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 methods are described in Gerard (2021) and Gerard (*in press*).

The main functions are:

`ldfast()`

: Fast, moment-based approach to estimate pairwise LD in the presence of genotype uncertainty.`ldest()`

: Estimates pairwise LD via maximum likelihood.`mldest()`

: Iteratively apply`ldest()`

across many pairs of SNPs.`sldest()`

: Iteratively apply`ldest()`

along a sliding window of fixed length.`plot.lddf()`

: Plot method for the output of`mldest()`

and`sldest()`

.`format_lddf()`

: Format the output of`mldest()`

and`sldest()`

into a matrix.`ldshrink()`

: Shrink correlation estimates using adaptive shrinkage (Stephens, 2017; Dey and Stephens, 2018).

You can install the released version of ldsep from CRAN with:

And the development version from GitHub with:

To cite `ldsep`

in publications use:

Gerard, David (2021). “Pairwise Linkage Disequilibrium Estimation for Polyploids.”

Molecular Ecology Resources,21(4), 1230–1242. doi:10.1111/1755-0998.13349.

A BibTeX entry for LaTeX users is

```
@Article{,
title = {Pairwise Linkage Disequilibrium Estimation for Polyploids},
author = {David Gerard},
journal = {Molecular Ecology Resources},
year = {2021},
doi = {10.1111/1755-0998.13349},
volume = {21},
number = {4},
pages = {1230--1242},
}
```

If you use `ldfast()`

, please cite:

Gerard, David (in press). “Scalable Bias-corrected Linkage Disequilibrium Estimation Under Genotype Uncertainty.”

Heredity. doi:10.1038/s41437-021-00462-5.

A BibTeX entry for LaTeX users is

```
@Article{,
title = {Scalable Bias-corrected Linkage Disequilibrium Estimation Under Genotype Uncertainty},
author = {David Gerard},
journal = {Heredity},
year = {in press},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41437-021-00462-5},
}
```

Please note that the ldsep project is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms.

Dey, Kushal K., and Matthew Stephens (2018). “CorShrink: Empirical Bayes shrinkage estimation of correlations, with applications.”

*bioRxiv*. doi:10.1101/368316Gerard, David (2021). “Pairwise Linkage Disequilibrium Estimation for Polyploids.”

*Molecular Ecology Resources*, 21(4), 1230–1242. doi:10.1111/1755-0998.13349.Gerard, David (in press). “Scalable Bias-corrected Linkage Disequilibrium Estimation Under Genotype Uncertainty.”

*Heredity*. doi:10.1038/s41437-021-00462-5.Stephens, Matthew (2017). “False discovery rates: a new deal.”

*Biostatistics*18(2), 275–294. doi:10.1093/biostatistics/kxw041