polyRAD v2.0

polyRAD 2.0.0 as it appears on CRAN. Multiploidy, i.e. ploidy varying among individuals, is now supported. There are a few other minor improvements (see NEWS.md). Although code will be backwards-compatible with previous versions of polyRAD, any RADdata objects saves as .rds or .RData will not be backwards-compatible.

polyRAD v1.6

polyRAD 1.6 as it appears on CRAN. This will probably be the last minor release before polyRAD 2.0.

Changes in v1.6

TestOverdispersion now prints a helpful suggestion for which overdispersion
parameter to use, as well as returning that value in its output.
The use of qqman has been eliminated from the vignettes.

ExpectedHindHe, ExpectedHindHeMapping, and SimAlleleDepth now have a contamRate
parameter to simulate sample cross contamination when sampling allelic read
depth, and an errorRate parameter to simulate sequencing error.

A bug has been fixed in Export_GWASpoly so that special characters in sample
names are not converted to periods.

polyRAD v1.5

polyRAD 1.5 as it appears on CRAN. SimGenotypesMapping, ExpectedHindHeMapping, Export_polymapR_probs, reverseComplement, and readDArTag functions have been added. Several bugs have been fixed, and a figure has been added to the vignettes to assist with estimating inbreeding.

polyRAD v1.4

polyRAD v1.4 as it appears on CRAN. This release was made primarily to resolve some dependency issues in the vignettes that were causing problems with CRAN checks. Additionally, Export_GWASpoly was modified to export continuous genotypes, and the Export_adegenet_genind function was added.

polyRAD v1.3

polyRAD 1.3 as it appears on CRAN. See NEWS page for new features and bug fixes.

polyRAD 1.2

polyRAD 1.2 as it appears on CRAN. See the NEWS file for a list of changes. Major improvements include the ability to export genotypes to VCF, introduction of the Hind/He statistic for evaluating marker quality, and Python scripts for variant calling in highly duplicated genomes.

polyRAD 1.1

polyRAD 1.1 as it appears on CRAN. With respect to version 1.0, a few utility functions have been added. There have also been some bug fixes and optimization.

polyRAD 1.0

polyRAD 1.0 as it appears on CRAN. The beta-binomial distribution is now used for estimating genotype likelihoods. RADdata objects are incompatible between v1.0 and v0.x due to the format of the depthSamplingPermutations slot changing. See the NEWS file for other updates.

polyRAD 0.5

polyRAD 0.5 as it appears on CRAN. With respect to version 0.4, the LocusInfo function has been added, and readStacks1 has been replaced with readStacks (for compatibility with Stacks 1 and 2).

polyRAD 0.4

With respect to version 0.3, version 0.4 introduces self-fertilization into the estimation of genotype prior probabilities for diversity panels. Documentation has also been cleaned up a bit.