Package: ldsep
Title: Linkage Disequilibrium Shrinkage Estimation for Polyploids
Version: 2.1.6
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)
RoxygenNote: 7.3.3
LinkingTo: Rcpp, RcppArmadillo
Imports: Rcpp, foreach, doParallel, ashr, corrplot, lpSolve, abind,
        modeest, matrixStats
Suggests: testthat, covr, knitr, rmarkdown, updog (>= 2.0.2),
        VariantAnnotation
Depends: R (>= 2.10)
VignetteBuilder: knitr
Repository: https://dcgerard.r-universe.dev
Date/Publication: 2025-09-18 16:41:12 UTC
RemoteUrl: https://github.com/dcgerard/ldsep
RemoteRef: HEAD
RemoteSha: 14b2be97c818bb6011cab98cf0b01000ed33bb41
NeedsCompilation: yes
Packaged: 2026-06-15 09:08:52 UTC; root
Author: David Gerard [aut, cre] (ORCID:
    <https://orcid.org/0000-0001-9450-5023>)
Maintainer: David Gerard <gerard.1787@gmail.com>