HaploDiploidEquilibrium

0.1.0

Calculate F Statistics Using Mixed Haploid and Diploid Organism Data

0packages depend

866downloads / year

–test coverage

13/13checks pass

Overview

About

Maintained by Francisco Pina-MartinsFirst published 2026-02-251 releasesCRAN page ↗

Provides functions to estimate population genetics summary statistics from haplo-diploid systems, where one sex is haploid and the other diploid (e.g. Hymenoptera insects). It implements a theoretical model assuming equal sex ratio, random mating, no selection, no mutation, and no gene flow, deriving expected genotype frequencies for both sexes under these equilibrium conditions. The package includes windowed calculations (operating over genomic sliding windows from VCF input) for allele and genotype frequencies, the inbreeding coefficient (Fis), pairwise Fst, Nei's H (gene diversity), Watterson's Theta, and sex-specific reference allele frequencies. Most statistics are agnostic to ploidy, allowing the package to be applied to both strictly haplo-diploid and fully diploid systems.

Install

R (CRAN)Ubuntu (r2u)Fedora (COPR)

install.packages("HaploDiploidEquilibrium")

Installs the current CRAN release. Prebuilt binaries on Windows and macOS.

Release

# one-time r2u setup for Ubuntu (noble)

curl -fsSL https://raw.githubusercontent.com/eddelbuettel/r2u/master/inst/scripts/add_cranapt_noble.sh | sudo bash

# then install

sudo apt install r-cran-haplodiploidequilibrium

Fast Ubuntu binaries via r2u (no compilation). Run the setup once per machine.

bspm (used by r2u) also needs make: sudo apt install make

sudo dnf copr enable iucar/cran

sudo dnf install R-CRAN-HaploDiploidEquilibrium

RPMs from the iucar/cran COPR, rebuilt from CRAN.

Health

CRAN checks

13OK

Code health

None

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

None

Vignettes

Yes

README

Dependencies · direct

Check history

OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Downloads

866

CRAN downloads in the past year

Rank #23,198 · ~2/day · ~72/mo

HaploDiploidEquilibrium Releases R versions

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20430 days

48690 days

8661 year

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Also on28 r2u

Source & community

Repository stars, issues, and contributor activity are not tracked yet.

Dependencies

Declared dependencies

4 external dependencies (excludes base and recommended)

Depends (1)

R >= 4.1.0

Imports (4)

dplyr vcfR data.table matrixStats

LinkingTo (0)

none

Suggests (0)

none

Enhances (0)

none

Reverse dependencies

0direct

–indirect (not tracked)

Nothing depends on this yet.

Code & Tests

Code Composition

R 1,202 (62%)Rd 743 (38%)

Test coverage

Line coverage

–

Expression

–

Tests / Examples

–

Functions

10 10 exported

Complexity

3.9 avg / 7 max

Call network

10 nodes / 0 edges

Test coverage has not been measured for this package yet; nodes fall back to a neutral fill.

Call graph

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Lowest coverage

Per-function coverage is not measured for this package yet.

People & History

People (2)

Maintainer (1)

Francisco Pina-Martins

Maintainer, Author

Authors (2)

Francisco Pina-Martins

Maintainer, Author

Paulo Sousa

Author

Release timeline

1 release. R releases are shown for context.

R
R 4.6.0 released · 2026-04-24
0.1.0Latest
2026-03-10 · current release
R
R 4.5.0 released · 2025-04-11

Package metadata

First published: 2026-02-25
Total releases: 1 / 1 yrs
License: GPL-3 OSI
Download size: not tracked yet
Installed size: not tracked yet
With dependencies: not tracked yet