Package: diemr
Title: Genome Polarization via Diagnostic Index Expectation
        Maximization
Version: 1.5.3
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
RoxygenNote: 7.3.3
Suggests: testthat (>= 3.0.0), knitr, rmarkdown
Config/testthat/edition: 3
Imports: zoo, vcfR, data.table, circlize
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2026-01-13 11:41:32 UTC; martinkova
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>
Repository: CRAN
Date/Publication: 2026-01-13 12:10:02 UTC
Built: R 4.5.2; ; 2026-03-04 03:57:21 UTC; windows
