R Observatory: Metrics for refuginator version 1.0.2

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

refuginator

1.0.2Package record

An Interactive Tool for Identifying Refugia

0packages depend

591downloads / year

34.7%test coverage

11/13flavors OK

Overview

About

Maintained by Nathaniel E. D. MorleyCRAN page ↗GitHub ↗Issues ↗

A 'shiny'-based browser application for reconstructing organismal distributions and identifying historical and geohistorical refugia using the methods published by Morley et al. (2026) doi:10.1038/s43247-026-03563-3.

Changes in 1.0.2

Fixed CRAN automated check issues

From NEWS.md in the release

Install

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

install.packages("refuginator", 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("nathanielmorley2000/refuginator")

Development version from nathanielmorley2000/refuginator. 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-refuginator

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-refuginator

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-refuginator

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

2NOTE11OK

Check messages

NOTEdependencies in R coder-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc

Namespaces in Imports field not imported from:
  ‘rnaturalearth’ ‘rnaturalearthdata’
All declared Imports should be used.

CRAN check page ↗

Slowest check: 1.5 min · r-oldrel-windows-x86_64

Status changes

NOTE11 OK, 2 NOTENow
NOTE5 OK, 2 NOTE2026-09-16

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.0.2

READMEYes · 177 wordsVignettesYes · 1 · dynamicNEWSYes · 100% structured · mentions 1.0.2Citation fileYes · cites a publicationWebsitenot declared in DESCRIPTION

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

Vignettes (1)

Launching and Using the Refuginator HTML

How these are measured

Downloads

591

CRAN downloads in the past year

Rank #22,225 · ~2/day · ~49/mo

Releases R versions

Daily download trend is not available in this view yet.

48730 days

59190 days

5911 year

Compare downloads with other packages →

Also on7 r2u1 autocran

How downloads are counted

Repository

nathanielmorley2000/refuginator ↗Account: nathanielmorley2000

0Stars

0Forks

1Open issues

0Open PRs

0Releases

License file reads as GPL-3.0 · Last activity 2026-09-05

Responsiveness

not measured

How these are measured

PracticesBeta

3 development-tooling and community-health practices detected across 2 families in the upstream repository

Checks run against github.com/nathanielmorley2000/refuginator on 2026-10-18.

CRAN release process (2)

cran-comments.mdCRAN-SUBMISSION

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 refuginator adds 105 packages (57 with compiled code, 112 MB of source tarballs). Heaviest: stringi 11 MB, sf 9.3 MB, ggplot2 6.0 MB.

Depends (0)

none

Imports (17)

dplyr gganimate ggplot2 leaflet neotoma2 plotly rlang rnaturalearth rnaturalearthdata scales sf shiny shinycssloaders shinyjs stringr tidyr viridis

LinkingTo (0)

none

Suggests (3)

knitr rmarkdown testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

How these are counted

Code & Tests

People & History

People (1)

Nathaniel E. D. Morley

Releases (1)

1.0.2Latest
record
2026-09-15 · current release
R
R 4.6.0 released · 2026-04-24

Package metadata

First published: 2026-09-15
Total releases: 1 / 1 yrs
License: GPL (>= 3) OSI
Download size: 4.7 MB

Cite

Cite this package

Run in R for the authors' entry:

citation("refuginator")

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

It points to 10.1038/s43247-026-03563-3.

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 refuginator version 1.0.2 [Data set]. HJJB, LLC. Data release v2026-10-20. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-20, 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 →