NEWS.md

In ldsep: Linkage Disequilibrium Shrinkage Estimation for Polyploids

ldsep 2.1.5

• Bug fix: Use && instead of & in C++ source.

ldsep 2.1.4

• Use unnamed formula argument in aggregate() to account for change in R.

ldsep 2.1.2

• DOUBLE_EPS -> DOUBLE_EPSILON.
• Modified citation to point to Heredity.
• Adds notes about the necessity of using adaptive priors in ldfast().

ldsep 2.1.0

• Includes a win argument in ldfast(), which implements the moment-based LD correction along a sliding window.
• Fixes a bug where monomorphic SNPs were causing errors when type = "Dprime" was selected in ldfast(). Now we just return NA's for LD with monomorphic SNPs.
• Uses the complete reference of Gerard (2021) (doi:10.1111/1755-0998.13349)

ldsep 2.0.2

• Removes ldfast_old() and ldfast_calc(), which were not used in any exported functions, because these functions had memory issues, detected by valgrind.

ldsep 2.0.1

• Added ldfast(), a new LD estimation approach based on sample moments of marginal posterior genotype moments.
• Unlike ldest(), mldest(), and sldest(), the new approach implemented in ldfast() is scalable to genome-wide applications, as these new estimators can be calculated in linear time in the sample size.
• Citation of MLE approach points to MER article.

ldsep 1.1.0

• I have changed the terminology from "gametic LD" to "haplotypic" LD, and so all instances of "gametic" have changed to "haplotypic". A breaking change is that all options that were "gam" are now "hap".
• Fixed an issue where the title in plot.lddf() was being cut off.
• Added a reference to the preprint where the methodology is developed.
• Updated the vignette to also take a user through uploading a VCF file into R using the VariantAnnotation package. We also provided examples on formatting genotype likelihoods from updog and fitpoly.

ldsep 1.0.0

• Initial release of package.

ldsep documentation built on Oct. 19, 2022, 1:08 a.m.