alleHap

0.9.9

Allele Imputation and Haplotype Reconstruction from Pedigree Databases

0packages depend

3.4Kdownloads / year

–test coverage

11/13checks pass

Overview

About

Maintained by Nathan Medina-RodriguezFirst published 2014-08-104 releasesCRAN page ↗

Tools to simulate alphanumeric alleles, impute genetic missing data and reconstruct non-recombinant haplotypes from pedigree databases in a deterministic way. Allelic simulations can be implemented taking into account many factors (such as number of families, markers, alleles per marker, probability and proportion of missing genotypes, recombination rate, etc). Genotype imputation can be used with simulated datasets or real databases (previously loaded in .ped format). Haplotype reconstruction can be carried out even with missing data, since the program firstly imputes each family genotype (without a reference panel), to later reconstruct the corresponding haplotypes for each family member. All this considering that each individual (due to meiosis) should unequivocally have two alleles per marker (one inherited from each parent) and thus imputation and reconstruction results can be deterministically calculated.

Install

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

install.packages("alleHap", repos = "https://cloud.r-project.org/")

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

Release

# enable cranapt (r2u) if it is not already set up, then install
grep -rqs r2u.stat.illinois.edu /etc/apt/sources.list /etc/apt/sources.list.d/ \
  || curl -fsSL https://raw.githubusercontent.com/eddelbuettel/r2u/master/inst/scripts/add_cranapt_noble.sh | sudo bash
sudo apt install -y r-cran-allehap

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled.

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

# enable the iucar/cran COPR if it is not already present, then install
ls /etc/yum.repos.d/*iucar*cran*.repo >/dev/null 2>&1 \
  || sudo dnf copr enable -y iucar/cran
sudo dnf install -y R-CRAN-alleHap

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

For install.packages() integration in R, also: sudo dnf install R-CoprManager

# add the autoCRAN OBS repo (Tumbleweed) if it is missing, then install
zypper -q lr | grep -qi autoCRAN \
  || sudo zypper addrepo https://download.opensuse.org/repositories/devel:/languages:/R:/autoCRAN/openSUSE_Tumbleweed/devel:languages:R:autoCRAN.repo
sudo zypper install -y R-alleHap

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed).

Health

CRAN checks

2NOTE11OK

Failing flavors

NOTE r-devel-linux-x86_64-debian-clang
NOTE r-devel-linux-x86_64-debian-gcc

Slowest check: 1.6 min · r-oldrel-macos-x86_64

Code health

None

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

Dependencies · direct

Check history

NOTE2026-03-10
12 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMENoVignettesYes · dynamicpkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 100%
Return-value docs: 100%
References docs: 100%

Downloads

3.4K

CRAN downloads in the past year

Rank #12,054 · ~9/day · ~286/mo

Releases R versions

Daily download trend is not available in this view yet.

26830 days

88590 days

3.4K1 year

Compare downloads with other packages →

Also on180 r2u47 autocran94 c2d4u

Dependencies

Declared dependencies

2 external dependencies (excludes base and recommended)

Depends (0)

none

Imports (4)

abindtoolsstatsutils

LinkingTo (0)

none

Suggests (1)

knitr

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

People & History

People (0)

Author records are not tracked yet for this package.

Listed in earlier versions (2)

Nathan Medina-Rodriguez

no longer listed · 0.7.2 to 0.9.9

Angelo Santana

no longer listed · 0.7.2 to 0.9.9

Package Timeline

4 releases. Pick two to compare their code metrics. R releases are shown for context.

R
R 4.6.0 released · 2026-04-24
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
R
R 4.3.0 released · 2023-04-21
R
R 4.2.0 released · 2022-04-22
R
R 4.1.0 released · 2021-05-18
R
R 4.0.0 released · 2020-04-24
R
R 3.6.0 released · 2019-04-26
R
R 3.5.0 released · 2018-04-23
0.9.9Latest
2017-08-19 · current release · diff ↗
R
R 3.4.0 released · 2017-04-21
0.9.7
2016-07-17 · diff ↗
R
R 3.3.0 released · 2016-05-03
0.9.2
2015-10-05 · diff ↗
R
R 3.2.0 released · 2015-04-16
0.7.2
2014-08-10

Show 1 earlier events

R
R 3.1.0 released · 2014-04-10

Package metadata

First published: 2014-08-10
Total releases: 4 / 12 yrs
License: GPL (>= 2) OSI
Download size: 543 KB
Installed size: not tracked yet
With dependencies: not tracked yet

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