R Observatory: Metrics for haplotypes version 1.1.3.2

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

haplotypes

1.1.3.2

Manipulating DNA Sequences and Estimating Unambiguous Haplotype Network with Statistical Parsimony

1packages depend

6.3Kdownloads / year

–test coverage

13/13checks pass

Overview

About

Maintained by Caner AktasFirst published 2015-04-267 releasesCRAN page ↗

Provides S4 classes and methods for reading and manipulating aligned DNA sequences, supporting an indel-coding method (only simple indel-coding method is available in the current version), showing base substitutions and indels, calculating absolute pairwise distances between DNA sequences, and collapsing identical DNA sequences into haplotypes or inferring haplotypes using user-provided absolute pairwise character difference matrix. This package also includes S4 classes and methods for estimating genealogical relationships among haplotypes using statistical parsimony and plotting parsimony networks.

Install

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

install.packages("haplotypes", 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-haplotypes

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-haplotypes

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-haplotypes

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

Health

CRAN checks

13OK

Slowest check: 2.9 min · r-oldrel-windows-x86_64

Code health

None

Tests · ratio 0.00

not tracked

Coverage

8

Dependencies · direct

Check history

OK2026-08-05
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-08-01
12 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-06-09
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-08
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 0 wordsVignettesNopkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 95%
Documented parameters: not tracked
Return-value docs: not tracked
References docs: 11%

Downloads

6.3K

CRAN downloads in the past year

Rank #10,071 · ~17/day · ~528/mo

Releases R versions

Daily download trend is not available in this view yet.

27430 days

95090 days

6.3K1 year

Compare downloads with other packages →

Also on115 r2u13 autocran

Dependencies

Declared dependencies

5 external dependencies (excludes base and recommended)

Depends (1)

R >= 4.1.0

Imports (8)

methodsstatsutilsnetwork sna ape phangorn plotrix

LinkingTo (0)

none

Suggests (0)

none

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

1direct

0indirect

RAINBOWR

Code & Tests

People & History

People (1)

Maintainer (1)

Caner Aktas

Author, Maintainer

Authors (1)

Caner Aktas

Author, Maintainer

Package Timeline

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

R
R 4.6.0 released · 2026-04-24
1.1.3.2Latest
2025-10-06 · current release · diff ↗
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
1.1.3.1
2023-07-15 · diff ↗
1.1.3
2023-06-29 · diff ↗
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
1.1.2
2020-02-28 · diff ↗
1.1.1
2020-02-20 · diff ↗
R
R 3.6.0 released · 2019-04-26
1.1
2019-03-16 · diff ↗
R
R 3.5.0 released · 2018-04-23
R
R 3.4.0 released · 2017-04-21

Show 3 earlier events

R
R 3.3.0 released · 2016-05-03
1.0
2015-04-26
R
R 3.2.0 released · 2015-04-16

Package metadata

First published: 2015-04-26
Total releases: 7 / 11 yrs
License: GPL-2 OSI
Minimum R: ≥ 4.1.0
Bundled data: 1.0 KB / 1 file
Download size: 42 KB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("haplotypes")

Format

Aktas, C. (2025). haplotypes: Manipulating DNA Sequences and Estimating Unambiguous Haplotype Network with Statistical Parsimony (Version 1.1.3.2) [Computer software]. https://doi.org/10.32614/CRAN.package.haplotypes

This is what citation() produces when a package has no citation file of its own. If it prints something else, use that.

Cite the R Observatory

For a number measured here: a download total, a coverage figure, an archival date.

Format

APA

Balamuta, J. J. (2026). R Observatory: Metrics for haplotypes version 1.1.3.2 [Data set]. HJJB, LLC. Data release v2026-08-18. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-18, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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