model = "s1pp" in flexdog. I was originally not constraining the levels of preferential pairing to be the same in both segregations of the same parent. This is now fixed. But the downside is that model = "s1pp" is now only supported for ploidy = 4 or ploidy = 6. This is because the optimization becomes more difficult for larger ploidy levels.I fixed some documentation. Perhaps the biggest error comes from this snippet from the original documentation of flexdog:
The value of
prop_misis a very intuitive measure for the quality of the SNP.prop_misis the posterior proportion of individuals mis-genotyped. So if you want only SNPS that accurately genotype, say, 95% of the individuals, you could discard all SNPs with aprop_misunder 0.95.
This now says
The value of prop_mis is a very intuitive measure for the quality of the SNP. prop_mis is the posterior proportion of individuals mis-genotyped. So if you want only SNPS that accurately genotype, say, 95% of the individuals, you could discard all SNPs with a prop_mis over 0.05.
I’ve now exported some C++ functions that I think are useful. You can call them in the usual way: http://r-pkgs.had.co.nz/src.html#cpp-import.
updog. The old version may be found in the updogAlpha package.flexdog.mupdog is now live. We provide no guarantees about mupdog’s performance.oracle_mis.rgeno.rflexdog.