resolveCompartments

Generates a list of logical vectors indicating which sites should be compartmentalized.
If <code>toBeCompartmentalized</code> is <code>"all"</code>, all sites are marked as <code>TRUE</code>. Otherwise, a logical vector
must be provided with a length matching the total number of sites.

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

resolveCompartments function

<dl><dt>files</dt>
<dd>Paths to diem input files.</dd>
<dt>toBeCompartmentalized</dt>
<dd>Either <code>"all"</code> or a logical vector specifying sites to compartmentalize.</dd>
<dt>compartmentSizes</dt>
<dd>Optional vector specifying the number of sites per file.</dd></dl>

Arguments

Resolve compartments for diem input files — resolveCompartments

<dl>

<dt>files</dt>
<dd>Paths to diem input files.</dd>


<dt>toBeCompartmentalized</dt>
<dd>Either <code>"all"</code> or a logical vector specifying sites to compartmentalize.</dd>


<dt>compartmentSizes</dt>
<dd>Optional vector specifying the number of sites per file.</dd>

</dl>

resolveCompartments: Resolve compartments for diem input files

Description

Usage

Value

Arguments