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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.

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.