R Observatory: Metrics for AlleleShift version 1.1-3

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

AlleleShift

1.1-3Package record

Predict and Visualize Population-Level Changes in Allele Frequencies in Response to Climate Change

0packages depend

4.2Kdownloads / year

–test coverage

13/13flavors OK

Overview

About

Maintained by Roeland KindtCRAN page ↗

Methods (doi:10.7717/peerj.11534) are provided of calibrating and predicting shifts in allele frequencies through redundancy analysis ('vegan::rda()') and generalized additive models ('mgcv::gam()'). Visualization functions for predicted changes in allele frequencies include 'shift.dot.ggplot()', 'shift.pie.ggplot()', 'shift.moon.ggplot()', 'shift.waffle.ggplot()' and 'shift.surf.ggplot()' that are made with input data sets that are prepared by helper functions for each visualization method. Examples in the documentation show how to prepare animated climate change graphics through a time series with the 'gganimate' package. Function 'amova.rda()' shows how Analysis of Molecular Variance can be directly conducted with the results from redundancy analysis.

Install

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

install.packages("AlleleShift", 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-alleleshift

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-AlleleShift

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-AlleleShift

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: 4.3 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 1.1-3

READMEYes · 232 wordsVignettesNoNEWSNoCitation fileYes · cites a publicationWebsitenot declared in DESCRIPTION

Help pages: 10
Examples that run: 60%6 run in a plain check · 3 only when donttest examples are enabled (R CMD check --as-cran) · 1 never run
Exported functions with examples: 100%
Documented parameters: 82%
Return-value docs: 100%
Help pages citing references: 50%

How these are measured

Downloads

4.2K

CRAN downloads in the past year

Rank #9,047 · ~11/day · ~348/mo

Releases R versions

Daily download trend is not available in this view yet.

40530 days

1.1K90 days

4.2K1 year

Compare downloads with other packages →

Also on131 r2u45 autocran

How downloads are counted

Dependencies

Declared dependencies

13 external dependencies (excludes base and recommended)

Installing AlleleShift adds 140 packages (71 with compiled code, 133 MB of source tarballs). Heaviest: stringi 11 MB, Rcmdr 8.7 MB, ggplot2 6.0 MB.

Depends (1)

R >= 4.1.0

Imports (3)

vegan BiodiversityR adegenet

LinkingTo (0)

none

Suggests (11)

popprmgcvdplyr ggplot2 GGally ggforce ggrepel ggsci gggibbous gganimate patchwork

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)

Roeland Kindt

Maintainer since 0.9 (2021), Author

Releases (7)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
1.1-3Latest
record
2025-10-16 · current release · diff ↗
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
unarchivedReturned to CRAN
2023-10-28
1.1-2
record
2023-10-28 · diff ↗
archivedRemoved from CRAN
2023-09-09
requires archived package 'BiodiversityR'
R
R 4.3.0 released · 2023-04-21
1.1
record
2022-09-07 · diff ↗
R
R 4.2.0 released · 2022-04-22
1.0-2
record
2021-08-14 · diff ↗
R
R 4.1.0 released · 2021-05-18
1.0-1
record
2021-04-07 · diff ↗ ·
added 1 export
environmental.novel
0.9-2
record
2021-01-29 · diff ↗
0.9
record
2021-01-26
R
R 4.0.0 released · 2020-04-24

Package metadata

First published: 2021-01-26
Total releases: 7 / 5 yrs
License: GPL-3 OSI
Minimum R: ≥ 4.1.0
Bundled data: 131 KB / 7 files
Download size: 787 KB

Cite

Cite this package

Run in R for the authors' entry:

citation("AlleleShift")

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

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 AlleleShift version 1.1-3 [Data set]. HJJB, LLC. Data release v2026-10-21. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-21, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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