sImport

Reads a diem genotype file, splits character data into a matrix, and optionally subsets individuals.
Unknown genotypes (<code>U</code>) are converted to <code>_</code>.

internal

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>.

Natalia Martinkova

diemr

Genome Polarization via Diagnostic Index Expectation
Maximization

Stuart Baird

sImport function

<dl><dt>file</dt>
<dd>Path to the diem-formatted genotype file.</dd>
<dt>ChosenInds</dt>
<dd>A vector of individual indices to keep, or <code>"all"</code> to retain all individuals.</dd></dl>

Arguments

Import a single diem-formatted genotype file — sImport

<dl>

<dt>file</dt>
<dd>Path to the diem-formatted genotype file.</dd>


<dt>ChosenInds</dt>
<dd>A vector of individual indices to keep, or <code>"all"</code> to retain all individuals.</dd>

</dl>

sImport: Import a single diem-formatted genotype file

Description

Usage

Value

Arguments