resolveChosenInds

Extracts the number of individuals encoded in the first line of a
diem-formatted genotype file and returns the corresponding index vector.
The first line contains one character per individual plus an initial label,
so the valid indices are <code>1:(nchar(line) - 1)</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

resolveChosenInds function

<dl><dt>file</dt>
<dd>Character path to a diem-formatted genotype file.</dd></dl>

Arguments

Resolve ChosenInds from a diem-formatted genotype file — resolveChosenInds

<dl>

<dt>file</dt>
<dd>Character path to a diem-formatted genotype file.</dd>

</dl>

resolveChosenInds: Resolve ChosenInds from a diem-formatted genotype file

Description

Usage

Value

Arguments