R Observatory: Metrics for malan version 1.0.4

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

malan

1.0.4

MAle Lineage ANalysis

0packages depend

3Kdownloads / year

75.0%test coverage

8/13checks pass

Overview

About

Maintained by Mikkel Meyer AndersenFirst published 2020-06-253 releasesCRAN page ↗GitHub ↗

MAle Lineage ANalysis by simulating genealogies backwards and imposing short tandem repeats (STR) mutations forwards. Intended for forensic Y chromosomal STR (Y-STR) haplotype analyses. Numerous analyses are possible, e.g. number of matches and meiotic distance to matches. Refer to papers mentioned in citation("malan") (DOI's: doi:10.1371/journal.pgen.1007028, doi:10.21105/joss.00684 and doi:10.1016/j.fsigen.2018.10.004).

Install

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

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

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

if (!requireNamespace("pak", quietly = TRUE))
  install.packages("pak", repos = "https://cloud.r-project.org/")
pak::pak("mikldk/malan")

Development version from mikldk/malan. Installs pak first if it is not already available.

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-malan

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-malan

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-malan

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

Health

CRAN checks

5NOTE8OK

Failing flavors

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

Slowest check: 8.4 min · r-devel-windows-x86_64

Code health

Yes

Tests · ratio 0.99

75.0%

Coverage · measured lines

100%

Documentation · exports

9

Dependencies · direct

Check history

NOTE2026-07-16
11 OK · 2 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
OK2026-04-25
12 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-04-22
12 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Show 4 earlier snapshots

ERROR2026-04-18
11 OK · 2 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
NOTE2026-04-10
12 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-09
11 OK · 2 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
NOTE2026-03-10
12 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 353 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 100%
Return-value docs: 68%
References docs: 1%

Downloads

3K

CRAN downloads in the past year

Rank #12,579 · ~8/day · ~250/mo

Releases R versions

Daily download trend is not available in this view yet.

24930 days

81290 days

3K1 year

Compare downloads with other packages →

Also on403 r2u22 autocran

Repository

GitHub ↗ mikldk/malan

0Stars

4Forks

1Open issues

0Open PRs

6Releases

271Commits

2Contributors

License GPL-2.0 · 271 commits · Last activity 2025-08-19

Forks over time

2019-08-25 · 32026-07-07 · 4

Repository practices

Upstream repositoryBeta

5 development-tooling and community-health practices detected across 3 families in the upstream repository

Checks run against github.com/mikldk/malan on 2026-08-23.

Continuous integration (2)

Travis CItic

Research and citation (2)

codemeta.jsonJOSS paper

Lint, format, editor (1)

RStudio project

How this is detected·Detection ruleset v1 (2026-07-18)

Dependencies

Declared dependencies

17 external dependencies (excludes base and recommended)

Depends (3)

R >= 3.6dplyr tidygraph

Imports (7)

Rcpp RcppProgress RcppArmadillo (>= 0.9.880.1.0)igraph tibble magrittr (>= 1.5)methods

LinkingTo (3)

Rcpp RcppArmadillo RcppProgress

Suggests (6)

knitr rmarkdown testthat ggraph dirmult Rmpfr

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Datasets

People & History

People (1)

Maintainer (1)

Mikkel Meyer Andersen

Author, Maintainer

Authors (1)

Mikkel Meyer Andersen

Author, Maintainer

Package Timeline

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

R
R 4.6.0 released · 2026-04-24
1.0.4Latest
2025-08-19 · current release · diff ↗
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
1.0.3
2023-11-28 · 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
1.0.2
2020-06-25
R
R 4.0.0 released · 2020-04-24

Package metadata

First published: 2020-06-25
Total releases: 3 / 6 yrs
License: GPL-2 | file LICENSE OSI
Minimum R: ≥ 3.6
Bundled data: 2.2 KB / 2 files
Download size: 764 KB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("malan")

The authors publish a JOSS paper, so they have said how they want this cited. Run citation() and use what it gives you.

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 malan version 1.0.4 [Data set]. HJJB, LLC. Data release v2026-08-24. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-24, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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