Package: diemr
Title: Genome Polarization via Diagnostic Index Expectation
        Maximization
Version: 1.5.5
Authors@R: c(
    person(given = "Natalia",
           family = "Martinkova",
           role = c("aut", "cre"),
           email = "martinkova@ivb.cz",
           comment = c(ORCID = "0000-0003-4556-4363")),
    person(given = "Stuart",
           family = "Baird",
           role = c("aut"),
           email = "stuartj.e.baird@gmail.com",
           comment = c(ORCID = "0000-0002-7144-9919")))
Description: Implements a likelihood-based method for genome
        polarization, identifying which alleles of SNV markers belong
        to either side of a barrier to gene flow. The approach
        co-estimates individual assignment, barrier strength, and
        divergence between sides, with direct application to studies of
        hybridization. Includes VCF-to-diem conversion and input
        checks, support for mixed ploidy and parallelization, and tools
        for visualization and diagnostic outputs. Based on diagnostic
        index expectation maximization as described in Baird et al.
        (2023) <doi:10.1111/2041-210X.14010>.
BugReports: https://github.com/nmartinkova/diemr/issues
URL: https://nmartinkova.github.io/genome-polarisation/
License: GPL (>= 3)
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.3
Suggests: testthat (>= 3.0.0), knitr, rmarkdown
Config/testthat/edition: 3
Imports: zoo, vcfR, data.table, circlize
VignetteBuilder: knitr
Config/pak/sysreqs: libicu-dev
Repository: https://nmartinkova.r-universe.dev
Date/Publication: 2026-03-18 07:55:50 UTC
RemoteUrl: https://github.com/nmartinkova/diemr
RemoteRef: HEAD
RemoteSha: 8dc3459a8abcee31ea8e075f4962a9094d8203e8
NeedsCompilation: no
Packaged: 2026-10-14 07:26:00 UTC; root
Author: Natalia Martinkova [aut, cre] (ORCID:
    <https://orcid.org/0000-0003-4556-4363>),
  Stuart Baird [aut] (ORCID: <https://orcid.org/0000-0002-7144-9919>)
Maintainer: Natalia Martinkova <martinkova@ivb.cz>