R Observatory: Metrics for ppgm version 1.1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

ppgm

1.1

PaleoPhyloGeographic Modeling of Climate Niches and Species Distributions

0packages depend

2.1Kdownloads / year

88.8%test coverage

13/13checks pass

Overview

About

Maintained by Alexandra HowardFirst published 2024-06-112 releasesCRAN page ↗

Reconstruction of paleoclimate niches using phylogenetic comparative methods and projection reconstructed niches onto paleoclimate maps. The user can specify various models of trait evolution or estimate the best fit model, include fossils, use one or multiple phylogenies for inference, and make animations of shifting suitable habitat through time. This model was first used in Lawing and Polly (2011), and further implemented in Lawing et al (2016) and Rivera et al (2020). Lawing and Polly (2011) doi:10.1371/journal.pone.0028554 "Pleistocene climate, phylogeny and climate envelope models: An integrative approach to better understand species' response to climate change" Lawing et al (2016) doi:10.1086/687202 "Including fossils in phylogenetic climate reconstructions: A deep time perspective on the climatic niche evolution and diversification of spiny lizards (Sceloporus)" Rivera et al (2020) doi:10.1111/jbi.13915 "Reconstructing historical shifts in suitable habitat of Sceloporus lineages using phylogenetic niche modelling.".

Install

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

install.packages("ppgm", 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-ppgm

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-ppgm

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-ppgm

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

Health

CRAN checks

13OK

Slowest check: 14.4 min · r-release-macos-x86_64

Code health

Yes

Tests · ratio 0.13

88.8%

Coverage · measured lines

100%

Documentation · exports

13

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
OK2026-06-09
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-08
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-04-25
12 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Show 1 earlier snapshots

NOTE2026-03-10
13 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 72 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 100%
Return-value docs: 100%
References docs: 10%

Downloads

2.1K

CRAN downloads in the past year

Rank #17,218 · ~6/day · ~176/mo

Releases R versions

Daily download trend is not available in this view yet.

19430 days

62290 days

2.1K1 year

Compare downloads with other packages →

Also on175 r2u15 autocran

Dependencies

Declared dependencies

14 external dependencies (excludes base and recommended)

Depends (4)

R >= 2.10sp sf

Imports (11)

ape fields geiger gifskimethodsphangorn phytools stringiparalleldoParallel foreach

LinkingTo (0)

none

Suggests (3)

knitr rmarkdown testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Datasets

People & History

People (3)

Maintainer (1)

Alexandra Howard

Author, Maintainer

Authors (3)

Alexandra Howard

Author, Maintainer

Maria-Aleja Hurtado-Materon

Author

A. Michelle Lawing

Author, Copyright holder

Copyright holders (1)

A. Michelle Lawing

Author, Copyright holder

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
1.1Latest
2025-03-12 · current release · diff ↗
1.0.3
2024-06-11
R
R 4.4.0 released · 2024-04-24

Package metadata

First published: 2024-06-11
Total releases: 2 / 2 yrs
License: GPL (>= 3) OSI
Minimum R: ≥ 4.4.0
Bundled data: 2.7 MB / 4 files
Download size: 4.4 MB
Installed size: not tracked yet
With dependencies: not tracked yet

Appears in task views

Paleontology

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("ppgm")

Format

Howard, A., Hurtado-Materon, M., & Lawing, A. M. (2025). ppgm: PaleoPhyloGeographic Modeling of Climate Niches and Species Distributions (Version 1.1) [Computer software]. https://doi.org/10.32614/CRAN.package.ppgm

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 ppgm version 1.1 [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.

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