polyRAD - 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.

- HTML
Published by lvclark over 3 years ago

polyRAD - 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.

- HTML
Published by lvclark about 4 years ago

polyRAD - polyRAD v1.5

polyRAD 1.5 as it appears on CRAN. SimGenotypesMapping, ExpectedHindHeMapping, ExportpolymapRprobs, 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.

- HTML
Published by lvclark over 4 years ago

polyRAD - 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.

- HTML
Published by lvclark almost 5 years ago

polyRAD - polyRAD v1.3

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

- HTML
Published by lvclark about 5 years ago

polyRAD - 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.

- HTML
Published by lvclark almost 6 years ago

polyRAD - 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.

- HTML
Published by lvclark over 6 years ago

polyRAD - 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.

- HTML
Published by lvclark over 7 years ago

polyRAD - 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).

- HTML
Published by lvclark over 7 years ago

polyRAD - 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.

- HTML
Published by lvclark over 7 years ago

polyRAD - polyRAD 0.3-1

With respect to version 0.3, 0.3-1 has several bug fixes pertaining to data import, especially from VCF files.

- HTML
Published by lvclark almost 8 years ago

polyRAD - polyRAD 0.3

Updates since version 0.2 include:

• Linked markers can now be used for updating genotype priors.
• Improvements have been made in estimation of parental genotypes for estimation of genotype priors in mapping populations.
• Several new utility functions have been added.

- HTML
Published by lvclark almost 8 years ago

polyRAD - polyRAD 0.2

This version includes new functions for subsetting RADdata objects and exporting genotypes to TASSEL. There are also bug fixes for importing from VCF. The package is ready to use, although more features will be added in the coming months.

- HTML
Published by lvclark about 8 years ago

polyRAD - polyRAD 0.1

This is the first release to include pipelines for diversity panels, as well as a variety of import and export functions. It is ready to be used, although more features will be added in the future.

- HTML
Published by lvclark about 8 years ago

polyRAD - polyRAD 0.0

This is a first prototype version of polyRAD, with functions for estimating genotype probabilities in mapping populations.

- HTML
Published by lvclark over 8 years ago