Package: ldsep
Title: Linkage Disequilibrium Shrinkage Estimation for Polyploids
Version: 2.1.7
Authors@R: 
    person(given = "David",
           family = "Gerard",
           role = c("aut", "cre"),
           email = "gerard.1787@gmail.com",
           comment = c(ORCID = "0000-0001-9450-5023"))
Description: 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>.
License: GPL (>= 3)
BugReports: https://github.com/dcgerard/ldsep/issues
URL: https://dcgerard.github.io/ldsep/
Encoding: UTF-8
LazyData: true
Roxygen: list(markdown = TRUE)
LinkingTo: Rcpp, RcppArmadillo
Imports: Rcpp, foreach, doParallel, ashr, corrplot, lpSolve, abind,
        matrixStats
Suggests: testthat, covr, knitr, rmarkdown, updog (>= 2.0.2),
        VariantAnnotation
Depends: R (>= 2.10)
VignetteBuilder: knitr
Config/roxygen2/version: 8.1.0
Repository: https://dcgerard.r-universe.dev
Date/Publication: 2026-09-09 19:32:29 UTC
RemoteUrl: https://github.com/dcgerard/ldsep
RemoteRef: HEAD
RemoteSha: bbe3912cdc6defff4dd293553166360d2d068083
NeedsCompilation: yes
Packaged: 2026-10-09 10:56:12 UTC; root
Author: David Gerard [aut, cre] (ORCID:
    <https://orcid.org/0000-0001-9450-5023>)
Maintainer: David Gerard <gerard.1787@gmail.com>