R Observatory: Metrics for mapmixture version 1.2.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

mapmixture

1.2.0Package record

Spatial Visualisation of Admixture on a Projected Map

0packages depend

3.1Kdownloads / year

25.8%test coverage

13/13flavors OK

Overview

About

Maintained by Tom JenkinsCRAN page ↗GitHub ↗Issues ↗

Visualise admixture as pie charts on a projected map, admixture as traditional structure barplots or facet barplots, and scatter plots from genotype principal components analysis. A 'shiny' app allows users to create admixture maps interactively. Jenkins TL (2024) doi:10.1111/1755-0998.13943.

Changes in 1.2.0

**Feature**. The pie_size argument now accepts a single value or a vector of values the same length as the number of sites. This allows users to plot pie of different sizes for different sites.
**Issue #28**. Changing the order of items in the legend. Fixed an issue when there are 10 or more clusters named cluster1, cluster2, ..., cluster10, clusterN. The main change is in the func_process_input_data.R script, whereby the renaming of cluster columns is now cluster01, cluster02, ..., instead of cluster1, cluster2, ..., to make sure the order is the same as the input.
**Shiny app**. Package dependencies for the Shiny app only are now on the Suggest list of dependencies rather than the Imports list. When launch_mapmixture() is executed, the function will check the dependencies are installed or ask the user to install them.
**Structure plot**. A permanent change in the default plotting of individuals on the structure plot. Previously, the individual column was sorted alphabetically, but users have indicated it is more ideal to preserve the original order of individuals for each site in the admixture data file. This is now the default behaviour for structure_plot().

From NEWS.md in the release

Install

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

install.packages("mapmixture", 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("Tom-Jenkins/mapmixture")

Development version from Tom-Jenkins/mapmixture. 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-mapmixture

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-mapmixture

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-mapmixture

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

13OK

CRAN check page ↗

Slowest check: 2.4 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-06-09
ERROR12 OK, 1 ERROR2026-06-08
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.2.0

READMEYes · 322 wordsVignettesNoNEWSYes · 100% structured · mentions 1.2.0Citation fileYes · cites a publicationWebsitenot declared in DESCRIPTION

Help pages: 13 (9 internal)
Examples that run: 100%13 run in a plain check (1 of them under a condition)
Exported functions with examples: 100%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 0%

How these are measured

Downloads

3.1K

CRAN downloads in the past year

Rank #10,372 · ~9/day · ~260/mo

Releases R versions

Daily download trend is not available in this view yet.

42730 days

97790 days

3.1K1 year

Compare downloads with other packages →

Also on102 r2u8 autocran

How downloads are counted

Repository

tom-jenkins/mapmixture ↗Account: Tom-Jenkins

48Stars

8Forks

0Open issues

0Open PRs

11Releases

246Commits

3Commit identities

admixturershinypopulation-structuremapmixtureancestry

License file reads as GPL-3.0 · 246 commits · Last activity 2025-02-06 · 0% stars, 30d

Responsiveness

How these are sampled

PRs merged (all time): 100%
Median days to close, 50 most recently updated closed issues: 6
Median days to close, 50 most recently updated closed PRs: 0

Stars over time

2025-03-30 · 442026-09-09 · 48

How these are measured

PracticesBeta

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

Checks run against github.com/tom-jenkins/mapmixture on 2026-10-11.

Continuous integration (2)

GitHub ActionsR CMD check workflow

The R CMD check workflow runs on Linux, macOS and Windows, and on R-devel

Docs source (1)

README.Rmd

Lint, format, editor (1)

RStudio project

How this is detected·Detection ruleset v3 (2026-09-26)

Dependencies

Declared dependencies

20 external dependencies (excludes base and recommended)

Installing mapmixture adds 49 packages (26 with compiled code, 53 MB of source tarballs). Heaviest: stringi 11 MB, sf 9.3 MB, ggplot2 6.0 MB.

Depends (1)

R >= 4.2

Imports (10)

dplyr ggplot2 ggspatialgridpurrr rlang rnaturalearthdata sf stringr tidyr

LinkingTo (0)

none

Suggests (11)

bslib colourpicker htmltools shiny shinyFeedback shinyjs shinytest2 shinyWidgets terra testthat waiter

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)

Tom Jenkins

Releases (5)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
R
R 4.5.0 released · 2025-04-11
1.2.0Latest
record
2025-01-23 · current release · diff ↗
1.1.4
record
2024-09-25 · diff ↗
1.1.3
record
2024-05-16 · diff ↗
1.1.2
record
2024-04-29 · diff ↗
R
R 4.4.0 released · 2024-04-24
1.1.1
record
2024-04-17
R
R 4.3.0 released · 2023-04-21

Package metadata

First published: 2024-04-17
Total releases: 5 / 2 yrs
License: GPL (>= 3) OSI
Minimum R: ≥ 4.2
Download size: 3.8 MB

Cite

Cite this package

Run in R for the authors' entry:

citation("mapmixture")

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

It points to 10.1111/1755-0998.13943.

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 mapmixture version 1.2.0 [Data set]. HJJB, LLC. Data release v2026-10-19. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-19, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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