R/qtl2 version 0.14

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Mar 9, 2018, 4:11:22 PM3/9/18

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I've just released a new version of R/qtl2 (ver 0.14). To update, use:

update.packages(ask=FALSE, repos="https://rqtl.org/qtl2cran")

Here are the main changes; nothing really big:

Added function clean_genoprob() which cleans genotype probabilities by setting small values to 0 and, for genotype columns where the maximum value is not large, setting all values to 0. This is intended to help with the problem of unstable estimates of genotype effects in scan1coef() and fit1() when there's a genotype that is largely absent.
Added function compare_maps() for comparing marker order between two marker maps.
Revised the order of arguments in reduce_markers() to match pick_marker_subset(), because I like the latter better. Removed the function pick_marker_subset() because it's identical to reduce_markers(). (Seriously, I implemented the same thing twice.)

plot_coef() now uses a named lodcolumn argument, if provided, to subset scan1_output, if that's provided.
In the documentation for scan1coef(), scan1blup(), and fit1(), revised the suggested contrasts for getting additive and dominance effects in an intercross.