--- /dev/null
+/* $Id$
+ $State$
+ $Log$
+ 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
+
+ Lot of changes in order to output the results with some covariates
+ After the Edimburgh REVES conference 2014, it seems mandatory to
+ improve the code.
+ No more memory valgrind error but a lot has to be done in order to
+ continue the work of splitting the code into subroutines.
+ Also, decodemodel has been improved. Tricode is still not
+ optimal. nbcode should be improved. Documentation has been added in
+ the source code.
+
+ Revision 1.143 2014/01/26 09:45:38 brouard
+ Summary: Version 0.98nR (to be improved, but gives same optimization results as 0.98k. Nice, promising
+
+ * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
+ (Module): Version 0.98nR Running ok, but output format still only works for three covariates.
+
+ Revision 1.142 2014/01/26 03:57:36 brouard
+ Summary: gnuplot changed plot w l 1 has to be changed to plot w l lt 2
+
+ * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
+
+ Revision 1.141 2014/01/26 02:42:01 brouard
+ * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
+
+ Revision 1.140 2011/09/02 10:37:54 brouard
+ Summary: times.h is ok with mingw32 now.
+
+ Revision 1.139 2010/06/14 07:50:17 brouard
+ After the theft of my laptop, I probably lost some lines of codes which were not uploaded to the CVS tree.
+ I remember having already fixed agemin agemax which are pointers now but not cvs saved.
+
+ Revision 1.138 2010/04/30 18:19:40 brouard
+ *** empty log message ***
+
+ Revision 1.137 2010/04/29 18:11:38 brouard
+ (Module): Checking covariates for more complex models
+ than V1+V2. A lot of change to be done. Unstable.
+
+ Revision 1.136 2010/04/26 20:30:53 brouard
+ (Module): merging some libgsl code. Fixing computation
+ of likelione (using inter/intrapolation if mle = 0) in order to
+ get same likelihood as if mle=1.
+ Some cleaning of code and comments added.
+
+ Revision 1.135 2009/10/29 15:33:14 brouard
+ (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
+
+ Revision 1.134 2009/10/29 13:18:53 brouard
+ (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
+
+ Revision 1.133 2009/07/06 10:21:25 brouard
+ just nforces
+
+ Revision 1.132 2009/07/06 08:22:05 brouard
+ Many tings
+
+ Revision 1.131 2009/06/20 16:22:47 brouard
+ Some dimensions resccaled
+
+ Revision 1.130 2009/05/26 06:44:34 brouard
+ (Module): Max Covariate is now set to 20 instead of 8. A
+ lot of cleaning with variables initialized to 0. Trying to make
+ V2+V3*age+V1+V4 strb=V3*age+V1+V4 working better.
+
+ Revision 1.129 2007/08/31 13:49:27 lievre
+ Modification of the way of exiting when the covariate is not binary in order to see on the window the error message before exiting
+
+ Revision 1.128 2006/06/30 13:02:05 brouard
+ (Module): Clarifications on computing e.j
+
+ Revision 1.127 2006/04/28 18:11:50 brouard
+ (Module): Yes the sum of survivors was wrong since
+ imach-114 because nhstepm was no more computed in the age
+ loop. Now we define nhstepma in the age loop.
+ (Module): In order to speed up (in case of numerous covariates) we
+ compute health expectancies (without variances) in a first step
+ and then all the health expectancies with variances or standard
+ deviation (needs data from the Hessian matrices) which slows the
+ computation.
+ In the future we should be able to stop the program is only health
+ expectancies and graph are needed without standard deviations.
+
+ Revision 1.126 2006/04/28 17:23:28 brouard
+ (Module): Yes the sum of survivors was wrong since
+ imach-114 because nhstepm was no more computed in the age
+ loop. Now we define nhstepma in the age loop.
+ Version 0.98h
+
+ Revision 1.125 2006/04/04 15:20:31 lievre
+ Errors in calculation of health expectancies. Age was not initialized.
+ Forecasting file added.
+
+ Revision 1.124 2006/03/22 17:13:53 lievre
+ Parameters are printed with %lf instead of %f (more numbers after the comma).
+ The log-likelihood is printed in the log file
+
+ Revision 1.123 2006/03/20 10:52:43 brouard
+ * imach.c (Module): <title> changed, corresponds to .htm file
+ name. <head> headers where missing.
+
+ * imach.c (Module): Weights can have a decimal point as for
+ English (a comma might work with a correct LC_NUMERIC environment,
+ otherwise the weight is truncated).
+ Modification of warning when the covariates values are not 0 or
+ 1.
+ Version 0.98g
+
+ Revision 1.122 2006/03/20 09:45:41 brouard
+ (Module): Weights can have a decimal point as for
+ English (a comma might work with a correct LC_NUMERIC environment,
+ otherwise the weight is truncated).
+ Modification of warning when the covariates values are not 0 or
+ 1.
+ Version 0.98g
+
+ Revision 1.121 2006/03/16 17:45:01 lievre
+ * imach.c (Module): Comments concerning covariates added
+
+ * imach.c (Module): refinements in the computation of lli if
+ status=-2 in order to have more reliable computation if stepm is
+ not 1 month. Version 0.98f
+
+ Revision 1.120 2006/03/16 15:10:38 lievre
+ (Module): refinements in the computation of lli if
+ status=-2 in order to have more reliable computation if stepm is
+ not 1 month. Version 0.98f
+
+ Revision 1.119 2006/03/15 17:42:26 brouard
+ (Module): Bug if status = -2, the loglikelihood was
+ computed as likelihood omitting the logarithm. Version O.98e
+
+ Revision 1.118 2006/03/14 18:20:07 brouard
+ (Module): varevsij Comments added explaining the second
+ table of variances if popbased=1 .
+ (Module): Covariances of eij, ekl added, graphs fixed, new html link.
+ (Module): Function pstamp added
+ (Module): Version 0.98d
+
+ Revision 1.117 2006/03/14 17:16:22 brouard
+ (Module): varevsij Comments added explaining the second
+ table of variances if popbased=1 .
+ (Module): Covariances of eij, ekl added, graphs fixed, new html link.
+ (Module): Function pstamp added
+ (Module): Version 0.98d
+
+ Revision 1.116 2006/03/06 10:29:27 brouard
+ (Module): Variance-covariance wrong links and
+ varian-covariance of ej. is needed (Saito).
+
+ Revision 1.115 2006/02/27 12:17:45 brouard
+ (Module): One freematrix added in mlikeli! 0.98c
+
+ Revision 1.114 2006/02/26 12:57:58 brouard
+ (Module): Some improvements in processing parameter
+ filename with strsep.
+
+ Revision 1.113 2006/02/24 14:20:24 brouard
+ (Module): Memory leaks checks with valgrind and:
+ datafile was not closed, some imatrix were not freed and on matrix
+ allocation too.
+
+ Revision 1.112 2006/01/30 09:55:26 brouard
+ (Module): Back to gnuplot.exe instead of wgnuplot.exe
+
+ Revision 1.111 2006/01/25 20:38:18 brouard
+ (Module): Lots of cleaning and bugs added (Gompertz)
+ (Module): Comments can be added in data file. Missing date values
+ can be a simple dot '.'.
+
+ Revision 1.110 2006/01/25 00:51:50 brouard
+ (Module): Lots of cleaning and bugs added (Gompertz)
+
+ Revision 1.109 2006/01/24 19:37:15 brouard
+ (Module): Comments (lines starting with a #) are allowed in data.
+
+ Revision 1.108 2006/01/19 18:05:42 lievre
+ Gnuplot problem appeared...
+ To be fixed
+
+ Revision 1.107 2006/01/19 16:20:37 brouard
+ Test existence of gnuplot in imach path
+
+ Revision 1.106 2006/01/19 13:24:36 brouard
+ Some cleaning and links added in html output
+
+ Revision 1.105 2006/01/05 20:23:19 lievre
+ *** empty log message ***
+
+ Revision 1.104 2005/09/30 16:11:43 lievre
+ (Module): sump fixed, loop imx fixed, and simplifications.
+ (Module): If the status is missing at the last wave but we know
+ that the person is alive, then we can code his/her status as -2
+ (instead of missing=-1 in earlier versions) and his/her
+ contributions to the likelihood is 1 - Prob of dying from last
+ health status (= 1-p13= p11+p12 in the easiest case of somebody in
+ the healthy state at last known wave). Version is 0.98
+
+ Revision 1.103 2005/09/30 15:54:49 lievre
+ (Module): sump fixed, loop imx fixed, and simplifications.
+
+ Revision 1.102 2004/09/15 17:31:30 brouard
+ Add the possibility to read data file including tab characters.
+
+ Revision 1.101 2004/09/15 10:38:38 brouard
+ Fix on curr_time
+
+ Revision 1.100 2004/07/12 18:29:06 brouard
+ Add version for Mac OS X. Just define UNIX in Makefile
+
+ Revision 1.99 2004/06/05 08:57:40 brouard
+ *** empty log message ***
+
+ Revision 1.98 2004/05/16 15:05:56 brouard
+ New version 0.97 . First attempt to estimate force of mortality
+ directly from the data i.e. without the need of knowing the health
+ state at each age, but using a Gompertz model: log u =a + b*age .
+ This is the basic analysis of mortality and should be done before any
+ other analysis, in order to test if the mortality estimated from the
+ cross-longitudinal survey is different from the mortality estimated
+ from other sources like vital statistic data.
+
+ The same imach parameter file can be used but the option for mle should be -3.
+
+ Agnès, who wrote this part of the code, tried to keep most of the
+ former routines in order to include the new code within the former code.
+
+ The output is very simple: only an estimate of the intercept and of
+ the slope with 95% confident intervals.
+
+ Current limitations:
+ A) Even if you enter covariates, i.e. with the
+ model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
+ B) There is no computation of Life Expectancy nor Life Table.
+
+ Revision 1.97 2004/02/20 13:25:42 lievre
+ Version 0.96d. Population forecasting command line is (temporarily)
+ suppressed.
+
+ Revision 1.96 2003/07/15 15:38:55 brouard
+ * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
+ rewritten within the same printf. Workaround: many printfs.
+
+ Revision 1.95 2003/07/08 07:54:34 brouard
+ * imach.c (Repository):
+ (Repository): Using imachwizard code to output a more meaningful covariance
+ matrix (cov(a12,c31) instead of numbers.
+
+ Revision 1.94 2003/06/27 13:00:02 brouard
+ Just cleaning
+
+ Revision 1.93 2003/06/25 16:33:55 brouard
+ (Module): On windows (cygwin) function asctime_r doesn't
+ exist so I changed back to asctime which exists.
+ (Module): Version 0.96b
+
+ Revision 1.92 2003/06/25 16:30:45 brouard
+ (Module): On windows (cygwin) function asctime_r doesn't
+ exist so I changed back to asctime which exists.
+
+ Revision 1.91 2003/06/25 15:30:29 brouard
+ * imach.c (Repository): Duplicated warning errors corrected.
+ (Repository): Elapsed time after each iteration is now output. It
+ helps to forecast when convergence will be reached. Elapsed time
+ is stamped in powell. We created a new html file for the graphs
+ concerning matrix of covariance. It has extension -cov.htm.
+
+ Revision 1.90 2003/06/24 12:34:15 brouard
+ (Module): Some bugs corrected for windows. Also, when
+ mle=-1 a template is output in file "or"mypar.txt with the design
+ of the covariance matrix to be input.
+
+ Revision 1.89 2003/06/24 12:30:52 brouard
+ (Module): Some bugs corrected for windows. Also, when
+ mle=-1 a template is output in file "or"mypar.txt with the design
+ of the covariance matrix to be input.
+
+ Revision 1.88 2003/06/23 17:54:56 brouard
+ * imach.c (Repository): Create a sub-directory where all the secondary files are. Only imach, htm, gp and r(imach) are on the main directory. Correct time and other things.
+
+ Revision 1.87 2003/06/18 12:26:01 brouard
+ Version 0.96
+
+ Revision 1.86 2003/06/17 20:04:08 brouard
+ (Module): Change position of html and gnuplot routines and added
+ routine fileappend.
+
+ Revision 1.85 2003/06/17 13:12:43 brouard
+ * imach.c (Repository): Check when date of death was earlier that
+ current date of interview. It may happen when the death was just
+ prior to the death. In this case, dh was negative and likelihood
+ was wrong (infinity). We still send an "Error" but patch by
+ assuming that the date of death was just one stepm after the
+ interview.
+ (Repository): Because some people have very long ID (first column)
+ we changed int to long in num[] and we added a new lvector for
+ memory allocation. But we also truncated to 8 characters (left
+ truncation)
+ (Repository): No more line truncation errors.
+
+ Revision 1.84 2003/06/13 21:44:43 brouard
+ * imach.c (Repository): Replace "freqsummary" at a correct
+ place. It differs from routine "prevalence" which may be called
+ many times. Probs is memory consuming and must be used with
+ parcimony.
+ Version 0.95a3 (should output exactly the same maximization than 0.8a2)
+
+ Revision 1.83 2003/06/10 13:39:11 lievre
+ *** empty log message ***
+
+ Revision 1.82 2003/06/05 15:57:20 brouard
+ Add log in imach.c and fullversion number is now printed.
+
+*/
+/*
+ Interpolated Markov Chain
+
+ 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
+ convergence.
+
+ The advantage of this computer programme, compared to a simple
+ multinomial logistic model, is clear when the delay between waves is not
+ identical for each individual. Also, if a individual missed an
+ intermediate interview, the information is lost, but taken into
+ account using an interpolation or extrapolation.
+
+ hPijx is the probability to be observed in state i at age x+h
+ conditional to the observed state i at age x. The delay 'h' can be
+ split into an exact number (nh*stepm) of unobserved intermediate
+ states. This elementary transition (by month, quarter,
+ semester or year) is modelled as a multinomial logistic. The hPx
+ matrix is simply the matrix product of nh*stepm elementary matrices
+ and the contribution of each individual to the likelihood is simply
+ hPijx.
+
+ Also this programme outputs the covariance matrix of the parameters but also
+ of the life expectancies. It also computes the period (stable) prevalence.
+
+ Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
+ Institut national d'études démographiques, Paris.
+ This software have been partly granted by Euro-REVES, a concerted action
+ from the European Union.
+ It is copyrighted identically to a GNU software product, ie programme and
+ software can be distributed freely for non commercial use. Latest version
+ can be accessed at http://euroreves.ined.fr/imach .
+
+ Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
+ or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
+
+ **********************************************************************/
+/*
+ main
+ read parameterfile
+ read datafile
+ concatwav
+ freqsummary
+ if (mle >= 1)
+ mlikeli
+ print results files
+ if mle==1
+ computes hessian
+ read end of parameter file: agemin, agemax, bage, fage, estepm
+ begin-prev-date,...
+ open gnuplot file
+ open html file
+ period (stable) prevalence | pl_nom 1-1 2-2 etc by covariate
+ for age prevalim() | #****** V1=0 V2=1 V3=1 V4=0 ******
+ | 65 1 0 2 1 3 1 4 0 0.96326 0.03674
+ freexexit2 possible for memory heap.
+
+ h Pij x | pij_nom ficrestpij
+ # Cov Agex agex+h hpijx with i,j= 1-1 1-2 1-3 2-1 2-2 2-3
+ 1 85 85 1.00000 0.00000 0.00000 0.00000 1.00000 0.00000
+ 1 85 86 0.68299 0.22291 0.09410 0.71093 0.00000 0.28907
+
+ 1 65 99 0.00364 0.00322 0.99314 0.00350 0.00310 0.99340
+ 1 65 100 0.00214 0.00204 0.99581 0.00206 0.00196 0.99597
+ variance of p one-step probabilities varprob | prob_nom ficresprob #One-step probabilities and stand. devi in ()
+ Standard deviation of one-step probabilities | probcor_nom ficresprobcor #One-step probabilities and correlation matrix
+ Matrix of variance covariance of one-step probabilities | probcov_nom ficresprobcov #One-step probabilities and covariance matrix
+
+ forecasting if prevfcast==1 prevforecast call prevalence()
+ health expectancies
+ Variance-covariance of DFLE
+ prevalence()
+ movingaverage()
+ varevsij()
+ if popbased==1 varevsij(,popbased)
+ total life expectancies
+ Variance of period (stable) prevalence
+ end
+*/
+
+
+
+
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+
+#ifdef _WIN32
+#include <io.h>
+#else
+#include <unistd.h>
+#endif
+
+#include <limits.h>
+#include <sys/types.h>
+#include <sys/stat.h>
+#include <errno.h>
+/* extern int errno; */
+
+/* #ifdef LINUX */
+/* #include <time.h> */
+/* #include "timeval.h" */
+/* #else */
+/* #include <sys/time.h> */
+/* #endif */
+
+#include <time.h>
+
+#ifdef GSL
+#include <gsl/gsl_errno.h>
+#include <gsl/gsl_multimin.h>
+#endif
+
+#ifdef NLOPT
+#include <nlopt.h>
+#endif
+
+/* #include <libintl.h> */
+/* #define _(String) gettext (String) */
+
+#define MAXLINE 1024 /* Was 256. Overflow with 312 with 2 states and 4 covariates. Should be ok */
+
+#define GNUPLOTPROGRAM "gnuplot"
+/*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
+#define FILENAMELENGTH 132
+
+#define GLOCK_ERROR_NOPATH -1 /* empty path */
+#define GLOCK_ERROR_GETCWD -2 /* cannot get cwd */
+
+#define MAXPARM 128 /**< Maximum number of parameters for the optimization */
+#define NPARMAX 64 /**< (nlstate+ndeath-1)*nlstate*ncovmodel */
+
+#define NINTERVMAX 8
+#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 MAXN 20000
+#define YEARM 12. /**< Number of months per year */
+#define AGESUP 130
+#define AGEBASE 40
+#define AGEGOMP 10. /**< Minimal age for Gompertz adjustment */
+#ifdef _WIN32
+#define DIRSEPARATOR '\\'
+#define CHARSEPARATOR "\\"
+#define ODIRSEPARATOR '/'
+#else
+#define DIRSEPARATOR '/'
+#define CHARSEPARATOR "/"
+#define ODIRSEPARATOR '\\'
+#endif
+
+/* $Id$ */
+/* $State$ */
+
+char version[]="Imach version 0.98nX, August 2014,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121)";
+char fullversion[]="$Revision$ $Date$";
+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 */
+/* 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 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 cptcov=0; /* Working variable */
+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 popbased=0;
+
+int *wav; /* Number of waves for this individuual 0 is possible */
+int maxwav=0; /* Maxim number of waves */
+int jmin=0, jmax=0; /* min, max spacing between 2 waves */
+int ijmin=0, ijmax=0; /* Individuals having jmin and jmax */
+int gipmx=0, gsw=0; /* Global variables on the number of contributions
+ to the likelihood and the sum of weights (done by funcone)*/
+int mle=1, weightopt=0;
+int **mw; /* mw[mi][i] is number of the mi wave for this individual */
+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 */
+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 */
+/*FILE *fic ; */ /* Used in readdata only */
+FILE *ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
+FILE *ficlog, *ficrespow;
+int globpr=0; /* Global variable for printing or not */
+double fretone; /* Only one call to likelihood */
+long ipmx=0; /* Number of contributions */
+double sw; /* Sum of weights */
+char filerespow[FILENAMELENGTH];
+char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
+FILE *ficresilk;
+FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
+FILE *ficresprobmorprev;
+FILE *fichtm, *fichtmcov; /* Html File */
+FILE *ficreseij;
+char filerese[FILENAMELENGTH];
+FILE *ficresstdeij;
+char fileresstde[FILENAMELENGTH];
+FILE *ficrescveij;
+char filerescve[FILENAMELENGTH];
+FILE *ficresvij;
+char fileresv[FILENAMELENGTH];
+FILE *ficresvpl;
+char fileresvpl[FILENAMELENGTH];
+char title[MAXLINE];
+char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH], filerespl[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 filelog[FILENAMELENGTH]; /* Log file */
+char filerest[FILENAMELENGTH];
+char fileregp[FILENAMELENGTH];
+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 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;
+long lval;
+double dval;
+
+#define NR_END 1
+#define FREE_ARG char*
+#define FTOL 1.0e-10
+
+#define NRANSI
+#define ITMAX 200
+
+#define TOL 2.0e-4
+
+#define CGOLD 0.3819660
+#define ZEPS 1.0e-10
+#define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);
+
+#define GOLD 1.618034
+#define GLIMIT 100.0
+#define TINY 1.0e-20
+
+static double maxarg1,maxarg2;
+#define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
+#define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
+
+#define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
+#define rint(a) floor(a+0.5)
+
+static double sqrarg;
+#define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
+#define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}
+int agegomp= AGEGOMP;
+
+int imx;
+int stepm=1;
+/* Stepm, step in month: minimum step interpolation*/
+
+int estepm;
+/* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
+
+int m,nb;
+long *num;
+int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
+double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
+double **pmmij, ***probs;
+double *ageexmed,*agecens;
+double dateintmean=0;
+
+double *weight;
+int **s; /* Status */
+double *agedc;
+double **covar; /**< covar[j,i], value of jth covariate for individual i,
+ * covar=matrix(0,NCOVMAX,1,n);
+ * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; */
+double idx;
+int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */
+int *Ndum; /** Freq of modality (tricode */
+int **codtab; /**< codtab=imatrix(1,100,1,10); */
+int **Tvard, *Tprod, cptcovprod, *Tvaraff;
+double *lsurv, *lpop, *tpop;
+
+double ftol=FTOL; /**< Tolerance for computing Max Likelihood */
+double ftolhess; /**< Tolerance for computing hessian */
+
+/**************** split *************************/
+static int split( char *path, char *dirc, char *name, char *ext, char *finame )
+{
+ /* From a file name with (full) path (either Unix or Windows) we extract the directory (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 */
+
+ l1 = strlen(path ); /* length of path */
+ if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
+ ss= strrchr( path, DIRSEPARATOR ); /* find last / */
+ if ( ss == NULL ) { /* no directory, so determine current directory */
+ strcpy( name, path ); /* we got the fullname name because no directory */
+ /*if(strrchr(path, ODIRSEPARATOR )==NULL)
+ 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 ) {
+ return( GLOCK_ERROR_GETCWD );
+ }
+ /* got dirc from getcwd*/
+ printf(" DIRC = %s \n",dirc);
+ } else { /* strip direcotry 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 */
+ printf(" DIRC2 = %s \n",dirc);
+ }
+ /* We add a separator at the end of dirc if not exists */
+ l1 = strlen( dirc ); /* length of directory */
+ if( dirc[l1-1] != DIRSEPARATOR ){
+ dirc[l1] = DIRSEPARATOR;
+ dirc[l1+1] = 0;
+ printf(" DIRC3 = %s \n",dirc);
+ }
+ ss = strrchr( name, '.' ); /* find last / */
+ if (ss >0){
+ ss++;
+ strcpy(ext,ss); /* save extension */
+ l1= strlen( name);
+ l2= strlen(ss)+1;
+ strncpy( finame, name, l1-l2);
+ finame[l1-l2]= 0;
+ }
+
+ return( 0 ); /* we're done */
+}
+
+
+/******************************************/
+
+void replace_back_to_slash(char *s, char*t)
+{
+ int i;
+ int lg=0;
+ i=0;
+ lg=strlen(t);
+ for(i=0; i<= lg; i++) {
+ (s[i] = t[i]);
+ if (t[i]== '\\') s[i]='/';
+ }
+}
+
+char *trimbb(char *out, char *in)
+{ /* Trim multiple blanks in line but keeps first blanks if line starts with blanks */
+ char *s;
+ s=out;
+ while (*in != '\0'){
+ while( *in == ' ' && *(in+1) == ' '){ /* && *(in+1) != '\0'){*/
+ in++;
+ }
+ *out++ = *in++;
+ }
+ *out='\0';
+ return s;
+}
+
+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'
+ and alocc starts after first 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 blocc
+ */
+ char *s, *t;
+ t=in;s=in;
+ while ((*in != occ) && (*in != '\0')){
+ *alocc++ = *in++;
+ }
+ if( *in == occ){
+ *(alocc)='\0';
+ s=++in;
+ }
+
+ if (s == t) {/* occ not found */
+ *(alocc-(in-s))='\0';
+ in=s;
+ }
+ while ( *in != '\0'){
+ *blocc++ = *in++;
+ }
+
+ *blocc='\0';
+ return t;
+}
+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'
+ 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
+ */
+ char *s, *t;
+ t=in;s=in;
+ while (*in != '\0'){
+ while( *in == occ){
+ *blocc++ = *in++;
+ s=in;
+ }
+ *blocc++ = *in++;
+ }
+ if (s == t) /* occ not found */
+ *(blocc-(in-s))='\0';
+ else
+ *(blocc-(in-s)-1)='\0';
+ in=s;
+ while ( *in != '\0'){
+ *alocc++ = *in++;
+ }
+
+ *alocc='\0';
+ return s;
+}
+
+int nbocc(char *s, char occ)
+{
+ int i,j=0;
+ int lg=20;
+ i=0;
+ lg=strlen(s);
+ for(i=0; i<= lg; i++) {
+ if (s[i] == occ ) j++;
+ }
+ return j;
+}
+
+/* void cutv(char *u,char *v, char*t, char occ) */
+/* { */
+/* /\* cuts string t into u and v where u ends before last occurence of char 'occ' */
+/* and v starts after last occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2') */
+/* gives u="abcdef2ghi" and v="j" *\/ */
+/* int i,lg,j,p=0; */
+/* i=0; */
+/* lg=strlen(t); */
+/* for(j=0; j<=lg-1; j++) { */
+/* if((t[j]!= occ) && (t[j+1]== occ)) p=j+1; */
+/* } */
+
+/* for(j=0; j<p; j++) { */
+/* (u[j] = t[j]); */
+/* } */
+/* u[p]='\0'; */
+
+/* for(j=0; j<= lg; j++) { */
+/* if (j>=(p+1))(v[j-p-1] = t[j]); */
+/* } */
+/* } */
+
+#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[])
+{
+ fprintf(stderr,"ERREUR ...\n");
+ fprintf(stderr,"%s\n",error_text);
+ exit(EXIT_FAILURE);
+}
+/*********************** vector *******************/
+double *vector(int nl, int nh)
+{
+ double *v;
+ v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
+ if (!v) nrerror("allocation failure in vector");
+ return v-nl+NR_END;
+}
+
+/************************ free vector ******************/
+void free_vector(double*v, int nl, int nh)
+{
+ free((FREE_ARG)(v+nl-NR_END));
+}
+
+/************************ivector *******************************/
+int *ivector(long nl,long nh)
+{
+ int *v;
+ v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
+ if (!v) nrerror("allocation failure in ivector");
+ return v-nl+NR_END;
+}
+
+/******************free ivector **************************/
+void free_ivector(int *v, long nl, long nh)
+{
+ free((FREE_ARG)(v+nl-NR_END));
+}
+
+/************************lvector *******************************/
+long *lvector(long nl,long nh)
+{
+ long *v;
+ v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
+ if (!v) nrerror("allocation failure in ivector");
+ return v-nl+NR_END;
+}
+
+/******************free lvector **************************/
+void free_lvector(long *v, long nl, long nh)
+{
+ free((FREE_ARG)(v+nl-NR_END));
+}
+
+/******************* imatrix *******************************/
+int **imatrix(long nrl, long nrh, long ncl, long nch)
+ /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */
+{
+ long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;
+ int **m;
+
+ /* allocate pointers to rows */
+ m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));
+ if (!m) nrerror("allocation failure 1 in matrix()");
+ m += NR_END;
+ m -= nrl;
+
+
+ /* allocate rows and set pointers to them */
+ m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));
+ if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
+ m[nrl] += NR_END;
+ m[nrl] -= ncl;
+
+ for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;
+
+ /* return pointer to array of pointers to rows */
+ return m;
+}
+
+/****************** free_imatrix *************************/
+void free_imatrix(m,nrl,nrh,ncl,nch)
+ int **m;
+ long nch,ncl,nrh,nrl;
+ /* free an int matrix allocated by imatrix() */
+{
+ free((FREE_ARG) (m[nrl]+ncl-NR_END));
+ free((FREE_ARG) (m+nrl-NR_END));
+}
+
+/******************* matrix *******************************/
+double **matrix(long nrl, long nrh, long ncl, long nch)
+{
+ long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
+ double **m;
+
+ m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
+ if (!m) nrerror("allocation failure 1 in matrix()");
+ m += NR_END;
+ m -= nrl;
+
+ m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
+ if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
+ m[nrl] += NR_END;
+ m[nrl] -= ncl;
+
+ for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
+ return m;
+ /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) or &(m[1][0])
+m[i] = address of ith row of the table. &(m[i]) is its value which is another adress
+that of m[i][0]. In order to get the value p m[i][0] but it is unitialized.
+ */
+}
+
+/*************************free matrix ************************/
+void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
+{
+ free((FREE_ARG)(m[nrl]+ncl-NR_END));
+ free((FREE_ARG)(m+nrl-NR_END));
+}
+
+/******************* ma3x *******************************/
+double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
+{
+ long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
+ double ***m;
+
+ m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
+ if (!m) nrerror("allocation failure 1 in matrix()");
+ m += NR_END;
+ m -= nrl;
+
+ m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
+ if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
+ m[nrl] += NR_END;
+ m[nrl] -= ncl;
+
+ for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
+
+ m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
+ if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
+ m[nrl][ncl] += NR_END;
+ m[nrl][ncl] -= nll;
+ for (j=ncl+1; j<=nch; j++)
+ m[nrl][j]=m[nrl][j-1]+nlay;
+
+ for (i=nrl+1; i<=nrh; i++) {
+ m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
+ for (j=ncl+1; j<=nch; j++)
+ m[i][j]=m[i][j-1]+nlay;
+ }
+ return m;
+ /* gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
+ &(m[i][j][k]) <=> *((*(m+i) + j)+k)
+ */
+}
+
+/*************************free ma3x ************************/
+void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
+{
+ free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
+ free((FREE_ARG)(m[nrl]+ncl-NR_END));
+ free((FREE_ARG)(m+nrl-NR_END));
+}
+
+/*************** function subdirf ***********/
+char *subdirf(char fileres[])
+{
+ /* Caution optionfilefiname is hidden */
+ strcpy(tmpout,optionfilefiname);
+ strcat(tmpout,"/"); /* Add to the right */
+ strcat(tmpout,fileres);
+ return tmpout;
+}
+
+/*************** function subdirf2 ***********/
+char *subdirf2(char fileres[], char *preop)
+{
+
+ /* Caution optionfilefiname is hidden */
+ strcpy(tmpout,optionfilefiname);
+ strcat(tmpout,"/");
+ strcat(tmpout,preop);
+ strcat(tmpout,fileres);
+ return tmpout;
+}
+
+/*************** function subdirf3 ***********/
+char *subdirf3(char fileres[], char *preop, char *preop2)
+{
+
+ /* Caution optionfilefiname is hidden */
+ strcpy(tmpout,optionfilefiname);
+ strcat(tmpout,"/");
+ strcat(tmpout,preop);
+ strcat(tmpout,preop2);
+ 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;
+}
+
+/*****************brent *************************/
+double brent(double ax, double bx, double cx, double (*f)(double), double tol, double *xmin)
+{
+ int iter;
+ double a,b,d,etemp;
+ double fu=0,fv,fw,fx;
+ double ftemp;
+ double p,q,r,tol1,tol2,u,v,w,x,xm;
+ double e=0.0;
+
+ a=(ax < cx ? ax : cx);
+ b=(ax > cx ? ax : cx);
+ x=w=v=bx;
+ fw=fv=fx=(*f)(x);
+ for (iter=1;iter<=ITMAX;iter++) {
+ xm=0.5*(a+b);
+ tol2=2.0*(tol1=tol*fabs(x)+ZEPS);
+ /* if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
+ printf(".");fflush(stdout);
+ fprintf(ficlog,".");fflush(ficlog);
+#ifdef DEBUG
+ 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)))) { */
+#endif
+ if (fabs(x-xm) <= (tol2-0.5*(b-a))){
+ *xmin=x;
+ return fx;
+ }
+ ftemp=fu;
+ if (fabs(e) > tol1) {
+ r=(x-w)*(fx-fv);
+ q=(x-v)*(fx-fw);
+ p=(x-v)*q-(x-w)*r;
+ q=2.0*(q-r);
+ if (q > 0.0) p = -p;
+ q=fabs(q);
+ 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));
+ else {
+ 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));
+ }
+ u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));
+ fu=(*f)(u);
+ 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;
+ }
+ }
+ }
+ nrerror("Too many iterations in brent");
+ *xmin=x;
+ return fx;
+}
+
+/****************** mnbrak ***********************/
+
+void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,
+ double (*func)(double))
+{
+ double ulim,u,r,q, dum;
+ double fu;
+
+ *fa=(*func)(*ax);
+ *fb=(*func)(*bx);
+ if (*fb > *fa) {
+ SHFT(dum,*ax,*bx,dum)
+ SHFT(dum,*fb,*fa,dum)
+ }
+ *cx=(*bx)+GOLD*(*bx-*ax);
+ *fc=(*func)(*cx);
+ while (*fb > *fc) {
+ r=(*bx-*ax)*(*fb-*fc);
+ q=(*bx-*cx)*(*fb-*fa);
+ 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) {
+ fu=(*func)(u);
+ } else if ((*cx-u)*(u-ulim) > 0.0) {
+ 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) {
+ u=ulim;
+ fu=(*func)(u);
+ } else {
+ u=(*cx)+GOLD*(*cx-*bx);
+ fu=(*func)(u);
+ }
+ SHFT(*ax,*bx,*cx,u)
+ SHFT(*fa,*fb,*fc,fu)
+ }
+}
+
+/*************** linmin ************************/
+
+int ncom;
+double *pcom,*xicom;
+double (*nrfunc)(double []);
+
+void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))
+{
+ double brent(double ax, double bx, double cx,
+ double (*f)(double), double tol, double *xmin);
+ double f1dim(double x);
+ void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,
+ double *fc, double (*func)(double));
+ int j;
+ double xx,xmin,bx,ax;
+ double fx,fb,fa;
+
+ 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];
+ }
+ ax=0.0;
+ xx=1.0;
+ mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);
+ *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);
+#ifdef DEBUG
+ printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
+ fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
+#endif
+ for (j=1;j<=n;j++) {
+ xi[j] *= xmin;
+ p[j] += xi[j];
+ }
+ 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 ************************/
+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,
+ double (*func)(double []));
+ int i,ibig,j;
+ double del,t,*pt,*ptt,*xit;
+ double fp,fptt;
+ double *xits;
+ int niterf, itmp;
+
+ pt=vector(1,n);
+ ptt=vector(1,n);
+ xit=vector(1,n);
+ 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);
+ ibig=0;
+ del=0.0;
+ 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++) {
+ printf(" %d %.12f",i, p[i]);
+ fprintf(ficlog," %d %.12lf",i, p[i]);
+ fprintf(ficrespow," %.12lf", p[i]);
+ }
+ printf("\n");
+ fprintf(ficlog,"\n");
+ fprintf(ficrespow,"\n");fflush(ficrespow);
+ if(*iter <=3){
+ tml = *localtime(&rcurr_time);
+ strcpy(strcurr,asctime(&tml));
+/* asctime_r(&tm,strcurr); */
+ 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,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){
+ rforecast_time=rcurr_time+(niterf-*iter)*(rcurr_time-rlast_time);
+ forecast_time = *localtime(&rforecast_time);
+/* asctime_r(&tmf,strfor); */
+ 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(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];
+ fptt=(*fret);
+#ifdef DEBUG
+ printf("fret=%lf \n",*fret);
+ fprintf(ficlog,"fret=%lf \n",*fret);
+#endif
+ printf("%d",i);fflush(stdout);
+ fprintf(ficlog,"%d",i);fflush(ficlog);
+ linmin(p,xit,n,fret,func);
+ if (fabs(fptt-(*fret)) > del) {
+ 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]);
+ }
+ for(j=1;j<=n;j++) {
+ printf(" p=%.12e",p[j]);
+ fprintf(ficlog," p=%.12e",p[j]);
+ }
+ printf("\n");
+ fprintf(ficlog,"\n");
+#endif
+ }
+ if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
+#ifdef DEBUG
+ int k[2],l;
+ k[0]=1;
+ k[1]=-1;
+ printf("Max: %.12e",(*func)(p));
+ fprintf(ficlog,"Max: %.12e",(*func)(p));
+ for (j=1;j<=n;j++) {
+ printf(" %.12e",p[j]);
+ fprintf(ficlog," %.12e",p[j]);
+ }
+ printf("\n");
+ fprintf(ficlog,"\n");
+ for(l=0;l<=1;l++) {
+ for (j=1;j<=n;j++) {
+ ptt[j]=p[j]+(p[j]-pt[j])*k[l];
+ printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
+ fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
+ }
+ printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
+ fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
+ }
+#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++) { /* Computes an extrapolated point */
+ ptt[j]=2.0*p[j]-pt[j];
+ xit[j]=p[j]-pt[j];
+ pt[j]=p[j];
+ }
+ fptt=(*func)(ptt);
+ if (fptt < fp) { /* If extrapolated point is better, decide if we keep that new direction or not */
+ /* x1 f1=fp x2 f2=*fret x3 f3=fptt, xm fm */
+ /* From x1 (P0) distance of x2 is at h and x3 is 2h */
+ /* Let f"(x2) be the 2nd derivative equal everywhere. Then the parabolic through (x1,f1), (x2,f2) and (x3,f3)
+ will reach at f3 = fm + h^2/2 f''m ; f" = (f1 -2f2 +f3 ) / h**2 */
+ /* f1-f3 = delta(2h) = 2 h**2 f'' = 2(f1- 2f2 +f3) */
+ /* Thus we compare delta(2h) with observed f1-f3 */
+ /* or best gain on one ancient line 'del' with total gain f1-f2 = f1 - f2 - 'del' with del */
+ /* t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); */
+ t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del);
+ t= t- del*SQR(fp-fptt);
+ printf("t1= %.12lf, t2= %.12lf, t=%.12lf\n", 2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del),del*SQR(fp-fptt),t);
+ fprintf(ficlog,"t1= %.12lf, t2= %.12lf, t=%.12lf\n", 2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del),del*SQR(fp-fptt),t);
+#ifdef DEBUG
+ 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
+ if (t < 0.0) { /* Then we use it for last direction */
+ linmin(p,xit,n,fret,func); /* computes mean on the extrapolated direction.*/
+ for (j=1;j<=n;j++) {
+ xi[j][ibig]=xi[j][n]; /* Replace the direction with biggest decrease by n */
+ xi[j][n]=xit[j]; /* and nth direction by the extrapolated */
+ }
+ printf("Gaining to use average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
+ fprintf(ficlog,"Gaining to use average direction of P0 P%d instead of biggest increase direction :\n",n,ibig);
+
+#ifdef DEBUG
+ for(j=1;j<=n;j++){
+ printf(" %.12e",xit[j]);
+ fprintf(ficlog," %.12e",xit[j]);
+ }
+ printf("\n");
+ fprintf(ficlog,"\n");
+#endif
+ }
+ }
+ }
+}
+
+/**** 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 */
+
+ int i, ii,j,k;
+ double min, max, maxmin, maxmax,sumnew=0.;
+ /* double **matprod2(); */ /* test */
+ double **out, cov[NCOVMAX+1], **pmij();
+ double **newm;
+ double agefin, delaymax=50 ; /* Max number of years to converge */
+
+ 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 */
+ for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
+ 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]]);*/
+ }
+ /* 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 *\/ */
+ 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];
+ 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]);
+ }
+ maxmin=max-min;
+ maxmax=FMAX(maxmax,maxmin);
+ }
+ if(maxmax < ftolpl){
+ return prlim;
+ }
+ }
+}
+
+/*************** 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-1)*ncovmodel
+ 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;
+
+ for(i=1; i<= nlstate; i++){
+ for(j=1; j<i;j++){
+ for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
+ /*lnpijopii += param[i][j][nc]*cov[nc];*/
+ lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
+/* printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
+ }
+ ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
+/* printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
+ }
+ for(j=i+1; j<=nlstate+ndeath;j++){
+ for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
+ /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
+ lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
+/* printf("Int j>i 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; j<i; j++){
+ s1+=exp(ps[i][j]); /* In fact sums pij/pii */
+ /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
+ }
+ for(j=i+1; j<=nlstate+ndeath; j++){
+ s1+=exp(ps[i][j]); /* In fact sums pij/pii */
+ /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
+ }
+ /* s1= sum_{j<>i} 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<i; j++)
+ ps[i][j]= exp(ps[i][j])*ps[i][i];
+ for(j=i+1; j<=nlstate+ndeath; j++)
+ ps[i][j]= exp(ps[i][j])*ps[i][i];
+ /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
+ } /* end i */
+
+ for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
+ for(jj=1; jj<= nlstate+ndeath; jj++){
+ ps[ii][jj]=0;
+ ps[ii][ii]=1;
+ }
+ }
+
+
+ /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
+ /* for(jj=1; jj<= nlstate+ndeath; jj++){ */
+ /* printf(" pmij ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
+ /* } */
+ /* printf("\n "); */
+ /* } */
+ /* printf("\n ");printf("%lf ",cov[2]);*/
+ /*
+ for(i=1; i<= npar; i++) printf("%f ",x[i]);
+ goto end;*/
+ return ps;
+}
+
+/**************** Product of 2 matrices ******************/
+
+double **matprod2(double **out, double **in,int nrl, int nrh, int ncl, int nch, int ncolol, int ncoloh, double **b)
+{
+ /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
+ b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
+ /* in, b, out are matrice of pointers which should have been initialized
+ before: only the contents of out is modified. The function returns
+ a pointer to pointers identical to out */
+ int i, j, k;
+ for(i=nrl; i<= nrh; i++)
+ for(k=ncolol; k<=ncoloh; k++){
+ out[i][k]=0.;
+ for(j=ncl; j<=nch; j++)
+ out[i][k] +=in[i][j]*b[j][k];
+ }
+ return out;
+}
+
+
+/************* Higher Matrix Product ***************/
+
+double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
+{
+ /* 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.
+ Output is stored in matrix po[i][j][h] for h every 'hstepm' step
+ (typically every 2 years instead of every month which is too big
+ for the memory).
+ Model is determined by parameters x and covariates have to be
+ included manually here.
+
+ */
+
+ int i, j, d, h, k;
+ double **out, cov[NCOVMAX+1];
+ double **newm;
+
+ /* Hstepm could be zero and should return the unit matrix */
+ for (i=1;i<=nlstate+ndeath;i++)
+ for (j=1;j<=nlstate+ndeath;j++){
+ oldm[i][j]=(i==j ? 1.0 : 0.0);
+ po[i][j][0]=(i==j ? 1.0 : 0.0);
+ }
+ /* Even if hstepm = 1, at least one multiplication by the unit matrix */
+ for(h=1; h <=nhstepm; h++){
+ for(d=1; d <=hstepm; d++){
+ newm=savm;
+ /* Covariates have to be included here again */
+ cov[1]=1.;
+ cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
+ 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];
+ for (k=1; k<=cptcovprod;k++) /* Useless because included in cptcovn */
+ cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
+
+
+ /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
+ /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
+ out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
+ pmij(pmmij,cov,ncovmodel,x,nlstate));
+ savm=oldm;
+ oldm=newm;
+ }
+ for(i=1; i<=nlstate+ndeath; i++)
+ for(j=1;j<=nlstate+ndeath;j++) {
+ po[i][j][h]=newm[i][j];
+ /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
+ }
+ /*printf("h=%d ",h);*/
+ } /* end h */
+/* printf("\n H=%d \n",h); */
+ return po;
+}
+
+double myfunc(unsigned n, const double *p, double *grad, double (*func) (double [])){
+ /* double (*nrfunc)(double []); */
+ /* double myfunc(unsigned n, const double *p, double *grad, void *my_func_data){ */
+ double fret;
+ double *xt;
+ int j;
+
+ xt=vector(1,n);
+ for (j=1;j<=n;j++)
+ xt[j]=p[j];
+ ++countcallfunc;
+
+ fret=(*func)(xt);
+ printf("Function = %.12lf ",fret);
+ for (j=1;j<=n;j++)
+ printf(" %d %.8lf", j, p[j]);
+ printf("\n");
+ free_vector(xt,1,n);
+ return fret;
+}
+/*************** log-likelihood *************/
+double func( double *x)
+{
+ int i, ii, j, k, mi, d, kk;
+ double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
+ double **out;
+ double sw; /* Sum of weights */
+ double lli; /* Individual log likelihood */
+ int s1, s2;
+ double bbh, survp;
+ long ipmx;
+ /*extern weight */
+ /* We are differentiating ll according to initial status */
+ /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
+ /*for(i=1;i<imx;i++)
+ printf(" %d\n",s[4][i]);
+ */
+ cov[1]=1.;
+
+ for(k=1; k<=nlstate; k++) ll[k]=0.;
+
+ if(mle==1){
+ for (i=1,ipmx=0, sw=0.; i<=imx; i++){
+ /* Computes the values of the ncovmodel covariates of the model
+ depending if the covariates are fixed or variying (age dependent) and stores them in cov[]
+ Then computes with function pmij which return a matrix p[i][j] giving the elementary probability
+ to be observed in j being in i according to the model.
+ */
+ for (k=1; k<=cptcovn;k++){ /* Simple and product covariates without age* products */
+ cov[2+k]=covar[Tvar[k]][i];
+ }
+ /* In model V2+V1*V4+age*V3+V3*V2 Tvar[1] is V2, Tvar[2=V1*V4]
+ is 6, Tvar[3=age*V3] should not be computed because of age Tvar[4=V3*V2]
+ has been calculated etc */
+ for(mi=1; mi<= wav[i]-1; mi++){
+ for (ii=1;ii<=nlstate+ndeath;ii++)
+ for (j=1;j<=nlstate+ndeath;j++){
+ oldm[ii][j]=(ii==j ? 1.0 : 0.0);
+ savm[ii][j]=(ii==j ? 1.0 : 0.0);
+ }
+ for(d=0; d<dh[mi][i]; d++){
+ newm=savm;
+ cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
+ for (kk=1; kk<=cptcovage;kk++) {
+ cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; /* Tage[kk] gives the data-covariate associated with age */
+ }
+ out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
+ 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
+ savm=oldm;
+ oldm=newm;
+ } /* end mult */
+
+ /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
+ /* But now since version 0.9 we anticipate for bias at large stepm.
+ * If stepm is larger than one month (smallest stepm) and if the exact delay
+ * (in months) between two waves is not a multiple of stepm, we rounded to
+ * the nearest (and in case of equal distance, to the lowest) interval but now
+ * we keep into memory the bias bh[mi][i] and also the previous matrix product
+ * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
+ * probability in order to take into account the bias as a fraction of the way
+ * 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;
+ /* bias bh is positive if real duration
+ * is higher than the multiple of stepm and negative otherwise.
+ */
+ /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
+ if( s2 > nlstate){
+ /* i.e. if s2 is a death state and if the date of death is known
+ then the contribution to the likelihood is the probability to
+ die between last step unit time and current step unit time,
+ 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.
+ */
+ lli=log(out[s1][s2] - savm[s1][s2]);
+
+
+ } else if (s2==-2) {
+ 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) {
+ 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++)
+ survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
+ 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 */
+ }
+ /*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;
+ sw += weight[i];
+ ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
+ } /* 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(mi=1; mi<= wav[i]-1; mi++){
+ for (ii=1;ii<=nlstate+ndeath;ii++)
+ for (j=1;j<=nlstate+ndeath;j++){
+ oldm[ii][j]=(ii==j ? 1.0 : 0.0);
+ savm[ii][j]=(ii==j ? 1.0 : 0.0);
+ }
+ for(d=0; d<=dh[mi][i]; d++){
+ newm=savm;
+ cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
+ for (kk=1; kk<=cptcovage;kk++) {
+ cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
+ }
+ out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
+ 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
+ savm=oldm;
+ oldm=newm;
+ } /* end mult */
+
+ s1=s[mw[mi][i]][i];
+ s2=s[mw[mi+1][i]][i];
+ bbh=(double)bh[mi][i]/(double)stepm;
+ 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 */
+ ipmx +=1;
+ sw += weight[i];
+ ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
+ } /* end of wave */
+ } /* 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(mi=1; mi<= wav[i]-1; mi++){
+ for (ii=1;ii<=nlstate+ndeath;ii++)
+ for (j=1;j<=nlstate+ndeath;j++){
+ oldm[ii][j]=(ii==j ? 1.0 : 0.0);
+ savm[ii][j]=(ii==j ? 1.0 : 0.0);
+ }
+ for(d=0; d<dh[mi][i]; d++){
+ newm=savm;
+ cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
+ for (kk=1; kk<=cptcovage;kk++) {
+ cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
+ }
+ out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
+ 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
+ savm=oldm;
+ oldm=newm;
+ } /* end mult */
+
+ s1=s[mw[mi][i]][i];
+ s2=s[mw[mi+1][i]][i];
+ bbh=(double)bh[mi][i]/(double)stepm;
+ lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
+ ipmx +=1;
+ sw += weight[i];
+ ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
+ } /* end of wave */
+ } /* end of individual */
+ }else if (mle==4){ /* ml=4 no 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(mi=1; mi<= wav[i]-1; mi++){
+ for (ii=1;ii<=nlstate+ndeath;ii++)
+ for (j=1;j<=nlstate+ndeath;j++){
+ oldm[ii][j]=(ii==j ? 1.0 : 0.0);
+ savm[ii][j]=(ii==j ? 1.0 : 0.0);
+ }
+ for(d=0; d<dh[mi][i]; d++){
+ newm=savm;
+ cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
+ for (kk=1; kk<=cptcovage;kk++) {
+ cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
+ }
+
+ out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
+ 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
+ savm=oldm;
+ oldm=newm;
+ } /* end mult */
+
+ s1=s[mw[mi][i]][i];
+ s2=s[mw[mi+1][i]][i];
+ if( s2 > nlstate){
+ lli=log(out[s1][s2] - savm[s1][s2]);
+ }else{
+ lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
+ }
+ ipmx +=1;
+ sw += weight[i];
+ 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]); */
+ } /* end of wave */
+ } /* 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(mi=1; mi<= wav[i]-1; mi++){
+ for (ii=1;ii<=nlstate+ndeath;ii++)
+ for (j=1;j<=nlstate+ndeath;j++){
+ oldm[ii][j]=(ii==j ? 1.0 : 0.0);
+ savm[ii][j]=(ii==j ? 1.0 : 0.0);
+ }
+ for(d=0; d<dh[mi][i]; d++){
+ newm=savm;
+ cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
+ for (kk=1; kk<=cptcovage;kk++) {
+ cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
+ }
+
+ out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
+ 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
+ savm=oldm;
+ oldm=newm;
+ } /* end mult */
+
+ s1=s[mw[mi][i]][i];
+ s2=s[mw[mi+1][i]][i];
+ lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
+ ipmx +=1;
+ sw += weight[i];
+ 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]);*/
+ } /* end of wave */
+ } /* end of individual */
+ } /* End of if */
+ 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 */
+ return -l;
+}
+
+/*************** log-likelihood *************/
+double funcone( double *x)
+{
+ /* Same as likeli but slower because of a lot of printf and if */
+ int i, ii, j, k, mi, d, kk;
+ double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
+ double **out;
+ double lli; /* Individual log likelihood */
+ double llt;
+ int s1, s2;
+ double bbh, survp;
+ /*extern weight */
+ /* We are differentiating ll according to initial status */
+ /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
+ /*for(i=1;i<imx;i++)
+ printf(" %d\n",s[4][i]);
+ */
+ cov[1]=1.;
+
+ for(k=1; k<=nlstate; k++) ll[k]=0.;
+
+ for (i=1,ipmx=0, sw=0.; i<=imx; i++){
+ for (k=1; k<=cptcovn;k++) cov[2+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++){
+ oldm[ii][j]=(ii==j ? 1.0 : 0.0);
+ savm[ii][j]=(ii==j ? 1.0 : 0.0);
+ }
+ for(d=0; d<dh[mi][i]; d++){
+ newm=savm;
+ cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
+ for (kk=1; kk<=cptcovage;kk++) {
+ cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
+ }
+ /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
+ out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
+ 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
+ /* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, */
+ /* 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); */
+ savm=oldm;
+ oldm=newm;
+ } /* end mult */
+
+ s1=s[mw[mi][i]][i];
+ s2=s[mw[mi+1][i]][i];
+ bbh=(double)bh[mi][i]/(double)stepm;
+ /* bias is positive if real duration
+ * is higher than the multiple of stepm and negative otherwise.
+ */
+ if( s2 > nlstate && (mle <5) ){ /* Jackson */
+ lli=log(out[s1][s2] - savm[s1][s2]);
+ } else if (s2==-2) {
+ for (j=1,survp=0. ; j<=nlstate; j++)
+ survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
+ lli= log(survp);
+ }else if (mle==1){
+ lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
+ } else if(mle==2){
+ 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 */
+ } else if(mle==3){ /* exponential inter-extrapolation */
+ lli= (savm[s1][s2]>(double)1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
+ } else if (mle==4){ /* mle=4 no inter-extrapolation */
+ lli=log(out[s1][s2]); /* Original formula */
+ } else{ /* mle=0 back to 1 */
+ lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
+ /*lli=log(out[s1][s2]); */ /* Original formula */
+ } /* End of if */
+ ipmx +=1;
+ sw += weight[i];
+ 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\
+ %11.6f %11.6f %11.6f ", \
+ num[i],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,llt=0.,l=0.; k<=nlstate; k++){
+ llt +=ll[k]*gipmx/gsw;
+ fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
+ }
+ 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;
+}
+
+
+/*************** function likelione ***********/
+void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
+{
+ /* This routine should help understanding what is done with
+ the selection of individuals/waves and
+ to check the exact contribution to the likelihood.
+ Plotting could be done.
+ */
+ int k;
+
+ if(*globpri !=0){ /* Just counts and sums, no printings */
+ strcpy(fileresilk,"ilk");
+ strcat(fileresilk,fileres);
+ 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 ");
+ /* 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);
+ fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
+ }
+
+ *fretone=(*funcone)(p);
+ if(*globpri !=0){
+ fclose(ficresilk);
+ fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
+ fflush(fichtm);
+ }
+ return;
+}
+
+
+/*********** Maximum Likelihood Estimation ***************/
+
+void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
+{
+ int i,j, iter;
+ double **xi;
+ double fret;
+ double fretone; /* Only one call to likelihood */
+ /* char filerespow[FILENAMELENGTH];*/
+ 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");
+ strcat(filerespow,fileres);
+ if((ficrespow=fopen(filerespow,"w"))==NULL) {
+ printf("Problem with resultfile: %s\n", filerespow);
+ fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
+ }
+ fprintf(ficrespow,"# Powell\n# iter -2*LL");
+ for (i=1;i<=nlstate;i++)
+ 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
+ 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 minf; /* the minimum objective value, upon return */
+ /* opt = nlopt_create(NLOPT_LN_NEWUOA,npar); */
+ opt = nlopt_create(NLOPT_LN_BOBYQA,npar);
+ nlopt_set_lower_bounds(opt, lb);
+ printf(" Func %.12lf \n",myfunc(npar,*(&p),NULL,func));
+ /* printf(" Func %.12lf /n",myfunc(npar,p,NULL,NULL)); */
+ /* nlopt_set_min_objective(opt, myfunc, NULL); */
+ nlopt_set_min_objective(opt, myfunc, func);
+ nlopt_set_xtol_rel(opt, ftol);
+ /* printf(" Func %.12lf /n",myfunc(npar,p,NULL,func)); */
+ if ((creturn=nlopt_optimize(opt, p, &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=countcallfunc; /* 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));
+
+}
+
+/**** Computes Hessian and covariance matrix ***/
+void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
+{
+ double **a,**y,*x,pd;
+ double **hess;
+ int i, j,jk;
+ 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);
+ 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);
+
+ 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);
+
+ hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
+
+ /* printf(" %f ",p[i]);
+ printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
+ }
+
+ 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);
+
+ hess[j][i]=hess[i][j];
+ /*printf(" %lf ",hess[i][j]);*/
+ }
+ }
+ }
+ printf("\n");
+ fprintf(ficlog,"\n");
+
+ printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
+ fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
+
+ a=matrix(1,npar,1,npar);
+ y=matrix(1,npar,1,npar);
+ x=vector(1,npar);
+ indx=ivector(1,npar);
+ for (i=1;i<=npar;i++)
+ for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
+ ludcmp(a,npar,indx,&pd);
+
+ 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++){
+ matcov[i][j]=x[i];
+ }
+ }
+
+ printf("\n#Hessian matrix#\n");
+ 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("\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);
+
+ /* 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");
+ }
+ */
+
+ 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);
+
+
+}
+
+/*************** hessian matrix ****************/
+double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
+{
+ int i;
+ int l=1, lmax=20;
+ double k1,k2;
+ 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;
+
+ fx=func(x);
+ for (i=1;i<=npar;i++) p2[i]=x[i];
+ for(l=0 ; l <=lmax; l++){ /* Enlarging the zone around the Maximum */
+ l1=pow(10,l);
+ delts=delt;
+ for(k=1 ; k <kmax; k=k+1){
+ delt = delta*(l1*k);
+ p2[theta]=x[theta] +delt;
+ k1=func(p2)-fx; /* Might be negative if too close to the theoretical maximum */
+ 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 */
+
+#ifdef DEBUGHESS
+ 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
+ /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
+ if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
+ 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.;
+ }
+ else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){
+ delts=delt;
+ }
+ }
+ }
+ delti[theta]=delts;
+ return res;
+
+}
+
+double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
+{
+ int i;
+ int l=1, l1, lmax=20;
+ double k1,k2,k3,k4,res,fx;
+ double p2[MAXPARM+1];
+ int k;
+
+ fx=func(x);
+ for (k=1; k<=2; k++) {
+ for (i=1;i<=npar;i++) p2[i]=x[i];
+ 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;
+ k2=func(p2)-fx;
+
+ 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;
+ 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);
+#endif
+ }
+ return res;
+}
+
+/************** Inverse of matrix **************/
+void ludcmp(double **a, int n, int *indx, double *d)
+{
+ int i,imax,j,k;
+ double big,dum,sum,temp;
+ double *vv;
+
+ vv=vector(1,n);
+ *d=1.0;
+ for (i=1;i<=n;i++) {
+ 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");
+ vv[i]=1.0/big;
+ }
+ for (j=1;j<=n;j++) {
+ for (i=1;i<j;i++) {
+ sum=a[i][j];
+ for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];
+ a[i][j]=sum;
+ }
+ big=0.0;
+ for (i=j;i<=n;i++) {
+ sum=a[i][j];
+ for (k=1;k<j;k++)
+ sum -= a[i][k]*a[k][j];
+ a[i][j]=sum;
+ if ( (dum=vv[i]*fabs(sum)) >= big) {
+ big=dum;
+ imax=i;
+ }
+ }
+ if (j != imax) {
+ for (k=1;k<=n;k++) {
+ dum=a[imax][k];
+ a[imax][k]=a[j][k];
+ a[j][k]=dum;
+ }
+ *d = -(*d);
+ vv[imax]=vv[j];
+ }
+ indx[j]=imax;
+ if (a[j][j] == 0.0) a[j][j]=TINY;
+ if (j != n) {
+ dum=1.0/(a[j][j]);
+ for (i=j+1;i<=n;i++) a[i][j] *= dum;
+ }
+ }
+ free_vector(vv,1,n); /* Doesn't work */
+;
+}
+
+void lubksb(double **a, int n, int *indx, double b[])
+{
+ int i,ii=0,ip,j;
+ double sum;
+
+ for (i=1;i<=n;i++) {
+ ip=indx[i];
+ sum=b[ip];
+ b[ip]=b[i];
+ if (ii)
+ for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];
+ else if (sum) ii=i;
+ b[i]=sum;
+ }
+ for (i=n;i>=1;i--) {
+ sum=b[i];
+ for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];
+ b[i]=sum/a[i][i];
+ }
+}
+
+void pstamp(FILE *fichier)
+{
+ fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,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 i, m, jk, k1,i1, j1, bool, z1,j;
+ int first;
+ double ***freq; /* Frequencies */
+ double *pp, **prop;
+ double pos,posprop, k2, dateintsum=0,k2cpt=0;
+ char fileresp[FILENAMELENGTH];
+
+ pp=vector(1,nlstate);
+ prop=matrix(1,nlstate,iagemin,iagemax+3);
+ strcpy(fileresp,"p");
+ strcat(fileresp,fileres);
+ 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;
+ if (cptcovn<1) {j=1;ncodemax[1]=1;}
+
+ first=1;
+
+ /* 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++){
+ /*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(m=iagemin; m <= iagemax+3; m++)
+ freq[i][jk][m]=0;
+
+ for (i=1; i<=nlstate; i++)
+ for(m=iagemin; m <= iagemax+3; m++)
+ prop[i][m]=0;
+
+ dateintsum=0;
+ k2cpt=0;
+ for (i=1; i<=imx; i++) {
+ 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 (m<lastpass) {
+ freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
+ freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
+ }
+
+ if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
+ dateintsum=dateintsum+k2;
+ k2cpt++;
+ }
+ /*}*/
+ }
+ }
+ } /* end i */
+
+ /* fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
+ pstamp(ficresp);
+ if (cptcovn>0) {
+ 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(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(i=1; i<=nlstate;i++)
+ fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
+ fprintf(ficresp, "\n");
+
+ for(i=iagemin; i <= iagemax+3; i++){
+ if(i==iagemax+3){
+ fprintf(ficlog,"Total");
+ }else{
+ if(first==1){
+ first=0;
+ printf("See log file for details...\n");
+ }
+ fprintf(ficlog,"Age %d", i);
+ }
+ for(jk=1; jk <=nlstate ; jk++){
+ for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
+ pp[jk] += freq[jk][m][i];
+ }
+ for(jk=1; jk <=nlstate ; jk++){
+ for(m=-1, pos=0; m <=0 ; m++)
+ pos += freq[jk][m][i];
+ if(pp[jk]>=1.e-10){
+ if(first==1){
+ printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
+ }
+ fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
+ }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);
+ }
+ }
+
+ 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(jk=1; jk <=nlstate ; jk++){
+ 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);
+ }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);
+ }
+ if( i <= 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]);*/
+ }
+ 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]);
+ }
+ if(i <= iagemax)
+ fprintf(ficresp,"\n");
+ if(first==1)
+ printf("Others in log...\n");
+ fprintf(ficlog,"\n");
+ }
+ /*}*/
+ }
+ dateintmean=dateintsum/k2cpt;
+
+ fclose(ficresp);
+ free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
+ free_vector(pp,1,nlstate);
+ free_matrix(prop,1,nlstate,iagemin, iagemax+3);
+ /* End of Freq */
+}
+
+/************ Prevalence ********************/
+void prevalence(double ***probs, double agemin, double agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, int firstpass, int lastpass)
+{
+ /* 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.
+ */
+
+ int i, m, jk, k1, i1, j1, bool, z1,j;
+ double ***freq; /* Frequencies */
+ double *pp, **prop;
+ double pos,posprop;
+ double y2; /* in fractional years */
+ int iagemin, iagemax;
+ int first; /** to stop verbosity which is redirected to log file */
+
+ iagemin= (int) agemin;
+ iagemax= (int) agemax;
+ /*pp=vector(1,nlstate);*/
+ prop=matrix(1,nlstate,iagemin,iagemax+3);
+ /* freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
+ j1=0;
+
+ /*j=cptcoveff;*/
+ 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]])
+ bool=0;
+ }
+ if (bool==1) {
+ for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
+ 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] <iagemin || (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(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];
+ }
+ }
+ } /* 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 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);
+} /* End of prevalence */
+
+/************* Waves Concatenation ***************/
+
+void concatwav(int wav[], int **dh, int **bh, int **mw, int **s, double *agedc, double **agev, int firstpass, int lastpass, int imx, int nlstate, int stepm)
+{
+ /* 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 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 j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
+ double sum=0., jmean=0.;*/
+ int first;
+ int j, k=0,jk, ju, jl;
+ double sum=0.;
+ first=0;
+ jmin=1e+5;
+ jmax=-1;
+ jmean=0.;
+ for(i=1; i<=imx; i++){
+ mi=0;
+ m=firstpass;
+ while(s[m][i] <= nlstate){
+ if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
+ mw[++mi][i]=m;
+ if(m >=lastpass)
+ break;
+ else
+ m++;
+ }/* end while */
+ if (s[m][i] > nlstate){
+ mi++; /* Death is another wave */
+ /* if(mi==0) never been interviewed correctly before death */
+ /* Only death is a correct wave */
+ mw[mi][i]=m;
+ }
+
+ wav[i]=mi;
+ if(mi==0){
+ nbwarn++;
+ if(first==0){
+ printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
+ first=1;
+ }
+ if(first==1){
+ fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
+ }
+ } /* end mi==0 */
+ } /* End individuals */
+
+ for(i=1; i<=imx; i++){
+ for(mi=1; mi<wav[i];mi++){
+ if (stepm <=0)
+ dh[mi][i]=1;
+ else{
+ if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
+ 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 */
+ else if(j<0){
+ nberr++;
+ printf("Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
+ j=1; /* Temporary Dangerous patch */
+ printf(" We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm);
+ fprintf(ficlog,"Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
+ fprintf(ficlog," We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm);
+ }
+ k=k+1;
+ if (j >= jmax){
+ jmax=j;
+ ijmax=i;
+ }
+ if (j <= jmin){
+ jmin=j;
+ ijmin=i;
+ }
+ sum=sum+j;
+ /*if (j<0) printf("j=%d num=%d \n",j,i);*/
+ /* printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
+ }
+ }
+ 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;
+ ijmax=i;
+ }
+ else if (j <= jmin){
+ jmin=j;
+ ijmin=i;
+ }
+ /* if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
+ /*printf("%d %lf %d %d %d\n", i,agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);*/
+ if(j<0){
+ nberr++;
+ printf("Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
+ fprintf(ficlog,"Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
+ }
+ sum=sum+j;
+ }
+ jk= j/stepm;
+ jl= j -jk*stepm;
+ ju= j -(jk+1)*stepm;
+ if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
+ if(jl==0){
+ dh[mi][i]=jk;
+ bh[mi][i]=0;
+ }else{ /* We want a negative bias in order to only have interpolation ie
+ * to avoid the price of an extra matrix product in likelihood */
+ dh[mi][i]=jk+1;
+ bh[mi][i]=ju;
+ }
+ }else{
+ if(jl <= -ju){
+ dh[mi][i]=jk;
+ bh[mi][i]=jl; /* bias is positive if real duration
+ * is higher than the multiple of stepm and negative otherwise.
+ */
+ }
+ else{
+ dh[mi][i]=jk+1;
+ bh[mi][i]=ju;
+ }
+ if(dh[mi][i]==0){
+ dh[mi][i]=1; /* At least one step */
+ bh[mi][i]=ju; /* At least one step */
+ /* printf(" bh=%d ju=%d jl=%d dh=%d jk=%d stepm=%d %d\n",bh[mi][i],ju,jl,dh[mi][i],jk,stepm,i);*/
+ }
+ } /* end if mle */
+ }
+ } /* end wave */
+ }
+ 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]=
+ */
+
+ 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;
+
+ for (k=-1; k < maxncov; k++) Ndum[k]=0;
+ 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;
+ }
+ 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[] )
+
+{
+ /* Health expectancies, no variances */
+ int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2;
+ int nhstepma, nstepma; /* Decreasing with age */
+ double age, agelim, hf;
+ double ***p3mat;
+ double eip;
+
+ 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++){
+ for(j=1; j<=nlstate;j++){
+ fprintf(ficreseij," e%1d%1d ",i,j);
+ }
+ fprintf(ficreseij," e%1d. ",i);
+ }
+ fprintf(ficreseij,"\n");
+
+
+ if(estepm < stepm){
+ printf ("Problem %d lower than %d\n",estepm, stepm);
+ }
+ else hstepm=estepm;
+ /* We compute the life expectancy from trapezoids spaced every estepm months
+ * This is mainly to measure the difference between two models: for example
+ * if stepm=24 months pijx are given only every 2 years and by summing them
+ * we are calculating an estimate of the Life Expectancy assuming a linear
+ * progression in between and thus overestimating or underestimating according
+ * to the curvature of the survival function. If, for the same date, we
+ * estimate the model with stepm=1 month, we can keep estepm to 24 months
+ * to compare the new estimate of Life expectancy with the same linear
+ * hypothesis. A more precise result, taking into account a more precise
+ * curvature will be obtained if estepm is as small as stepm. */
+
+ /* 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 hpijx to understand the reason of that which relies in memory size
+ and note for a fixed period like estepm months */
+ /* 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 only each 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;
+ /* If stepm=6 months */
+ /* Computed by stepm unit matrices, product of hstepm matrices, stored
+ in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
+
+/* nhstepm age range expressed in number of stepm */
+ nstepm=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
+ /* Typically if 20 years nstepm = 20*12/6=40 stepm */
+ /* if (stepm >= YEARM) hstepm=1;*/
+ nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
+ p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+
+ for (age=bage; age<=fage; age ++){
+ nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
+ /* 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 */
+
+ hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
+
+ hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
+
+ printf("%d|",(int)age);fflush(stdout);
+ fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
+
+ /* Computing expectancies */
+ 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] += (p3mat[i][j][h]+p3mat[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(ficreseij,"%3.0f",age );
+ for(i=1; i<=nlstate;i++){
+ eip=0;
+ for(j=1; j<=nlstate;j++){
+ eip +=eij[i][j][(int)age];
+ fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
+ }
+ fprintf(ficreseij,"%9.4f", eip );
+ }
+ fprintf(ficreseij,"\n");
+
+ }
+ free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+ printf("\n");
+ fprintf(ficlog,"\n");
+
+}
+
+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[] )
+
+{
+ /* Covariances of health expectancies eij and of total life expectancies according
+ 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 */
+ double age, agelim, hf;
+ double ***p3matp, ***p3matm, ***varhe;
+ double **dnewm,**doldm;
+ double *xp, *xm;
+ double **gp, **gm;
+ double ***gradg, ***trgradg;
+ int theta;
+
+ double eip, vip;
+
+ varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
+ xp=vector(1,npar);
+ xm=vector(1,npar);
+ dnewm=matrix(1,nlstate*nlstate,1,npar);
+ doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
+
+ pstamp(ficresstdeij);
+ fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
+ fprintf(ficresstdeij,"# Age");
+ for(i=1; i<=nlstate;i++){
+ for(j=1; j<=nlstate;j++)
+ fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
+ fprintf(ficresstdeij," e%1d. ",i);
+ }
+ fprintf(ficresstdeij,"\n");
+
+ pstamp(ficrescveij);
+ fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
+ fprintf(ficrescveij,"# Age");
+ for(i=1; i<=nlstate;i++)
+ for(j=1; j<=nlstate;j++){
+ cptj= (j-1)*nlstate+i;
+ for(i2=1; i2<=nlstate;i2++)
+ for(j2=1; j2<=nlstate;j2++){
+ cptj2= (j2-1)*nlstate+i2;
+ if(cptj2 <= cptj)
+ fprintf(ficrescveij," %1d%1d,%1d%1d",i,j,i2,j2);
+ }
+ }
+ fprintf(ficrescveij,"\n");
+
+ if(estepm < stepm){
+ printf ("Problem %d lower than %d\n",estepm, stepm);
+ }
+ else hstepm=estepm;
+ /* We compute the life expectancy from trapezoids spaced every estepm months
+ * This is mainly to measure the difference between two models: for example
+ * if stepm=24 months pijx are given only every 2 years and by summing them
+ * we are calculating an estimate of the Life Expectancy assuming a linear
+ * progression in between and thus overestimating or underestimating according
+ * to the curvature of the survival function. If, for the same date, we
+ * estimate the model with stepm=1 month, we can keep estepm to 24 months
+ * to compare the new estimate of Life expectancy with the same linear
+ * hypothesis. A more precise result, taking into account a more precise
+ * curvature will be obtained if estepm is as small as stepm. */
+
+ /* 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 hpijx to understand the reason of that which relies in memory size
+ and note for a fixed period like estepm months */
+ /* 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 only each 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 */
+
+ /* If stepm=6 months */
+ /* nhstepm age range expressed in number of stepm */
+ agelim=AGESUP;
+ nstepm=(int) rint((agelim-bage)*YEARM/stepm);
+ /* Typically if 20 years nstepm = 20*12/6=40 stepm */
+ /* if (stepm >= YEARM) hstepm=1;*/
+ nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
+
+ p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+ p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+ gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
+ trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
+ gp=matrix(0,nhstepm,1,nlstate*nlstate);
+ gm=matrix(0,nhstepm,1,nlstate*nlstate);
+
+ for (age=bage; age<=fage; age ++){
+ nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
+ /* 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 */
+ for(theta=1; theta <=npar; theta++){
+ for(i=1; i<=npar; i++){
+ 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);
+
+ for(j=1; j<= nlstate; j++){
+ for(i=1; i<=nlstate; i++){
+ for(h=0; h<=nhstepm-1; h++){
+ gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
+ gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
+ }
+ }
+ }
+
+ 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];
+ }
+ }/* End theta */
+
+
+ for(h=0; h<=nhstepm-1; h++)
+ for(j=1; j<=nlstate*nlstate;j++)
+ for(theta=1; theta <=npar; theta++)
+ trgradg[h][j][theta]=gradg[h][theta][j];
+
+
+ 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++){
+ 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]);
+ for(ij=1;ij<=nlstate*nlstate;ij++)
+ for(ji=1;ji<=nlstate*nlstate;ji++)
+ varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
+ }
+ }
+
+ /* Computing expectancies */
+ hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
+ 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.;
+ vip=0.;
+ for(j=1; j<=nlstate;j++){
+ eip += eij[i][j][(int)age];
+ for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
+ vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
+ fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
+ }
+ 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++){
+ cptj= (j-1)*nlstate+i;
+ for(i2=1; i2<=nlstate;i2++)
+ for(j2=1; j2<=nlstate;j2++){
+ cptj2= (j2-1)*nlstate+i2;
+ if(cptj2 <= cptj)
+ fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
+ }
+ }
+ fprintf(ficrescveij,"\n");
+
+ }
+ free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
+ free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
+ free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
+ free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
+ free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+ 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<li><h4> Computing probabilities of dying over estepm months as a weighted average (i.e global mortality independent of initial healh state)</h4></li>\n");
+ fprintf(fichtm,"\n<br>%s <br>\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.;
+
+ 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 */
+ 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.
+ */
+ 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");
+ /* 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<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
+ fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"%s%s.png\"> <br>\n", estepm,subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
+ /* fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months and then divided by estepm and multiplied by %.0f in order to have the probability to die over a year <br> <img src=\"varmuptjgr%s%s.png\"> <br>\n", stepm,YEARM,digitp,digit);
+*/
+/* 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 */
+
+/************ 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[])
+{
+ /* Variance of prevalence limit */
+ /* 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 age,agelim;
+ int theta;
+
+ pstamp(ficresvpl);
+ fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
+ fprintf(ficresvpl,"# Age");
+ for(i=1; i<=nlstate;i++)
+ fprintf(ficresvpl," %1d-%1d",i,i);
+ fprintf(ficresvpl,"\n");
+
+ xp=vector(1,npar);
+ dnewm=matrix(1,nlstate,1,npar);
+ doldm=matrix(1,nlstate,1,nlstate);
+
+ hstepm=1*YEARM; /* Every year of age */
+ hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
+ agelim = AGESUP;
+ for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
+ nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
+ if (stepm >= YEARM) hstepm=1;
+ nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
+ gradg=matrix(1,npar,1,nlstate);
+ gp=vector(1,nlstate);
+ gm=vector(1,nlstate);
+
+ for(theta=1; theta <=npar; theta++){
+ 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++)
+ gp[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++)
+ gm[i] = prlim[i][i];
+
+ for(i=1;i<=nlstate;i++)
+ gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
+ } /* End theta */
+
+ trgradg =matrix(1,nlstate,1,npar);
+
+ for(j=1; j<=nlstate;j++)
+ for(theta=1; theta <=npar; theta++)
+ trgradg[j][theta]=gradg[theta][j];
+
+ for(i=1;i<=nlstate;i++)
+ varpl[i][(int)age] =0.;
+ 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 );
+ 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(gradg,1,npar,1,nlstate);
+ free_matrix(trgradg,1,nlstate,1,npar);
+ } /* End age */
+
+ free_vector(xp,1,npar);
+ free_matrix(doldm,1,nlstate,1,npar);
+ free_matrix(dnewm,1,nlstate,1,nlstate);
+
+}
+
+/************ 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<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
+ fprintf(fichtm,"\n");
+
+ fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
+ fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
+ file %s<br>\n",optionfilehtmcov);
+ fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
+and drawn. It helps understanding how is the covariance between two incidences.\
+ They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
+ fprintf(fichtmcov,"\n<br> Contour plot corresponding to x'cov<sup>-1</sup>x = 4 (where x is the column vector (pij,pkl)) are drawn. \
+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. <br>\
+ Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
+ and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
+To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \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<hr size=\"2\" color=\"#EC5E5E\">********** Variable ");
+ for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
+ fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
+
+ 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<br>Probability with confidence intervals expressed in year<sup>-1</sup> :<a href=\"pijgr%s.png\">pijgr%s.png</A>, ",optionfilefiname,optionfilefiname);
+ fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",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,"\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<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
+ :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
+%s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
+ subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
+ subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
+ fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
+ fprintf(fichtmcov,"\n<br> 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);
+}
+
+
+/******************* Printing html file ***********/
+void printinghtml(char fileres[], 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;
+
+ fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
+ <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
+</ul>");
+ fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \
+ - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
+ jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
+ fprintf(fichtm,"\
+ - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
+ stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
+ fprintf(fichtm,"\
+ - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
+ subdirf2(fileres,"pl"),subdirf2(fileres,"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): \
+ <a href=\"%s\">%s</a> <br>\n",
+ estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
+ fprintf(fichtm,"\
+ - Population projections by age and states: \
+ <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileres,"f"),subdirf2(fileres,"f"));
+
+fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
+
+ 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++;
+ if (cptcovn > 0) {
+ fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
+ for (cpt=1; cpt<=cptcoveff;cpt++)
+ fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
+ fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
+ }
+ /* Pij */
+ fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i, %d (stepm) months before: <a href=\"%s%d_1.png\">%s%d_1.png</a><br> \
+<img src=\"%s%d_1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
+ /* Quasi-incidences */
+ fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
+ before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: <a href=\"%s%d_2.png\">%s%d_2.png</a><br> \
+<img src=\"%s%d_2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
+ /* Period (stable) prevalence in each health state */
+ for(cpt=1; cpt<=nlstate;cpt++){
+ fprintf(fichtm,"<br>- Convergence from each state (1 to %d) to period (stable) prevalence in state %d <a href=\"%s%d_%d.png\">%s%d_%d.png</a><br> \
+<img src=\"%s%d_%d.png\">",nlstate, cpt, subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
+ }
+ for(cpt=1; cpt<=nlstate;cpt++) {
+ fprintf(fichtm,"\n<br>- Life expectancy by health state (%d) at initial age and its decomposition into health expectancies in each alive state (1 to %d) : <a href=\"%s%d%d.png\">%s%d%d.png</a> <br> \
+<img src=\"%s%d%d.png\">",cpt,nlstate,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
+ }
+ } /* end i1 */
+ }/* End k1 */
+ fprintf(fichtm,"</ul>");
+
+
+ fprintf(fichtm,"\
+\n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
+ - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);
+
+ fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
+ subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
+ fprintf(fichtm,"\
+ - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
+ subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
+
+ fprintf(fichtm,"\
+ - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
+ subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
+ fprintf(fichtm,"\
+ - Variances and covariances of health expectancies by age and <b>initial health status</b> (cov(e<sup>ij</sup>,e<sup>kl</sup>)(estepm=%2d months): \
+ <a href=\"%s\">%s</a> <br>\n</li>",
+ estepm,subdirf2(fileres,"cve"),subdirf2(fileres,"cve"));
+ fprintf(fichtm,"\
+ - (a) Health expectancies by health status at initial age (e<sup>ij</sup>) and standard errors (in parentheses) (b) life expectancies and standard errors (e<sup>i.</sup>=e<sup>i1</sup>+e<sup>i2</sup>+...)(estepm=%2d months): \
+ <a href=\"%s\">%s</a> <br>\n</li>",
+ estepm,subdirf2(fileres,"stde"),subdirf2(fileres,"stde"));
+ fprintf(fichtm,"\
+ - Variances and covariances of health expectancies by age. Status (i) based health expectancies (in state j), e<sup>ij</sup> are weighted by the period prevalences in each state i (if popbased=1, an additional computation is done using the cross-sectional prevalences, i.e population based) (estepm=%d months): <a href=\"%s\">%s</a><br>\n",
+ estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
+ fprintf(fichtm,"\
+ - Total life expectancy and total health expectancies to be spent in each health state e<sup>.j</sup> with their standard errors (if popbased=1, an additional computation is done using the cross-sectional prevalences, i.e population based) (estepm=%d months): <a href=\"%s\">%s</a> <br>\n",
+ estepm, subdirf2(fileres,"t"),subdirf2(fileres,"t"));
+ fprintf(fichtm,"\
+ - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
+ subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
+
+/* if(popforecast==1) fprintf(fichtm,"\n */
+/* - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
+/* - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
+/* <br>",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 .)<br><br></li>\n",popforecast, stepm, model); */
+ fflush(fichtm);
+ fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
+
+ 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++;
+ if (cptcovn > 0) {
+ fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
+ for (cpt=1; cpt<=cptcoveff;cpt++)
+ fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
+ fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
+ }
+ for(cpt=1; cpt<=nlstate;cpt++) {
+ fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
+prevalence (with 95%% confidence interval) in state (%d): %s%d_%d.png <br>\
+<img src=\"%s%d_%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);
+ }
+ fprintf(fichtm,"\n<br>- 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<br>\
+<img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
+ } /* end i1 */
+ }/* End k1 */
+ fprintf(fichtm,"</ul>");
+ fflush(fichtm);
+}
+
+/******************* Gnuplot file **************/
+void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , 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;
+ int ng=0;
+/* if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
+/* printf("Problem with file %s",optionfilegnuplot); */
+/* fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
+/* } */
+
+ /*#ifdef windows */
+ fprintf(ficgp,"cd \"%s\" \n",pathc);
+ /*#endif */
+ m=pow(2,cptcoveff);
+
+ strcpy(dirfileres,optionfilefiname);
+ strcpy(optfileres,"vpl");
+ /* 1eme*/
+ fprintf(ficgp,"\n# 1st: Period (stable) prevalence with CI: 'vpl' files\n");
+ 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*/
+ fprintf(ficgp,"\n# 2nd: Total life expectancy with CI: 't' files\n");
+ 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+$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
+ for (j=1; j<= nlstate+1 ; j ++) {
+ if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
+ else fprintf(ficgp," \%%*lf (\%%*lf)");
+ }
+ if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l lt 0");
+ else fprintf(ficgp,"\" t\"\" w l lt 0,");
+ }
+ }
+
+ /*3eme*/
+
+ for (k1=1; k1<= m ; k1 ++) {
+ for (cpt=1; cpt<= nlstate ; cpt ++) {
+ /* k=2+nlstate*(2*cpt-2); */
+ k=2+(nlstate+1)*(cpt-1);
+ fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
+ fprintf(ficgp,"set ter png small size 320, 240\n\
+plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
+ /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%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 (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," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+nlstate,cpt);
+ }
+ }
+
+ /* CV preval stable (period) */
+ for (k1=1; k1<= m ; k1 ++) { /* For each multivariate if any */
+ for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
+ k=3;
+ fprintf(ficgp,"\n#\n#\n#CV preval stable (period): 'pij' files, cov=%d state=%d",k1, cpt);
+ 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] ", ageminpar, agemaxpar);
+ for (i=1; i<= nlstate ; i ++){
+ if(i==1)
+ fprintf(ficgp,"\"%s\"",subdirf2(fileres,"pij"));
+ else
+ fprintf(ficgp,", '' ");
+ l=(nlstate+ndeath)*(i-1)+1;
+ fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
+ for (j=1; j<= (nlstate-1) ; j ++)
+ fprintf(ficgp,"+$%d",k+l+j);
+ fprintf(ficgp,")) t \"prev(%d,%d)\" w l",i,cpt);
+ } /* nlstate */
+ fprintf(ficgp,"\n");
+ } /* end cpt state*/
+ } /* end covariate */
+
+ /* proba elementaires */
+ for(i=1,jk=1; i <=nlstate; i++){
+ for(k=1; k <=(nlstate+ndeath); k++){
+ if (k != i) {
+ for(j=1; j <=ncovmodel; j++){
+ fprintf(ficgp,"p%d=%f ",jk,p[jk]);
+ jk++;
+ fprintf(ficgp,"\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);
+} /* 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 */
+
+
+/************** 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){
+ /* 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;
+ double agec; /* generic age */
+ double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
+ double *popeffectif,*popcount;
+ double ***p3mat;
+ double ***mobaverage;
+ char fileresf[FILENAMELENGTH];
+
+ agelim=AGESUP;
+ prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
+
+ strcpy(fileresf,"f");
+ strcat(fileresf,fileres);
+ 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);
+
+ 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;}
+
+ 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 (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);
+ }
+ }/* 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(ficresf);
+}
+
+/************** 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;
+
+ prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
+
+
+ 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);
+
+ 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;
+
+ agelim=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<imx;i++) popeffectif[popage[i]]=popcount[i];
+ }
+
+ for(cptcov=1,k=0;cptcov<=i2;cptcov++){
+ for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
+ k=k+1;
+ fprintf(ficrespop,"\n#******");
+ for(j=1;j<=cptcoveff;j++) {
+ fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+ }
+ fprintf(ficrespop,"******\n");
+ fprintf(ficrespop,"# Age");
+ for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
+ if (popforecast==1) fprintf(ficrespop," [Population]");
+
+ for (cpt=0; cpt<=0;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(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 */
+
+int fileappend(FILE *fichier, char *optionfich)
+{
+ if((fichier=fopen(optionfich,"a"))==NULL) {
+ printf("Problem with file: %s\n", optionfich);
+ fprintf(ficlog,"Problem with file: %s\n", optionfich);
+ return (0);
+ }
+ fflush(fichier);
+ return (1);
+}
+
+
+/**************** function prwizard **********************/
+void prwizard(int ncovmodel, int nlstate, int ndeath, char model[], FILE *ficparo)
+{
+
+ /* 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;
+ int numlinepar;
+
+ printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
+ fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
+ for(i=1; i <=nlstate; i++){
+ jj=0;
+ for(j=1; j <=nlstate+ndeath; j++){
+ if(j==i) continue;
+ jj++;
+ /*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]); */
+ printf(" 0.");
+ fprintf(ficparo," 0.");
+ }
+ printf("\n");
+ fprintf(ficparo,"\n");
+ }
+ }
+ printf("# Scales (for hessian or gradient estimation)\n");
+ fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
+ npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
+ for(i=1; i <=nlstate; i++){
+ jj=0;
+ for(j=1; j <=nlstate+ndeath; j++){
+ if(j==i) continue;
+ jj++;
+ fprintf(ficparo,"%1d%1d",i,j);
+ printf("%1d%1d",i,j);
+ fflush(stdout);
+ for(k=1; k<=ncovmodel;k++){
+ /* printf(" %le",delti3[i][j][k]); */
+ /* fprintf(ficparo," %le",delti3[i][j][k]); */
+ printf(" 0.");
+ fprintf(ficparo," 0.");
+ }
+ numlinepar++;
+ printf("\n");
+ fprintf(ficparo,"\n");
+ }
+ }
+ printf("# Covariance matrix\n");
+/* # 121 Var(a12)\n\ */
+/* # 122 Cov(b12,a12) Var(b12)\n\ */
+/* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
+/* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
+/* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
+/* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
+/* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
+/* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
+ fflush(stdout);
+ fprintf(ficparo,"# 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" */
+
+ for(itimes=1;itimes<=2;itimes++){
+ jj=0;
+ for(i=1; i <=nlstate; i++){
+ for(j=1; j <=nlstate+ndeath; j++){
+ if(j==i) continue;
+ for(k=1; k<=ncovmodel;k++){
+ jj++;
+ ca[0]= k+'a'-1;ca[1]='\0';
+ if(itimes==1){
+ printf("#%1d%1d%d",i,j,k);
+ fprintf(ficparo,"#%1d%1d%d",i,j,k);
+ }else{
+ printf("%1d%1d%d",i,j,k);
+ fprintf(ficparo,"%1d%1d%d",i,j,k);
+ /* printf(" %.5le",matcov[i][j]); */
+ }
+ ll=0;
+ for(li=1;li <=nlstate; li++){
+ for(lj=1;lj <=nlstate+ndeath; lj++){
+ if(lj==li) continue;
+ for(lk=1;lk<=ncovmodel;lk++){
+ ll++;
+ if(ll<=jj){
+ cb[0]= lk +'a'-1;cb[1]='\0';
+ if(ll<jj){
+ if(itimes==1){
+ printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
+ fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
+ }else{
+ printf(" 0.");
+ fprintf(ficparo," 0.");
+ }
+ }else{
+ if(itimes==1){
+ printf(" Var(%s%1d%1d)",ca,i,j);
+ fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
+ }else{
+ printf(" 0.");
+ fprintf(ficparo," 0.");
+ }
+ }
+ }
+ } /* end lk */
+ } /* end lj */
+ } /* end li */
+ printf("\n");
+ fprintf(ficparo,"\n");
+ numlinepar++;
+ } /* end k*/
+ } /*end j */
+ } /* end i */
+ } /* end itimes */
+
+} /* end of prwizard */
+/******************* Gompertz Likelihood ******************************/
+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++) {
+ sump=sump+weight[i];
+ /* sump=sump+1;*/
+ num=num+1;
+ }
+
+
+ /* for (i=0; i<=imx; i++)
+ if (wav[i]>0) printf("i=%d ageex=%lf agecens=%lf agedc=%lf cens=%d %d\n" ,i,ageexmed[i],agecens[i],agedc[i],cens[i],wav[i]);*/
+
+ for (i=1;i<=imx ; i++)
+ {
+ if (cens[i] == 1 && wav[i]>1)
+ A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
+
+ if (cens[i] == 0 && wav[i]>1)
+ A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
+ +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);
+
+ /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
+ if (wav[i] > 1 ) { /* ??? */
+ L=L+A*weight[i];
+ /* printf("\ni=%d A=%f L=%lf x[1]=%lf x[2]=%lf ageex=%lf agecens=%lf cens=%d agedc=%lf weight=%lf\n",i,A,L,x[1],x[2],ageexmed[i]*12,agecens[i]*12,cens[i],agedc[i]*12,weight[i]);*/
+ }
+ }
+
+ /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
+
+ return -2*L*num/sump;
+}
+
+#ifdef GSL
+/******************* Gompertz_f Likelihood ******************************/
+double gompertz_f(const gsl_vector *v, void *params)
+{
+ double A,B,LL=0.0,sump=0.,num=0.;
+ double *x= (double *) v->data;
+ int i,n=0; /* n is the size of the sample */
+
+ for (i=0;i<=imx-1 ; i++) {
+ sump=sump+weight[i];
+ /* sump=sump+1;*/
+ num=num+1;
+ }
+
+
+ /* for (i=0; i<=imx; i++)
+ if (wav[i]>0) printf("i=%d ageex=%lf agecens=%lf agedc=%lf cens=%d %d\n" ,i,ageexmed[i],agecens[i],agedc[i],cens[i],wav[i]);*/
+ printf("x[0]=%lf x[1]=%lf\n",x[0],x[1]);
+ for (i=1;i<=imx ; i++)
+ {
+ if (cens[i] == 1 && wav[i]>1)
+ A=-x[0]/(x[1])*(exp(x[1]*(agecens[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)));
+
+ if (cens[i] == 0 && wav[i]>1)
+ A=-x[0]/(x[1])*(exp(x[1]*(agedc[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)))
+ +log(x[0]/YEARM)+x[1]*(agedc[i]-agegomp)+log(YEARM);
+
+ /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
+ if (wav[i] > 1 ) { /* ??? */
+ LL=LL+A*weight[i];
+ /* printf("\ni=%d A=%f L=%lf x[1]=%lf x[2]=%lf ageex=%lf agecens=%lf cens=%d agedc=%lf weight=%lf\n",i,A,L,x[1],x[2],ageexmed[i]*12,agecens[i]*12,cens[i],agedc[i]*12,weight[i]);*/
+ }
+ }
+
+ /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
+ printf("x[0]=%lf x[1]=%lf -2*LL*num/sump=%lf\n",x[0],x[1],-2*LL*num/sump);
+
+ return -2*LL*num/sump;
+}
+#endif
+
+/******************* Printing html file ***********/
+void printinghtmlmort(char fileres[], 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;
+
+ fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
+ fprintf(fichtm," mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
+ for (i=1;i<=2;i++)
+ fprintf(fichtm," p[%d] = %lf [%f ; %f]<br>\n",i,p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
+ fprintf(fichtm,"<br><br><img src=\"graphmort.png\">");
+ fprintf(fichtm,"</ul>");
+
+fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
+
+ fprintf(fichtm,"\nAge l<inf>x</inf> q<inf>x</inf> d(x,x+1) L<inf>x</inf> T<inf>x</inf> e<infx</inf><br>");
+
+ for (k=agegomp;k<(agemortsup-2);k++)
+ fprintf(fichtm,"%d %.0lf %lf %.0lf %.0lf %.0lf %lf<br>\n",k,lsurv[k],p[1]*exp(p[2]*(k-agegomp)),(p[1]*exp(p[2]*(k-agegomp)))*lsurv[k],lpop[k],tpop[k],tpop[k]/lsurv[k]);
+
+
+ fflush(fichtm);
+}
+
+/******************* Gnuplot file **************/
+void printinggnuplotmort(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
+
+ char dirfileres[132],optfileres[132];
+ int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
+ int ng;
+
+
+ /*#ifdef windows */
+ fprintf(ficgp,"cd \"%s\" \n",pathc);
+ /*#endif */
+
+
+ strcpy(dirfileres,optionfilefiname);
+ strcpy(optfileres,"vpl");
+ fprintf(ficgp,"set out \"graphmort.png\"\n ");
+ fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n ");
+ fprintf(ficgp, "set ter png small size 320, 240\n set log y\n");
+ /* fprintf(ficgp, "set size 0.65,0.65\n"); */
+ fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
+
+}
+
+int readdata(char datafile[], int firstobs, int lastobs, int *imax)
+{
+
+ /*-------- data file ----------*/
+ FILE *fic;
+ char dummy[]=" ";
+ int i, j, n;
+ int linei, month, year,iout;
+ char line[MAXLINE], linetmp[MAXLINE];
+ char stra[80], strb[80];
+ char *stratrunc;
+ int lstra;
+
+
+ if((fic=fopen(datafile,"r"))==NULL) {
+ printf("Problem while opening datafile: %s\n", datafile);return 1;
+ fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);return 1;
+ }
+
+ i=1;
+ linei=0;
+ while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
+ linei=linei+1;
+ for(j=strlen(line); j>=0;j--){ /* Untabifies line */
+ if(line[j] == '\t')
+ line[j] = ' ';
+ }
+ for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){
+ ;
+ };
+ line[j+1]=0; /* Trims blanks at end of line */
+ if(line[0]=='#'){
+ fprintf(ficlog,"Comment line\n%s\n",line);
+ printf("Comment line\n%s\n",line);
+ continue;
+ }
+ trimbb(linetmp,line); /* Trims multiple blanks in line */
+ for (j=0; line[j]!='\0';j++){
+ line[j]=linetmp[j];
+ }
+
+
+ for (j=maxwav;j>=1;j--){
+ cutv(stra, strb, line, ' ');
+ if(strb[0]=='.') { /* Missing status */
+ 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 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;
+
+ strcpy(line,stra);
+ cutv(stra, strb,line,' ');
+ if(iout=sscanf(strb,"%d/%d",&month, &year) != 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 interview (mm/yyyy or .) at wave %d. Exiting.\n",strb, linei,i, line,j);
+ fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of interview (mm/yyyy or .) at wave %d. Exiting.\n",strb, linei,i, line,j);fflush(ficlog);
+ return 1;
+ }
+ anint[j][i]= (double) year;
+ mint[j][i]= (double)month;
+ strcpy(line,stra);
+ } /* ENd Waves */
+
+ cutv(stra, strb,line,' ');
+ if(iout=sscanf(strb,"%d/%d",&month, &year) != 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;
+ }
+ andc[i]=(double) year;
+ moisdc[i]=(double) month;
+ strcpy(line,stra);
+
+ cutv(stra, strb,line,' ');
+ if(iout=sscanf(strb,"%d/%d",&month, &year) != 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;
+ }
+ 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;
+
+ }
+ annais[i]=(double)(year);
+ moisnais[i]=(double)(month);
+ strcpy(line,stra);
+
+ cutv(stra, strb,line,' ');
+ errno=0;
+ dval=strtod(strb,&endptr);
+ if( strb[0]=='\0' || (*endptr != '\0')){
+ printf("Error reading data around '%f' at line number %d, \"%s\" for individual %d\nShould be a weight. Exiting.\n",dval, i,line,linei);
+ fprintf(ficlog,"Error reading data around '%f' at line number %d, \"%s\" for individual %d\nShould be a weight. Exiting.\n",dval, i,line,linei);
+ fflush(ficlog);
+ return 1;
+ }
+ weight[i]=dval;
+ strcpy(line,stra);
+
+ for (j=ncovcol;j>=1;j--){
+ cutv(stra, strb,line,' ');
+ if(strb[0]=='.') { /* Missing status */
+ lval=-1;
+ }else{
+ errno=0;
+ lval=strtol(strb,&endptr,10);
+ if( strb[0]=='\0' || (*endptr != '\0')){
+ printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\nShould be a covariate value (=0 for the reference or 1 for alternative). Exiting.\n",lval, linei,i, line);
+ fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\nShould be a covariate value (=0 for the reference or 1 for alternative). Exiting.\n",lval, linei,i, line);fflush(ficlog);
+ 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;
+ }
+ covar[j][i]=(double)(lval);
+ 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);
+ }
+ else
+ num[i]=atol(stra);
+ /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
+ printf("%ld %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]), (mint[2][i]), (anint[2][i]), (s[2][i]), (mint[3][i]), (anint[3][i]), (s[3][i]), (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/
+
+ 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);
+
+
+
+}
+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 i, j, k, ks;
+ int i1, j1, k1, k2;
+ char modelsav[80];
+ char stra[80], strb[80], strc[80], strd[80],stre[80];
+
+ /*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);
+ return 1;
+ }
+ if (strstr(model,"v") !=0){
+ printf("Error. 'v' must be in upper case 'V' model=%s ",model);
+ 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 */
+
+ /*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);*/
+
+
+ return (0); /* with covar[new additional covariate if product] and Tage if age */
+ endread:
+ printf("Exiting decodemodel: ");
+ return (1);
+}
+
+calandcheckages(int imx, int maxwav, double *agemin, double *agemax, int *nberr, int *nbwarn )
+{
+ int i, m;
+
+ for (i=1; i<=imx; i++) {
+ for(m=2; (m<= maxwav); m++) {
+ if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
+ anint[m][i]=9999;
+ s[m][i]=-1;
+ }
+ if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>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;
+ }
+ 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 */
+ }
+ }
+ }
+
+ 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] >= nlstate+1) {
+ 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 ((int)andc[i]!=9999){
+ nbwarn++;
+ printf("Warning negative age at death: %ld line:%d\n",num[i],i);
+ fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
+ agev[m][i]=-1;
+ }
+ }
+ }
+ 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]);
+ if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
+ agev[m][i]=1;
+ else if(agev[m][i] < *agemin){
+ *agemin=agev[m][i];
+ printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], *agemin);
+ }
+ 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);*/
+ }
+ /*agev[m][i]=anint[m][i]-annais[i];*/
+ /* agev[m][i] = age[i]+2*m;*/
+ }
+ else { /* =9 */
+ agev[m][i]=1;
+ s[m][i]=-1;
+ }
+ }
+ else /*= 0 Unknown */
+ agev[m][i]=1;
+ }
+
+ }
+ for (i=1; i<=imx; i++) {
+ for(m=firstpass; (m<=lastpass); m++){
+ if (s[m][i] > (nlstate+ndeath)) {
+ *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;
+ }
+ }
+ }
+
+ /*for (i=1; i<=imx; i++){
+ for (m=firstpass; (m<lastpass); m++){
+ printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
+}
+
+}*/
+
+
+ printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
+ fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
+
+ return (0);
+ endread:
+ printf("Exiting calandcheckages: ");
+ return (1);
+}
+
+
+/***********************************************/
+/**************** Main Program *****************/
+/***********************************************/
+
+int main(int argc, char *argv[])
+{
+#ifdef GSL
+ const gsl_multimin_fminimizer_type *T;
+ size_t iteri = 0, it;
+ int rval = GSL_CONTINUE;
+ int status = GSL_SUCCESS;
+ 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 numlinepar=0; /* Current linenumber of parameter file */
+ int itimes;
+ int NDIM=2;
+ int vpopbased=0;
+
+ char ca[32], cb[32], cc[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 fret;
+ double **xi,tmp,delta;
+
+ double dum; /* Dummy variable */
+ double ***p3mat;
+ double ***mobaverage;
+ int *indx;
+ char line[MAXLINE], linepar[MAXLINE];
+ char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
+ char pathr[MAXLINE], pathimach[MAXLINE];
+ char **bp, *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 mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
+ int mobilav=0,popforecast=0;
+ int hstepm, nhstepm;
+ 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 ftolpl=FTOL;
+ double **prlim;
+ double ***param; /* Matrix of parameters */
+ double *p;
+ double **matcov; /* Matrix of covariance */
+ 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 **ximort;
+ char *alph[]={"a","a","b","c","d","e"}, str[4]="1234";
+ int *dcwave;
+
+ char z[1]="c", occ;
+
+ /*char *strt;*/
+ char strtend[80];
+
+ long total_usecs;
+
+/* setlocale (LC_ALL, ""); */
+/* bindtextdomain (PACKAGE, LOCALEDIR); */
+/* textdomain (PACKAGE); */
+/* setlocale (LC_CTYPE, ""); */
+/* setlocale (LC_MESSAGES, ""); */
+
+ /* gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
+ rstart_time = time(NULL);
+ /* (void) gettimeofday(&start_time,&tzp);*/
+ start_time = *localtime(&rstart_time);
+ curr_time=start_time;
+ /*tml = *localtime(&start_time.tm_sec);*/
+ /* strcpy(strstart,asctime(&tml)); */
+ strcpy(strstart,asctime(&start_time));
+
+/* printf("Localtime (at start)=%s",strstart); */
+/* 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.tm_sec = mktime(&tmg); */
+/* strt=asctime(&tmg); */
+/* printf("Time(after) =%s",strstart); */
+/* (void) time (&time_value);
+* printf("time=%d,t-=%d\n",time_value,time_value-86400);
+* tm = *localtime(&time_value);
+* strstart=asctime(&tm);
+* printf("tim_value=%d,asctime=%s\n",time_value,strstart);
+*/
+
+ nberr=0; /* Number of errors and warnings */
+ nbwarn=0;
+ getcwd(pathcd, size);
+
+ printf("\n%s\n%s",version,fullversion);
+ if(argc <=1){
+ printf("\nEnter the parameter file name: ");
+ fgets(pathr,FILENAMELENGTH,stdin);
+ i=strlen(pathr);
+ if(pathr[i-1]=='\n')
+ pathr[i-1]='\0';
+ i=strlen(pathr);
+ if(pathr[i-1]==' ') /* This may happen when dragging on oS/X! */
+ pathr[i-1]='\0';
+ 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);
+ strcpy (pathtot, val);
+ if(pathr[0] == '\0') break; /* Dirty */
+ }
+ }
+ else{
+ strcpy(pathtot,argv[1]);
+ }
+ /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
+ /*cygwin_split_path(pathtot,path,optionfile);
+ printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
+ /* cutv(path,optionfile,pathtot,'\\');*/
+
+ /* Split argv[0], imach program to get pathimach */
+ printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
+ split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
+ printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
+ /* strcpy(pathimach,argv[0]); */
+ /* 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);
+ chdir(path); /* Can be a relative path */
+ if(getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */
+ 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);
+ /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
+ /* fclose(ficlog); */
+/* exit(1); */
+ }
+/* if((imk=mkdir(optionfilefiname))<0){ */
+/* perror("mkdir"); */
+/* } */
+
+ /*-------- arguments in the command line --------*/
+
+ /* Log file */
+ strcat(filelog, optionfilefiname);
+ strcat(filelog,".log"); /* */
+ if((ficlog=fopen(filelog,"w"))==NULL) {
+ printf("Problem with logfile %s\n",filelog);
+ goto end;
+ }
+ fprintf(ficlog,"Log filename:%s\n",filelog);
+ fprintf(ficlog,"\n%s\n%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);
+
+ 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.tm_sec-start_time.tm_sec,tmpout)); */
+
+ /* */
+ strcpy(fileres,"r");
+ strcat(fileres, optionfilefiname);
+ strcat(fileres,".txt"); /* Other files have txt extension */
+
+ /*---------arguments file --------*/
+
+ if((ficpar=fopen(optionfile,"r"))==NULL) {
+ 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; */
+ exit(70);
+ }
+
+
+
+ strcpy(filereso,"o");
+ strcat(filereso,fileres);
+ 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);
+ fflush(ficlog);
+ goto end;
+ }
+
+ /* Reads comments: lines beginning with '#' */
+ numlinepar=0;
+ while((c=getc(ficpar))=='#' && c!= EOF){
+ ungetc(c,ficpar);
+ fgets(line, MAXLINE, ficpar);
+ numlinepar++;
+ fputs(line,stdout);
+ fputs(line,ficparo);
+ fputs(line,ficlog);
+ }
+ 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);
+ fflush(ficlog);
+ while((c=getc(ficpar))=='#' && c!= EOF){
+ ungetc(c,ficpar);
+ fgets(line, MAXLINE, ficpar);
+ numlinepar++;
+ fputs(line, stdout);
+ //puts(line);
+ fputs(line,ficparo);
+ fputs(line,ficlog);
+ }
+ ungetc(c,ficpar);
+
+
+ covar=matrix(0,NCOVMAX,1,n); /**< used in readdata */
+ 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*/
+ else
+ ncovmodel=2;
+ nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
+ 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){
+ printf("Too complex model for current IMaCh: npar=(nlstate+ndeath-1)*nlstate*ncovmodel=%d >= %d(MAXPARM) or nlstate=%d >= %d(NLSTATEMAX) or ndeath=%d >= %d(NDEATHMAX) or ncovmodel=(k+age+#of+signs)=%d(NCOVMAX) >= %d\n",npar, MAXPARM, nlstate, NLSTATEMAX, ndeath, NDEATHMAX, ncovmodel, NCOVMAX);
+ fprintf(ficlog,"Too complex model for current IMaCh: %d >=%d(MAXPARM) or %d >=%d(NLSTATEMAX) or %d >=%d(NDEATHMAX) or %d(NCOVMAX) >=%d\n",npar, MAXPARM, nlstate, NLSTATEMAX, ndeath, NDEATHMAX, ncovmodel, NCOVMAX);
+ fflush(stdout);
+ fclose (ficlog);
+ goto end;
+ }
+ delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
+ 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 */
+ prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
+ printf(" You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
+ fprintf(ficlog," You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
+ free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
+ fclose (ficparo);
+ fclose (ficlog);
+ goto end;
+ exit(0);
+ }
+ else if(mle==-3) {
+ prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
+ printf(" You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
+ fprintf(ficlog," You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
+ param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
+ matcov=matrix(1,npar,1,npar);
+ }
+ else{
+ /* Read guessed parameters */
+ /* Reads comments: lines beginning with '#' */
+ while((c=getc(ficpar))=='#' && c!= EOF){
+ ungetc(c,ficpar);
+ fgets(line, MAXLINE, ficpar);
+ numlinepar++;
+ fputs(line,stdout);
+ fputs(line,ficparo);
+ fputs(line,ficlog);
+ }
+ ungetc(c,ficpar);
+
+ param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
+ for(i=1; i <=nlstate; i++){
+ j=0;
+ for(jj=1; jj <=nlstate+ndeath; jj++){
+ if(jj==i) continue;
+ j++;
+ fscanf(ficpar,"%1d%1d",&i1,&j1);
+ if ((i1 != i) && (j1 != j)){
+ printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \
+It might be a problem of design; if ncovcol and the model are correct\n \
+run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1);
+ exit(1);
+ }
+ fprintf(ficparo,"%1d%1d",i1,j1);
+ if(mle==1)
+ printf("%1d%1d",i,j);
+ fprintf(ficlog,"%1d%1d",i,j);
+ for(k=1; k<=ncovmodel;k++){
+ fscanf(ficpar," %lf",¶m[i][j][k]);
+ if(mle==1){
+ printf(" %lf",param[i][j][k]);
+ fprintf(ficlog," %lf",param[i][j][k]);
+ }
+ else
+ fprintf(ficlog," %lf",param[i][j][k]);
+ fprintf(ficparo," %lf",param[i][j][k]);
+ }
+ fscanf(ficpar,"\n");
+ numlinepar++;
+ if(mle==1)
+ printf("\n");
+ fprintf(ficlog,"\n");
+ fprintf(ficparo,"\n");
+ }
+ }
+ fflush(ficlog);
+
+ /* Reads scales values */
+ p=param[1][1];
+
+ /* Reads comments: lines beginning with '#' */
+ while((c=getc(ficpar))=='#' && c!= EOF){
+ ungetc(c,ficpar);
+ fgets(line, MAXLINE, ficpar);
+ numlinepar++;
+ fputs(line,stdout);
+ fputs(line,ficparo);
+ fputs(line,ficlog);
+ }
+ ungetc(c,ficpar);
+
+ for(i=1; i <=nlstate; i++){
+ for(j=1; j <=nlstate+ndeath-1; j++){
+ fscanf(ficpar,"%1d%1d",&i1,&j1);
+ if ((i1-i)*(j1-j)!=0){
+ printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
+ exit(1);
+ }
+ printf("%1d%1d",i,j);
+ fprintf(ficparo,"%1d%1d",i1,j1);
+ fprintf(ficlog,"%1d%1d",i1,j1);
+ for(k=1; k<=ncovmodel;k++){
+ fscanf(ficpar,"%le",&delti3[i][j][k]);
+ printf(" %le",delti3[i][j][k]);
+ fprintf(ficparo," %le",delti3[i][j][k]);
+ fprintf(ficlog," %le",delti3[i][j][k]);
+ }
+ fscanf(ficpar,"\n");
+ numlinepar++;
+ printf("\n");
+ fprintf(ficparo,"\n");
+ fprintf(ficlog,"\n");
+ }
+ }
+ fflush(ficlog);
+
+ /* Reads covariance matrix */
+ delti=delti3[1][1];
+
+
+ /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
+
+ /* Reads comments: lines beginning with '#' */
+ while((c=getc(ficpar))=='#' && c!= EOF){
+ ungetc(c,ficpar);
+ fgets(line, MAXLINE, ficpar);
+ numlinepar++;
+ fputs(line,stdout);
+ fputs(line,ficparo);
+ fputs(line,ficlog);
+ }
+ ungetc(c,ficpar);
+
+ matcov=matrix(1,npar,1,npar);
+ for(i=1; i <=npar; i++)
+ for(j=1; j <=npar; j++) matcov[i][j]=0.;
+
+ for(i=1; i <=npar; i++){
+ fscanf(ficpar,"%s",str);
+ if(mle==1)
+ printf("%s",str);
+ fprintf(ficlog,"%s",str);
+ fprintf(ficparo,"%s",str);
+ for(j=1; j <=i; j++){
+ fscanf(ficpar," %le",&matcov[i][j]);
+ if(mle==1){
+ printf(" %.5le",matcov[i][j]);
+ }
+ fprintf(ficlog," %.5le",matcov[i][j]);
+ fprintf(ficparo," %.5le",matcov[i][j]);
+ }
+ fscanf(ficpar,"\n");
+ numlinepar++;
+ if(mle==1)
+ printf("\n");
+ fprintf(ficlog,"\n");
+ fprintf(ficparo,"\n");
+ }
+ for(i=1; i <=npar; i++)
+ for(j=i+1;j<=npar;j++)
+ matcov[i][j]=matcov[j][i];
+
+ if(mle==1)
+ printf("\n");
+ fprintf(ficlog,"\n");
+
+ fflush(ficlog);
+
+ /*-------- Rewriting parameter file ----------*/
+ strcpy(rfileres,"r"); /* "Rparameterfile */
+ strcat(rfileres,optionfilefiname); /* Parameter file first name*/
+ strcat(rfileres,"."); /* */
+ strcat(rfileres,optionfilext); /* Other files have txt extension */
+ if((ficres =fopen(rfileres,"w"))==NULL) {
+ printf("Problem writing new parameter file: %s\n", fileres);goto end;
+ fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
+ }
+ fprintf(ficres,"#%s\n",version);
+ } /* End of mle != -3 */
+
+
+ n= lastobs;
+ num=lvector(1,n);
+ moisnais=vector(1,n);
+ annais=vector(1,n);
+ moisdc=vector(1,n);
+ andc=vector(1,n);
+ agedc=vector(1,n);
+ cod=ivector(1,n);
+ weight=vector(1,n);
+ for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
+ mint=matrix(1,maxwav,1,n);
+ anint=matrix(1,maxwav,1,n);
+ s=imatrix(1,maxwav+1,1,n); /* s[i][j] health state for wave i and individual j */
+ tab=ivector(1,NCOVMAX);
+ ncodemax=ivector(1,NCOVMAX); /* Number of code per covariate; if 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
+ 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. */
+ /* 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.
+ */
+ /* 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
+ Tvar[3=V1*V4]=4+1 etc */
+ Tprod=ivector(1,NCOVMAX); /* Gives the position of a product */
+ /* 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)
+ */
+ 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
+ * For V3*V2 (in V2+V1+V1*V4+age*V3+V3*V2), V3*V2 position is 2nd.
+ * Tvard[k1=2][1]=3 (V3) Tvard[k1=2][2]=2(V2) */
+ Tage=ivector(1,NCOVMAX); /* Gives the covariate id of covariates associated with age: V2 + V1 + age*V4 + V3*age
+ 4 covariates (3 plus signs)
+ Tage[1=V3*age]= 4; Tage[2=age*V4] = 3
+ */
+
+ if(decodemodel(model, lastobs) == 1)
+ goto end;
+
+ if((double)(lastobs-imx)/(double)imx > 1.10){
+ nbwarn++;
+ printf("Warning: The value of parameter lastobs=%d is big compared to the \n effective number of cases imx=%d, please adjust, \n otherwise you are allocating more memory than necessary.\n",lastobs, imx);
+ fprintf(ficlog,"Warning: The value of parameter lastobs=%d is big compared to the \n effective number of cases imx=%d, please adjust, \n otherwise you are allocating more memory than necessary.\n",lastobs, imx);
+ }
+ /* if(mle==1){*/
+ if (weightopt != 1) { /* Maximisation without weights. We can have weights different from 1 but want no weight*/
+ for(i=1;i<=imx;i++) weight[i]=1.0; /* changed to imx */
+ }
+
+ /*-calculation of age at interview from date of interview and age at death -*/
+ agev=matrix(1,maxwav,1,imx);
+
+ if(calandcheckages(imx, maxwav, &agemin, &agemax, &nberr, &nbwarn) == 1)
+ goto end;
+
+
+ agegomp=(int)agemin;
+ free_vector(moisnais,1,n);
+ 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);
+ /* */
+
+ 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);
+
+ /* Concatenates waves */
+ concatwav(wav, dh, bh, mw, s, agedc, agev, firstpass, lastpass, imx, nlstate, stepm);
+ /* */
+
+ /* 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]; */
+
+ codtab=imatrix(1,100,1,10); /* codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) */
+ /*printf(" codtab[1,1],codtab[100,10]=%d,%d\n", codtab[1][1],codtab[100][10]);*/
+ h=0;
+
+
+ /*if (cptcovn > 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
+ *______________________________
+ * 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);*/
+
+ free_ivector(Ndum,-1,NCOVMAX);
+
+
+
+ /*------------ gnuplot -------------*/
+ strcpy(optionfilegnuplot,optionfilefiname);
+ if(mle==-3)
+ 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,"# %s\n", optionfilegnuplot);
+ //fprintf(ficgp,"set missing 'NaNq'\n");
+ fprintf(ficgp,"set datafile missing 'NaNq'\n");
+ }
+ /* fclose(ficgp);*/
+ /*--------- index.htm --------*/
+
+ strcpy(optionfilehtm,optionfilefiname); /* Main html file */
+ if(mle==-3)
+ strcat(optionfilehtm,"-mort");
+ strcat(optionfilehtm,".htm");
+ if((fichtm=fopen(optionfilehtm,"w"))==NULL) {
+ printf("Problem with %s \n",optionfilehtm);
+ exit(0);
+ }
+
+ strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
+ strcat(optionfilehtmcov,"-cov.htm");
+ if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL) {
+ printf("Problem with %s \n",optionfilehtmcov), exit(0);
+ }
+ else{
+ fprintf(fichtmcov,"<html><head>\n<title>IMaCh Cov %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
+<hr size=\"2\" color=\"#EC5E5E\"> \n\
+Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n",\
+ optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
+ }
+
+ fprintf(fichtm,"<html><head>\n<title>IMaCh %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
+<hr size=\"2\" color=\"#EC5E5E\"> \n\
+Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
+\n\
+<hr size=\"2\" color=\"#EC5E5E\">\
+ <ul><li><h4>Parameter files</h4>\n\
+ - Parameter file: <a href=\"%s.%s\">%s.%s</a><br>\n\
+ - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
+ - Log file of the run: <a href=\"%s\">%s</a><br>\n\
+ - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
+ - Date and time at start: %s</ul>\n",\
+ optionfilehtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
+ optionfilefiname,optionfilext,optionfilefiname,optionfilext,\
+ fileres,fileres,\
+ filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
+ fflush(fichtm);
+
+ strcpy(pathr,path);
+ strcat(pathr,optionfilefiname);
+ chdir(optionfilefiname); /* Move to directory named optionfile */
+
+ /* Calculates basic frequencies. Computes observed prevalence at single age
+ and prints on file fileres'p'. */
+ freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart);
+
+ fprintf(fichtm,"\n");
+ fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
+Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
+Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\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 */
+
+
+ /* 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*/
+
+ if (mle==-3){
+ ximort=matrix(1,NDIM,1,NDIM);
+/* 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++)
+ if (s[m][i]>nlstate) {
+ dcwave[i]=m;
+ /* printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
+ 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;
+ }else if (ageexmed[i]< 1)
+ cens[i]= -1;
+ if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
+ cens[i]=0 ;
+ }
+ else cens[i]=-1;
+ }
+
+ for (i=1;i<=NDIM;i++) {
+ for (j=1;j<=NDIM;j++)
+ ximort[i][j]=(i == j ? 1.0 : 0.0);
+ }
+
+ /*p[1]=0.0268; p[NDIM]=0.083;*/
+ /*printf("%lf %lf", p[1], p[2]);*/
+
+
+#ifdef GSL
+ printf("GSL optimization\n"); fprintf(ficlog,"Powell\n");
+#else
+ printf("Powell\n"); fprintf(ficlog,"Powell\n");
+#endif
+ strcpy(filerespow,"pow-mort");
+ strcat(filerespow,fileres);
+ 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");
+#else
+ fprintf(ficrespow,"# Powell\n# iter -2*LL");
+#endif
+ /* for (i=1;i<=nlstate;i++)
+ for(j=1;j<=nlstate+ndeath;j++)
+ if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
+ */
+ fprintf(ficrespow,"\n");
+#ifdef GSL
+ /* gsl starts here */
+ T = gsl_multimin_fminimizer_nmsimplex;
+ gsl_multimin_fminimizer *sfm = NULL;
+ gsl_vector *ss, *x;
+ gsl_multimin_function minex_func;
+
+ /* Initial vertex size vector */
+ ss = gsl_vector_alloc (NDIM);
+
+ if (ss == NULL){
+ GSL_ERROR_VAL ("failed to allocate space for ss", GSL_ENOMEM, 0);
+ }
+ /* Set all step sizes to 1 */
+ gsl_vector_set_all (ss, 0.001);
+
+ /* Starting point */
+
+ x = gsl_vector_alloc (NDIM);
+
+ if (x == NULL){
+ gsl_vector_free(ss);
+ GSL_ERROR_VAL ("failed to allocate space for x", GSL_ENOMEM, 0);
+ }
+
+ /* 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, p[1]);
+ gsl_vector_set(x, 1, p[2]);
+
+ minex_func.f = &gompertz_f;
+ minex_func.n = NDIM;
+ minex_func.params = (void *)&p; /* ??? */
+
+ sfm = gsl_multimin_fminimizer_alloc (T, NDIM);
+ gsl_multimin_fminimizer_set (sfm, &minex_func, x, ss);
+
+ printf("Iterations beginning .....\n\n");
+ printf("Iter. # Intercept Slope -Log Likelihood Simplex size\n");
+
+ iteri=0;
+ while (rval == GSL_CONTINUE){
+ iteri++;
+ status = gsl_multimin_fminimizer_iterate(sfm);
+
+ if (status) printf("error: %s\n", gsl_strerror (status));
+ fflush(0);
+
+ if (status)
+ break;
+
+ rval = gsl_multimin_test_size (gsl_multimin_fminimizer_size (sfm), 1e-6);
+ ssval = gsl_multimin_fminimizer_size (sfm);
+
+ if (rval == GSL_SUCCESS)
+ printf ("converged to a local maximum at\n");
+
+ printf("%5d ", iteri);
+ for (it = 0; it < NDIM; it++){
+ printf ("%10.5f ", gsl_vector_get (sfm->x, it));
+ }
+ printf("f() = %-10.5f ssize = %.7f\n", sfm->fval, ssval);
+ }
+
+ printf("\n\n Please note: Program should be run many times with varying starting points to detemine global maximum\n\n");
+
+ gsl_vector_free(x); /* initial values */
+ gsl_vector_free(ss); /* inital step size */
+ for (it=0; it<NDIM; it++){
+ p[it+1]=gsl_vector_get(sfm->x,it);
+ fprintf(ficrespow," %.12lf", p[it]);
+ }
+ gsl_multimin_fminimizer_free (sfm); /* p *(sfm.x.data) et p *(sfm.x.data+1) */
+#endif
+#ifdef POWELL
+ powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
+#endif
+ fclose(ficrespow);
+
+ hesscov(matcov, 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];
+
+ printf("\nCovariance matrix\n ");
+ for(i=1; i <=NDIM; i++) {
+ for(j=1;j<=NDIM;j++){
+ printf("%f ",matcov[i][j]);
+ }
+ printf("\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++)
+ printf("%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);
+ lsurv[agegomp]=100000;
+
+ for (k=agegomp;k<=AGESUP;k++) {
+ agemortsup=k;
+ if (p[1]*exp(p[2]*(k-agegomp))>1) break;
+ }
+
+ for (k=agegomp;k<agemortsup;k++)
+ lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
+
+ for (k=agegomp;k<agemortsup;k++){
+ lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
+ sumlpop=sumlpop+lpop[k];
+ }
+
+ tpop[agegomp]=sumlpop;
+ for (k=agegomp;k<(agemortsup-3);k++){
+ /* tpop[k+1]=2;*/
+ tpop[k+1]=tpop[k]-lpop[k];
+ }
+
+
+ printf("\nAge lx qx dx Lx Tx e(x)\n");
+ for (k=agegomp;k<(agemortsup-2);k++)
+ printf("%d %.0lf %lf %.0lf %.0lf %.0lf %lf\n",k,lsurv[k],p[1]*exp(p[2]*(k-agegomp)),(p[1]*exp(p[2]*(k-agegomp)))*lsurv[k],lpop[k],tpop[k],tpop[k]/lsurv[k]);
+
+
+ replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
+ printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
+
+ printinghtmlmort(fileres,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_ivector(cens,1,n);
+ free_vector(agecens,1,n);
+ free_ivector(dcwave,1,n);
+ free_matrix(ximort,1,NDIM,1,NDIM);
+#endif
+ } /* Endof if mle==-3 */
+
+ else{ /* For mle >=1 */
+ globpr=0;/* debug */
+ 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 */
+ likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
+ printf("Second 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");
+ if(mle>=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,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
+ printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
+ fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\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);
+ 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]);
+ jk++;
+ }
+ printf("\n");
+ fprintf(ficlog,"\n");
+ fprintf(ficres,"\n");
+ }
+ }
+ }
+ if(mle!=0){
+ /* Computing hessian and covariance matrix */
+ ftolhess=ftol; /* Usually correct */
+ hesscov(matcov, p, npar, delti, ftolhess, func);
+ }
+ 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");
+ for(i=1,jk=1; i <=nlstate; i++){
+ for(j=1; j <=nlstate+ndeath; j++){
+ if (j!=i) {
+ fprintf(ficres,"%1d%1d",i,j);
+ printf("%1d%1d",i,j);
+ fprintf(ficlog,"%1d%1d",i,j);
+ for(k=1; k<=ncovmodel;k++){
+ printf(" %.5e",delti[jk]);
+ fprintf(ficlog," %.5e",delti[jk]);
+ fprintf(ficres," %.5e",delti[jk]);
+ jk++;
+ }
+ printf("\n");
+ fprintf(ficlog,"\n");
+ fprintf(ficres,"\n");
+ }
+ }
+ }
+
+ 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)
+ 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\ */
+ /* # 122 Cov(b12,a12) Var(b12)\n\ */
+ /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
+ /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
+ /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
+ /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
+ /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
+ /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
+
+
+ /* Just to have a covariance matrix which will be more understandable
+ even is we still don't want to manage dictionary of variables
+ */
+ for(itimes=1;itimes<=2;itimes++){
+ jj=0;
+ for(i=1; i <=nlstate; i++){
+ for(j=1; j <=nlstate+ndeath; j++){
+ if(j==i) continue;
+ for(k=1; k<=ncovmodel;k++){
+ jj++;
+ ca[0]= k+'a'-1;ca[1]='\0';
+ if(itimes==1){
+ if(mle>=1)
+ printf("#%1d%1d%d",i,j,k);
+ fprintf(ficlog,"#%1d%1d%d",i,j,k);
+ fprintf(ficres,"#%1d%1d%d",i,j,k);
+ }else{
+ if(mle>=1)
+ printf("%1d%1d%d",i,j,k);
+ fprintf(ficlog,"%1d%1d%d",i,j,k);
+ fprintf(ficres,"%1d%1d%d",i,j,k);
+ }
+ ll=0;
+ for(li=1;li <=nlstate; li++){
+ for(lj=1;lj <=nlstate+ndeath; lj++){
+ if(lj==li) continue;
+ for(lk=1;lk<=ncovmodel;lk++){
+ ll++;
+ if(ll<=jj){
+ cb[0]= lk +'a'-1;cb[1]='\0';
+ if(ll<jj){
+ if(itimes==1){
+ if(mle>=1)
+ printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
+ fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
+ fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
+ }else{
+ if(mle>=1)
+ printf(" %.5e",matcov[jj][ll]);
+ fprintf(ficlog," %.5e",matcov[jj][ll]);
+ fprintf(ficres," %.5e",matcov[jj][ll]);
+ }
+ }else{
+ if(itimes==1){
+ if(mle>=1)
+ printf(" Var(%s%1d%1d)",ca,i,j);
+ fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
+ 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]);
+ }
+ }
+ }
+ } /* end lk */
+ } /* end lj */
+ } /* end li */
+ if(mle>=1)
+ printf("\n");
+ fprintf(ficlog,"\n");
+ fprintf(ficres,"\n");
+ numlinepar++;
+ } /* end k*/
+ } /*end j */
+ } /* end i */
+ } /* end itimes */
+
+ fflush(ficlog);
+ fflush(ficres);
+
+ 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 (estepm==0 || estepm < stepm) estepm=stepm;
+ if (fage <= 2) {
+ bage = ageminpar;
+ fage = agemaxpar;
+ }
+
+ 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);
+ }
+ 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);
+ }
+ 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);
+ }
+ 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.*/
+
+
+
+ /* 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);
+ 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);
+
+
+ /*--------------- Prevalence limit (period or stable prevalence) --------------*/
+#include "prevlim.h" /* Use ficrespl, ficlog */
+ fclose(ficrespl);
+
+#ifdef FREEEXIT2
+#include "freeexit2.h"
+#endif
+
+ /*------------- h Pij x at various ages ------------*/
+#include "hpijx.h"
+ fclose(ficrespij);
+
+ /*-------------- 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);
+ for(i=1;i<=AGESUP;i++)
+ for(j=1;j<=NCOVMAX;j++)
+ for(k=1;k<=NCOVMAX;k++)
+ probs[i][j][k]=0.;
+
+ /*---------- 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); */
+ /* } */
+ }
+
+
+ /* 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);
+ }
+ }
+
+
+ /*---------- Health expectancies, no variances ------------*/
+
+ strcpy(filerese,"e");
+ strcat(filerese,fileres);
+ 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");
+
+ 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);
+
+ free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
+ /*}*/
+ }
+ fclose(ficreseij);
+
+
+ /*---------- Health expectancies and variances ------------*/
+
+
+ strcpy(filerest,"t");
+ strcat(filerest,fileres);
+ 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);
+
+
+ strcpy(fileresstde,"stde");
+ strcat(fileresstde,fileres);
+ 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("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);
+
+ strcpy(filerescve,"cve");
+ strcat(filerescve,fileres);
+ 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("Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
+ fprintf(ficlog,"Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
+
+ strcpy(fileresv,"v");
+ strcat(fileresv,fileres);
+ 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);
+
+ /*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 */
+ cptcod= 0; /* To be deleted */
+ varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,vpopbased,mobilav, strstart); /* cptcod not initialized Intel */
+ 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];
+ }
+
+ 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);
+ /*}*/
+ }
+ free_vector(weight,1,n);
+ free_imatrix(Tvard,1,NCOVMAX,1,2);
+ free_imatrix(s,1,maxwav+1,1,n);
+ free_matrix(anint,1,maxwav,1,n);
+ free_matrix(mint,1,maxwav,1,n);
+ free_ivector(cod,1,n);
+ free_ivector(tab,1,NCOVMAX);
+ fclose(ficresstdeij);
+ fclose(ficrescveij);
+ 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:
+ 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);
+ 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);
+ }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);*/
+ 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(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,"<br>Local time at start %s<br>Local time at end %s<br>\n</body></html>",strstart, strtend);
+ fclose(fichtm);
+ fprintf(fichtmcov,"<br>Local time at start %s<br>Local time at end %s<br>\n</body></html>",strstart, strtend);
+ fclose(fichtmcov);
+ fclose(ficgp);
+ fclose(ficlog);
+ /*------ End -----------*/
+
+
+ printf("Before Current directory %s!\n",pathcd);
+ if(chdir(pathcd) != 0)
+ printf("Can't move to directory %s!\n",path);
+ if(getcwd(pathcd,MAXLINE) > 0)
+ printf("Current directory %s!\n",pathcd);
+ /*strcat(plotcmd,CHARSEPARATOR);*/
+ sprintf(plotcmd,"gnuplot");
+#ifdef _WIN32
+ sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
+#endif
+ if(!stat(plotcmd,&info)){
+ printf("Error or gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
+ if(!stat(getenv("GNUPLOTBIN"),&info)){
+ printf("Error or gnuplot program not found: '%s' Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);
+ }else
+ strcpy(pplotcmd,plotcmd);
+#ifdef __unix
+ strcpy(plotcmd,GNUPLOTPROGRAM);
+ if(!stat(plotcmd,&info)){
+ printf("Error gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
+ }else
+ strcpy(pplotcmd,plotcmd);
+#endif
+ }else
+ strcpy(pplotcmd,plotcmd);
+
+ sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
+ printf("Starting graphs with: '%s'\n",plotcmd);fflush(stdout);
+
+ if((outcmd=system(plotcmd)) != 0){
+ 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(" Successful, please wait...");
+ while (z[0] != 'q') {
+ /* chdir(path); */
+ 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') {
+#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:
+ while (z[0] != 'q') {
+ printf("\nType q for exiting: ");
+ scanf("%s",z);
+ }
+}
git://henry.ined.fr / .git / commitdiff