R Observatory: Metrics for malan version 1.0.4

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

malan

1.0.4Package record

MAle Lineage ANalysis

0packages depend

3.1Kdownloads / year

75.0%test coverage

8/13flavors OK

Overview

About

Maintained by Mikkel Meyer AndersenCRAN page ↗GitHub ↗Website ↗Issues ↗

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).

Changes in 1.0.4

Fixed Rd's \link anchors

From NEWS in the release

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. We list this channel from recorded r2u download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

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). We list this channel from recorded autoCRAN download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

Health

CRAN checks

5NOTE8OK

Check messages

NOTER code for possible problemsr-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-x86_64

Found calls to structure() using deprecated special names:
  malan/tests/testthat/test-autosomal.R (.Dim: 18, .Names: 4)
'.Dim' should be changed to 'dim'.
'.Names' should be changed to 'names'.

CRAN check page ↗

Slowest check: 8.3 min · r-oldrel-windows-x86_64

Status changes

NOTE8 OK, 5 NOTENow
NOTE11 OK, 2 NOTE2026-07-16
OK13 OK2026-06-09
ERROR12 OK, 1 ERROR2026-06-08
OK12 OK2026-04-25
NOTE12 OK, 2 NOTE2026-04-22

Show 4 earlier changesHide 4 earlier changes

ERROR11 OK, 2 NOTE, 1 ERROR2026-04-18
NOTE12 OK, 2 NOTE2026-04-10
ERROR11 OK, 2 NOTE, 1 ERROR2026-04-09
NOTE12 OK, 2 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.0.4

READMEYes · 353 wordsVignettesYes · 2 · dynamicNEWSYes · 100% structured · mentions 1.0.4Citation fileYes · cites a publicationWebsiteYes · pkgdown

Cites a JOSS paper

Help pages: 101includes a package overview page
Examples that run: 100%21 run in a plain check
Exported functions with examples: 25%
Documented parameters: 100%
Return-value docs: 68%
Help pages citing references: 1%

Vignettes (2)

Case study: Partial profiles HTML
Introduction HTML

How these are measured

Downloads

3.1K

CRAN downloads in the past year

Rank #14,140 · ~8/day · ~259/mo

Releases R versions

Daily download trend is not available in this view yet.

25030 days

83490 days

3.1K1 year

Compare downloads with other packages →

Also on355 r2u4 autocran

How downloads are counted

Repository

mikldk/malan ↗Account: mikldk

0Stars

4Forks

1Open issues

0Open PRs

6Releases

271Commits

2Commit identities

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

Responsiveness

How these are sampled

PRs merged (all time): 100%
Median days to close, 50 most recently updated closed issues: 2
Median days to close, 50 most recently updated closed PRs: 0

Forks over time

2019-08-25 · 32026-07-07 · 4

How these are measured

PracticesBeta

6 development-tooling and community-health practices detected across 4 families in the upstream repository

Checks run against github.com/mikldk/malan on 2026-10-22.

Continuous integration (2)

Travis CI (config file)tic

Docs source (1)

GitHub Pages site last deployed 2025-08-19

Research and citation (2)

codemeta.jsonJOSS paper

Lint, format, editor (1)

RStudio project

How this is detected·Detection ruleset v4 (2026-10-20)

Dependencies

Declared dependencies

17 external dependencies (excludes base and recommended)

Installing malan adds 25 packages (16 with compiled code, 25 MB of source tarballs). Heaviest: stringi 11 MB, igraph 4.8 MB, Rcpp 1.8 MB.

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.

How these are counted

Code & Tests

Datasets

People & History

People (1)

Mikkel Meyer Andersen

Author, Maintainer since 1.0.2 (2020)

Releases (3)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
1.0.4Latest
record
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
record
2023-11-28 · diff ↗ ·
added 5 exports
infer_generation, load_haplotypes, meiotic_dist_threshold, meiotic_radius, set_generation
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
record
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

Cite

Cite this package

Run in R for the authors' entry:

citation("malan")

The package provides a citation file, so citation() returns the authors' own entry.

It points to 10.1371/journal.pgen.1007028, 10.21105/joss.00684, 10.1016/j.fsigen.2018.10.004.

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 v2026-10-23. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-23, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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