ldsep

Estimate haplotypic or composite pairwise linkage disequilibrium (LD) in polyploids, using either genotypes or genotype likelihoods. Support is provided to estimate the popular measures of LD: the LD coefficient D, the standardized LD coefficient D', and the Pearson correlation coefficient r. All estimates are returned with corresponding standard errors. These estimates and standard errors can then be used for shrinkage estimation. The main functions are ldfast(), ldest(), mldest(), sldest(), plot.lddf(), format_lddf(), and ldshrink(). Details of the methods are available in Gerard (2021a) doi:10.1111/1755-0998.13349 and Gerard (2021b) doi:10.1038/s41437-021-00462-5.

Last 30 days

This package has been downloaded 228 times in the last 30 days. More than a random curiosity, but not quite a blockbuster. Still, it's gaining traction! The following heatmap shows the distribution of downloads per day. Yesterday, it was downloaded 3 times.

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Last 365 days

This package has been downloaded 3,005 times in the last 365 days. That's enough downloads to impress a room full of undergrads. A commendable achievement indeed. The day with the most downloads was Jan 30, 2025 with 52 downloads.

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