--- imach/src/ChangeLog	2006/02/09 14:30:41	1.17
+++ imach/src/ChangeLog	2022/05/24 08:09:48	1.51
@@ -1,5 +1,614 @@
+2022-05-24  Nicolas Brouard   <brouard@ined.fr>
+
+	* imach.c (Module): Some attempts to find a bug of wrong estimates
+	of confidencce intervals with product in the equation modelC
+
+2022-05-15  Nicolas Brouard   <brouard@ined.fr>
+
+	* imach.c (Module):  Some minor improvements
+
+2022-04-13  Brouard Nicolas  <brouard@brouard.name>
+
+	* imach.c (Module): Adding link to text data files
+
+2022-04-11  Nicolas Brouard   <brouard@ined.fr>
+
+	* imach.c (Module): Error in rewriting the 'r' file with yearsfproj or yearsbproj fixed
+
+2022-04-05  Brouard Nicolas  <brouard@ined.fr>
+
+	* imach.c (Module): Fixed covariates (dummy or quantitative)
+	with missing values have never been allowed but are ERRORS and
+	program quits. Standard deviations of fixed covariates were
+	wrongly computed. Mean and standard deviations of time varying
+	covariates are still not computed.
+
+2022-03-17  Brouard Nicolas  <brouard@ined.fr>
+
+	* 99r25 Improvements in fixing discrepancies between covariates
+	missing in result line but in model. 
+
+*Wed Mar 31 2021  Nicolas Brouard   <brouard@ined.fr>
+	* imach.c (Module): Still bugs in the result loop. Thank to Holly Benett
+
+*2021-03-08  Nicolas Brouard   <brouard@ined.fr>
+
+	* ./ (Module): Fixed bug on result:
+
+*2021-02-20  Nicolas Brouard   <brouard@ined.fr>
+
+	* imach.c (Module): Fix bug on quitting after result lines!
+	(Module): Version 0.99r21
+
+2021-02-12  Nicolas Brouard   <brouard@ined.fr>
+
+	* imach.c (Module): The use of a Windows BOM (huge) file is now an error
+
+
+2021-02-11  Nicolas  Brouard   <brouard@ined.fr>
+
+	*  (Module): imach.c Someone entered 'results:' instead of 'result:'. Now it is an error which is printed.
+
+2020-02-22  Brouard Nicolas  <brouard@ined.fr>
+
+	*  (Module): imach.c Update mle=-3 (for computing Life expectancy
+	and life table from the data without any state)
+
+2019-05-20  Brouard Nicolas  <brouard@ined.fr>
+
+	* version.h: Summary: version 0.99.r19
+
+	* imach.c: Summary: Projection syntax simplified
+	We can now start projections, forward or backward, from the mean date
+	of inteviews up to or down to a number of years of projection:
+	prevforecast=1 yearsfproj=15.3 mobil_average=0
+	or
+	prevforecast=1 starting-proj-date=1/1/2007 final-proj-date=12/31/2017 mobil_average=0
+	or
+	prevbackcast=1 yearsbproj=12.3 mobil_average=1
+	or
+	prevbackcast=1 starting-back-date=1/10/1999 final-back-date=1/1/1985 mobil_average=1
+
+2019-05-18  Brouard Nicolas  <brouard@ined.fr>
+
+	* imach.c: Summary: doxygen tex bug
+
+2019-05-16  Brouard Nicolas  <brouard@ined.fr>
+
+	* imach.c: Summary: There was some wrong lines added
+
+2019-05-09  Brouard Nicolas  <brouard@ined.fr>
+
+	* Makefile, imach.c: *** empty log message ***
+
+	* ChangeLog: Summary: C=
+
+	* imach.c: Summary: Some updates
+
+	* imach.c: Summary: Before ncovmax
+
+	* version.h: *** empty log message ***
+
+	* imach.c: Summary: 0.99r18 unlimited number of individuals
+	The number n which was limited to 20,000 cases is now unlimited, from firstobs to lastobs. If the number is too for the virtual memory, probably an error will occur.
+
+2018-12-13  Brouard Nicolas  <brouard@ined.fr>
+
+	* imach.c: Summary: Bug for young ages (<-30) will be in r17
+
+2018-12-05  Brouard Nicolas  <brouard@ined.fr>
+
+	* Makefile: Summary: 0.99r16
+
+2018-05-02  Brouard Nicolas  <brouard@ined.fr>
+
+	* imach.c: Summary: Some bugs fixed
+
+2018-05-02  Brouard Nicolas  <brouard@ined.fr>
+
+	* imach.c:  Summary: Bug for young ages (<-30) will be in r17
+
+2018-05-02  Brouard Nicolas  <brouard@ined.fr>
+
+	* imach.c: Summary: Some bugs fixed
+
+2018-05-01  Brouard Nicolas  <brouard@ined.fr>
+
+	* imach.c:
+	Summary: Bug fixed by providing frequencies only for non missing covariates
+
+2018-04-27  Brouard Nicolas  <brouard@ined.fr>
+
+	* imach.c: Summary: some minor bugs
+
+2018-04-21  Brouard Nicolas  <brouard@ined.fr>
+
+	* README.txt: *** empty log message ***
+
+	* imach.c: Summary: Some bugs fixed, valgrind tested
+
+2018-04-20  Brouard Nicolas  <brouard@ined.fr>
+
+	* Makefile, README.txt, setup.iss: Summary: imach 0.99r16
+
+	* imach.c:
+	Summary: Computing mean and stdeviation of fixed quantitative variables
+
+2018-04-19  Brouard Nicolas  <brouard@ined.fr>
+
+	* imach.c: Summary: Some minor bugs fixed
+
+	* version.h: *** empty log message ***
+
+2018-02-27  Brouard Nicolas  <brouard@ined.fr>
+
+	* imach.c: *** empty log message ***
+
+	* imach.c: Summary: Adding second argument for quitting
+
+2018-02-21  Brouard Nicolas  <brouard@ined.fr>
+
+	* Makefile, README.txt, imach.c: Summary: 0.99r15
+	New Makefile with recent VirtualBox 5.26. Bug in sqrt negatve in imach.c
+
+2017-07-20  Brouard Nicolas  <brouard@ined.fr>
+
+	* imach.c: Summary: temporary working
+
+2017-07-19  Brouard Nicolas  <brouard@ined.fr>
+
+	* imach.c: Summary: Bug for mobil_average=0 and prevforecast fixed(?)
+
+2017-07-17  Brouard Nicolas  <brouard@ined.fr>
+
+	* imach.c: Summary: BOM files can be read now
+
+2017-06-30  Brouard Nicolas  <brouard@ined.fr>
+
+	* imach.c: Summary: Graphs improvements
+
+	* imach.c: Summary: Saito's color
+
+2017-06-29  Brouard Nicolas  <brouard@ined.fr>
+
+	* imach.c: Summary: Version 0.99r14
+
+2017-06-27  Brouard Nicolas  <brouard@ined.fr>
+
+	* imach.c: Summary: More documentation on projections
+
+	* imach.c: Summary: Color of backprojection changed from 6 to 5(yellow)
+
+	* imach.c: Summary: Some bug with rint
+
+2017-05-24  Brouard Nicolas  <brouard@ined.fr>
+
+	* imach.c: *** empty log message ***
+
+2017-05-23  Brouard Nicolas  <brouard@ined.fr>
+
+	* imach.c: Summary: Code into subroutine, cleanings
+
+2017-05-18  Brouard Nicolas  <brouard@ined.fr>
+
+	* imach.c:
+	Summary: backprojection and confidence intervals of backprevalence
+
+2017-05-13  Brouard Nicolas  <brouard@ined.fr>
+
+	* imach.c: Summary: temporary save for backprojection
+
+	* imach.c: Summary: Version 0.99r13 (improvements and bugs fixed)
+
+2017-04-26  Brouard Nicolas  <brouard@ined.fr>
+
+	* imach.c: Summary: imach 0.99r13 Some bugs fixed
+
+	* imach.c: Summary: Labels in graphs
+
+2017-04-24  Brouard Nicolas  <brouard@ined.fr>
+
+	* imach.c: Summary: to save
+
+2017-04-18  Brouard Nicolas  <brouard@ined.fr>
+
+	* imach.c: *** empty log message ***
+
+2017-04-05  Brouard Nicolas  <brouard@ined.fr>
+
+	* imach.c: Summary: Bug in E_ as well as in T_ fixed nres-1 vs k1-1
+
+2017-04-04  Brouard Nicolas  <brouard@ined.fr>
+
+	* imach.c: Summary: Gnuplot indexations fixed (humm)
+
+	* imach.c:
+	Summary: Some errors to warnings only if date of death is unknown but status is death we could set to pi3
+
+2017-04-03  Brouard Nicolas  <brouard@ined.fr>
+
+	* imach.c: Summary: Version 0.99r12
+	Some cleanings, conformed with updated documentation.
+
+2017-03-30  Brouard Nicolas  <brouard@ined.fr>
+
+	* version.h: *** empty log message ***
+
+	* version.h: Summary:0.99r11
+
+2017-03-29  Brouard Nicolas  <brouard@ined.fr>
+
+	* imach.c: Summary: Temp
+
+2017-03-27  Brouard Nicolas  <brouard@ined.fr>
+
+	* imach.c: Summary: Temporary
+
+2017-03-08  Brouard Nicolas  <brouard@ined.fr>
+
+	* imach.c: Summary: IMaCh version 0.99r10 bugs in gnuplot fixed
+
+	* imach.c: Summary: Fixing data parameter line
+
+2016-12-15  Brouard Nicolas  <brouard@ined.fr>
+
+	* imach.c: Summary: 0.99 in progress
+
+2016-09-15  Brouard Nicolas  <brouard@ined.fr>
+
+	* imach.c: *** empty log message ***
+
+	* imach.c: Summary: not working
+
+2016-09-08  Brouard Nicolas  <brouard@ined.fr>
+
+	* imach.c: Summary: continue
+
+2016-09-07  Brouard Nicolas  <brouard@ined.fr>
+
+	* imach.c: Summary: Starting values from frequencies
+
+	* imach.c: *** empty log message ***
+
+2016-09-02  Brouard Nicolas  <brouard@ined.fr>
+
+	* imach.c: *** empty log message ***
+
+2016-08-30  Brouard Nicolas  <brouard@ined.fr>
+
+	* imach.c: Summary: Fixing a lots
+
+2016-08-29  Brouard Nicolas  <brouard@ined.fr>
+
+	* imach.c: Summary: gnuplot problem in Back projection to fix
+
+	* imach.c: Summary: Better
+
+2016-08-26  Brouard Nicolas  <brouard@ined.fr>
+
+	* imach.c:
+	Summary: Improvement in Powell output in order to copy and paste
+
+	* imach.c: Summary: Starting tests of 0.99
+
+	* imach.c: Summary: to valgrind
+
+2016-08-25  Brouard Nicolas  <brouard@ined.fr>
+
+	* imach.c: *** empty log message ***
+
+2016-08-23  Brouard Nicolas  <brouard@ined.fr>
+
+	* imach.c: *** empty log message ***
+
+	* imach.c: Summary: not working
+
+2016-08-22  Brouard Nicolas  <brouard@ined.fr>
+
+	* imach.c: Summary: not working
+
+	* imach.c: Summary: Not working
+
+2016-07-23  Brouard Nicolas  <brouard@ined.fr>
+
+	* imach.c: Summary: Completing for func too
+
+2016-07-22  Brouard Nicolas  <brouard@ined.fr>
+
+	* imach.c: Summary: Fixing some arrays, still debugging
+
+2016-07-21  Brouard Nicolas  <brouard@ined.fr>
+
+	* imach.c:
+	Summary: 0.99 working (more or less) for Asian Workshop on multitate methods
+
+2016-07-12  Brouard Nicolas  <brouard@ined.fr>
+
+	* imach.c: Summary: temp
+
+	* imach.c: Summary: saving but not running
+
+2016-07-01  Brouard Nicolas  <brouard@ined.fr>
+
+	* imach.c: Summary: Fixes
+
+2016-02-19  Brouard Nicolas  <brouard@ined.fr>
+
+	* imach-0.98r.c: Summary: Kind of 0.98r? series, starting with r7
+
+	* setup.iss, Makefile, version.h: *** empty log message ***
+
+	* imach.c: Summary: temporary
+
+2016-02-17  Brouard Nicolas  <brouard@ined.fr>
+
+	* imach.c: Summary: Probably last 0.98 stable version 0.98r6
+
+2016-02-16  Brouard Nicolas  <brouard@ined.fr>
+
+	* imach.c: Summary: minor bug
+
+	* imach.c: Summary: 0.99r2
+
+2016-02-15  Brouard Nicolas  <brouard@ined.fr>
+
+	* imach.c: *** empty log message ***
+
+2016-02-12  Brouard Nicolas  <brouard@ined.fr>
+
+	* imach.c: Summary: 0.99 Back projections
+
+2015-12-23  Brouard Nicolas  <brouard@ined.fr>
+
+	* imach.c: Summary: Experimental backcast
+
+2015-12-18  Brouard Nicolas  <brouard@ined.fr>
+
+	* imach.c: Summary: 0.98r4 Warning and status=-2
+
+	Version 0.98r4 is now:
+	 - displaying an error when status is -1, date of interview unknown and date of death known;
+	 - permitting a status -2 when the vital status is unknown at a known date of right truncation.
+	Older changes concerning s=-2, dating from 2005 have been supersed.
+
+	* Makefile: *** empty log message ***
+
+2015-12-16  Brouard Nicolas  <brouard@ined.fr>
+
+	* Makefile: *** empty log message ***
+
+	* imach.c: Summary: 0.98r4 working
+
+	* Makefile: Summary: linuxrpm added
+
+	* Makefile: *** empty log message ***
+
+	* imach.c: Summary: temporary not working
+
+2015-12-11  Brouard Nicolas  <brouard@ined.fr>
+
+	* imach.c: Summary: 0.98r4
+
+2015-12-08  Brouard Nicolas  <brouard@ined.fr>
+
+	* Makefile: *** empty log message ***
+
+2015-11-21  Brouard Nicolas  <brouard@ined.fr>
+
+	* Makefile:
+	Summary: VBoxManage change from execute --image to run --exe and --wait-exit doesn't exist any more
+
+	* imach.c: Summary: minor typo
+
+	* imach.c: Summary: 0.98r3 with some graph of projected cross-sectional
+
+	Author: Nicolas Brouard
+
+2015-11-18  Brouard Nicolas  <brouard@ined.fr>
+
+	* imach.c: Summary: Start working on projected prevalences
+
+2015-11-17  Brouard Nicolas  <brouard@ined.fr>
+
+	* imach.c: Summary: Adding ftolpl parameter
+	Author: N Brouard
+
+	We had difficulties to get smoothed confidence intervals. It was due
+	to the period prevalence which wasn't computed accurately. The inner
+	parameter ftolpl is now an outer parameter of the .imach parameter
+	file after estepm. If ftolpl is small 1.e-4 and estepm too,
+	computation are long.
+
+	* version.h: *** empty log message ***
+
+	* imach.c: Summary: temporary
+
+2015-10-27  Brouard Nicolas  <brouard@ined.fr>
+
+	* Makefile: *** empty log message ***
+
+	* setup.iss.in: Summary: some new subdirs
+
+	* imach.c: *** empty log message ***
+
+	* setup.iss.in:
+	Summary: Adding gnuplot 5.1 with bin and etc for pango fonts
+
+2015-10-24  Brouard Nicolas  <brouard@ined.fr>
+
+	* imach.c: *** empty log message ***
+
+2015-10-23  Brouard Nicolas  <brouard@ined.fr>
+
+	* imach.c:
+	Summary: 0.98r3 some clarification for graphs on likelihood contributions
+
+2015-10-01  Brouard Nicolas  <brouard@ined.fr>
+
+	* imach.c: Summary: Some new graphs of contribution to likelihood
+
+2015-09-30  Brouard Nicolas  <brouard@ined.fr>
+
+	* Makefile:
+	Summary: Version read from version.h, itself read with cmake
+
+	* imach.c: Summary: looking at better estimation of the hessian
+
+	Also a better criteria for convergence to the period prevalence And
+	therefore adding the number of years needed to converge. (The
+	prevalence in any alive state shold sum to one
+
+	* Makefile: *** empty log message ***
+
+2015-09-22  Brouard Nicolas  <brouard@ined.fr>
+
+	* imach.c:
+	Summary: Adding some overall graph on contribution to likelihood. Might change
+
+2015-09-15  Brouard Nicolas  <brouard@ined.fr>
+
+	* Makefile: *** empty log message ***
+
+	* imach.c: Summary: 0.98r0
+
+	- Some new graphs like survival functions
+	- Some bugs fixed like model=1+age+V2.
+
+	* ChangeLog, Makefile: Summary: 0.98r0
+
+	* CMakeLists.txt: Summary: Some tests for setup.iss
+
+2015-09-15  Nicolas J Brouard   <nbrouard@tugault.ined.fr>
+
+	*  (Module): 0.98r0 Some new graphs, some bugs fixed: model=1+age+V2. etc
+
+2015-08-18  Nicolas J Brouard   <nbrouard@tugault.local>
+
+	*  (Module): Adding error when the covariance matrix doesn't contain the exact number of lines required by the model line.
+
+2015-08-03  Nicolas J Brouard   <nbrouard@tugault.ined.fr>
+
+	*  (Module): Changing Variance of one-step probabilities into Standard deviation (thanks to Yao-Chi Shih)
+
+2014-12-16  Nicolas J Brouard   <nbrouard@tugault.local>
+
+	* imach.c (Module): Merging 1.61 to 1.162
+
+2014-09-02  Nicolas J Brouard   <nbrouard@njbrouard.ined.fr>
+
+	* prevlim.h (Module): 
+
+2014-01-26  Nicolas J Brouard   <nbrouard@ledermann-2.local>
+
+	* 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.
+
+2010-04-29  brouard  <brouard@ined.fr>
+
+	* imach.c (Module): Checking covariates for more complex models
+	than V1+V2. A lot of change to be done. Unstable.
+
+2010-04-26  brouard  <brouard@ined.fr>
+
+	* imach.c (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.
+
+2009-10-29  brouard  <brouard@ined.fr>
+
+	* imach.c (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
+
+2006-06-30  Brouard Nicolas  <brouard@localhost>
+
+	* imach.c (Module): Clarifications on computing e.j
+
+2006-04-28  Brouard Nicolas  <brouard@localhost>
+
+	* imach.c (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.
+
+2006-04-04  LIEVRE Agnes  <lievre@PC_00697.ined.fr>
+
+	* imach.iss (Module): 
+
+	* imach.c (Module): bugs in evsi + population file added in htm output file
+
+2006-03-22  LIEVRE Agnes  <lievre@PC_00697.ined.fr>
+
+	* imach.c (Module): 
+
+2006-03-20  Brouard Nicolas  <brouard@localhost>
+
+	* imach.c (Module): <title> changed, corresponds to .htm file
+	name. <head> headers where missing.
+
+	* Makefile (Module): 0.98g
+
+	* 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
+
+2006-03-16  LIEVRE Agnes  <lievre@PC_00697.ined.fr>
+
+	* imach.c (Module): Comments concerning covariates added
+
+	* noreg-setup.iss (Module): Version 0.98f
+
+	* Makefile (Module): Version 0.98f make _windows=1 imachcyg-setup
+
+	* 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
+
+2006-03-15  Brouard Nicolas  <brouard@localhost>
+
+	* imach.c (Module): Bug if status = -2, the loglikelihood was
+	computed as likelihood omitting the logarithm. Version O.98e
+
+2006-03-14  Brouard Nicolas  <brouard@localhost>
+
+	* imach.c (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 
+
+2006-03-06  Brouard Nicolas  <brouard@localhost>
+
+	* imach.c (Module): Variance-covariance wrong links and
+	varian-covariance of ej. is needed (Saito).
+
+2006-02-27  Brouard Nicolas  <brouard@localhost>
+
+	* imach.c (Module): One freematrix added in mlikeli!
+
+2006-02-26  Brouard Nicolas  <brouard@localhost>
+
+	* imach.c (Module): Some improvements in processing parameter
+	filename with strsep.
+
+2006-02-24  Brouard Nicolas  <brouard@localhost>
+
+	* imach.c (Module): Memory leaks checks with valgrind and:
+	datafile was not closed, some imatrix were not freed and on matrix
+	allocation too.
+
 2006-02-09  LIEVRE Agnes  <lievre@PC_00697.ined.fr>
 
+	* strsep.c (Module): Inclusion because not in mingw32!!!
+
 	* setup.iss.in (Module): IMACHSETUPVERSION added
 
 	* noreg-setup.iss (Module): added to cvs tree
@@ -8,6 +617,8 @@
 
 2006-01-30  BROUARD Nicolas  <brouard@localhost>
 
+	* Makefile (Module, Module): Latest Makefile
+
 	* imach.c (Module): Back to gnuplot.exe instead of wgnuplot.exe
 
 2006-01-27  BROUARD Nicolas  <brouard@localhost>
@@ -137,32 +748,12 @@
 	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.
 
-
-
-
-
 2002-05-30    <brouard@BROUARD>
-
-
-
-
-
 	* 
-
-
-
-
-
 	* imach.c (Module): Add correlation matrix of one-step
-
-
 	probabilities and covariance matrix