Package: diemr 1.5.5

diemr: Genome Polarization via Diagnostic Index Expectation Maximization

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>.

Authors:Natalia Martinkova [aut, cre], Stuart Baird [aut]

diemr_1.5.5.tar.gz
diemr_1.5.5.zip(r-4.7-any)diemr_1.5.5.zip(r-4.6-any)diemr_1.5.5.zip(r-4.5-any)
diemr_1.5.5.tgz(r-4.6-any)diemr_1.5.5.tgz(r-4.5-any)
diemr_1.5.5.tar.gz(r-4.7-any)diemr_1.5.5.tar.gz(r-4.6-any)
diemr_1.5.5.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
diemr/json (API)

# Install 'diemr' in R:
install.packages('diemr', repos = c('https://nmartinkova.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/nmartinkova/diemr/issues

On CRAN:

Conda:

bioinformaticsdiemdiemrgenome-admixturegenome-polarisationgenome-polarizationgenomicshybridisationhybridizationpopulation-geneticspopulation-genomicsspeciation

5.02 score 1 scripts 576 downloads 15 exports 38 dependencies

Last updated from:8dc3459a8a. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-develOK151
source / vignettesOK257
linux-releaseOK139
macos-releaseOK198
macos-oldrelOK203
windows-develOK125
windows-releaseOK102
windows-oldrelOK72
wasm-releaseOK100

Exports:CheckDiemFormatdiememPolarisehybridIndeximportPolarizedpHetErrOnStateCountplotDeFinettiplotMarkerAxisplotPolarizedrank2mapreadIncludedSitessmoothPolarizedGenotypessStateCountvariantSitesvcf2diem

Dependencies:apecirclizecliclustercolorspacedata.tabledigestdplyrgenericsGlobalOptionsgluelatticelifecyclemagrittrMASSMatrixmemusemgcvnlmepermutepillarpinfsc50pkgconfigR6Rcpprlangshapestringistringrtibbletidyselectutf8vcfRvctrsveganviridisLitewithrzoo

diemr: Diagnostic index expectation maximisation in R
Quick start | Input data | Multiple compartments with different ploidies | Frequently asked questions
Rendered fromdiemr-diagnostic-index-expecation-maximisation-in-r.Rmdusingknitr::rmarkdown

Last update: 2025-09-11
Started: 2025-09-11

Importing data for genome polarisation
Quick start | Principle of conversion to diem format | Invariant sites and indels | Sites not informative for genome polarisation | Haploid data | Diploid data | Heterozygotes in DNA sequence alignments | Variant call format | Polyploid data
Rendered fromImporting-data-for-genome-polarisation.Rmdusingknitr::rmarkdown

Last update: 2025-09-11
Started: 2025-09-11

Understanding genome polarisation output files
Obligatory outputs | MarkerDiagnosticsWithOptimalPolarities | HIwithOptimalPolarities | I4withOptimalPolarities | Optional outputs | The user perspective | NullMarkerPolarities | MarkersWithChangedPolarities | MarkersWithChangedPolarities-(compartmentNumber) | MarkerDiagnostics(iteration)-(compartmentNumber) | Iteration-specific graphics | WarpSwitch files | Hybrid index files | The log file | References
Rendered fromUnderstanding-genome-polarisation-output-files.Rmdusingknitr::rmarkdown

Last update: 2025-09-11
Started: 2025-09-11