--- imach/src/README.txt 2004/06/17 17:36:38 1.1 +++ imach/src/README.txt 2019/05/21 15:55:06 1.8 @@ -1,74 +1,119 @@ +Version IMaCh 0.99 +Parameter files have new undocumented parameters. +Look at the archives of imach-users@listes.ined.fr for information. + +Current documentation on the web site is for 0.98 (before the +introduction of varying covariates). + Interpolated Marlov Chain (IMaCh program) -This program is GPL licensed for the part the code that we wrote at -INED. But currently (version 0.97b may 2004) maximization routines use -a modified version of the patented routines from "Numerical Recipes in -C". If you have the right to use the sources of their software you can -get access to the source code and to the CVS tree of IMaCh. - -The program estimates Health Expectancies from Cross-longitudinal -studies. -The main publication is Lievre, A. Brouard. N, Heathcote -Ch. Estimating Health Expectancies from Corss-longitudinal surveys, -Mathematical Population Studies, 10(1), 2003, pp. 1-52. - -To be brief, for each people interviewed we have the age and health -states at each interview. Also the month of death is known. We model -the probability to be observed in any state at any age via a -parametric model and estimate the parameters and their confidence interval -by maximum likelihood, many tables and graphs are output in -HTML. Graphs are built using gnuplot. - -In the Windows version, gnuplot is also distributed. Version 4 is out -since early 2004 and is used by latest version of Imach (at least -version 0.38i is required). -IMaCh is supposed to work on Linux, MacIntosh and Windows (9X or -NT/XP). - -WINDOWS -On Windows it is distributed via a setup file (no more a zip file). As -usual you can put the 'imach' directory in Program Files or -wherever. The directory contains at least 2 directories, 'bin' for the -binaries which are imach.exe and gnuplot.exe, doc for some of the +This program is licensed under the GNU GNU GENERAL PUBLIC LICENSE. + +The program estimates Life Expectancies from Cross-longitudinal +studies as well as age-specific forward and backward prevalences in each state. +The main publications are: +(1) Lièvre, A. Brouard. N, Heathcote Ch. Estimating Health +Expectancies from Cross-longitudinal surveys, Mathematical Population Studies, 10(1), 2003, pp. 1-52. +(2) Nicolas Brouard, 2019, "Theory and applications of backward probabilities and prevalences in cross-longitudinal surveys". In: Arni S. R. Srinivasa Rao (Ed.) and C.R. Rao (Ed.), Handbook of Statistics. +Integrated population biology and modeling, Part B, Elsevier, p. 435-486. +http://hdl.handle.net/20.500.12204/AWltfxMuXMQCvuZmm9UI + +To be brief, for each people interviewed we need the age and +state at each interview. Also the month and year of death should be +known as for birth. We model the probability to be observed in any +state at any age via a parametric model and estimate the parameters +and their confidence interval by maximum likelihood. Many tables and +graphs are output in HTML. Graphs are built using gnuplot. + +First versions appeared around year 2000. Currently (May 2019) +version 0.99r19 can run on any Unix, including OS/X and on Windows 10 +(64bit) as well as Windows XP (32bit). + +Binaries are usually provided for OS/X (DMG for 64bit), Linux (rpm) +and Windows installer (32 and 64bit). + + +STRUCTURE of the binary + +IMaCh is a command line program (no time for a GUI) which means that +it can be run on a shell by "$ imach foo.imach" where foo.imach is your +'parameter' file which is a simple text file with a few lines that +your must edit in order to describe your data as well as your model +line. In this parameter file you give the name and path of your data +file which is also a text file. + +Even if it is command line program, most operating systems offer +simplifications of use: + +- On Windows, you can click on the imach.exe icon (which opens a DOS +window) and drag your parameter file into the DOS windows and enter +return. You can use the right click (once your mouse cursor is on an +foo.imach file) to either edit the parameter file (with notepad) or +execute this parameter file via imach. At the end of the run, your are +asked to enter a character and the terminal will not disappear. + +- On OSX, you can click on the IMaCh application and a terminal window will be + opened: either type in the name and path of your parameter file or + drag it from the finder. + +The output of your run consists in many text files which are grouped +into a sub-directory having the same name as of your parameter +filename 'foo'. In addition, you will find two other important files +on the same directory as your parameter file: + +-1- a text file named 'foo.gp' which is a gnuplot file. This gnuplot +is automatically runned by imach in order to create the graphs from +the various result text files. + +You can edit this gnuplot file, customize it at your will and run it +to get additional figures or modified figures to be published. Just +click on gnuplot executable and type "load foo.gp" for example. + +Gnuplot is a well known grapher under the GPL license too. As it is +changing often, the OS/X and Windows installers are providing binaries +for gnuplot 2.6.5. + +-2- a text file named 'foo.htm' which is an html file. It can be +opened by your browser and it will display various hyperlinks to most +of your results as well as your graphs. + + +Since the era of 64bit processors and their wide use on OS/X and +Windows 7, 8 or 10, we discovered that our usual GNU compiler were not +efficient on Windows 64 and current binaries are compiled with the +Intel C compiler. On OS/X the native LLVM C compiler from Apple is +very efficient too. + +Usually IMaCh binaries are distributed under two subdirectories, 'bin' for the +binaries which are imach.exe and gnuplot.exe and 'html' for some of the documentation, and 'mytry' in order to test the program on a parameter -file name 'mypar.imach'. +file named 'mypar.imach'. -You still can click on the imach.exe icon (which opens a DOS window) -and drag your parameter file into the DOS windows and enter -return. But with the newly installable version (>0.97) you can use the right -click (once your mouse cursor is on an foo.imach file) to either edit the -parameter file (with wordpad) or execute this parameter file via -imach. -If the program runs well you get a main foo.htm file which can be viewed -with your browser and which includes all the results. - -As the program output a file named foo.gp which is executed by gnuplot -in order to draw all the graphs, you can edit it and customize it at -your will. - -By default the file gnuplot.exe is located on the same directory as -imach and is used by imach with its absolute path. Thus if you have -another gnuplot program which is in your path it will not be used by +By default the file 'gnuplot.exe' is located on the same directory as +imach and is used by imach with its absolute path. Thus, if you have +another gnuplot program which is already in your path it will not be used by imach (we tried to simplify the installation process). -If you download a newer version of IMaCh you are supposed to Uninstall the +If you download a newer version of IMaCh, you are supposed to Uninstall the former version with the standard Install/Uninstall process of Windows. -The Windows version is compiled via cygwin (gcc -mno-cygwin -o imach -imach.c). It can be used on a command line with the command "imach -foo.imach". But then imach.exe must be in your path. -The program can be used (with more comfort?) on Linux or on a -MacIntosh. - Enjoy (?) using IMaCh. You may subscribe to imach-users@listes.ined.fr by sending a mail at imach-users-subscribe@listes.ined.fr and you can unsubscribe with a mail to imach-users-unsubscribe@listes.ined.fr . +Other comments are included on the Wiki server +http://euroreves.ined.fr/imach/wiki, please use it ask questions too. + Nicolas Brouard (brouard at ined point fr) -Agnès Lièvre (lievre chez ined dot fr) -Christopher Heathcote +Institut national d'études démographiques +133 Boulevard Davout +75014 Paris + +Earlier versions were also written by +Agnès Lièvre (former PHD student at INED) +Christopher Heathcote (ANU)