R Observatory: Metrics for GapAnalysis version 2.1.1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

GapAnalysis

2.1.1Package record

Conservation Indicators Using Spatial Information

0packages depend

19.4Kdownloads / year

72.2%test coverage

13/13flavors OK

Overview

About

Maintained by Dan CarverCRAN page ↗GitHub ↗Issues ↗

Supports the assessment of the degree of conservation of taxa in conservation systems, both in ex situ (in genebanks, botanical gardens, and other repositories), and in situ (in protected natural areas). Methods are described in Carver et al. (2021) doi:10.1111/ecog.05430, building on Khoury et al. (2020) doi:10.1073/pnas.2007029117, Khoury et al. (2019) doi:10.1016/j.ecolind.2018.11.016, Khoury et al. (2019) doi:10.1111/DDI.13008, Castaneda-Alvarez et al. (2016) doi:10.1038/nplants.2016.22, and Ramirez-Villegas et al. (2010) doi:10.1371/journal.pone.0013497.

Changes in 2.1.1

Method addition: The workflow now supports taxa for which no species distribution model is available (for example, taxa with records but no usable coordinates). SRSin, ERSin, and ERSex accept sdm = NULL; SRSin then evaluates all occurrence points against protected areas, and the ERS metrics return 0 with the ecoregion counts set accordingly. The results tables and leaflet maps reflect the missing model.
Method addition: Added the noModel parameter to FCSex and FCSin. When TRUE, GRS and ERS are assigned 0 and the final conservation score is the mean of the three metrics, consistent with the treatment of unmodelled taxa in Khoury et al. (2019) <doi:10.1016/j.ecolind.2018.11.016>. GRSex and GRSin require a model and should be skipped for these taxa.
Bug fix: getDatasets wrote the ecoregions file into the protected areas folder and used a misspelled filename for the protected areas raster. Both paths are corrected, and the function gains an out_dir argument (defaulting to the previous tools::R_user_dir() location) and returns the file paths invisibly.
Bug fix: ERSex and ERSin no longer error when limitByPoints = TRUE leaves no ecoregions to evaluate.
Infrastructure: Replaced data-masked column references in ERSex with the .data pronoun.
Infrastructure: Added a testthat file covering taxa with no coordinates, taxa with no model, taxa with no G records, and the noModel behaviour of FCSex and FCSin.

From NEWS.md in the release

Install

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

install.packages("GapAnalysis", 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("CIAT-DAPA/GapAnalysis")

Development version from CIAT-DAPA/GapAnalysis. 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-gapanalysis

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-GapAnalysis

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-GapAnalysis

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: 5.9 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
OK13 OK2026-05-16

Show 2 earlier changesHide 2 earlier changes

ERROR11 OK, 2 ERROR2026-05-06
OK5 OK2026-04-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 2.1.1

README· In the repository, left out of the releaseVignettesYes · 1 · dynamicNEWSYes · 100% structured · mentions 2.1.1Citation fileNoWebsitenot declared in DESCRIPTION

Help pages: 21
Examples that run: 75%12 run in a plain check · 4 hold no code
Exported functions with examples: 94%
Documented parameters: 97%
Return-value docs: 100%
Help pages citing references: 95%

Vignettes (1)

Gap analysis workflow for multiple species HTML

How these are measured

Downloads

19.4K

CRAN downloads in the past year

Rank #7,629 · ~53/day · ~1.6K/mo

Releases R versions

Daily download trend is not available in this view yet.

55230 days

1.2K90 days

19.4K1 year

Compare downloads with other packages →

Also on92 r2u7 autocran

How downloads are counted

Repository

ciat-dapa/gapanalysis ↗Organization: CIAT-DAPA

17Stars

13Forks

4Open issues

0Open PRs

3Releases

350Commits

8Commit identities

350 commits · Last activity 2026-09-22 · 0% stars, 30d

Responsiveness

How these are sampled

PRs merged (all time): 83%
Median days to close, 50 most recently updated closed issues: 468
Median days to close, 50 most recently updated closed PRs: 2

Stars over time

2025-09-23 · 152026-07-24 · 17

How these are measured

PracticesBeta

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

Checks run against github.com/ciat-dapa/gapanalysis on 2026-10-18.

CRAN release process (1)

cran-comments.md

Lint, format, editor (1)

RStudio project

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

Dependencies

Declared dependencies

19 external dependencies (excludes base and recommended)

Installing GapAnalysis adds 79 packages (47 with compiled code, 55 MB of source tarballs). Heaviest: sf 9.3 MB, bslib 5.6 MB, sp 4.3 MB.

Depends (1)

R >= 4.3.0

Imports (4)

dataverse dplyr leaflet terra

LinkingTo (0)

none

Suggests (15)

sf knitr rmarkdown devtools remotes tidyr stringr openxlsx ggplot2 ggtext cowplot htmltools htmlwidgets kableExtra testthat

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 (11)

Dan Carver

Sarah Gore

Author, Copyright holder · added in 2.0.0

Colin Khoury

Author, Copyright holder

Julian Ramirez-Villegas

Author, Copyright holder

Chrystian Sosa

Author, Copyright holder

Harold Achicanoy

Contributor, Copyright holder

Nora Castaneda-Alvarez

Contributor, Copyright holder

Kaue De Sousa

Contributor

Maria Victoria Diaz

Contributor, Copyright holder

Steven Sotelo

Contributor, Copyright holder

Valentin Stefan

Contributor

Previously maintained by Julian Ramirez-Villegas (1.0.1 to 1.0.2).

Releases (6)

Pick two releases to compare their code metrics.

2.1.1Latest
record
2026-07-23 · current release · diff ↗
2.1.0
record
2026-07-23 · diff ↗
2.0.2
record
2026-05-12 · diff ↗
R
R 4.6.0 released · 2026-04-24
unarchivedReturned to CRAN
2026-04-09
2.0.0
record
2026-04-09 · diff ↗ ·
removed 6 exports
Gbuffer, GetDatasets, OccurrenceCounts, ParamTest, SummaryHTML, indicator

added 8 exports
checkEcoregion, checkOccurrences, checkProtectedAreas, checksdm, generateCounts, generateEcoSelection, generateGBuffers, getDatasets
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
archivedRemoved from CRAN
2023-06-09
issues were not corrected in time
R
R 4.3.0 released · 2023-04-21
R
R 4.2.0 released · 2022-04-22
unarchivedReturned to CRAN
2021-06-14
1.0.2
record
2021-06-14 · diff ↗
R
R 4.1.0 released · 2021-05-18
archivedRemoved from CRAN
2021-02-16
depends on archived package 'dataverse'
1.0.1
record
2020-08-10

Show 1 earlier eventHide 1 earlier event

R
R 4.0.0 released · 2020-04-24

Package metadata

First published: 2020-08-10
Total releases: 6 / 6 yrs
License: GPL-3 OSI
Minimum R: ≥ 4.3.0
Bundled data: 605 KB / 4 files
Download size: 664 KB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("GapAnalysis")

Format

Carver, D., Achicanoy, H., Castaneda-Alvarez, N., De Sousa, K., Diaz, M. V., Gore, S., Khoury, C., Ramirez-Villegas, J., Sosa, C., Sotelo, S., & Stefan, V. (2026). GapAnalysis: Conservation Indicators Using Spatial Information (Version 2.1.1) [Computer software]. https://doi.org/10.32614/CRAN.package.GapAnalysis

This package has no citation file, so citation() returns this entry built from DESCRIPTION.

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 GapAnalysis version 2.1.1 [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 →