R/qtl version 1.17-39

[Karl Broman]

A new version of R/qtl (1.17-39) has been released at its web site
(http://www.rqtl.org). It should be on CRAN within a couple of days.

See http://www.rqtl.org/STATUS.txt for a list of changes. The major
changes are below.

Karl Broman
kbr...@biostat.wisc.edu

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Version 1.17, 7/28/2010:

Major changes:

Implemented the fit of models for binary traits in fitqtl(), by
Haley-Knott regression and multiple imputation. This model can also
be used in refineqtl, scanqtl, addqtl, addpair, addint, stepwiseqtl,
and addcovarint.

Implemented Haley-Knott regression for binary traits in scanone and
scantwo.

In mqmscan(), replaced the arguments step.min and step.max with
a single argument, off.end (to be more like scanone).

Added functions for the joint analysis of multiple crosses, in order
to map QTL to a phylogenetic tree. (A paper describing the methods
is in preparation.) The key function is scanPhyloQTL. simPhyloQTL
is used to simulate data. plot.scanPhyloQTL, max.scanPhyloQTL, and
summary.scanPhyloQTL are the plot, max, and summary functions for
the output from scanPhyloQTL.