R Observatory: Metrics for reems version 0.1.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

reems

0.1.0

Estimating Effective Migration Surfaces from Single Nucleotide Polymorphism Data

0packages depend

805downloads / year

76.0%test coverage

13/13checks pass

Overview

About

Maintained by Felix WeitkämperFirst published 2026-05-061 releasesCRAN page ↗Codeberg ↗

Wrapper and plotting utilities for the spatial population genetics tool 'EEMS' (Estimated Effective Migration Surfaces) for SNP (Single Nucleotide Polymorphism) data, originally provided as a command-line tool written in 'C++' together with an accompanying 'R' package for plotting the output of the 'EEMS' tool itself (https://github.com/dipetkov/eems/). There are four main motivations for offering this to 'R' users as a package. Firstly, to remove the installation and configuration burden for the 'EEMS' command-line tool, which relies on manually installed 'Boost' and 'Eigen' system libraries and configuring their location; secondly, to streamline the workflow by having a singe environment (the 'R' system) for the entire analysis rather than a file-based command-line executable whose output files are then to be imported and analysed by a separate 'R' script; thirdly, to make the input formats compatible with other, 'R'-based spatial population genetics tools such as the 'ConStruct' package; and lastly, to allow for easily running several chains in parallel and combining them for plotting and further analysis. The package also adds more intuitive, streamlined tooling around creating more complex habitats. The method of estimating effective migration surfaces was first described by Petkova, D., Novembre, J. & Stephens, M. (2016) doi:10.1038/ng.3464.

Install

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

install.packages("reems", 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-reems

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-reems

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-reems

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

Health

CRAN checks

13OK

Slowest check: 13.6 min · r-oldrel-windows-x86_64

Code health

Yes

Tests · ratio 0.09

76.0%

Coverage · measured lines

100%

Documentation · exports

7

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
OK2026-05-06
7 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 142 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 67% structuredCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 99%
Return-value docs: 100%
References docs: 45%

Downloads

805

CRAN downloads in the past year

Rank #19,494 · ~2/day · ~67/mo

Releases R versions

Daily download trend is not available in this view yet.

16930 days

56290 days

8051 year

Compare downloads with other packages →

Also on27 r2u3 autocran

Repository

Codeberg ↗ felix_weitkaemper/reems

Repository practices

Upstream repositoryBeta

Repository codeberg.org/felix_weitkaemper/reems is linked, but repository-practices checks have not run for it yet. Checks are GitHub-only for now.

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

Dependencies

Declared dependencies

17 external dependencies (excludes base and recommended)

Depends (1)

R >= 4.1.0

Imports (7)

Rcppmethodsraster sp sfstatsutils

LinkingTo (3)

BH Rcpp RcppEigen

Suggests (11)

future future.applyMatrixRColorBrewer (>= 1.1)deldir dichromat rworldmap rworldxtra knitr rmarkdown testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

People & History

People (2)

Maintainer (1)

Felix Weitkämper

Author, Maintainer, Copyright holder

Authors (1)

Felix Weitkämper

Author, Maintainer, Copyright holder

Copyright holders (2)

Felix Weitkämper

Author, Maintainer, Copyright holder

Desislava Petkova

Copyright holder

Package Timeline

1 release. R releases are shown for context.

0.1.0Latest
2026-05-06 · current release
R
R 4.6.0 released · 2026-04-24

Package metadata

First published: 2026-05-06
Total releases: 1 / 1 yrs
License: GPL-2 OSI
Minimum R: ≥ 4.1.0
Bundled data: 41 KB / 2 files
Download size: 556 KB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("reems")

Format

Weitkämper, F., & Petkova, D. (2026). reems: Estimating Effective Migration Surfaces from Single Nucleotide Polymorphism Data (Version 0.1.0) [Computer software]. https://doi.org/10.32614/CRAN.package.reems

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 reems version 0.1.0 [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.

Report a problem with this page →