R Observatory: Metrics for palaeoverse version 1.5.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

palaeoverse

1.5.0Package record

Prepare and Explore Data for Palaeobiological Analyses

1packages dependsuggested by 3

6.3Kdownloads / year

96.5%test coverage

13/13flavors OK

Overview

About

Maintained by Lewis A. JonesCRAN page ↗GitHub ↗Website ↗Issues ↗

Provides functionality to support data preparation and exploration for palaeobiological analyses, improving code reproducibility and accessibility. The wider aim of 'palaeoverse' is to bring the palaeobiological community together to establish agreed standards. The package currently includes functionality for data cleaning, binning (time and space), exploration, summarisation and visualisation. Reference datasets (i.e. Geological Time Scales https://stratigraphy.org/chart/) and auxiliary functions are also provided. Details can be found in: Jones et al., (2023) <doi: 10.1111/2041-210X.14099>.

Changes in 1.5.0

New features

Added tax_certainty() (#109)
Added group argument to tax_range_time() and tax_range_strat() and improved plotting (#120)
Made bin durations more even and added n_bins option in time_bins() (#131)
Added autofit argument to axis_geo() which, when enabled, automatically adjusts the sizes of individual interval labels to fit within the interval boxes (#21)
Added title argument to axis_geo() which can be used to add a title to the axis with the timescale (#133)
Increased efficiency and reduced hackiness of group_apply() (#135)
Downloads related to the palaeorotate() function are now retried if they fail (#137)

Other changes

tax_range_time() and tax_range_strat() now reset row names of the output (#120).

From NEWS.md in the release

Install

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

install.packages("palaeoverse", 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("palaeoverse/palaeoverse")

Development version from palaeoverse/palaeoverse. 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-palaeoverse

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-palaeoverse

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-palaeoverse

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: 3.9 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-06-22
ERROR12 OK, 1 ERROR2026-06-19
OK13 OK2026-05-24

Show 2 earlier changesHide 2 earlier changes

ERROR11 OK, 2 ERROR2026-05-17
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.5.0

READMEYes · 528 wordsVignettesYes · 3 · staticNEWSYes · 100% structured · mentions 1.5.0Citation fileYes · cites a publicationWebsiteYes · pkgdown

Help pages: 26 (1 internal)includes a package overview page
Examples that run: 89%17 run in a plain check (2 of them under a condition) · 2 never run
Exported functions with examples: 95%
Documented parameters: 100%
Return-value docs: 95%
Help pages citing references: 0%

Vignettes (3)

How these are measured

Downloads

6.3K

CRAN downloads in the past year

Rank #6,243 · ~17/day · ~522/mo

Releases R versions

Daily download trend is not available in this view yet.

43330 days

1.3K90 days

6.3K1 year

Compare downloads with other packages →

Also on83 r2u4 autocran443 conda_forge

How downloads are counted

Repository

palaeoverse/palaeoverse ↗Organization: palaeoverse

29Stars

9Forks

63Open issues

14Open PRs

8Releases

665Commits

13Commit identities

biodiversityfossilpalaeobiologyr-packagepaleobiology

License file reads as GPL-3.0 · 665 commits · Last activity 2026-10-23 · 0% stars, 30d · Default branch at 1.5.0.9000, ahead of CRAN 1.5.0 (checked 2026-10-22)

Responsiveness

How these are sampled

PRs merged (all time): 93%
Median days to close, 50 most recently updated closed issues: 94
Median days to close, 50 most recently updated closed PRs: 6

Stars over time

2025-10-18 · 242026-07-07 · 29

How these are measured

PracticesBeta

15 development-tooling and community-health practices detected across 7 families in the upstream repository

Checks run against github.com/palaeoverse/palaeoverse on 2026-10-22.

Continuous integration (2)

GitHub ActionsR CMD check workflow

The R CMD check workflow runs on Linux, macOS and Windows, and on R-devel

Governance and community (4)

Code of conductContributing guideIssue templatesPR template

Docs source (3)

pkgdown

GitHub Pages site last deployed 2026-10-19 · The repository has a site deploy workflow

pkgdown site last built 2026-08-20

Coverage (1)

Coverage reporting (Codecov)

Show all practicesHide 3 practices

CRAN release process (1)

cran-comments.md

Research and citation (1)

CITATION.cff

Lint, format, editor (3)

Lint workflowjarlRStudio project

How this is detected·Detection ruleset v4 (2026-10-20)

AI coding toolsBeta

This repository shows signs of AI coding tools.

Claude Codefirst seen 2026-06-08
Named in .Rbuildignore: .claude
Commits: at least 11 crediting it in the message

Models named in its commits

Claude Opus 511 commits · Sep 2026

Counts are commits, not lines of code. Commits by a tool's accounts count once across all of its accounts. Commits crediting it are the largest count among its credit lines, a minimum.How this is detected·Detection ruleset v4 (updated 2026-09-27)

Dependencies

Declared dependencies

16 external dependencies (excludes base and recommended)

Installing palaeoverse adds 48 packages (35 with compiled code, 44 MB of source tarballs). Heaviest: stringi 11 MB, sf 9.3 MB, s2 2.8 MB.

Depends (1)

R >= 4.0

Imports (13)

ape curl geospheregraphicsh3jsr httr lifecyclemethodspbapply sfstatsstringdistutils

LinkingTo (0)

none

Suggests (7)

covr knitr paleotree phytools rmarkdown testthat (>= 3.0.0)vdiffr

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

1direct

0indirect

Imports 1

Suggested by 3

Depends, Imports or LinkingTo, most downloaded first

rTARDIS

Suggests, most downloaded first

rphylopic deeptime rmacrostrat

How these are counted

Code & Tests

Datasets

People & History

People (14)

Lewis A. Jones

Author, Maintainer since 1.0.0 (2022)

Bethany J. Allen

Author

Etienne Bacher

Author · added in 1.5.0

Christopher D. Dean

Author

Kilian Eichenseer

Author

Joseph T. Flannery-Sutherland

Author

William Gearty

Author

Lucas Buffan

Contributor

A. Alessandro Chiarenza

Contributor

Contributor

Contributor

Contributor

Contributor

Contributor

Releases (8)

Pick two releases to compare their code metrics.

1.5.0Latest
record
2026-06-11 · current release · diff ↗ ·
added 1 export
tax_certainty
R
R 4.6.0 released · 2026-04-24
R
R 4.5.0 released · 2025-04-11
1.4.0
record
2024-10-14 · diff ↗ ·
added 2 exports
lat_bins_area, lat_bins_degrees
R
R 4.4.0 released · 2024-04-24
1.3.0
record
2024-04-16 · diff ↗ ·
added 1 export
tax_range_strat
1.2.1
record
2023-08-17 · diff ↗
R
R 4.3.0 released · 2023-04-21
1.2.0
record
2023-04-18 · diff ↗
1.1.1
record
2023-02-16 · diff ↗
1.1.0
record
2023-01-12 · diff ↗ ·
added 1 export
axis_geo_phylo
1.0.0
record
2022-10-31
R
R 4.2.0 released · 2022-04-22

Package metadata

First published: 2022-10-31
Total releases: 8 / 4 yrs
License: GPL (>= 3) OSI
Minimum R: ≥ 4.0
Bundled data: 381 KB / 5 files
Download size: 3.2 MB

Appears in task views

Paleontology

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("palaeoverse")

The package provides a citation file that builds its entry when R runs it. Run citation() to see it.

The repository also keeps a CITATION.cff.

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 palaeoverse version 1.5.0 [Data set]. HJJB, LLC. Data release v2026-10-23. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-23, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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