R Observatory: Metrics for nichevol version 0.1.20

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

nichevol

0.1.20

Tools for Ecological Niche Evolution Assessment Considering Uncertainty

0packages depend

2.3Kdownloads / year

–test coverage

0/13checks pass

Overview

About

Maintained by Marlon E. CobosFirst published 2020-03-022 releasesCRAN page ↗GitHub ↗

A collection of tools that allow users to perform critical steps in the process of assessing ecological niche evolution over phylogenies, with uncertainty incorporated explicitly in reconstructions. The method proposed here for ancestral reconstruction of ecological niches characterizes species' niches using a bin-based approach that incorporates uncertainty in estimations. Compared to other existing methods, the approaches presented here reduce risk of overestimation of amounts and rates of ecological niche evolution. The main analyses include: initial exploration of environmental data in occurrence records and accessible areas, preparation of data for phylogenetic analyses, executing comparative phylogenetic analyses of ecological niches, and plotting for interpretations. Details on the theoretical background and methods used can be found in: Owens et al. (2020) doi:10.1002/ece3.6359, Peterson et al. (1999) doi:10.1126/science.285.5431.1265, Soberón and Peterson (2005) doi:10.17161/bi.v2i0.4, Peterson (2011) doi:10.1111/j.1365-2699.2010.02456.x, Barve et al. (2011) doi:10.1111/ecog.02671, Machado-Stredel et al. (2021) doi:10.21425/F5FBG48814, Owens et al. (2013) doi:10.1016/j.ecolmodel.2013.04.011, Saupe et al. (2018) doi:10.1093/sysbio/syx084, and Cobos et al. (2021) doi:10.1111/jav.02868.

Install

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

install.packages("nichevol", 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("marlonecobos/nichevol")

Development version from marlonecobos/nichevol. 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-nichevol

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-nichevol

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-nichevol

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

Health

CRAN checks

13NOTE

Failing flavors

NOTE r-devel-linux-x86_64-debian-clang
NOTE r-devel-linux-x86_64-debian-gcc
NOTE r-devel-linux-x86_64-fedora-clang
NOTE r-devel-linux-x86_64-fedora-gcc
NOTE r-devel-windows-x86_64
NOTE r-oldrel-macos-arm64
NOTE r-oldrel-macos-x86_64
NOTE r-oldrel-windows-x86_64
NOTE r-patched-linux-x86_64
NOTE r-release-linux-x86_64
NOTE r-release-macos-arm64
NOTE r-release-macos-x86_64
NOTE r-release-windows-x86_64

Slowest check: 5.5 min · r-oldrel-windows-x86_64

Code health

None

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

9

Dependencies · direct

Check history

NOTE2026-06-09
0 OK · 13 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-08
0 OK · 12 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
NOTE2026-03-10
0 OK · 14 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 5,321 wordsVignettesNopkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 100%
Return-value docs: 80%
References docs: 0%

Downloads

2.3K

CRAN downloads in the past year

Rank #18,480 · ~6/day · ~195/mo

Releases R versions

Daily download trend is not available in this view yet.

16930 days

59290 days

2.3K1 year

Compare downloads with other packages →

Also on95 r2u18 autocran

Repository

GitHub ↗ marlonecobos/nichevol

15Stars

4Forks

0Open issues

0Open PRs

0Releases

263Commits

2Contributors

263 commits · Last activity 2023-03-10

Stars over time

2025-03-22 · 152026-07-07 · 15

Repository practices

Upstream repositoryBeta

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

Checks run against github.com/marlonecobos/nichevol on 2026-08-09.

Continuous integration (2)

GitHub ActionsTravis CI

CRAN release process (2)

cran-comments.mdCRAN-SUBMISSION

Docs source (1)

README.Rmd

Lint, format, editor (1)

RStudio project

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

Dependencies

Declared dependencies

7 external dependencies (excludes base and recommended)

Depends (2)

R >= 3.5.0ape

Imports (8)

castor geigergraphicsgrDevicesstringrstatsterrautils

LinkingTo (0)

none

Suggests (2)

knitr phytools

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

People & History

People (3)

Maintainer (1)

Marlon E. Cobos

Author, Maintainer

Authors (3)

Marlon E. Cobos

Author, Maintainer

Hannah L. Owens

Author

A. Townsend Peterson

Author

Package Timeline

2 releases. Pick two to compare their code metrics. R releases are shown for context.

R
R 4.6.0 released · 2026-04-24
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
R
R 4.3.0 released · 2023-04-21
0.1.20Latest
2023-03-11 · current release · diff ↗
unarchivedReturned to CRAN
2023-03-11
archivedRemoved from CRAN
2022-05-27
check problems were not corrected in time
R
R 4.2.0 released · 2022-04-22
R
R 4.1.0 released · 2021-05-18
R
R 4.0.0 released · 2020-04-24
0.1.19
2020-03-02
R
R 3.6.0 released · 2019-04-26

Package metadata

First published: 2020-03-02
Total releases: 2 / 6 yrs
License: GPL-3 OSI
Minimum R: ≥ 3.5.0
Bundled data: 13 KB / 6 files
Download size: 276 KB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("nichevol")

Format

Cobos, M. E., Owens, H. L., & Peterson, A. T. (2023). nichevol: Tools for Ecological Niche Evolution Assessment Considering Uncertainty (Version 0.1.20) [Computer software]. https://doi.org/10.32614/CRAN.package.nichevol

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 nichevol version 0.1.20 [Data set]. HJJB, LLC. Data release v2026-08-15. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-15, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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