (*nrfunc)(double []); + +double f1dim(double x) { + int j; + double f; + double *xt; + + xt=vector(1,ncom); + for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; + f=(*nrfunc)(xt); + free_vector(xt,1,ncom); + return f; +} + +/*****************brent *************************/ +double brent(double ax, double bx, double cx, double (*f)(double), double tol, double *xmin) +{ + /* Given a function f, and given a bracketing triplet of abscissas ax, bx, cx (such that bx is + * between ax and cx, and f(bx) is less than both f(ax) and f(cx) ), this routine isolates + * the minimum to a fractional precision of about tol using Brent’s method. The abscissa of + * the minimum is returned as xmin, and the minimum function value is returned as brent , the + * returned function value. + */ int iter; double a,b,d,etemp; - double fu,fv,fw,fx; - double ftemp; + double fu=0,fv,fw,fx; + double ftemp=0.; double p,q,r,tol1,tol2,u,v,w,x,xm; double e=0.0; @@ -1035,7 +1797,7 @@ double brent(double ax, double bx, doubl /* if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/ printf(".");fflush(stdout); fprintf(ficlog,".");fflush(ficlog); -#ifdef DEBUG +#ifdef DEBUGBRENT 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); 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); /* if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */ @@ -1055,12 +1817,12 @@ double brent(double ax, double bx, doubl etemp=e; e=d; if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) - d=CGOLD*(e=(x >= xm ? a-x : b-x)); + d=CGOLD*(e=(x >= xm ? a-x : b-x)); else { - d=p/q; - u=x+d; - if (u-a < tol2 || b-u < tol2) - d=SIGN(tol1,xm-x); + d=p/q; + u=x+d; + if (u-a < tol2 || b-u < tol2) + d=SIGN(tol1,xm-x); } } else { d=CGOLD*(e=(x >= xm ? a-x : b-x)); @@ -1070,19 +1832,19 @@ double brent(double ax, double bx, doubl if (fu <= fx) { if (u >= x) a=x; else b=x; SHFT(v,w,x,u) - SHFT(fv,fw,fx,fu) - } else { - if (u < x) a=u; else b=u; - if (fu <= fw || w == x) { - v=w; - w=u; - fv=fw; - fw=fu; - } else if (fu <= fv || v == x || v == w) { - v=u; - fv=fu; - } - } + SHFT(fv,fw,fx,fu) + } else { + if (u < x) a=u; else b=u; + if (fu <= fw || w == x) { + v=w; + w=u; + fv=fw; + fw=fu; + } else if (fu <= fv || v == x || v == w) { + v=u; + fv=fu; + } + } } nrerror("Too many iterations in brent"); *xmin=x; @@ -1093,51 +1855,158 @@ double brent(double ax, double bx, doubl void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, double (*func)(double)) -{ +{ /* Given a function func , and given distinct initial points ax and bx , this routine searches in +the downhill direction (defined by the function as evaluated at the initial points) and returns +new points ax , bx , cx that bracket a minimum of the function. Also returned are the function +values at the three points, fa, fb , and fc such that fa > fb and fb < fc. + */ double ulim,u,r,q, dum; double fu; - - *fa=(*func)(*ax); - *fb=(*func)(*bx); + + double scale=10.; + int iterscale=0; + + *fa=(*func)(*ax); /* xta[j]=pcom[j]+(*ax)*xicom[j]; fa=f(xta[j])*/ + *fb=(*func)(*bx); /* xtb[j]=pcom[j]+(*bx)*xicom[j]; fb=f(xtb[j]) */ + + + /* while(*fb != *fb){ /\* *ax should be ok, reducing distance to *ax *\/ */ + /* printf("Warning mnbrak *fb = %lf, *bx=%lf *ax=%lf *fa==%lf iter=%d\n",*fb, *bx, *ax, *fa, iterscale++); */ + /* *bx = *ax - (*ax - *bx)/scale; */ + /* *fb=(*func)(*bx); /\* xtb[j]=pcom[j]+(*bx)*xicom[j]; fb=f(xtb[j]) *\/ */ + /* } */ + if (*fb > *fa) { SHFT(dum,*ax,*bx,dum) - SHFT(dum,*fb,*fa,dum) - } + SHFT(dum,*fb,*fa,dum) + } *cx=(*bx)+GOLD*(*bx-*ax); *fc=(*func)(*cx); - while (*fb > *fc) { +#ifdef DEBUG + printf("mnbrak0 a=%lf *fa=%lf, b=%lf *fb=%lf, c=%lf *fc=%lf\n",*ax,*fa,*bx,*fb,*cx, *fc); + fprintf(ficlog,"mnbrak0 a=%lf *fa=%lf, b=%lf *fb=%lf, c=%lf *fc=%lf\n",*ax,*fa,*bx,*fb,*cx, *fc); +#endif + while (*fb > *fc) { /* Declining a,b,c with fa> fb > fc. If fc=inf it exits and if flat fb=fc it exits too.*/ r=(*bx-*ax)*(*fb-*fc); - q=(*bx-*cx)*(*fb-*fa); + q=(*bx-*cx)*(*fb-*fa); /* What if fa=inf */ u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ - (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); - ulim=(*bx)+GLIMIT*(*cx-*bx); - if ((*bx-u)*(u-*cx) > 0.0) { + (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); /* Minimum abscissa of a parabolic estimated from (a,fa), (b,fb) and (c,fc). */ + ulim=(*bx)+GLIMIT*(*cx-*bx); /* Maximum abscissa where function should be evaluated */ + if ((*bx-u)*(u-*cx) > 0.0) { /* if u_p is between b and c */ fu=(*func)(u); - } else if ((*cx-u)*(u-ulim) > 0.0) { +#ifdef DEBUG + /* f(x)=A(x-u)**2+f(u) */ + double A, fparabu; + A= (*fb - *fa)/(*bx-*ax)/(*bx+*ax-2*u); + fparabu= *fa - A*(*ax-u)*(*ax-u); + printf("\nmnbrak (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf), (*u=%.12f, fu=%.12lf, fparabu=%.12f, q=%lf < %lf=r)\n",*ax,*fa,*bx,*fb,*cx,*fc,u,fu, fparabu,q,r); + fprintf(ficlog,"\nmnbrak (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf), (*u=%.12f, fu=%.12lf, fparabu=%.12f, q=%lf < %lf=r)\n",*ax,*fa,*bx,*fb,*cx,*fc,u,fu, fparabu,q,r); + /* And thus,it can be that fu > *fc even if fparabu < *fc */ + /* mnbrak (*ax=7.666299858533, *fa=299039.693133272231), (*bx=8.595447774979, *fb=298976.598289369489), + (*cx=10.098840694817, *fc=298946.631474258087), (*u=9.852501168332, fu=298948.773013752128, fparabu=298945.434711494134) */ + /* In that case, there is no bracket in the output! Routine is wrong with many consequences.*/ +#endif +#ifdef MNBRAKORIGINAL +#else +/* if (fu > *fc) { */ +/* #ifdef DEBUG */ +/* printf("mnbrak4 fu > fc \n"); */ +/* fprintf(ficlog, "mnbrak4 fu > fc\n"); */ +/* #endif */ +/* /\* 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 *\\/ *\/ */ +/* /\* SHFT(*fa,*fc,fu,*fc) /\\* (b, u, c) is a bracket while test fb > fc will be fu > fc will exit *\\/ *\/ */ +/* dum=u; /\* Shifting c and u *\/ */ +/* u = *cx; */ +/* *cx = dum; */ +/* dum = fu; */ +/* fu = *fc; */ +/* *fc =dum; */ +/* } else { /\* end *\/ */ +/* #ifdef DEBUG */ +/* printf("mnbrak3 fu < fc \n"); */ +/* fprintf(ficlog, "mnbrak3 fu < fc\n"); */ +/* #endif */ +/* dum=u; /\* Shifting c and u *\/ */ +/* u = *cx; */ +/* *cx = dum; */ +/* dum = fu; */ +/* fu = *fc; */ +/* *fc =dum; */ +/* } */ +#ifdef DEBUGMNBRAK + double A, fparabu; + A= (*fb - *fa)/(*bx-*ax)/(*bx+*ax-2*u); + fparabu= *fa - A*(*ax-u)*(*ax-u); + printf("\nmnbrak35 ax=%lf fa=%lf bx=%lf fb=%lf, u=%lf fp=%lf fu=%lf < or >= fc=%lf cx=%lf, q=%lf < %lf=r \n",*ax, *fa, *bx,*fb,u,fparabu,fu,*fc,*cx,q,r); + fprintf(ficlog,"\nmnbrak35 ax=%lf fa=%lf bx=%lf fb=%lf, u=%lf fp=%lf fu=%lf < or >= fc=%lf cx=%lf, q=%lf < %lf=r \n",*ax, *fa, *bx,*fb,u,fparabu,fu,*fc,*cx,q,r); +#endif + dum=u; /* Shifting c and u */ + u = *cx; + *cx = dum; + dum = fu; + fu = *fc; + *fc =dum; +#endif + } else if ((*cx-u)*(u-ulim) > 0.0) { /* u is after c but before ulim */ +#ifdef DEBUG + printf("\nmnbrak2 u=%lf after c=%lf but before ulim\n",u,*cx); + fprintf(ficlog,"\nmnbrak2 u=%lf after c=%lf but before ulim\n",u,*cx); +#endif fu=(*func)(u); if (fu < *fc) { - SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) - SHFT(*fb,*fc,fu,(*func)(u)) - } - } else if ((u-ulim)*(ulim-*cx) >= 0.0) { +#ifdef DEBUG + printf("\nmnbrak2 u=%lf after c=%lf but before ulim=%lf AND fu=%lf < %lf=fc\n",u,*cx,ulim,fu, *fc); + fprintf(ficlog,"\nmnbrak2 u=%lf after c=%lf but before ulim=%lf AND fu=%lf < %lf=fc\n",u,*cx,ulim,fu, *fc); +#endif + SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) + SHFT(*fb,*fc,fu,(*func)(u)) +#ifdef DEBUG + printf("\nmnbrak2 shift GOLD c=%lf",*cx+GOLD*(*cx-*bx)); +#endif + } + } else if ((u-ulim)*(ulim-*cx) >= 0.0) { /* u outside ulim (verifying that ulim is beyond c) */ +#ifdef DEBUG + printf("\nmnbrak2 u=%lf outside ulim=%lf (verifying that ulim is beyond c=%lf)\n",u,ulim,*cx); + fprintf(ficlog,"\nmnbrak2 u=%lf outside ulim=%lf (verifying that ulim is beyond c=%lf)\n",u,ulim,*cx); +#endif u=ulim; fu=(*func)(u); - } else { + } else { /* u could be left to b (if r > q parabola has a maximum) */ +#ifdef DEBUG + printf("\nmnbrak2 u=%lf could be left to b=%lf (if r=%lf > q=%lf parabola has a maximum)\n",u,*bx,r,q); + fprintf(ficlog,"\nmnbrak2 u=%lf could be left to b=%lf (if r=%lf > q=%lf parabola has a maximum)\n",u,*bx,r,q); +#endif u=(*cx)+GOLD*(*cx-*bx); fu=(*func)(u); - } +#ifdef DEBUG + printf("\nmnbrak2 new u=%lf fu=%lf shifted gold left from c=%lf and b=%lf \n",u,fu,*cx,*bx); + fprintf(ficlog,"\nmnbrak2 new u=%lf fu=%lf shifted gold left from c=%lf and b=%lf \n",u,fu,*cx,*bx); +#endif + } /* end tests */ SHFT(*ax,*bx,*cx,u) - SHFT(*fa,*fb,*fc,fu) - } + SHFT(*fa,*fb,*fc,fu) +#ifdef DEBUG + printf("\nmnbrak2 shift (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf)\n",*ax,*fa,*bx,*fb,*cx,*fc); + fprintf(ficlog, "\nmnbrak2 shift (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf)\n",*ax,*fa,*bx,*fb,*cx,*fc); +#endif + } /* end while; ie return (a, b, c, fa, fb, fc) such that a < b < c with f(a) > f(b) and fb < f(c) */ } /*************** linmin ************************/ - +/* Given an n -dimensional point p[1..n] and an n -dimensional direction xi[1..n] , moves and +resets p to where the function func(p) takes on a minimum along the direction xi from p , +and replaces xi by the actual vector displacement that p was moved. Also returns as fret +the value of func at the returned location p . This is actually all accomplished by calling the +routines mnbrak and brent .*/ int ncom; double *pcom,*xicom; double (*nrfunc)(double []); +#ifdef LINMINORIGINAL void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) +#else +void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []), int *flat) +#endif { double brent(double ax, double bx, double cx, double (*f)(double), double tol, double *xmin); @@ -1147,55 +2016,151 @@ void linmin(double p[], double xi[], int int j; double xx,xmin,bx,ax; double fx,fb,fa; - + +#ifdef LINMINORIGINAL +#else + double scale=10., axs, xxs; /* Scale added for infinity */ +#endif + ncom=n; pcom=vector(1,n); xicom=vector(1,n); nrfunc=func; for (j=1;j<=n;j++) { pcom[j]=p[j]; - xicom[j]=xi[j]; + xicom[j]=xi[j]; /* Former scale xi[j] of currrent direction i */ } - ax=0.0; - xx=1.0; - mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); - *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); + +#ifdef LINMINORIGINAL + xx=1.; +#else + axs=0.0; + xxs=1.; + do{ + xx= xxs; +#endif + ax=0.; + mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); /* Outputs: xtx[j]=pcom[j]+(*xx)*xicom[j]; fx=f(xtx[j]) */ + /* brackets with inputs ax=0 and xx=1, but points, pcom=p, and directions values, xicom=xi, are sent via f1dim(x) */ + /* 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)) */ + /* Outputs: fa=f(p(j)) and fx=f(p(j) + xxs * xi(j) ) and f(bx)= f(p(j)+ bx* xi(j)) */ + /* Given input ax=axs and xx=xxs, xx might be too far from ax to get a finite f(xx) */ + /* Searches on line, outputs (ax, xx, bx) such that fx < min(fa and fb) */ + /* 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]]*/ +#ifdef LINMINORIGINAL +#else + if (fx != fx){ + xxs=xxs/scale; /* Trying a smaller xx, closer to initial ax=0 */ + printf("|"); + fprintf(ficlog,"|"); +#ifdef DEBUGLINMIN + 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); +#endif + } + }while(fx != fx && xxs > 1.e-5); +#endif + +#ifdef DEBUGLINMIN + 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); + fprintf(ficlog,"\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); +#endif +#ifdef LINMINORIGINAL +#else + if(fb == fx){ /* Flat function in the direction */ + xmin=xx; + *flat=1; + }else{ + *flat=0; +#endif + /*Flat mnbrak2 shift (*ax=0.000000000000, *fa=51626.272983130431), (*bx=-1.618034000000, *fb=51590.149499362531), (*cx=-4.236068025156, *fc=51590.149499362531) */ + *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); /* Giving a bracketting triplet (ax, xx, bx), find a minimum, xmin, according to f1dim, *fret(xmin),*/ + /* fa = f(p[j] + ax * xi[j]), fx = f(p[j] + xx * xi[j]), fb = f(p[j] + bx * xi[j]) */ + /* fmin = f(p[j] + xmin * xi[j]) */ + /* P+lambda n in that direction (lambdamin), with TOL between abscisses */ + /* f1dim(xmin): for (j=1;j<=ncom;j++) xt[j]=pcom[j]+xmin*xicom[j]; */ #ifdef DEBUG - printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin); - fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin); + printf("retour brent from bracket (a=%lf fa=%lf, xx=%lf fx=%lf, b=%lf fb=%lf): fret=%lf xmin=%lf\n",ax,fa,xx,fx,bx,fb,*fret,xmin); + fprintf(ficlog,"retour brent from bracket (a=%lf fa=%lf, xx=%lf fx=%lf, b=%lf fb=%lf): fret=%lf xmin=%lf\n",ax,fa,xx,fx,bx,fb,*fret,xmin); +#endif +#ifdef LINMINORIGINAL +#else + } +#endif +#ifdef DEBUGLINMIN + printf("linmin end "); + fprintf(ficlog,"linmin end "); #endif for (j=1;j<=n;j++) { +#ifdef LINMINORIGINAL xi[j] *= xmin; - p[j] += xi[j]; +#else +#ifdef DEBUGLINMIN + if(xxs <1.0) + printf(" before xi[%d]=%12.8f", j,xi[j]); +#endif + xi[j] *= xmin*xxs; /* xi rescaled by xmin and number of loops: if xmin=-1.237 and xi=(1,0,...,0) xi=(-1.237,0,...,0) */ +#ifdef DEBUGLINMIN + if(xxs <1.0) + 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 ); +#endif +#endif + p[j] += xi[j]; /* Parameters values are updated accordingly */ } +#ifdef DEBUGLINMIN + printf("\n"); + printf("Comparing last *frec(xmin=%12.8f)=%12.8f from Brent and frec(0.)=%12.8f \n", xmin, *fret, (*func)(p)); + fprintf(ficlog,"Comparing last *frec(xmin=%12.8f)=%12.8f from Brent and frec(0.)=%12.8f \n", xmin, *fret, (*func)(p)); + for (j=1;j<=n;j++) { + printf(" xi[%d]= %14.10f p[%d]= %12.7f",j,xi[j],j,p[j]); + fprintf(ficlog," xi[%d]= %14.10f p[%d]= %12.7f",j,xi[j],j,p[j]); + if(j % ncovmodel == 0){ + printf("\n"); + fprintf(ficlog,"\n"); + } + } +#else +#endif free_vector(xicom,1,n); free_vector(pcom,1,n); } -char *asc_diff_time(long time_sec, char ascdiff[]) -{ - long sec_left, days, hours, minutes; - days = (time_sec) / (60*60*24); - sec_left = (time_sec) % (60*60*24); - hours = (sec_left) / (60*60) ; - sec_left = (sec_left) %(60*60); - minutes = (sec_left) /60; - sec_left = (sec_left) % (60); - sprintf(ascdiff,"%ld day(s) %ld hour(s) %ld minute(s) %ld second(s)",days, hours, minutes, sec_left); - return ascdiff; -} /*************** powell ************************/ +/* +Minimization of a function func of n variables. Input consists of an initial starting point +p[1..n] ; an initial matrix xi[1..n][1..n] , whose columns contain the initial set of di- +rections (usually the n unit vectors); and ftol , the fractional tolerance in the function value +such that failure to decrease by more than this amount on one iteration signals doneness. On +output, p is set to the best point found, xi is the then-current direction set, fret is the returned +function value at p , and iter is the number of iterations taken. The routine linmin is used. + */ +#ifdef LINMINORIGINAL +#else + int *flatdir; /* Function is vanishing in that direction */ + int flat=0, flatd=0; /* Function is vanishing in that direction */ +#endif void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, double (*func)(double [])) { - void linmin(double p[], double xi[], int n, double *fret, +#ifdef LINMINORIGINAL + void linmin(double p[], double xi[], int n, double *fret, double (*func)(double [])); - int i,ibig,j; +#else + void linmin(double p[], double xi[], int n, double *fret, + double (*func)(double []),int *flat); +#endif + int i,ibig,j,jk,k; double del,t,*pt,*ptt,*xit; + double directest; double fp,fptt; double *xits; int niterf, itmp; +#ifdef LINMINORIGINAL +#else + + flatdir=ivector(1,n); + for (j=1;j<=n;j++) flatdir[j]=0; +#endif pt=vector(1,n); ptt=vector(1,n); @@ -1203,76 +2168,144 @@ void powell(double p[], double **xi, int xits=vector(1,n); *fret=(*func)(p); for (j=1;j<=n;j++) pt[j]=p[j]; + rcurr_time = time(NULL); for (*iter=1;;++(*iter)) { - fp=(*fret); + fp=(*fret); /* From former iteration or initial value */ ibig=0; del=0.0; - last_time=curr_time; - (void) gettimeofday(&curr_time,&tzp); - printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, curr_time.tv_sec-last_time.tv_sec, curr_time.tv_sec-start_time.tv_sec);fflush(stdout); - fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, curr_time.tv_sec-last_time.tv_sec, curr_time.tv_sec-start_time.tv_sec); fflush(ficlog); -/* fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tv_sec-start_time.tv_sec); */ - for (i=1;i<=n;i++) { - printf(" %d %.12f",i, p[i]); - fprintf(ficlog," %d %.12lf",i, p[i]); + rlast_time=rcurr_time; + /* (void) gettimeofday(&curr_time,&tzp); */ + rcurr_time = time(NULL); + curr_time = *localtime(&rcurr_time); + printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, rcurr_time-rlast_time, rcurr_time-rstart_time);fflush(stdout); + fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret,rcurr_time-rlast_time, rcurr_time-rstart_time); fflush(ficlog); +/* fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tm_sec-start_time.tm_sec); */ + for (i=1;i<=n;i++) { fprintf(ficrespow," %.12lf", p[i]); } + fprintf(ficrespow,"\n");fflush(ficrespow); + printf("\n#model= 1 + age "); + fprintf(ficlog,"\n#model= 1 + age "); + if(nagesqr==1){ + printf(" + age*age "); + fprintf(ficlog," + age*age "); + } + for(j=1;j <=ncovmodel-2;j++){ + if(Typevar[j]==0) { + printf(" + V%d ",Tvar[j]); + fprintf(ficlog," + V%d ",Tvar[j]); + }else if(Typevar[j]==1) { + printf(" + V%d*age ",Tvar[j]); + fprintf(ficlog," + V%d*age ",Tvar[j]); + }else if(Typevar[j]==2) { + printf(" + V%d*V%d ",Tvard[Tposprod[j]][1],Tvard[Tposprod[j]][2]); + fprintf(ficlog," + V%d*V%d ",Tvard[Tposprod[j]][1],Tvard[Tposprod[j]][2]); + } + } printf("\n"); +/* printf("12 47.0114589 0.0154322 33.2424412 0.3279905 2.3731903 */ +/* 13 -21.5392400 0.1118147 1.2680506 1.2973408 -1.0663662 */ fprintf(ficlog,"\n"); - fprintf(ficrespow,"\n");fflush(ficrespow); - if(*iter <=3){ - tm = *localtime(&curr_time.tv_sec); - strcpy(strcurr,asctime(&tm)); -/* asctime_r(&tm,strcurr); */ - forecast_time=curr_time; + for(i=1,jk=1; i <=nlstate; i++){ + for(k=1; k <=(nlstate+ndeath); k++){ + if (k != i) { + printf("%d%d ",i,k); + fprintf(ficlog,"%d%d ",i,k); + for(j=1; j <=ncovmodel; j++){ + printf("%12.7f ",p[jk]); + fprintf(ficlog,"%12.7f ",p[jk]); + jk++; + } + printf("\n"); + fprintf(ficlog,"\n"); + } + } + } + if(*iter <=3 && *iter >1){ + tml = *localtime(&rcurr_time); + strcpy(strcurr,asctime(&tml)); + rforecast_time=rcurr_time; itmp = strlen(strcurr); if(strcurr[itmp-1]=='\n') /* Windows outputs with a new line */ strcurr[itmp-1]='\0'; - printf("\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec); - fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec); + printf("\nConsidering the time needed for the last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time); + fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time); for(niterf=10;niterf<=30;niterf+=10){ - forecast_time.tv_sec=curr_time.tv_sec+(niterf-*iter)*(curr_time.tv_sec-last_time.tv_sec); - tmf = *localtime(&forecast_time.tv_sec); -/* asctime_r(&tmf,strfor); */ - strcpy(strfor,asctime(&tmf)); + rforecast_time=rcurr_time+(niterf-*iter)*(rcurr_time-rlast_time); + forecast_time = *localtime(&rforecast_time); + strcpy(strfor,asctime(&forecast_time)); itmp = strlen(strfor); if(strfor[itmp-1]=='\n') - strfor[itmp-1]='\0'; - 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(forecast_time.tv_sec-curr_time.tv_sec,tmpout),strfor,strcurr); - 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(forecast_time.tv_sec-curr_time.tv_sec,tmpout),strfor,strcurr); + strfor[itmp-1]='\0'; + 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); + 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); } } - for (i=1;i<=n;i++) { - for (j=1;j<=n;j++) xit[j]=xi[j][i]; + for (i=1;i<=n;i++) { /* For each direction i */ + for (j=1;j<=n;j++) xit[j]=xi[j][i]; /* Directions stored from previous iteration with previous scales */ fptt=(*fret); #ifdef DEBUG - printf("fret=%lf \n",*fret); - fprintf(ficlog,"fret=%lf \n",*fret); + printf("fret=%lf, %lf, %lf \n", *fret, *fret, *fret); + fprintf(ficlog, "fret=%lf, %lf, %lf \n", *fret, *fret, *fret); #endif - printf("%d",i);fflush(stdout); + printf("%d",i);fflush(stdout); /* print direction (parameter) i */ fprintf(ficlog,"%d",i);fflush(ficlog); - linmin(p,xit,n,fret,func); - if (fabs(fptt-(*fret)) > del) { - del=fabs(fptt-(*fret)); - ibig=i; +#ifdef LINMINORIGINAL + linmin(p,xit,n,fret,func); /* Point p[n]. xit[n] has been loaded for direction i as input.*/ +#else + linmin(p,xit,n,fret,func,&flat); /* Point p[n]. xit[n] has been loaded for direction i as input.*/ + flatdir[i]=flat; /* Function is vanishing in that direction i */ +#endif + /* Outputs are fret(new point p) p is updated and xit rescaled */ + if (fabs(fptt-(*fret)) > del) { /* We are keeping the max gain on each of the n directions */ + /* because that direction will be replaced unless the gain del is small */ + /* in comparison with the 'probable' gain, mu^2, with the last average direction. */ + /* Unless the n directions are conjugate some gain in the determinant may be obtained */ + /* with the new direction. */ + del=fabs(fptt-(*fret)); + ibig=i; } #ifdef DEBUG printf("%d %.12e",i,(*fret)); fprintf(ficlog,"%d %.12e",i,(*fret)); for (j=1;j<=n;j++) { - xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5); - printf(" x(%d)=%.12e",j,xit[j]); - fprintf(ficlog," x(%d)=%.12e",j,xit[j]); + xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5); + printf(" x(%d)=%.12e",j,xit[j]); + fprintf(ficlog," x(%d)=%.12e",j,xit[j]); } for(j=1;j<=n;j++) { - printf(" p=%.12e",p[j]); - fprintf(ficlog," p=%.12e",p[j]); + printf(" p(%d)=%.12e",j,p[j]); + fprintf(ficlog," p(%d)=%.12e",j,p[j]); } printf("\n"); fprintf(ficlog,"\n"); #endif - } - if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) { + } /* end loop on each direction i */ + /* Convergence test will use last linmin estimation (fret) and compare former iteration (fp) */ + /* But p and xit have been updated at the end of linmin, *fret corresponds to new p, xit */ + /* New value of last point Pn is not computed, P(n-1) */ + for(j=1;j<=n;j++) { + if(flatdir[j] >0){ + printf(" p(%d)=%lf flat=%d ",j,p[j],flatdir[j]); + fprintf(ficlog," p(%d)=%lf flat=%d ",j,p[j],flatdir[j]); + } + /* printf("\n"); */ + /* fprintf(ficlog,"\n"); */ + } + /* if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) { /\* Did we reach enough precision? *\/ */ + if (2.0*fabs(fp-(*fret)) <= ftol) { /* Did we reach enough precision? */ + /* We could compare with a chi^2. chisquare(0.95,ddl=1)=3.84 */ + /* By adding age*age in a model, the new -2LL should be lower and the difference follows a */ + /* a chisquare statistics with 1 degree. To be significant at the 95% level, it should have */ + /* decreased of more than 3.84 */ + /* By adding age*age and V1*age the gain (-2LL) should be more than 5.99 (ddl=2) */ + /* By using V1+V2+V3, the gain should be 7.82, compared with basic 1+age. */ + /* By adding 10 parameters more the gain should be 18.31 */ + + /* Starting the program with initial values given by a former maximization will simply change */ + /* the scales of the directions and the directions, because the are reset to canonical directions */ + /* Thus the first calls to linmin will give new points and better maximizations until fp-(*fret) is */ + /* under the tolerance value. If the tolerance is very small 1.e-9, it could last long. */ #ifdef DEBUG int k[2],l; k[0]=1; @@ -1296,190 +2329,703 @@ void powell(double p[], double **xi, int } #endif - +#ifdef LINMINORIGINAL +#else + free_ivector(flatdir,1,n); +#endif free_vector(xit,1,n); free_vector(xits,1,n); free_vector(ptt,1,n); free_vector(pt,1,n); return; - } - if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); - for (j=1;j<=n;j++) { + } /* enough precision */ + if (*iter == ITMAX*n) nrerror("powell exceeding maximum iterations."); + for (j=1;j<=n;j++) { /* Computes the extrapolated point P_0 + 2 (P_n-P_0) */ ptt[j]=2.0*p[j]-pt[j]; xit[j]=p[j]-pt[j]; pt[j]=p[j]; } - fptt=(*func)(ptt); - if (fptt < fp) { - t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); - if (t < 0.0) { - linmin(p,xit,n,fret,func); + fptt=(*func)(ptt); /* f_3 */ +#ifdef NODIRECTIONCHANGEDUNTILNITER /* No change in drections until some iterations are done */ + if (*iter <=4) { +#else +#endif +#ifdef POWELLNOF3INFF1TEST /* skips test F3 0 */ + /* mu² and del² are equal when f3=f1 */ + /* f3 < f1 : mu² < del <= lambda^2 both test are equivalent */ + /* f3 < f1 : mu² < lambda^2 < del then directtest is negative and powell t is positive */ + /* f3 > f1 : lambda² < mu^2 < del then t is negative and directest >0 */ + /* f3 > f1 : lambda² < del < mu^2 then t is positive and directest >0 */ +#ifdef NRCORIGINAL + t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)- del*SQR(fp-fptt); /* Original Numerical Recipes in C*/ +#else + t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del); /* Intel compiler doesn't work on one line; bug reported */ + t= t- del*SQR(fp-fptt); +#endif + directest = fp-2.0*(*fret)+fptt - 2.0 * del; /* If delta was big enough we change it for a new direction */ +#ifdef DEBUG + 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); + 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); + printf("t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt), + (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt)); + fprintf(ficlog,"t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt), + (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt)); + 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); + 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); +#endif +#ifdef POWELLORIGINAL + if (t < 0.0) { /* Then we use it for new direction */ +#else + if (directest*t < 0.0) { /* Contradiction between both tests */ + printf("directest= %.12lf (if <0 we include P0 Pn as new direction), t= %.12lf, f1= %.12lf,f2= %.12lf,f3= %.12lf, del= %.12lf\n",directest, t, fp,(*fret),fptt,del); + printf("f1-2f2+f3= %.12lf, f1-f2-del= %.12lf, f1-f3= %.12lf\n",fp-2.0*(*fret)+fptt, fp -(*fret) -del, fp-fptt); + fprintf(ficlog,"directest= %.12lf (if directest<0 or t<0 we include P0 Pn as new direction), t= %.12lf, f1= %.12lf,f2= %.12lf,f3= %.12lf, del= %.12lf\n",directest, t, fp,(*fret),fptt, del); + fprintf(ficlog,"f1-2f2+f3= %.12lf, f1-f2-del= %.12lf, f1-f3= %.12lf\n",fp-2.0*(*fret)+fptt, fp -(*fret) -del, fp-fptt); + } + if (directest < 0.0) { /* Then we use it for new direction */ +#endif +#ifdef DEBUGLINMIN + printf("Before linmin in direction P%d-P0\n",n); + for (j=1;j<=n;j++) { + printf(" Before xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]); + fprintf(ficlog," Before xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]); + if(j % ncovmodel == 0){ + printf("\n"); + fprintf(ficlog,"\n"); + } + } +#endif +#ifdef LINMINORIGINAL + linmin(p,xit,n,fret,func); /* computes minimum on the extrapolated direction: changes p and rescales xit.*/ +#else + linmin(p,xit,n,fret,func,&flat); /* computes minimum on the extrapolated direction: changes p and rescales xit.*/ + flatdir[i]=flat; /* Function is vanishing in that direction i */ +#endif + +#ifdef DEBUGLINMIN for (j=1;j<=n;j++) { - xi[j][ibig]=xi[j][n]; - xi[j][n]=xit[j]; + printf("After xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]); + fprintf(ficlog,"After xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]); + if(j % ncovmodel == 0){ + printf("\n"); + fprintf(ficlog,"\n"); + } + } +#endif + for (j=1;j<=n;j++) { + xi[j][ibig]=xi[j][n]; /* Replace direction with biggest decrease by last direction n */ + xi[j][n]=xit[j]; /* and this nth direction by the by the average p_0 p_n */ + } +#ifdef LINMINORIGINAL +#else + for (j=1, flatd=0;j<=n;j++) { + if(flatdir[j]>0) + flatd++; + } + if(flatd >0){ + printf("%d flat directions: ",flatd); + fprintf(ficlog,"%d flat directions :",flatd); + for (j=1;j<=n;j++) { + if(flatdir[j]>0){ + printf("%d ",j); + fprintf(ficlog,"%d ",j); + } + } + printf("\n"); + fprintf(ficlog,"\n"); } +#endif + printf("Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig); + fprintf(ficlog,"Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig); + #ifdef DEBUG printf("Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig); fprintf(ficlog,"Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig); for(j=1;j<=n;j++){ - printf(" %.12e",xit[j]); - fprintf(ficlog," %.12e",xit[j]); + printf(" %lf",xit[j]); + fprintf(ficlog," %lf",xit[j]); } printf("\n"); fprintf(ficlog,"\n"); #endif - } - } - } + } /* end of t or directest negative */ +#ifdef POWELLNOF3INFF1TEST +#else + } /* end if (fptt < fp) */ +#endif +#ifdef NODIRECTIONCHANGEDUNTILNITER /* No change in drections until some iterations are done */ + } /*NODIRECTIONCHANGEDUNTILNITER No change in drections until some iterations are done */ +#else +#endif + } /* loop iteration */ } - + /**** Prevalence limit (stable or period prevalence) ****************/ - -double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij) -{ - /* Computes the prevalence limit in each live state at age x by left multiplying the unit - matrix by transitions matrix until convergence is reached */ - + + double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int *ncvyear, int ij, int nres) + { + /* Computes the prevalence limit in each live state at age x and for covariate combination ij + (and selected quantitative values in nres) + by left multiplying the unit + matrix by transitions matrix until convergence is reached with precision ftolpl */ + /* Wx= Wx-1 Px-1= Wx-2 Px-2 Px-1 = Wx-n Px-n ... Px-2 Px-1 I */ + /* Wx is row vector: population in state 1, population in state 2, population dead */ + /* or prevalence in state 1, prevalence in state 2, 0 */ + /* newm is the matrix after multiplications, its rows are identical at a factor */ + /* Initial matrix pimij */ + /* {0.85204250825084937, 0.13044499163996345, 0.017512500109187184, */ + /* 0.090851990222114765, 0.88271245433047185, 0.026435555447413338, */ + /* 0, 0 , 1} */ + /* + * and after some iteration: */ + /* {0.45504275246439968, 0.42731458730878791, 0.11764266022681241, */ + /* 0.45201005341706885, 0.42865420071559901, 0.11933574586733192, */ + /* 0, 0 , 1} */ + /* And prevalence by suppressing the deaths are close to identical rows in prlim: */ + /* {0.51571254859325999, 0.4842874514067399, */ + /* 0.51326036147820708, 0.48673963852179264} */ + /* If we start from prlim again, prlim tends to a constant matrix */ + int i, ii,j,k; - double min, max, maxmin, maxmax,sumnew=0.; + double *min, *max, *meandiff, maxmax,sumnew=0.; /* double **matprod2(); */ /* test */ - double **out, cov[NCOVMAX+1], **pmij(); + double **out, cov[NCOVMAX+1], **pmij(); /* **pmmij is a global variable feeded with oldms etc */ double **newm; - double agefin, delaymax=50 ; /* Max number of years to converge */ + double agefin, delaymax=200. ; /* 100 Max number of years to converge */ + int ncvloop=0; + + min=vector(1,nlstate); + max=vector(1,nlstate); + meandiff=vector(1,nlstate); + /* Starting with matrix unity */ for (ii=1;ii<=nlstate+ndeath;ii++) for (j=1;j<=nlstate+ndeath;j++){ oldm[ii][j]=(ii==j ? 1.0 : 0.0); } - - cov[1]=1.; - - /* Even if hstepm = 1, at least one multiplication by the unit matrix */ + + cov[1]=1.; + + /* Even if hstepm = 1, at least one multiplication by the unit matrix */ + /* Start at agefin= age, computes the matrix of passage and loops decreasing agefin until convergence is reached */ for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){ + ncvloop++; newm=savm; /* Covariates have to be included here again */ cov[2]=agefin; - - for (k=1; k<=cptcovn;k++) { - cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]]; - /*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]]);*/ + if(nagesqr==1) + cov[3]= agefin*agefin;; + for (k=1; k<=nsd;k++) { /* For single dummy covariates only */ + /* Here comes the value of the covariate 'ij' after renumbering k with single dummy covariates */ + cov[2+nagesqr+TvarsDind[k]]=nbcode[TvarsD[k]][codtabm(ij,k)]; + /* printf("prevalim Dummy combi=%d k=%d TvarsD[%d]=V%d TvarsDind[%d]=%d nbcode=%d cov=%lf codtabm(%d,Tvar[%d])=%d \n",ij,k, k, TvarsD[k],k,TvarsDind[k],nbcode[TvarsD[k]][codtabm(ij,k)],cov[2+nagesqr+TvarsDind[k]], ij, k, codtabm(ij,k)); */ + } + for (k=1; k<=nsq;k++) { /* For single varying covariates only */ + /* Here comes the value of quantitative after renumbering k with single quantitative covariates */ + cov[2+nagesqr+TvarsQind[k]]=Tqresult[nres][k]; + /* printf("prevalim Quantitative k=%d TvarsQind[%d]=%d, TvarsQ[%d]=V%d,Tqresult[%d][%d]=%f\n",k,k,TvarsQind[k],k,TvarsQ[k],nres,k,Tqresult[nres][k]); */ + } + for (k=1; k<=cptcovage;k++){ /* For product with age */ + if(Dummy[Tvar[Tage[k]]]){ + cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2]; + } else{ + cov[2+nagesqr+Tage[k]]=Tqresult[nres][k]; + } + /* printf("prevalim Age combi=%d k=%d Tage[%d]=V%d Tqresult[%d][%d]=%f\n",ij,k,k,Tage[k],nres,k,Tqresult[nres][k]); */ + } + for (k=1; k<=cptcovprod;k++){ /* For product without age */ + /* printf("prevalim Prod ij=%d k=%d Tprod[%d]=%d Tvard[%d][1]=V%d, Tvard[%d][2]=V%d\n",ij,k,k,Tprod[k], k,Tvard[k][1], k,Tvard[k][2]); */ + if(Dummy[Tvard[k][1]==0]){ + if(Dummy[Tvard[k][2]==0]){ + cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)]; + }else{ + cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * Tqresult[nres][k]; + } + }else{ + if(Dummy[Tvard[k][2]==0]){ + cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][2]][codtabm(ij,k)] * Tqinvresult[nres][Tvard[k][1]]; + }else{ + cov[2+nagesqr+Tprod[k]]=Tqinvresult[nres][Tvard[k][1]]* Tqinvresult[nres][Tvard[k][2]]; + } + } } - /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */ - /* for (k=1; k<=cptcovprod;k++) /\* Useless *\/ */ - /* cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]] * nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]]; */ - /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/ /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/ /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/ /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */ /* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind *\/ */ + /* age and covariate values of ij are in 'cov' */ out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /* Bug Valgrind */ savm=oldm; oldm=newm; - maxmax=0.; - for(j=1;j<=nlstate;j++){ - min=1.; - max=0.; - for(i=1; i<=nlstate; i++) { - sumnew=0; - for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k]; + + for(j=1; j<=nlstate; j++){ + max[j]=0.; + min[j]=1.; + } + for(i=1;i<=nlstate;i++){ + sumnew=0; + for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k]; + for(j=1; j<=nlstate; j++){ prlim[i][j]= newm[i][j]/(1-sumnew); - /*printf(" prevalim i=%d, j=%d, prmlim[%d][%d]=%f, agefin=%d \n", i, j, i, j, prlim[i][j],(int)agefin);*/ - max=FMAX(max,prlim[i][j]); - min=FMIN(min,prlim[i][j]); + max[j]=FMAX(max[j],prlim[i][j]); + min[j]=FMIN(min[j],prlim[i][j]); } - maxmin=max-min; - maxmax=FMAX(maxmax,maxmin); } + + maxmax=0.; + for(j=1; j<=nlstate; j++){ + meandiff[j]=(max[j]-min[j])/(max[j]+min[j])*2.; /* mean difference for each column */ + maxmax=FMAX(maxmax,meandiff[j]); + /* printf(" age= %d meandiff[%d]=%f, agefin=%d max[%d]=%f min[%d]=%f maxmax=%f\n", (int)age, j, meandiff[j],(int)agefin, j, max[j], j, min[j],maxmax); */ + } /* j loop */ + *ncvyear= (int)age- (int)agefin; + /* printf("maxmax=%lf maxmin=%lf ncvloop=%d, age=%d, agefin=%d ncvyear=%d \n", maxmax, maxmin, ncvloop, (int)age, (int)agefin, *ncvyear); */ if(maxmax < ftolpl){ + /* printf("maxmax=%lf ncvloop=%ld, age=%d, agefin=%d ncvyear=%d \n", maxmax, ncvloop, (int)age, (int)agefin, *ncvyear); */ + free_vector(min,1,nlstate); + free_vector(max,1,nlstate); + free_vector(meandiff,1,nlstate); return prlim; } - } + } /* age loop */ + /* After some age loop it doesn't converge */ + printf("Warning: the stable prevalence at age %d did not converge with the required precision (%g > ftolpl=%g) within %.0f years. Try to lower 'ftolpl'. \n\ +Earliest age to start was %d-%d=%d, ncvloop=%d, ncvyear=%d\n", (int)age, maxmax, ftolpl, delaymax, (int)age, (int)delaymax, (int)agefin, ncvloop, *ncvyear); + /* Try to lower 'ftol', for example from 1.e-8 to 6.e-9.\n", ftolpl, (int)age, (int)delaymax, (int)agefin, ncvloop, (int)age-(int)agefin); */ + free_vector(min,1,nlstate); + free_vector(max,1,nlstate); + free_vector(meandiff,1,nlstate); + + return prlim; /* should not reach here */ } -/*************** transition probabilities ***************/ -double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate ) -{ - /* According to parameters values stored in x and the covariate's values stored in cov, - computes the probability to be observed in state j being in state i by appying the - model to the ncovmodel covariates (including constant and age). - lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc] - and, according on how parameters are entered, the position of the coefficient xij(nc) of the - ncth covariate in the global vector x is given by the formula: - j=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel - Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation, - sums on j different of i to get 1-pii/pii, deduces pii, and then all pij. - Outputs ps[i][j] the probability to be observed in j being in j according to - the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij] - */ - double s1, lnpijopii; - /*double t34;*/ - int i,j,j1, nc, ii, jj; + /**** Back Prevalence limit (stable or period prevalence) ****************/ + + /* double **bprevalim(double **bprlim, double ***prevacurrent, int nlstate, double x[], double age, double ageminpar, double agemaxpar, double **oldm, double **savm, double **dnewm, double **doldm, double **dsavm, double ftolpl, int *ncvyear, int ij) */ + /* double **bprevalim(double **bprlim, double ***prevacurrent, int nlstate, double x[], double age, double **oldm, double **savm, double **dnewm, double **doldm, double **dsavm, double ftolpl, int *ncvyear, int ij) */ + double **bprevalim(double **bprlim, double ***prevacurrent, int nlstate, double x[], double age, double ftolpl, int *ncvyear, int ij, int nres) +{ + /* Computes the prevalence limit in each live state at age x and for covariate combination ij (<=2**cptcoveff) by left multiplying the unit + matrix by transitions matrix until convergence is reached with precision ftolpl */ + /* Wx= Wx-1 Px-1= Wx-2 Px-2 Px-1 = Wx-n Px-n ... Px-2 Px-1 I */ + /* Wx is row vector: population in state 1, population in state 2, population dead */ + /* or prevalence in state 1, prevalence in state 2, 0 */ + /* newm is the matrix after multiplications, its rows are identical at a factor */ + /* Initial matrix pimij */ + /* {0.85204250825084937, 0.13044499163996345, 0.017512500109187184, */ + /* 0.090851990222114765, 0.88271245433047185, 0.026435555447413338, */ + /* 0, 0 , 1} */ + /* + * and after some iteration: */ + /* {0.45504275246439968, 0.42731458730878791, 0.11764266022681241, */ + /* 0.45201005341706885, 0.42865420071559901, 0.11933574586733192, */ + /* 0, 0 , 1} */ + /* And prevalence by suppressing the deaths are close to identical rows in prlim: */ + /* {0.51571254859325999, 0.4842874514067399, */ + /* 0.51326036147820708, 0.48673963852179264} */ + /* If we start from prlim again, prlim tends to a constant matrix */ - for(i=1; i<= nlstate; i++){ - for(j=1; ji s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */ - } - ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */ - } - } - - for(i=1; i<= nlstate; i++){ - s1=0; - for(j=1; ji} pij/pii=(1-pii)/pii and thus pii is known from s1 */ - ps[i][i]=1./(s1+1.); - /* Computing other pijs */ - for(j=1; j ftolpl=%g) within %.0f years. Try to lower 'ftolpl'. Others in log file only...\n\ +Oldest age to start was %d-%d=%d, ncvloop=%d, ncvyear=%d\n", (int)age, maxmax, ftolpl, delaymax, (int)age, (int)delaymax, (int)agefin, ncvloop, *ncvyear); + } + fprintf(ficlog,"Warning: the back stable prevalence at age %d did not converge with the required precision (%g > ftolpl=%g) within %.0f years. Try to lower 'ftolpl'. \n\ +Oldest age to start was %d-%d=%d, ncvloop=%d, ncvyear=%d\n", (int)age, maxmax, ftolpl, delaymax, (int)age, (int)delaymax, (int)agefin, ncvloop, *ncvyear); + /* Try to lower 'ftol', for example from 1.e-8 to 6.e-9.\n", ftolpl, (int)age, (int)delaymax, (int)agefin, ncvloop, (int)age-(int)agefin); */ + free_vector(min,1,nlstate); + free_vector(max,1,nlstate); + free_vector(meandiff,1,nlstate); + + return bprlim; /* should not reach here */ +} + +/*************** transition probabilities ***************/ + +double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate ) +{ + /* According to parameters values stored in x and the covariate's values stored in cov, + computes the probability to be observed in state j being in state i by appying the + model to the ncovmodel covariates (including constant and age). + lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc] + and, according on how parameters are entered, the position of the coefficient xij(nc) of the + ncth covariate in the global vector x is given by the formula: + j=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel + Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation, + sums on j different of i to get 1-pii/pii, deduces pii, and then all pij. + Outputs ps[i][j] the probability to be observed in j being in j according to + the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij] + */ + double s1, lnpijopii; + /*double t34;*/ + int i,j, nc, ii, jj; + + for(i=1; i<= nlstate; i++){ + for(j=1; ji s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */ + } + ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */ + } + } + + for(i=1; i<= nlstate; i++){ + s1=0; + for(j=1; ji} pij/pii=(1-pii)/pii and thus pii is known from s1 */ + ps[i][i]=1./(s1+1.); + /* Computing other pijs */ + for(j=1; j= 1.e-10){ + /* if(agefin >= agemaxpar && agefin <= agemaxpar+stepm/YEARM){ */ + /* doldm[ii][j]=(ii==j ? 1./sumnew : 0.0); */ + /* }else if(agefin >= agemaxpar+stepm/YEARM){ */ + /* doldm[ii][j]=(ii==j ? 1./sumnew : 0.0); */ + /* }else */ + doldm[ii][j]=(ii==j ? 1./sumnew : 0.0); + }else{ + ; + /* printf("ii=%d, i=%d, doldm=%lf dsavm=%lf, probs=%lf, sumnew=%lf,agefin=%d\n",ii,j,doldm[ii][j],dsavm[ii][j],prevacurrent[(int)agefin][ii][ij],sumnew, (int)agefin); */ + } + } /*End ii */ + } /* End j, At the end doldm is diag[1/(w_1p1i+w_2 p2i)] */ + /* left Product of this diag matrix by dsavm=Px (newm=dsavm*doldm) */ + bbmij=matprod2(dnewm, dsavm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, doldm); /* Bug Valgrind */ + /* dsavm=doldm; /\* dsavm is now diag [1/(w_1p1i+w_2 p2i)] but can be overwritten*\/ */ + /* doldm=dnewm; /\* doldm is now Px * diag [1/(w_1p1i+w_2 p2i)] *\/ */ + /* dnewm=dsavm; /\* doldm is now Px * diag [1/(w_1p1i+w_2 p2i)] *\/ */ + /* left Product of this matrix by diag matrix of prevalences (savm) */ + for (j=1;j<=nlstate+ndeath;j++){ + for (ii=1;ii<=nlstate+ndeath;ii++){ + dsavm[ii][j]=(ii==j ? prevacurrent[(int)agefin][ii][ij] : 0.0); + } + } /* End j, At the end oldm is diag[1/(w_1p1i+w_2 p2i)] */ + ps=matprod2(doldm, dsavm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, dnewm); /* Bug Valgrind */ + /* newm or out is now diag[w_i] * Px * diag [1/(w_1p1i+w_2 p2i)] */ + /* end bmij */ + return ps; +} +/*************** transition probabilities ***************/ + +double **bpmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate ) +{ + /* According to parameters values stored in x and the covariate's values stored in cov, + computes the probability to be observed in state j being in state i by appying the + model to the ncovmodel covariates (including constant and age). + lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc] + and, according on how parameters are entered, the position of the coefficient xij(nc) of the + ncth covariate in the global vector x is given by the formula: + j=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel + Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation, + sums on j different of i to get 1-pii/pii, deduces pii, and then all pij. + Outputs ps[i][j] the probability to be observed in j being in j according to + the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij] + */ + double s1, lnpijopii; + /*double t34;*/ + int i,j, nc, ii, jj; + + for(i=1; i<= nlstate; i++){ + for(j=1; ji s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */ + } + ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */ + } + } + + for(i=1; i<= nlstate; i++){ + s1=0; + for(j=1; ji} pij/pii=(1-pii)/pii and thus pii is known from s1 */ + ps[i][i]=1./(s1+1.); + /* Computing other pijs */ + for(j=1; jfunction)(xt); /* p xt[1]@8 is fine */ + /* fret=(*func)(xt); /\* p xt[1]@8 is fine *\/ */ + printf("Function = %.12lf ",fret); + for (j=1;j<=n;j++) printf(" %d %.8lf", j, xt[j]); + printf("\n"); + free_vector(xt,1,n); + return fret; +} +#endif + /*************** log-likelihood *************/ double func( double *x) { int i, ii, j, k, mi, d, kk; + int ioffset=0; double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1]; double **out; - double sw; /* Sum of weights */ double lli; /* Individual log likelihood */ int s1, s2; + int iv=0, iqv=0, itv=0, iqtv=0 ; /* Index of varying covariate, fixed quantitative cov, time varying covariate, quantitative time varying covariate */ double bbh, survp; long ipmx; + double agexact; /*extern weight */ /* We are differentiating ll according to initial status */ /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/ /*for(i=1;i 1 the results are less biased than in previous versions. - */ + * from savm to out if bh is negative or even beyond if bh is positive. bh varies + * -stepm/2 to stepm/2 . + * For stepm=1 the results are the same as for previous versions of Imach. + * For stepm > 1 the results are less biased than in previous versions. + */ s1=s[mw[mi][i]][i]; s2=s[mw[mi+1][i]][i]; bbh=(double)bh[mi][i]/(double)stepm; @@ -1639,45 +3362,61 @@ double func( double *x) which is also equal to probability to die before dh minus probability to die before dh-stepm . In version up to 0.92 likelihood was computed - as if date of death was unknown. Death was treated as any other - health state: the date of the interview describes the actual state - and not the date of a change in health state. The former idea was - to consider that at each interview the state was recorded - (healthy, disable or death) and IMaCh was corrected; but when we - introduced the exact date of death then we should have modified - the contribution of an exact death to the likelihood. This new - contribution is smaller and very dependent of the step unit - stepm. It is no more the probability to die between last interview - and month of death but the probability to survive from last - interview up to one month before death multiplied by the - probability to die within a month. Thanks to Chris - Jackson for correcting this bug. Former versions increased - mortality artificially. The bad side is that we add another loop - which slows down the processing. The difference can be up to 10% - lower mortality. + as if date of death was unknown. Death was treated as any other + health state: the date of the interview describes the actual state + and not the date of a change in health state. The former idea was + to consider that at each interview the state was recorded + (healthy, disable or death) and IMaCh was corrected; but when we + introduced the exact date of death then we should have modified + the contribution of an exact death to the likelihood. This new + contribution is smaller and very dependent of the step unit + stepm. It is no more the probability to die between last interview + and month of death but the probability to survive from last + interview up to one month before death multiplied by the + probability to die within a month. Thanks to Chris + Jackson for correcting this bug. Former versions increased + mortality artificially. The bad side is that we add another loop + which slows down the processing. The difference can be up to 10% + lower mortality. */ + /* If, at the beginning of the maximization mostly, the + cumulative probability or probability to be dead is + constant (ie = 1) over time d, the difference is equal to + 0. out[s1][3] = savm[s1][3]: probability, being at state + s1 at precedent wave, to be dead a month before current + wave is equal to probability, being at state s1 at + precedent wave, to be dead at mont of the current + wave. Then the observed probability (that this person died) + is null according to current estimated parameter. In fact, + it should be very low but not zero otherwise the log go to + infinity. + */ +/* #ifdef INFINITYORIGINAL */ +/* lli=log(out[s1][s2] - savm[s1][s2]); */ +/* #else */ +/* if ((out[s1][s2] - savm[s1][s2]) < mytinydouble) */ +/* lli=log(mytinydouble); */ +/* else */ +/* lli=log(out[s1][s2] - savm[s1][s2]); */ +/* #endif */ lli=log(out[s1][s2] - savm[s1][s2]); - - - } else if (s2==-2) { + + } else if ( s2==-1 ) { /* alive */ for (j=1,survp=0. ; j<=nlstate; j++) survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j]; /*survp += out[s1][j]; */ lli= log(survp); } - - else if (s2==-4) { + else if (s2==-4) { for (j=3,survp=0. ; j<=nlstate; j++) survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j]; - lli= log(survp); - } - - else if (s2==-5) { - for (j=1,survp=0. ; j<=2; j++) + lli= log(survp); + } + else if (s2==-5) { + for (j=1,survp=0. ; j<=2; j++) survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j]; - lli= log(survp); - } - + lli= log(survp); + } else{ lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */ /* 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 */ @@ -1685,14 +3424,18 @@ double func( double *x) /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/ /*if(lli ==000.0)*/ /*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); */ - ipmx +=1; + ipmx +=1; sw += weight[i]; ll[s[mw[mi][i]][i]] += 2*weight[i]*lli; + /* if (lli < log(mytinydouble)){ */ + /* 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); */ + /* 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]); */ + /* } */ } /* end of wave */ } /* end of individual */ } else if(mle==2){ for (i=1,ipmx=0, sw=0.; i<=imx; i++){ - for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i]; + for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i]; for(mi=1; mi<= wav[i]-1; mi++){ for (ii=1;ii<=nlstate+ndeath;ii++) for (j=1;j<=nlstate+ndeath;j++){ @@ -1701,9 +3444,12 @@ double func( double *x) } for(d=0; d<=dh[mi][i]; d++){ newm=savm; - cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM; + agexact=agev[mw[mi][i]][i]+d*stepm/YEARM; + cov[2]=agexact; + if(nagesqr==1) + cov[3]= agexact*agexact; for (kk=1; kk<=cptcovage;kk++) { - cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; + cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact; } out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); @@ -1722,7 +3468,7 @@ double func( double *x) } /* end of individual */ } else if(mle==3){ /* exponential inter-extrapolation */ for (i=1,ipmx=0, sw=0.; i<=imx; i++){ - for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i]; + for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i]; for(mi=1; mi<= wav[i]-1; mi++){ for (ii=1;ii<=nlstate+ndeath;ii++) for (j=1;j<=nlstate+ndeath;j++){ @@ -1731,9 +3477,12 @@ double func( double *x) } for(d=0; d nlstate){ lli=log(out[s1][s2] - savm[s1][s2]); + } else if ( s2==-1 ) { /* alive */ + for (j=1,survp=0. ; j<=nlstate; j++) + survp += out[s1][j]; + lli= log(survp); }else{ lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */ } @@ -1787,7 +3543,7 @@ double func( double *x) } /* end of individual */ }else{ /* ml=5 no inter-extrapolation no jackson =0.8a */ for (i=1,ipmx=0, sw=0.; i<=imx; i++){ - for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i]; + for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i]; for(mi=1; mi<= wav[i]-1; mi++){ for (ii=1;ii<=nlstate+ndeath;ii++) for (j=1;j<=nlstate+ndeath;j++){ @@ -1796,9 +3552,12 @@ double func( double *x) } for(d=0; d nlstate && (mle <5) ){ /* Jackson */ lli=log(out[s1][s2] - savm[s1][s2]); - } else if (s2==-2) { + } else if ( s2==-1 ) { /* alive */ for (j=1,survp=0. ; j<=nlstate; j++) survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j]; lli= log(survp); @@ -1896,9 +3717,9 @@ double funcone( double *x) ll[s[mw[mi][i]][i]] += 2*weight[i]*lli; /*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]); */ if(globpr){ - fprintf(ficresilk,"%9ld %6d %2d %2d %1d %1d %3d %11.6f %8.4f\ + fprintf(ficresilk,"%09ld %6.1f %6.1f %6d %2d %2d %2d %2d %3d %15.6f %8.4f %8.3f\ %11.6f %11.6f %11.6f ", \ - num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i], + num[i], agebegin, ageend, i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],weight[i]*gipmx/gsw, 2*weight[i]*lli,out[s1][s2],savm[s1][s2]); for(k=1,llt=0.,l=0.; k<=nlstate; k++){ llt +=ll[k]*gipmx/gsw; @@ -1906,16 +3727,16 @@ double funcone( double *x) } fprintf(ficresilk," %10.6f\n", -llt); } - } /* end of wave */ - } /* end of individual */ - for(k=1,l=0.; k<=nlstate; k++) l += ll[k]; - /* printf("l1=%f l2=%f ",ll[1],ll[2]); */ - l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */ - if(globpr==0){ /* First time we count the contributions and weights */ - gipmx=ipmx; - gsw=sw; - } - return -l; + } /* end of wave */ +} /* end of individual */ +for(k=1,l=0.; k<=nlstate; k++) l += ll[k]; +/* printf("l1=%f l2=%f ",ll[1],ll[2]); */ +l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */ +if(globpr==0){ /* First time we count the contributions and weights */ + gipmx=ipmx; + gsw=sw; +} +return -l; } @@ -1930,14 +3751,14 @@ void likelione(FILE *ficres,double p[], int k; if(*globpri !=0){ /* Just counts and sums, no printings */ - strcpy(fileresilk,"ilk"); - strcat(fileresilk,fileres); + strcpy(fileresilk,"ILK_"); + strcat(fileresilk,fileresu); if((ficresilk=fopen(fileresilk,"w"))==NULL) { printf("Problem with resultfile: %s\n", fileresilk); fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk); } - 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"); - fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav "); + fprintf(ficresilk, "#individual(line's_record) count ageb ageend s1 s2 wave# effective_wave# number_of_matrices_product pij weight weight/gpw -2ln(pij)*weight 0pij_x 0pij_(x-stepm) cumulating_loglikeli_by_health_state(reweighted=-2ll*weightXnumber_of_contribs/sum_of_weights) and_total\n"); + fprintf(ficresilk, "#num_i ageb agend i s1 s2 mi mw dh likeli weight %%weight 2wlli out sav "); /* i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */ for(k=1; k<=nlstate; k++) fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k); @@ -1947,9 +3768,23 @@ void likelione(FILE *ficres,double p[], *fretone=(*funcone)(p); if(*globpri !=0){ fclose(ficresilk); - fprintf(fichtm,"\n
File of contributions to the likelihood: %s
\n",subdirf(fileresilk),subdirf(fileresilk)); - fflush(fichtm); - } + if (mle ==0) + fprintf(fichtm,"\n
File of contributions to the likelihood computed with initial parameters and mle = %d.",mle); + else if(mle >=1) + fprintf(fichtm,"\n
File of contributions to the likelihood computed with optimized parameters mle = %d.",mle); + fprintf(fichtm," You should at least run with mle >= 1 to get starting values corresponding to the optimized parameters in order to visualize the real contribution of each individual/wave: %s
\n",subdirf(fileresilk),subdirf(fileresilk)); + + + for (k=1; k<= nlstate ; k++) { + fprintf(fichtm,"
- Probability p%dj by origin %d and destination j. Dot's sizes are related to corresponding weight: %s-p%dj.png
\ +",k,k,subdirf2(optionfilefiname,"ILK_"),k,subdirf2(optionfilefiname,"ILK_"),k,subdirf2(optionfilefiname,"ILK_"),k); + } + fprintf(fichtm,"
- The function drawn is -2Log(L) in Log scale: by state of origin %s-ori.png
\ +",subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_")); + fprintf(fichtm,"
- and by state of destination %s-dest.png
\ +",subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_")); + fflush(fichtm); + } return; } @@ -1958,17 +3793,29 @@ void likelione(FILE *ficres,double p[], void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double [])) { - int i,j, iter; + int i,j, iter=0; double **xi; double fret; double fretone; /* Only one call to likelihood */ /* char filerespow[FILENAMELENGTH];*/ + +#ifdef NLOPT + int creturn; + nlopt_opt opt; + /* double lb[9] = { -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL }; /\* lower bounds *\/ */ + double *lb; + double minf; /* the minimum objective value, upon return */ + double * p1; /* Shifted parameters from 0 instead of 1 */ + myfunc_data dinst, *d = &dinst; +#endif + + xi=matrix(1,npar,1,npar); for (i=1;i<=npar;i++) for (j=1;j<=npar;j++) xi[i][j]=(i==j ? 1.0 : 0.0); printf("Powell\n"); fprintf(ficlog,"Powell\n"); - strcpy(filerespow,"pow"); + strcpy(filerespow,"POW_"); strcat(filerespow,fileres); if((ficrespow=fopen(filerespow,"w"))==NULL) { printf("Problem with resultfile: %s\n", filerespow); @@ -1979,37 +3826,64 @@ void mlikeli(FILE *ficres,double p[], in for(j=1;j<=nlstate+ndeath;j++) if(j!=i)fprintf(ficrespow," p%1d%1d",i,j); fprintf(ficrespow,"\n"); - +#ifdef POWELL powell(p,xi,npar,ftol,&iter,&fret,func); +#endif +#ifdef NLOPT +#ifdef NEWUOA + opt = nlopt_create(NLOPT_LN_NEWUOA,npar); +#else + opt = nlopt_create(NLOPT_LN_BOBYQA,npar); +#endif + lb=vector(0,npar-1); + for (i=0;ifunction = func; + printf(" Func %.12lf \n",myfunc(npar,p1,NULL,d)); + nlopt_set_min_objective(opt, myfunc, d); + nlopt_set_xtol_rel(opt, ftol); + if ((creturn=nlopt_optimize(opt, p1, &minf)) < 0) { + printf("nlopt failed! %d\n",creturn); + } + else { + printf("found minimum after %d evaluations (NLOPT=%d)\n", countcallfunc ,NLOPT); + printf("found minimum at f(%g,%g) = %0.10g\n", p[0], p[1], minf); + iter=1; /* not equal */ + } + nlopt_destroy(opt); +#endif free_matrix(xi,1,npar,1,npar); fclose(ficrespow); - printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p)); - fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p)); - fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p)); + printf("\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p)); + fprintf(ficlog,"\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p)); + fprintf(ficres,"#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p)); } /**** Computes Hessian and covariance matrix ***/ -void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double [])) +void hesscov(double **matcov, double **hess, double p[], int npar, double delti[], double ftolhess, double (*func)(double [])) { double **a,**y,*x,pd; - double **hess; - int i, j,jk; + /* double **hess; */ + int i, j; int *indx; double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar); - double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar); + double hessij(double p[], double **hess, double delti[], int i, int j,double (*func)(double []),int npar); void lubksb(double **a, int npar, int *indx, double b[]) ; void ludcmp(double **a, int npar, int *indx, double *d) ; double gompertz(double p[]); - hess=matrix(1,npar,1,npar); + /* hess=matrix(1,npar,1,npar); */ printf("\nCalculation of the hessian matrix. Wait...\n"); fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n"); for (i=1;i<=npar;i++){ - printf("%d",i);fflush(stdout); - fprintf(ficlog,"%d",i);fflush(ficlog); + printf("%d-",i);fflush(stdout); + fprintf(ficlog,"%d-",i);fflush(ficlog); hess[i][i]=hessii(p,ftolhess,i,delti,func,npar); @@ -2020,9 +3894,9 @@ void hesscov(double **matcov, double p[] for (i=1;i<=npar;i++) { for (j=1;j<=npar;j++) { if (j>i) { - printf(".%d%d",i,j);fflush(stdout); - fprintf(ficlog,".%d%d",i,j);fflush(ficlog); - hess[i][j]=hessij(p,delti,i,j,func,npar); + printf(".%d-%d",i,j);fflush(stdout); + fprintf(ficlog,".%d-%d",i,j);fflush(ficlog); + hess[i][j]=hessij(p,hess, delti,i,j,func,npar); hess[j][i]=hess[i][j]; /*printf(" %lf ",hess[i][j]);*/ @@ -2056,53 +3930,78 @@ void hesscov(double **matcov, double p[] fprintf(ficlog,"\n#Hessian matrix#\n"); for (i=1;i<=npar;i++) { for (j=1;j<=npar;j++) { - printf("%.3e ",hess[i][j]); - fprintf(ficlog,"%.3e ",hess[i][j]); + printf("%.6e ",hess[i][j]); + fprintf(ficlog,"%.6e ",hess[i][j]); } printf("\n"); fprintf(ficlog,"\n"); } + /* printf("\n#Covariance matrix#\n"); */ + /* fprintf(ficlog,"\n#Covariance matrix#\n"); */ + /* for (i=1;i<=npar;i++) { */ + /* for (j=1;j<=npar;j++) { */ + /* printf("%.6e ",matcov[i][j]); */ + /* fprintf(ficlog,"%.6e ",matcov[i][j]); */ + /* } */ + /* printf("\n"); */ + /* fprintf(ficlog,"\n"); */ + /* } */ + /* Recompute Inverse */ - for (i=1;i<=npar;i++) - for (j=1;j<=npar;j++) a[i][j]=matcov[i][j]; - ludcmp(a,npar,indx,&pd); + /* for (i=1;i<=npar;i++) */ + /* for (j=1;j<=npar;j++) a[i][j]=matcov[i][j]; */ + /* ludcmp(a,npar,indx,&pd); */ + + /* printf("\n#Hessian matrix recomputed#\n"); */ + + /* for (j=1;j<=npar;j++) { */ + /* for (i=1;i<=npar;i++) x[i]=0; */ + /* x[j]=1; */ + /* lubksb(a,npar,indx,x); */ + /* for (i=1;i<=npar;i++){ */ + /* y[i][j]=x[i]; */ + /* printf("%.3e ",y[i][j]); */ + /* fprintf(ficlog,"%.3e ",y[i][j]); */ + /* } */ + /* printf("\n"); */ + /* fprintf(ficlog,"\n"); */ + /* } */ + + /* Verifying the inverse matrix */ +#ifdef DEBUGHESS + y=matprod2(y,hess,1,npar,1,npar,1,npar,matcov); - /* printf("\n#Hessian matrix recomputed#\n"); + printf("\n#Verification: multiplying the matrix of covariance by the Hessian matrix, should be unity:#\n"); + fprintf(ficlog,"\n#Verification: multiplying the matrix of covariance by the Hessian matrix. Should be unity:#\n"); for (j=1;j<=npar;j++) { - for (i=1;i<=npar;i++) x[i]=0; - x[j]=1; - lubksb(a,npar,indx,x); for (i=1;i<=npar;i++){ - y[i][j]=x[i]; - printf("%.3e ",y[i][j]); - fprintf(ficlog,"%.3e ",y[i][j]); + printf("%.2f ",y[i][j]); + fprintf(ficlog,"%.2f ",y[i][j]); } printf("\n"); fprintf(ficlog,"\n"); } - */ +#endif free_matrix(a,1,npar,1,npar); free_matrix(y,1,npar,1,npar); free_vector(x,1,npar); free_ivector(indx,1,npar); - free_matrix(hess,1,npar,1,npar); + /* free_matrix(hess,1,npar,1,npar); */ } /*************** hessian matrix ****************/ double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar) -{ +{ /* Around values of x, computes the function func and returns the scales delti and hessian */ int i; int l=1, lmax=20; - double k1,k2; + double k1,k2, res, fx; double p2[MAXPARM+1]; /* identical to x */ - double res; double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4; - double fx; int k=0,kmax=10; double l1; @@ -2118,9 +4017,9 @@ double hessii(double x[], double delta, p2[theta]=x[theta]-delt; k2=func(p2)-fx; /*res= (k1-2.0*fx+k2)/delt/delt; */ - res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */ + res= (k1+k2)/delt/delt/2.; /* Divided by 2 because L and not 2*L */ -#ifdef DEBUGHESS +#ifdef DEBUGHESSII 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); 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); #endif @@ -2129,53 +4028,130 @@ double hessii(double x[], double delta, k=kmax; } else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */ - k=kmax; l=lmax*10.; + k=kmax; l=lmax*10; } else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ delts=delt; } - } + } /* End loop k */ } delti[theta]=delts; return res; } -double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar) +double hessij( double x[], double **hess, double delti[], int thetai,int thetaj,double (*func)(double []),int npar) { int i; - int l=1, l1, lmax=20; + int l=1, lmax=20; double k1,k2,k3,k4,res,fx; double p2[MAXPARM+1]; - int k; + int k, kmax=1; + double v1, v2, cv12, lc1, lc2; + int firstime=0; + fx=func(x); - for (k=1; k<=2; k++) { + for (k=1; k<=kmax; k=k+10) { for (i=1;i<=npar;i++) p2[i]=x[i]; - p2[thetai]=x[thetai]+delti[thetai]/k; - p2[thetaj]=x[thetaj]+delti[thetaj]/k; + p2[thetai]=x[thetai]+delti[thetai]*k; + p2[thetaj]=x[thetaj]+delti[thetaj]*k; k1=func(p2)-fx; - p2[thetai]=x[thetai]+delti[thetai]/k; - p2[thetaj]=x[thetaj]-delti[thetaj]/k; + p2[thetai]=x[thetai]+delti[thetai]*k; + p2[thetaj]=x[thetaj]-delti[thetaj]*k; k2=func(p2)-fx; - p2[thetai]=x[thetai]-delti[thetai]/k; - p2[thetaj]=x[thetaj]+delti[thetaj]/k; + p2[thetai]=x[thetai]-delti[thetai]*k; + p2[thetaj]=x[thetaj]+delti[thetaj]*k; k3=func(p2)-fx; - p2[thetai]=x[thetai]-delti[thetai]/k; - p2[thetaj]=x[thetaj]-delti[thetaj]/k; + p2[thetai]=x[thetai]-delti[thetai]*k; + p2[thetaj]=x[thetaj]-delti[thetaj]*k; k4=func(p2)-fx; - res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */ -#ifdef DEBUG - 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); - 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); + res=(k1-k2-k3+k4)/4.0/delti[thetai]/k/delti[thetaj]/k/2.; /* Because of L not 2*L */ + if(k1*k2*k3*k4 <0.){ + firstime=1; + kmax=kmax+10; + } + if(kmax >=10 || firstime ==1){ + printf("Warning: directions %d-%d, you are not estimating the Hessian at the exact maximum likelihood; you could increase ftol=%.2e\n",thetai,thetaj, ftol); + fprintf(ficlog,"Warning: directions %d-%d, you are not estimating the Hessian at the exact maximum likelihood; you could increase ftol=%.2e\n",thetai,thetaj, ftol); + 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); + 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); + } +#ifdef DEBUGHESSIJ + v1=hess[thetai][thetai]; + v2=hess[thetaj][thetaj]; + cv12=res; + /* Computing eigen value of Hessian matrix */ + lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.; + lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.; + if ((lc2 <0) || (lc1 <0) ){ + printf("Warning: sub Hessian matrix '%d%d' does not have positive eigen values \n",thetai,thetaj); + fprintf(ficlog, "Warning: sub Hessian matrix '%d%d' does not have positive eigen values \n",thetai,thetaj); + 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); + 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); + } #endif } return res; } + /* Not done yet: Was supposed to fix if not exactly at the maximum */ +/* double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar) */ +/* { */ +/* int i; */ +/* int l=1, lmax=20; */ +/* double k1,k2,k3,k4,res,fx; */ +/* double p2[MAXPARM+1]; */ +/* double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4; */ +/* int k=0,kmax=10; */ +/* double l1; */ + +/* fx=func(x); */ +/* for(l=0 ; l <=lmax; l++){ /\* Enlarging the zone around the Maximum *\/ */ +/* l1=pow(10,l); */ +/* delts=delt; */ +/* for(k=1 ; k khi/nkhif) || (k2 >khi/nkhif) || (k4 >khi/nkhif) || (k4 >khi/nkhif)){ /\* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. *\/ */ +/* k=kmax; l=lmax*10; */ +/* } */ +/* else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ */ +/* delts=delt; */ +/* } */ +/* } /\* End loop k *\/ */ +/* } */ +/* delti[theta]=delts; */ +/* return res; */ +/* } */ + + /************** Inverse of matrix **************/ void ludcmp(double **a, int n, int *indx, double *d) { @@ -2189,7 +4165,16 @@ void ludcmp(double **a, int n, int *indx big=0.0; for (j=1;j<=n;j++) if ((temp=fabs(a[i][j])) > big) big=temp; - if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); + if (big == 0.0){ + printf(" Singular Hessian matrix at row %d:\n",i); + for (j=1;j<=n;j++) { + printf(" a[%d][%d]=%f,",i,j,a[i][j]); + fprintf(ficlog," a[%d][%d]=%f,",i,j,a[i][j]); + } + fflush(ficlog); + fclose(ficlog); + nrerror("Singular matrix in routine ludcmp"); + } vv[i]=1.0/big; } for (j=1;j<=n;j++) { @@ -2252,184 +4237,625 @@ void lubksb(double **a, int n, int *indx void pstamp(FILE *fichier) { - fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart); + fprintf(fichier,"# %s.%s\n#IMaCh version %s, %s\n#%s\n# %s", optionfilefiname,optionfilext,version,copyright, fullversion, strstart); } -/************ Frequencies ********************/ -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[]) -{ /* Some frequencies */ +int linreg(int ifi, int ila, int *no, const double x[], const double y[], double* a, double* b, double* r, double* sa, double * sb) { + + /* y=a+bx regression */ + double sumx = 0.0; /* sum of x */ + double sumx2 = 0.0; /* sum of x**2 */ + double sumxy = 0.0; /* sum of x * y */ + double sumy = 0.0; /* sum of y */ + double sumy2 = 0.0; /* sum of y**2 */ + double sume2; /* sum of square or residuals */ + double yhat; + + double denom=0; + int i; + int ne=*no; + + for ( i=ifi, ne=0;i<=ila;i++) { + if(!isfinite(x[i]) || !isfinite(y[i])){ + /* printf(" x[%d]=%f, y[%d]=%f\n",i,x[i],i,y[i]); */ + continue; + } + ne=ne+1; + sumx += x[i]; + sumx2 += x[i]*x[i]; + sumxy += x[i] * y[i]; + sumy += y[i]; + sumy2 += y[i]*y[i]; + denom = (ne * sumx2 - sumx*sumx); + /* printf("ne=%d, i=%d,x[%d]=%f, y[%d]=%f sumx=%f, sumx2=%f, sumxy=%f, sumy=%f, sumy2=%f, denom=%f\n",ne,i,i,x[i],i,y[i], sumx, sumx2,sumxy, sumy, sumy2,denom); */ + } + + denom = (ne * sumx2 - sumx*sumx); + if (denom == 0) { + // vertical, slope m is infinity + *b = INFINITY; + *a = 0; + if (r) *r = 0; + return 1; + } + + *b = (ne * sumxy - sumx * sumy) / denom; + *a = (sumy * sumx2 - sumx * sumxy) / denom; + if (r!=NULL) { + *r = (sumxy - sumx * sumy / ne) / /* compute correlation coeff */ + sqrt((sumx2 - sumx*sumx/ne) * + (sumy2 - sumy*sumy/ne)); + } + *no=ne; + for ( i=ifi, ne=0;i<=ila;i++) { + if(!isfinite(x[i]) || !isfinite(y[i])){ + /* printf(" x[%d]=%f, y[%d]=%f\n",i,x[i],i,y[i]); */ + continue; + } + ne=ne+1; + yhat = y[i] - *a -*b* x[i]; + sume2 += yhat * yhat ; + + denom = (ne * sumx2 - sumx*sumx); + /* printf("ne=%d, i=%d,x[%d]=%f, y[%d]=%f sumx=%f, sumx2=%f, sumxy=%f, sumy=%f, sumy2=%f, denom=%f\n",ne,i,i,x[i],i,y[i], sumx, sumx2,sumxy, sumy, sumy2,denom); */ + } + *sb = sqrt(sume2/(ne-2)/(sumx2 - sumx * sumx /ne)); + *sa= *sb * sqrt(sumx2/ne); - int i, m, jk, k1,i1, j1, bool, z1,j; + return 0; +} + +/************ Frequencies ********************/ +void freqsummary(char fileres[], double p[], double pstart[], int iagemin, int iagemax, int **s, double **agev, int nlstate, int imx, \ + int *Tvaraff, int *invalidvarcomb, int **nbcode, int *ncodemax,double **mint,double **anint, char strstart[], \ + int firstpass, int lastpass, int stepm, int weightopt, char model[]) +{ /* Some frequencies as well as proposing some starting values */ + + int i, m, jk, j1, bool, z1,j, nj, nl, k, iv, jj=0, s1=1, s2=1; + int iind=0, iage=0; + int mi; /* Effective wave */ int first; double ***freq; /* Frequencies */ - double *pp, **prop; - double pos,posprop, k2, dateintsum=0,k2cpt=0; - char fileresp[FILENAMELENGTH]; - + double *x, *y, a,b,r, sa, sb; /* for regression, y=b+m*x and r is the correlation coefficient */ + int no; + double *meanq; + double **meanqt; + double *pp, **prop, *posprop, *pospropt; + double pos=0., posproptt=0., pospropta=0., k2, dateintsum=0,k2cpt=0; + char fileresp[FILENAMELENGTH], fileresphtm[FILENAMELENGTH], fileresphtmfr[FILENAMELENGTH]; + double agebegin, ageend; + pp=vector(1,nlstate); - prop=matrix(1,nlstate,iagemin,iagemax+3); - strcpy(fileresp,"p"); - strcat(fileresp,fileres); + prop=matrix(1,nlstate,iagemin-AGEMARGE,iagemax+4+AGEMARGE); + posprop=vector(1,nlstate); /* Counting the number of transition starting from a live state per age */ + pospropt=vector(1,nlstate); /* Counting the number of transition starting from a live state */ + /* prop=matrix(1,nlstate,iagemin,iagemax+3); */ + meanq=vector(1,nqfveff); /* Number of Quantitative Fixed Variables Effective */ + meanqt=matrix(1,lastpass,1,nqtveff); + strcpy(fileresp,"P_"); + strcat(fileresp,fileresu); + /*strcat(fileresphtm,fileresu);*/ if((ficresp=fopen(fileresp,"w"))==NULL) { printf("Problem with prevalence resultfile: %s\n", fileresp); fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp); exit(0); } - freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3); - j1=0; - j=cptcoveff; + strcpy(fileresphtm,subdirfext(optionfilefiname,"PHTM_",".htm")); + if((ficresphtm=fopen(fileresphtm,"w"))==NULL) { + printf("Problem with prevalence HTM resultfile '%s' with errno='%s'\n",fileresphtm,strerror(errno)); + fprintf(ficlog,"Problem with prevalence HTM resultfile '%s' with errno='%s'\n",fileresphtm,strerror(errno)); + fflush(ficlog); + exit(70); + } + else{ + fprintf(ficresphtm,"\nIMaCh PHTM_ %s\n %s
%s \ +
\n \ +Title=%s
Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s
\n",\ + fileresphtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model); + } + fprintf(ficresphtm,"Current page is file %s
\n\n

Frequencies and prevalence by age at begin of transition and dummy covariate value at beginning of transition

\n",fileresphtm, fileresphtm); + + strcpy(fileresphtmfr,subdirfext(optionfilefiname,"PHTMFR_",".htm")); + if((ficresphtmfr=fopen(fileresphtmfr,"w"))==NULL) { + printf("Problem with frequency table HTM resultfile '%s' with errno='%s'\n",fileresphtmfr,strerror(errno)); + fprintf(ficlog,"Problem with frequency table HTM resultfile '%s' with errno='%s'\n",fileresphtmfr,strerror(errno)); + fflush(ficlog); + exit(70); + } else{ + fprintf(ficresphtmfr,"\nIMaCh PHTM_Frequency table %s\n %s
%s \ +
\n \ +Title=%s
Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s
\n",\ + fileresphtmfr,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model); + } + fprintf(ficresphtmfr,"Current page is file %s
\n\n

Frequencies of all effective transitions of the model, by age at begin of transition, and covariate value at the begin of transition (if the covariate is a varying covariate)

Unknown status is -1
\n",fileresphtmfr, fileresphtmfr); + + y= vector(iagemin-AGEMARGE,iagemax+4+AGEMARGE); + x= vector(iagemin-AGEMARGE,iagemax+4+AGEMARGE); + freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin-AGEMARGE,iagemax+4+AGEMARGE); + j1=0; + + /* j=ncoveff; /\* Only fixed dummy covariates *\/ */ + j=cptcoveff; /* Only dummy covariates of the model */ if (cptcovn<1) {j=1;ncodemax[1]=1;} + + + /* Detects if a combination j1 is empty: for a multinomial variable like 3 education levels: + reference=low_education V1=0,V2=0 + med_educ V1=1 V2=0, + high_educ V1=0 V2=1 + Then V1=1 and V2=1 is a noisy combination that we want to exclude for the list 2**cptcoveff + */ + dateintsum=0; + k2cpt=0; - first=1; + if(cptcoveff == 0 ) + nl=1; /* Constant and age model only */ + else + nl=2; - /* for(k1=1; k1<=j ; k1++){ /* Loop on covariates */ - /* for(i1=1; i1<=ncodemax[k1];i1++){ /* Now it is 2 */ - /* j1++; -*/ - for (j1 = 1; j1 <= (int) pow(2,cptcoveff); j1++){ + /* if a constant only model, one pass to compute frequency tables and to write it on ficresp */ + /* Loop on nj=1 or 2 if dummy covariates j!=0 + * Loop on j1(1 to 2**cptcoveff) covariate combination + * freq[s1][s2][iage] =0. + * Loop on iind + * ++freq[s1][s2][iage] weighted + * end iind + * if covariate and j!0 + * headers Variable on one line + * endif cov j!=0 + * header of frequency table by age + * Loop on age + * pp[s1]+=freq[s1][s2][iage] weighted + * pos+=freq[s1][s2][iage] weighted + * Loop on s1 initial state + * fprintf(ficresp + * end s1 + * end age + * if j!=0 computes starting values + * end compute starting values + * end j1 + * end nl + */ + for (nj = 1; nj <= nl; nj++){ /* nj= 1 constant model, nl number of loops. */ + if(nj==1) + j=0; /* First pass for the constant */ + else{ + j=cptcoveff; /* Other passes for the covariate values */ + } + first=1; + for (j1 = 1; j1 <= (int) pow(2,j); j1++){ /* Loop on all covariates combination of the model, excluding quantitatives, V4=0, V3=0 for example, fixed or varying covariates */ + posproptt=0.; /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]); scanf("%d", i);*/ for (i=-5; i<=nlstate+ndeath; i++) - for (jk=-5; jk<=nlstate+ndeath; jk++) + for (s2=-5; s2<=nlstate+ndeath; s2++) for(m=iagemin; m <= iagemax+3; m++) - freq[i][jk][m]=0; + freq[i][s2][m]=0; - for (i=1; i<=nlstate; i++) + for (i=1; i<=nlstate; i++) { for(m=iagemin; m <= iagemax+3; m++) prop[i][m]=0; + posprop[i]=0; + pospropt[i]=0; + } + /* for (z1=1; z1<= nqfveff; z1++) { */ + /* meanq[z1]+=0.; */ + /* for(m=1;m<=lastpass;m++){ */ + /* meanqt[m][z1]=0.; */ + /* } */ + /* } */ + + /* dateintsum=0; */ + /* k2cpt=0; */ - dateintsum=0; - k2cpt=0; - for (i=1; i<=imx; i++) { + /* For that combination of covariates j1 (V4=1 V3=0 for example), we count and print the frequencies in one pass */ + for (iind=1; iind<=imx; iind++) { /* For each individual iind */ bool=1; - if (cptcovn>0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */ - for (z1=1; z1<=cptcoveff; z1++) - if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]){ - /* Tests if the value of each of the covariates of i is equal to filter j1 */ - bool=0; - /* 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", - bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtab[j1][z1], - j1,z1,nbcode[Tvaraff[z1]][codtab[j1][z1]],j1);*/ - /* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtab[7][3]=1 and nbcde[3][?]=1*/ - } - } - - if (bool==1){ - for(m=firstpass; m<=lastpass; m++){ - k2=anint[m][i]+(mint[m][i]/12.); - /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/ - if(agev[m][i]==0) agev[m][i]=iagemax+1; - if(agev[m][i]==1) agev[m][i]=iagemax+2; - if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i]; - if (m1) && (agev[m][i]< (iagemax+3))) { - dateintsum=dateintsum+k2; + if(j !=0){ + if(anyvaryingduminmodel==0){ /* If All fixed covariates */ + if (cptcoveff >0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */ + /* for (z1=1; z1<= nqfveff; z1++) { */ + /* meanq[z1]+=coqvar[Tvar[z1]][iind]; /\* Computes mean of quantitative with selected filter *\/ */ + /* } */ + for (z1=1; z1<=cptcoveff; z1++) { /* loops on covariates in the model */ + /* if(Tvaraff[z1] ==-20){ */ + /* /\* sumnew+=cotvar[mw[mi][iind]][z1][iind]; *\/ */ + /* }else if(Tvaraff[z1] ==-10){ */ + /* /\* sumnew+=coqvar[z1][iind]; *\/ */ + /* }else */ + if (covar[Tvaraff[z1]][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]){ /* for combination j1 of covariates */ + /* Tests if the value of the covariate z1 for this individual iind responded to combination j1 (V4=1 V3=0) */ + bool=0; /* bool should be equal to 1 to be selected, one covariate value failed */ + /* printf("bool=%d i=%d, z1=%d, Tvaraff[%d]=%d, covar[Tvarff][%d]=%2f, codtabm(%d,%d)=%d, nbcode[Tvaraff][codtabm(%d,%d)=%d, j1=%d\n", + bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtabm(j1,z1), + j1,z1,nbcode[Tvaraff[z1]][codtabm(j1,z1)],j1);*/ + /* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtabm(7,3)=1 and nbcde[3][?]=1*/ + } /* Onlyf fixed */ + } /* end z1 */ + } /* cptcovn > 0 */ + } /* end any */ + }/* end j==0 */ + if (bool==1){ /* We selected an individual iind satisfying combination j1 (V4=1 V3=0) or all fixed covariates */ + /* for(m=firstpass; m<=lastpass; m++){ */ + for(mi=1; mi=firstpass && m <=lastpass){ + k2=anint[m][iind]+(mint[m][iind]/12.); + /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/ + if(agev[m][iind]==0) agev[m][iind]=iagemax+1; /* All ages equal to 0 are in iagemax+1 */ + if(agev[m][iind]==1) agev[m][iind]=iagemax+2; /* All ages equal to 1 are in iagemax+2 */ + if (s[m][iind]>0 && s[m][iind]<=nlstate) /* If status at wave m is known and a live state */ + prop[s[m][iind]][(int)agev[m][iind]] += weight[iind]; /* At age of beginning of transition, where status is known */ + if (m1) && (agev[m][iind]< (iagemax+3)) && (anint[m][iind]!=9999) && (mint[m][iind]!=99) && (j==0)) { + dateintsum=dateintsum+k2; /* on all covariates ?*/ k2cpt++; + /* printf("iind=%ld dateintmean = %lf dateintsum=%lf k2cpt=%lf k2=%lf\n",iind, dateintsum/k2cpt, dateintsum,k2cpt, k2); */ } - /*}*/ - } - } - } /* end i */ - + }else{ + bool=1; + }/* end bool 2 */ + } /* end m */ + } /* end bool */ + } /* end iind = 1 to imx */ + /* prop[s][age] is feeded for any initial and valid live state as well as + freq[s1][s2][age] at single age of beginning the transition, for a combination j1 */ + + /* fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/ - pstamp(ficresp); - if (cptcovn>0) { + if(cptcoveff==0 && nj==1) /* no covariate and first pass */ + pstamp(ficresp); + if (cptcoveff>0 && j!=0){ + pstamp(ficresp); + printf( "\n#********** Variable "); fprintf(ficresp, "\n#********** Variable "); - for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]); - fprintf(ficresp, "**********\n#"); + fprintf(ficresphtm, "\n

********** Variable "); + fprintf(ficresphtmfr, "\n

********** Variable "); fprintf(ficlog, "\n#********** Variable "); - for (z1=1; z1<=cptcoveff; z1++) fprintf(ficlog, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]); - fprintf(ficlog, "**********\n#"); + for (z1=1; z1<=cptcoveff; z1++){ + if(!FixedV[Tvaraff[z1]]){ + printf( "V%d(fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]); + fprintf(ficresp, "V%d(fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]); + fprintf(ficresphtm, "V%d(fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]); + fprintf(ficresphtmfr, "V%d(fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]); + fprintf(ficlog, "V%d(fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]); + }else{ + printf( "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]); + fprintf(ficresp, "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]); + fprintf(ficresphtm, "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]); + fprintf(ficresphtmfr, "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]); + fprintf(ficlog, "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]); + } + } + printf( "**********\n#"); + fprintf(ficresp, "**********\n#"); + fprintf(ficresphtm, "**********

\n"); + fprintf(ficresphtmfr, "**********\n"); + fprintf(ficlog, "**********\n"); + } + fprintf(ficresphtm,""); + if((cptcoveff==0 && nj==1)|| nj==2 ) /* no covariate and first pass */ + fprintf(ficresp, " Age"); + if(nj==2) for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, " V%d=%d",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]); + for(i=1; i<=nlstate;i++) { + if((cptcoveff==0 && nj==1)|| nj==2 ) fprintf(ficresp," Prev(%d) N(%d) N ",i,i); + fprintf(ficresphtm, "",i,i); } - for(i=1; i<=nlstate;i++) - fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i); - fprintf(ficresp, "\n"); + if((cptcoveff==0 && nj==1)|| nj==2 ) fprintf(ficresp, "\n"); + fprintf(ficresphtm, "\n"); - for(i=iagemin; i <= iagemax+3; i++){ - if(i==iagemax+3){ + /* Header of frequency table by age */ + fprintf(ficresphtmfr,"
AgePrev(%d)N(%d)N
"); + fprintf(ficresphtmfr," "); + for(s2=-1; s2 <=nlstate+ndeath; s2++){ + for(m=-1; m <=nlstate+ndeath; m++){ + if(s2!=0 && m!=0) + fprintf(ficresphtmfr," ",s2,m); + } + } + fprintf(ficresphtmfr, "\n"); + + /* For each age */ + for(iage=iagemin; iage <= iagemax+3; iage++){ + fprintf(ficresphtm,""); + if(iage==iagemax+1){ + fprintf(ficlog,"1"); + fprintf(ficresphtmfr," "); + }else if(iage==iagemax+2){ + fprintf(ficlog,"0"); + fprintf(ficresphtmfr," "); + }else if(iage==iagemax+3){ fprintf(ficlog,"Total"); + fprintf(ficresphtmfr," "); }else{ if(first==1){ first=0; printf("See log file for details...\n"); } - fprintf(ficlog,"Age %d", i); + fprintf(ficresphtmfr," ",iage); + fprintf(ficlog,"Age %d", iage); } - for(jk=1; jk <=nlstate ; jk++){ - for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++) - pp[jk] += freq[jk][m][i]; + for(s1=1; s1 <=nlstate ; s1++){ + for(m=-1, pp[s1]=0; m <=nlstate+ndeath ; m++) + pp[s1] += freq[s1][m][iage]; } - for(jk=1; jk <=nlstate ; jk++){ + for(s1=1; s1 <=nlstate ; s1++){ for(m=-1, pos=0; m <=0 ; m++) - pos += freq[jk][m][i]; - if(pp[jk]>=1.e-10){ + pos += freq[s1][m][iage]; + if(pp[s1]>=1.e-10){ if(first==1){ - printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]); + printf(" %d.=%.0f loss[%d]=%.1f%%",s1,pp[s1],s1,100*pos/pp[s1]); } - fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]); + fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",s1,pp[s1],s1,100*pos/pp[s1]); }else{ if(first==1) - printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk); - fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk); + printf(" %d.=%.0f loss[%d]=NaNQ%%",s1,pp[s1],s1); + fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",s1,pp[s1],s1); } } - - for(jk=1; jk <=nlstate ; jk++){ - for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++) - pp[jk] += freq[jk][m][i]; - } - for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){ - pos += pp[jk]; - posprop += prop[jk][i]; + + for(s1=1; s1 <=nlstate ; s1++){ + /* posprop[s1]=0; */ + for(m=0, pp[s1]=0; m <=nlstate+ndeath; m++)/* Summing on all ages */ + pp[s1] += freq[s1][m][iage]; + } /* pp[s1] is the total number of transitions starting from state s1 and any ending status until this age */ + + for(s1=1,pos=0, pospropta=0.; s1 <=nlstate ; s1++){ + pos += pp[s1]; /* pos is the total number of transitions until this age */ + posprop[s1] += prop[s1][iage]; /* prop is the number of transitions from a live state + from s1 at age iage prop[s[m][iind]][(int)agev[m][iind]] += weight[iind] */ + pospropta += prop[s1][iage]; /* prop is the number of transitions from a live state + from s1 at age iage prop[s[m][iind]][(int)agev[m][iind]] += weight[iind] */ } - for(jk=1; jk <=nlstate ; jk++){ + + /* Writing ficresp */ + if(cptcoveff==0 && nj==1){ /* no covariate and first pass */ + if( iage <= iagemax){ + fprintf(ficresp," %d",iage); + } + }else if( nj==2){ + if( iage <= iagemax){ + fprintf(ficresp," %d",iage); + for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, " %d %d",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]); + } + } + for(s1=1; s1 <=nlstate ; s1++){ if(pos>=1.e-5){ if(first==1) - printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos); - fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos); + printf(" %d.=%.0f prev[%d]=%.1f%%",s1,pp[s1],s1,100*pp[s1]/pos); + fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",s1,pp[s1],s1,100*pp[s1]/pos); }else{ if(first==1) - printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk); - fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk); + printf(" %d.=%.0f prev[%d]=NaNQ%%",s1,pp[s1],s1); + fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",s1,pp[s1],s1); } - if( i <= iagemax){ + if( iage <= iagemax){ if(pos>=1.e-5){ - fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop); - /*probs[i][jk][j1]= pp[jk]/pos;*/ - /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/ + if(cptcoveff==0 && nj==1){ /* no covariate and first pass */ + fprintf(ficresp," %.5f %.0f %.0f",prop[s1][iage]/pospropta, prop[s1][iage],pospropta); + }else if( nj==2){ + fprintf(ficresp," %.5f %.0f %.0f",prop[s1][iage]/pospropta, prop[s1][iage],pospropta); + } + fprintf(ficresphtm,"",iage,prop[s1][iage]/pospropta, prop[s1][iage],pospropta); + /*probs[iage][s1][j1]= pp[s1]/pos;*/ + /*printf("\niage=%d s1=%d j1=%d %.5f %.0f %.0f %f",iage,s1,j1,pp[s1]/pos, pp[s1],pos,probs[iage][s1][j1]);*/ + } else{ + if((cptcoveff==0 && nj==1)|| nj==2 ) fprintf(ficresp," NaNq %.0f %.0f",prop[s1][iage],pospropta); + fprintf(ficresphtm,"",iage, prop[s1][iage],pospropta); } - else - fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop); } - } - - for(jk=-1; jk <=nlstate+ndeath; jk++) - for(m=-1; m <=nlstate+ndeath; m++) - if(freq[jk][m][i] !=0 ) { - if(first==1) - printf(" %d%d=%.0f",jk,m,freq[jk][m][i]); - fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]); + pospropt[s1] +=posprop[s1]; + } /* end loop s1 */ + /* pospropt=0.; */ + for(s1=-1; s1 <=nlstate+ndeath; s1++){ + for(m=-1; m <=nlstate+ndeath; m++){ + if(freq[s1][m][iage] !=0 ) { /* minimizing output */ + if(first==1){ + printf(" %d%d=%.0f",s1,m,freq[s1][m][iage]); + } + /* printf(" %d%d=%.0f",s1,m,freq[s1][m][iage]); */ + fprintf(ficlog," %d%d=%.0f",s1,m,freq[s1][m][iage]); } - if(i <= iagemax) - fprintf(ficresp,"\n"); + if(s1!=0 && m!=0) + fprintf(ficresphtmfr," ",freq[s1][m][iage]); + } + } /* end loop s1 */ + posproptt=0.; + for(s1=1; s1 <=nlstate; s1++){ + posproptt += pospropt[s1]; + } + fprintf(ficresphtmfr,"\n "); + fprintf(ficresphtm,"\n"); + if((cptcoveff==0 && nj==1)|| nj==2 ) { + if(iage <= iagemax) + fprintf(ficresp,"\n"); + } if(first==1) printf("Others in log...\n"); fprintf(ficlog,"\n"); + } /* end loop age iage */ + + fprintf(ficresphtm,""); + for(s1=1; s1 <=nlstate ; s1++){ + if(posproptt < 1.e-5){ + fprintf(ficresphtm,"",pospropt[s1],posproptt); + }else{ + fprintf(ficresphtm,"",pospropt[s1]/posproptt,pospropt[s1],posproptt); + } } - /*}*/ - } + fprintf(ficresphtm,"\n"); + fprintf(ficresphtm,"
Age%d%d
0
Unknown
Total
%d%d%.5f%.0f%.0f%dNaNq%.0f%.0f%.0f
TotNanq%.0f%.0f%.5f%.0f%.0f
\n"); + fprintf(ficresphtmfr,"\n"); + if(posproptt < 1.e-5){ + fprintf(ficresphtm,"\n

This combination (%d) is not valid and no result will be produced

",j1); + fprintf(ficresphtmfr,"\n

This combination (%d) is not valid and no result will be produced

",j1); + fprintf(ficlog,"# This combination (%d) is not valid and no result will be produced\n",j1); + printf("# This combination (%d) is not valid and no result will be produced\n",j1); + invalidvarcomb[j1]=1; + }else{ + fprintf(ficresphtm,"\n

This combination (%d) is valid and result will be produced.

",j1); + invalidvarcomb[j1]=0; + } + fprintf(ficresphtmfr,"\n"); + fprintf(ficlog,"\n"); + if(j!=0){ + printf("#Freqsummary: Starting values for combination j1=%d:\n", j1); + for(i=1,s1=1; i <=nlstate; i++){ + for(k=1; k <=(nlstate+ndeath); k++){ + if (k != i) { + for(jj=1; jj <=ncovmodel; jj++){ /* For counting s1 */ + if(jj==1){ /* Constant case (in fact cste + age) */ + if(j1==1){ /* All dummy covariates to zero */ + freq[i][k][iagemax+4]=freq[i][k][iagemax+3]; /* Stores case 0 0 0 */ + freq[i][i][iagemax+4]=freq[i][i][iagemax+3]; /* Stores case 0 0 0 */ + printf("%d%d ",i,k); + fprintf(ficlog,"%d%d ",i,k); + printf("%12.7f ln(%.0f/%.0f)= %f, OR=%f sd=%f \n",p[s1],freq[i][k][iagemax+3],freq[i][i][iagemax+3], log(freq[i][k][iagemax+3]/freq[i][i][iagemax+3]),freq[i][k][iagemax+3]/freq[i][i][iagemax+3], sqrt(1/freq[i][k][iagemax+3]+1/freq[i][i][iagemax+3])); + fprintf(ficlog,"%12.7f ln(%.0f/%.0f)= %12.7f \n",p[s1],freq[i][k][iagemax+3],freq[i][i][iagemax+3], log(freq[i][k][iagemax+3]/freq[i][i][iagemax+3])); + pstart[s1]= log(freq[i][k][iagemax+3]/freq[i][i][iagemax+3]); + } + }else if((j1==1) && (jj==2 || nagesqr==1)){ /* age or age*age parameter without covariate V4*age (to be done later) */ + for(iage=iagemin; iage <= iagemax+3; iage++){ + x[iage]= (double)iage; + y[iage]= log(freq[i][k][iage]/freq[i][i][iage]); + /* printf("i=%d, k=%d, s1=%d, j1=%d, jj=%d, y[%d]=%f\n",i,k,s1,j1,jj, iage, y[iage]); */ + } + linreg(iagemin,iagemax,&no,x,y,&a,&b,&r, &sa, &sb ); /* y= a+b*x with standard errors */ + pstart[s1]=b; + pstart[s1-1]=a; + }else if( j1!=1 && (j1==2 || (log(j1-1.)/log(2.)-(int)(log(j1-1.)/log(2.))) <0.010) && ( TvarsDind[(int)(log(j1-1.)/log(2.))+1]+2+nagesqr == jj) && Dummy[jj-2-nagesqr]==0){ /* We want only if the position, jj, in model corresponds to unique covariate equal to 1 in j1 combination */ + printf("j1=%d, jj=%d, (int)(log(j1-1.)/log(2.))+1=%d, TvarsDind[(int)(log(j1-1.)/log(2.))+1]=%d\n",j1, jj,(int)(log(j1-1.)/log(2.))+1,TvarsDind[(int)(log(j1-1.)/log(2.))+1]); + printf("j1=%d, jj=%d, (log(j1-1.)/log(2.))+1=%f, TvarsDind[(int)(log(j1-1.)/log(2.))+1]=%d\n",j1, jj,(log(j1-1.)/log(2.))+1,TvarsDind[(int)(log(j1-1.)/log(2.))+1]); + pstart[s1]= log((freq[i][k][iagemax+3]/freq[i][i][iagemax+3])/(freq[i][k][iagemax+4]/freq[i][i][iagemax+4])); + printf("%d%d ",i,k); + fprintf(ficlog,"%d%d ",i,k); + printf("s1=%d,i=%d,k=%d,p[%d]=%12.7f ln((%.0f/%.0f)/(%.0f/%.0f))= %f, OR=%f sd=%f \n",s1,i,k,s1,p[s1],freq[i][k][iagemax+3],freq[i][i][iagemax+3],freq[i][k][iagemax+4],freq[i][i][iagemax+4], log((freq[i][k][iagemax+3]/freq[i][i][iagemax+3])/(freq[i][k][iagemax+4]/freq[i][i][iagemax+4])),(freq[i][k][iagemax+3]/freq[i][i][iagemax+3])/(freq[i][k][iagemax+4]/freq[i][i][iagemax+4]), sqrt(1/freq[i][k][iagemax+3]+1/freq[i][i][iagemax+3]+1/freq[i][k][iagemax+4]+1/freq[i][i][iagemax+4])); + }else{ /* Other cases, like quantitative fixed or varying covariates */ + ; + } + /* printf("%12.7f )", param[i][jj][k]); */ + /* fprintf(ficlog,"%12.7f )", param[i][jj][k]); */ + s1++; + } /* end jj */ + } /* end k!= i */ + } /* end k */ + } /* end i, s1 */ + } /* end j !=0 */ + } /* end selected combination of covariate j1 */ + if(j==0){ /* We can estimate starting values from the occurences in each case */ + printf("#Freqsummary: Starting values for the constants:\n"); + fprintf(ficlog,"\n"); + for(i=1,s1=1; i <=nlstate; i++){ + for(k=1; k <=(nlstate+ndeath); k++){ + if (k != i) { + printf("%d%d ",i,k); + fprintf(ficlog,"%d%d ",i,k); + for(jj=1; jj <=ncovmodel; jj++){ + pstart[s1]=p[s1]; /* Setting pstart to p values by default */ + if(jj==1){ /* Age has to be done */ + pstart[s1]= log(freq[i][k][iagemax+3]/freq[i][i][iagemax+3]); + printf("%12.7f ln(%.0f/%.0f)= %12.7f ",p[s1],freq[i][k][iagemax+3],freq[i][i][iagemax+3], log(freq[i][k][iagemax+3]/freq[i][i][iagemax+3])); + fprintf(ficlog,"%12.7f ln(%.0f/%.0f)= %12.7f ",p[s1],freq[i][k][iagemax+3],freq[i][i][iagemax+3], log(freq[i][k][iagemax+3]/freq[i][i][iagemax+3])); + } + /* printf("%12.7f )", param[i][jj][k]); */ + /* fprintf(ficlog,"%12.7f )", param[i][jj][k]); */ + s1++; + } + printf("\n"); + fprintf(ficlog,"\n"); + } + } + } + printf("#Freqsummary\n"); + fprintf(ficlog,"\n"); + for(s1=-1; s1 <=nlstate+ndeath; s1++){ + for(s2=-1; s2 <=nlstate+ndeath; s2++){ + /* param[i]|j][k]= freq[s1][s2][iagemax+3] */ + printf(" %d%d=%.0f",s1,s2,freq[s1][s2][iagemax+3]); + fprintf(ficlog," %d%d=%.0f",s1,s2,freq[s1][s2][iagemax+3]); + /* if(freq[s1][s2][iage] !=0 ) { /\* minimizing output *\/ */ + /* printf(" %d%d=%.0f",s1,s2,freq[s1][s2][iagemax+3]); */ + /* fprintf(ficlog," %d%d=%.0f",s1,s2,freq[s1][s2][iagemax+3]); */ + /* } */ + } + } /* end loop s1 */ + + printf("\n"); + fprintf(ficlog,"\n"); + } /* end j=0 */ + } /* end j */ + + if(mle == -2){ /* We want to use these values as starting values */ + for(i=1, jk=1; i <=nlstate; i++){ + for(j=1; j <=nlstate+ndeath; j++){ + if(j!=i){ + /*ca[0]= k+'a'-1;ca[1]='\0';*/ + printf("%1d%1d",i,j); + fprintf(ficparo,"%1d%1d",i,j); + for(k=1; k<=ncovmodel;k++){ + /* printf(" %lf",param[i][j][k]); */ + /* fprintf(ficparo," %lf",param[i][j][k]); */ + p[jk]=pstart[jk]; + printf(" %f ",pstart[jk]); + fprintf(ficparo," %f ",pstart[jk]); + jk++; + } + printf("\n"); + fprintf(ficparo,"\n"); + } + } + } + } /* end mle=-2 */ dateintmean=dateintsum/k2cpt; - + fclose(ficresp); - free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3); + fclose(ficresphtm); + fclose(ficresphtmfr); + free_vector(meanq,1,nqfveff); + free_matrix(meanqt,1,lastpass,1,nqtveff); + free_vector(x, iagemin-AGEMARGE, iagemax+4+AGEMARGE); + free_vector(y, iagemin-AGEMARGE, iagemax+4+AGEMARGE); + free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin-AGEMARGE, iagemax+4+AGEMARGE); + free_vector(pospropt,1,nlstate); + free_vector(posprop,1,nlstate); + free_matrix(prop,1,nlstate,iagemin-AGEMARGE, iagemax+4+AGEMARGE); free_vector(pp,1,nlstate); - free_matrix(prop,1,nlstate,iagemin, iagemax+3); - /* End of Freq */ + /* End of freqsummary */ } /************ Prevalence ********************/ @@ -2440,10 +4866,13 @@ void prevalence(double ***probs, double We still use firstpass and lastpass as another selection. */ - int i, m, jk, k1, i1, j1, bool, z1,j; - double ***freq; /* Frequencies */ - double *pp, **prop; - double pos,posprop; + int i, m, jk, j1, bool, z1,j, iv; + int mi; /* Effective wave */ + int iage; + double agebegin, ageend; + + double **prop; + double posprop; double y2; /* in fractional years */ int iagemin, iagemax; int first; /** to stop verbosity which is redirected to log file */ @@ -2451,7 +4880,7 @@ void prevalence(double ***probs, double iagemin= (int) agemin; iagemax= (int) agemax; /*pp=vector(1,nlstate);*/ - prop=matrix(1,nlstate,iagemin,iagemax+3); + prop=matrix(1,nlstate,iagemin-AGEMARGE,iagemax+4+AGEMARGE); /* freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/ j1=0; @@ -2459,61 +4888,77 @@ void prevalence(double ***probs, double if (cptcovn<1) {j=1;ncodemax[1]=1;} first=1; - for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){ - /*for(i1=1; i1<=ncodemax[k1];i1++){ - j1++;*/ - - for (i=1; i<=nlstate; i++) - for(m=iagemin; m <= iagemax+3; m++) - prop[i][m]=0.0; - - for (i=1; i<=imx; i++) { /* Each individual */ - bool=1; - if (cptcovn>0) { - for (z1=1; z1<=cptcoveff; z1++) - if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) + for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){ /* For each combination of covariate */ + for (i=1; i<=nlstate; i++) + for(iage=iagemin-AGEMARGE; iage <= iagemax+4+AGEMARGE; iage++) + prop[i][iage]=0.0; + printf("Prevalence combination of varying and fixed dummies %d\n",j1); + /* fprintf(ficlog," V%d=%d ",Tvaraff[j1],nbcode[Tvaraff[j1]][codtabm(k,j1)]); */ + fprintf(ficlog,"Prevalence combination of varying and fixed dummies %d\n",j1); + + for (i=1; i<=imx; i++) { /* Each individual */ + bool=1; + /* for(m=firstpass; m<=lastpass; m++){/\* Other selection (we can limit to certain interviews*\/ */ + for(mi=1; mi=firstpass && m <=lastpass){ y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */ if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */ if(agev[m][i]==0) agev[m][i]=iagemax+1; if(agev[m][i]==1) agev[m][i]=iagemax+2; - if((int)agev[m][i] iagemax+3) printf("Error on individual =%d agev[m][i]=%f m=%d\n",i, agev[m][i],m); - if (s[m][i]>0 && s[m][i]<=nlstate) { + if((int)agev[m][i] iagemax+4+AGEMARGE){ + printf("Error on individual # %d agev[m][i]=%f <%d-%d or > %d+3+%d m=%d; either change agemin or agemax or fix data\n",i, agev[m][i],iagemin,AGEMARGE, iagemax,AGEMARGE,m); + exit(1); + } + if (s[m][i]>0 && s[m][i]<=nlstate) { /*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]]);*/ - prop[s[m][i]][(int)agev[m][i]] += weight[i]; - prop[s[m][i]][iagemax+3] += weight[i]; - } - } + prop[s[m][i]][(int)agev[m][i]] += weight[i];/* At age of beginning of transition, where status is known */ + prop[s[m][i]][iagemax+3] += weight[i]; + } /* end valid statuses */ + } /* end selection of dates */ } /* end selection of waves */ - } - } - for(i=iagemin; i <= iagemax+3; i++){ - for(jk=1,posprop=0; jk <=nlstate ; jk++) { - posprop += prop[jk][i]; - } - - for(jk=1; jk <=nlstate ; jk++){ - if( i <= iagemax){ - if(posprop>=1.e-5){ - probs[i][jk][j1]= prop[jk][i]/posprop; - } else{ - if(first==1){ - first=0; - 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]); - } + } /* end bool */ + } /* end wave */ + } /* end individual */ + for(i=iagemin; i <= iagemax+3; i++){ + for(jk=1,posprop=0; jk <=nlstate ; jk++) { + posprop += prop[jk][i]; + } + + for(jk=1; jk <=nlstate ; jk++){ + if( i <= iagemax){ + if(posprop>=1.e-5){ + probs[i][jk][j1]= prop[jk][i]/posprop; + } else{ + if(first==1){ + first=0; + printf("Warning Observed prevalence probs[%d][%d][%d]=%lf because of lack of cases\nSee others in log file...\n",jk,i,j1,probs[i][jk][j1]); } - } - }/* end jk */ - }/* end i */ - /*} *//* end i1 */ + } + } + }/* end jk */ + }/* end i */ + /*} *//* end i1 */ } /* end j1 */ /* free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/ /*free_vector(pp,1,nlstate);*/ - free_matrix(prop,1,nlstate, iagemin,iagemax+3); + free_matrix(prop,1,nlstate, iagemin-AGEMARGE,iagemax+4+AGEMARGE); } /* End of prevalence */ /************* Waves Concatenation ***************/ @@ -2525,37 +4970,105 @@ void concatwav(int wav[], int **dh, int mw[mi][i] is the mi (mi=1 to wav[i]) effective wave of individual i dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i] and mw[mi+1][i]. dh depends on stepm. - */ + */ - int i, mi, m; + int i=0, mi=0, m=0, mli=0; /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1; double sum=0., jmean=0.;*/ - int first; + int first=0, firstwo=0, firsthree=0, firstfour=0, firstfiv=0; int j, k=0,jk, ju, jl; double sum=0.; first=0; - jmin=1e+5; + firstwo=0; + firsthree=0; + firstfour=0; + jmin=100000; jmax=-1; jmean=0.; - for(i=1; i<=imx; i++){ - mi=0; + +/* Treating live states */ + for(i=1; i<=imx; i++){ /* For simple cases and if state is death */ + mi=0; /* First valid wave */ + mli=0; /* Last valid wave */ m=firstpass; - while(s[m][i] <= nlstate){ - if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5) + while(s[m][i] <= nlstate){ /* a live state */ + if(m >firstpass && s[m][i]==s[m-1][i] && mint[m][i]==mint[m-1][i] && anint[m][i]==anint[m-1][i]){/* Two succesive identical information on wave m */ + mli=m-1;/* mw[++mi][i]=m-1; */ + }else if(s[m][i]>=1 || s[m][i]==-4 || s[m][i]==-5){ /* Since 0.98r4 if status=-2 vital status is really unknown, wave should be skipped */ mw[++mi][i]=m; - if(m >=lastpass) + mli=m; + } /* else might be a useless wave -1 and mi is not incremented and mw[mi] not updated */ + if(m < lastpass){ /* m < lastpass, standard case */ + m++; /* mi gives the "effective" current wave, m the current wave, go to next wave by incrementing m */ + } + else{ /* m >= lastpass, eventual special issue with warning */ +#ifdef UNKNOWNSTATUSNOTCONTRIBUTING break; - else - m++; +#else + if(s[m][i]==-1 && (int) andc[i] == 9999 && (int)anint[m][i] != 9999){ + if(firsthree == 0){ + printf("Information! Unknown status for individual %ld line=%d occurred at last wave %d at known date %d/%d. Please, check if your unknown date of death %d/%d means a live state %d at wave %d. This case(%d)/wave(%d) contributes to the likelihood as 1-p%d%d .\nOthers in log file only\n",num[i],i,lastpass,(int)mint[m][i],(int)anint[m][i], (int) moisdc[i], (int) andc[i], s[m][i], m, i, m, s[m][i], nlstate+ndeath); + firsthree=1; + } + fprintf(ficlog,"Information! Unknown status for individual %ld line=%d occurred at last wave %d at known date %d/%d. Please, check if your unknown date of death %d/%d means a live state %d at wave %d. This case(%d)/wave(%d) contributes to the likelihood as 1-p%d%d .\n",num[i],i,lastpass,(int)mint[m][i],(int)anint[m][i], (int) moisdc[i], (int) andc[i], s[m][i], m, i, m, s[m][i], nlstate+ndeath); + mw[++mi][i]=m; + mli=m; + } + if(s[m][i]==-2){ /* Vital status is really unknown */ + nbwarn++; + if((int)anint[m][i] == 9999){ /* Has the vital status really been verified? */ + printf("Warning! Vital status for individual %ld (line=%d) at last wave %d interviewed at date %d/%d is unknown %d. Please, check if the vital status and the date of death %d/%d are really unknown. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\nOthers in log file only\n",num[i],i,lastpass,(int)mint[m][i],(int)anint[m][i], s[m][i], (int) moisdc[i], (int) andc[i], i, m); + fprintf(ficlog,"Warning! Vital status for individual %ld (line=%d) at last wave %d interviewed at date %d/%d is unknown %d. Please, check if the vital status and the date of death %d/%d are really unknown. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\n",num[i],i,lastpass,(int)mint[m][i],(int)anint[m][i], s[m][i], (int) moisdc[i], (int) andc[i], i, m); + } + break; + } + break; +#endif + }/* End m >= lastpass */ }/* end while */ - if (s[m][i] > nlstate){ + + /* mi is the last effective wave, m is lastpass, mw[j][i] gives the # of j-th effective wave for individual i */ + /* After last pass */ +/* Treating death states */ + if (s[m][i] > nlstate){ /* In a death state */ + /* if( mint[m][i]==mdc[m][i] && anint[m][i]==andc[m][i]){ /\* same date of death and date of interview *\/ */ + /* } */ mi++; /* Death is another wave */ /* if(mi==0) never been interviewed correctly before death */ - /* Only death is a correct wave */ + /* Only death is a correct wave */ mw[mi][i]=m; - } - - wav[i]=mi; + } /* else not in a death state */ +#ifndef DISPATCHINGKNOWNDEATHAFTERLASTWAVE + else if ((int) andc[i] != 9999) { /* Date of death is known */ + if ((int)anint[m][i]!= 9999) { /* date of last interview is known */ + if((andc[i]+moisdc[i]/12.) <=(anint[m][i]+mint[m][i]/12.)){ /* death occured before last wave and status should have been death instead of -1 */ + nbwarn++; + if(firstfiv==0){ + printf("Warning! Death for individual %ld line=%d occurred at %d/%d before last wave %d interviewed at %d/%d and should have been coded as death instead of '%d'. This case (%d)/wave (%d) is contributing to likelihood.\nOthers in log file only\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], s[m][i], i,m ); + firstfiv=1; + }else{ + fprintf(ficlog,"Warning! Death for individual %ld line=%d occurred at %d/%d before last wave %d interviewed at %d/%d and should have been coded as death instead of '%d'. This case (%d)/wave (%d) is contributing to likelihood.\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], s[m][i], i,m ); + } + }else{ /* Death occured afer last wave potential bias */ + nberr++; + if(firstwo==0){ + printf("Error! Death for individual %ld line=%d occurred at %d/%d after last wave %d interviewed at %d/%d. Potential bias if other individuals are still alive at this date but ignored. This case (%d)/wave (%d) is skipped, no contribution to likelihood. Please add a new fictive wave at the date of last vital status scan, with a dead status or alive but unknown state status (-1). See documentation\nOthers in log file only\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], i,m ); + firstwo=1; + } + fprintf(ficlog,"Error! Death for individual %ld line=%d occurred at %d/%d after last wave %d interviewed at %d/%d. Potential bias if other individuals are still alive at this date but ignored. This case (%d)/wave (%d) is skipped, no contribution to likelihood. Please add a new fictive wave at the date of last vital status scan, with a dead status or alive but unknown state status (-1). See documentation\n\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], i,m ); + } + }else{ /* if date of interview is unknown */ + /* death is known but not confirmed by death status at any wave */ + if(firstfour==0){ + printf("Error! Death for individual %ld line=%d occurred %d/%d but not confirmed by any death status for any wave, including last wave %d at unknown date %d/%d. Potential bias if other individuals are still alive at this date but ignored. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\nOthers in log file only\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], i,m ); + firstfour=1; + } + fprintf(ficlog,"Error! Death for individual %ld line=%d occurred %d/%d but not confirmed by any death status for any wave, including last wave %d at unknown date %d/%d. Potential bias if other individuals are still alive at this date but ignored. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], i,m ); + } + } /* end if date of death is known */ +#endif + wav[i]=mi; /* mi should be the last effective wave (or mli) */ + /* wav[i]=mw[mi][i]; */ if(mi==0){ nbwarn++; if(first==0){ @@ -2567,13 +5080,15 @@ void concatwav(int wav[], int **dh, int } } /* end mi==0 */ } /* End individuals */ - + /* wav and mw are no more changed */ + + for(i=1; i<=imx; i++){ for(mi=1; mi nlstate) { /* A death */ + if (s[mw[mi+1][i]][i] > nlstate) { /* A death, but what if date is unknown? */ if (agedc[i] < 2*AGESUP) { j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); if(j==0) j=1; /* Survives at least one month after exam */ @@ -2602,7 +5117,7 @@ void concatwav(int wav[], int **dh, int else{ j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12)); /* 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]); */ - + k=k+1; if (j >= jmax) { jmax=j; @@ -2656,131 +5171,192 @@ void concatwav(int wav[], int **dh, int jmean=sum/k; 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); 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); - } +} /*********** Tricode ****************************/ -void tricode(int *Tvar, int **nbcode, int imx, int *Ndum) -{ - /**< Uses cptcovn+2*cptcovprod as the number of covariates */ - /* Tvar[i]=atoi(stre); find 'n' in Vn and stores in Tvar. If model=V2+V1 Tvar[1]=2 and Tvar[2]=1 - /* Boring subroutine which should only output nbcode[Tvar[j]][k] - * Tvar[5] in V2+V1+V3*age+V2*V4 is 2 (V2) - /* nbcode[Tvar[j]][1]= - */ + void tricode(int *cptcov, int *Tvar, int **nbcode, int imx, int *Ndum) + { + /**< Uses cptcovn+2*cptcovprod as the number of covariates */ + /* Tvar[i]=atoi(stre); find 'n' in Vn and stores in Tvar. If model=V2+V1 Tvar[1]=2 and Tvar[2]=1 + * Boring subroutine which should only output nbcode[Tvar[j]][k] + * Tvar[5] in V2+V1+V3*age+V2*V4 is 4 (V4) even it is a time varying or quantitative variable + * nbcode[Tvar[5]][1]= nbcode[4][1]=0, nbcode[4][2]=1 (usually); + */ - int ij=1, k=0, j=0, i=0, maxncov=NCOVMAX; - int modmaxcovj=0; /* Modality max of covariates j */ - int cptcode=0; /* Modality max of covariates j */ - int modmincovj=0; /* Modality min of covariates j */ + int ij=1, k=0, j=0, i=0, maxncov=NCOVMAX; + int modmaxcovj=0; /* Modality max of covariates j */ + int cptcode=0; /* Modality max of covariates j */ + int modmincovj=0; /* Modality min of covariates j */ - cptcoveff=0; + /* cptcoveff=0; */ + /* *cptcov=0; */ - for (k=-1; k < maxncov; k++) Ndum[k]=0; - for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */ + for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */ - /* Loop on covariates without age and products */ - for (j=1; j<=(cptcovs); j++) { /* model V1 + V2*age+ V3 + V3*V4 : V1 + V3 = 2 only */ - for (i=1; i<=imx; i++) { /* Lopp on individuals: reads the data file to get the maximum value of the - modality of this covariate Vj*/ - ij=(int)(covar[Tvar[j]][i]); /* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i - * If product of Vn*Vm, still boolean *: - * If it was coded 1, 2, 3, 4 should be splitted into 3 boolean variables - * 1 => 0 0 0, 2 => 0 0 1, 3 => 0 1 1, 4=1 0 0 */ - /* Finds for covariate j, n=Tvar[j] of Vn . ij is the - modality of the nth covariate of individual i. */ - if (ij > modmaxcovj) - modmaxcovj=ij; - else if (ij < modmincovj) - modmincovj=ij; - if ((ij < -1) && (ij > NCOVMAX)){ - printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX ); - exit(1); - }else - Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/ - /* If coded 1, 2, 3 , counts the number of 1 Ndum[1], number of 2, Ndum[2], etc */ - /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/ - /* getting the maximum value of the modality of the covariate - (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and - female is 1, then modmaxcovj=1.*/ - } - printf(" Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", j, Tvar[j], modmincovj, modmaxcovj); - cptcode=modmaxcovj; - /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */ - /*for (i=0; i<=cptcode; i++) {*/ - for (i=modmincovj; i<=modmaxcovj; i++) { /* i=-1 ? 0 and 1*//* For each value of the modality of model-cov j */ - printf("Frequencies of covariates %d V%d %d\n", j, Tvar[j], Ndum[i]); - if( Ndum[i] != 0 ){ /* Counts if nobody answered, empty modality */ - ncodemax[j]++; /* ncodemax[j]= Number of non-null modalities of the j th covariate. */ - } - /* In fact ncodemax[j]=2 (dichotom. variables only) but it could be more for - historical reasons: 3 if coded 1, 2, 3 and 4 and Ndum[2]=0 */ - } /* Ndum[-1] number of undefined modalities */ - - /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */ - /* For covariate j, modalities could be 1, 2, 3, 4. If Ndum[2]=0 ncodemax[j] is not 4 but 3 */ - /* If Ndum[3}= 635; Ndum[4]=0; Ndum[5]=0; Ndum[6]=27; Ndum[7]=125; - modmincovj=3; modmaxcovj = 7; - There are only 3 modalities non empty (or 2 if 27 is too few) : ncodemax[j]=3; - which will be coded 0, 1, 2 which in binary on 3-1 digits are 0=00 1=01, 2=10; defining two dummy - variables V1_1 and V1_2. - nbcode[Tvar[j]][ij]=k; - nbcode[Tvar[j]][1]=0; - nbcode[Tvar[j]][2]=1; - nbcode[Tvar[j]][3]=2; - */ - ij=1; /* ij is similar to i but can jumps over null modalities */ - for (i=modmincovj; i<=modmaxcovj; i++) { /* i= 1 to 2 for dichotomous, or from 1 to 3 */ - for (k=0; k<= cptcode; k++) { /* k=-1 ? k=0 to 1 *//* Could be 1 to 4 */ - /*recode from 0 */ - if (Ndum[k] != 0) { /* If at least one individual responded to this modality k */ - nbcode[Tvar[j]][ij]=k; /* stores the modality in an array nbcode. - k is a modality. If we have model=V1+V1*sex - then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */ - ij++; - } - if (ij > ncodemax[j]) break; - } /* end of loop on */ - } /* end of loop on modality */ - } /* end of loop on model-covariate j. nbcode[Tvarj][1]=0 and nbcode[Tvarj][2]=1 sets the value of covariate j*/ - - for (k=-1; k< maxncov; k++) Ndum[k]=0; - - for (i=1; i<=ncovmodel-2; i++) { /* -2, cste and age */ - /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/ - ij=Tvar[i]; /* Tvar might be -1 if status was unknown */ - Ndum[ij]++; - } - - ij=1; - for (i=0; i<= maxncov-1; i++) { /* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) */ - /*printf("Ndum[%d]=%d\n",i, Ndum[i]);*/ - if((Ndum[i]!=0) && (i<=ncovcol)){ - /*printf("diff Ndum[%d]=%d\n",i, Ndum[i]);*/ - Tvaraff[ij]=i; /*For printing (unclear) */ - ij++; - }else - Tvaraff[ij]=0; + /* Loop on covariates without age and products and no quantitative variable */ + /* for (j=1; j<=(cptcovs); j++) { /\* From model V1 + V2*age+ V3 + V3*V4 keeps V1 + V3 = 2 only *\/ */ + for (k=1; k<=cptcovt; k++) { /* From model V1 + V2*age + V3 + V3*V4 keeps V1 + V3 = 2 only */ + for (j=-1; (j < maxncov); j++) Ndum[j]=0; + if(Dummy[k]==0 && Typevar[k] !=1){ /* Dummy covariate and not age product */ + switch(Fixed[k]) { + case 0: /* Testing on fixed dummy covariate, simple or product of fixed */ + for (i=1; i<=imx; i++) { /* Loop on individuals: reads the data file to get the maximum value of the modality of this covariate Vj*/ + ij=(int)(covar[Tvar[k]][i]); + /* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i + * If product of Vn*Vm, still boolean *: + * If it was coded 1, 2, 3, 4 should be splitted into 3 boolean variables + * 1 => 0 0 0, 2 => 0 0 1, 3 => 0 1 1, 4=1 0 0 */ + /* Finds for covariate j, n=Tvar[j] of Vn . ij is the + modality of the nth covariate of individual i. */ + if (ij > modmaxcovj) + modmaxcovj=ij; + else if (ij < modmincovj) + modmincovj=ij; + if ((ij < -1) && (ij > NCOVMAX)){ + printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX ); + exit(1); + }else + Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/ + /* If coded 1, 2, 3 , counts the number of 1 Ndum[1], number of 2, Ndum[2], etc */ + /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/ + /* getting the maximum value of the modality of the covariate + (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and + female ies 1, then modmaxcovj=1. + */ + } /* end for loop on individuals i */ + printf(" Minimal and maximal values of %d th (fixed) covariate V%d: min=%d max=%d \n", k, Tvar[k], modmincovj, modmaxcovj); + fprintf(ficlog," Minimal and maximal values of %d th (fixed) covariate V%d: min=%d max=%d \n", k, Tvar[k], modmincovj, modmaxcovj); + cptcode=modmaxcovj; + /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */ + /*for (i=0; i<=cptcode; i++) {*/ + for (j=modmincovj; j<=modmaxcovj; j++) { /* j=-1 ? 0 and 1*//* For each value j of the modality of model-cov k */ + printf("Frequencies of (fixed) covariate %d ie V%d with value %d: %d\n", k, Tvar[k], j, Ndum[j]); + fprintf(ficlog, "Frequencies of (fixed) covariate %d ie V%d with value %d: %d\n", k, Tvar[k], j, Ndum[j]); + if( Ndum[j] != 0 ){ /* Counts if nobody answered modality j ie empty modality, we skip it and reorder */ + if( j != -1){ + ncodemax[k]++; /* ncodemax[k]= Number of modalities of the k th + covariate for which somebody answered excluding + undefined. Usually 2: 0 and 1. */ + } + ncodemaxwundef[k]++; /* ncodemax[j]= Number of modalities of the k th + covariate for which somebody answered including + undefined. Usually 3: -1, 0 and 1. */ + } /* In fact ncodemax[k]=2 (dichotom. variables only) but it could be more for + * historical reasons: 3 if coded 1, 2, 3 and 4 and Ndum[2]=0 */ + } /* Ndum[-1] number of undefined modalities */ + + /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */ + /* For covariate j, modalities could be 1, 2, 3, 4, 5, 6, 7. */ + /* If Ndum[1]=0, Ndum[2]=0, Ndum[3]= 635, Ndum[4]=0, Ndum[5]=0, Ndum[6]=27, Ndum[7]=125; */ + /* modmincovj=3; modmaxcovj = 7; */ + /* There are only 3 modalities non empty 3, 6, 7 (or 2 if 27 is too few) : ncodemax[j]=3; */ + /* which will be coded 0, 1, 2 which in binary on 2=3-1 digits are 0=00 1=01, 2=10; */ + /* defining two dummy variables: variables V1_1 and V1_2.*/ + /* nbcode[Tvar[j]][ij]=k; */ + /* nbcode[Tvar[j]][1]=0; */ + /* nbcode[Tvar[j]][2]=1; */ + /* nbcode[Tvar[j]][3]=2; */ + /* To be continued (not working yet). */ + ij=0; /* ij is similar to i but can jump over null modalities */ + for (i=modmincovj; i<=modmaxcovj; i++) { /* i= 1 to 2 for dichotomous, or from 1 to 3 or from -1 or 0 to 1 currently*/ + if (Ndum[i] == 0) { /* If nobody responded to this modality k */ + break; + } + ij++; + nbcode[Tvar[k]][ij]=i; /* stores the original value of modality i in an array nbcode, ij modality from 1 to last non-nul modality. nbcode[1][1]=0 nbcode[1][2]=1*/ + cptcode = ij; /* New max modality for covar j */ + } /* end of loop on modality i=-1 to 1 or more */ + break; + case 1: /* Testing on varying covariate, could be simple and + * should look at waves or product of fixed * + * varying. No time to test -1, assuming 0 and 1 only */ + ij=0; + for(i=0; i<=1;i++){ + nbcode[Tvar[k]][++ij]=i; + } + break; + default: + break; + } /* end switch */ + } /* end dummy test */ + + /* for (k=0; k<= cptcode; k++) { /\* k=-1 ? k=0 to 1 *\//\* Could be 1 to 4 *\//\* cptcode=modmaxcovj *\/ */ + /* /\*recode from 0 *\/ */ + /* k is a modality. If we have model=V1+V1*sex */ + /* then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */ + /* But if some modality were not used, it is recoded from 0 to a newer modmaxcovj=cptcode *\/ */ + /* } */ + /* /\* cptcode = ij; *\/ /\* New max modality for covar j *\/ */ + /* if (ij > ncodemax[j]) { */ + /* printf( " Error ij=%d > ncodemax[%d]=%d\n", ij, j, ncodemax[j]); */ + /* fprintf(ficlog, " Error ij=%d > ncodemax[%d]=%d\n", ij, j, ncodemax[j]); */ + /* break; */ + /* } */ + /* } /\* end of loop on modality k *\/ */ + } /* end of loop on model-covariate j. nbcode[Tvarj][1]=0 and nbcode[Tvarj][2]=1 sets the value of covariate j*/ + + for (k=-1; k< maxncov; k++) Ndum[k]=0; + /* Look at fixed dummy (single or product) covariates to check empty modalities */ + for (i=1; i<=ncovmodel-2-nagesqr; i++) { /* -2, cste and age and eventually age*age */ + /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/ + ij=Tvar[i]; /* Tvar 5,4,3,6,5,7,1,4 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V4*age */ + Ndum[ij]++; /* Count the # of 1, 2 etc: {1,1,1,2,2,1,1} because V1 once, V2 once, two V4 and V5 in above */ + /* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, {2, 1, 1, 1, 2, 1, 1, 0, 0} */ + } /* V4+V3+V5, Ndum[1]@5={0, 0, 1, 1, 1} */ + + ij=0; + /* for (i=0; i<= maxncov-1; i++) { /\* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) *\/ */ + for (k=1; k<= cptcovt; k++) { /* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) */ + /*printf("Ndum[%d]=%d\n",i, Ndum[i]);*/ + /* if((Ndum[i]!=0) && (i<=ncovcol)){ /\* Tvar[i] <= ncovmodel ? *\/ */ + if(Ndum[Tvar[k]]!=0 && Dummy[k] == 0 && Typevar[k]==0){ /* Only Dummy and non empty in the model */ + /* If product not in single variable we don't print results */ + /*printf("diff Ndum[%d]=%d\n",i, Ndum[i]);*/ + ++ij;/* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, */ + Tvaraff[ij]=Tvar[k]; /* For printing combination *//* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, Tvar {5, 4, 3, 6, 5, 2, 7, 1, 1} Tvaraff={4, 3, 1} V4, V3, V1*/ + Tmodelind[ij]=k; /* Tmodelind: index in model of dummies Tmodelind[1]=2 V4: pos=2; V3: pos=3, V1=9 {2, 3, 9, ?, ?,} */ + TmodelInvind[ij]=Tvar[k]- ncovcol-nqv; /* Inverse TmodelInvind[2=V4]=2 second dummy varying cov (V4)4-1-1 {0, 2, 1, } TmodelInvind[3]=1 */ + if(Fixed[k]!=0) + anyvaryingduminmodel=1; + /* }else if((Ndum[i]!=0) && (i<=ncovcol+nqv)){ */ + /* Tvaraff[++ij]=-10; /\* Dont'n know how to treat quantitative variables yet *\/ */ + /* }else if((Ndum[i]!=0) && (i<=ncovcol+nqv+ntv)){ */ + /* Tvaraff[++ij]=i; /\*For printing (unclear) *\/ */ + /* }else if((Ndum[i]!=0) && (i<=ncovcol+nqv+ntv+nqtv)){ */ + /* Tvaraff[++ij]=-20; /\* Dont'n know how to treat quantitative variables yet *\/ */ + } + } /* Tvaraff[1]@5 {3, 4, -20, 0, 0} Very strange */ + /* ij--; */ + /* cptcoveff=ij; /\*Number of total covariates*\/ */ + *cptcov=ij; /*Number of total real effective covariates: effective + * because they can be excluded from the model and real + * if in the model but excluded because missing values, but how to get k from ij?*/ + for(j=ij+1; j<= cptcovt; j++){ + Tvaraff[j]=0; + Tmodelind[j]=0; + } + for(j=ntveff+1; j<= cptcovt; j++){ + TmodelInvind[j]=0; + } + /* To be sorted */ + ; } - ij--; - cptcoveff=ij; /*Number of total covariates*/ - -} /*********** Health Expectancies ****************/ -void evsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,char strstart[] ) + void evsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,char strstart[], int nres ) { /* Health expectancies, no variances */ - int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2; + int i, j, nhstepm, hstepm, h, nstepm; int nhstepma, nstepma; /* Decreasing with age */ double age, agelim, hf; double ***p3mat; double eip; - pstamp(ficreseij); + /* pstamp(ficreseij); */ fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n"); fprintf(ficreseij,"# Age"); for(i=1; i<=nlstate;i++){ @@ -2843,7 +5419,7 @@ void evsij(double ***eij, double x[], in /* Computed by stepm unit matrices, product of hstepma matrices, stored in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */ - hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij); + hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij, nres); hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */ @@ -2878,11 +5454,11 @@ void evsij(double ***eij, double x[], in } -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[] ) + 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[], int nres ) { /* Covariances of health expectancies eij and of total life expectancies according - to initial status i, ei. . + to initial status i, ei. . */ int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji; int nhstepma, nstepma; /* Decreasing with age */ @@ -2976,13 +5552,13 @@ void cvevsij(double ***eij, double x[], /* Typically if 20 years nstepm = 20*12/6=40 stepm */ /* if (stepm >= YEARM) hstepm=1;*/ nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */ - + /* If stepm=6 months */ /* Computed by stepm unit matrices, product of hstepma matrices, stored in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */ hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */ - + /* Computing Variances of health expectancies */ /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to decrease memory allocation */ @@ -2991,9 +5567,9 @@ void cvevsij(double ***eij, double x[], xp[i] = x[i] + (i==theta ?delti[theta]:0); xm[i] = x[i] - (i==theta ?delti[theta]:0); } - hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij); - hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij); - + hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij, nres); + hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij, nres); + for(j=1; j<= nlstate; j++){ for(i=1; i<=nlstate; i++){ for(h=0; h<=nhstepm-1; h++){ @@ -3002,7 +5578,7 @@ void cvevsij(double ***eij, double x[], } } } - + for(ij=1; ij<= nlstate*nlstate; ij++) for(h=0; h<=nhstepm-1; h++){ gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta]; @@ -3015,14 +5591,14 @@ void cvevsij(double ***eij, double x[], for(theta=1; theta <=npar; theta++) trgradg[h][j][theta]=gradg[h][theta][j]; - - for(ij=1;ij<=nlstate*nlstate;ij++) + + for(ij=1;ij<=nlstate*nlstate;ij++) for(ji=1;ji<=nlstate*nlstate;ji++) varhe[ij][ji][(int)age] =0.; - - printf("%d|",(int)age);fflush(stdout); - fprintf(ficlog,"%d|",(int)age);fflush(ficlog); - for(h=0;h<=nhstepm-1;h++){ + + printf("%d|",(int)age);fflush(stdout); + fprintf(ficlog,"%d|",(int)age);fflush(ficlog); + for(h=0;h<=nhstepm-1;h++){ for(k=0;k<=nhstepm-1;k++){ matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov); matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]); @@ -3031,18 +5607,18 @@ void cvevsij(double ***eij, double x[], varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf; } } - + /* Computing expectancies */ - hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij); + hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij,nres); for(i=1; i<=nlstate;i++) for(j=1; j<=nlstate;j++) for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){ eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf; - + /* 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]);*/ - + } - + fprintf(ficresstdeij,"%3.0f",age ); for(i=1; i<=nlstate;i++){ eip=0.; @@ -3056,7 +5632,7 @@ void cvevsij(double ***eij, double x[], fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip)); } fprintf(ficresstdeij,"\n"); - + fprintf(ficrescveij,"%3.0f",age ); for(i=1; i<=nlstate;i++) for(j=1; j<=nlstate;j++){ @@ -3069,7 +5645,7 @@ void cvevsij(double ***eij, double x[], } } fprintf(ficrescveij,"\n"); - + } free_matrix(gm,0,nhstepm,1,nlstate*nlstate); free_matrix(gp,0,nhstepm,1,nlstate*nlstate); @@ -3079,336 +5655,356 @@ void cvevsij(double ***eij, double x[], free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); printf("\n"); fprintf(ficlog,"\n"); - + free_vector(xm,1,npar); free_vector(xp,1,npar); free_matrix(dnewm,1,nlstate*nlstate,1,npar); free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate); free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage); } - -/************ Variance ******************/ -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[]) -{ - /* Variance of health expectancies */ - /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/ - /* double **newm;*/ - double **dnewm,**doldm; - double **dnewmp,**doldmp; - int i, j, nhstepm, hstepm, h, nstepm ; - int k, cptcode; - double *xp; - double **gp, **gm; /* for var eij */ - double ***gradg, ***trgradg; /*for var eij */ - double **gradgp, **trgradgp; /* for var p point j */ - double *gpp, *gmp; /* for var p point j */ - double **varppt; /* for var p point j nlstate to nlstate+ndeath */ - double ***p3mat; - double age,agelim, hf; - double ***mobaverage; - int theta; - char digit[4]; - char digitp[25]; - - char fileresprobmorprev[FILENAMELENGTH]; - - if(popbased==1){ - if(mobilav!=0) - strcpy(digitp,"-populbased-mobilav-"); - else strcpy(digitp,"-populbased-nomobil-"); - } - else - strcpy(digitp,"-stablbased-"); - - if (mobilav!=0) { - mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); - if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){ - fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav); - printf(" Error in movingaverage mobilav=%d\n",mobilav); - } - } - - strcpy(fileresprobmorprev,"prmorprev"); - sprintf(digit,"%-d",ij); - /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/ - strcat(fileresprobmorprev,digit); /* Tvar to be done */ - strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */ - strcat(fileresprobmorprev,fileres); - if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) { - printf("Problem with resultfile: %s\n", fileresprobmorprev); - fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev); - } - printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev); - fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev); - pstamp(ficresprobmorprev); - 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); - fprintf(ficresprobmorprev,"# Age cov=%-d",ij); - for(j=nlstate+1; j<=(nlstate+ndeath);j++){ - fprintf(ficresprobmorprev," p.%-d SE",j); - for(i=1; i<=nlstate;i++) - fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j); - } - fprintf(ficresprobmorprev,"\n"); - fprintf(ficgp,"\n# Routine varevsij"); - /* fprintf(fichtm, "#Local time at start: %s", strstart);*/ - fprintf(fichtm,"\n

  • Computing probabilities of dying over estepm months as a weighted average (i.e global mortality independent of initial healh state)

    • \n"); - fprintf(fichtm,"\n
    %s
    \n",digitp); -/* } */ - varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath); - pstamp(ficresvij); - fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n# (weighted average of eij where weights are "); - if(popbased==1) - 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); - else - fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n"); - fprintf(ficresvij,"# Age"); - for(i=1; i<=nlstate;i++) - for(j=1; j<=nlstate;j++) - fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j); - fprintf(ficresvij,"\n"); - - xp=vector(1,npar); - dnewm=matrix(1,nlstate,1,npar); - doldm=matrix(1,nlstate,1,nlstate); - dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar); - doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath); - - gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath); - gpp=vector(nlstate+1,nlstate+ndeath); - gmp=vector(nlstate+1,nlstate+ndeath); - trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/ - - if(estepm < stepm){ - printf ("Problem %d lower than %d\n",estepm, stepm); - } - else hstepm=estepm; - /* For example we decided to compute the life expectancy with the smallest unit */ - /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. - nhstepm is the number of hstepm from age to agelim - nstepm is the number of stepm from age to agelin. - Look at function hpijx to understand why (it is linked to memory size questions) */ - /* We decided (b) to get a life expectancy respecting the most precise curvature of the - survival function given by stepm (the optimization length). Unfortunately it - means that if the survival funtion is printed every two years of age and if - you sum them up and add 1 year (area under the trapezoids) you won't get the same - results. So we changed our mind and took the option of the best precision. - */ - hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ - agelim = AGESUP; - for (age=bage; age<=fage; age ++){ /* If stepm=6 months */ - nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ - nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */ - p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); - gradg=ma3x(0,nhstepm,1,npar,1,nlstate); - gp=matrix(0,nhstepm,1,nlstate); - gm=matrix(0,nhstepm,1,nlstate); - - - for(theta=1; theta <=npar; theta++){ - for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/ - xp[i] = x[i] + (i==theta ?delti[theta]:0); - } - hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij); - prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij); - - if (popbased==1) { - if(mobilav ==0){ - for(i=1; i<=nlstate;i++) - prlim[i][i]=probs[(int)age][i][ij]; - }else{ /* mobilav */ - for(i=1; i<=nlstate;i++) - prlim[i][i]=mobaverage[(int)age][i][ij]; - } - } - - for(j=1; j<= nlstate; j++){ - for(h=0; h<=nhstepm; h++){ - for(i=1, gp[h][j]=0.;i<=nlstate;i++) - gp[h][j] += prlim[i][i]*p3mat[i][j][h]; - } - } - /* This for computing probability of death (h=1 means - computed over hstepm matrices product = hstepm*stepm months) - as a weighted average of prlim. - */ - for(j=nlstate+1;j<=nlstate+ndeath;j++){ - for(i=1,gpp[j]=0.; i<= nlstate; i++) - gpp[j] += prlim[i][i]*p3mat[i][j][1]; - } - /* end probability of death */ - - for(i=1; i<=npar; i++) /* Computes gradient x - delta */ - xp[i] = x[i] - (i==theta ?delti[theta]:0); - hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij); - prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij); - - if (popbased==1) { - if(mobilav ==0){ - for(i=1; i<=nlstate;i++) - prlim[i][i]=probs[(int)age][i][ij]; - }else{ /* mobilav */ - for(i=1; i<=nlstate;i++) - prlim[i][i]=mobaverage[(int)age][i][ij]; - } - } - - for(j=1; j<= nlstate; j++){ /* Sum of wi * eij = e.j */ - for(h=0; h<=nhstepm; h++){ - for(i=1, gm[h][j]=0.;i<=nlstate;i++) - gm[h][j] += prlim[i][i]*p3mat[i][j][h]; - } - } - /* This for computing probability of death (h=1 means - computed over hstepm matrices product = hstepm*stepm months) - as a weighted average of prlim. - */ - for(j=nlstate+1;j<=nlstate+ndeath;j++){ - for(i=1,gmp[j]=0.; i<= nlstate; i++) - gmp[j] += prlim[i][i]*p3mat[i][j][1]; - } - /* end probability of death */ - - for(j=1; j<= nlstate; j++) /* vareij */ - for(h=0; h<=nhstepm; h++){ - gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta]; - } - - for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */ - gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta]; - } - - } /* End theta */ - - trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */ - - for(h=0; h<=nhstepm; h++) /* veij */ - for(j=1; j<=nlstate;j++) - for(theta=1; theta <=npar; theta++) - trgradg[h][j][theta]=gradg[h][theta][j]; - - for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */ - for(theta=1; theta <=npar; theta++) - trgradgp[j][theta]=gradgp[theta][j]; - - - hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */ - for(i=1;i<=nlstate;i++) - for(j=1;j<=nlstate;j++) - vareij[i][j][(int)age] =0.; +/************ Variance ******************/ + 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 *ncvyearp, int ij, int estepm, int cptcov, int cptcod, int popbased, int mobilav, char strstart[], int nres) + { + /* Variance of health expectancies */ + /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/ + /* double **newm;*/ + /* int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav)*/ + + /* int movingaverage(); */ + double **dnewm,**doldm; + double **dnewmp,**doldmp; + int i, j, nhstepm, hstepm, h, nstepm ; + int k; + double *xp; + double **gp, **gm; /* for var eij */ + double ***gradg, ***trgradg; /*for var eij */ + double **gradgp, **trgradgp; /* for var p point j */ + double *gpp, *gmp; /* for var p point j */ + double **varppt; /* for var p point j nlstate to nlstate+ndeath */ + double ***p3mat; + double age,agelim, hf; + /* double ***mobaverage; */ + int theta; + char digit[4]; + char digitp[25]; + + char fileresprobmorprev[FILENAMELENGTH]; + + if(popbased==1){ + if(mobilav!=0) + strcpy(digitp,"-POPULBASED-MOBILAV_"); + else strcpy(digitp,"-POPULBASED-NOMOBIL_"); + } + else + strcpy(digitp,"-STABLBASED_"); - for(h=0;h<=nhstepm;h++){ - for(k=0;k<=nhstepm;k++){ - matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov); - matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]); - for(i=1;i<=nlstate;i++) - for(j=1;j<=nlstate;j++) - vareij[i][j][(int)age] += doldm[i][j]*hf*hf; - } - } + /* if (mobilav!=0) { */ + /* mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */ + /* if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){ */ + /* fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav); */ + /* printf(" Error in movingaverage mobilav=%d\n",mobilav); */ + /* } */ + /* } */ + + strcpy(fileresprobmorprev,"PRMORPREV-"); + sprintf(digit,"%-d",ij); + /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/ + strcat(fileresprobmorprev,digit); /* Tvar to be done */ + strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */ + strcat(fileresprobmorprev,fileresu); + if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) { + printf("Problem with resultfile: %s\n", fileresprobmorprev); + fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev); + } + printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev); + fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev); + pstamp(ficresprobmorprev); + 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); + fprintf(ficresprobmorprev,"# Selected quantitative variables and dummies"); + for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */ + fprintf(ficresprobmorprev," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]); + } + for(j=1;j<=cptcoveff;j++) + fprintf(ficresprobmorprev,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(ij,j)]); + fprintf(ficresprobmorprev,"\n"); + + fprintf(ficresprobmorprev,"# Age cov=%-d",ij); + for(j=nlstate+1; j<=(nlstate+ndeath);j++){ + fprintf(ficresprobmorprev," p.%-d SE",j); + for(i=1; i<=nlstate;i++) + fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j); + } + fprintf(ficresprobmorprev,"\n"); + + fprintf(ficgp,"\n# Routine varevsij"); + fprintf(ficgp,"\nunset title \n"); + /* fprintf(fichtm, "#Local time at start: %s", strstart);*/ + fprintf(fichtm,"\n

  • Computing probabilities of dying over estepm months as a weighted average (i.e global mortality independent of initial healh state)

    • \n"); + fprintf(fichtm,"\n
    %s
    \n",digitp); + /* } */ + varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath); + pstamp(ficresvij); + fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n# (weighted average of eij where weights are "); + if(popbased==1) + 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); + else + fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n"); + fprintf(ficresvij,"# Age"); + for(i=1; i<=nlstate;i++) + for(j=1; j<=nlstate;j++) + fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j); + fprintf(ficresvij,"\n"); + + xp=vector(1,npar); + dnewm=matrix(1,nlstate,1,npar); + doldm=matrix(1,nlstate,1,nlstate); + dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar); + doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath); + + gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath); + gpp=vector(nlstate+1,nlstate+ndeath); + gmp=vector(nlstate+1,nlstate+ndeath); + trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/ - /* pptj */ - matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov); - matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp); - for(j=nlstate+1;j<=nlstate+ndeath;j++) - for(i=nlstate+1;i<=nlstate+ndeath;i++) - varppt[j][i]=doldmp[j][i]; - /* end ppptj */ - /* x centered again */ - hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij); - prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij); - - if (popbased==1) { - if(mobilav ==0){ - for(i=1; i<=nlstate;i++) - prlim[i][i]=probs[(int)age][i][ij]; - }else{ /* mobilav */ - for(i=1; i<=nlstate;i++) - prlim[i][i]=mobaverage[(int)age][i][ij]; - } - } - - /* This for computing probability of death (h=1 means - computed over hstepm (estepm) matrices product = hstepm*stepm months) - as a weighted average of prlim. + if(estepm < stepm){ + printf ("Problem %d lower than %d\n",estepm, stepm); + } + else hstepm=estepm; + /* For example we decided to compute the life expectancy with the smallest unit */ + /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. + nhstepm is the number of hstepm from age to agelim + nstepm is the number of stepm from age to agelim. + Look at function hpijx to understand why because of memory size limitations, + we decided (b) to get a life expectancy respecting the most precise curvature of the + survival function given by stepm (the optimization length). Unfortunately it + means that if the survival funtion is printed every two years of age and if + you sum them up and add 1 year (area under the trapezoids) you won't get the same + results. So we changed our mind and took the option of the best precision. + */ + hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ + agelim = AGESUP; + for (age=bage; age<=fage; age ++){ /* If stepm=6 months */ + nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ + nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */ + p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); + gradg=ma3x(0,nhstepm,1,npar,1,nlstate); + gp=matrix(0,nhstepm,1,nlstate); + gm=matrix(0,nhstepm,1,nlstate); + + + for(theta=1; theta <=npar; theta++){ + for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/ + xp[i] = x[i] + (i==theta ?delti[theta]:0); + } + + prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij, nres); + + if (popbased==1) { + if(mobilav ==0){ + for(i=1; i<=nlstate;i++) + prlim[i][i]=probs[(int)age][i][ij]; + }else{ /* mobilav */ + for(i=1; i<=nlstate;i++) + prlim[i][i]=mobaverage[(int)age][i][ij]; + } + } + + hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij,nres); /* Returns p3mat[i][j][h] for h=1 to nhstepm */ + for(j=1; j<= nlstate; j++){ + for(h=0; h<=nhstepm; h++){ + for(i=1, gp[h][j]=0.;i<=nlstate;i++) + gp[h][j] += prlim[i][i]*p3mat[i][j][h]; + } + } + /* Next for computing probability of death (h=1 means + computed over hstepm matrices product = hstepm*stepm months) + as a weighted average of prlim. + */ + for(j=nlstate+1;j<=nlstate+ndeath;j++){ + for(i=1,gpp[j]=0.; i<= nlstate; i++) + gpp[j] += prlim[i][i]*p3mat[i][j][1]; + } + /* end probability of death */ + + for(i=1; i<=npar; i++) /* Computes gradient x - delta */ + xp[i] = x[i] - (i==theta ?delti[theta]:0); + + prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp, ij, nres); + + if (popbased==1) { + if(mobilav ==0){ + for(i=1; i<=nlstate;i++) + prlim[i][i]=probs[(int)age][i][ij]; + }else{ /* mobilav */ + for(i=1; i<=nlstate;i++) + prlim[i][i]=mobaverage[(int)age][i][ij]; + } + } + + hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij,nres); + + for(j=1; j<= nlstate; j++){ /* Sum of wi * eij = e.j */ + for(h=0; h<=nhstepm; h++){ + for(i=1, gm[h][j]=0.;i<=nlstate;i++) + gm[h][j] += prlim[i][i]*p3mat[i][j][h]; + } + } + /* This for computing probability of death (h=1 means + computed over hstepm matrices product = hstepm*stepm months) + as a weighted average of prlim. + */ + for(j=nlstate+1;j<=nlstate+ndeath;j++){ + for(i=1,gmp[j]=0.; i<= nlstate; i++) + gmp[j] += prlim[i][i]*p3mat[i][j][1]; + } + /* end probability of death */ + + for(j=1; j<= nlstate; j++) /* vareij */ + for(h=0; h<=nhstepm; h++){ + gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta]; + } + + for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */ + gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta]; + } + + } /* End theta */ + + trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */ + + for(h=0; h<=nhstepm; h++) /* veij */ + for(j=1; j<=nlstate;j++) + for(theta=1; theta <=npar; theta++) + trgradg[h][j][theta]=gradg[h][theta][j]; + + for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */ + for(theta=1; theta <=npar; theta++) + trgradgp[j][theta]=gradgp[theta][j]; + + + hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */ + for(i=1;i<=nlstate;i++) + for(j=1;j<=nlstate;j++) + vareij[i][j][(int)age] =0.; + + for(h=0;h<=nhstepm;h++){ + for(k=0;k<=nhstepm;k++){ + matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov); + matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]); + for(i=1;i<=nlstate;i++) + for(j=1;j<=nlstate;j++) + vareij[i][j][(int)age] += doldm[i][j]*hf*hf; + } + } + + /* pptj */ + matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov); + matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp); + for(j=nlstate+1;j<=nlstate+ndeath;j++) + for(i=nlstate+1;i<=nlstate+ndeath;i++) + varppt[j][i]=doldmp[j][i]; + /* end ppptj */ + /* x centered again */ + + prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ncvyearp,ij, nres); + + if (popbased==1) { + if(mobilav ==0){ + for(i=1; i<=nlstate;i++) + prlim[i][i]=probs[(int)age][i][ij]; + }else{ /* mobilav */ + for(i=1; i<=nlstate;i++) + prlim[i][i]=mobaverage[(int)age][i][ij]; + } + } + + /* This for computing probability of death (h=1 means + computed over hstepm (estepm) matrices product = hstepm*stepm months) + as a weighted average of prlim. + */ + hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij, nres); + for(j=nlstate+1;j<=nlstate+ndeath;j++){ + for(i=1,gmp[j]=0.;i<= nlstate; i++) + gmp[j] += prlim[i][i]*p3mat[i][j][1]; + } + /* end probability of death */ + + fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij); + for(j=nlstate+1; j<=(nlstate+ndeath);j++){ + fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j])); + for(i=1; i<=nlstate;i++){ + fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]); + } + } + fprintf(ficresprobmorprev,"\n"); + + fprintf(ficresvij,"%.0f ",age ); + for(i=1; i<=nlstate;i++) + for(j=1; j<=nlstate;j++){ + fprintf(ficresvij," %.4f", vareij[i][j][(int)age]); + } + fprintf(ficresvij,"\n"); + free_matrix(gp,0,nhstepm,1,nlstate); + free_matrix(gm,0,nhstepm,1,nlstate); + free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate); + free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar); + free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); + } /* End age */ + free_vector(gpp,nlstate+1,nlstate+ndeath); + free_vector(gmp,nlstate+1,nlstate+ndeath); + free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath); + free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/ + /* fprintf(ficgp,"\nunset parametric;unset label; set ter png small size 320, 240"); */ + fprintf(ficgp,"\nunset parametric;unset label; set ter svg size 640, 480"); + /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */ + fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";"); + fprintf(ficgp,"\nset out \"%s%s.svg\";",subdirf3(optionfilefiname,"VARMUPTJGR-",digitp),digit); + /* fprintf(ficgp,"\n plot \"%s\" u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */ + /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */ + /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */ + fprintf(ficgp,"\n plot \"%s\" u 1:($3) not w l lt 1 ",subdirf(fileresprobmorprev)); + fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)) t \"95%% interval\" w l lt 2 ",subdirf(fileresprobmorprev)); + fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)) not w l lt 2 ",subdirf(fileresprobmorprev)); + fprintf(fichtm,"\n
    File (multiple files are possible if covariates are present): %s\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev)); + fprintf(fichtm,"\n
    Probability is computed over estepm=%d months.

    \n", estepm,subdirf3(optionfilefiname,"VARMUPTJGR-",digitp),digit); + /* 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

    \n", stepm,YEARM,digitp,digit); */ - for(j=nlstate+1;j<=nlstate+ndeath;j++){ - for(i=1,gmp[j]=0.;i<= nlstate; i++) - gmp[j] += prlim[i][i]*p3mat[i][j][1]; - } - /* end probability of death */ - - fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij); - for(j=nlstate+1; j<=(nlstate+ndeath);j++){ - fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j])); - for(i=1; i<=nlstate;i++){ - fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]); - } - } - fprintf(ficresprobmorprev,"\n"); + /* fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.svg\";replot;",digitp,optionfilefiname,digit); */ + fprintf(ficgp,"\nset out;\nset out \"%s%s.svg\";replot;set out;\n",subdirf3(optionfilefiname,"VARMUPTJGR-",digitp),digit); - fprintf(ficresvij,"%.0f ",age ); - for(i=1; i<=nlstate;i++) - for(j=1; j<=nlstate;j++){ - fprintf(ficresvij," %.4f", vareij[i][j][(int)age]); - } - fprintf(ficresvij,"\n"); - free_matrix(gp,0,nhstepm,1,nlstate); - free_matrix(gm,0,nhstepm,1,nlstate); - free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate); - free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar); - free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); - } /* End age */ - free_vector(gpp,nlstate+1,nlstate+ndeath); - free_vector(gmp,nlstate+1,nlstate+ndeath); - free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath); - free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/ - fprintf(ficgp,"\nunset parametric;unset label; set ter png small size 320, 240"); - /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */ - fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";"); -/* fprintf(ficgp,"\n plot \"%s\" u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */ -/* fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */ -/* fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */ - fprintf(ficgp,"\n plot \"%s\" u 1:($3) not w l lt 1 ",subdirf(fileresprobmorprev)); - fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)) t \"95\%% interval\" w l lt 2 ",subdirf(fileresprobmorprev)); - fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)) not w l lt 2 ",subdirf(fileresprobmorprev)); - fprintf(fichtm,"\n
    File (multiple files are possible if covariates are present): %s\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev)); - fprintf(fichtm,"\n
    Probability is computed over estepm=%d months.

    \n", estepm,subdirf3(optionfilefiname,"varmuptjgr",digitp),digit); - /* 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

    \n", stepm,YEARM,digitp,digit); -*/ -/* fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */ - fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit); - - free_vector(xp,1,npar); - free_matrix(doldm,1,nlstate,1,nlstate); - free_matrix(dnewm,1,nlstate,1,npar); - free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath); - free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar); - free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath); - if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); - fclose(ficresprobmorprev); - fflush(ficgp); - fflush(fichtm); -} /* end varevsij */ + free_vector(xp,1,npar); + free_matrix(doldm,1,nlstate,1,nlstate); + free_matrix(dnewm,1,nlstate,1,npar); + free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath); + free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar); + free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath); + /* if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */ + fclose(ficresprobmorprev); + fflush(ficgp); + fflush(fichtm); + } /* end varevsij */ /************ Variance of prevlim ******************/ -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[]) + 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 *ncvyearp, int ij, char strstart[], int nres) { - /* Variance of prevalence limit */ + /* Variance of prevalence limit for each state ij using current parameters x[] and estimates of neighbourhood give by delti*/ /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/ - double **newm; + double **dnewm,**doldm; int i, j, nhstepm, hstepm; - int k, cptcode; double *xp; double *gp, *gm; double **gradg, **trgradg; + double **mgm, **mgp; double age,agelim; int theta; pstamp(ficresvpl); fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n"); - fprintf(ficresvpl,"# Age"); + fprintf(ficresvpl,"# Age "); + if(nresult >=1) + fprintf(ficresvpl," Result# "); for(i=1; i<=nlstate;i++) fprintf(ficresvpl," %1d-%1d",i,i); fprintf(ficresvpl,"\n"); @@ -3425,6 +6021,8 @@ void varprevlim(char fileres[], double * if (stepm >= YEARM) hstepm=1; nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */ gradg=matrix(1,npar,1,nlstate); + mgp=matrix(1,npar,1,nlstate); + mgm=matrix(1,npar,1,nlstate); gp=vector(1,nlstate); gm=vector(1,nlstate); @@ -3432,18 +6030,27 @@ void varprevlim(char fileres[], double * for(i=1; i<=npar; i++){ /* Computes gradient */ xp[i] = x[i] + (i==theta ?delti[theta]:0); } - prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij); - for(i=1;i<=nlstate;i++) + if((int)age==79 ||(int)age== 80 ||(int)age== 81 ) + prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij,nres); + else + prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij,nres); + for(i=1;i<=nlstate;i++){ gp[i] = prlim[i][i]; - + mgp[theta][i] = prlim[i][i]; + } for(i=1; i<=npar; i++) /* Computes gradient */ xp[i] = x[i] - (i==theta ?delti[theta]:0); - prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij); - for(i=1;i<=nlstate;i++) + if((int)age==79 ||(int)age== 80 ||(int)age== 81 ) + prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij,nres); + else + prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij,nres); + for(i=1;i<=nlstate;i++){ gm[i] = prlim[i][i]; - + mgm[theta][i] = prlim[i][i]; + } for(i=1;i<=nlstate;i++) gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta]; + /* gradg[theta][2]= -gradg[theta][1]; */ /* For testing if nlstate=2 */ } /* End theta */ trgradg =matrix(1,nlstate,1,npar); @@ -3451,20 +6058,47 @@ void varprevlim(char fileres[], double * for(j=1; j<=nlstate;j++) for(theta=1; theta <=npar; theta++) trgradg[j][theta]=gradg[theta][j]; + /* if((int)age==79 ||(int)age== 80 ||(int)age== 81 ){ */ + /* printf("\nmgm mgp %d ",(int)age); */ + /* for(j=1; j<=nlstate;j++){ */ + /* printf(" %d ",j); */ + /* for(theta=1; theta <=npar; theta++) */ + /* printf(" %d %lf %lf",theta,mgm[theta][j],mgp[theta][j]); */ + /* printf("\n "); */ + /* } */ + /* } */ + /* if((int)age==79 ||(int)age== 80 ||(int)age== 81 ){ */ + /* printf("\n gradg %d ",(int)age); */ + /* for(j=1; j<=nlstate;j++){ */ + /* printf("%d ",j); */ + /* for(theta=1; theta <=npar; theta++) */ + /* printf("%d %lf ",theta,gradg[theta][j]); */ + /* printf("\n "); */ + /* } */ + /* } */ for(i=1;i<=nlstate;i++) varpl[i][(int)age] =0.; + if((int)age==79 ||(int)age== 80 ||(int)age== 81){ matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov); matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg); + }else{ + matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov); + matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg); + } for(i=1;i<=nlstate;i++) varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */ fprintf(ficresvpl,"%.0f ",age ); + if(nresult >=1) + fprintf(ficresvpl,"%d ",nres ); for(i=1; i<=nlstate;i++) fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age])); fprintf(ficresvpl,"\n"); free_vector(gp,1,nlstate); free_vector(gm,1,nlstate); + free_matrix(mgm,1,npar,1,nlstate); + free_matrix(mgp,1,npar,1,nlstate); free_matrix(gradg,1,npar,1,nlstate); free_matrix(trgradg,1,nlstate,1,npar); } /* End age */ @@ -3477,87 +6111,86 @@ void varprevlim(char fileres[], double * /************ Variance of one-step probabilities ******************/ 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[]) -{ - int i, j=0, i1, k1, l1, t, tj; - int k2, l2, j1, z1; - int k=0,l, cptcode; - int first=1, first1, first2; - double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp; - double **dnewm,**doldm; - double *xp; - double *gp, *gm; - double **gradg, **trgradg; - double **mu; - double age,agelim, cov[NCOVMAX+1]; - double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */ - int theta; - char fileresprob[FILENAMELENGTH]; - char fileresprobcov[FILENAMELENGTH]; - char fileresprobcor[FILENAMELENGTH]; - double ***varpij; - - strcpy(fileresprob,"prob"); - strcat(fileresprob,fileres); - if((ficresprob=fopen(fileresprob,"w"))==NULL) { - printf("Problem with resultfile: %s\n", fileresprob); - fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob); - } - strcpy(fileresprobcov,"probcov"); - strcat(fileresprobcov,fileres); - if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) { - printf("Problem with resultfile: %s\n", fileresprobcov); - fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov); - } - strcpy(fileresprobcor,"probcor"); - strcat(fileresprobcor,fileres); - if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) { - printf("Problem with resultfile: %s\n", fileresprobcor); - fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor); - } - printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob); - fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob); - printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov); - fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov); - printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor); - fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor); - pstamp(ficresprob); - fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n"); - fprintf(ficresprob,"# Age"); - pstamp(ficresprobcov); - fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n"); - fprintf(ficresprobcov,"# Age"); - pstamp(ficresprobcor); - fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n"); - fprintf(ficresprobcor,"# Age"); - - - for(i=1; i<=nlstate;i++) - for(j=1; j<=(nlstate+ndeath);j++){ - fprintf(ficresprob," p%1d-%1d (SE)",i,j); - fprintf(ficresprobcov," p%1d-%1d ",i,j); - fprintf(ficresprobcor," p%1d-%1d ",i,j); - } - /* fprintf(ficresprob,"\n"); - fprintf(ficresprobcov,"\n"); - fprintf(ficresprobcor,"\n"); - */ - xp=vector(1,npar); - dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar); - doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath)); - mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage); - varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage); - first=1; - fprintf(ficgp,"\n# Routine varprob"); - fprintf(fichtm,"\n

  • Computing and drawing one step probabilities with their confidence intervals

    • \n"); - fprintf(fichtm,"\n"); - - fprintf(fichtm,"\n

  • Matrix of variance-covariance of pairs of step probabilities (drawings)

    • \n",optionfilehtmcov); - fprintf(fichtmcov,"\n

    Matrix of variance-covariance of pairs of step probabilities

    \n\ - file %s
    \n",optionfilehtmcov); - fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (pij, pkl) are estimated\ + { + int i, j=0, k1, l1, tj; + int k2, l2, j1, z1; + int k=0, l; + int first=1, first1, first2; + double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp; + double **dnewm,**doldm; + double *xp; + double *gp, *gm; + double **gradg, **trgradg; + double **mu; + double age, cov[NCOVMAX+1]; + double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */ + int theta; + char fileresprob[FILENAMELENGTH]; + char fileresprobcov[FILENAMELENGTH]; + char fileresprobcor[FILENAMELENGTH]; + double ***varpij; + + strcpy(fileresprob,"PROB_"); + strcat(fileresprob,fileres); + if((ficresprob=fopen(fileresprob,"w"))==NULL) { + printf("Problem with resultfile: %s\n", fileresprob); + fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob); + } + strcpy(fileresprobcov,"PROBCOV_"); + strcat(fileresprobcov,fileresu); + if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) { + printf("Problem with resultfile: %s\n", fileresprobcov); + fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov); + } + strcpy(fileresprobcor,"PROBCOR_"); + strcat(fileresprobcor,fileresu); + if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) { + printf("Problem with resultfile: %s\n", fileresprobcor); + fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor); + } + printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob); + fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob); + printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov); + fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov); + printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor); + fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor); + pstamp(ficresprob); + fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n"); + fprintf(ficresprob,"# Age"); + pstamp(ficresprobcov); + fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n"); + fprintf(ficresprobcov,"# Age"); + pstamp(ficresprobcor); + fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n"); + fprintf(ficresprobcor,"# Age"); + + + for(i=1; i<=nlstate;i++) + for(j=1; j<=(nlstate+ndeath);j++){ + fprintf(ficresprob," p%1d-%1d (SE)",i,j); + fprintf(ficresprobcov," p%1d-%1d ",i,j); + fprintf(ficresprobcor," p%1d-%1d ",i,j); + } + /* fprintf(ficresprob,"\n"); + fprintf(ficresprobcov,"\n"); + fprintf(ficresprobcor,"\n"); + */ + xp=vector(1,npar); + dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar); + doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath)); + mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage); + varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage); + first=1; + fprintf(ficgp,"\n# Routine varprob"); + fprintf(fichtm,"\n

  • Computing and drawing one step probabilities with their confidence intervals

    • \n"); + fprintf(fichtm,"\n"); + + fprintf(fichtm,"\n

  • Matrix of variance-covariance of one-step probabilities (drawings)

    this page is important in order to visualize confidence intervals and especially correlation between disability and recovery, or more generally, way in and way back.
    • \n",optionfilehtmcov); + fprintf(fichtmcov,"Current page is file %s
    \n\n

    Matrix of variance-covariance of pairs of step probabilities

    \n",optionfilehtmcov, optionfilehtmcov); + fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (pij, pkl) are estimated \ and drawn. It helps understanding how is the covariance between two incidences.\ They are expressed in year-1 in order to be less dependent of stepm.
    \n"); - fprintf(fichtmcov,"\n
    Contour plot corresponding to x'cov-1x = 4 (where x is the column vector (pij,pkl)) are drawn. \ + fprintf(fichtmcov,"\n
    Contour plot corresponding to x'cov-1x = 4 (where x is the column vector (pij,pkl)) are drawn. \ It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \ would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \ standard deviations wide on each axis.
    \ @@ -3565,343 +6198,465 @@ standard deviations wide on each axis. < and made the appropriate rotation to look at the uncorrelated principal directions.
    \ To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.
    \n"); - cov[1]=1; - /* tj=cptcoveff; */ - tj = (int) pow(2,cptcoveff); - if (cptcovn<1) {tj=1;ncodemax[1]=1;} - j1=0; - for(j1=1; j1<=tj;j1++){ - /*for(i1=1; i1<=ncodemax[t];i1++){ */ - /*j1++;*/ - if (cptcovn>0) { - fprintf(ficresprob, "\n#********** Variable "); - for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]); - fprintf(ficresprob, "**********\n#\n"); - fprintf(ficresprobcov, "\n#********** Variable "); - for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]); - fprintf(ficresprobcov, "**********\n#\n"); - - fprintf(ficgp, "\n#********** Variable "); - for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]); - fprintf(ficgp, "**********\n#\n"); - - - fprintf(fichtmcov, "\n
    ********** Variable "); - for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]); - fprintf(fichtmcov, "**********\n
    "); - - fprintf(ficresprobcor, "\n#********** Variable "); - for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]); - fprintf(ficresprobcor, "**********\n#"); - } - - gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath)); - trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar); - gp=vector(1,(nlstate)*(nlstate+ndeath)); - gm=vector(1,(nlstate)*(nlstate+ndeath)); - for (age=bage; age<=fage; age ++){ - cov[2]=age; - for (k=1; k<=cptcovn;k++) { - cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];/* j1 1 2 3 4 - * 1 1 1 1 1 - * 2 2 1 1 1 - * 3 1 2 1 1 - */ - /* nbcode[1][1]=0 nbcode[1][2]=1;*/ - } - for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; - for (k=1; k<=cptcovprod;k++) - cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]]; - - - for(theta=1; theta <=npar; theta++){ - for(i=1; i<=npar; i++) - xp[i] = x[i] + (i==theta ?delti[theta]:(double)0); - - pmij(pmmij,cov,ncovmodel,xp,nlstate); - - k=0; - for(i=1; i<= (nlstate); i++){ - for(j=1; j<=(nlstate+ndeath);j++){ - k=k+1; - gp[k]=pmmij[i][j]; - } - } - - for(i=1; i<=npar; i++) - xp[i] = x[i] - (i==theta ?delti[theta]:(double)0); - - pmij(pmmij,cov,ncovmodel,xp,nlstate); - k=0; - for(i=1; i<=(nlstate); i++){ - for(j=1; j<=(nlstate+ndeath);j++){ - k=k+1; - gm[k]=pmmij[i][j]; - } - } - - for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) - gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta]; - } - - for(j=1; j<=(nlstate)*(nlstate+ndeath);j++) - for(theta=1; theta <=npar; theta++) - trgradg[j][theta]=gradg[theta][j]; - - matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov); - matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg); - - pmij(pmmij,cov,ncovmodel,x,nlstate); - - k=0; - for(i=1; i<=(nlstate); i++){ - for(j=1; j<=(nlstate+ndeath);j++){ - k=k+1; - mu[k][(int) age]=pmmij[i][j]; - } - } - for(i=1;i<=(nlstate)*(nlstate+ndeath);i++) - for(j=1;j<=(nlstate)*(nlstate+ndeath);j++) - varpij[i][j][(int)age] = doldm[i][j]; - - /*printf("\n%d ",(int)age); - for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){ - printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i])); - fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i])); - }*/ - - fprintf(ficresprob,"\n%d ",(int)age); - fprintf(ficresprobcov,"\n%d ",(int)age); - fprintf(ficresprobcor,"\n%d ",(int)age); - - for (i=1; i<=(nlstate)*(nlstate+ndeath);i++) - fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age])); - for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){ - fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]); - fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]); - } - i=0; - for (k=1; k<=(nlstate);k++){ - for (l=1; l<=(nlstate+ndeath);l++){ - i++; - fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l); - fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l); - for (j=1; j<=i;j++){ - /* printf(" k=%d l=%d i=%d j=%d\n",k,l,i,j);fflush(stdout); */ - fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]); - fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age])); - } - } - }/* end of loop for state */ - } /* end of loop for age */ - free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath)); - free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath)); - free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar); - free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar); - - /* Confidence intervalle of pij */ - /* - fprintf(ficgp,"\nunset parametric;unset label"); - fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\""); - fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65"); - fprintf(fichtm,"\n
    Probability with confidence intervals expressed in year-1 :pijgr%s.png, ",optionfilefiname,optionfilefiname); - fprintf(fichtm,"\n
    ",optionfilefiname); - fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname); - fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob); - */ - - /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/ - first1=1;first2=2; - for (k2=1; k2<=(nlstate);k2++){ - for (l2=1; l2<=(nlstate+ndeath);l2++){ - if(l2==k2) continue; - j=(k2-1)*(nlstate+ndeath)+l2; - for (k1=1; k1<=(nlstate);k1++){ - for (l1=1; l1<=(nlstate+ndeath);l1++){ - if(l1==k1) continue; - i=(k1-1)*(nlstate+ndeath)+l1; - if(i<=j) continue; - for (age=bage; age<=fage; age ++){ - if ((int)age %5==0){ - v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM; - v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM; - cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM; - mu1=mu[i][(int) age]/stepm*YEARM ; - mu2=mu[j][(int) age]/stepm*YEARM; - c12=cv12/sqrt(v1*v2); - /* Computing eigen value of matrix of covariance */ - lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.; - lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.; - if ((lc2 <0) || (lc1 <0) ){ - if(first2==1){ - first1=0; - 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); - } - 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); - /* lc1=fabs(lc1); */ /* If we want to have them positive */ - /* lc2=fabs(lc2); */ - } + cov[1]=1; + /* tj=cptcoveff; */ + tj = (int) pow(2,cptcoveff); + if (cptcovn<1) {tj=1;ncodemax[1]=1;} + j1=0; + for(j1=1; j1<=tj;j1++){ /* For each valid combination of covariates or only once*/ + if (cptcovn>0) { + fprintf(ficresprob, "\n#********** Variable "); + for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]); + fprintf(ficresprob, "**********\n#\n"); + fprintf(ficresprobcov, "\n#********** Variable "); + for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]); + fprintf(ficresprobcov, "**********\n#\n"); + + fprintf(ficgp, "\n#********** Variable "); + for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]); + fprintf(ficgp, "**********\n#\n"); + + + fprintf(fichtmcov, "\n
    ********** Variable "); + for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]); + fprintf(fichtmcov, "**********\n
    "); + + fprintf(ficresprobcor, "\n#********** Variable "); + for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]); + fprintf(ficresprobcor, "**********\n#"); + if(invalidvarcomb[j1]){ + fprintf(ficgp,"\n#Combination (%d) ignored because no cases \n",j1); + fprintf(fichtmcov,"\n

    Combination (%d) ignored because no cases

    \n",j1); + continue; + } + } + gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath)); + trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar); + gp=vector(1,(nlstate)*(nlstate+ndeath)); + gm=vector(1,(nlstate)*(nlstate+ndeath)); + for (age=bage; age<=fage; age ++){ + cov[2]=age; + if(nagesqr==1) + cov[3]= age*age; + for (k=1; k<=cptcovn;k++) { + cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(j1,k)]; + /*cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(j1,Tvar[k])];*//* j1 1 2 3 4 + * 1 1 1 1 1 + * 2 2 1 1 1 + * 3 1 2 1 1 + */ + /* nbcode[1][1]=0 nbcode[1][2]=1;*/ + } + /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */ + for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2]; + for (k=1; k<=cptcovprod;k++) + cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)]; + + + for(theta=1; theta <=npar; theta++){ + for(i=1; i<=npar; i++) + xp[i] = x[i] + (i==theta ?delti[theta]:(double)0); + + pmij(pmmij,cov,ncovmodel,xp,nlstate); + + k=0; + for(i=1; i<= (nlstate); i++){ + for(j=1; j<=(nlstate+ndeath);j++){ + k=k+1; + gp[k]=pmmij[i][j]; + } + } + + for(i=1; i<=npar; i++) + xp[i] = x[i] - (i==theta ?delti[theta]:(double)0); + + pmij(pmmij,cov,ncovmodel,xp,nlstate); + k=0; + for(i=1; i<=(nlstate); i++){ + for(j=1; j<=(nlstate+ndeath);j++){ + k=k+1; + gm[k]=pmmij[i][j]; + } + } + + for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) + gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta]; + } - /* Eigen vectors */ - v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12)); - /*v21=sqrt(1.-v11*v11); *//* error */ - v21=(lc1-v1)/cv12*v11; - v12=-v21; - v22=v11; - tnalp=v21/v11; - if(first1==1){ - first1=0; - 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); - } - 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); - /*printf(fignu*/ - /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */ - /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */ - if(first==1){ - first=0; - fprintf(ficgp,"\nset parametric;unset label"); - 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); - fprintf(ficgp,"\nset ter png small size 320, 240"); - fprintf(fichtmcov,"\n
    Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year-1\ - :\ -%s%d%1d%1d-%1d%1d.png, ",k1,l1,k2,l2,\ - subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\ - subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2); - fprintf(fichtmcov,"\n
    ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2); - fprintf(fichtmcov,"\n
    Correlation at age %d (%.3f),",(int) age, c12); - fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2); - fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2); - fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2); - 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",\ - mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\ - mu2,std,v21,sqrt(lc1),v22,sqrt(lc2)); - }else{ - first=0; - fprintf(fichtmcov," %d (%.3f),",(int) age, c12); - fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2); - fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2); - 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",\ - mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\ - mu2,std,v21,sqrt(lc1),v22,sqrt(lc2)); - }/* if first */ - } /* age mod 5 */ - } /* end loop age */ - fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2); - first=1; - } /*l12 */ - } /* k12 */ - } /*l1 */ - }/* k1 */ - /* } /* loop covariates */ - } - free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage); - free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage); - free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath)); - free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar); - free_vector(xp,1,npar); - fclose(ficresprob); - fclose(ficresprobcov); - fclose(ficresprobcor); - fflush(ficgp); - fflush(fichtmcov); -} + for(j=1; j<=(nlstate)*(nlstate+ndeath);j++) + for(theta=1; theta <=npar; theta++) + trgradg[j][theta]=gradg[theta][j]; + + matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov); + matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg); + + pmij(pmmij,cov,ncovmodel,x,nlstate); + + k=0; + for(i=1; i<=(nlstate); i++){ + for(j=1; j<=(nlstate+ndeath);j++){ + k=k+1; + mu[k][(int) age]=pmmij[i][j]; + } + } + for(i=1;i<=(nlstate)*(nlstate+ndeath);i++) + for(j=1;j<=(nlstate)*(nlstate+ndeath);j++) + varpij[i][j][(int)age] = doldm[i][j]; + + /*printf("\n%d ",(int)age); + for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){ + printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i])); + fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i])); + }*/ + + fprintf(ficresprob,"\n%d ",(int)age); + fprintf(ficresprobcov,"\n%d ",(int)age); + fprintf(ficresprobcor,"\n%d ",(int)age); + + for (i=1; i<=(nlstate)*(nlstate+ndeath);i++) + fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age])); + for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){ + fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]); + fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]); + } + i=0; + for (k=1; k<=(nlstate);k++){ + for (l=1; l<=(nlstate+ndeath);l++){ + i++; + fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l); + fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l); + for (j=1; j<=i;j++){ + /* printf(" k=%d l=%d i=%d j=%d\n",k,l,i,j);fflush(stdout); */ + fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]); + fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age])); + } + } + }/* end of loop for state */ + } /* end of loop for age */ + free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath)); + free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath)); + free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar); + free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar); + + /* Confidence intervalle of pij */ + /* + fprintf(ficgp,"\nunset parametric;unset label"); + fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\""); + fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65"); + fprintf(fichtm,"\n
    Probability with confidence intervals expressed in year-1 :pijgr%s.png, ",optionfilefiname,optionfilefiname); + fprintf(fichtm,"\n
    ",optionfilefiname); + fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname); + fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob); + */ + + /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/ + first1=1;first2=2; + for (k2=1; k2<=(nlstate);k2++){ + for (l2=1; l2<=(nlstate+ndeath);l2++){ + if(l2==k2) continue; + j=(k2-1)*(nlstate+ndeath)+l2; + for (k1=1; k1<=(nlstate);k1++){ + for (l1=1; l1<=(nlstate+ndeath);l1++){ + if(l1==k1) continue; + i=(k1-1)*(nlstate+ndeath)+l1; + if(i<=j) continue; + for (age=bage; age<=fage; age ++){ + if ((int)age %5==0){ + v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM; + v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM; + cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM; + mu1=mu[i][(int) age]/stepm*YEARM ; + mu2=mu[j][(int) age]/stepm*YEARM; + c12=cv12/sqrt(v1*v2); + /* Computing eigen value of matrix of covariance */ + lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.; + lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.; + if ((lc2 <0) || (lc1 <0) ){ + if(first2==1){ + first1=0; + 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); + } + 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); + /* lc1=fabs(lc1); */ /* If we want to have them positive */ + /* lc2=fabs(lc2); */ + } + + /* Eigen vectors */ + v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12)); + /*v21=sqrt(1.-v11*v11); *//* error */ + v21=(lc1-v1)/cv12*v11; + v12=-v21; + v22=v11; + tnalp=v21/v11; + if(first1==1){ + first1=0; + 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); + } + 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); + /*printf(fignu*/ + /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */ + /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */ + if(first==1){ + first=0; + fprintf(ficgp,"\n# Ellipsoids of confidence\n#\n"); + fprintf(ficgp,"\nset parametric;unset label"); + 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); + fprintf(ficgp,"\nset ter svg size 640, 480"); + fprintf(fichtmcov,"\n
    Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year-1\ + : \ +%s_%d%1d%1d-%1d%1d.svg, ",k1,l1,k2,l2,\ + subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2, \ + subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2); + fprintf(fichtmcov,"\n
    ",subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2); + fprintf(fichtmcov,"\n
    Correlation at age %d (%.3f),",(int) age, c12); + fprintf(ficgp,"\nset out \"%s_%d%1d%1d-%1d%1d.svg\"",subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2); + fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2); + fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2); + 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", \ + mu1,std,v11,sqrt(lc1),v12,sqrt(lc2), \ + mu2,std,v21,sqrt(lc1),v22,sqrt(lc2)); + }else{ + first=0; + fprintf(fichtmcov," %d (%.3f),",(int) age, c12); + fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2); + fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2); + 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", \ + mu1,std,v11,sqrt(lc1),v12,sqrt(lc2), \ + mu2,std,v21,sqrt(lc1),v22,sqrt(lc2)); + }/* if first */ + } /* age mod 5 */ + } /* end loop age */ + fprintf(ficgp,"\nset out;\nset out \"%s_%d%1d%1d-%1d%1d.svg\";replot;set out;",subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2); + first=1; + } /*l12 */ + } /* k12 */ + } /*l1 */ + }/* k1 */ + } /* loop on combination of covariates j1 */ + free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage); + free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage); + free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath)); + free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar); + free_vector(xp,1,npar); + fclose(ficresprob); + fclose(ficresprobcov); + fclose(ficresprobcor); + fflush(ficgp); + fflush(fichtmcov); + } /******************* Printing html file ***********/ -void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \ +void printinghtml(char fileresu[], char title[], char datafile[], int firstpass, \ int lastpass, int stepm, int weightopt, char model[],\ int imx,int jmin, int jmax, double jmeanint,char rfileres[],\ - int popforecast, int estepm ,\ - double jprev1, double mprev1,double anprev1, \ - double jprev2, double mprev2,double anprev2){ - int jj1, k1, i1, cpt; + int popforecast, int mobilav, int prevfcast, int mobilavproj, int backcast, int estepm , \ + double jprev1, double mprev1,double anprev1, double dateprev1, \ + double jprev2, double mprev2,double anprev2, double dateprev2){ + int jj1, k1, i1, cpt, k4, nres; fprintf(fichtm,""); - fprintf(fichtm,"

    • Result files (first order: no variance)

      \n \ - - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): %s
      \n ", - jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p")); + fprintf(fichtm,"
      • model=1+age+%s\n \ +
      ", model); + fprintf(fichtm,"

      • Result files (first order: no variance)

        \n"); + fprintf(fichtm,"
      • - Observed frequency between two states (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): %s (html file)
        \n", + jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirfext3(optionfilefiname,"PHTMFR_",".htm"),subdirfext3(optionfilefiname,"PHTMFR_",".htm")); + fprintf(fichtm,"
      • - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): %s (html file) ", + jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirfext3(optionfilefiname,"PHTM_",".htm"),subdirfext3(optionfilefiname,"PHTM_",".htm")); + fprintf(fichtm,", %s (text file)
        \n",subdirf2(fileresu,"P_"),subdirf2(fileresu,"P_")); fprintf(fichtm,"\ - Estimated transition probabilities over %d (stepm) months: %s
        \n ", - stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij")); + stepm,subdirf2(fileresu,"PIJ_"),subdirf2(fileresu,"PIJ_")); + fprintf(fichtm,"\ + - Estimated back transition probabilities over %d (stepm) months: %s
        \n ", + stepm,subdirf2(fileresu,"PIJB_"),subdirf2(fileresu,"PIJB_")); fprintf(fichtm,"\ - Period (stable) prevalence in each health state: %s
        \n", - subdirf2(fileres,"pl"),subdirf2(fileres,"pl")); + subdirf2(fileresu,"PL_"),subdirf2(fileresu,"PL_")); fprintf(fichtm,"\ - - (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): \ - %s
        \n", - estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e")); + - Period (stable) back prevalence in each health state: %s
        \n", + subdirf2(fileresu,"PLB_"),subdirf2(fileresu,"PLB_")); fprintf(fichtm,"\ - - Population projections by age and states: \ - %s
        \n
        • ", subdirf2(fileres,"f"),subdirf2(fileres,"f")); + - (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): \ + %s
        \n", + estepm,subdirf2(fileresu,"E_"),subdirf2(fileresu,"E_")); + if(prevfcast==1){ + fprintf(fichtm,"\ + - Prevalence projections by age and states: \ + %s
        \n", subdirf2(fileresu,"F_"),subdirf2(fileresu,"F_")); + } + -fprintf(fichtm," \n"); - fprintf(fichtm,"\ + fprintf(fichtm,"\ \n

      • Result files (second order: variances)

        \n\ - - Parameter file with estimated parameters and covariance matrix: %s
        \n", rfileres,rfileres); + - Parameter file with estimated parameters and covariance matrix: %s
        \ + - 95%% confidence intervals and Wald tests of the estimated parameters are in the log file if optimization has been done (mle != 0).
        \ +But because parameters are usually highly correlated (a higher incidence of disability \ +and a higher incidence of recovery can give very close observed transition) it might \ +be very useful to look not only at linear confidence intervals estimated from the \ +variances but at the covariance matrix. And instead of looking at the estimated coefficients \ +(parameters) of the logistic regression, it might be more meaningful to visualize the \ +covariance matrix of the one-step probabilities. \ +See page 'Matrix of variance-covariance of one-step probabilities' below. \n", rfileres,rfileres); - fprintf(fichtm," - Variance of one-step probabilities: %s
        \n", - subdirf2(fileres,"prob"),subdirf2(fileres,"prob")); - fprintf(fichtm,"\ + fprintf(fichtm," - Standard deviation of one-step probabilities: %s
        \n", + subdirf2(fileresu,"PROB_"),subdirf2(fileresu,"PROB_")); + fprintf(fichtm,"\ - Variance-covariance of one-step probabilities: %s
        \n", - subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov")); + subdirf2(fileresu,"PROBCOV_"),subdirf2(fileresu,"PROBCOV_")); - fprintf(fichtm,"\ + fprintf(fichtm,"\ - Correlation matrix of one-step probabilities: %s
        \n", - subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor")); - fprintf(fichtm,"\ + subdirf2(fileresu,"PROBCOR_"),subdirf2(fileresu,"PROBCOR_")); + fprintf(fichtm,"\ - Variances and covariances of health expectancies by age and initial health status (cov(eij,ekl)(estepm=%2d months): \ %s
        \n
        • ", - estepm,subdirf2(fileres,"cve"),subdirf2(fileres,"cve")); - fprintf(fichtm,"\ + estepm,subdirf2(fileresu,"CVE_"),subdirf2(fileresu,"CVE_")); + fprintf(fichtm,"\ - (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): \ %s
        \n", - estepm,subdirf2(fileres,"stde"),subdirf2(fileres,"stde")); - fprintf(fichtm,"\ + estepm,subdirf2(fileresu,"STDE_"),subdirf2(fileresu,"STDE_")); + fprintf(fichtm,"\ - 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): %s
        \n", - estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v")); - fprintf(fichtm,"\ + estepm, subdirf2(fileresu,"V_"),subdirf2(fileresu,"V_")); + fprintf(fichtm,"\ - 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): %s
        \n", - estepm, subdirf2(fileres,"t"),subdirf2(fileres,"t")); - fprintf(fichtm,"\ + estepm, subdirf2(fileresu,"T_"),subdirf2(fileresu,"T_")); + fprintf(fichtm,"\ - Standard deviation of period (stable) prevalences: %s
        \n",\ - subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl")); + subdirf2(fileresu,"VPL_"),subdirf2(fileresu,"VPL_")); /* if(popforecast==1) fprintf(fichtm,"\n */ /* - Prevalences forecasting: f%s
        \n */ @@ -3909,45 +6664,66 @@ fprintf(fichtm," \n
        • Graphs /*
          ",fileres,fileres,fileres,fileres); */ /* else */ /* fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)

          • \n",popforecast, stepm, model); */ - fflush(fichtm); - fprintf(fichtm,"
          • Graphs

            • "); + fflush(fichtm); + fprintf(fichtm,"

            • Graphs

              • "); - m=pow(2,cptcoveff); - if (cptcovn < 1) {m=1;ncodemax[1]=1;} + m=pow(2,cptcoveff); + if (cptcovn < 1) {m=1;ncodemax[1]=1;} - jj1=0; - for(k1=1; k1<=m;k1++){ - for(i1=1; i1<=ncodemax[k1];i1++){ + jj1=0; + + for(nres=1; nres <= nresult; nres++){ /* For each resultline */ + for(k1=1; k1<=m;k1++){ + if(m != 1 && TKresult[nres]!= k1) + continue; + /* for(i1=1; i1<=ncodemax[k1];i1++){ */ jj1++; if (cptcovn > 0) { fprintf(fichtm,"

              ************ Results for covariates"); - for (cpt=1; cpt<=cptcoveff;cpt++) - fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]); + for (cpt=1; cpt<=cptcoveff;cpt++) /**< cptcoveff number of variables */ + fprintf(fichtm," V%d=%d ",Tvresult[nres][cpt],Tresult[nres][cpt]); + /* fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]); */ + for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */ + fprintf(fichtm," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]); + } + fprintf(fichtm," ************\n
              "); + + if(invalidvarcomb[k1]){ + fprintf(fichtm,"\n

              Combination (%d) ignored because no cases

              \n",k1); + continue; + } } for(cpt=1; cpt<=nlstate;cpt++) { - fprintf(fichtm,"
              - Observed (cross-sectional) and period (incidence based) \ -prevalence (with 95%% confidence interval) in state (%d): %s%d_%d.png
              \ -",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1); + fprintf(fichtm,"\n
              - Observed (cross-sectional with mov_average=%d) and period (incidence based) \ +prevalence (with 95%% confidence interval) in state (%d): %s_%d-%d-%d.svg\n
              \ +",mobilav,cpt,subdirf2(optionfilefiname,"V_"),cpt,k1,nres,subdirf2(optionfilefiname,"V_"),cpt,k1,nres,subdirf2(optionfilefiname,"V_"),cpt,k1,nres); } fprintf(fichtm,"\n
              - Total life expectancy by age and \ health expectancies in states (1) and (2). If popbased=1 the smooth (due to the model) \ true period expectancies (those weighted with period prevalences are also\ drawn in addition to the population based expectancies computed using\ - observed and cahotic prevalences: %s%d.png
              \ -",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1); - } /* end i1 */ - }/* End k1 */ - fprintf(fichtm,"
            "); - fflush(fichtm); + observed and cahotic prevalences: %s_%d-%d.svg\n
            \ +",subdirf2(optionfilefiname,"E_"),k1,nres,subdirf2(optionfilefiname,"E_"),k1,nres,subdirf2(optionfilefiname,"E_"),k1,nres); + /* } /\* end i1 *\/ */ + }/* End k1 */ + }/* End nres */ + fprintf(fichtm,"
          "); + fflush(fichtm); } /******************* Gnuplot file **************/ -void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){ +void printinggnuplot(char fileresu[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , int prevfcast, int backcast, char pathc[], double p[]){ char dirfileres[132],optfileres[132]; - int m0,cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,ij=0,l=0; + char gplotcondition[132], gplotlabel[132]; + int cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,k4=0,ij=0, ijp=0, l=0; + int lv=0, vlv=0, kl=0; int ng=0; + int vpopbased; + int ioffset; /* variable offset for columns */ + int nres=0; /* Index of resultline */ + /* if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */ /* printf("Problem with file %s",optionfilegnuplot); */ /* fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */ @@ -3955,265 +6731,981 @@ void printinggnuplot(char fileres[], cha /*#ifdef windows */ fprintf(ficgp,"cd \"%s\" \n",pathc); - /*#endif */ + /*#endif */ m=pow(2,cptcoveff); + /* Contribution to likelihood */ + /* Plot the probability implied in the likelihood */ + fprintf(ficgp,"\n# Contributions to the Likelihood, mle >=1. For mle=4 no interpolation, pure matrix products.\n#\n"); + fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Likelihood (-2Log(L))\";"); + /* fprintf(ficgp,"\nset ter svg size 640, 480"); */ /* Too big for svg */ + fprintf(ficgp,"\nset ter pngcairo size 640, 480"); +/* nice for mle=4 plot by number of matrix products. + replot "rrtest1/toto.txt" u 2:($4 == 1 && $5==2 ? $9 : 1/0):5 t "p12" with point lc 1 */ +/* replot exp(p1+p2*x)/(1+exp(p1+p2*x)+exp(p3+p4*x)+exp(p5+p6*x)) t "p12(x)" */ + /* fprintf(ficgp,"\nset out \"%s.svg\";",subdirf2(optionfilefiname,"ILK_")); */ + fprintf(ficgp,"\nset out \"%s-dest.png\";",subdirf2(optionfilefiname,"ILK_")); + fprintf(ficgp,"\nset log y;plot \"%s\" u 2:(-$13):6 t \"All sample, transitions colored by destination\" with dots lc variable; set out;\n",subdirf(fileresilk)); + fprintf(ficgp,"\nset out \"%s-ori.png\";",subdirf2(optionfilefiname,"ILK_")); + fprintf(ficgp,"\nset log y;plot \"%s\" u 2:(-$13):5 t \"All sample, transitions colored by origin\" with dots lc variable; set out;\n\n",subdirf(fileresilk)); + for (i=1; i<= nlstate ; i ++) { + fprintf(ficgp,"\nset out \"%s-p%dj.png\";set ylabel \"Probability for each individual/wave\";",subdirf2(optionfilefiname,"ILK_"),i); + fprintf(ficgp,"unset log;\n# plot weighted, mean weight should have point size of 0.5\n plot \"%s\"",subdirf(fileresilk)); + fprintf(ficgp," u 2:($5 == %d && $6==%d ? $10 : 1/0):($12/4.):6 t \"p%d%d\" with points pointtype 7 ps variable lc variable \\\n",i,1,i,1); + for (j=2; j<= nlstate+ndeath ; j ++) { + fprintf(ficgp,",\\\n \"\" u 2:($5 == %d && $6==%d ? $10 : 1/0):($12/4.):6 t \"p%d%d\" with points pointtype 7 ps variable lc variable ",i,j,i,j); + } + fprintf(ficgp,";\nset out; unset ylabel;\n"); + } + /* unset log; plot "rrtest1_sorted_4/ILK_rrtest1_sorted_4.txt" u 2:($4 == 1 && $5==2 ? $9 : 1/0):5 t "p12" with points lc variable */ + /* fprintf(ficgp,"\nset log y;plot \"%s\" u 2:(-$11):3 t \"All sample, all transitions\" with dots lc variable",subdirf(fileresilk)); */ + /* fprintf(ficgp,"\nreplot \"%s\" u 2:($3 <= 3 ? -$11 : 1/0):3 t \"First 3 individuals\" with line lc variable", subdirf(fileresilk)); */ + fprintf(ficgp,"\nset out;unset log\n"); + /* fprintf(ficgp,"\nset out \"%s.svg\"; replot; set out; # bug gnuplot",subdirf2(optionfilefiname,"ILK_")); */ + strcpy(dirfileres,optionfilefiname); strcpy(optfileres,"vpl"); - /* 1eme*/ - for (cpt=1; cpt<= nlstate ; cpt ++) { - for (k1=1; k1<= m ; k1 ++) { /* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */ - fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1); - fprintf(ficgp,"\n#set out \"v%s%d_%d.png\" \n",optionfilefiname,cpt,k1); - fprintf(ficgp,"set xlabel \"Age\" \n\ -set ylabel \"Probability\" \n\ -set ter png small size 320, 240\n\ -plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1); - - for (i=1; i<= nlstate ; i ++) { - if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)"); - else fprintf(ficgp," \%%*lf (\%%*lf)"); - } - 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); - for (i=1; i<= nlstate ; i ++) { - if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)"); - else fprintf(ficgp," \%%*lf (\%%*lf)"); - } - fprintf(ficgp,"\" t\"95\%% CI\" w l lt 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1); - for (i=1; i<= nlstate ; i ++) { - if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)"); - else fprintf(ficgp," \%%*lf (\%%*lf)"); - } - fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l lt 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1)); - } - } - /*2 eme*/ - - for (k1=1; k1<= m ; k1 ++) { - fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1); - fprintf(ficgp,"set ylabel \"Years\" \nset ter png small size 320, 240\nplot [%.f:%.f] ",ageminpar,fage); - - for (i=1; i<= nlstate+1 ; i ++) { - k=2*i; - fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1); - for (j=1; j<= nlstate+1 ; j ++) { - if (j==i) fprintf(ficgp," \%%lf (\%%lf)"); - else fprintf(ficgp," \%%*lf (\%%*lf)"); - } - if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,"); - else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1); - fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1); - for (j=1; j<= nlstate+1 ; j ++) { - if (j==i) fprintf(ficgp," \%%lf (\%%lf)"); - else fprintf(ficgp," \%%*lf (\%%*lf)"); - } - fprintf(ficgp,"\" t\"\" w l lt 0,"); - fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1); - for (j=1; j<= nlstate+1 ; j ++) { - if (j==i) fprintf(ficgp," \%%lf (\%%lf)"); - else fprintf(ficgp," \%%*lf (\%%*lf)"); - } - if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l lt 0"); - else fprintf(ficgp,"\" t\"\" w l lt 0,"); - } - } + /* 1eme*/ + for (cpt=1; cpt<= nlstate ; cpt ++){ /* For each live state */ + for (k1=1; k1<= m ; k1 ++){ /* For each valid combination of covariate */ + for(nres=1; nres <= nresult; nres++){ /* For each resultline */ + /* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */ + if(m != 1 && TKresult[nres]!= k1) + continue; + /* We are interested in selected combination by the resultline */ + /* printf("\n# 1st: Period (stable) prevalence with CI: 'VPL_' files and live state =%d ", cpt); */ + fprintf(ficgp,"\n# 1st: Period (stable) prevalence with CI: 'VPL_' files and live state =%d ", cpt); + strcpy(gplotlabel,"("); + for (k=1; k<=cptcoveff; k++){ /* For each covariate k get corresponding value lv for combination k1 */ + lv= decodtabm(k1,k,cptcoveff); /* Should be the value of the covariate corresponding to k1 combination */ + /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */ + /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */ + /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */ + vlv= nbcode[Tvaraff[k]][lv]; /* vlv is the value of the covariate lv, 0 or 1 */ + /* For each combination of covariate k1 (V1=1, V3=0), we printed the current covariate k and its value vlv */ + /* printf(" V%d=%d ",Tvaraff[k],vlv); */ + fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv); + sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv); + } + for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */ + /* printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]); */ + fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]); + sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]); + } + strcpy(gplotlabel+strlen(gplotlabel),")"); + /* printf("\n#\n"); */ + fprintf(ficgp,"\n#\n"); + if(invalidvarcomb[k1]){ + /*k1=k1-1;*/ /* To be checked */ + fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1); + continue; + } + + fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"V_"),cpt,k1,nres); + fprintf(ficgp,"\n#set out \"V_%s_%d-%d-%d.svg\" \n",optionfilefiname,cpt,k1,nres); + fprintf(ficgp,"set label \"Alive state %d %s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",cpt,gplotlabel); + fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter svg size 640, 480\nplot [%.f:%.f] \"%s\" every :::%d::%d u 1:($2==%d ? $3:1/0) \"%%lf %%lf",ageminpar,fage,subdirf2(fileresu,"VPL_"),nres-1,nres-1,nres); + /* fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter svg size 640, 480\nplot [%.f:%.f] \"%s\" every :::%d::%d u 1:($2==%d ? $3:1/0) \"%%lf %%lf",ageminpar,fage,subdirf2(fileresu,"VPL_"),k1-1,k1-1,nres); */ + /* k1-1 error should be nres-1*/ + for (i=1; i<= nlstate ; i ++) { + if (i==cpt) fprintf(ficgp," %%lf (%%lf)"); + else fprintf(ficgp," %%*lf (%%*lf)"); + } + fprintf(ficgp,"\" t\"Period (stable) prevalence\" w l lt 0,\"%s\" every :::%d::%d u 1:($2==%d ? $3+1.96*$4 : 1/0) \"%%lf %%lf",subdirf2(fileresu,"VPL_"),nres-1,nres-1,nres); + for (i=1; i<= nlstate ; i ++) { + if (i==cpt) fprintf(ficgp," %%lf (%%lf)"); + else fprintf(ficgp," %%*lf (%%*lf)"); + } + fprintf(ficgp,"\" t\"95%% CI\" w l lt 1,\"%s\" every :::%d::%d u 1:($2==%d ? $3-1.96*$4 : 1/0) \"%%lf %%lf",subdirf2(fileresu,"VPL_"),nres-1,nres-1,nres); + for (i=1; i<= nlstate ; i ++) { + if (i==cpt) fprintf(ficgp," %%lf (%%lf)"); + else fprintf(ficgp," %%*lf (%%*lf)"); + } + /* fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence\" w l lt 2",subdirf2(fileresu,"P_"),k1-1,k1-1,2+4*(cpt-1)); */ + + fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" u 1:((",subdirf2(fileresu,"P_")); + if(cptcoveff ==0){ + fprintf(ficgp,"$%d)) t 'Observed prevalence in state %d' with line lt 3", 2+(cpt-1), cpt ); + }else{ + kl=0; + for (k=1; k<=cptcoveff; k++){ /* For each combination of covariate */ + lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */ + /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */ + /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */ + /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */ + vlv= nbcode[Tvaraff[k]][lv]; + kl++; + /* kl=6+(cpt-1)*(nlstate+1)+1+(i-1); /\* 6+(1-1)*(2+1)+1+(1-1)=7, 6+(2-1)(2+1)+1+(1-1)=10 *\/ */ + /*6+(cpt-1)*(nlstate+1)+1+(i-1)+(nlstate+1)*nlstate; 6+(1-1)*(2+1)+1+(1-1) +(2+1)*2=13 */ + /*6+1+(i-1)+(nlstate+1)*nlstate; 6+1+(1-1) +(2+1)*2=13 */ + /* '' u 6:(($1==1 && $2==0 && $3==2 && $4==0)? $9/(1.-$15) : 1/0):($5==2000? 3:2) t 'p.1' with line lc variable*/ + if(k==cptcoveff){ + fprintf(ficgp,"$%d==%d && $%d==%d)? $%d : 1/0) t 'Observed prevalence in state %d' w l lt 2",kl+1, Tvaraff[k],kl+1+1,nbcode[Tvaraff[k]][lv], \ + 2+cptcoveff*2+3*(cpt-1), cpt ); /* 4 or 6 ?*/ + }else{ + fprintf(ficgp,"$%d==%d && $%d==%d && ",kl+1, Tvaraff[k],kl+1+1,nbcode[Tvaraff[k]][lv]); + kl++; + } + } /* end covariate */ + } /* end if no covariate */ + + if(backcast==1){ /* We need to get the corresponding values of the covariates involved in this combination k1 */ + /* fprintf(ficgp,",\"%s\" every :::%d::%d u 1:($%d) t\"Backward stable prevalence\" w l lt 3",subdirf2(fileresu,"PLB_"),k1-1,k1-1,1+cpt); */ + fprintf(ficgp,",\"%s\" u 1:((",subdirf2(fileresu,"PLB_")); /* Age is in 1, nres in 2 to be fixed */ + if(cptcoveff ==0){ + fprintf(ficgp,"$%d)) t 'Backward prevalence in state %d' with line lt 3", 2+(cpt-1), cpt ); + }else{ + kl=0; + for (k=1; k<=cptcoveff; k++){ /* For each combination of covariate */ + lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */ + /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */ + /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */ + /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */ + vlv= nbcode[Tvaraff[k]][lv]; + kl++; + /* kl=6+(cpt-1)*(nlstate+1)+1+(i-1); /\* 6+(1-1)*(2+1)+1+(1-1)=7, 6+(2-1)(2+1)+1+(1-1)=10 *\/ */ + /*6+(cpt-1)*(nlstate+1)+1+(i-1)+(nlstate+1)*nlstate; 6+(1-1)*(2+1)+1+(1-1) +(2+1)*2=13 */ + /*6+1+(i-1)+(nlstate+1)*nlstate; 6+1+(1-1) +(2+1)*2=13 */ + /* '' u 6:(($1==1 && $2==0 && $3==2 && $4==0)? $9/(1.-$15) : 1/0):($5==2000? 3:2) t 'p.1' with line lc variable*/ + if(k==cptcoveff){ + fprintf(ficgp,"$%d==%d && $%d==%d)? $%d : 1/0) t 'Backward prevalence in state %d' w l lt 3",kl+1, Tvaraff[k],kl+1+1,nbcode[Tvaraff[k]][lv], \ + 2+cptcoveff*2+(cpt-1), cpt ); /* 4 or 6 ?*/ + }else{ + fprintf(ficgp,"$%d==%d && $%d==%d && ",kl+1, Tvaraff[k],kl+1+1,nbcode[Tvaraff[k]][lv]); + kl++; + } + } /* end covariate */ + } /* end if no covariate */ + } /* end if backcast */ + fprintf(ficgp,"\nset out ;unset label;\n"); + } /* nres */ + } /* k1 */ + } /* cpt */ + + /*2 eme*/ + for (k1=1; k1<= m ; k1 ++){ + for(nres=1; nres <= nresult; nres++){ /* For each resultline */ + if(m != 1 && TKresult[nres]!= k1) + continue; + fprintf(ficgp,"\n# 2nd: Total life expectancy with CI: 't' files "); + strcpy(gplotlabel,"("); + for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */ + lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */ + /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */ + /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */ + /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */ + vlv= nbcode[Tvaraff[k]][lv]; + fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv); + sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv); + } + /* for(k=1; k <= ncovds; k++){ */ + for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */ + printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]); + fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]); + sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]); + } + strcpy(gplotlabel+strlen(gplotlabel),")"); + fprintf(ficgp,"\n#\n"); + if(invalidvarcomb[k1]){ + fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1); + continue; + } + + fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"E_"),k1,nres); + for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/ + fprintf(ficgp,"\nset label \"popbased %d %s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",vpopbased,gplotlabel); + if(vpopbased==0){ + fprintf(ficgp,"set ylabel \"Years\" \nset ter svg size 640, 480\nplot [%.f:%.f] ",ageminpar,fage); + }else + fprintf(ficgp,"\nreplot "); + for (i=1; i<= nlstate+1 ; i ++) { + k=2*i; + fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2==%d && $4!=0 ?$4 : 1/0) \"%%lf %%lf %%lf",subdirf2(fileresu,"T_"),nres-1,nres-1, vpopbased); + for (j=1; j<= nlstate+1 ; j ++) { + if (j==i) fprintf(ficgp," %%lf (%%lf)"); + else fprintf(ficgp," %%*lf (%%*lf)"); + } + if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l lt %d, \\\n",i); + else fprintf(ficgp,"\" t\"LE in state (%d)\" w l lt %d, \\\n",i-1,i+1); + fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2==%d && $4!=0 ? $4-$5*2 : 1/0) \"%%lf %%lf %%lf",subdirf2(fileresu,"T_"),nres-1,nres-1,vpopbased); + for (j=1; j<= nlstate+1 ; j ++) { + if (j==i) fprintf(ficgp," %%lf (%%lf)"); + else fprintf(ficgp," %%*lf (%%*lf)"); + } + fprintf(ficgp,"\" t\"\" w l lt 0,"); + fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2==%d && $4!=0 ? $4+$5*2 : 1/0) \"%%lf %%lf %%lf",subdirf2(fileresu,"T_"),nres-1,nres-1,vpopbased); + for (j=1; j<= nlstate+1 ; j ++) { + if (j==i) fprintf(ficgp," %%lf (%%lf)"); + else fprintf(ficgp," %%*lf (%%*lf)"); + } + if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l lt 0"); + else fprintf(ficgp,"\" t\"\" w l lt 0,\\\n"); + } /* state */ + } /* vpopbased */ + fprintf(ficgp,"\nset out;set out \"%s_%d-%d.svg\"; replot; set out; unset label;\n",subdirf2(optionfilefiname,"E_"),k1,nres); /* Buggy gnuplot */ + } /* end nres */ + } /* k1 end 2 eme*/ + + /*3eme*/ - - for (k1=1; k1<= m ; k1 ++) { - for (cpt=1; cpt<= nlstate ; cpt ++) { - /* k=2+nlstate*(2*cpt-2); */ - k=2+(nlstate+1)*(cpt-1); - fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1); - fprintf(ficgp,"set ter png small size 320, 240\n\ -plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt); - /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1); - for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) "); - fprintf(ficgp,"\" t \"e%d1\" w l",cpt); - fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1); - for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) "); - fprintf(ficgp,"\" t \"e%d1\" w l",cpt); + for (k1=1; k1<= m ; k1 ++){ + for(nres=1; nres <= nresult; nres++){ /* For each resultline */ + if(m != 1 && TKresult[nres]!= k1) + continue; + + for (cpt=1; cpt<= nlstate ; cpt ++) { + fprintf(ficgp,"\n\n# 3d: Life expectancy with EXP_ files: combination=%d state=%d",k1, cpt); + strcpy(gplotlabel,"("); + for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */ + lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */ + /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */ + /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */ + /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */ + vlv= nbcode[Tvaraff[k]][lv]; + fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv); + sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv); + } + for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */ + fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]); + sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]); + } + strcpy(gplotlabel+strlen(gplotlabel),")"); + fprintf(ficgp,"\n#\n"); + if(invalidvarcomb[k1]){ + fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1); + continue; + } + + /* k=2+nlstate*(2*cpt-2); */ + k=2+(nlstate+1)*(cpt-1); + fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"EXP_"),cpt,k1,nres); + fprintf(ficgp,"set label \"%s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",gplotlabel); + fprintf(ficgp,"set ter svg size 640, 480\n\ +plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileresu,"E_"),nres-1,nres-1,k,cpt); + /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1); + for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) "); + fprintf(ficgp,"\" t \"e%d1\" w l",cpt); + fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1); + for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) "); + fprintf(ficgp,"\" t \"e%d1\" w l",cpt); + + */ + for (i=1; i< nlstate ; i ++) { + fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileresu,"E_"),nres-1,nres-1,k+i,cpt,i+1); + /* 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);*/ + + } + fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileresu,"E_"),nres-1,nres-1,k+nlstate,cpt); + } + fprintf(ficgp,"\nunset label;\n"); + } /* end nres */ + } /* end kl 3eme */ + + /* 4eme */ + /* Survival functions (period) from state i in state j by initial state i */ + for (k1=1; k1<=m; k1++){ /* For each covariate and each value */ + for(nres=1; nres <= nresult; nres++){ /* For each resultline */ + if(m != 1 && TKresult[nres]!= k1) + continue; + for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state cpt*/ + strcpy(gplotlabel,"("); + fprintf(ficgp,"\n#\n#\n# Survival functions in state j : 'LIJ_' files, cov=%d state=%d",k1, cpt); + for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */ + lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */ + /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */ + /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */ + /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */ + vlv= nbcode[Tvaraff[k]][lv]; + fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv); + sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv); + } + for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */ + fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]); + sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]); + } + strcpy(gplotlabel+strlen(gplotlabel),")"); + fprintf(ficgp,"\n#\n"); + if(invalidvarcomb[k1]){ + fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1); + continue; + } + + fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"LIJ_"),cpt,k1,nres); + fprintf(ficgp,"set label \"Alive state %d %s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",cpt,gplotlabel); + fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability to be alive\" \n\ +set ter svg size 640, 480\nunset log y\nplot [%.f:%.f] ", ageminpar, agemaxpar); + k=3; + for (i=1; i<= nlstate ; i ++){ + if(i==1){ + fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_")); + }else{ + fprintf(ficgp,", '' "); + } + l=(nlstate+ndeath)*(i-1)+1; + fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l); + for (j=2; j<= nlstate+ndeath ; j ++) + fprintf(ficgp,"+$%d",k+l+j-1); + fprintf(ficgp,")) t \"l(%d,%d)\" w l",i,cpt); + } /* nlstate */ + fprintf(ficgp,"\nset out; unset label;\n"); + } /* end cpt state*/ + } /* end nres */ + } /* end covariate k1 */ + +/* 5eme */ + /* Survival functions (period) from state i in state j by final state j */ + for (k1=1; k1<= m ; k1++){ /* For each covariate combination if any */ + for(nres=1; nres <= nresult; nres++){ /* For each resultline */ + if(m != 1 && TKresult[nres]!= k1) + continue; + for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each inital state */ + strcpy(gplotlabel,"("); + fprintf(ficgp,"\n#\n#\n# Survival functions in state j and all livestates from state i by final state j: 'lij' files, cov=%d state=%d",k1, cpt); + for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */ + lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */ + /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */ + /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */ + /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */ + vlv= nbcode[Tvaraff[k]][lv]; + fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv); + sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv); + } + for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */ + fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]); + sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]); + } + strcpy(gplotlabel+strlen(gplotlabel),")"); + fprintf(ficgp,"\n#\n"); + if(invalidvarcomb[k1]){ + fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1); + continue; + } + + fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"LIJT_"),cpt,k1,nres); + fprintf(ficgp,"set label \"Alive state %d %s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",cpt,gplotlabel); + fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability to be alive\" \n\ +set ter svg size 640, 480\nunset log y\nplot [%.f:%.f] ", ageminpar, agemaxpar); + k=3; + for (j=1; j<= nlstate ; j ++){ /* Lived in state j */ + if(j==1) + fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_")); + else + fprintf(ficgp,", '' "); + l=(nlstate+ndeath)*(cpt-1) +j; + fprintf(ficgp," u (($1==%d && (floor($2)%%5 == 0)) ? ($3):1/0):($%d",k1,k+l); + /* for (i=2; i<= nlstate+ndeath ; i ++) */ + /* fprintf(ficgp,"+$%d",k+l+i-1); */ + fprintf(ficgp,") t \"l(%d,%d)\" w l",cpt,j); + } /* nlstate */ + fprintf(ficgp,", '' "); + fprintf(ficgp," u (($1==%d && (floor($2)%%5 == 0)) ? ($3):1/0):(",k1); + for (j=1; j<= nlstate ; j ++){ /* Lived in state j */ + l=(nlstate+ndeath)*(cpt-1) +j; + if(j < nlstate) + fprintf(ficgp,"$%d +",k+l); + else + fprintf(ficgp,"$%d) t\"l(%d,.)\" w l",k+l,cpt); + } + fprintf(ficgp,"\nset out; unset label;\n"); + } /* end cpt state*/ + } /* end covariate */ + } /* end nres */ + +/* 6eme */ + /* CV preval stable (period) for each covariate */ + for (k1=1; k1<= m ; k1 ++) /* For each covariate combination if any */ + for(nres=1; nres <= nresult; nres++){ /* For each resultline */ + if(m != 1 && TKresult[nres]!= k1) + continue; + for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state of arrival */ + strcpy(gplotlabel,"("); + fprintf(ficgp,"\n#\n#\n#CV preval stable (period): 'pij' files, covariatecombination#=%d state=%d",k1, cpt); + for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */ + lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */ + /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */ + /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */ + /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */ + vlv= nbcode[Tvaraff[k]][lv]; + fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv); + sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv); + } + for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */ + fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]); + sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]); + } + strcpy(gplotlabel+strlen(gplotlabel),")"); + fprintf(ficgp,"\n#\n"); + if(invalidvarcomb[k1]){ + fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1); + continue; + } + + fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"P_"),cpt,k1,nres); + fprintf(ficgp,"set label \"Alive state %d %s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",cpt,gplotlabel); + fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\ +set ter svg size 640, 480\nunset log y\nplot [%.f:%.f] ", ageminpar, agemaxpar); + k=3; /* Offset */ + for (i=1; i<= nlstate ; i ++){ /* State of origin */ + if(i==1) + fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_")); + else + fprintf(ficgp,", '' "); + l=(nlstate+ndeath)*(i-1)+1; /* 1, 1+ nlstate+ndeath, 1+2*(nlstate+ndeath) */ + fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l); + for (j=2; j<= nlstate ; j ++) + fprintf(ficgp,"+$%d",k+l+j-1); + fprintf(ficgp,")) t \"prev(%d,%d)\" w l",i,cpt); + } /* nlstate */ + fprintf(ficgp,"\nset out; unset label;\n"); + } /* end cpt state*/ + } /* end covariate */ + + +/* 7eme */ + if(backcast == 1){ + /* CV back preval stable (period) for each covariate */ + for (k1=1; k1<= m ; k1 ++) /* For each covariate combination if any */ + for(nres=1; nres <= nresult; nres++){ /* For each resultline */ + if(m != 1 && TKresult[nres]!= k1) + continue; + for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life ending state */ + strcpy(gplotlabel,"("); + fprintf(ficgp,"\n#\n#\n#CV Back preval stable (period): 'pijb' files, covariatecombination#=%d state=%d",k1, cpt); + for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */ + lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */ + /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */ + /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */ + /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */ + vlv= nbcode[Tvaraff[k]][lv]; + fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv); + sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv); + } + for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */ + fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]); + sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]); + } + strcpy(gplotlabel+strlen(gplotlabel),")"); + fprintf(ficgp,"\n#\n"); + if(invalidvarcomb[k1]){ + fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1); + continue; + } - */ - for (i=1; i< nlstate ; i ++) { - 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); - /* 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);*/ + fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"PB_"),cpt,k1,nres); + fprintf(ficgp,"set label \"Ending alive state %d %s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",cpt,gplotlabel); + fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\ +set ter svg size 640, 480\nunset log y\nplot [%.f:%.f] ", ageminpar, agemaxpar); + k=3; /* Offset */ + for (i=1; i<= nlstate ; i ++){ /* State of origin */ + if(i==1) + fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJB_")); + else + fprintf(ficgp,", '' "); + /* l=(nlstate+ndeath)*(i-1)+1; */ + l=(nlstate+ndeath)*(cpt-1)+1; /* fixed for i; cpt=1 1, cpt=2 1+ nlstate+ndeath, 1+2*(nlstate+ndeath) */ + /* fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l); /\* a vérifier *\/ */ + /* fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l+(cpt-1)+i-1); /\* a vérifier *\/ */ + fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d",k1,k+l+i-1); /* To be verified */ + /* for (j=2; j<= nlstate ; j ++) */ + /* fprintf(ficgp,"+$%d",k+l+j-1); */ + /* /\* fprintf(ficgp,"+$%d",k+l+j-1); *\/ */ + fprintf(ficgp,") t \"bprev(%d,%d)\" w l",i,cpt); + } /* nlstate */ + fprintf(ficgp,"\nset out; unset label;\n"); + } /* end cpt state*/ + } /* end covariate */ + } /* End if backcast */ + + /* 8eme */ + if(prevfcast==1){ + /* Projection from cross-sectional to stable (period) for each covariate */ + + for (k1=1; k1<= m ; k1 ++) /* For each covariate combination if any */ + for(nres=1; nres <= nresult; nres++){ /* For each resultline */ + if(m != 1 && TKresult[nres]!= k1) + continue; + for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */ + strcpy(gplotlabel,"("); + fprintf(ficgp,"\n#\n#\n#Projection of prevalence to stable (period): 'PROJ_' files, covariatecombination#=%d state=%d",k1, cpt); + for (k=1; k<=cptcoveff; k++){ /* For each correspondig covariate value */ + lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */ + /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */ + /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */ + /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */ + vlv= nbcode[Tvaraff[k]][lv]; + fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv); + sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv); + } + for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */ + fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]); + sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]); + } + strcpy(gplotlabel+strlen(gplotlabel),")"); + fprintf(ficgp,"\n#\n"); + if(invalidvarcomb[k1]){ + fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1); + continue; + } - } - fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+nlstate,cpt); - } - } + fprintf(ficgp,"# hpijx=probability over h years, hp.jx is weighted by observed prev\n "); + fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"PROJ_"),cpt,k1,nres); + fprintf(ficgp,"set label \"Alive state %d %s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",cpt,gplotlabel); + fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Prevalence\" \n\ +set ter svg size 640, 480\nunset log y\nplot [%.f:%.f] ", ageminpar, agemaxpar); + for (i=1; i<= nlstate+1 ; i ++){ /* nlstate +1 p11 p21 p.1 */ + /*# V1 = 1 V2 = 0 yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/ + /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 */ + /*# yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/ + /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 */ + if(i==1){ + fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"F_")); + }else{ + fprintf(ficgp,",\\\n '' "); + } + if(cptcoveff ==0){ /* No covariate */ + ioffset=2; /* Age is in 2 */ + /*# yearproj age p11 p21 p31 p.1 p12 p22 p32 p.2 p13 p23 p33 p.3 p14 p24 p34 p.4*/ + /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 */ + /*# V1 = 1 yearproj age p11 p21 p31 p.1 p12 p22 p32 p.2 p13 p23 p33 p.3 p14 p24 p34 p.4*/ + /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 */ + fprintf(ficgp," u %d:(", ioffset); + if(i==nlstate+1) + fprintf(ficgp," $%d/(1.-$%d)) t 'pw.%d' with line ", \ + ioffset+(cpt-1)*(nlstate+1)+1+(i-1), ioffset+1+(i-1)+(nlstate+1)*nlstate,cpt ); + else + fprintf(ficgp," $%d/(1.-$%d)) t 'p%d%d' with line ", \ + ioffset+(cpt-1)*(nlstate+1)+1+(i-1), ioffset+1+(i-1)+(nlstate+1)*nlstate,i,cpt ); + }else{ /* more than 2 covariates */ + if(cptcoveff ==1){ + ioffset=4; /* Age is in 4 */ + }else{ + ioffset=6; /* Age is in 6 */ + /*# V1 = 1 V2 = 0 yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/ + /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 */ + } + fprintf(ficgp," u %d:(",ioffset); + kl=0; + strcpy(gplotcondition,"("); + for (k=1; k<=cptcoveff; k++){ /* For each covariate writing the chain of conditions */ + lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to combination k1 and covariate k */ + /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */ + /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */ + /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */ + vlv= nbcode[Tvaraff[k]][lv]; /* Value of the modality of Tvaraff[k] */ + kl++; + sprintf(gplotcondition+strlen(gplotcondition),"$%d==%d && $%d==%d " ,kl,Tvaraff[k], kl+1, nbcode[Tvaraff[k]][lv]); + kl++; + if(k 1) + sprintf(gplotcondition+strlen(gplotcondition)," && "); + } + strcpy(gplotcondition+strlen(gplotcondition),")"); + /* kl=6+(cpt-1)*(nlstate+1)+1+(i-1); /\* 6+(1-1)*(2+1)+1+(1-1)=7, 6+(2-1)(2+1)+1+(1-1)=10 *\/ */ + /*6+(cpt-1)*(nlstate+1)+1+(i-1)+(nlstate+1)*nlstate; 6+(1-1)*(2+1)+1+(1-1) +(2+1)*2=13 */ + /*6+1+(i-1)+(nlstate+1)*nlstate; 6+1+(1-1) +(2+1)*2=13 */ + /* '' u 6:(($1==1 && $2==0 && $3==2 && $4==0)? $9/(1.-$15) : 1/0):($5==2000? 3:2) t 'p.1' with line lc variable*/ + if(i==nlstate+1){ + fprintf(ficgp,"%s ? $%d/(1.-$%d) : 1/0) t 'p.%d' with line ", gplotcondition, \ + ioffset+(cpt-1)*(nlstate+1)+1+(i-1), ioffset+1+(i-1)+(nlstate+1)*nlstate,cpt ); + }else{ + fprintf(ficgp,"%s ? $%d/(1.-$%d) : 1/0) t 'p%d%d' with line ", gplotcondition, \ + ioffset+(cpt-1)*(nlstate+1)+1+(i-1), ioffset +1+(i-1)+(nlstate+1)*nlstate,i,cpt ); + } + } /* end if covariate */ + } /* nlstate */ + fprintf(ficgp,"\nset out; unset label;\n"); + } /* end cpt state*/ + } /* end covariate */ + } /* End if prevfcast */ - /* CV preval stable (period) */ - for (k1=1; k1<= m ; k1 ++) { - for (cpt=1; cpt<=nlstate ; cpt ++) { - k=3; - fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1); - fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\ -set ter png small size 320, 240\n\ -unset log y\n\ -plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,subdirf2(fileres,"pij"),k1,k+cpt+1,k+1); - - for (i=1; i< nlstate ; i ++) - fprintf(ficgp,"+$%d",k+i+1); - fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1); - - l=3+(nlstate+ndeath)*cpt; - fprintf(ficgp,",\"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",subdirf2(fileres,"pij"),k1,l+cpt+1,l+1); - for (i=1; i< nlstate ; i ++) { - l=3+(nlstate+ndeath)*cpt; - fprintf(ficgp,"+$%d",l+i+1); - } - fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1); - } - } - /* proba elementaires */ + /* 9eme writing MLE parameters */ + fprintf(ficgp,"\n##############\n#9eme MLE estimated parameters\n#############\n"); for(i=1,jk=1; i <=nlstate; i++){ + fprintf(ficgp,"# initial state %d\n",i); for(k=1; k <=(nlstate+ndeath); k++){ if (k != i) { + fprintf(ficgp,"# current state %d\n",k); for(j=1; j <=ncovmodel; j++){ - fprintf(ficgp,"p%d=%f ",jk,p[jk]); + fprintf(ficgp,"p%d=%f; ",jk,p[jk]); jk++; - fprintf(ficgp,"\n"); } + fprintf(ficgp,"\n"); } } - } + } + fprintf(ficgp,"##############\n#\n"); + /*goto avoid;*/ - for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/ - for(jk=1; jk <=m; jk++) { - fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng); - if (ng==2) - fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n"); - else - fprintf(ficgp,"\nset title \"Probability\"\n"); - fprintf(ficgp,"\nset ter png small size 320, 240\nset log y\nplot [%.f:%.f] ",ageminpar,agemaxpar); - i=1; - for(k2=1; k2<=nlstate; k2++) { - k3=i; - for(k=1; k<=(nlstate+ndeath); k++) { - if (k != k2){ - if(ng==2) - fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1); - else - fprintf(ficgp," exp(p%d+p%d*x",i,i+1); - ij=1;/* To be checked else nbcode[0][0] wrong */ - for(j=3; j <=ncovmodel; j++) { - /* if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) { /\* Bug valgrind *\/ */ - /* /\*fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);*\/ */ - /* ij++; */ - /* } */ - /* else */ - fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]); - } - fprintf(ficgp,")/(1"); - - for(k1=1; k1 <=nlstate; k1++){ - fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1); - ij=1; - for(j=3; j <=ncovmodel; j++){ - /* if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) { */ - /* fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]); */ - /* ij++; */ - /* } */ - /* else */ - fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]); - } - fprintf(ficgp,")"); - } - fprintf(ficgp,") t \"p%d%d\" ", k2,k); - if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,","); - i=i+ncovmodel; - } - } /* end k */ - } /* end k2 */ - } /* end jk */ - } /* end ng */ - avoid: - fflush(ficgp); + /* 10eme Graphics of probabilities or incidences using written MLE parameters */ + fprintf(ficgp,"\n##############\n#10eme Graphics of probabilities or incidences\n#############\n"); + fprintf(ficgp,"# logi(p12/p11)=a12+b12*age+c12age*age+d12*V1+e12*V1*age\n"); + fprintf(ficgp,"# logi(p12/p11)=p1 +p2*age +p3*age*age+ p4*V1+ p5*V1*age\n"); + fprintf(ficgp,"# logi(p13/p11)=a13+b13*age+c13age*age+d13*V1+e13*V1*age\n"); + fprintf(ficgp,"# logi(p13/p11)=p6 +p7*age +p8*age*age+ p9*V1+ p10*V1*age\n"); + fprintf(ficgp,"# p12+p13+p14+p11=1=p11(1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n"); + fprintf(ficgp,"# +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age)+...)\n"); + fprintf(ficgp,"# p11=1/(1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n"); + fprintf(ficgp,"# +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age)+...)\n"); + fprintf(ficgp,"# p12=exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)/\n"); + fprintf(ficgp,"# (1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n"); + fprintf(ficgp,"# +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age))\n"); + fprintf(ficgp,"# +exp(a14+b14*age+c14age*age+d14*V1+e14*V1*age)+...)\n"); + fprintf(ficgp,"#\n"); + for(ng=1; ng<=3;ng++){ /* Number of graphics: first is logit, 2nd is probabilities, third is incidences per year*/ + fprintf(ficgp,"#Number of graphics: first is logit, 2nd is probabilities, third is incidences per year\n"); + fprintf(ficgp,"#model=%s \n",model); + fprintf(ficgp,"# Type of graphic ng=%d\n",ng); + fprintf(ficgp,"# k1=1 to 2^%d=%d\n",cptcoveff,m);/* to be checked */ + for(k1=1; k1 <=m; k1++) /* For each combination of covariate */ + for(nres=1; nres <= nresult; nres++){ /* For each resultline */ + if(m != 1 && TKresult[nres]!= k1) + continue; + fprintf(ficgp,"\n\n# Combination of dummy k1=%d which is ",k1); + strcpy(gplotlabel,"("); + sprintf(gplotlabel+strlen(gplotlabel)," Dummy combination %d ",k1); + for (k=1; k<=cptcoveff; k++){ /* For each correspondig covariate value */ + lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */ + /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */ + /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */ + /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */ + vlv= nbcode[Tvaraff[k]][lv]; + fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv); + sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv); + } + for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */ + fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]); + sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]); + } + strcpy(gplotlabel+strlen(gplotlabel),")"); + fprintf(ficgp,"\n#\n"); + fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" ",subdirf2(optionfilefiname,"PE_"),k1,ng,nres); + fprintf(ficgp,"\nset label \"%s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",gplotlabel); + fprintf(ficgp,"\nset ter svg size 640, 480 "); + if (ng==1){ + fprintf(ficgp,"\nset ylabel \"Value of the logit of the model\"\n"); /* exp(a12+b12*x) could be nice */ + fprintf(ficgp,"\nunset log y"); + }else if (ng==2){ + fprintf(ficgp,"\nset ylabel \"Probability\"\n"); + fprintf(ficgp,"\nset log y"); + }else if (ng==3){ + fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n"); + fprintf(ficgp,"\nset log y"); + }else + fprintf(ficgp,"\nunset title "); + fprintf(ficgp,"\nplot [%.f:%.f] ",ageminpar,agemaxpar); + i=1; + for(k2=1; k2<=nlstate; k2++) { + k3=i; + for(k=1; k<=(nlstate+ndeath); k++) { + if (k != k2){ + switch( ng) { + case 1: + if(nagesqr==0) + fprintf(ficgp," p%d+p%d*x",i,i+1); + else /* nagesqr =1 */ + fprintf(ficgp," p%d+p%d*x+p%d*x*x",i,i+1,i+1+nagesqr); + break; + case 2: /* ng=2 */ + if(nagesqr==0) + fprintf(ficgp," exp(p%d+p%d*x",i,i+1); + else /* nagesqr =1 */ + fprintf(ficgp," exp(p%d+p%d*x+p%d*x*x",i,i+1,i+1+nagesqr); + break; + case 3: + if(nagesqr==0) + fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1); + else /* nagesqr =1 */ + fprintf(ficgp," %f*exp(p%d+p%d*x+p%d*x*x",YEARM/stepm,i,i+1,i+1+nagesqr); + break; + } + ij=1;/* To be checked else nbcode[0][0] wrong */ + ijp=1; /* product no age */ + /* for(j=3; j <=ncovmodel-nagesqr; j++) { */ + for(j=1; j <=cptcovt; j++) { /* For each covariate of the simplified model */ + /* printf("Tage[%d]=%d, j=%d\n", ij, Tage[ij], j); */ + if(j==Tage[ij]) { /* Product by age */ + if(ij <=cptcovage) { /* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, 2 V5 and V1 */ + if(DummyV[j]==0){ + fprintf(ficgp,"+p%d*%d*x",i+j+2+nagesqr-1,Tinvresult[nres][Tvar[j]]);; + }else{ /* quantitative */ + fprintf(ficgp,"+p%d*%f*x",i+j+2+nagesqr-1,Tqinvresult[nres][Tvar[j]]); /* Tqinvresult in decoderesult */ + /* fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(k1,Tvar[j-2])]); */ + } + ij++; + } + }else if(j==Tprod[ijp]) { /* */ + /* printf("Tprod[%d]=%d, j=%d\n", ij, Tprod[ijp], j); */ + if(ijp <=cptcovprod) { /* Product */ + if(DummyV[Tvard[ijp][1]]==0){/* Vn is dummy */ + if(DummyV[Tvard[ijp][2]]==0){/* Vn and Vm are dummy */ + /* fprintf(ficgp,"+p%d*%d*%d",i+j+2+nagesqr-1,nbcode[Tvard[ijp][1]][codtabm(k1,j)],nbcode[Tvard[ijp][2]][codtabm(k1,j)]); */ + fprintf(ficgp,"+p%d*%d*%d",i+j+2+nagesqr-1,Tinvresult[nres][Tvard[ijp][1]],Tinvresult[nres][Tvard[ijp][2]]); + }else{ /* Vn is dummy and Vm is quanti */ + /* fprintf(ficgp,"+p%d*%d*%f",i+j+2+nagesqr-1,nbcode[Tvard[ijp][1]][codtabm(k1,j)],Tqinvresult[nres][Tvard[ijp][2]]); */ + fprintf(ficgp,"+p%d*%d*%f",i+j+2+nagesqr-1,Tinvresult[nres][Tvard[ijp][1]],Tqinvresult[nres][Tvard[ijp][2]]); + } + }else{ /* Vn*Vm Vn is quanti */ + if(DummyV[Tvard[ijp][2]]==0){ + fprintf(ficgp,"+p%d*%d*%f",i+j+2+nagesqr-1,Tinvresult[nres][Tvard[ijp][2]],Tqinvresult[nres][Tvard[ijp][1]]); + }else{ /* Both quanti */ + fprintf(ficgp,"+p%d*%f*%f",i+j+2+nagesqr-1,Tqinvresult[nres][Tvard[ijp][1]],Tqinvresult[nres][Tvard[ijp][2]]); + } + } + ijp++; + } + } else{ /* simple covariate */ + /* fprintf(ficgp,"+p%d*%d",i+j+2+nagesqr-1,nbcode[Tvar[j]][codtabm(k1,j)]); /\* Valgrind bug nbcode *\/ */ + if(Dummy[j]==0){ + fprintf(ficgp,"+p%d*%d",i+j+2+nagesqr-1,Tinvresult[nres][Tvar[j]]); /* */ + }else{ /* quantitative */ + fprintf(ficgp,"+p%d*%f",i+j+2+nagesqr-1,Tqinvresult[nres][Tvar[j]]); /* */ + /* fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(k1,Tvar[j-2])]); */ + } + } /* end simple */ + } /* end j */ + }else{ + i=i-ncovmodel; + if(ng !=1 ) /* For logit formula of log p11 is more difficult to get */ + fprintf(ficgp," (1."); + } + + if(ng != 1){ + fprintf(ficgp,")/(1"); + + for(cpt=1; cpt <=nlstate; cpt++){ + if(nagesqr==0) + fprintf(ficgp,"+exp(p%d+p%d*x",k3+(cpt-1)*ncovmodel,k3+(cpt-1)*ncovmodel+1); + else /* nagesqr =1 */ + fprintf(ficgp,"+exp(p%d+p%d*x+p%d*x*x",k3+(cpt-1)*ncovmodel,k3+(cpt-1)*ncovmodel+1,k3+(cpt-1)*ncovmodel+1+nagesqr); + + ij=1; + for(j=3; j <=ncovmodel-nagesqr; j++){ + if((j-2)==Tage[ij]) { /* Bug valgrind */ + if(ij <=cptcovage) { /* Bug valgrind */ + fprintf(ficgp,"+p%d*%d*x",k3+(cpt-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(k1,j-2)]); + /* fprintf(ficgp,"+p%d*%d*x",k3+(cpt-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(k1,Tvar[j-2])]); */ + ij++; + } + } + else + fprintf(ficgp,"+p%d*%d",k3+(cpt-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(k1,j-2)]);/* Valgrind bug nbcode */ + } + fprintf(ficgp,")"); + } + fprintf(ficgp,")"); + if(ng ==2) + fprintf(ficgp," t \"p%d%d\" ", k2,k); + else /* ng= 3 */ + fprintf(ficgp," t \"i%d%d\" ", k2,k); + }else{ /* end ng <> 1 */ + if( k !=k2) /* logit p11 is hard to draw */ + fprintf(ficgp," t \"logit(p%d%d)\" ", k2,k); + } + if ((k+k2)!= (nlstate*2+ndeath) && ng != 1) + fprintf(ficgp,","); + if (ng == 1 && k!=k2 && (k+k2)!= (nlstate*2+ndeath)) + fprintf(ficgp,","); + i=i+ncovmodel; + } /* end k */ + } /* end k2 */ + fprintf(ficgp,"\n set out; unset label;\n"); + } /* end k1 */ + } /* end ng */ + /* avoid: */ + fflush(ficgp); } /* end gnuplot */ /*************** Moving average **************/ -int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){ - - int i, cpt, cptcod; - int modcovmax =1; - int mobilavrange, mob; - double age; - - modcovmax=2*cptcoveff;/* Max number of modalities. We suppose - a covariate has 2 modalities */ - if (cptcovn<1) modcovmax=1; /* At least 1 pass */ - - if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){ - if(mobilav==1) mobilavrange=5; /* default */ - else mobilavrange=mobilav; - for (age=bage; age<=fage; age++) - for (i=1; i<=nlstate;i++) - for (cptcod=1;cptcod<=modcovmax;cptcod++) - mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod]; - /* We keep the original values on the extreme ages bage, fage and for - fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2 - we use a 5 terms etc. until the borders are no more concerned. - */ - for (mob=3;mob <=mobilavrange;mob=mob+2){ - for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){ - for (i=1; i<=nlstate;i++){ - for (cptcod=1;cptcod<=modcovmax;cptcod++){ - mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod]; - for (cpt=1;cpt<=(mob-1)/2;cpt++){ - mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod]; - mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod]; - } - mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob; - } - } - }/* end age */ - }/* end mob */ - }else return -1; - return 0; -}/* End movingaverage */ +/* int movingaverage(double ***probs, double bage, double fage, double ***mobaverage, int mobilav, double bageout, double fageout){ */ + int movingaverage(double ***probs, double bage, double fage, double ***mobaverage, int mobilav){ + + int i, cpt, cptcod; + int modcovmax =1; + int mobilavrange, mob; + int iage=0; + + double sum=0.; + double age; + double *sumnewp, *sumnewm; + double *agemingood, *agemaxgood; /* Currently identical for all covariates */ + + + /* modcovmax=2*cptcoveff;/\* Max number of modalities. We suppose */ + /* a covariate has 2 modalities, should be equal to ncovcombmax *\/ */ + + sumnewp = vector(1,ncovcombmax); + sumnewm = vector(1,ncovcombmax); + agemingood = vector(1,ncovcombmax); + agemaxgood = vector(1,ncovcombmax); + + for (cptcod=1;cptcod<=ncovcombmax;cptcod++){ + sumnewm[cptcod]=0.; + sumnewp[cptcod]=0.; + agemingood[cptcod]=0; + agemaxgood[cptcod]=0; + } + if (cptcovn<1) ncovcombmax=1; /* At least 1 pass */ + + if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){ + if(mobilav==1) mobilavrange=5; /* default */ + else mobilavrange=mobilav; + for (age=bage; age<=fage; age++) + for (i=1; i<=nlstate;i++) + for (cptcod=1;cptcod<=ncovcombmax;cptcod++) + mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod]; + /* We keep the original values on the extreme ages bage, fage and for + fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2 + we use a 5 terms etc. until the borders are no more concerned. + */ + for (mob=3;mob <=mobilavrange;mob=mob+2){ + for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){ + for (i=1; i<=nlstate;i++){ + for (cptcod=1;cptcod<=ncovcombmax;cptcod++){ + mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod]; + for (cpt=1;cpt<=(mob-1)/2;cpt++){ + mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod]; + mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod]; + } + mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob; + } + } + }/* end age */ + }/* end mob */ + }else + return -1; + for (cptcod=1;cptcod<=ncovcombmax;cptcod++){ + /* for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){ */ + if(invalidvarcomb[cptcod]){ + printf("\nCombination (%d) ignored because no cases \n",cptcod); + continue; + } + agemingood[cptcod]=fage-(mob-1)/2; + for (age=fage-(mob-1)/2; age>=bage; age--){/* From oldest to youngest, finding the youngest wrong */ + sumnewm[cptcod]=0.; + for (i=1; i<=nlstate;i++){ + sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod]; + } + if(fabs(sumnewm[cptcod] - 1.) <= 1.e-3) { /* good */ + agemingood[cptcod]=age; + }else{ /* bad */ + for (i=1; i<=nlstate;i++){ + mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemingood[cptcod]][i][cptcod]; + } /* i */ + } /* end bad */ + }/* age */ + sum=0.; + for (i=1; i<=nlstate;i++){ + sum+=mobaverage[(int)agemingood[cptcod]][i][cptcod]; + } + if(fabs(sum - 1.) > 1.e-3) { /* bad */ + printf("For this combination of covariate cptcod=%d, we can't get a smoothed prevalence which sums to one at any descending age!\n",cptcod); + /* for (i=1; i<=nlstate;i++){ */ + /* mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemingood[cptcod]][i][cptcod]; */ + /* } /\* i *\/ */ + } /* end bad */ + /* else{ /\* We found some ages summing to one, we will smooth the oldest *\/ */ + /* From youngest, finding the oldest wrong */ + agemaxgood[cptcod]=bage+(mob-1)/2; + for (age=bage+(mob-1)/2; age<=fage; age++){ + sumnewm[cptcod]=0.; + for (i=1; i<=nlstate;i++){ + sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod]; + } + if(fabs(sumnewm[cptcod] - 1.) <= 1.e-3) { /* good */ + agemaxgood[cptcod]=age; + }else{ /* bad */ + for (i=1; i<=nlstate;i++){ + mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemaxgood[cptcod]][i][cptcod]; + } /* i */ + } /* end bad */ + }/* age */ + sum=0.; + for (i=1; i<=nlstate;i++){ + sum+=mobaverage[(int)agemaxgood[cptcod]][i][cptcod]; + } + if(fabs(sum - 1.) > 1.e-3) { /* bad */ + printf("For this combination of covariate cptcod=%d, we can't get a smoothed prevalence which sums to one at any ascending age!\n",cptcod); + /* for (i=1; i<=nlstate;i++){ */ + /* mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemingood[cptcod]][i][cptcod]; */ + /* } /\* i *\/ */ + } /* end bad */ + + for (age=bage; age<=fage; age++){ + /* printf("%d %d ", cptcod, (int)age); */ + sumnewp[cptcod]=0.; + sumnewm[cptcod]=0.; + for (i=1; i<=nlstate;i++){ + sumnewp[cptcod]+=probs[(int)age][i][cptcod]; + sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod]; + /* printf("%.4f %.4f ",probs[(int)age][i][cptcod], mobaverage[(int)age][i][cptcod]); */ + } + /* printf("%.4f %.4f \n",sumnewp[cptcod], sumnewm[cptcod]); */ + } + /* printf("\n"); */ + /* } */ + /* brutal averaging */ + for (i=1; i<=nlstate;i++){ + for (age=1; age<=bage; age++){ + mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemingood[cptcod]][i][cptcod]; + /* printf("age=%d i=%d cptcod=%d mobaverage=%.4f \n",(int)age,i, cptcod, mobaverage[(int)age][i][cptcod]); */ + } + for (age=fage; age<=AGESUP; age++){ + mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemaxgood[cptcod]][i][cptcod]; + /* printf("age=%d i=%d cptcod=%d mobaverage=%.4f \n",(int)age,i, cptcod, mobaverage[(int)age][i][cptcod]); */ + } + } /* end i status */ + for (i=nlstate+1; i<=nlstate+ndeath;i++){ + for (age=1; age<=AGESUP; age++){ + /*printf("i=%d, age=%d, cptcod=%d\n",i, (int)age, cptcod);*/ + mobaverage[(int)age][i][cptcod]=0.; + } + } + }/* end cptcod */ + free_vector(sumnewm,1, ncovcombmax); + free_vector(sumnewp,1, ncovcombmax); + free_vector(agemaxgood,1, ncovcombmax); + free_vector(agemingood,1, ncovcombmax); + return 0; + }/* End movingaverage */ + /************** Forecasting ******************/ -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){ + 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){ /* proj1, year, month, day of starting projection agemin, agemax range of age dateprev1 dateprev2 range of dates during which prevalence is computed anproj2 year of en of projection (same day and month as proj1). */ - int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1; - int *popage; + int yearp, stepsize, hstepm, nhstepm, j, k, cptcod, i, h, i1, k4, nres=0; double agec; /* generic age */ double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean; double *popeffectif,*popcount; double ***p3mat; - double ***mobaverage; + /* double ***mobaverage; */ char fileresf[FILENAMELENGTH]; agelim=AGESUP; - prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass); + /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people + in each health status at the date of interview (if between dateprev1 and dateprev2). + We still use firstpass and lastpass as another selection. + */ + /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart,\ */ + /* firstpass, lastpass, stepm, weightopt, model); */ - strcpy(fileresf,"f"); - strcat(fileresf,fileres); + strcpy(fileresf,"F_"); + strcat(fileresf,fileresu); if((ficresf=fopen(fileresf,"w"))==NULL) { printf("Problem with forecast resultfile: %s\n", fileresf); fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf); } - printf("Computing forecasting: result on file '%s' \n", fileresf); - fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf); + printf("\nComputing forecasting: result on file '%s', please wait... \n", fileresf); + fprintf(ficlog,"\nComputing forecasting: result on file '%s', please wait... \n", fileresf); if (cptcoveff==0) ncodemax[cptcoveff]=1; - if (mobilav!=0) { - mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); - if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){ - fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav); - printf(" Error in movingaverage mobilav=%d\n",mobilav); - } - } stepsize=(int) (stepm+YEARM-1)/YEARM; if (stepm<=12) stepsize=1; @@ -4233,234 +7725,371 @@ prevforecast(char fileres[], double anpr if(jprojmean==0) jprojmean=1; if(mprojmean==0) jprojmean=1; - i1=cptcoveff; + i1=pow(2,cptcoveff); if (cptcovn < 1){i1=1;} fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2); fprintf(ficresf,"#****** Routine prevforecast **\n"); - + /* if (h==(int)(YEARM*yearp)){ */ - for(cptcov=1, k=0;cptcov<=i1;cptcov++){ - for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){ - k=k+1; - fprintf(ficresf,"\n#******"); - for(j=1;j<=cptcoveff;j++) { - 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]]); - } - fprintf(ficresf,"******\n"); - fprintf(ficresf,"# Covariate valuofcovar yearproj age"); - for(j=1; j<=nlstate+ndeath;j++){ - for(i=1; i<=nlstate;i++) - fprintf(ficresf," p%d%d",i,j); - fprintf(ficresf," p.%d",j); - } - for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) { - fprintf(ficresf,"\n"); - fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp); - - for (agec=fage; agec>=(ageminpar-1); agec--){ - nhstepm=(int) rint((agelim-agec)*YEARM/stepm); - nhstepm = nhstepm/hstepm; - p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); - oldm=oldms;savm=savms; - hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k); + for(nres=1; nres <= nresult; nres++) /* For each resultline */ + for(k=1; k<=i1;k++){ + if(i1 != 1 && TKresult[nres]!= k) + continue; + if(invalidvarcomb[k]){ + printf("\nCombination (%d) projection ignored because no cases \n",k); + continue; + } + fprintf(ficresf,"\n#****** hpijx=probability over h years, hp.jx is weighted by observed prev \n#"); + for(j=1;j<=cptcoveff;j++) { + fprintf(ficresf," V%d (=) %d",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); + } + for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */ + fprintf(ficresf," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]); + } + fprintf(ficresf," yearproj age"); + for(j=1; j<=nlstate+ndeath;j++){ + for(i=1; i<=nlstate;i++) + fprintf(ficresf," p%d%d",i,j); + fprintf(ficresf," wp.%d",j); + } + for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) { + fprintf(ficresf,"\n"); + fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp); + for (agec=fage; agec>=(ageminpar-1); agec--){ + nhstepm=(int) rint((agelim-agec)*YEARM/stepm); + nhstepm = nhstepm/hstepm; + p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); + oldm=oldms;savm=savms; + hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k,nres); - for (h=0; h<=nhstepm; h++){ - if (h*hstepm/YEARM*stepm ==yearp) { - fprintf(ficresf,"\n"); - for(j=1;j<=cptcoveff;j++) - fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]); - fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm); - } - for(j=1; j<=nlstate+ndeath;j++) { - ppij=0.; - for(i=1; i<=nlstate;i++) { - if (mobilav==1) - ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod]; - else { - ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod]; - } - if (h*hstepm/YEARM*stepm== yearp) { - fprintf(ficresf," %.3f", p3mat[i][j][h]); - } - } /* end i */ - if (h*hstepm/YEARM*stepm==yearp) { - fprintf(ficresf," %.3f", ppij); + for (h=0; h<=nhstepm; h++){ + if (h*hstepm/YEARM*stepm ==yearp) { + fprintf(ficresf,"\n"); + for(j=1;j<=cptcoveff;j++) + fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); + fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm); + } + for(j=1; j<=nlstate+ndeath;j++) { + ppij=0.; + for(i=1; i<=nlstate;i++) { + if (mobilav==1) + ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][k]; + else { + ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][k]; } - }/* end j */ - } /* end h */ - free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); - } /* end agec */ - } /* end yearp */ - } /* end cptcod */ - } /* end cptcov */ - - if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); - + if (h*hstepm/YEARM*stepm== yearp) { + fprintf(ficresf," %.3f", p3mat[i][j][h]); + } + } /* end i */ + if (h*hstepm/YEARM*stepm==yearp) { + fprintf(ficresf," %.3f", ppij); + } + }/* end j */ + } /* end h */ + free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); + } /* end agec */ + } /* end yearp */ + } /* end k */ + fclose(ficresf); -} + printf("End of Computing forecasting \n"); + fprintf(ficlog,"End of Computing forecasting\n"); -/************** Forecasting *****not tested NB*************/ -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){ - - int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h; - int *popage; - double calagedatem, agelim, kk1, kk2; - double *popeffectif,*popcount; - double ***p3mat,***tabpop,***tabpopprev; - double ***mobaverage; - char filerespop[FILENAMELENGTH]; +} - tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); - tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); - agelim=AGESUP; - calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM; +/* /\************** Back Forecasting ******************\/ */ +/* void prevbackforecast(char fileres[], double anback1, double mback1, double jback1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double anback2, double p[], int cptcoveff){ */ +/* /\* back1, year, month, day of starting backection */ +/* agemin, agemax range of age */ +/* dateprev1 dateprev2 range of dates during which prevalence is computed */ +/* anback2 year of en of backection (same day and month as back1). */ +/* *\/ */ +/* int yearp, stepsize, hstepm, nhstepm, j, k, cptcod, i, h, i1; */ +/* double agec; /\* generic age *\/ */ +/* double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean; */ +/* double *popeffectif,*popcount; */ +/* double ***p3mat; */ +/* /\* double ***mobaverage; *\/ */ +/* char fileresfb[FILENAMELENGTH]; */ + +/* agelim=AGESUP; */ +/* /\* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people */ +/* in each health status at the date of interview (if between dateprev1 and dateprev2). */ +/* We still use firstpass and lastpass as another selection. */ +/* *\/ */ +/* /\* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart,\ *\/ */ +/* /\* firstpass, lastpass, stepm, weightopt, model); *\/ */ +/* prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass); */ + +/* strcpy(fileresfb,"FB_"); */ +/* strcat(fileresfb,fileresu); */ +/* if((ficresfb=fopen(fileresfb,"w"))==NULL) { */ +/* printf("Problem with back forecast resultfile: %s\n", fileresfb); */ +/* fprintf(ficlog,"Problem with back forecast resultfile: %s\n", fileresfb); */ +/* } */ +/* printf("Computing back forecasting: result on file '%s', please wait... \n", fileresfb); */ +/* fprintf(ficlog,"Computing back forecasting: result on file '%s', please wait... \n", fileresfb); */ + +/* if (cptcoveff==0) ncodemax[cptcoveff]=1; */ + +/* /\* if (mobilav!=0) { *\/ */ +/* /\* mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); *\/ */ +/* /\* if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){ *\/ */ +/* /\* fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav); *\/ */ +/* /\* printf(" Error in movingaverage mobilav=%d\n",mobilav); *\/ */ +/* /\* } *\/ */ +/* /\* } *\/ */ + +/* stepsize=(int) (stepm+YEARM-1)/YEARM; */ +/* if (stepm<=12) stepsize=1; */ +/* if(estepm < stepm){ */ +/* printf ("Problem %d lower than %d\n",estepm, stepm); */ +/* } */ +/* else hstepm=estepm; */ + +/* hstepm=hstepm/stepm; */ +/* yp1=modf(dateintmean,&yp);/\* extracts integral of datemean in yp and */ +/* fractional in yp1 *\/ */ +/* anprojmean=yp; */ +/* yp2=modf((yp1*12),&yp); */ +/* mprojmean=yp; */ +/* yp1=modf((yp2*30.5),&yp); */ +/* jprojmean=yp; */ +/* if(jprojmean==0) jprojmean=1; */ +/* if(mprojmean==0) jprojmean=1; */ + +/* i1=cptcoveff; */ +/* if (cptcovn < 1){i1=1;} */ - prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass); +/* fprintf(ficresfb,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2); */ +/* fprintf(ficresfb,"#****** Routine prevbackforecast **\n"); */ + +/* /\* if (h==(int)(YEARM*yearp)){ *\/ */ +/* for(cptcov=1, k=0;cptcov<=i1;cptcov++){ */ +/* for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){ */ +/* k=k+1; */ +/* fprintf(ficresfb,"\n#****** hbijx=probability over h years, hp.jx is weighted by observed prev \n#"); */ +/* for(j=1;j<=cptcoveff;j++) { */ +/* fprintf(ficresfb," V%d (=) %d",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); */ +/* } */ +/* fprintf(ficresfb," yearbproj age"); */ +/* for(j=1; j<=nlstate+ndeath;j++){ */ +/* for(i=1; i<=nlstate;i++) */ +/* fprintf(ficresfb," p%d%d",i,j); */ +/* fprintf(ficresfb," p.%d",j); */ +/* } */ +/* for (yearp=0; yearp>=(anback2-anback1);yearp -=stepsize) { */ +/* /\* for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) { *\/ */ +/* fprintf(ficresfb,"\n"); */ +/* fprintf(ficresfb,"\n# Back Forecasting at date %.lf/%.lf/%.lf ",jback1,mback1,anback1+yearp); */ +/* for (agec=fage; agec>=(ageminpar-1); agec--){ */ +/* nhstepm=(int) rint((agelim-agec)*YEARM/stepm); */ +/* nhstepm = nhstepm/hstepm; */ +/* p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); */ +/* oldm=oldms;savm=savms; */ +/* hbxij(p3mat,nhstepm,agec,hstepm,p,prevacurrent,nlstate,stepm,oldm,savm,oldm,savm, dnewm, doldm, dsavm, k); */ +/* for (h=0; h<=nhstepm; h++){ */ +/* if (h*hstepm/YEARM*stepm ==yearp) { */ +/* fprintf(ficresfb,"\n"); */ +/* for(j=1;j<=cptcoveff;j++) */ +/* fprintf(ficresfb,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); */ +/* fprintf(ficresfb,"%.f %.f ",anback1+yearp,agec+h*hstepm/YEARM*stepm); */ +/* } */ +/* for(j=1; j<=nlstate+ndeath;j++) { */ +/* ppij=0.; */ +/* for(i=1; i<=nlstate;i++) { */ +/* if (mobilav==1) */ +/* ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod]; */ +/* else { */ +/* ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod]; */ +/* } */ +/* if (h*hstepm/YEARM*stepm== yearp) { */ +/* fprintf(ficresfb," %.3f", p3mat[i][j][h]); */ +/* } */ +/* } /\* end i *\/ */ +/* if (h*hstepm/YEARM*stepm==yearp) { */ +/* fprintf(ficresfb," %.3f", ppij); */ +/* } */ +/* }/\* end j *\/ */ +/* } /\* end h *\/ */ +/* free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); */ +/* } /\* end agec *\/ */ +/* } /\* end yearp *\/ */ +/* } /\* end cptcod *\/ */ +/* } /\* end cptcov *\/ */ + +/* /\* if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); *\/ */ + +/* fclose(ficresfb); */ +/* printf("End of Computing Back forecasting \n"); */ +/* fprintf(ficlog,"End of Computing Back forecasting\n"); */ + +/* } */ + +/************** Forecasting *****not tested NB*************/ +/* void populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2s, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){ */ - strcpy(filerespop,"pop"); - strcat(filerespop,fileres); - if((ficrespop=fopen(filerespop,"w"))==NULL) { - printf("Problem with forecast resultfile: %s\n", filerespop); - fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop); - } - printf("Computing forecasting: result on file '%s' \n", filerespop); - fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop); +/* int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h; */ +/* int *popage; */ +/* double calagedatem, agelim, kk1, kk2; */ +/* double *popeffectif,*popcount; */ +/* double ***p3mat,***tabpop,***tabpopprev; */ +/* /\* double ***mobaverage; *\/ */ +/* char filerespop[FILENAMELENGTH]; */ + +/* tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */ +/* tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */ +/* agelim=AGESUP; */ +/* calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM; */ + +/* prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass); */ + + +/* strcpy(filerespop,"POP_"); */ +/* strcat(filerespop,fileresu); */ +/* if((ficrespop=fopen(filerespop,"w"))==NULL) { */ +/* printf("Problem with forecast resultfile: %s\n", filerespop); */ +/* fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop); */ +/* } */ +/* printf("Computing forecasting: result on file '%s' \n", filerespop); */ +/* fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop); */ - if (cptcoveff==0) ncodemax[cptcoveff]=1; +/* if (cptcoveff==0) ncodemax[cptcoveff]=1; */ - if (mobilav!=0) { - mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); - if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){ - fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav); - printf(" Error in movingaverage mobilav=%d\n",mobilav); - } - } +/* /\* if (mobilav!=0) { *\/ */ +/* /\* mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); *\/ */ +/* /\* if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){ *\/ */ +/* /\* fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav); *\/ */ +/* /\* printf(" Error in movingaverage mobilav=%d\n",mobilav); *\/ */ +/* /\* } *\/ */ +/* /\* } *\/ */ - stepsize=(int) (stepm+YEARM-1)/YEARM; - if (stepm<=12) stepsize=1; - - agelim=AGESUP; +/* stepsize=(int) (stepm+YEARM-1)/YEARM; */ +/* if (stepm<=12) stepsize=1; */ - hstepm=1; - hstepm=hstepm/stepm; +/* agelim=AGESUP; */ - if (popforecast==1) { - if((ficpop=fopen(popfile,"r"))==NULL) { - printf("Problem with population file : %s\n",popfile);exit(0); - fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0); - } - popage=ivector(0,AGESUP); - popeffectif=vector(0,AGESUP); - popcount=vector(0,AGESUP); +/* hstepm=1; */ +/* hstepm=hstepm/stepm; */ + +/* if (popforecast==1) { */ +/* if((ficpop=fopen(popfile,"r"))==NULL) { */ +/* printf("Problem with population file : %s\n",popfile);exit(0); */ +/* fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0); */ +/* } */ +/* popage=ivector(0,AGESUP); */ +/* popeffectif=vector(0,AGESUP); */ +/* popcount=vector(0,AGESUP); */ - i=1; - while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1; - - imx=i; - for (i=1; i=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ - nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); - nhstepm = nhstepm/hstepm; +/* for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ */ +/* nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); */ +/* nhstepm = nhstepm/hstepm; */ - p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); - oldm=oldms;savm=savms; - hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k); - - for (h=0; h<=nhstepm; h++){ - if (h==(int) (calagedatem+YEARM*cpt)) { - fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm); - } - for(j=1; j<=nlstate+ndeath;j++) { - kk1=0.;kk2=0; - for(i=1; i<=nlstate;i++) { - if (mobilav==1) - kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod]; - else { - kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod]; - } - } - if (h==(int)(calagedatem+12*cpt)){ - tabpop[(int)(agedeb)][j][cptcod]=kk1; - /*fprintf(ficrespop," %.3f", kk1); - if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/ - } - } - for(i=1; i<=nlstate;i++){ - kk1=0.; - for(j=1; j<=nlstate;j++){ - kk1= kk1+tabpop[(int)(agedeb)][j][cptcod]; - } - tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)]; - } - - if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++) - fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]); - } - free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); - } - } - - /******/ - - for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) { - fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt); - for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ - nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); - nhstepm = nhstepm/hstepm; +/* p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); */ +/* oldm=oldms;savm=savms; */ +/* hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k); */ - p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); - oldm=oldms;savm=savms; - hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k); - for (h=0; h<=nhstepm; h++){ - if (h==(int) (calagedatem+YEARM*cpt)) { - fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm); - } - for(j=1; j<=nlstate+ndeath;j++) { - kk1=0.;kk2=0; - for(i=1; i<=nlstate;i++) { - kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod]; - } - if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1); - } - } - free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); - } - } - } - } +/* for (h=0; h<=nhstepm; h++){ */ +/* if (h==(int) (calagedatem+YEARM*cpt)) { */ +/* fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm); */ +/* } */ +/* for(j=1; j<=nlstate+ndeath;j++) { */ +/* kk1=0.;kk2=0; */ +/* for(i=1; i<=nlstate;i++) { */ +/* if (mobilav==1) */ +/* kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod]; */ +/* else { */ +/* kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod]; */ +/* } */ +/* } */ +/* if (h==(int)(calagedatem+12*cpt)){ */ +/* tabpop[(int)(agedeb)][j][cptcod]=kk1; */ +/* /\*fprintf(ficrespop," %.3f", kk1); */ +/* if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*\/ */ +/* } */ +/* } */ +/* for(i=1; i<=nlstate;i++){ */ +/* kk1=0.; */ +/* for(j=1; j<=nlstate;j++){ */ +/* kk1= kk1+tabpop[(int)(agedeb)][j][cptcod]; */ +/* } */ +/* tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)]; */ +/* } */ + +/* if (h==(int)(calagedatem+12*cpt)) */ +/* for(j=1; j<=nlstate;j++) */ +/* fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]); */ +/* } */ +/* free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); */ +/* } */ +/* } */ + +/* /\******\/ */ + +/* for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) { */ +/* fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt); */ +/* for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ */ +/* nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); */ +/* nhstepm = nhstepm/hstepm; */ + +/* p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); */ +/* oldm=oldms;savm=savms; */ +/* hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k); */ +/* for (h=0; h<=nhstepm; h++){ */ +/* if (h==(int) (calagedatem+YEARM*cpt)) { */ +/* fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm); */ +/* } */ +/* for(j=1; j<=nlstate+ndeath;j++) { */ +/* kk1=0.;kk2=0; */ +/* for(i=1; i<=nlstate;i++) { */ +/* kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod]; */ +/* } */ +/* if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1); */ +/* } */ +/* } */ +/* free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); */ +/* } */ +/* } */ +/* } */ +/* } */ + +/* /\* if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); *\/ */ + +/* if (popforecast==1) { */ +/* free_ivector(popage,0,AGESUP); */ +/* free_vector(popeffectif,0,AGESUP); */ +/* free_vector(popcount,0,AGESUP); */ +/* } */ +/* free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */ +/* free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */ +/* fclose(ficrespop); */ +/* } /\* End of popforecast *\/ */ - if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); - - if (popforecast==1) { - free_ivector(popage,0,AGESUP); - free_vector(popeffectif,0,AGESUP); - free_vector(popcount,0,AGESUP); - } - free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); - free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); - fclose(ficrespop); -} /* End of popforecast */ - int fileappend(FILE *fichier, char *optionfich) { if((fichier=fopen(optionfich,"a"))==NULL) { @@ -4479,8 +8108,8 @@ void prwizard(int ncovmodel, int nlstate /* Wizard to print covariance matrix template */ - char ca[32], cb[32], cc[32]; - int i,j, k, l, li, lj, lk, ll, jj, npar, itimes; + char ca[32], cb[32]; + int i,j, k, li, lj, lk, ll, jj, npar, itimes; int numlinepar; printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n"); @@ -4601,7 +8230,7 @@ double gompertz(double x[]) double A,B,L=0.0,sump=0.,num=0.; int i,n=0; /* n is the size of the sample */ - for (i=0;i<=imx-1 ; i++) { + for (i=1;i<=imx ; i++) { sump=sump+weight[i]; /* sump=sump+1;*/ num=num+1; @@ -4674,7 +8303,7 @@ double gompertz_f(const gsl_vector *v, v #endif /******************* Printing html file ***********/ -void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \ +void printinghtmlmort(char fileresu[], char title[], char datafile[], int firstpass, \ int lastpass, int stepm, int weightopt, char model[],\ int imx, double p[],double **matcov,double agemortsup){ int i,k; @@ -4683,7 +8312,7 @@ void printinghtmlmort(char fileres[], ch fprintf(fichtm," mu(age) =%lf*exp(%lf*(age-%d)) per year

          ",p[1],p[2],agegomp); for (i=1;i<=2;i++) 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])); - fprintf(fichtm,"

          "); + fprintf(fichtm,"

          "); fprintf(fichtm,"
        "); fprintf(fichtm,"

        • Life table

          \n
          "); @@ -4698,10 +8327,10 @@ fprintf(fichtm,"

          • Life table=1;j--){ + for (iv=nqtv;iv>=1;iv--){ /* Loop on time varying quantitative variables */ + cutv(stra, strb, line, ' '); + if(strb[0]=='.') { /* Missing value */ + lval=-1; + cotqvar[j][iv][i]=-1; /* 0.0/0.0 */ + cotvar[j][ntv+iv][i]=-1; /* For performance reasons */ + if(isalpha(strb[1])) { /* .m or .d Really Missing value */ + printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be the %d th quantitative value out of %d measured at wave %d. If missing, you should remove this individual or impute a value. Exiting.\n", strb, linei,i,line,iv, nqtv, j); + fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be the %d th quantitative value out of %d measured at wave %d. If missing, you should remove this individual or impute a value. Exiting.\n", strb, linei,i,line,iv, nqtv, j);fflush(ficlog); + return 1; + } + }else{ + errno=0; + /* what_kind_of_number(strb); */ + dval=strtod(strb,&endptr); + /* if( strb[0]=='\0' || (*endptr != '\0')){ */ + /* if(strb != endptr && *endptr == '\0') */ + /* dval=dlval; */ + /* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN)) */ + if( strb[0]=='\0' || (*endptr != '\0')){ + printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be the %d th quantitative value out of %d measured at wave %d. Setting maxwav=%d might be wrong. Exiting.\n", strb, linei,i,line,iv, nqtv, j,maxwav); + fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be the %d th quantitative value out of %d measured at wave %d. Setting maxwav=%d might be wrong. Exiting.\n", strb, linei,i,line, iv, nqtv, j,maxwav);fflush(ficlog); + return 1; + } + cotqvar[j][iv][i]=dval; + cotvar[j][ntv+iv][i]=dval; + } + strcpy(line,stra); + }/* end loop ntqv */ + + for (iv=ntv;iv>=1;iv--){ /* Loop on time varying dummies */ + cutv(stra, strb, line, ' '); + if(strb[0]=='.') { /* Missing value */ + lval=-1; + }else{ + errno=0; + lval=strtol(strb,&endptr,10); + /* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/ + if( strb[0]=='\0' || (*endptr != '\0')){ + printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be the %d th dummy covariate out of %d measured at wave %d. Setting maxwav=%d might be wrong. Exiting.\n", strb, linei,i,line,iv, ntv, j,maxwav); + fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be the %d dummy covariate out of %d measured wave %d. Setting maxwav=%d might be wrong. Exiting.\n", strb, linei,i,line,iv, ntv,j,maxwav);fflush(ficlog); + return 1; + } + } + if(lval <-1 || lval >1){ + printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\n \ + Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \ + for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \ + For example, for multinomial values like 1, 2 and 3,\n \ + build V1=0 V2=0 for the reference value (1),\n \ + V1=1 V2=0 for (2) \n \ + and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \ + output of IMaCh is often meaningless.\n \ + Exiting.\n",lval,linei, i,line,j); + fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\n \ + Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \ + for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \ + For example, for multinomial values like 1, 2 and 3,\n \ + build V1=0 V2=0 for the reference value (1),\n \ + V1=1 V2=0 for (2) \n \ + and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \ + output of IMaCh is often meaningless.\n \ + Exiting.\n",lval,linei, i,line,j);fflush(ficlog); + return 1; + } + cotvar[j][iv][i]=(double)(lval); + strcpy(line,stra); + }/* end loop ntv */ + + /* Statuses at wave */ cutv(stra, strb, line, ' '); - if(strb[0]=='.') { /* Missing status */ + if(strb[0]=='.') { /* Missing value */ lval=-1; }else{ errno=0; lval=strtol(strb,&endptr,10); - /* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/ + /* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/ if( strb[0]=='\0' || (*endptr != '\0')){ 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); 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); return 1; } } + s[j][i]=lval; + /* Date of Interview */ strcpy(line,stra); cutv(stra, strb,line,' '); - if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){ + if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){ } - else if(iout=sscanf(strb,"%s.",dummy) != 0){ + else if( (iout=sscanf(strb,"%s.",dummy)) != 0){ month=99; year=9999; }else{ @@ -4793,44 +8515,47 @@ int readdata(char datafile[], int firsto anint[j][i]= (double) year; mint[j][i]= (double)month; strcpy(line,stra); - } /* ENd Waves */ + } /* End loop on waves */ + /* Date of death */ cutv(stra, strb,line,' '); - if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){ + if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){ } - else if(iout=sscanf(strb,"%s.",dummy) != 0){ + else if( (iout=sscanf(strb,"%s.",dummy)) != 0){ month=99; year=9999; }else{ 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); - 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); - return 1; + 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); + return 1; } andc[i]=(double) year; moisdc[i]=(double) month; strcpy(line,stra); + /* Date of birth */ cutv(stra, strb,line,' '); - if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){ + if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){ } - else if(iout=sscanf(strb,"%s.", dummy) != 0){ + else if( (iout=sscanf(strb,"%s.", dummy)) != 0){ month=99; year=9999; }else{ 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); 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); - return 1; + return 1; } if (year==9999) { 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); 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); - return 1; - + return 1; + } annais[i]=(double)(year); moisnais[i]=(double)(month); strcpy(line,stra); + /* Sample weight */ cutv(stra, strb,line,' '); errno=0; dval=strtod(strb,&endptr); @@ -4843,9 +8568,32 @@ int readdata(char datafile[], int firsto weight[i]=dval; strcpy(line,stra); + for (iv=nqv;iv>=1;iv--){ /* Loop on fixed quantitative variables */ + cutv(stra, strb, line, ' '); + if(strb[0]=='.') { /* Missing value */ + lval=-1; + }else{ + errno=0; + /* what_kind_of_number(strb); */ + dval=strtod(strb,&endptr); + /* if(strb != endptr && *endptr == '\0') */ + /* dval=dlval; */ + /* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN)) */ + if( strb[0]=='\0' || (*endptr != '\0')){ + printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be the %d th quantitative value (out of %d) constant for all waves. Setting maxwav=%d might be wrong. Exiting.\n", strb, linei,i,line, iv, nqv, maxwav); + fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be the %d th quantitative value (out of %d) constant for all waves. Setting maxwav=%d might be wrong. Exiting.\n", strb, linei,i,line, iv, nqv, maxwav);fflush(ficlog); + return 1; + } + coqvar[iv][i]=dval; + covar[ncovcol+iv][i]=dval; /* including qvar in standard covar for performance reasons */ + } + strcpy(line,stra); + }/* end loop nqv */ + + /* Covariate values */ for (j=ncovcol;j>=1;j--){ cutv(stra, strb,line,' '); - if(strb[0]=='.') { /* Missing status */ + if(strb[0]=='.') { /* Missing covariate value */ lval=-1; }else{ errno=0; @@ -4860,20 +8608,20 @@ int readdata(char datafile[], int firsto printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\n \ Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \ for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \ - For example, for multinomial values like 1, 2 and 3,\n \ - build V1=0 V2=0 for the reference value (1),\n \ - V1=1 V2=0 for (2) \n \ + For example, for multinomial values like 1, 2 and 3,\n \ + build V1=0 V2=0 for the reference value (1),\n \ + V1=1 V2=0 for (2) \n \ and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \ - output of IMaCh is often meaningless.\n \ + output of IMaCh is often meaningless.\n \ Exiting.\n",lval,linei, i,line,j); fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\n \ Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \ for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \ - For example, for multinomial values like 1, 2 and 3,\n \ - build V1=0 V2=0 for the reference value (1),\n \ - V1=1 V2=0 for (2) \n \ + For example, for multinomial values like 1, 2 and 3,\n \ + build V1=0 V2=0 for the reference value (1),\n \ + V1=1 V2=0 for (2) \n \ and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \ - output of IMaCh is often meaningless.\n \ + output of IMaCh is often meaningless.\n \ Exiting.\n",lval,linei, i,line,j);fflush(ficlog); return 1; } @@ -4881,7 +8629,7 @@ int readdata(char datafile[], int firsto strcpy(line,stra); } lstra=strlen(stra); - + if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */ stratrunc = &(stra[lstra-9]); num[i]=atol(stratrunc); @@ -4893,61 +8641,181 @@ int readdata(char datafile[], int firsto i=i+1; } /* End loop reading data */ - + *imax=i-1; /* Number of individuals */ fclose(fic); - + return (0); - endread: - printf("Exiting readdata: "); - fclose(fic); - return (1); + /* endread: */ + printf("Exiting readdata: "); + fclose(fic); + return (1); +} +void removefirstspace(char **stri){/*, char stro[]) {*/ + char *p1 = *stri, *p2 = *stri; + while (*p2 == ' ') + p2++; + /* while ((*p1++ = *p2++) !=0) */ + /* ; */ + /* do */ + /* while (*p2 == ' ') */ + /* p2++; */ + /* while (*p1++ == *p2++); */ + *stri=p2; +} + +int decoderesult ( char resultline[], int nres) +/**< This routine decode one result line and returns the combination # of dummy covariates only **/ +{ + int j=0, k=0, k1=0, k2=0, k3=0, k4=0, match=0, k2q=0, k3q=0, k4q=0; + char resultsav[MAXLINE]; + int resultmodel[MAXLINE]; + int modelresult[MAXLINE]; + char stra[80], strb[80], strc[80], strd[80],stre[80]; + removefirstspace(&resultline); + printf("decoderesult:%s\n",resultline); + if (strstr(resultline,"v") !=0){ + printf("Error. 'v' must be in upper case 'V' result: %s ",resultline); + fprintf(ficlog,"Error. 'v' must be in upper case result: %s ",resultline);fflush(ficlog); + return 1; + } + trimbb(resultsav, resultline); + if (strlen(resultsav) >1){ + j=nbocc(resultsav,'='); /**< j=Number of covariate values'=' */ + } + if(j == 0){ /* Resultline but no = */ + TKresult[nres]=0; /* Combination for the nresult and the model */ + return (0); + } + + if( j != cptcovs ){ /* Be careful if a variable is in a product but not single */ + printf("ERROR: the number of variable in the resultline, %d, differs from the number of variable used in the model line, %d.\n",j, cptcovs); + fprintf(ficlog,"ERROR: the number of variable in the resultline, %d, differs from the number of variable used in the model line, %d.\n",j, cptcovs); + } + for(k=1; k<=j;k++){ /* Loop on any covariate of the result line */ + if(nbocc(resultsav,'=') >1){ + cutl(stra,strb,resultsav,' '); /* keeps in strb after the first ' ' + resultsav= V4=1 V5=25.1 V3=0 strb=V3=0 stra= V4=1 V5=25.1 */ + cutl(strc,strd,strb,'='); /* strb:V4=1 strc=1 strd=V4 */ + }else + cutl(strc,strd,resultsav,'='); + Tvalsel[k]=atof(strc); /* 1 */ + + cutl(strc,stre,strd,'V'); /* strd='V4' strc=4 stre='V' */; + Tvarsel[k]=atoi(strc); + /* Typevarsel[k]=1; /\* 1 for age product *\/ */ + /* cptcovsel++; */ + if (nbocc(stra,'=') >0) + strcpy(resultsav,stra); /* and analyzes it */ + } + /* Checking for missing or useless values in comparison of current model needs */ + for(k1=1; k1<= cptcovt ;k1++){ /* model line V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ + if(Typevar[k1]==0){ /* Single covariate in model */ + match=0; + for(k2=1; k2 <=j;k2++){/* result line V4=1 V5=24.1 V3=1 V2=8 V1=0 */ + if(Tvar[k1]==Tvarsel[k2]) {/* Tvar[1]=5 == Tvarsel[2]=5 */ + modelresult[k2]=k1;/* modelresult[2]=1 modelresult[1]=2 modelresult[3]=3 modelresult[6]=4 modelresult[9]=5 */ + match=1; + break; + } + } + if(match == 0){ + printf("Error in result line: %d value missing; result: %s, model=%s\n",k1, resultline, model); + } + } + } + /* Checking for missing or useless values in comparison of current model needs */ + for(k2=1; k2 <=j;k2++){ /* result line V4=1 V5=24.1 V3=1 V2=8 V1=0 */ + match=0; + for(k1=1; k1<= cptcovt ;k1++){ /* model line V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ + if(Typevar[k1]==0){ /* Single */ + if(Tvar[k1]==Tvarsel[k2]) { /* Tvar[2]=4 == Tvarsel[1]=4 */ + resultmodel[k1]=k2; /* resultmodel[2]=1 resultmodel[1]=2 resultmodel[3]=3 resultmodel[6]=4 resultmodel[9]=5 */ + ++match; + } + } + } + if(match == 0){ + printf("Error in result line: %d value missing; result: %s, model=%s\n",k1, resultline, model); + }else if(match > 1){ + printf("Error in result line: %d doubled; result: %s, model=%s\n",k2, resultline, model); + } + } + + /* We need to deduce which combination number is chosen and save quantitative values */ + /* model line V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ + /* result line V4=1 V5=25.1 V3=0 V2=8 V1=1 */ + /* should give a combination of dummy V4=1, V3=0, V1=1 => V4*2**(0) + V3*2**(1) + V1*2**(2) = 5 + (1offset) = 6*/ + /* result line V4=1 V5=24.1 V3=1 V2=8 V1=0 */ + /* should give a combination of dummy V4=1, V3=1, V1=0 => V4*2**(0) + V3*2**(1) + V1*2**(2) = 3 + (1offset) = 4*/ + /* 1 0 0 0 */ + /* 2 1 0 0 */ + /* 3 0 1 0 */ + /* 4 1 1 0 */ /* V4=1, V3=1, V1=0 */ + /* 5 0 0 1 */ + /* 6 1 0 1 */ /* V4=1, V3=0, V1=1 */ + /* 7 0 1 1 */ + /* 8 1 1 1 */ + /* V(Tvresult)=Tresult V4=1 V3=0 V1=1 Tresult[nres=1][2]=0 */ + /* V(Tvqresult)=Tqresult V5=25.1 V2=8 Tqresult[nres=1][1]=25.1 */ + /* V5*age V5 known which value for nres? */ + /* Tqinvresult[2]=8 Tqinvresult[1]=25.1 */ + for(k1=1, k=0, k4=0, k4q=0; k1 <=cptcovt;k1++){ /* model line */ + if( Dummy[k1]==0 && Typevar[k1]==0 ){ /* Single dummy */ + k3= resultmodel[k1]; /* resultmodel[2(V4)] = 1=k3 */ + k2=(int)Tvarsel[k3]; /* Tvarsel[resultmodel[2]]= Tvarsel[1] = 4=k2 */ + k+=Tvalsel[k3]*pow(2,k4); /* Tvalsel[1]=1 */ + Tresult[nres][k4+1]=Tvalsel[k3];/* Tresult[nres][1]=1(V4=1) Tresult[nres][2]=0(V3=0) */ + Tvresult[nres][k4+1]=(int)Tvarsel[k3];/* Tvresult[nres][1]=4 Tvresult[nres][3]=1 */ + Tinvresult[nres][(int)Tvarsel[k3]]=Tvalsel[k3]; /* Tinvresult[nres][4]=1 */ + printf("Decoderesult Dummy k=%d, V(k2=V%d)= Tvalsel[%d]=%d, 2**(%d)\n",k, k2, k3, (int)Tvalsel[k3], k4); + k4++;; + } else if( Dummy[k1]==1 && Typevar[k1]==0 ){ /* Single quantitative */ + k3q= resultmodel[k1]; /* resultmodel[2] = 1=k3 */ + k2q=(int)Tvarsel[k3q]; /* Tvarsel[resultmodel[2]]= Tvarsel[1] = 4=k2 */ + Tqresult[nres][k4q+1]=Tvalsel[k3q]; /* Tqresult[nres][1]=25.1 */ + Tvqresult[nres][k4q+1]=(int)Tvarsel[k3q]; /* Tvqresult[nres][1]=5 */ + Tqinvresult[nres][(int)Tvarsel[k3q]]=Tvalsel[k3q]; /* Tqinvresult[nres][5]=25.1 */ + printf("Decoderesult Quantitative nres=%d, V(k2q=V%d)= Tvalsel[%d]=%d, Tvarsel[%d]=%f\n",nres, k2q, k3q, Tvarsel[k3q], k3q, Tvalsel[k3q]); + k4q++;; + } + } + + TKresult[nres]=++k; /* Combination for the nresult and the model */ + return (0); } -void removespace(char *str) { - char *p1 = str, *p2 = str; - do - while (*p2 == ' ') - p2++; - while (*p1++ = *p2++); -} - -int decodemodel ( char model[], int lastobs) /**< This routine decode the model and returns: - * Model V1+V2+V3+V8+V7*V8+V5*V6+V8*age+V3*age - * - cptcovt total number of covariates of the model nbocc(+)+1 = 8 - * - cptcovn or number of covariates k of the models excluding age*products =6 - * - cptcovage number of covariates with age*products =2 - * - cptcovs number of simple covariates - * - 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 - * which is a new column after the 9 (ncovcol) variables. - * - if k is a product Vn*Vm covar[k][i] is filled with correct values for each individual - * - Tprod[l] gives the kth covariates of the product Vn*Vm l=1 to cptcovprod-cptcovage - * Tprod[1]@2 {5, 6}: position of first product V7*V8 is 5, and second V5*V6 is 6. - * - Tvard[k] p Tvard[1][1]@4 {7, 8, 5, 6} for V7*V8 and V5*V6 . - */ + +int decodemodel( char model[], int lastobs) + /**< This routine decodes the model and returns: + * Model V1+V2+V3+V8+V7*V8+V5*V6+V8*age+V3*age+age*age + * - nagesqr = 1 if age*age in the model, otherwise 0. + * - cptcovt total number of covariates of the model nbocc(+)+1 = 8 excepting constant and age and age*age + * - cptcovn or number of covariates k of the models excluding age*products =6 and age*age + * - cptcovage number of covariates with age*products =2 + * - cptcovs number of simple covariates + * - 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 + * which is a new column after the 9 (ncovcol) variables. + * - if k is a product Vn*Vm covar[k][i] is filled with correct values for each individual + * - Tprod[l] gives the kth covariates of the product Vn*Vm l=1 to cptcovprod-cptcovage + * Tprod[1]@2 {5, 6}: position of first product V7*V8 is 5, and second V5*V6 is 6. + * - Tvard[k] p Tvard[1][1]@4 {7, 8, 5, 6} for V7*V8 and V5*V6 . + */ { - int i, j, k, ks; - int i1, j1, k1, k2; + int i, j, k, ks, v; + int j1, k1, k2, k3, k4; char modelsav[80]; char stra[80], strb[80], strc[80], strd[80],stre[80]; + char *strpt; /*removespace(model);*/ if (strlen(model) >1){ /* If there is at least 1 covariate */ j=0, j1=0, k1=0, k2=-1, ks=0, cptcovn=0; - j=nbocc(model,'+'); /**< j=Number of '+' */ - j1=nbocc(model,'*'); /**< j1=Number of '*' */ - cptcovs=j+1-j1; /**< Number of simple covariates V1+V2*age+V3 +V3*V4=> V1 + V3 =2 */ - cptcovt= j+1; /* Number of total covariates in the model V1 + V2*age+ V3 + V3*V4=> 4*/ - /* including age products which are counted in cptcovage. - /* but the covariates which are products must be treated separately: ncovn=4- 2=2 (V1+V3). */ - cptcovprod=j1; /**< Number of products V1*V2 +v3*age = 2 */ - cptcovprodnoage=0; /**< Number of covariate products without age: V3*V4 =1 */ - strcpy(modelsav,model); if (strstr(model,"AGE") !=0){ - printf("Error. AGE must be in lower case 'age' model=%s ",model); - fprintf(ficlog,"Error. AGE must be in lower case model=%s ",model);fflush(ficlog); + printf("Error. AGE must be in lower case 'age' model=1+age+%s. ",model); + fprintf(ficlog,"Error. AGE must be in lower case model=1+age+%s. ",model);fflush(ficlog); return 1; } if (strstr(model,"v") !=0){ @@ -4955,155 +8823,498 @@ int decodemodel ( char model[], int last fprintf(ficlog,"Error. 'v' must be in upper case model=%s ",model);fflush(ficlog); return 1; } - - /* Design - * V1 V2 V3 V4 V5 V6 V7 V8 V9 Weight - * < ncovcol=8 > - * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8 - * k= 1 2 3 4 5 6 7 8 - * cptcovn number of covariates (not including constant and age ) = # of + plus 1 = 7+1=8 - * covar[k,i], value of kth covariate if not including age for individual i: - * covar[1][i]= (V2), covar[4][i]=(V3), covar[8][i]=(V8) - * Tvar[k] # of the kth covariate: Tvar[1]=2 Tvar[4]=3 Tvar[8]=8 - * if multiplied by age: V3*age Tvar[3=V3*age]=3 (V3) Tvar[7]=8 and - * Tage[++cptcovage]=k - * if products, new covar are created after ncovcol with k1 - * Tvar[k]=ncovcol+k1; # of the kth covariate product: Tvar[5]=ncovcol+1=10 Tvar[6]=ncovcol+1=11 - * Tprod[k1]=k; Tprod[1]=5 Tprod[2]= 6; gives the position of the k1th product - * 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 - * Tvar[cptcovn+k2]=Tvard[k1][1];Tvar[cptcovn+k2+1]=Tvard[k1][2]; - * Tvar[8+1]=5;Tvar[8+2]=6;Tvar[8+3]=7;Tvar[8+4]=8 inverted - * V1 V2 V3 V4 V5 V6 V7 V8 V9 V10 V11 - * < ncovcol=8 > - * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8 d1 d1 d2 d2 - * k= 1 2 3 4 5 6 7 8 9 10 11 12 - * Tvar[k]= 2 1 3 3 10 11 8 8 5 6 7 8 - * p Tvar[1]@12={2, 1, 3, 3, 11, 10, 8, 8, 7, 8, 5, 6} - * p Tprod[1]@2={ 6, 5} - *p Tvard[1][1]@4= {7, 8, 5, 6} - * covar[k][i]= V2 V1 ? V3 V5*V6? V7*V8? ? V8 - * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; - *How to reorganize? - * Model V1 + V2 + V3 + V8 + V5*V6 + V7*V8 + V3*age + V8*age - * Tvars {2, 1, 3, 3, 11, 10, 8, 8, 7, 8, 5, 6} - * {2, 1, 4, 8, 5, 6, 3, 7} - * Struct [] - */ - - /* This loop fills the array Tvar from the string 'model'.*/ - /* j is the number of + signs in the model V1+V2+V3 j=2 i=3 to 1 */ - /* modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4 */ - /* k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tage[cptcovage=1]=4 */ - /* k=3 V4 Tvar[k=3]= 4 (from V4) */ - /* k=2 V1 Tvar[k=2]= 1 (from V1) */ - /* k=1 Tvar[1]=2 (from V2) */ - /* k=5 Tvar[5] */ - /* for (k=1; k<=cptcovn;k++) { */ - /* cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]]; */ - /* } */ - /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */ - /* - * Treating invertedly V2+V1+V3*age+V2*V4 is as if written V2*V4 +V3*age + V1 + V2 */ - for(k=cptcovt; k>=1;k--) /**< Number of covariates */ - Tvar[k]=0; - cptcovage=0; - for(k=1; k<=cptcovt;k++){ /* Loop on total covariates of the model */ - cutl(stra,strb,modelsav,'+'); /* keeps in strb after the first '+' - modelsav==V2+V1+V4+V3*age strb=V3*age stra=V2+V1+V4 */ - if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */ - /* printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/ - /*scanf("%d",i);*/ - if (strchr(strb,'*')) { /**< Model includes a product V2+V1+V4+V3*age strb=V3*age */ - cutl(strc,strd,strb,'*'); /**< strd*strc Vm*Vn: strb=V3*age(input) strc=age strd=V3 ; V3*V2 strc=V2, strd=V3 */ - if (strcmp(strc,"age")==0) { /**< Model includes age: Vn*age */ - /* covar is not filled and then is empty */ - cptcovprod--; - cutl(stre,strb,strd,'V'); /* strd=V3(input): stre="3" */ - Tvar[k]=atoi(stre); /* V2+V1+V4+V3*age Tvar[4]=3 ; V1+V2*age Tvar[2]=2 */ - cptcovage++; /* Sums the number of covariates which include age as a product */ - Tage[cptcovage]=k; /* Tage[1] = 4 */ - /*printf("stre=%s ", stre);*/ - } else if (strcmp(strd,"age")==0) { /* or age*Vn */ - cptcovprod--; - cutl(stre,strb,strc,'V'); - Tvar[k]=atoi(stre); - cptcovage++; - Tage[cptcovage]=k; - } else { /* Age is not in the model product V2+V1+V1*V4+V3*age+V3*V2 strb=V3*V2*/ - /* loops on k1=1 (V3*V2) and k1=2 V4*V3 */ - cptcovn++; - cptcovprodnoage++;k1++; - cutl(stre,strb,strc,'V'); /* strc= Vn, stre is n; strb=V3*V2 stre=3 strc=*/ - Tvar[k]=ncovcol+k1; /* For model-covariate k tells which data-covariate to use but - because this model-covariate is a construction we invent a new column - ncovcol + k1 - If already ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2 - Tvar[3=V1*V4]=4+1 Tvar[5=V3*V2]=4 + 2= 6, etc */ - cutl(strc,strb,strd,'V'); /* strd was Vm, strc is m */ - Tprod[k1]=k; /* Tprod[1]=3(=V1*V4) for V2+V1+V1*V4+age*V3+V3*V2 */ - Tvard[k1][1] =atoi(strc); /* m 1 for V1*/ - Tvard[k1][2] =atoi(stre); /* n 4 for V4*/ - k2=k2+2; - Tvar[cptcovt+k2]=Tvard[k1][1]; /* Tvar[(cptcovt=4+k2=1)=5]= 1 (V1) */ - Tvar[cptcovt+k2+1]=Tvard[k1][2]; /* Tvar[(cptcovt=4+(k2=1)+1)=6]= 4 (V4) */ - for (i=1; i<=lastobs;i++){ - /* Computes the new covariate which is a product of - covar[n][i]* covar[m][i] and stores it at ncovol+k1 May not be defined */ - covar[ncovcol+k1][i]=covar[atoi(stre)][i]*covar[atoi(strc)][i]; - } - } /* End age is not in the model */ - } /* End if model includes a product */ - else { /* no more sum */ - /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/ - /* scanf("%d",i);*/ - cutl(strd,strc,strb,'V'); - ks++; /**< Number of simple covariates */ - cptcovn++; - Tvar[k]=atoi(strd); - } - strcpy(modelsav,stra); /* modelsav=V2+V1+V4 stra=V2+V1+V4 */ - /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav); - scanf("%d",i);*/ - } /* end of loop + */ - } /* end model */ + strcpy(modelsav,model); + if ((strpt=strstr(model,"age*age")) !=0){ + printf(" strpt=%s, model=%s\n",strpt, model); + if(strpt != model){ + printf("Error in model: 'model=%s'; 'age*age' should in first place before other covariates\n \ + 'model=1+age+age*age+V1.' or 'model=1+age+age*age+V1+V1*age.', please swap as well as \n \ + corresponding column of parameters.\n",model); + fprintf(ficlog,"Error in model: 'model=%s'; 'age*age' should in first place before other covariates\n \ + 'model=1+age+age*age+V1.' or 'model=1+age+age*age+V1+V1*age.', please swap as well as \n \ + corresponding column of parameters.\n",model); fflush(ficlog); + return 1; + } + nagesqr=1; + if (strstr(model,"+age*age") !=0) + substrchaine(modelsav, model, "+age*age"); + else if (strstr(model,"age*age+") !=0) + substrchaine(modelsav, model, "age*age+"); + else + substrchaine(modelsav, model, "age*age"); + }else + nagesqr=0; + if (strlen(modelsav) >1){ + j=nbocc(modelsav,'+'); /**< j=Number of '+' */ + j1=nbocc(modelsav,'*'); /**< j1=Number of '*' */ + cptcovs=j+1-j1; /**< Number of simple covariates V1+V1*age+V3 +V3*V4+age*age=> V1 + V3 =5-3=2 */ + cptcovt= j+1; /* Number of total covariates in the model, not including + * cst, age and age*age + * V1+V1*age+ V3 + V3*V4+age*age=> 3+1=4*/ + /* including age products which are counted in cptcovage. + * but the covariates which are products must be treated + * separately: ncovn=4- 2=2 (V1+V3). */ + cptcovprod=j1; /**< Number of products V1*V2 +v3*age = 2 */ + cptcovprodnoage=0; /**< Number of covariate products without age: V3*V4 =1 */ + + + /* Design + * V1 V2 V3 V4 V5 V6 V7 V8 V9 Weight + * < ncovcol=8 > + * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8 + * k= 1 2 3 4 5 6 7 8 + * cptcovn number of covariates (not including constant and age ) = # of + plus 1 = 7+1=8 + * covar[k,i], value of kth covariate if not including age for individual i: + * covar[1][i]= (V1), covar[4][i]=(V4), covar[8][i]=(V8) + * Tvar[k] # of the kth covariate: Tvar[1]=2 Tvar[2]=1 Tvar[4]=3 Tvar[8]=8 + * if multiplied by age: V3*age Tvar[3=V3*age]=3 (V3) Tvar[7]=8 and + * Tage[++cptcovage]=k + * if products, new covar are created after ncovcol with k1 + * Tvar[k]=ncovcol+k1; # of the kth covariate product: Tvar[5]=ncovcol+1=10 Tvar[6]=ncovcol+1=11 + * Tprod[k1]=k; Tprod[1]=5 Tprod[2]= 6; gives the position of the k1th product + * 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 + * Tvar[cptcovn+k2]=Tvard[k1][1];Tvar[cptcovn+k2+1]=Tvard[k1][2]; + * Tvar[8+1]=5;Tvar[8+2]=6;Tvar[8+3]=7;Tvar[8+4]=8 inverted + * V1 V2 V3 V4 V5 V6 V7 V8 V9 V10 V11 + * < ncovcol=8 > + * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8 d1 d1 d2 d2 + * k= 1 2 3 4 5 6 7 8 9 10 11 12 + * Tvar[k]= 2 1 3 3 10 11 8 8 5 6 7 8 + * p Tvar[1]@12={2, 1, 3, 3, 11, 10, 8, 8, 7, 8, 5, 6} + * p Tprod[1]@2={ 6, 5} + *p Tvard[1][1]@4= {7, 8, 5, 6} + * covar[k][i]= V2 V1 ? V3 V5*V6? V7*V8? ? V8 + * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; + *How to reorganize? + * Model V1 + V2 + V3 + V8 + V5*V6 + V7*V8 + V3*age + V8*age + * Tvars {2, 1, 3, 3, 11, 10, 8, 8, 7, 8, 5, 6} + * {2, 1, 4, 8, 5, 6, 3, 7} + * Struct [] + */ + + /* This loop fills the array Tvar from the string 'model'.*/ + /* j is the number of + signs in the model V1+V2+V3 j=2 i=3 to 1 */ + /* modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4 */ + /* k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tage[cptcovage=1]=4 */ + /* k=3 V4 Tvar[k=3]= 4 (from V4) */ + /* k=2 V1 Tvar[k=2]= 1 (from V1) */ + /* k=1 Tvar[1]=2 (from V2) */ + /* k=5 Tvar[5] */ + /* for (k=1; k<=cptcovn;k++) { */ + /* cov[2+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; */ + /* } */ + /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,Tvar[Tage[k])]]*cov[2]; */ + /* + * Treating invertedly V2+V1+V3*age+V2*V4 is as if written V2*V4 +V3*age + V1 + V2 */ + for(k=cptcovt; k>=1;k--){ /**< Number of covariates not including constant and age, neither age*age*/ + Tvar[k]=0; Tprod[k]=0; Tposprod[k]=0; + } + cptcovage=0; + for(k=1; k<=cptcovt;k++){ /* Loop on total covariates of the model */ + cutl(stra,strb,modelsav,'+'); /* keeps in strb after the first '+' + modelsav==V2+V1+V4+V3*age strb=V3*age stra=V2+V1+V4 */ + if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */ + /* printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/ + /*scanf("%d",i);*/ + if (strchr(strb,'*')) { /**< Model includes a product V2+V1+V4+V3*age strb=V3*age */ + cutl(strc,strd,strb,'*'); /**< strd*strc Vm*Vn: strb=V3*age(input) strc=age strd=V3 ; V3*V2 strc=V2, strd=V3 */ + if (strcmp(strc,"age")==0) { /**< Model includes age: Vn*age */ + /* covar is not filled and then is empty */ + cptcovprod--; + cutl(stre,strb,strd,'V'); /* strd=V3(input): stre="3" */ + Tvar[k]=atoi(stre); /* V2+V1+V4+V3*age Tvar[4]=3 ; V1+V2*age Tvar[2]=2; V1+V1*age Tvar[2]=1 */ + Typevar[k]=1; /* 1 for age product */ + cptcovage++; /* Sums the number of covariates which include age as a product */ + Tage[cptcovage]=k; /* Tvar[4]=3, Tage[1] = 4 or V1+V1*age Tvar[2]=1, Tage[1]=2 */ + /*printf("stre=%s ", stre);*/ + } else if (strcmp(strd,"age")==0) { /* or age*Vn */ + cptcovprod--; + cutl(stre,strb,strc,'V'); + Tvar[k]=atoi(stre); + Typevar[k]=1; /* 1 for age product */ + cptcovage++; + Tage[cptcovage]=k; + } else { /* Age is not in the model product V2+V1+V1*V4+V3*age+V3*V2 strb=V3*V2*/ + /* loops on k1=1 (V3*V2) and k1=2 V4*V3 */ + cptcovn++; + cptcovprodnoage++;k1++; + cutl(stre,strb,strc,'V'); /* strc= Vn, stre is n; strb=V3*V2 stre=3 strc=*/ + Tvar[k]=ncovcol+nqv+ntv+nqtv+k1; /* For model-covariate k tells which data-covariate to use but + because this model-covariate is a construction we invent a new column + which is after existing variables ncovcol+nqv+ntv+nqtv + k1 + If already ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2 + Tvar[3=V1*V4]=4+1 Tvar[5=V3*V2]=4 + 2= 6, etc */ + Typevar[k]=2; /* 2 for double fixed dummy covariates */ + cutl(strc,strb,strd,'V'); /* strd was Vm, strc is m */ + Tprod[k1]=k; /* Tprod[1]=3(=V1*V4) for V2+V1+V1*V4+age*V3+V3*V2 */ + Tposprod[k]=k1; /* Tpsprod[3]=1, Tposprod[2]=5 */ + Tvard[k1][1] =atoi(strc); /* m 1 for V1*/ + Tvard[k1][2] =atoi(stre); /* n 4 for V4*/ + k2=k2+2; /* k2 is initialize to -1, We want to store the n and m in Vn*Vm at the end of Tvar */ + /* Tvar[cptcovt+k2]=Tvard[k1][1]; /\* Tvar[(cptcovt=4+k2=1)=5]= 1 (V1) *\/ */ + /* Tvar[cptcovt+k2+1]=Tvard[k1][2]; /\* Tvar[(cptcovt=4+(k2=1)+1)=6]= 4 (V4) *\/ */ + /*ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2, Tvar[3]=5, Tvar[4]=6, cptcovt=5 */ + /* 1 2 3 4 5 | Tvar[5+1)=1, Tvar[7]=2 */ + for (i=1; i<=lastobs;i++){ + /* Computes the new covariate which is a product of + covar[n][i]* covar[m][i] and stores it at ncovol+k1 May not be defined */ + covar[ncovcol+k1][i]=covar[atoi(stre)][i]*covar[atoi(strc)][i]; + } + } /* End age is not in the model */ + } /* End if model includes a product */ + else { /* no more sum */ + /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/ + /* scanf("%d",i);*/ + cutl(strd,strc,strb,'V'); + ks++; /**< Number of simple covariates dummy or quantitative, fixe or varying */ + cptcovn++; /** V4+V3+V5: V4 and V3 timevarying dummy covariates, V5 timevarying quantitative */ + Tvar[k]=atoi(strd); + Typevar[k]=0; /* 0 for simple covariates */ + } + strcpy(modelsav,stra); /* modelsav=V2+V1+V4 stra=V2+V1+V4 */ + /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav); + scanf("%d",i);*/ + } /* end of loop + on total covariates */ + } /* end if strlen(modelsave == 0) age*age might exist */ + } /* end if strlen(model == 0) */ /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products. If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/ - + /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]); - printf("cptcovprod=%d ", cptcovprod); - fprintf(ficlog,"cptcovprod=%d ", cptcovprod); - - scanf("%d ",i);*/ - - + printf("cptcovprod=%d ", cptcovprod); + fprintf(ficlog,"cptcovprod=%d ", cptcovprod); + scanf("%d ",i);*/ + + +/* Until here, decodemodel knows only the grammar (simple, product, age*) of the model but not what kind + of variable (dummy vs quantitative, fixed vs time varying) is behind. But we know the # of each. */ +/* ncovcol= 1, nqv=1 | ntv=2, nqtv= 1 = 5 possible variables data: 2 fixed 3, varying + model= V5 + V4 +V3 + V4*V3 + V5*age + V2 + V1*V2 + V1*age + V5*age, V1 is not used saving its place + k = 1 2 3 4 5 6 7 8 9 + Tvar[k]= 5 4 3 1+1+2+1+1=6 5 2 7 1 5 + Typevar[k]= 0 0 0 2 1 0 2 1 1 + Fixed[k] 1 1 1 1 3 0 0 or 2 2 3 + Dummy[k] 1 0 0 0 3 1 1 2 3 + Tmodelind[combination of covar]=k; +*/ +/* Dispatching between quantitative and time varying covariates */ + /* If Tvar[k] >ncovcol it is a product */ + /* Tvar[k] is the value n of Vn with n varying for 1 to nvcol, or p Vp=Vn*Vm for product */ + /* Computing effective variables, ie used by the model, that is from the cptcovt variables */ + printf("Model=%s\n\ +Typevar: 0 for simple covariate (dummy, quantitative, fixed or varying), 1 for age product, 2 for product \n\ +Fixed[k] 0=fixed (product or simple), 1 varying, 2 fixed with age product, 3 varying with age product \n\ +Dummy[k] 0=dummy (0 1), 1 quantitative (single or product without age), 2 dummy with age product, 3 quant with age product\n",model); + fprintf(ficlog,"Model=%s\n\ +Typevar: 0 for simple covariate (dummy, quantitative, fixed or varying), 1 for age product, 2 for product \n\ +Fixed[k] 0=fixed (product or simple), 1 varying, 2 fixed with age product, 3 varying with age product \n\ +Dummy[k] 0=dummy (0 1), 1 quantitative (single or product without age), 2 dummy with age product, 3 quant with age product\n",model); + for(k=1;k<=cptcovt; k++){ Fixed[k]=0; Dummy[k]=0;} + for(k=1, ncovf=0, nsd=0, nsq=0, ncovv=0, ncova=0, ncoveff=0, nqfveff=0, ntveff=0, nqtveff=0;k<=cptcovt; k++){ /* or cptocvt */ + if (Tvar[k] <=ncovcol && Typevar[k]==0 ){ /* Simple fixed dummy (<=ncovcol) covariates */ + Fixed[k]= 0; + Dummy[k]= 0; + ncoveff++; + ncovf++; + nsd++; + modell[k].maintype= FTYPE; + TvarsD[nsd]=Tvar[k]; + TvarsDind[nsd]=k; + TvarF[ncovf]=Tvar[k]; + TvarFind[ncovf]=k; + TvarFD[ncoveff]=Tvar[k]; /* TvarFD[1]=V1 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ + TvarFDind[ncoveff]=k; /* TvarFDind[1]=9 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ + }else if( Tvar[k] <=ncovcol && Typevar[k]==2){ /* Product of fixed dummy (<=ncovcol) covariates */ + Fixed[k]= 0; + Dummy[k]= 0; + ncoveff++; + ncovf++; + modell[k].maintype= FTYPE; + TvarF[ncovf]=Tvar[k]; + TvarFind[ncovf]=k; + TvarFD[ncoveff]=Tvar[k]; /* TvarFD[1]=V1 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ + TvarFDind[ncoveff]=k; /* TvarFDind[1]=9 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ + }else if( Tvar[k] <=ncovcol+nqv && Typevar[k]==0){/* Remind that product Vn*Vm are added in k Only simple fixed quantitative variable */ + Fixed[k]= 0; + Dummy[k]= 1; + nqfveff++; + modell[k].maintype= FTYPE; + modell[k].subtype= FQ; + nsq++; + TvarsQ[nsq]=Tvar[k]; + TvarsQind[nsq]=k; + ncovf++; + TvarF[ncovf]=Tvar[k]; + TvarFind[ncovf]=k; + TvarFQ[nqfveff]=Tvar[k]-ncovcol; /* TvarFQ[1]=V2-1=1st in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple fixed quantitative variable */ + TvarFQind[nqfveff]=k; /* TvarFQind[1]=6 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple fixed quantitative variable */ + }else if( Tvar[k] <=ncovcol+nqv+ntv && Typevar[k]==0){/* Only simple time varying dummy variables */ + Fixed[k]= 1; + Dummy[k]= 0; + ntveff++; /* Only simple time varying dummy variable */ + modell[k].maintype= VTYPE; + modell[k].subtype= VD; + nsd++; + TvarsD[nsd]=Tvar[k]; + TvarsDind[nsd]=k; + ncovv++; /* Only simple time varying variables */ + TvarV[ncovv]=Tvar[k]; + TvarVind[ncovv]=k; /* TvarVind[2]=2 TvarVind[3]=3 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Any time varying singele */ + TvarVD[ntveff]=Tvar[k]; /* TvarVD[1]=V4 TvarVD[2]=V3 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple time varying dummy variable */ + TvarVDind[ntveff]=k; /* TvarVDind[1]=2 TvarVDind[2]=3 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple time varying dummy variable */ + printf("Quasi Tmodelind[%d]=%d,Tvar[Tmodelind[%d]]=V%d, ncovcol=%d, nqv=%d,Tvar[k]- ncovcol-nqv=%d\n",ntveff,k,ntveff,Tvar[k], ncovcol, nqv,Tvar[k]- ncovcol-nqv); + printf("Quasi TmodelInvind[%d]=%d\n",k,Tvar[k]- ncovcol-nqv); + }else if( Tvar[k] <=ncovcol+nqv+ntv+nqtv && Typevar[k]==0){ /* Only simple time varying quantitative variable V5*/ + Fixed[k]= 1; + Dummy[k]= 1; + nqtveff++; + modell[k].maintype= VTYPE; + modell[k].subtype= VQ; + ncovv++; /* Only simple time varying variables */ + nsq++; + TvarsQ[nsq]=Tvar[k]; + TvarsQind[nsq]=k; + TvarV[ncovv]=Tvar[k]; + TvarVind[ncovv]=k; /* TvarVind[1]=1 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Any time varying singele */ + TvarVQ[nqtveff]=Tvar[k]; /* TvarVQ[1]=V5 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple time varying quantitative variable */ + TvarVQind[nqtveff]=k; /* TvarVQind[1]=1 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple time varying quantitative variable */ + TmodelInvQind[nqtveff]=Tvar[k]- ncovcol-nqv-ntv;/* Only simple time varying quantitative variable */ + /* Tmodeliqind[k]=nqtveff;/\* Only simple time varying quantitative variable *\/ */ + printf("Quasi TmodelQind[%d]=%d,Tvar[TmodelQind[%d]]=V%d, ncovcol=%d, nqv=%d, ntv=%d,Tvar[k]- ncovcol-nqv-ntv=%d\n",nqtveff,k,nqtveff,Tvar[k], ncovcol, nqv, ntv, Tvar[k]- ncovcol-nqv-ntv); + printf("Quasi TmodelInvQind[%d]=%d\n",k,Tvar[k]- ncovcol-nqv-ntv); + }else if (Typevar[k] == 1) { /* product with age */ + ncova++; + TvarA[ncova]=Tvar[k]; + TvarAind[ncova]=k; + if (Tvar[k] <=ncovcol ){ /* Product age with fixed dummy covariatee */ + Fixed[k]= 2; + Dummy[k]= 2; + modell[k].maintype= ATYPE; + modell[k].subtype= APFD; + /* ncoveff++; */ + }else if( Tvar[k] <=ncovcol+nqv) { /* Remind that product Vn*Vm are added in k*/ + Fixed[k]= 2; + Dummy[k]= 3; + modell[k].maintype= ATYPE; + modell[k].subtype= APFQ; /* Product age * fixed quantitative */ + /* nqfveff++; /\* Only simple fixed quantitative variable *\/ */ + }else if( Tvar[k] <=ncovcol+nqv+ntv ){ + Fixed[k]= 3; + Dummy[k]= 2; + modell[k].maintype= ATYPE; + modell[k].subtype= APVD; /* Product age * varying dummy */ + /* ntveff++; /\* Only simple time varying dummy variable *\/ */ + }else if( Tvar[k] <=ncovcol+nqv+ntv+nqtv){ + Fixed[k]= 3; + Dummy[k]= 3; + modell[k].maintype= ATYPE; + modell[k].subtype= APVQ; /* Product age * varying quantitative */ + /* nqtveff++;/\* Only simple time varying quantitative variable *\/ */ + } + }else if (Typevar[k] == 2) { /* product without age */ + k1=Tposprod[k]; + if(Tvard[k1][1] <=ncovcol){ + if(Tvard[k1][2] <=ncovcol){ + Fixed[k]= 1; + Dummy[k]= 0; + modell[k].maintype= FTYPE; + modell[k].subtype= FPDD; /* Product fixed dummy * fixed dummy */ + ncovf++; /* Fixed variables without age */ + TvarF[ncovf]=Tvar[k]; + TvarFind[ncovf]=k; + }else if(Tvard[k1][2] <=ncovcol+nqv){ + Fixed[k]= 0; /* or 2 ?*/ + Dummy[k]= 1; + modell[k].maintype= FTYPE; + modell[k].subtype= FPDQ; /* Product fixed dummy * fixed quantitative */ + ncovf++; /* Varying variables without age */ + TvarF[ncovf]=Tvar[k]; + TvarFind[ncovf]=k; + }else if(Tvard[k1][2] <=ncovcol+nqv+ntv){ + Fixed[k]= 1; + Dummy[k]= 0; + modell[k].maintype= VTYPE; + modell[k].subtype= VPDD; /* Product fixed dummy * varying dummy */ + ncovv++; /* Varying variables without age */ + TvarV[ncovv]=Tvar[k]; + TvarVind[ncovv]=k; + }else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){ + Fixed[k]= 1; + Dummy[k]= 1; + modell[k].maintype= VTYPE; + modell[k].subtype= VPDQ; /* Product fixed dummy * varying quantitative */ + ncovv++; /* Varying variables without age */ + TvarV[ncovv]=Tvar[k]; + TvarVind[ncovv]=k; + } + }else if(Tvard[k1][1] <=ncovcol+nqv){ + if(Tvard[k1][2] <=ncovcol){ + Fixed[k]= 0; /* or 2 ?*/ + Dummy[k]= 1; + modell[k].maintype= FTYPE; + modell[k].subtype= FPDQ; /* Product fixed quantitative * fixed dummy */ + ncovf++; /* Fixed variables without age */ + TvarF[ncovf]=Tvar[k]; + TvarFind[ncovf]=k; + }else if(Tvard[k1][2] <=ncovcol+nqv+ntv){ + Fixed[k]= 1; + Dummy[k]= 1; + modell[k].maintype= VTYPE; + modell[k].subtype= VPDQ; /* Product fixed quantitative * varying dummy */ + ncovv++; /* Varying variables without age */ + TvarV[ncovv]=Tvar[k]; + TvarVind[ncovv]=k; + }else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){ + Fixed[k]= 1; + Dummy[k]= 1; + modell[k].maintype= VTYPE; + modell[k].subtype= VPQQ; /* Product fixed quantitative * varying quantitative */ + ncovv++; /* Varying variables without age */ + TvarV[ncovv]=Tvar[k]; + TvarVind[ncovv]=k; + ncovv++; /* Varying variables without age */ + TvarV[ncovv]=Tvar[k]; + TvarVind[ncovv]=k; + } + }else if(Tvard[k1][1] <=ncovcol+nqv+ntv){ + if(Tvard[k1][2] <=ncovcol){ + Fixed[k]= 1; + Dummy[k]= 1; + modell[k].maintype= VTYPE; + modell[k].subtype= VPDD; /* Product time varying dummy * fixed dummy */ + ncovv++; /* Varying variables without age */ + TvarV[ncovv]=Tvar[k]; + TvarVind[ncovv]=k; + }else if(Tvard[k1][2] <=ncovcol+nqv){ + Fixed[k]= 1; + Dummy[k]= 1; + modell[k].maintype= VTYPE; + modell[k].subtype= VPDQ; /* Product time varying dummy * fixed quantitative */ + ncovv++; /* Varying variables without age */ + TvarV[ncovv]=Tvar[k]; + TvarVind[ncovv]=k; + }else if(Tvard[k1][2] <=ncovcol+nqv+ntv){ + Fixed[k]= 1; + Dummy[k]= 0; + modell[k].maintype= VTYPE; + modell[k].subtype= VPDD; /* Product time varying dummy * time varying dummy */ + ncovv++; /* Varying variables without age */ + TvarV[ncovv]=Tvar[k]; + TvarVind[ncovv]=k; + }else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){ + Fixed[k]= 1; + Dummy[k]= 1; + modell[k].maintype= VTYPE; + modell[k].subtype= VPDQ; /* Product time varying dummy * time varying quantitative */ + ncovv++; /* Varying variables without age */ + TvarV[ncovv]=Tvar[k]; + TvarVind[ncovv]=k; + } + }else if(Tvard[k1][1] <=ncovcol+nqv+ntv+nqtv){ + if(Tvard[k1][2] <=ncovcol){ + Fixed[k]= 1; + Dummy[k]= 1; + modell[k].maintype= VTYPE; + modell[k].subtype= VPDQ; /* Product time varying quantitative * fixed dummy */ + ncovv++; /* Varying variables without age */ + TvarV[ncovv]=Tvar[k]; + TvarVind[ncovv]=k; + }else if(Tvard[k1][2] <=ncovcol+nqv){ + Fixed[k]= 1; + Dummy[k]= 1; + modell[k].maintype= VTYPE; + modell[k].subtype= VPQQ; /* Product time varying quantitative * fixed quantitative */ + ncovv++; /* Varying variables without age */ + TvarV[ncovv]=Tvar[k]; + TvarVind[ncovv]=k; + }else if(Tvard[k1][2] <=ncovcol+nqv+ntv){ + Fixed[k]= 1; + Dummy[k]= 1; + modell[k].maintype= VTYPE; + modell[k].subtype= VPDQ; /* Product time varying quantitative * time varying dummy */ + ncovv++; /* Varying variables without age */ + TvarV[ncovv]=Tvar[k]; + TvarVind[ncovv]=k; + }else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){ + Fixed[k]= 1; + Dummy[k]= 1; + modell[k].maintype= VTYPE; + modell[k].subtype= VPQQ; /* Product time varying quantitative * time varying quantitative */ + ncovv++; /* Varying variables without age */ + TvarV[ncovv]=Tvar[k]; + TvarVind[ncovv]=k; + } + }else{ + printf("Error unknown type of covariate: Tvard[%d][1]=%d,Tvard[%d][2]=%d\n",k1,Tvard[k1][1],k1,Tvard[k1][2]); + fprintf(ficlog,"Error unknown type of covariate: Tvard[%d][1]=%d,Tvard[%d][2]=%d\n",k1,Tvard[k1][1],k1,Tvard[k1][2]); + } /*end k1*/ + }else{ + printf("Error, current version can't treat for performance reasons, Tvar[%d]=%d, Typevar[%d]=%d\n", k, Tvar[k], k, Typevar[k]); + fprintf(ficlog,"Error, current version can't treat for performance reasons, Tvar[%d]=%d, Typevar[%d]=%d\n", k, Tvar[k], k, Typevar[k]); + } + printf("Decodemodel, k=%d, Tvar[%d]=V%d,Typevar=%d, Fixed=%d, Dummy=%d\n",k, k,Tvar[k],Typevar[k],Fixed[k],Dummy[k]); + printf(" modell[%d].maintype=%d, modell[%d].subtype=%d\n",k,modell[k].maintype,k,modell[k].subtype); + fprintf(ficlog,"Decodemodel, k=%d, Tvar[%d]=V%d,Typevar=%d, Fixed=%d, Dummy=%d\n",k, k,Tvar[k],Typevar[k],Fixed[k],Dummy[k]); + } + /* Searching for doublons in the model */ + for(k1=1; k1<= cptcovt;k1++){ + for(k2=1; k2 nlstate){ - *nberr++; - printf("Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i); - fprintf(ficlog,"Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i); - s[m][i]=-1; + *nberr = *nberr + 1; + if(firstone == 0){ + firstone=1; + printf("Warning (#%d)! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown but status is a death state %d at wave %d. If you don't know the vital status, please enter -2. If he/she is still alive but don't know the state, please code with '-1 or '.'. Here, we do not believe in a death, skipped.\nOther similar cases in log file\n", *nberr,(int)moisdc[i],(int)andc[i],num[i],i,s[m][i],m); + } + fprintf(ficlog,"Warning (#%d)! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown but status is a death state %d at wave %d. If you don't know the vital status, please enter -2. If he/she is still alive but don't know the state, please code with '-1 or '.'. Here, we do not believe in a death, skipped.\n", *nberr,(int)moisdc[i],(int)andc[i],num[i],i,s[m][i],m); + s[m][i]=-1; /* Droping the death status */ } if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){ - *nberr++; - 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]); - 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]); - s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */ + (*nberr)++; + printf("Error (#%d)! Month of death of individual %ld on line %d was unknown (%2d) (year of death is %4d) and status is a death state %d at wave %d. Please impute an arbitrary (or not) month and rerun. Currently this transition to death will be skipped (status is set to -2).\nOther similar cases in log file\n", *nberr, num[i],i,(int)moisdc[i],(int)andc[i],s[m][i],m); + fprintf(ficlog,"Error (#%d)! Month of death of individual %ld on line %d was unknown (%2d) (year of death is %4d) and status is a death state %d at wave %d. Please impute an arbitrary (or not) month and rerun. Currently this transition to death will be skipped (status is set to -2).\n", *nberr, num[i],i,(int)moisdc[i],(int)andc[i],s[m][i],m); + s[m][i]=-2; /* We prefer to skip it (and to skip it in version 0.8a1 too */ } } } @@ -5111,13 +9322,13 @@ calandcheckages(int imx, int maxwav, dou for (i=1; i<=imx; i++) { agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]); for(m=firstpass; (m<= lastpass); m++){ - if(s[m][i] >0 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){ + if(s[m][i] >0 || s[m][i]==-1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){ /* What if s[m][i]=-1 */ if (s[m][i] >= nlstate+1) { - if(agedc[i]>0) - if((int)moisdc[i]!=99 && (int)andc[i]!=9999) + if(agedc[i]>0){ + if((int)moisdc[i]!=99 && (int)andc[i]!=9999){ agev[m][i]=agedc[i]; - /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/ - else { + /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/ + }else { if ((int)andc[i]!=9999){ nbwarn++; printf("Warning negative age at death: %ld line:%d\n",num[i],i); @@ -5125,7 +9336,8 @@ calandcheckages(int imx, int maxwav, dou agev[m][i]=-1; } } - } + } /* agedc > 0 */ + } /* end if */ else if(s[m][i] !=9){ /* Standard case, age in fractional years but with the precision of a month */ agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]); @@ -5137,25 +9349,31 @@ calandcheckages(int imx, int maxwav, dou } else if(agev[m][i] >*agemax){ *agemax=agev[m][i]; - printf(" Max anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.2f\n",m,i,anint[m][i], i,annais[i], *agemax); + /* printf(" Max anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.2f\n",m,i,anint[m][i], i,annais[i], *agemax);*/ } /*agev[m][i]=anint[m][i]-annais[i];*/ /* agev[m][i] = age[i]+2*m;*/ - } + } /* en if 9*/ else { /* =9 */ + /* printf("Debug num[%d]=%ld s[%d][%d]=%d\n",i,num[i], m,i, s[m][i]); */ agev[m][i]=1; s[m][i]=-1; } } - else /*= 0 Unknown */ + else if(s[m][i]==0) /*= 0 Unknown */ agev[m][i]=1; - } - + else{ + printf("Warning, num[%d]=%ld, s[%d][%d]=%d\n", i, num[i], m, i,s[m][i]); + fprintf(ficlog, "Warning, num[%d]=%ld, s[%d][%d]=%d\n", i, num[i], m, i,s[m][i]); + agev[m][i]=0; + } + } /* End for lastpass */ } + for (i=1; i<=imx; i++) { for(m=firstpass; (m<=lastpass); m++){ if (s[m][i] > (nlstate+ndeath)) { - *nberr++; + (*nberr)++; 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); 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); return 1; @@ -5175,11 +9393,569 @@ calandcheckages(int imx, int maxwav, dou fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax); return (0); - endread: + /* endread:*/ printf("Exiting calandcheckages: "); return (1); } +#if defined(_MSC_VER) +/*printf("Visual C++ compiler: %s \n;", _MSC_FULL_VER);*/ +/*fprintf(ficlog, "Visual C++ compiler: %s \n;", _MSC_FULL_VER);*/ +//#include "stdafx.h" +//#include +//#include +//#include +//#include +typedef BOOL(WINAPI *LPFN_ISWOW64PROCESS) (HANDLE, PBOOL); + +LPFN_ISWOW64PROCESS fnIsWow64Process; + +BOOL IsWow64() +{ + BOOL bIsWow64 = FALSE; + + //typedef BOOL (APIENTRY *LPFN_ISWOW64PROCESS) + // (HANDLE, PBOOL); + + //LPFN_ISWOW64PROCESS fnIsWow64Process; + + HMODULE module = GetModuleHandle(_T("kernel32")); + const char funcName[] = "IsWow64Process"; + fnIsWow64Process = (LPFN_ISWOW64PROCESS) + GetProcAddress(module, funcName); + + if (NULL != fnIsWow64Process) + { + if (!fnIsWow64Process(GetCurrentProcess(), + &bIsWow64)) + //throw std::exception("Unknown error"); + printf("Unknown error\n"); + } + return bIsWow64 != FALSE; +} +#endif + +void syscompilerinfo(int logged) + { + /* #include "syscompilerinfo.h"*/ + /* command line Intel compiler 32bit windows, XP compatible:*/ + /* /GS /W3 /Gy + /Zc:wchar_t /Zi /O2 /Fd"Release\vc120.pdb" /D "WIN32" /D "NDEBUG" /D + "_CONSOLE" /D "_LIB" /D "_USING_V110_SDK71_" /D "_UNICODE" /D + "UNICODE" /Qipo /Zc:forScope /Gd /Oi /MT /Fa"Release\" /EHsc /nologo + /Fo"Release\" /Qprof-dir "Release\" /Fp"Release\IMaCh.pch" + */ + /* 64 bits */ + /* + /GS /W3 /Gy + /Zc:wchar_t /Zi /O2 /Fd"x64\Release\vc120.pdb" /D "WIN32" /D "NDEBUG" + /D "_CONSOLE" /D "_LIB" /D "_UNICODE" /D "UNICODE" /Qipo /Zc:forScope + /Oi /MD /Fa"x64\Release\" /EHsc /nologo /Fo"x64\Release\" /Qprof-dir + "x64\Release\" /Fp"x64\Release\IMaCh.pch" */ + /* Optimization are useless and O3 is slower than O2 */ + /* + /GS /W3 /Gy /Zc:wchar_t /Zi /O3 /Fd"x64\Release\vc120.pdb" /D "WIN32" + /D "NDEBUG" /D "_CONSOLE" /D "_LIB" /D "_UNICODE" /D "UNICODE" /Qipo + /Zc:forScope /Oi /MD /Fa"x64\Release\" /EHsc /nologo /Qparallel + /Fo"x64\Release\" /Qprof-dir "x64\Release\" /Fp"x64\Release\IMaCh.pch" + */ + /* Link is */ /* /OUT:"visual studio + 2013\Projects\IMaCh\Release\IMaCh.exe" /MANIFEST /NXCOMPAT + /PDB:"visual studio + 2013\Projects\IMaCh\Release\IMaCh.pdb" /DYNAMICBASE + "kernel32.lib" "user32.lib" "gdi32.lib" "winspool.lib" + "comdlg32.lib" "advapi32.lib" "shell32.lib" "ole32.lib" + "oleaut32.lib" "uuid.lib" "odbc32.lib" "odbccp32.lib" + /MACHINE:X86 /OPT:REF /SAFESEH /INCREMENTAL:NO + /SUBSYSTEM:CONSOLE",5.01" /MANIFESTUAC:"level='asInvoker' + uiAccess='false'" + /ManifestFile:"Release\IMaCh.exe.intermediate.manifest" /OPT:ICF + /NOLOGO /TLBID:1 + */ +#if defined __INTEL_COMPILER +#if defined(__GNUC__) + struct utsname sysInfo; /* For Intel on Linux and OS/X */ +#endif +#elif defined(__GNUC__) +#ifndef __APPLE__ +#include /* Only on gnu */ +#endif + struct utsname sysInfo; + int cross = CROSS; + if (cross){ + printf("Cross-"); + if(logged) fprintf(ficlog, "Cross-"); + } +#endif + +#include + + printf("Compiled with:");if(logged)fprintf(ficlog,"Compiled with:"); +#if defined(__clang__) + printf(" Clang/LLVM");if(logged)fprintf(ficlog," Clang/LLVM"); /* Clang/LLVM. ---------------------------------------------- */ +#endif +#if defined(__ICC) || defined(__INTEL_COMPILER) + printf(" Intel ICC/ICPC");if(logged)fprintf(ficlog," Intel ICC/ICPC");/* Intel ICC/ICPC. ------------------------------------------ */ +#endif +#if defined(__GNUC__) || defined(__GNUG__) + printf(" GNU GCC/G++");if(logged)fprintf(ficlog," GNU GCC/G++");/* GNU GCC/G++. --------------------------------------------- */ +#endif +#if defined(__HP_cc) || defined(__HP_aCC) + printf(" Hewlett-Packard C/aC++");if(logged)fprintf(fcilog," Hewlett-Packard C/aC++"); /* Hewlett-Packard C/aC++. ---------------------------------- */ +#endif +#if defined(__IBMC__) || defined(__IBMCPP__) + printf(" IBM XL C/C++"); if(logged) fprintf(ficlog," IBM XL C/C++");/* IBM XL C/C++. -------------------------------------------- */ +#endif +#if defined(_MSC_VER) + printf(" Microsoft Visual Studio");if(logged)fprintf(ficlog," Microsoft Visual Studio");/* Microsoft Visual Studio. --------------------------------- */ +#endif +#if defined(__PGI) + printf(" Portland Group PGCC/PGCPP");if(logged) fprintf(ficlog," Portland Group PGCC/PGCPP");/* Portland Group PGCC/PGCPP. ------------------------------- */ +#endif +#if defined(__SUNPRO_C) || defined(__SUNPRO_CC) + printf(" Oracle Solaris Studio");if(logged)fprintf(ficlog," Oracle Solaris Studio\n");/* Oracle Solaris Studio. ----------------------------------- */ +#endif + printf(" for "); if (logged) fprintf(ficlog, " for "); + +// http://stackoverflow.com/questions/4605842/how-to-identify-platform-compiler-from-preprocessor-macros +#ifdef _WIN32 // note the underscore: without it, it's not msdn official! + // Windows (x64 and x86) + printf("Windows (x64 and x86) ");if(logged) fprintf(ficlog,"Windows (x64 and x86) "); +#elif __unix__ // all unices, not all compilers + // Unix + printf("Unix ");if(logged) fprintf(ficlog,"Unix "); +#elif __linux__ + // linux + printf("linux ");if(logged) fprintf(ficlog,"linux "); +#elif __APPLE__ + // Mac OS, not sure if this is covered by __posix__ and/or __unix__ though.. + printf("Mac OS ");if(logged) fprintf(ficlog,"Mac OS "); +#endif + +/* __MINGW32__ */ +/* __CYGWIN__ */ +/* __MINGW64__ */ +// http://msdn.microsoft.com/en-us/library/b0084kay.aspx +/* _MSC_VER //the Visual C++ compiler is 17.00.51106.1, the _MSC_VER macro evaluates to 1700. Type cl /? */ +/* _MSC_FULL_VER //the Visual C++ compiler is 15.00.20706.01, the _MSC_FULL_VER macro evaluates to 150020706 */ +/* _WIN64 // Defined for applications for Win64. */ +/* _M_X64 // Defined for compilations that target x64 processors. */ +/* _DEBUG // Defined when you compile with /LDd, /MDd, and /MTd. */ + +#if UINTPTR_MAX == 0xffffffff + printf(" 32-bit"); if(logged) fprintf(ficlog," 32-bit");/* 32-bit */ +#elif UINTPTR_MAX == 0xffffffffffffffff + printf(" 64-bit"); if(logged) fprintf(ficlog," 64-bit");/* 64-bit */ +#else + printf(" wtf-bit"); if(logged) fprintf(ficlog," wtf-bit");/* wtf */ +#endif + +#if defined(__GNUC__) +# if defined(__GNUC_PATCHLEVEL__) +# define __GNUC_VERSION__ (__GNUC__ * 10000 \ + + __GNUC_MINOR__ * 100 \ + + __GNUC_PATCHLEVEL__) +# else +# define __GNUC_VERSION__ (__GNUC__ * 10000 \ + + __GNUC_MINOR__ * 100) +# endif + printf(" using GNU C version %d.\n", __GNUC_VERSION__); + if(logged) fprintf(ficlog, " using GNU C version %d.\n", __GNUC_VERSION__); + + if (uname(&sysInfo) != -1) { + printf("Running on: %s %s %s %s %s\n",sysInfo.sysname, sysInfo.nodename, sysInfo.release, sysInfo.version, sysInfo.machine); + if(logged) fprintf(ficlog,"Running on: %s %s %s %s %s\n ",sysInfo.sysname, sysInfo.nodename, sysInfo.release, sysInfo.version, sysInfo.machine); + } + else + perror("uname() error"); + //#ifndef __INTEL_COMPILER +#if !defined (__INTEL_COMPILER) && !defined(__APPLE__) + printf("GNU libc version: %s\n", gnu_get_libc_version()); + if(logged) fprintf(ficlog,"GNU libc version: %s\n", gnu_get_libc_version()); +#endif +#endif + + // void main() + // { +#if defined(_MSC_VER) + if (IsWow64()){ + printf("\nThe program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n"); + if (logged) fprintf(ficlog, "\nThe program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n"); + } + else{ + printf("\nThe program is not running under WOW64 (i.e probably on a 64bit Windows).\n"); + if (logged) fprintf(ficlog, "\nThe programm is not running under WOW64 (i.e probably on a 64bit Windows).\n"); + } + // printf("\nPress Enter to continue..."); + // getchar(); + // } + +#endif + + +} + +int prevalence_limit(double *p, double **prlim, double ageminpar, double agemaxpar, double ftolpl, int *ncvyearp){ + /*--------------- Prevalence limit (period or stable prevalence) --------------*/ + int i, j, k, i1, k4=0, nres=0 ; + /* double ftolpl = 1.e-10; */ + double age, agebase, agelim; + double tot; + + strcpy(filerespl,"PL_"); + strcat(filerespl,fileresu); + if((ficrespl=fopen(filerespl,"w"))==NULL) { + printf("Problem with period (stable) prevalence resultfile: %s\n", filerespl);return 1; + fprintf(ficlog,"Problem with period (stable) prevalence resultfile: %s\n", filerespl);return 1; + } + printf("\nComputing period (stable) prevalence: result on file '%s' \n", filerespl); + fprintf(ficlog,"\nComputing period (stable) prevalence: result on file '%s' \n", filerespl); + pstamp(ficrespl); + fprintf(ficrespl,"# Period (stable) prevalence. Precision given by ftolpl=%g \n", ftolpl); + fprintf(ficrespl,"#Age "); + for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i); + fprintf(ficrespl,"\n"); + + /* prlim=matrix(1,nlstate,1,nlstate);*/ /* back in main */ + + agebase=ageminpar; + agelim=agemaxpar; + + /* i1=pow(2,ncoveff); */ + i1=pow(2,cptcoveff); /* Number of combination of dummy covariates */ + if (cptcovn < 1){i1=1;} + + for(k=1; k<=i1;k++){ /* For each combination k of dummy covariates in the model */ + for(nres=1; nres <= nresult; nres++){ /* For each resultline */ + if(i1 != 1 && TKresult[nres]!= k) + continue; + + /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */ + /* for(cptcov=1,k=0;cptcov<=1;cptcov++){ */ + //for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){ + /* k=k+1; */ + /* to clean */ + //printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtabm(cptcod,cptcov)); + fprintf(ficrespl,"#******"); + printf("#******"); + fprintf(ficlog,"#******"); + for(j=1;j<=cptcoveff ;j++) {/* all covariates */ + fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); /* Here problem for varying dummy*/ + printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); + fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); + } + for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */ + printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]); + fprintf(ficrespl," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]); + fprintf(ficlog," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]); + } + fprintf(ficrespl,"******\n"); + printf("******\n"); + fprintf(ficlog,"******\n"); + if(invalidvarcomb[k]){ + printf("\nCombination (%d) ignored because no case \n",k); + fprintf(ficrespl,"#Combination (%d) ignored because no case \n",k); + fprintf(ficlog,"\nCombination (%d) ignored because no case \n",k); + continue; + } + + fprintf(ficrespl,"#Age "); + for(j=1;j<=cptcoveff;j++) { + fprintf(ficrespl,"V%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); + } + for(i=1; i<=nlstate;i++) fprintf(ficrespl," %d-%d ",i,i); + fprintf(ficrespl,"Total Years_to_converge\n"); + + for (age=agebase; age<=agelim; age++){ + /* for (age=agebase; age<=agebase; age++){ */ + prevalim(prlim, nlstate, p, age, oldm, savm, ftolpl, ncvyearp, k, nres); + fprintf(ficrespl,"%.0f ",age ); + for(j=1;j<=cptcoveff;j++) + fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); + tot=0.; + for(i=1; i<=nlstate;i++){ + tot += prlim[i][i]; + fprintf(ficrespl," %.5f", prlim[i][i]); + } + fprintf(ficrespl," %.3f %d\n", tot, *ncvyearp); + } /* Age */ + /* was end of cptcod */ + } /* cptcov */ + } /* nres */ + return 0; +} + +int back_prevalence_limit(double *p, double **bprlim, double ageminpar, double agemaxpar, double ftolpl, int *ncvyearp, double dateprev1,double dateprev2, int firstpass, int lastpass, int mobilavproj){ + /*--------------- Back Prevalence limit (period or stable prevalence) --------------*/ + + /* Computes the back prevalence limit for any combination of covariate values + * at any age between ageminpar and agemaxpar + */ + int i, j, k, i1, nres=0 ; + /* double ftolpl = 1.e-10; */ + double age, agebase, agelim; + double tot; + /* double ***mobaverage; */ + /* double **dnewm, **doldm, **dsavm; /\* for use *\/ */ + + strcpy(fileresplb,"PLB_"); + strcat(fileresplb,fileresu); + if((ficresplb=fopen(fileresplb,"w"))==NULL) { + printf("Problem with period (stable) back prevalence resultfile: %s\n", fileresplb);return 1; + fprintf(ficlog,"Problem with period (stable) back prevalence resultfile: %s\n", fileresplb);return 1; + } + printf("Computing period (stable) back prevalence: result on file '%s' \n", fileresplb); + fprintf(ficlog,"Computing period (stable) back prevalence: result on file '%s' \n", fileresplb); + pstamp(ficresplb); + fprintf(ficresplb,"# Period (stable) back prevalence. Precision given by ftolpl=%g \n", ftolpl); + fprintf(ficresplb,"#Age "); + for(i=1; i<=nlstate;i++) fprintf(ficresplb,"%d-%d ",i,i); + fprintf(ficresplb,"\n"); + + + /* prlim=matrix(1,nlstate,1,nlstate);*/ /* back in main */ + + agebase=ageminpar; + agelim=agemaxpar; + + + i1=pow(2,cptcoveff); + if (cptcovn < 1){i1=1;} + + for(nres=1; nres <= nresult; nres++){ /* For each resultline */ + for(k=1; k<=i1;k++){ /* For any combination of dummy covariates, fixed and varying */ + if(i1 != 1 && TKresult[nres]!= k) + continue; + //printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtabm(cptcod,cptcov)); + fprintf(ficresplb,"#******"); + printf("#******"); + fprintf(ficlog,"#******"); + for(j=1;j<=cptcoveff ;j++) {/* all covariates */ + fprintf(ficresplb," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); + printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); + fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); + } + for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */ + printf(" V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]); + fprintf(ficresplb," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]); + fprintf(ficlog," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]); + } + fprintf(ficresplb,"******\n"); + printf("******\n"); + fprintf(ficlog,"******\n"); + if(invalidvarcomb[k]){ + printf("\nCombination (%d) ignored because no cases \n",k); + fprintf(ficresplb,"#Combination (%d) ignored because no cases \n",k); + fprintf(ficlog,"\nCombination (%d) ignored because no cases \n",k); + continue; + } + + fprintf(ficresplb,"#Age "); + for(j=1;j<=cptcoveff;j++) { + fprintf(ficresplb,"V%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); + } + for(i=1; i<=nlstate;i++) fprintf(ficresplb," %d-%d ",i,i); + fprintf(ficresplb,"Total Years_to_converge\n"); + + + for (age=agebase; age<=agelim; age++){ + /* for (age=agebase; age<=agebase; age++){ */ + if(mobilavproj > 0){ + /* bprevalim(bprlim, mobaverage, nlstate, p, age, ageminpar, agemaxpar, oldm, savm, doldm, dsavm, ftolpl, ncvyearp, k); */ + /* bprevalim(bprlim, mobaverage, nlstate, p, age, oldm, savm, dnewm, doldm, dsavm, ftolpl, ncvyearp, k); */ + bprevalim(bprlim, mobaverage, nlstate, p, age, ftolpl, ncvyearp, k, nres); + }else if (mobilavproj == 0){ + printf("There is no chance to get back prevalence limit if data aren't non zero and summing to 1, please try a non null mobil_average(=%d) parameter or mobil_average=-1 if you want to try at your own risk.\n",mobilavproj); + fprintf(ficlog,"There is no chance to get back prevalence limit if data aren't non zero and summing to 1, please try a non null mobil_average(=%d) parameter or mobil_average=-1 if you want to try at your own risk.\n",mobilavproj); + exit(1); + }else{ + /* bprevalim(bprlim, probs, nlstate, p, age, oldm, savm, dnewm, doldm, dsavm, ftolpl, ncvyearp, k); */ + bprevalim(bprlim, probs, nlstate, p, age, ftolpl, ncvyearp, k,nres); + } + fprintf(ficresplb,"%.0f ",age ); + for(j=1;j<=cptcoveff;j++) + fprintf(ficresplb,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); + tot=0.; + for(i=1; i<=nlstate;i++){ + tot += bprlim[i][i]; + fprintf(ficresplb," %.5f", bprlim[i][i]); + } + fprintf(ficresplb," %.3f %d\n", tot, *ncvyearp); + } /* Age */ + /* was end of cptcod */ + /*fprintf(ficresplb,"\n");*/ /* Seems to be necessary for gnuplot only if two result lines and no covariate. */ + } /* end of any combination */ + } /* end of nres */ + /* hBijx(p, bage, fage); */ + /* fclose(ficrespijb); */ + + return 0; +} + +int hPijx(double *p, int bage, int fage){ + /*------------- h Pij x at various ages ------------*/ + + int stepsize; + int agelim; + int hstepm; + int nhstepm; + int h, i, i1, j, k, k4, nres=0; + + double agedeb; + double ***p3mat; + + strcpy(filerespij,"PIJ_"); strcat(filerespij,fileresu); + if((ficrespij=fopen(filerespij,"w"))==NULL) { + printf("Problem with Pij resultfile: %s\n", filerespij); return 1; + fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij); return 1; + } + printf("Computing pij: result on file '%s' \n", filerespij); + fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij); + + stepsize=(int) (stepm+YEARM-1)/YEARM; + /*if (stepm<=24) stepsize=2;*/ + + agelim=AGESUP; + hstepm=stepsize*YEARM; /* Every year of age */ + hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */ + + /* hstepm=1; aff par mois*/ + pstamp(ficrespij); + fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x "); + i1= pow(2,cptcoveff); + /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */ + /* /\*for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*\/ */ + /* k=k+1; */ + for(nres=1; nres <= nresult; nres++) /* For each resultline */ + for(k=1; k<=i1;k++){ + if(i1 != 1 && TKresult[nres]!= k) + continue; + fprintf(ficrespij,"\n#****** "); + for(j=1;j<=cptcoveff;j++) + fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); + for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */ + printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]); + fprintf(ficrespij," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]); + } + fprintf(ficrespij,"******\n"); + + for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */ + nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ + nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */ + + /* nhstepm=nhstepm*YEARM; aff par mois*/ + + p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); + oldm=oldms;savm=savms; + hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k, nres); + fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j="); + for(i=1; i<=nlstate;i++) + for(j=1; j<=nlstate+ndeath;j++) + fprintf(ficrespij," %1d-%1d",i,j); + fprintf(ficrespij,"\n"); + for (h=0; h<=nhstepm; h++){ + /*agedebphstep = agedeb + h*hstepm/YEARM*stepm;*/ + fprintf(ficrespij,"%d %3.f %3.f",k, agedeb, agedeb + h*hstepm/YEARM*stepm ); + for(i=1; i<=nlstate;i++) + for(j=1; j<=nlstate+ndeath;j++) + fprintf(ficrespij," %.5f", p3mat[i][j][h]); + fprintf(ficrespij,"\n"); + } + free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); + fprintf(ficrespij,"\n"); + } + /*}*/ + } + return 0; +} + + int hBijx(double *p, int bage, int fage, double ***prevacurrent){ + /*------------- h Bij x at various ages ------------*/ + + int stepsize; + /* int agelim; */ + int ageminl; + int hstepm; + int nhstepm; + int h, i, i1, j, k, nres; + + double agedeb; + double ***p3mat; + + strcpy(filerespijb,"PIJB_"); strcat(filerespijb,fileresu); + if((ficrespijb=fopen(filerespijb,"w"))==NULL) { + printf("Problem with Pij back resultfile: %s\n", filerespijb); return 1; + fprintf(ficlog,"Problem with Pij back resultfile: %s\n", filerespijb); return 1; + } + printf("Computing pij back: result on file '%s' \n", filerespijb); + fprintf(ficlog,"Computing pij back: result on file '%s' \n", filerespijb); + + stepsize=(int) (stepm+YEARM-1)/YEARM; + /*if (stepm<=24) stepsize=2;*/ + + /* agelim=AGESUP; */ + ageminl=30; + hstepm=stepsize*YEARM; /* Every year of age */ + hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */ + + /* hstepm=1; aff par mois*/ + pstamp(ficrespijb); + fprintf(ficrespijb,"#****** h Bij x Back probability to be in state i at age x-h being in j at x: B1j+B2j+...=1 "); + i1= pow(2,cptcoveff); + /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */ + /* /\*for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*\/ */ + /* k=k+1; */ + for(nres=1; nres <= nresult; nres++){ /* For each resultline */ + for(k=1; k<=i1;k++){ /* For any combination of dummy covariates, fixed and varying */ + if(i1 != 1 && TKresult[nres]!= k) + continue; + fprintf(ficrespijb,"\n#****** "); + for(j=1;j<=cptcoveff;j++) + fprintf(ficrespijb,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); + for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */ + fprintf(ficrespijb," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]); + } + fprintf(ficrespijb,"******\n"); + if(invalidvarcomb[k]){ /* Is it necessary here? */ + fprintf(ficrespijb,"\n#Combination (%d) ignored because no cases \n",k); + continue; + } + + /* for (agedeb=fage; agedeb>=bage; agedeb--){ /\* If stepm=6 months *\/ */ + for (agedeb=bage; agedeb<=fage; agedeb++){ /* If stepm=6 months and estepm=24 (2 years) */ + /* nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /\* Typically 20 years = 20*12/6=40 *\/ */ + nhstepm=(int) rint((agedeb-ageminl)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ + nhstepm = nhstepm/hstepm; /* Typically 40/4=10, because estepm=24 stepm=6 => hstepm=24/6=4 */ + + /* nhstepm=nhstepm*YEARM; aff par mois*/ + + p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); + /* oldm=oldms;savm=savms; */ + /* hbxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k); */ + hbxij(p3mat,nhstepm,agedeb,hstepm,p,prevacurrent,nlstate,stepm, k); + /* hbxij(p3mat,nhstepm,agedeb,hstepm,p,prevacurrent,nlstate,stepm,oldm,savm, dnewm, doldm, dsavm, k); */ + fprintf(ficrespijb,"# Cov Agex agex-h hbijx with i,j="); + for(i=1; i<=nlstate;i++) + for(j=1; j<=nlstate+ndeath;j++) + fprintf(ficrespijb," %1d-%1d",i,j); + fprintf(ficrespijb,"\n"); + for (h=0; h<=nhstepm; h++){ + /*agedebphstep = agedeb + h*hstepm/YEARM*stepm;*/ + fprintf(ficrespijb,"%d %3.f %3.f",k, agedeb, agedeb - h*hstepm/YEARM*stepm ); + /* fprintf(ficrespijb,"%d %3.f %3.f",k, agedeb, agedeb + h*hstepm/YEARM*stepm ); */ + for(i=1; i<=nlstate;i++) + for(j=1; j<=nlstate+ndeath;j++) + fprintf(ficrespijb," %.5f", p3mat[i][j][h]); + fprintf(ficrespijb,"\n"); + } + free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); + fprintf(ficrespijb,"\n"); + } /* end age deb */ + } /* end combination */ + } /* end nres */ + return 0; + } /* hBijx */ + /***********************************************/ /**************** Main Program *****************/ @@ -5195,70 +9971,83 @@ int main(int argc, char *argv[]) double ssval; #endif int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav); - int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod; - int linei, month, year,iout; - int jj, ll, li, lj, lk, imk; + int i,j, k, n=MAXN,iter=0,m,size=100, cptcod; + int ncvyear=0; /* Number of years needed for the period prevalence to converge */ + int jj, ll, li, lj, lk; int numlinepar=0; /* Current linenumber of parameter file */ + int num_filled; int itimes; int NDIM=2; int vpopbased=0; + int nres=0; + int endishere=0; - char ca[32], cb[32], cc[32]; + char ca[32], cb[32]; /* FILE *fichtm; *//* Html File */ /* FILE *ficgp;*/ /*Gnuplot File */ struct stat info; - double agedeb, agefin,hf; - double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20; + double agedeb=0.; - double fret; - double **xi,tmp,delta; + double ageminpar=AGEOVERFLOW,agemin=AGEOVERFLOW, agemaxpar=-AGEOVERFLOW, agemax=-AGEOVERFLOW; + double ageminout=-AGEOVERFLOW,agemaxout=AGEOVERFLOW; /* Smaller Age range redefined after movingaverage */ - double dum; /* Dummy variable */ + double fret; + double dum=0.; /* Dummy variable */ double ***p3mat; - double ***mobaverage; - int *indx; - char line[MAXLINE], linepar[MAXLINE]; - char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE]; + /* double ***mobaverage; */ + + char line[MAXLINE]; + char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE]; + + char modeltemp[MAXLINE]; + char resultline[MAXLINE]; + char pathr[MAXLINE], pathimach[MAXLINE]; - char **bp, *tok, *val; /* pathtot */ + char *tok, *val; /* pathtot */ int firstobs=1, lastobs=10; - int sdeb, sfin; /* Status at beginning and end */ - int c, h , cpt,l; - int ju,jl, mi; - int i1,j1, jk,aa,bb, stepsize, ij; - int jnais,jdc,jint4,jint1,jint2,jint3,*tab; + int c, h , cpt, c2; + int jl=0; + int i1, j1, jk, stepsize=0; + int count=0; + + int *tab; int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */ + int backcast=0; int mobilav=0,popforecast=0; - int hstepm, nhstepm; + int hstepm=0, nhstepm=0; int agemortsup; float sumlpop=0.; double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000; double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000; - double bage, fage, age, agelim, agebase; + double bage=0, fage=110., age, agelim=0., agebase=0.; double ftolpl=FTOL; double **prlim; + double **bprlim; double ***param; /* Matrix of parameters */ - double *p; + double ***paramstart; /* Matrix of starting parameter values */ + double *p, *pstart; /* p=param[1][1] pstart is for starting values guessed by freqsummary */ double **matcov; /* Matrix of covariance */ + double **hess; /* Hessian matrix */ double ***delti3; /* Scale */ double *delti; /* Scale */ double ***eij, ***vareij; double **varpl; /* Variances of prevalence limits by age */ double *epj, vepp; - double kk1, kk2; + double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000; + double jback1=1,mback1=1,anback1=2000,jback2=1,mback2=1,anback2=2000; + double **ximort; char *alph[]={"a","a","b","c","d","e"}, str[4]="1234"; int *dcwave; - char z[1]="c", occ; + char z[1]="c"; /*char *strt;*/ char strtend[80]; - long total_usecs; - + /* setlocale (LC_ALL, ""); */ /* bindtextdomain (PACKAGE, LOCALEDIR); */ /* textdomain (PACKAGE); */ @@ -5266,19 +10055,21 @@ int main(int argc, char *argv[]) /* setlocale (LC_MESSAGES, ""); */ /* gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */ - (void) gettimeofday(&start_time,&tzp); + rstart_time = time(NULL); + /* (void) gettimeofday(&start_time,&tzp);*/ + start_time = *localtime(&rstart_time); curr_time=start_time; - tm = *localtime(&start_time.tv_sec); - tmg = *gmtime(&start_time.tv_sec); - strcpy(strstart,asctime(&tm)); + /*tml = *localtime(&start_time.tm_sec);*/ + /* strcpy(strstart,asctime(&tml)); */ + strcpy(strstart,asctime(&start_time)); /* printf("Localtime (at start)=%s",strstart); */ -/* tp.tv_sec = tp.tv_sec +86400; */ -/* tm = *localtime(&start_time.tv_sec); */ +/* tp.tm_sec = tp.tm_sec +86400; */ +/* tm = *localtime(&start_time.tm_sec); */ /* tmg.tm_year=tmg.tm_year +dsign*dyear; */ /* tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */ /* tmg.tm_hour=tmg.tm_hour + 1; */ -/* tp.tv_sec = mktime(&tmg); */ +/* tp.tm_sec = mktime(&tmg); */ /* strt=asctime(&tmg); */ /* printf("Time(after) =%s",strstart); */ /* (void) time (&time_value); @@ -5290,16 +10081,32 @@ int main(int argc, char *argv[]) nberr=0; /* Number of errors and warnings */ nbwarn=0; +#ifdef WIN32 + _getcwd(pathcd, size); +#else getcwd(pathcd, size); - - printf("\n%s\n%s",version,fullversion); +#endif + syscompilerinfo(0); + printf("\nIMaCh version %s, %s\n%s",version, copyright, fullversion); if(argc <=1){ printf("\nEnter the parameter file name: "); - fgets(pathr,FILENAMELENGTH,stdin); + if(!fgets(pathr,FILENAMELENGTH,stdin)){ + printf("ERROR Empty parameter file name\n"); + goto end; + } i=strlen(pathr); if(pathr[i-1]=='\n') pathr[i-1]='\0'; - for (tok = pathr; tok != NULL; ){ + i=strlen(pathr); + if(i >= 1 && pathr[i-1]==' ') {/* This may happen when dragging on oS/X! */ + pathr[i-1]='\0'; + } + i=strlen(pathr); + if( i==0 ){ + printf("ERROR Empty parameter file name\n"); + goto end; + } + for (tok = pathr; tok != NULL; ){ printf("Pathr |%s|\n",pathr); while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0'); printf("val= |%s| pathr=%s\n",val,pathr); @@ -5323,13 +10130,18 @@ int main(int argc, char *argv[]) /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */ split(pathtot,path,optionfile,optionfilext,optionfilefiname); printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname); +#ifdef WIN32 + _chdir(path); /* Can be a relative path */ + if(_getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */ +#else chdir(path); /* Can be a relative path */ - if(getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */ - printf("Current directory %s!\n",pathcd); + if (getcwd(pathcd, MAXLINE) > 0) /* So pathcd is the full path */ +#endif + printf("Current directory %s!\n",pathcd); strcpy(command,"mkdir "); strcat(command,optionfilefiname); if((outcmd=system(command)) != 0){ - printf("Problem creating directory or it already exists %s%s, err=%d\n",path,optionfilefiname,outcmd); + printf("Directory already exists (or can't create it) %s%s, err=%d\n",path,optionfilefiname,outcmd); /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */ /* fclose(ficlog); */ /* exit(1); */ @@ -5340,7 +10152,7 @@ int main(int argc, char *argv[]) /*-------- arguments in the command line --------*/ - /* Log file */ + /* Main Log file */ strcat(filelog, optionfilefiname); strcat(filelog,".log"); /* */ if((ficlog=fopen(filelog,"w"))==NULL) { @@ -5348,38 +10160,43 @@ int main(int argc, char *argv[]) goto end; } fprintf(ficlog,"Log filename:%s\n",filelog); - fprintf(ficlog,"\n%s\n%s",version,fullversion); + fprintf(ficlog,"Version %s %s",version,fullversion); fprintf(ficlog,"\nEnter the parameter file name: \n"); fprintf(ficlog,"pathimach=%s\npathtot=%s\n\ path=%s \n\ optionfile=%s\n\ optionfilext=%s\n\ - optionfilefiname=%s\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname); + optionfilefiname='%s'\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname); + + syscompilerinfo(1); printf("Local time (at start):%s",strstart); fprintf(ficlog,"Local time (at start): %s",strstart); fflush(ficlog); /* (void) gettimeofday(&curr_time,&tzp); */ -/* printf("Elapsed time %d\n", asc_diff_time(curr_time.tv_sec-start_time.tv_sec,tmpout)); */ +/* printf("Elapsed time %d\n", asc_diff_time(curr_time.tm_sec-start_time.tm_sec,tmpout)); */ /* */ strcpy(fileres,"r"); strcat(fileres, optionfilefiname); + strcat(fileresu, optionfilefiname); /* Without r in front */ strcat(fileres,".txt"); /* Other files have txt extension */ + strcat(fileresu,".txt"); /* Other files have txt extension */ - /*---------arguments file --------*/ + /* Main ---------arguments file --------*/ if((ficpar=fopen(optionfile,"r"))==NULL) { - printf("Problem with optionfile %s\n",optionfile); - fprintf(ficlog,"Problem with optionfile %s\n",optionfile); + printf("Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno)); + fprintf(ficlog,"Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno)); fflush(ficlog); - goto end; + /* goto end; */ + exit(70); } strcpy(filereso,"o"); - strcat(filereso,fileres); + strcat(filereso,fileresu); if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */ printf("Problem with Output resultfile: %s\n", filereso); fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso); @@ -5389,26 +10206,107 @@ int main(int argc, char *argv[]) /* Reads comments: lines beginning with '#' */ numlinepar=0; - while((c=getc(ficpar))=='#' && c!= EOF){ - ungetc(c,ficpar); - fgets(line, MAXLINE, ficpar); + + /* First parameter line */ + while(fgets(line, MAXLINE, ficpar)) { + /* If line starts with a # it is a comment */ + if (line[0] == '#') { + numlinepar++; + fputs(line,stdout); + fputs(line,ficparo); + fputs(line,ficlog); + continue; + }else + break; + } + if((num_filled=sscanf(line,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", \ + title, datafile, &lastobs, &firstpass,&lastpass)) !=EOF){ + if (num_filled != 5) { + printf("Should be 5 parameters\n"); + } numlinepar++; - fputs(line,stdout); - fputs(line,ficparo); - fputs(line,ficlog); + printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", title, datafile, lastobs, firstpass,lastpass); } - ungetc(c,ficpar); - - fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model); - numlinepar++; - printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model); - fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model); - fprintf(ficlog,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model); + /* Second parameter line */ + while(fgets(line, MAXLINE, ficpar)) { + /* If line starts with a # it is a comment */ + if (line[0] == '#') { + numlinepar++; + fputs(line,stdout); + fputs(line,ficparo); + fputs(line,ficlog); + continue; + }else + break; + } + if((num_filled=sscanf(line,"ftol=%lf stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\n", \ + &ftol, &stepm, &ncovcol, &nqv, &ntv, &nqtv, &nlstate, &ndeath, &maxwav, &mle, &weightopt)) !=EOF){ + if (num_filled != 11) { + printf("Not 11 parameters, for example:ftol=1.e-8 stepm=12 ncovcol=2 nqv=1 ntv=2 nqtv=1 nlstate=2 ndeath=1 maxwav=3 mle=1 weight=1\n"); + printf("but line=%s\n",line); + } + printf("ftol=%e stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\n",ftol, stepm, ncovcol, nqv, ntv, nqtv, nlstate, ndeath, maxwav, mle, weightopt); + } + /* ftolpl=6*ftol*1.e5; /\* 6.e-3 make convergences in less than 80 loops for the prevalence limit *\/ */ + /*ftolpl=6.e-4; *//* 6.e-3 make convergences in less than 80 loops for the prevalence limit */ + /* Third parameter line */ + while(fgets(line, MAXLINE, ficpar)) { + /* If line starts with a # it is a comment */ + if (line[0] == '#') { + numlinepar++; + fputs(line,stdout); + fputs(line,ficparo); + fputs(line,ficlog); + continue; + }else + break; + } + if((num_filled=sscanf(line,"model=1+age%[^.\n]", model)) !=EOF){ + if (num_filled == 0){ + printf("ERROR %d: Model should be at minimum 'model=1+age.' WITHOUT space:'%s'\n",num_filled, line); + fprintf(ficlog,"ERROR %d: Model should be at minimum 'model=1+age.' WITHOUT space:'%s'\n",num_filled, line); + model[0]='\0'; + goto end; + } else if (num_filled != 1){ + printf("ERROR %d: Model should be at minimum 'model=1+age.' %s\n",num_filled, line); + fprintf(ficlog,"ERROR %d: Model should be at minimum 'model=1+age.' %s\n",num_filled, line); + model[0]='\0'; + goto end; + } + else{ + if (model[0]=='+'){ + for(i=1; i<=strlen(model);i++) + modeltemp[i-1]=model[i]; + strcpy(model,modeltemp); + } + } + /* printf(" model=1+age%s modeltemp= %s, model=%s\n",model, modeltemp, model);fflush(stdout); */ + printf("model=1+age+%s\n",model);fflush(stdout); + } + /* 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); */ + /* numlinepar=numlinepar+3; /\* In general *\/ */ + /* 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); */ + fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=1+age+%s.\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol, nqv, ntv, nqtv, nlstate,ndeath,maxwav, mle, weightopt,model); + fprintf(ficlog,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=1+age+%s.\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol, nqv, ntv, nqtv, nlstate,ndeath,maxwav, mle, weightopt,model); fflush(ficlog); + /* if(model[0]=='#'|| model[0]== '\0'){ */ + if(model[0]=='#'){ + printf("Error in 'model' line: model should start with 'model=1+age+' and end with '.' \n \ + 'model=1+age+.' or 'model=1+age+V1.' or 'model=1+age+age*age+V1+V1*age.' or \n \ + 'model=1+age+V1+V2.' or 'model=1+age+V1+V2+V1*V2.' etc. \n"); \ + if(mle != -1){ + printf("Fix the model line and run imach with mle=-1 to get a correct template of the parameter file.\n"); + exit(1); + } + } while((c=getc(ficpar))=='#' && c!= EOF){ ungetc(c,ficpar); fgets(line, MAXLINE, ficpar); numlinepar++; + if(line[1]=='q'){ /* This #q will quit imach (the answer is q) */ + z[0]=line[1]; + } + /* printf("****line [1] = %c \n",line[1]); */ fputs(line, stdout); //puts(line); fputs(line,ficparo); @@ -5418,15 +10316,17 @@ int main(int argc, char *argv[]) covar=matrix(0,NCOVMAX,1,n); /**< used in readdata */ + coqvar=matrix(1,nqv,1,n); /**< Fixed quantitative covariate */ + cotvar=ma3x(1,maxwav,1,ntv+nqtv,1,n); /**< Time varying covariate (dummy and quantitative)*/ + cotqvar=ma3x(1,maxwav,1,nqtv,1,n); /**< Time varying quantitative covariate */ cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement plus one, indepently of n in Vn*/ /* v1+v2+v3+v2*v4+v5*age makes cptcovn = 5 v1+v2*age+v2*v3 makes cptcovn = 3 */ if (strlen(model)>1) - 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*/ + 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*/ else - ncovmodel=2; - nvar=ncovmodel-1; /* Suppressing age as a basic covariate */ + ncovmodel=2; /* Constant and age */ nforce= (nlstate+ndeath-1)*nlstate; /* Number of forces ij from state i to j */ npar= nforce*ncovmodel; /* Number of parameters like aij*/ if(npar >MAXPARM || nlstate >NLSTATEMAX || ndeath >NDEATHMAX || ncovmodel>NCOVMAX){ @@ -5440,23 +10340,28 @@ int main(int argc, char *argv[]) delti=delti3[1][1]; /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/ if(mle==-1){ /* Print a wizard for help writing covariance matrix */ +/* We could also provide initial parameters values giving by simple logistic regression + * only one way, that is without matrix product. We will have nlstate maximizations */ + /* for(i=1;i16 */ + ncodemaxwundef=ivector(1,NCOVMAX); /* Number of code per covariate; if - 1 O and 1 only, 2**ncov; V1+V2+V3+V4=>16 */ /* Reads data from file datafile */ if (readdata(datafile, firstobs, lastobs, &imx)==1) goto end; /* Calculation of the number of parameters from char model */ - /* modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4 + /* modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4 k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tag[cptcovage=1]=4 k=3 V4 Tvar[k=3]= 4 (from V4) k=2 V1 Tvar[k=2]= 1 (from V1) k=1 Tvar[1]=2 (from V2) - */ + */ + Tvar=ivector(1,NCOVMAX); /* Was 15 changed to NCOVMAX. */ + TvarsDind=ivector(1,NCOVMAX); /* */ + TvarsD=ivector(1,NCOVMAX); /* */ + TvarsQind=ivector(1,NCOVMAX); /* */ + TvarsQ=ivector(1,NCOVMAX); /* */ + TvarF=ivector(1,NCOVMAX); /* */ + TvarFind=ivector(1,NCOVMAX); /* */ + TvarV=ivector(1,NCOVMAX); /* */ + TvarVind=ivector(1,NCOVMAX); /* */ + TvarA=ivector(1,NCOVMAX); /* */ + TvarAind=ivector(1,NCOVMAX); /* */ + TvarFD=ivector(1,NCOVMAX); /* */ + TvarFDind=ivector(1,NCOVMAX); /* */ + TvarFQ=ivector(1,NCOVMAX); /* */ + TvarFQind=ivector(1,NCOVMAX); /* */ + TvarVD=ivector(1,NCOVMAX); /* */ + TvarVDind=ivector(1,NCOVMAX); /* */ + TvarVQ=ivector(1,NCOVMAX); /* */ + TvarVQind=ivector(1,NCOVMAX); /* */ + + Tvalsel=vector(1,NCOVMAX); /* */ + Tvarsel=ivector(1,NCOVMAX); /* */ + Typevar=ivector(-1,NCOVMAX); /* -1 to 2 */ + Fixed=ivector(-1,NCOVMAX); /* -1 to 3 */ + Dummy=ivector(-1,NCOVMAX); /* -1 to 3 */ /* V2+V1+V4+age*V3 is a model with 4 covariates (3 plus signs). For each model-covariate stores the data-covariate id. Tvar[1]=2, Tvar[2]=1, Tvar[3]=4, Tvar[4=age*V3] is 3 and 'age' is recorded in Tage. @@ -5647,9 +10603,11 @@ run imach with mle=-1 to get a correct t ncovcol + k1 If already ncovcol=4 and model=V2+V1+V1*V4+age*V3 Tvar[3=V1*V4]=4+1 etc */ - Tprod=ivector(1,NCOVMAX); /* Gives the position of a product */ + Tprod=ivector(1,NCOVMAX); /* Gives the k position of the k1 product */ + Tposprod=ivector(1,NCOVMAX); /* Gives the k1 product from the k position */ /* Tprod[k1=1]=3(=V1*V4) for V2+V1+V1*V4+age*V3 if V2+V1+V1*V4+age*V3+V3*V2 TProd[k1=2]=5 (V3*V2) + Tposprod[k]=k1 , Tposprod[3]=1, Tposprod[5]=2 */ Tvaraff=ivector(1,NCOVMAX); /* Unclear */ 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 @@ -5659,8 +10617,23 @@ run imach with mle=-1 to get a correct t 4 covariates (3 plus signs) Tage[1=V3*age]= 4; Tage[2=age*V4] = 3 */ + Tmodelind=ivector(1,NCOVMAX);/** gives the k model position of an + * individual dummy, fixed or varying: + * Tmodelind[Tvaraff[3]]=9,Tvaraff[1]@9={4, + * 3, 1, 0, 0, 0, 0, 0, 0}, + * model=V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 , + * V1 df, V2 qf, V3 & V4 dv, V5 qv + * Tmodelind[1]@9={9,0,3,2,}*/ + TmodelInvind=ivector(1,NCOVMAX); /* TmodelInvind=Tvar[k]- ncovcol-nqv={5-2-1=2,*/ + TmodelInvQind=ivector(1,NCOVMAX);/** gives the k model position of an + * individual quantitative, fixed or varying: + * Tmodelqind[1]=1,Tvaraff[1]@9={4, + * 3, 1, 0, 0, 0, 0, 0, 0}, + * model=V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1*/ +/* Main decodemodel */ + - if(decodemodel(model, lastobs) == 1) + if(decodemodel(model, lastobs) == 1) /* In order to get Tvar[k] V4+V3+V5 p Tvar[1]@3 = {4, 3, 5}*/ goto end; if((double)(lastobs-imx)/(double)imx > 1.10){ @@ -5685,106 +10658,159 @@ run imach with mle=-1 to get a correct t free_vector(annais,1,n); /* free_matrix(mint,1,maxwav,1,n); free_matrix(anint,1,maxwav,1,n);*/ - free_vector(moisdc,1,n); - free_vector(andc,1,n); + /* free_vector(moisdc,1,n); */ + /* free_vector(andc,1,n); */ /* */ wav=ivector(1,imx); - dh=imatrix(1,lastpass-firstpass+1,1,imx); - bh=imatrix(1,lastpass-firstpass+1,1,imx); - mw=imatrix(1,lastpass-firstpass+1,1,imx); + /* dh=imatrix(1,lastpass-firstpass+1,1,imx); */ + /* bh=imatrix(1,lastpass-firstpass+1,1,imx); */ + /* mw=imatrix(1,lastpass-firstpass+1,1,imx); */ + dh=imatrix(1,lastpass-firstpass+2,1,imx); /* We are adding a wave if status is unknown at last wave but death occurs after last wave.*/ + bh=imatrix(1,lastpass-firstpass+2,1,imx); + mw=imatrix(1,lastpass-firstpass+2,1,imx); /* Concatenates waves */ + /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i. + Death is a valid wave (if date is known). + mw[mi][i] is the number of (mi=1 to wav[i]) effective wave out of mi of individual i + dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i] + and mw[mi+1][i]. dh depends on stepm. + */ + concatwav(wav, dh, bh, mw, s, agedc, agev, firstpass, lastpass, imx, nlstate, stepm); - /* */ + /* Concatenates waves */ - /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */ + free_vector(moisdc,1,n); + free_vector(andc,1,n); + /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */ nbcode=imatrix(0,NCOVMAX,0,NCOVMAX); ncodemax[1]=1; Ndum =ivector(-1,NCOVMAX); - if (ncovmodel > 2) - tricode(Tvar,nbcode,imx, Ndum); /**< Fills nbcode[Tvar[j]][l]; */ + cptcoveff=0; + if (ncovmodel-nagesqr > 2 ){ /* That is if covariate other than cst, age and age*age */ + tricode(&cptcoveff,Tvar,nbcode,imx, Ndum); /**< Fills nbcode[Tvar[j]][l]; */ + } + + ncovcombmax=pow(2,cptcoveff); + invalidvarcomb=ivector(1, ncovcombmax); + for(i=1;i 0) */ - - m=pow(2,cptcoveff); - for(k=1;k<=cptcoveff; k++){ /* scans any effective covariate */ - 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 */ - for(j=1; j <= ncodemax[k]; j++){ /* For each modality of this covariate ncodemax=2*/ - for(cpt=1; cpt <=pow(2,k-1); cpt++){ /* cpt=1 to 8/2**(3+1-1 or 3+1-3) =1 or 4 */ - h++; - if (h>m) - h=1; /**< codtab(h,k) k = codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) + 1 - * h 1 2 3 4 + * For k=4 covariates, h goes from 1 to m=2**k + * codtabm(h,k)= (1 & (h-1) >> (k-1)) + 1; + * #define codtabm(h,k) (1 & (h-1) >> (k-1))+1 + * h\k 1 2 3 4 *______________________________ * 1 i=1 1 i=1 1 i=1 1 i=1 1 * 2 2 1 1 1 * 3 i=2 1 2 1 1 * 4 2 2 1 1 - * 5 i=3 1 i=2 1 2 1 - * 6 2 1 2 1 - * 7 i=4 1 2 2 1 - * 8 2 2 2 1 - * 9 i=5 1 i=3 1 i=2 1 1 - * 10 2 1 1 1 - * 11 i=6 1 2 1 1 - * 12 2 2 1 1 - * 13 i=7 1 i=4 1 2 1 - * 14 2 1 2 1 - * 15 i=8 1 2 2 1 - * 16 2 2 2 1 - */ - codtab[h][k]=j; - /*codtab[h][Tvar[k]]=j;*/ - 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]]); - } - } - } - } - /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]); - codtab[1][2]=1;codtab[2][2]=2; */ - /* for(i=1; i <=m ;i++){ - for(k=1; k <=cptcovn; k++){ - printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff); - } - printf("\n"); - } - scanf("%d",i);*/ + * 5 i=3 1 i=2 1 2 1 + * 6 2 1 2 1 + * 7 i=4 1 2 2 1 + * 8 2 2 2 1 + * 9 i=5 1 i=3 1 i=2 1 2 + * 10 2 1 1 2 + * 11 i=6 1 2 1 2 + * 12 2 2 1 2 + * 13 i=7 1 i=4 1 2 2 + * 14 2 1 2 2 + * 15 i=8 1 2 2 2 + * 16 2 2 2 2 + */ + /* How to do the opposite? From combination h (=1 to 2**k) how to get the value on the covariates? */ + /* from h=5 and m, we get then number of covariates k=log(m)/log(2)=4 + * and the value of each covariate? + * V1=1, V2=1, V3=2, V4=1 ? + * h-1=4 and 4 is 0100 or reverse 0010, and +1 is 1121 ok. + * h=6, 6-1=5, 5 is 0101, 1010, 2121, V1=2nd, V2=1st, V3=2nd, V4=1st. + * In order to get the real value in the data, we use nbcode + * nbcode[Tvar[3][2nd]]=1 and nbcode[Tvar[4][1]]=0 + * We are keeping this crazy system in order to be able (in the future?) + * to have more than 2 values (0 or 1) for a covariate. + * #define codtabm(h,k) (1 & (h-1) >> (k-1))+1 + * h=6, k=2? h-1=5=0101, reverse 1010, +1=2121, k=2nd position: value is 1: codtabm(6,2)=1 + * bbbbbbbb + * 76543210 + * h-1 00000101 (6-1=5) + *(h-1)>>(k-1)= 00000010 >> (2-1) = 1 right shift + * & + * 1 00000001 (1) + * 00000000 = 1 & ((h-1) >> (k-1)) + * +1= 00000001 =1 + * + * h=14, k=3 => h'=h-1=13, k'=k-1=2 + * h' 1101 =2^3+2^2+0x2^1+2^0 + * >>k' 11 + * & 00000001 + * = 00000001 + * +1 = 00000010=2 = codtabm(14,3) + * Reverse h=6 and m=16? + * cptcoveff=log(16)/log(2)=4 covariate: 6-1=5=0101 reversed=1010 +1=2121 =>V1=2, V2=1, V3=2, V4=1. + * for (j=1 to cptcoveff) Vj=decodtabm(j,h,cptcoveff) + * decodtabm(h,j,cptcoveff)= (((h-1) >> (j-1)) & 1) +1 + * decodtabm(h,j,cptcoveff)= (h <= (1<> (j-1)) & 1) +1 : -1) + * V3=decodtabm(14,3,2**4)=2 + * h'=13 1101 =2^3+2^2+0x2^1+2^0 + *(h-1) >> (j-1) 0011 =13 >> 2 + * &1 000000001 + * = 000000001 + * +1= 000000010 =2 + * 2211 + * V1=1+1, V2=0+1, V3=1+1, V4=1+1 + * V3=2 + * codtabm and decodtabm are identical + */ + free_ivector(Ndum,-1,NCOVMAX); - /*------------ gnuplot -------------*/ + /* Initialisation of ----------- gnuplot -------------*/ strcpy(optionfilegnuplot,optionfilefiname); if(mle==-3) - strcat(optionfilegnuplot,"-mort"); + strcat(optionfilegnuplot,"-MORT_"); strcat(optionfilegnuplot,".gp"); if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) { printf("Problem with file %s",optionfilegnuplot); } else{ - fprintf(ficgp,"\n# %s\n", version); + fprintf(ficgp,"\n# IMaCh-%s\n", version); fprintf(ficgp,"# %s\n", optionfilegnuplot); //fprintf(ficgp,"set missing 'NaNq'\n"); fprintf(ficgp,"set datafile missing 'NaNq'\n"); } /* fclose(ficgp);*/ - /*--------- index.htm --------*/ + + + /* Initialisation of --------- index.htm --------*/ strcpy(optionfilehtm,optionfilefiname); /* Main html file */ if(mle==-3) - strcat(optionfilehtm,"-mort"); + strcat(optionfilehtm,"-MORT_"); strcat(optionfilehtm,".htm"); if((fichtm=fopen(optionfilehtm,"w"))==NULL) { printf("Problem with %s \n",optionfilehtm); @@ -5799,13 +10825,15 @@ run imach with mle=-1 to get a correct t else{ fprintf(fichtmcov,"\nIMaCh Cov %s\n %s
            %s             \
            \n\ -Title=%s
            Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s
            \n",\ +Title=%s
            Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s
            \n",\ optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model); } - fprintf(fichtm,"\nIMaCh %s\n %s
            %s             \ + fprintf(fichtm,"\n\n\nIMaCh %s\n IMaCh for Interpolated Markov Chain
            \nSponsored by Copyright (C) 2002-2015 INED-EUROREVES-Institut de longévité-2013-2016-Japan Society for the Promotion of Sciences 日本学術振興会 (Grant-in-Aid for Scientific Research 25293121) - Intel Software 2015-2018
            \ +
            \n\ +IMaCh-%s
            %s             \
            \n\ -Title=%s
            Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s
            \n\ +Title=%s
            Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s
            \n\ \n\
            \

            • Parameter files

              \n\ @@ -5822,11 +10850,18 @@ Title=%s
              Datafile=%s Firstpass=%d La strcpy(pathr,path); strcat(pathr,optionfilefiname); +#ifdef WIN32 + _chdir(optionfilefiname); /* Move to directory named optionfile */ +#else chdir(optionfilefiname); /* Move to directory named optionfile */ +#endif + - /* Calculates basic frequencies. Computes observed prevalence at single age + /* Calculates basic frequencies. Computes observed prevalence at single age + and for any valid combination of covariates and prints on file fileres'p'. */ - freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart); + freqsummary(fileres, p, pstart, agemin, agemax, s, agev, nlstate, imx, Tvaraff, invalidvarcomb, nbcode, ncodemax,mint,anint,strstart, \ + firstpass, lastpass, stepm, weightopt, model); fprintf(fichtm,"\n"); fprintf(fichtm,"
              Total number of observations=%d
              \n\ @@ -5834,26 +10869,28 @@ Youngest age at first (selected) pass %. Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf
              \n",\ imx,agemin,agemax,jmin,jmax,jmean); pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */ - oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */ - newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */ - savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */ - oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */ - - + oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */ + newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */ + savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */ + oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */ + /* For Powell, parameters are in a vector p[] starting at p[1] so we point p on param[1][1] so that p[1] maps on param[1][1][1] */ p=param[1][1]; /* *(*(*(param +1)+1)+0) */ globpr=0; /* To get the number ipmx of contributions and the sum of weights*/ - + /* For mortality only */ if (mle==-3){ ximort=matrix(1,NDIM,1,NDIM); -/* ximort=gsl_matrix_alloc(1,NDIM,1,NDIM); */ + for(i=1;i<=NDIM;i++) + for(j=1;j<=NDIM;j++) + ximort[i][j]=0.; + /* ximort=gsl_matrix_alloc(1,NDIM,1,NDIM); */ cens=ivector(1,n); ageexmed=vector(1,n); agecens=vector(1,n); dcwave=ivector(1,n); - + for (i=1; i<=imx; i++){ dcwave[i]=-1; for (m=firstpass; m<=lastpass; m++) @@ -5863,13 +10900,13 @@ Interval (in months) between two waves: break; } } - + for (i=1; i<=imx; i++) { if (wav[i]>0){ ageexmed[i]=agev[mw[1][i]][i]; j=wav[i]; agecens[i]=1.; - + if (ageexmed[i]> 1 && wav[i] > 0){ agecens[i]=agev[mw[j][i]][i]; cens[i]= 1; @@ -5892,18 +10929,18 @@ Interval (in months) between two waves: #ifdef GSL printf("GSL optimization\n"); fprintf(ficlog,"Powell\n"); -#elsedef +#else printf("Powell\n"); fprintf(ficlog,"Powell\n"); #endif - strcpy(filerespow,"pow-mort"); - strcat(filerespow,fileres); + strcpy(filerespow,"POW-MORT_"); + strcat(filerespow,fileresu); if((ficrespow=fopen(filerespow,"w"))==NULL) { printf("Problem with resultfile: %s\n", filerespow); fprintf(ficlog,"Problem with resultfile: %s\n", filerespow); } #ifdef GSL fprintf(ficrespow,"# GSL optimization\n# iter -2*LL"); -#elsedef +#else fprintf(ficrespow,"# Powell\n# iter -2*LL"); #endif /* for (i=1;i<=nlstate;i++) @@ -5938,8 +10975,8 @@ Interval (in months) between two waves: /* Initialize method and iterate */ /* p[1]=0.0268; p[NDIM]=0.083; */ -/* gsl_vector_set(x, 0, 0.0268); */ -/* gsl_vector_set(x, 1, 0.083); */ + /* gsl_vector_set(x, 0, 0.0268); */ + /* gsl_vector_set(x, 1, 0.083); */ gsl_vector_set(x, 0, p[1]); gsl_vector_set(x, 1, p[2]); @@ -5992,24 +11029,27 @@ Interval (in months) between two waves: #endif fclose(ficrespow); - hesscov(matcov, p, NDIM, delti, 1e-4, gompertz); + hesscov(matcov, hess, p, NDIM, delti, 1e-4, gompertz); for(i=1; i <=NDIM; i++) for(j=i+1;j<=NDIM;j++) - matcov[i][j]=matcov[j][i]; + matcov[i][j]=matcov[j][i]; printf("\nCovariance matrix\n "); + fprintf(ficlog,"\nCovariance matrix\n "); for(i=1; i <=NDIM; i++) { for(j=1;j<=NDIM;j++){ - printf("%f ",matcov[i][j]); + printf("%f ",matcov[i][j]); + fprintf(ficlog,"%f ",matcov[i][j]); } - printf("\n "); + printf("\n "); fprintf(ficlog,"\n "); } printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp); - for (i=1;i<=NDIM;i++) + for (i=1;i<=NDIM;i++) { printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i])); - + fprintf(ficlog,"%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i])); + } lsurv=vector(1,AGESUP); lpop=vector(1,AGESUP); tpop=vector(1,AGESUP); @@ -6041,42 +11081,65 @@ Interval (in months) between two waves: replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */ - printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p); - - printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \ + ageminpar=50; + agemaxpar=100; + if(ageminpar == AGEOVERFLOW ||agemaxpar == AGEOVERFLOW){ + printf("Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\ +This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\ +Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar); + fprintf(ficlog,"Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\ +This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\ +Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar); + }else{ + printf("Warning! ageminpar %f and agemaxpar %f have been fixed because for simplification until it is fixed...\n\n",ageminpar,agemaxpar); + fprintf(ficlog,"Warning! ageminpar %f and agemaxpar %f have been fixed because for simplification until it is fixed...\n\n",ageminpar,agemaxpar); + printinggnuplotmort(fileresu, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p); + } + printinghtmlmort(fileresu,title,datafile, firstpass, lastpass, \ stepm, weightopt,\ model,imx,p,matcov,agemortsup); free_vector(lsurv,1,AGESUP); free_vector(lpop,1,AGESUP); free_vector(tpop,1,AGESUP); -#ifdef GSL + free_matrix(ximort,1,NDIM,1,NDIM); free_ivector(cens,1,n); free_vector(agecens,1,n); free_ivector(dcwave,1,n); - free_matrix(ximort,1,NDIM,1,NDIM); +#ifdef GSL #endif - } /* Endof if mle==-3 */ - - else{ /* For mle >=1 */ - globpr=0;/* debug */ + } /* Endof if mle==-3 mortality only */ + /* Standard */ + else{ /* For mle !=- 3, could be 0 or 1 or 4 etc. */ + globpr=0;/* Computes sum of likelihood for globpr=1 and funcone */ + /* Computes likelihood for initial parameters, uses funcone to compute gpimx and gsw */ likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */ printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw); for (k=1; k<=npar;k++) printf(" %d %8.5f",k,p[k]); printf("\n"); - globpr=1; /* to print the contributions */ + if(mle>=1){ /* Could be 1 or 2, Real Maximization */ + /* mlikeli uses func not funcone */ + /* for(i=1;i=1){ /* Could be 1 or 2 */ - mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func); - } /*--------- results files --------------*/ - fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate, ndeath, maxwav, weightopt,model); + fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=1+age+%s.\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nqv, ntv, nqtv, nlstate, ndeath, maxwav, weightopt,model); fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n"); @@ -6089,9 +11152,9 @@ Interval (in months) between two waves: fprintf(ficlog,"%d%d ",i,k); fprintf(ficres,"%1d%1d ",i,k); for(j=1; j <=ncovmodel; j++){ - printf("%lf ",p[jk]); - fprintf(ficlog,"%lf ",p[jk]); - fprintf(ficres,"%lf ",p[jk]); + printf("%12.7f ",p[jk]); + fprintf(ficlog,"%12.7f ",p[jk]); + fprintf(ficres,"%12.7f ",p[jk]); jk++; } printf("\n"); @@ -6100,11 +11163,30 @@ Interval (in months) between two waves: } } } - if(mle!=0){ - /* Computing hessian and covariance matrix */ + if(mle != 0){ + /* Computing hessian and covariance matrix only at a peak of the Likelihood, that is after optimization */ ftolhess=ftol; /* Usually correct */ - hesscov(matcov, p, npar, delti, ftolhess, func); - } + hesscov(matcov, hess, p, npar, delti, ftolhess, func); + printf("Parameters and 95%% confidence intervals\n W is simply the result of the division of the parameter by the square root of covariance of the parameter.\n And Wald-based confidence intervals plus and minus 1.96 * W .\n But be careful that parameters are highly correlated because incidence of disability is highly correlated to incidence of recovery.\n It might be better to visualize the covariance matrix. See the page 'Matrix of variance-covariance of one-step probabilities' and its graphs.\n"); + fprintf(ficlog, "Parameters, Wald tests and Wald-based confidence intervals\n W is simply the result of the division of the parameter by the square root of covariance of the parameter.\n And Wald-based confidence intervals plus and minus 1.96 * W \n It might be better to visualize the covariance matrix. See the page 'Matrix of variance-covariance of one-step probabilities' and its graphs.\n"); + for(i=1,jk=1; i <=nlstate; i++){ + for(k=1; k <=(nlstate+ndeath); k++){ + if (k != i) { + printf("%d%d ",i,k); + fprintf(ficlog,"%d%d ",i,k); + for(j=1; j <=ncovmodel; j++){ + printf("%12.7f W=%8.3f CI=[%12.7f ; %12.7f] ",p[jk], p[jk]/sqrt(matcov[jk][jk]), p[jk]-1.96*sqrt(matcov[jk][jk]),p[jk]+1.96*sqrt(matcov[jk][jk])); + fprintf(ficlog,"%12.7f W=%8.3f CI=[%12.7f ; %12.7f] ",p[jk], p[jk]/sqrt(matcov[jk][jk]), p[jk]-1.96*sqrt(matcov[jk][jk]),p[jk]+1.96*sqrt(matcov[jk][jk])); + jk++; + } + printf("\n"); + fprintf(ficlog,"\n"); + } + } + } + } /* end of hesscov and Wald tests */ + + /* */ fprintf(ficres,"# Scales (for hessian or gradient estimation)\n"); printf("# Scales (for hessian or gradient estimation)\n"); fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n"); @@ -6128,7 +11210,7 @@ Interval (in months) between two waves: } 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"); - if(mle>=1) + if(mle >= 1) /* To big for the screen */ 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"); 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"); /* # 121 Var(a12)\n\ */ @@ -6191,9 +11273,9 @@ Interval (in months) between two waves: fprintf(ficres," Var(%s%1d%1d)",ca,i,j); }else{ if(mle>=1) - printf(" %.5e",matcov[jj][ll]); - fprintf(ficlog," %.5e",matcov[jj][ll]); - fprintf(ficres," %.5e",matcov[jj][ll]); + printf(" %.7e",matcov[jj][ll]); + fprintf(ficlog," %.7e",matcov[jj][ll]); + fprintf(ficres," %.7e",matcov[jj][ll]); } } } @@ -6212,17 +11294,40 @@ Interval (in months) between two waves: fflush(ficlog); fflush(ficres); - - while((c=getc(ficpar))=='#' && c!= EOF){ - ungetc(c,ficpar); - fgets(line, MAXLINE, ficpar); - fputs(line,stdout); - fputs(line,ficparo); + while(fgets(line, MAXLINE, ficpar)) { + /* If line starts with a # it is a comment */ + if (line[0] == '#') { + numlinepar++; + fputs(line,stdout); + fputs(line,ficparo); + fputs(line,ficlog); + continue; + }else + break; } - ungetc(c,ficpar); + + /* while((c=getc(ficpar))=='#' && c!= EOF){ */ + /* ungetc(c,ficpar); */ + /* fgets(line, MAXLINE, ficpar); */ + /* fputs(line,stdout); */ + /* fputs(line,ficparo); */ + /* } */ + /* ungetc(c,ficpar); */ estepm=0; - fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm); + if((num_filled=sscanf(line,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d ftolpl=%lf\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm, &ftolpl)) !=EOF){ + + if (num_filled != 6) { + printf("Error: Not 6 parameters in line, for example:agemin=60 agemax=95 bage=55 fage=95 estepm=24 ftolpl=6e-4\n, your line=%s . Probably you are running an older format.\n",line); + fprintf(ficlog,"Error: Not 6 parameters in line, for example:agemin=60 agemax=95 bage=55 fage=95 estepm=24 ftolpl=6e-4\n, your line=%s . Probably you are running an older format.\n",line); + goto end; + } + printf("agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d ftolpl=%lf\n",ageminpar,agemaxpar, bage, fage, estepm, ftolpl); + } + /* ftolpl=6*ftol*1.e5; /\* 6.e-3 make convergences in less than 80 loops for the prevalence limit *\/ */ + /*ftolpl=6.e-4;*/ /* 6.e-3 make convergences in less than 80 loops for the prevalence limit */ + + /* fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d ftolpl=%\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm); */ if (estepm==0 || estepm < stepm) estepm=stepm; if (fage <= 2) { bage = ageminpar; @@ -6230,288 +11335,536 @@ Interval (in months) between two waves: } fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n"); - fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm); - fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm); - - while((c=getc(ficpar))=='#' && c!= EOF){ - ungetc(c,ficpar); - fgets(line, MAXLINE, ficpar); - fputs(line,stdout); - fputs(line,ficparo); + fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d ftolpl=%e\n",ageminpar,agemaxpar,bage,fage, estepm, ftolpl); + fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d, ftolpl=%e\n",ageminpar,agemaxpar,bage,fage, estepm, ftolpl); + + /* Other stuffs, more or less useful */ + while(fgets(line, MAXLINE, ficpar)) { + /* If line starts with a # it is a comment */ + if (line[0] == '#') { + numlinepar++; + fputs(line,stdout); + fputs(line,ficparo); + fputs(line,ficlog); + continue; + }else + break; } - ungetc(c,ficpar); - - 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); - 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); - 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); - printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav); - 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); - - while((c=getc(ficpar))=='#' && c!= EOF){ - ungetc(c,ficpar); - fgets(line, MAXLINE, ficpar); - fputs(line,stdout); - fputs(line,ficparo); + + if((num_filled=sscanf(line,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf mov_average=%d\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2,&mobilav)) !=EOF){ + + if (num_filled != 7) { + printf("Error: Not 7 (data)parameters in line but %d, for example:begin-prev-date=1/1/1990 end-prev-date=1/6/2004 mov_average=0\n, your line=%s . Probably you are running an older format.\n",num_filled,line); + fprintf(ficlog,"Error: Not 7 (data)parameters in line but %d, for example:begin-prev-date=1/1/1990 end-prev-date=1/6/2004 mov_average=0\n, your line=%s . Probably you are running an older format.\n",num_filled,line); + goto end; + } + printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav); + 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); + 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); + 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); + } + + while(fgets(line, MAXLINE, ficpar)) { + /* If line starts with a # it is a comment */ + if (line[0] == '#') { + numlinepar++; + fputs(line,stdout); + fputs(line,ficparo); + fputs(line,ficlog); + continue; + }else + break; } - ungetc(c,ficpar); dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.; dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.; - fscanf(ficpar,"pop_based=%d\n",&popbased); - fprintf(ficparo,"pop_based=%d\n",popbased); - fprintf(ficres,"pop_based=%d\n",popbased); - - while((c=getc(ficpar))=='#' && c!= EOF){ - ungetc(c,ficpar); - fgets(line, MAXLINE, ficpar); - fputs(line,stdout); - fputs(line,ficparo); + if((num_filled=sscanf(line,"pop_based=%d\n",&popbased)) !=EOF){ + if (num_filled != 1) { + printf("Error: Not 1 (data)parameters in line but %d, for example:pop_based=0\n, your line=%s . Probably you are running an older format.\n",num_filled,line); + fprintf(ficlog,"Error: Not 1 (data)parameters in line but %d, for example: pop_based=1\n, your line=%s . Probably you are running an older format.\n",num_filled,line); + goto end; + } + printf("pop_based=%d\n",popbased); + fprintf(ficlog,"pop_based=%d\n",popbased); + fprintf(ficparo,"pop_based=%d\n",popbased); + fprintf(ficres,"pop_based=%d\n",popbased); } - ungetc(c,ficpar); - - 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); - 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); - 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); - 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); - 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); - /* day and month of proj2 are not used but only year anproj2.*/ - - + + /* Results */ + nresult=0; + do{ + if(!fgets(line, MAXLINE, ficpar)){ + endishere=1; + parameterline=14; + }else if (line[0] == '#') { + /* If line starts with a # it is a comment */ + numlinepar++; + fputs(line,stdout); + fputs(line,ficparo); + fputs(line,ficlog); + continue; + }else if(sscanf(line,"prevforecast=%[^\n]\n",modeltemp)) + parameterline=11; + else if(sscanf(line,"backcast=%[^\n]\n",modeltemp)) + parameterline=12; + else if(sscanf(line,"result:%[^\n]\n",modeltemp)) + parameterline=13; + else{ + parameterline=14; + } + switch (parameterline){ + case 11: + if((num_filled=sscanf(line,"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)) !=EOF){ + if (num_filled != 8) { + printf("Error: Not 8 (data)parameters in line but %d, for example:prevforecast=1 starting-proj-date=1/1/1990 final-proj-date=1/1/2000 mobil_average=0\n, your line=%s . Probably you are running an older format.\n",num_filled,line); + fprintf(ficlog,"Error: Not 8 (data)parameters in line but %d, for example:prevforecast=1 starting-proj-date=1/1/1990 final-proj-date=1/1/2000 mov_average=0\n, your line=%s . Probably you are running an older format.\n",num_filled,line); + goto end; + } + 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); + 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); + 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); + 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); + /* day and month of proj2 are not used but only year anproj2.*/ + } + break; + case 12: + /*fscanf(ficpar,"backcast=%d starting-back-date=%lf/%lf/%lf final-back-date=%lf/%lf/%lf mobil_average=%d\n",&backcast,&jback1,&mback1,&anback1,&jback2,&mback2,&anback2,&mobilavproj);*/ + if((num_filled=sscanf(line,"backcast=%d starting-back-date=%lf/%lf/%lf final-back-date=%lf/%lf/%lf mobil_average=%d\n",&backcast,&jback1,&mback1,&anback1,&jback2,&mback2,&anback2,&mobilavproj)) !=EOF){ + if (num_filled != 8) { + printf("Error: Not 8 (data)parameters in line but %d, for example:backcast=1 starting-back-date=1/1/1990 final-back-date=1/1/1970 mobil_average=1\n, your line=%s . Probably you are running an older format.\n",num_filled,line); + fprintf(ficlog,"Error: Not 8 (data)parameters in line but %d, for example:backcast=1 starting-back-date=1/1/1990 final-back-date=1/1/1970 mobil_average=1\n, your line=%s . Probably you are running an older format.\n",num_filled,line); + goto end; + } + printf("backcast=%d starting-back-date=%.lf/%.lf/%.lf final-back-date=%.lf/%.lf/%.lf mobil_average=%d\n",backcast,jback1,mback1,anback1,jback2,mback2,anback2,mobilavproj); + fprintf(ficparo,"backcast=%d starting-back-date=%.lf/%.lf/%.lf final-back-date=%.lf/%.lf/%.lf mobil_average=%d\n",backcast,jback1,mback1,anback1,jback2,mback2,anback2,mobilavproj); + fprintf(ficlog,"backcast=%d starting-back-date=%.lf/%.lf/%.lf final-back-date=%.lf/%.lf/%.lf mobil_average=%d\n",backcast,jback1,mback1,anback1,jback2,mback2,anback2,mobilavproj); + fprintf(ficres,"backcast=%d starting-back-date=%.lf/%.lf/%.lf final-back-date=%.lf/%.lf/%.lf mobil_average=%d\n",backcast,jback1,mback1,anback1,jback2,mback2,anback2,mobilavproj); + /* day and month of proj2 are not used but only year anproj2.*/ + } + break; + case 13: + if((num_filled=sscanf(line,"result:%[^\n]\n",resultline)) !=EOF){ + if (num_filled == 0){ + resultline[0]='\0'; + printf("Warning %d: no result line! It should be at minimum 'result: V2=0 V1=1 or result:.\n%s\n", num_filled, line); + fprintf(ficlog,"Warning %d: no result line! It should be at minimum 'result: V2=0 V1=1 or result:.\n%s\n", num_filled, line); + break; + } else if (num_filled != 1){ + printf("ERROR %d: result line! It should be at minimum 'result: V2=0 V1=1 or result:.' %s\n",num_filled, line); + fprintf(ficlog,"ERROR %d: result line! It should be at minimum 'result: V2=0 V1=1 or result:.' %s\n",num_filled, line); + } + nresult++; /* Sum of resultlines */ + printf("Result %d: result=%s\n",nresult, resultline); + if(nresult > MAXRESULTLINES){ + printf("ERROR: Current version of IMaCh limits the number of resultlines to %d, you used %d\n",MAXRESULTLINES,nresult); + fprintf(ficlog,"ERROR: Current version of IMaCh limits the number of resultlines to %d, you used %d\n",MAXRESULTLINES,nresult); + goto end; + } + decoderesult(resultline, nresult); /* Fills TKresult[nresult] combination and Tresult[nresult][k4+1] combination values */ + fprintf(ficparo,"result: %s\n",resultline); + fprintf(ficres,"result: %s\n",resultline); + fprintf(ficlog,"result: %s\n",resultline); + break; + case 14: + if(ncovmodel >2 && nresult==0 ){ + printf("ERROR: no result lines! It should be at minimum 'result: V2=0 V1=1 or result:.' %s\n",line); + goto end; + } + break; + default: + nresult=1; + decoderesult(".",nresult ); /* No covariate */ + } + } /* End switch parameterline */ + }while(endishere==0); /* End do */ - /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint); */ + /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint); */ /* ,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2); */ replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */ - printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p); - - printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\ - model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\ - jprev1,mprev1,anprev1,jprev2,mprev2,anprev2); - - /*------------ free_vector -------------*/ - /* chdir(path); */ - - free_ivector(wav,1,imx); - free_imatrix(dh,1,lastpass-firstpass+1,1,imx); - free_imatrix(bh,1,lastpass-firstpass+1,1,imx); - free_imatrix(mw,1,lastpass-firstpass+1,1,imx); + if(ageminpar == AGEOVERFLOW ||agemaxpar == -AGEOVERFLOW){ + printf("Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\ +This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\ +Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar); + fprintf(ficlog,"Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\ +This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\ +Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar); + }else{ + printinggnuplot(fileresu, optionfilefiname,ageminpar,agemaxpar,fage, prevfcast, backcast, pathc,p); + } + printinghtml(fileresu,title,datafile, firstpass, lastpass, stepm, weightopt, \ + model,imx,jmin,jmax,jmean,rfileres,popforecast,mobilav,prevfcast,mobilavproj,backcast, estepm, \ + jprev1,mprev1,anprev1,dateprev1,jprev2,mprev2,anprev2,dateprev2); + + /*------------ free_vector -------------*/ + /* chdir(path); */ + + /* free_ivector(wav,1,imx); */ /* Moved after last prevalence call */ + /* free_imatrix(dh,1,lastpass-firstpass+2,1,imx); */ + /* free_imatrix(bh,1,lastpass-firstpass+2,1,imx); */ + /* free_imatrix(mw,1,lastpass-firstpass+2,1,imx); */ free_lvector(num,1,n); free_vector(agedc,1,n); /*free_matrix(covar,0,NCOVMAX,1,n);*/ /*free_matrix(covar,1,NCOVMAX,1,n);*/ fclose(ficparo); fclose(ficres); - - + + + /* Other results (useful)*/ + + /*--------------- Prevalence limit (period or stable prevalence) --------------*/ -#include "prevlim.h" /* Use ficrespl, ficlog */ + /*#include "prevlim.h"*/ /* Use ficrespl, ficlog */ + prlim=matrix(1,nlstate,1,nlstate); + prevalence_limit(p, prlim, ageminpar, agemaxpar, ftolpl, &ncvyear); fclose(ficrespl); -#ifdef FREEEXIT2 -#include "freeexit2.h" -#endif - /*------------- h Pij x at various ages ------------*/ -#include "hpijx.h" + /*#include "hpijx.h"*/ + hPijx(p, bage, fage); fclose(ficrespij); - - /*-------------- Variance of one-step probabilities---*/ + + /* ncovcombmax= pow(2,cptcoveff); */ + /*-------------- Variance of one-step probabilities---*/ k=1; varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart); - - - probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX); + + /* Prevalence for each covariates in probs[age][status][cov] */ + probs= ma3x(1,AGESUP,1,nlstate+ndeath, 1,ncovcombmax); for(i=1;i<=AGESUP;i++) - for(j=1;j<=NCOVMAX;j++) - for(k=1;k<=NCOVMAX;k++) + for(j=1;j<=nlstate+ndeath;j++) /* ndeath is useless but a necessity to be compared with mobaverages */ + for(k=1;k<=ncovcombmax;k++) probs[i][j][k]=0.; - + prevalence(probs, ageminpar, agemaxpar, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass); + if (mobilav!=0 ||mobilavproj !=0 ) { + mobaverages= ma3x(1, AGESUP,1,nlstate+ndeath, 1,ncovcombmax); + for(i=1;i<=AGESUP;i++) + for(j=1;j<=nlstate;j++) + for(k=1;k<=ncovcombmax;k++) + mobaverages[i][j][k]=0.; + mobaverage=mobaverages; + if (mobilav!=0) { + printf("Movingaveraging observed prevalence\n"); + fprintf(ficlog,"Movingaveraging observed prevalence\n"); + if (movingaverage(probs, ageminpar, agemaxpar, mobaverage, mobilav)!=0){ + fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav); + printf(" Error in movingaverage mobilav=%d\n",mobilav); + } + } + /* /\* Prevalence for each covariates in probs[age][status][cov] *\/ */ + /* prevalence(probs, ageminpar, agemaxpar, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass); */ + else if (mobilavproj !=0) { + printf("Movingaveraging projected observed prevalence\n"); + fprintf(ficlog,"Movingaveraging projected observed prevalence\n"); + if (movingaverage(probs, ageminpar, agemaxpar, mobaverage, mobilavproj)!=0){ + fprintf(ficlog," Error in movingaverage mobilavproj=%d\n",mobilavproj); + printf(" Error in movingaverage mobilavproj=%d\n",mobilavproj); + } + } + }/* end if moving average */ + /*---------- Forecasting ------------------*/ /*if((stepm == 1) && (strcmp(model,".")==0)){*/ if(prevfcast==1){ /* if(stepm ==1){*/ - prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff); - /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/ - /* } */ - /* else{ */ - /* erreur=108; */ - /* 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); */ - /* 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); */ - /* } */ + prevforecast(fileresu, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff); } - - - /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */ - - prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass); - /* 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",\ - ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass); - */ - - if (mobilav!=0) { - mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); - if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){ - fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav); - printf(" Error in movingaverage mobilav=%d\n",mobilav); - } + if(backcast==1){ + ddnewms=matrix(1,nlstate+ndeath,1,nlstate+ndeath); + ddoldms=matrix(1,nlstate+ndeath,1,nlstate+ndeath); + ddsavms=matrix(1,nlstate+ndeath,1,nlstate+ndeath); + + /*--------------- Back Prevalence limit (period or stable prevalence) --------------*/ + + bprlim=matrix(1,nlstate,1,nlstate); + back_prevalence_limit(p, bprlim, ageminpar, agemaxpar, ftolpl, &ncvyear, dateprev1, dateprev2, firstpass, lastpass, mobilavproj); + fclose(ficresplb); + + hBijx(p, bage, fage, mobaverage); + fclose(ficrespijb); + free_matrix(bprlim,1,nlstate,1,nlstate); /*here or after loop ? */ + + /* prevbackforecast(fileresu, anback1, mback1, jback1, agemin, agemax, dateprev1, dateprev2, mobilavproj, + bage, fage, firstpass, lastpass, anback2, p, cptcoveff); */ + free_matrix(ddnewms, 1, nlstate+ndeath, 1, nlstate+ndeath); + free_matrix(ddsavms, 1, nlstate+ndeath, 1, nlstate+ndeath); + free_matrix(ddoldms, 1, nlstate+ndeath, 1, nlstate+ndeath); } + + + /* ------ Other prevalence ratios------------ */ - + free_ivector(wav,1,imx); + free_imatrix(dh,1,lastpass-firstpass+2,1,imx); + free_imatrix(bh,1,lastpass-firstpass+2,1,imx); + free_imatrix(mw,1,lastpass-firstpass+2,1,imx); + + /*---------- Health expectancies, no variances ------------*/ - - strcpy(filerese,"e"); - strcat(filerese,fileres); + + strcpy(filerese,"E_"); + strcat(filerese,fileresu); if((ficreseij=fopen(filerese,"w"))==NULL) { printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0); fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0); } - printf("Computing Health Expectancies: result on file '%s' \n", filerese); - fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese); - /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){ - for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/ - - for (k=1; k <= (int) pow(2,cptcoveff); k++){ - fprintf(ficreseij,"\n#****** "); - for(j=1;j<=cptcoveff;j++) { - fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]); - } - fprintf(ficreseij,"******\n"); + printf("Computing Health Expectancies: result on file '%s' ...", filerese);fflush(stdout); + fprintf(ficlog,"Computing Health Expectancies: result on file '%s' ...", filerese);fflush(ficlog); - eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage); - oldm=oldms;savm=savms; - evsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart); + pstamp(ficreseij); + + i1=pow(2,cptcoveff); /* Number of combination of dummy covariates */ + if (cptcovn < 1){i1=1;} + + for(nres=1; nres <= nresult; nres++) /* For each resultline */ + for(k=1; k<=i1;k++){ /* For any combination of dummy covariates, fixed and varying */ + if(i1 != 1 && TKresult[nres]!= k) + continue; + fprintf(ficreseij,"\n#****** "); + printf("\n#****** "); + for(j=1;j<=cptcoveff;j++) { + fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); + printf("V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); + } + for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */ + printf(" V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]); + fprintf(ficreseij," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]); + } + fprintf(ficreseij,"******\n"); + printf("******\n"); - free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage); - /*}*/ + eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage); + oldm=oldms;savm=savms; + evsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart, nres); + + free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage); } fclose(ficreseij); - - - /*---------- Health expectancies and variances ------------*/ - - - strcpy(filerest,"t"); - strcat(filerest,fileres); + printf("done evsij\n");fflush(stdout); + fprintf(ficlog,"done evsij\n");fflush(ficlog); + + /*---------- State-specific expectancies and variances ------------*/ + + + strcpy(filerest,"T_"); + strcat(filerest,fileresu); if((ficrest=fopen(filerest,"w"))==NULL) { printf("Problem with total LE resultfile: %s\n", filerest);goto end; fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end; } - printf("Computing Total Life expectancies with their standard errors: file '%s' \n", filerest); - fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' \n", filerest); - + printf("Computing Total Life expectancies with their standard errors: file '%s' ...\n", filerest); fflush(stdout); + fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' ...\n", filerest); fflush(ficlog); + - strcpy(fileresstde,"stde"); - strcat(fileresstde,fileres); + strcpy(fileresstde,"STDE_"); + strcat(fileresstde,fileresu); if((ficresstdeij=fopen(fileresstde,"w"))==NULL) { - printf("Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0); - fprintf(ficlog,"Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0); + printf("Problem with State specific Exp. and std errors resultfile: %s\n", fileresstde); exit(0); + fprintf(ficlog,"Problem with State specific Exp. and std errors resultfile: %s\n", fileresstde); exit(0); } - printf("Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde); - fprintf(ficlog,"Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde); + printf(" Computing State-specific Expectancies and standard errors: result on file '%s' \n", fileresstde); + fprintf(ficlog," Computing State-specific Expectancies and standard errors: result on file '%s' \n", fileresstde); - strcpy(filerescve,"cve"); - strcat(filerescve,fileres); + strcpy(filerescve,"CVE_"); + strcat(filerescve,fileresu); if((ficrescveij=fopen(filerescve,"w"))==NULL) { - printf("Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0); - fprintf(ficlog,"Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0); + printf("Problem with Covar. State-specific Exp. resultfile: %s\n", filerescve); exit(0); + fprintf(ficlog,"Problem with Covar. State-specific Exp. resultfile: %s\n", filerescve); exit(0); } - printf("Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve); - fprintf(ficlog,"Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve); + printf(" Computing Covar. of State-specific Expectancies: result on file '%s' \n", filerescve); + fprintf(ficlog," Computing Covar. of State-specific Expectancies: result on file '%s' \n", filerescve); - strcpy(fileresv,"v"); - strcat(fileresv,fileres); + strcpy(fileresv,"V_"); + strcat(fileresv,fileresu); if((ficresvij=fopen(fileresv,"w"))==NULL) { printf("Problem with variance resultfile: %s\n", fileresv);exit(0); fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0); } - printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv); - fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv); + printf(" Computing Variance-covariance of State-specific Expectancies: file '%s' ... ", fileresv);fflush(stdout); + fprintf(ficlog," Computing Variance-covariance of State-specific Expectancies: file '%s' ... ", fileresv);fflush(ficlog); /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){ for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/ - for (k=1; k <= (int) pow(2,cptcoveff); k++){ - fprintf(ficrest,"\n#****** "); - for(j=1;j<=cptcoveff;j++) - fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]); - fprintf(ficrest,"******\n"); - - fprintf(ficresstdeij,"\n#****** "); - fprintf(ficrescveij,"\n#****** "); - for(j=1;j<=cptcoveff;j++) { - fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]); - fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]); - } - fprintf(ficresstdeij,"******\n"); - fprintf(ficrescveij,"******\n"); - - fprintf(ficresvij,"\n#****** "); - for(j=1;j<=cptcoveff;j++) - fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]); - fprintf(ficresvij,"******\n"); - - eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage); - oldm=oldms;savm=savms; - cvevsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart); - /* - */ - /* goto endfree; */ - - vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage); - pstamp(ficrest); - - - for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/ - oldm=oldms;savm=savms; /* Segmentation fault */ - varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,vpopbased,mobilav, strstart); - 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 "); - if(vpopbased==1) - 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); - else - fprintf(ficrest,"the age specific period (stable) prevalences in each health state \n"); - fprintf(ficrest,"# Age e.. (std) "); - for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i); - fprintf(ficrest,"\n"); - - epj=vector(1,nlstate+1); - for(age=bage; age <=fage ;age++){ - prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k); - if (vpopbased==1) { - if(mobilav ==0){ - for(i=1; i<=nlstate;i++) - prlim[i][i]=probs[(int)age][i][k]; - }else{ /* mobilav */ - for(i=1; i<=nlstate;i++) - prlim[i][i]=mobaverage[(int)age][i][k]; - } - } - - fprintf(ficrest," %4.0f",age); - for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){ - for(i=1, epj[j]=0.;i <=nlstate;i++) { - epj[j] += prlim[i][i]*eij[i][j][(int)age]; - /* printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/ - } - epj[nlstate+1] +=epj[j]; + i1=pow(2,cptcoveff); /* Number of combination of dummy covariates */ + if (cptcovn < 1){i1=1;} + + for(nres=1; nres <= nresult; nres++) /* For each resultline */ + for(k=1; k<=i1;k++){ /* For any combination of dummy covariates, fixed and varying */ + if(i1 != 1 && TKresult[nres]!= k) + continue; + printf("\n#****** Result for:"); + fprintf(ficrest,"\n#****** Result for:"); + fprintf(ficlog,"\n#****** Result for:"); + for(j=1;j<=cptcoveff;j++){ + printf("V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); + fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); + fprintf(ficlog,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); + } + for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */ + printf(" V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]); + fprintf(ficrest," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]); + fprintf(ficlog," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]); + } + fprintf(ficrest,"******\n"); + fprintf(ficlog,"******\n"); + printf("******\n"); + + fprintf(ficresstdeij,"\n#****** "); + fprintf(ficrescveij,"\n#****** "); + for(j=1;j<=cptcoveff;j++) { + fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); + fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); + } + for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */ + fprintf(ficresstdeij," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]); + fprintf(ficrescveij," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]); + } + fprintf(ficresstdeij,"******\n"); + fprintf(ficrescveij,"******\n"); + + fprintf(ficresvij,"\n#****** "); + /* pstamp(ficresvij); */ + for(j=1;j<=cptcoveff;j++) + fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); + for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */ + fprintf(ficresvij," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]); + } + fprintf(ficresvij,"******\n"); + + eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage); + oldm=oldms;savm=savms; + printf(" cvevsij "); + fprintf(ficlog, " cvevsij "); + cvevsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart, nres); + printf(" end cvevsij \n "); + fprintf(ficlog, " end cvevsij \n "); + + /* + */ + /* goto endfree; */ + + vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage); + pstamp(ficrest); + + + for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/ + oldm=oldms;savm=savms; /* ZZ Segmentation fault */ + cptcod= 0; /* To be deleted */ + printf("varevsij vpopbased=%d \n",vpopbased); + fprintf(ficlog, "varevsij vpopbased=%d \n",vpopbased); + varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl, &ncvyear, k, estepm, cptcov,cptcod,vpopbased,mobilav, strstart, nres); /* cptcod not initialized Intel */ + 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 "); + if(vpopbased==1) + 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); + else + fprintf(ficrest,"the age specific period (stable) prevalences in each health state \n"); + fprintf(ficrest,"# Age popbased mobilav e.. (std) "); + for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i); + fprintf(ficrest,"\n"); + /* printf("Which p?\n"); for(i=1;i<=npar;i++)printf("p[i=%d]=%lf,",i,p[i]);printf("\n"); */ + epj=vector(1,nlstate+1); + printf("Computing age specific period (stable) prevalences in each health state \n"); + fprintf(ficlog,"Computing age specific period (stable) prevalences in each health state \n"); + for(age=bage; age <=fage ;age++){ + prevalim(prlim, nlstate, p, age, oldm, savm, ftolpl, &ncvyear, k, nres); /*ZZ Is it the correct prevalim */ + if (vpopbased==1) { + if(mobilav ==0){ + for(i=1; i<=nlstate;i++) + prlim[i][i]=probs[(int)age][i][k]; + }else{ /* mobilav */ + for(i=1; i<=nlstate;i++) + prlim[i][i]=mobaverage[(int)age][i][k]; } - - for(i=1, vepp=0.;i <=nlstate;i++) - for(j=1;j <=nlstate;j++) - vepp += vareij[i][j][(int)age]; - fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp)); - for(j=1;j <=nlstate;j++){ - fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age])); + } + + fprintf(ficrest," %4.0f %d %d",age, vpopbased, mobilav); + /* fprintf(ficrest," %4.0f %d %d %d %d",age, vpopbased, mobilav,Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); */ /* to be done */ + /* printf(" age %4.0f ",age); */ + for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){ + for(i=1, epj[j]=0.;i <=nlstate;i++) { + epj[j] += prlim[i][i]*eij[i][j][(int)age]; + /*ZZZ printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/ + /* printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]); */ } - fprintf(ficrest,"\n"); + epj[nlstate+1] +=epj[j]; + } + /* printf(" age %4.0f \n",age); */ + + for(i=1, vepp=0.;i <=nlstate;i++) + for(j=1;j <=nlstate;j++) + vepp += vareij[i][j][(int)age]; + fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp)); + for(j=1;j <=nlstate;j++){ + fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age])); } + fprintf(ficrest,"\n"); } - free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage); - free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage); - free_vector(epj,1,nlstate+1); + } /* End vpopbased */ + free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage); + free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage); + free_vector(epj,1,nlstate+1); + printf("done selection\n");fflush(stdout); + fprintf(ficlog,"done selection\n");fflush(ficlog); + + /*}*/ + } /* End k selection */ + + printf("done State-specific expectancies\n");fflush(stdout); + fprintf(ficlog,"done State-specific expectancies\n");fflush(ficlog); + + /*------- Variance of period (stable) prevalence------*/ + + strcpy(fileresvpl,"VPL_"); + strcat(fileresvpl,fileresu); + if((ficresvpl=fopen(fileresvpl,"w"))==NULL) { + printf("Problem with variance of period (stable) prevalence resultfile: %s\n", fileresvpl); + exit(0); + } + printf("Computing Variance-covariance of period (stable) prevalence: file '%s' ...", fileresvpl);fflush(stdout); + fprintf(ficlog, "Computing Variance-covariance of period (stable) prevalence: file '%s' ...", fileresvpl);fflush(ficlog); + + /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){ + for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/ + + i1=pow(2,cptcoveff); + if (cptcovn < 1){i1=1;} + + for(nres=1; nres <= nresult; nres++) /* For each resultline */ + for(k=1; k<=i1;k++){ + if(i1 != 1 && TKresult[nres]!= k) + continue; + fprintf(ficresvpl,"\n#****** "); + printf("\n#****** "); + fprintf(ficlog,"\n#****** "); + for(j=1;j<=cptcoveff;j++) { + fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); + fprintf(ficlog,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); + printf("V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); + } + for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */ + printf(" V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]); + fprintf(ficresvpl," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]); + fprintf(ficlog," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]); + } + fprintf(ficresvpl,"******\n"); + printf("******\n"); + fprintf(ficlog,"******\n"); + + varpl=matrix(1,nlstate,(int) bage, (int) fage); + oldm=oldms;savm=savms; + varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl, &ncvyear, k, strstart, nres); + free_matrix(varpl,1,nlstate,(int) bage, (int)fage); /*}*/ } + + fclose(ficresvpl); + printf("done variance-covariance of period prevalence\n");fflush(stdout); + fprintf(ficlog,"done variance-covariance of period prevalence\n");fflush(ficlog); + free_vector(weight,1,n); free_imatrix(Tvard,1,NCOVMAX,1,2); free_imatrix(s,1,maxwav+1,1,n); @@ -6524,84 +11877,94 @@ Interval (in months) between two waves: fclose(ficresvij); fclose(ficrest); fclose(ficpar); - - /*------- Variance of period (stable) prevalence------*/ - - strcpy(fileresvpl,"vpl"); - strcat(fileresvpl,fileres); - if((ficresvpl=fopen(fileresvpl,"w"))==NULL) { - printf("Problem with variance of period (stable) prevalence resultfile: %s\n", fileresvpl); - exit(0); - } - printf("Computing Variance-covariance of period (stable) prevalence: file '%s' \n", fileresvpl); - - /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){ - for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/ - - for (k=1; k <= (int) pow(2,cptcoveff); k++){ - fprintf(ficresvpl,"\n#****** "); - for(j=1;j<=cptcoveff;j++) - fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]); - fprintf(ficresvpl,"******\n"); - - varpl=matrix(1,nlstate,(int) bage, (int) fage); - oldm=oldms;savm=savms; - varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k,strstart); - free_matrix(varpl,1,nlstate,(int) bage, (int)fage); - /*}*/ - } - - fclose(ficresvpl); - + + /*---------- End : free ----------------*/ - if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); - free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX); - } /* mle==-3 arrives here for freeing */ - endfree: + if (mobilav!=0 ||mobilavproj !=0) + free_ma3x(mobaverages,1, AGESUP,1,nlstate+ndeath, 1,ncovcombmax); /* We need to have a squared matrix with prevalence of the dead! */ + free_ma3x(probs,1,AGESUP,1,nlstate+ndeath, 1,ncovcombmax); free_matrix(prlim,1,nlstate,1,nlstate); /*here or after loop ? */ free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath); - free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath); - free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath); - free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath); - free_matrix(covar,0,NCOVMAX,1,n); - free_matrix(matcov,1,npar,1,npar); - /*free_vector(delti,1,npar);*/ - free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); - free_matrix(agev,1,maxwav,1,imx); - free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); - - free_ivector(ncodemax,1,NCOVMAX); - free_ivector(Tvar,1,NCOVMAX); - free_ivector(Tprod,1,NCOVMAX); - free_ivector(Tvaraff,1,NCOVMAX); - free_ivector(Tage,1,NCOVMAX); - - free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX); - free_imatrix(codtab,1,100,1,10); + } /* mle==-3 arrives here for freeing */ + /* endfree:*/ + free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath); + free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath); + free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath); + free_ma3x(cotqvar,1,maxwav,1,nqtv,1,n); + free_ma3x(cotvar,1,maxwav,1,ntv+nqtv,1,n); + free_matrix(coqvar,1,maxwav,1,n); + free_matrix(covar,0,NCOVMAX,1,n); + free_matrix(matcov,1,npar,1,npar); + free_matrix(hess,1,npar,1,npar); + /*free_vector(delti,1,npar);*/ + free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); + free_matrix(agev,1,maxwav,1,imx); + free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); + + free_ivector(ncodemax,1,NCOVMAX); + free_ivector(ncodemaxwundef,1,NCOVMAX); + free_ivector(Dummy,-1,NCOVMAX); + free_ivector(Fixed,-1,NCOVMAX); + free_ivector(DummyV,1,NCOVMAX); + free_ivector(FixedV,1,NCOVMAX); + free_ivector(Typevar,-1,NCOVMAX); + free_ivector(Tvar,1,NCOVMAX); + free_ivector(TvarsQ,1,NCOVMAX); + free_ivector(TvarsQind,1,NCOVMAX); + free_ivector(TvarsD,1,NCOVMAX); + free_ivector(TvarsDind,1,NCOVMAX); + free_ivector(TvarFD,1,NCOVMAX); + free_ivector(TvarFDind,1,NCOVMAX); + free_ivector(TvarF,1,NCOVMAX); + free_ivector(TvarFind,1,NCOVMAX); + free_ivector(TvarV,1,NCOVMAX); + free_ivector(TvarVind,1,NCOVMAX); + free_ivector(TvarA,1,NCOVMAX); + free_ivector(TvarAind,1,NCOVMAX); + free_ivector(TvarFQ,1,NCOVMAX); + free_ivector(TvarFQind,1,NCOVMAX); + free_ivector(TvarVD,1,NCOVMAX); + free_ivector(TvarVDind,1,NCOVMAX); + free_ivector(TvarVQ,1,NCOVMAX); + free_ivector(TvarVQind,1,NCOVMAX); + free_ivector(Tvarsel,1,NCOVMAX); + free_vector(Tvalsel,1,NCOVMAX); + free_ivector(Tposprod,1,NCOVMAX); + free_ivector(Tprod,1,NCOVMAX); + free_ivector(Tvaraff,1,NCOVMAX); + free_ivector(invalidvarcomb,1,ncovcombmax); + free_ivector(Tage,1,NCOVMAX); + free_ivector(Tmodelind,1,NCOVMAX); + free_ivector(TmodelInvind,1,NCOVMAX); + free_ivector(TmodelInvQind,1,NCOVMAX); + + free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX); + /* free_imatrix(codtab,1,100,1,10); */ fflush(fichtm); fflush(ficgp); - + if((nberr >0) || (nbwarn>0)){ - printf("End of Imach with %d errors and/or %d warnings\n",nberr,nbwarn); - fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn); + printf("End of Imach with %d errors and/or %d warnings. Please look at the log file for details.\n",nberr,nbwarn); + fprintf(ficlog,"End of Imach with %d errors and/or warnings %d. Please look at the log file for details.\n",nberr,nbwarn); }else{ printf("End of Imach\n"); fprintf(ficlog,"End of Imach\n"); } printf("See log file on %s\n",filelog); /* gettimeofday(&end_time, (struct timezone*)0);*/ /* after time */ - (void) gettimeofday(&end_time,&tzp); - tm = *localtime(&end_time.tv_sec); - tmg = *gmtime(&end_time.tv_sec); - strcpy(strtend,asctime(&tm)); + /*(void) gettimeofday(&end_time,&tzp);*/ + rend_time = time(NULL); + end_time = *localtime(&rend_time); + /* tml = *localtime(&end_time.tm_sec); */ + strcpy(strtend,asctime(&end_time)); printf("Local time at start %s\nLocal time at end %s",strstart, strtend); fprintf(ficlog,"Local time at start %s\nLocal time at end %s\n",strstart, strtend); - printf("Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout)); - - printf("Total time was %ld Sec.\n", end_time.tv_sec -start_time.tv_sec); - fprintf(ficlog,"Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout)); - fprintf(ficlog,"Total time was %ld Sec.\n", end_time.tv_sec -start_time.tv_sec); + printf("Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout)); + + printf("Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time)); + fprintf(ficlog,"Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout)); + fprintf(ficlog,"Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time)); /* printf("Total time was %d uSec.\n", total_usecs);*/ /* if(fileappend(fichtm,optionfilehtm)){ */ fprintf(fichtm,"
              Local time at start %s
              Local time at end %s
              \n",strstart, strtend); @@ -6611,28 +11974,34 @@ Interval (in months) between two waves: fclose(ficgp); fclose(ficlog); /*------ End -----------*/ - - - printf("Before Current directory %s!\n",pathcd); - if(chdir(pathcd) != 0) + + + printf("Before Current directory %s!\n",pathcd); +#ifdef WIN32 + if (_chdir(pathcd) != 0) printf("Can't move to directory %s!\n",path); - if(getcwd(pathcd,MAXLINE) > 0) + if(_getcwd(pathcd,MAXLINE) > 0) +#else + if(chdir(pathcd) != 0) + printf("Can't move to directory %s!\n", path); + if (getcwd(pathcd, MAXLINE) > 0) +#endif printf("Current directory %s!\n",pathcd); /*strcat(plotcmd,CHARSEPARATOR);*/ sprintf(plotcmd,"gnuplot"); -#ifndef UNIX +#ifdef _WIN32 sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach); #endif if(!stat(plotcmd,&info)){ - printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout); + printf("Error or gnuplot program not found: '%s'\n",plotcmd);fflush(stdout); if(!stat(getenv("GNUPLOTBIN"),&info)){ - printf("Error gnuplot program not found: %s Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout); + printf("Error or gnuplot program not found: '%s' Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout); }else strcpy(pplotcmd,plotcmd); -#ifdef UNIX +#ifdef __unix strcpy(plotcmd,GNUPLOTPROGRAM); if(!stat(plotcmd,&info)){ - printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout); + printf("Error gnuplot program not found: '%s'\n",plotcmd);fflush(stdout); }else strcpy(pplotcmd,plotcmd); #endif @@ -6640,30 +12009,38 @@ Interval (in months) between two waves: strcpy(pplotcmd,plotcmd); sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot); - printf("Starting graphs with: %s\n",plotcmd);fflush(stdout); - + printf("Starting graphs with: '%s'\n",plotcmd);fflush(stdout); + if((outcmd=system(plotcmd)) != 0){ - printf("\n Problem with gnuplot\n"); + printf("gnuplot command might not be in your path: '%s', err=%d\n", plotcmd, outcmd); + printf("\n Trying if gnuplot resides on the same directory that IMaCh\n"); + sprintf(plotcmd,"%sgnuplot %s", pathimach, optionfilegnuplot); + if((outcmd=system(plotcmd)) != 0) + printf("\n Still a problem with gnuplot command %s, err=%d\n", plotcmd, outcmd); } - printf(" Wait..."); + printf(" Successful, please wait..."); while (z[0] != 'q') { /* chdir(path); */ - printf("\nType e to edit output files, g to graph again and q for exiting: "); + printf("\nType e to edit results with your browser, g to graph again and q for exit: "); scanf("%s",z); /* if (z[0] == 'c') system("./imach"); */ if (z[0] == 'e') { - printf("Starting browser with: %s",optionfilehtm);fflush(stdout); - system(optionfilehtm); +#ifdef __APPLE__ + sprintf(pplotcmd, "open %s", optionfilehtm); +#elif __linux + sprintf(pplotcmd, "xdg-open %s", optionfilehtm); +#else + sprintf(pplotcmd, "%s", optionfilehtm); +#endif + printf("Starting browser with: %s",pplotcmd);fflush(stdout); + system(pplotcmd); } else if (z[0] == 'g') system(plotcmd); else if (z[0] == 'q') exit(0); } - end: +end: while (z[0] != 'q') { - printf("\nType q for exiting: "); + printf("\nType q for exiting: "); fflush(stdout); scanf("%s",z); } } - - -