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
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
NeedsCompilation: yes
Packaged: 2025-09-18 16:42:02 UTC; dgerard
Author: David Gerard [aut, cre] (ORCID:
    <https://orcid.org/0000-0001-9450-5023>)
Maintainer: David Gerard <gerard.1787@gmail.com>
Repository: CRAN
Date/Publication: 2025-09-18 17:10:03 UTC
Built: R 4.4.3; x86_64-w64-mingw32; 2026-01-12 19:57:09 UTC; windows
Archs: x64
