Brief Description:

The compositeLD package computes composite measures of Linkage
Disequilibrium, their variances and covariances, and statistical 
tests, for all pairs of alleles from two loci when linkage phase is
unkown.

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Installation procedures for compositeLD

Intallation procedures in this file are for setting up a 'local
library' for a user. If a large group of users plan to use the same
library, then install on a system-wide 'library' location designated
by a system administrator. 

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S-PLUS Installation

The compositeLD S-PLUS functions are written for S-PLUS version 7.0.6 

To install the software for local use in S-PLUS, move
compositeLD_x.y.z_S.tar.gz to your installation directory and follow
the series of commands:

1) gunzip compositeLD_x.y.z_S.tar.gz
2) tar -xvf compositeLD_x.y.z_S.tar
3) cd compositeLD
4) cd src
5) Splus CHAPTER -m
6) Splus make -f makefile.compLD

Note that the installation for S-PLUS 8 will be more like the R installation below.

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R Installation

The compositeLD package is not available for distribution through any
R websites. To install, downloading the README.compositeLD file with
compositeLD_x.y.z.tar.gz and execute the following command with the local
"INSTALL LIBRARY DIR PATH" correctly specified.

R CMD INSTALL -l /INSTALL LIBRARY DIR PATH/ compositeLD_x.y.z.tar.gz

Additional details on R may be found on the R project website 
(http://www.r-project.org).

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User Documenation:

There is a demo file located in the /compositeLD/demo/ directory that
shows a simple example for using compositeLD.  We warn that
compositeLD has computing limits (run-time and memory limits) for when
the number of alleles is high, which is roughly 10 alleles for each
locus.