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Annotation of imach/src/README.txt, revision 1.8

1.7       brouard     1: Version IMaCh 0.99
1.5       brouard     2: Parameter files have new undocumented parameters.
                      3: Look at the archives of imach-users@listes.ined.fr for information.
                      4: 
                      5: Current documentation on the web site is for 0.98 (before the
                      6: introduction of varying covariates).
                      7: 
1.1       brouard     8: Interpolated Marlov Chain (IMaCh program)
                      9: 
1.8     ! brouard    10: This program is licensed under the GNU GNU GENERAL PUBLIC LICENSE.
1.1       brouard    11: 
1.8     ! brouard    12: The program estimates Life Expectancies from Cross-longitudinal
        !            13: studies as well as age-specific forward and backward prevalences in each state.
        !            14: The main publications are:
        !            15: (1) Lièvre, A. Brouard. N, Heathcote Ch. Estimating Health
        !            16: Expectancies from Cross-longitudinal surveys, Mathematical Population Studies, 10(1), 2003, pp. 1-52.
        !            17: (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.
        !            18: Integrated population biology and modeling, Part B, Elsevier, p. 435-486.
        !            19: http://hdl.handle.net/20.500.12204/AWltfxMuXMQCvuZmm9UI
1.1       brouard    20: 
1.8     ! brouard    21: To be brief, for each people interviewed we need the age and 
        !            22: state at each interview. Also the month and year of death should be
1.2       brouard    23: known as for birth.  We model the probability to be observed in any
                     24: state at any age via a parametric model and estimate the parameters
                     25: and their confidence interval by maximum likelihood. Many tables and
                     26: graphs are output in HTML. Graphs are built using gnuplot.
                     27: 
1.8     ! brouard    28: First versions appeared around year 2000. Currently (May 2019)
        !            29: version 0.99r19 can run on any Unix, including OS/X and on Windows 10
1.4       brouard    30: (64bit) as well as Windows XP (32bit).
                     31: 
                     32: Binaries are usually provided for OS/X (DMG for 64bit), Linux (rpm)
                     33: and Windows installer (32 and 64bit).
                     34: 
                     35: 
                     36: STRUCTURE of the binary
                     37: 
                     38: IMaCh is a command line program (no time for a GUI) which means that
1.8     ! brouard    39: it can be run on a shell by "$ imach foo.imach" where foo.imach is your
1.4       brouard    40: 'parameter' file which is a simple text file with a few lines that
                     41: your must edit in order to describe your data as well as your model
                     42: line. In this parameter file you give the name and path of your data
                     43: file which is also a text file.
                     44: 
                     45: Even if it is command line program, most operating systems offer
                     46: simplifications of use:
                     47: 
1.6       brouard    48: - On Windows, you can click on the imach.exe icon (which opens a DOS
                     49: window) and drag your parameter file into the DOS windows and enter
                     50: return. You can use the right click (once your mouse cursor is on an
                     51: foo.imach file) to either edit the parameter file (with notepad) or
1.4       brouard    52: execute this parameter file via imach. At the end of the run, your are
                     53: asked to enter a character and the terminal will not disappear.
                     54: 
1.6       brouard    55: - On OSX, you can click on the IMaCh application and a terminal window will be
                     56:   opened: either type in the name and path of your parameter file or
1.4       brouard    57:   drag it from the finder.
                     58: 
1.6       brouard    59: The output of your run consists in many text files which are grouped
                     60: into a sub-directory having the same name as of your parameter
                     61: filename 'foo'. In addition, you will find two other important files
                     62: on the same directory as your parameter file:
                     63: 
                     64: -1- a text file named 'foo.gp' which is a gnuplot file. This gnuplot
                     65: is automatically runned by imach in order to create the graphs from
                     66: the various result text files.
                     67: 
                     68: You can edit this gnuplot file, customize it at your will and run it
                     69: to get additional figures or modified figures to be published. Just
                     70: click on gnuplot executable and type "load foo.gp" for example.
1.4       brouard    71: 
                     72: Gnuplot is a well known grapher under the GPL license too. As it is
                     73: changing often, the OS/X and Windows installers are providing binaries
                     74: for gnuplot 2.6.5.
                     75: 
1.6       brouard    76: -2- a text file named 'foo.htm' which is an html file. It can be
                     77: opened by your browser and it will display various hyperlinks to most
                     78: of your results as well as your graphs.
                     79: 
                     80: 
1.4       brouard    81: Since the era of 64bit processors and their wide use on OS/X and
                     82: Windows 7, 8 or 10, we discovered that our usual GNU compiler were not
                     83: efficient on Windows 64 and current binaries are compiled with the
                     84: Intel C compiler.  On OS/X the native LLVM C compiler from Apple is
                     85: very efficient too.
                     86: 
                     87: Usually IMaCh binaries are distributed under two subdirectories, 'bin' for the
                     88: binaries which are imach.exe and gnuplot.exe and 'html' for some of the
1.1       brouard    89: documentation, and 'mytry' in order to test the program on a parameter
1.4       brouard    90: file named 'mypar.imach'.
1.3       lievre     91: 
                     92: By default the file 'gnuplot.exe' is located on the same directory as
                     93: imach and is used by imach with its absolute path. Thus, if you have
                     94: another gnuplot program which is already in your path it will not be used by
1.1       brouard    95: imach (we tried to simplify the installation process).
                     96: 
1.3       lievre     97: If you download a newer version of IMaCh, you are supposed to Uninstall the
1.1       brouard    98: former version with the standard Install/Uninstall process of Windows.
                     99: 
                    100: Enjoy (?) using IMaCh.
                    101: 
                    102: You may subscribe to imach-users@listes.ined.fr by sending a mail at
                    103: imach-users-subscribe@listes.ined.fr and you can unsubscribe with a
                    104: mail to imach-users-unsubscribe@listes.ined.fr .
                    105: 
1.2       brouard   106: Other comments are included on the Wiki server
                    107: http://euroreves.ined.fr/imach/wiki, please use it ask questions too.
                    108: 
1.1       brouard   109: Nicolas Brouard (brouard at ined point fr)
1.4       brouard   110: Institut national d'études démographiques
                    111: 133 Boulevard Davout
                    112: 75014 Paris
                    113: 
                    114: Earlier versions were also written by 
                    115: Agnès Lièvre (former PHD student at INED)
                    116: Christopher Heathcote (ANU)
1.1       brouard   117: 
                    118:  
                    119: