Revision history for the R/xoi package
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copyright (c) 1999-2011, Karl W Broman

    The R/xoi package is free software; you can redistribute it and/or
    modify it under the terms of the GNU General Public License,
    version 3, as published by the Free Software Foundation.
    
    This program is distributed in the hope that it will be useful,
    but without any warranty; without even the implied warranty of
    merchantability or fitness for a particular purpose.  See the GNU
    General Public License for more details.
    
    A copy of the GNU General Public License, version 3, is available
    at http://www.r-project.org/Licenses/GPL-3
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Version 0.58-2, 11/7/2001:

   Added NAMESPACE.

   Compressed bssbsb data.


Version 0.57-5, 7/28/2011:

   Added functions intensity() and coincidence(), plus internal
   functions get_n_xo and identify_xo, from Il youp Kwak


Version 0.56-4, 5/9/2011:

   Removed a few extraneous .'s from titles in help files


Version 0.56-3, 5/4/2010:

   Removed a few unused variables from C code.


Version 0.56-2, 4/11/2010:

   Revised chiasma() slightly, so that "Done!" is printed only if
   verbose=TRUE.


Version 0.56-1, 10/26/2009:

   Fixed a bug in find.breaks (changing call to locate.xo to
   locateXO). 

   Fixed links in help files.


Version 0.55-2, 6/2/2009:

   Added functions stahlLoglik and fitStahl, for calculating the log
   likelihood under the Stahl model and for obtaining MLEs and the log
   LR for testing p=0.

   Revised convertxoloc() so that the output is a data frame.


Version 0.54-1, 5/18/2009:

   In est.recrate, modified the default positions at which the
   recombination rate is calculated (that is, if the "pos" argument is
   not specified) so that calculations will be done at the marker
   positions and at a grid with 4 positions per Mbp. 

   Added a function recrate2scanone for converting est.recrate results
   for multiple chromosomes to the form of the output of scanone (from
   R/qtl), but I'll leave it undocumented for now.


Version 0.53-4, 4/28/2009:

   Changed the license to GPL-3.


Version 0.53-3, 4/28/2009:

   Commented out an empty example in a help file.


Version 0.53-2, 10/16/2008:

   Fixed a bug in fitGamma.


Version 0.53-1, 8/25/2008:

   Added a function est.recrate for obtaining a smoothed estimate of
   the recombination rate along a chromosome, using the cM and Mbp
   position of markers.


Version 0.52-8, 8/21/2008:

   Fixed a slight error in the help file for fitGamma.


Version 0.52-7, 10/9/2007:

   Fixed some slight problems in the help files.


Version 0.52-6, 9/20/2007:

    Changed my email address, etc., due to my move to UW-Madison


Version 0.52-5, 4/26/2007:

    Added a function joint.given.two for calculating the joint density
    of the crossover locations, given that there are two.

    Added a function est.coi, for estimating the three-point
    coincidence along a chromosome.


Version 0.51-3, 12/20/2006:

    Added function est.intensity and est.kfunc to estimate the
    intensity and K_inhom functions for an inhomogeneous point
    process.

    Revised most of the functions for calculating densities and
    such so that you may specify (via the argument "x") the
    exact values at which these functions are to be calculated.
    If x is unspecified, we calculate things at n equally spaced
    points between 0 and L.


Version 0.50-18, 12/18/2006:

    A newly created package.

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end of STATUS.txt