R Observatory: Metrics for FossilSim version 2.4.4

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

FossilSim

2.4.4Package record

Simulation and Plots for Fossil and Taxonomy Data

2packages dependsuggested by 2

5.9Kdownloads / year

–test coverage

13/13flavors OK

Overview

About

Maintained by Joëlle Barido-SottaniCRAN page ↗

Simulating and plotting taxonomy and fossil data on phylogenetic trees under mechanistic models of speciation, preservation and sampling.

Changes in 2.4.4

some dependencies were made optional to make installation easier

From NEWS.md in the release

Install

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

install.packages("FossilSim", 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-fossilsim

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-FossilSim

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-FossilSim

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: 5.5 min · r-oldrel-macos-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 OK2026-05-10

Show 2 earlier changesHide 2 earlier changes

ERROR12 OK, 1 ERROR2026-05-03
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 2.4.4

READMEYes · 144 wordsVignettesYes · 6 · dynamicNEWSYes · 100% structured · mentions 2.4.4Citation fileNoWebsitenot declared in DESCRIPTION

Help pages: 50includes a package overview page
Examples that run: 100%41 run in a plain check (1 of them under a condition)
Exported functions with examples: 82%
Documented parameters: 100%
Return-value docs: 89%
Help pages citing references: 4%

Vignettes (6)

Converting from and to paleotree format HTML
Exporting sampled ancestor trees HTML
Introduction to FossilSim HTML
Simulating fossils HTML
Simulating taxonomy HTML
Simulating trees from the fossilized birth-death process HTML

How these are measured

Downloads

5.9K

CRAN downloads in the past year

Rank #7,391 · ~16/day · ~496/mo

Releases R versions

Daily download trend is not available in this view yet.

46930 days

1.2K90 days

5.9K1 year

Compare downloads with other packages →

Also on166 r2u8 autocran91 c2d4u

How downloads are counted

Dependencies

Declared dependencies

13 external dependencies (excludes base and recommended)

Installing FossilSim adds 28 packages (18 with compiled code, 23 MB of source tarballs). Heaviest: stringi 11 MB, Rcpp 1.8 MB, ape 1.4 MB.

Depends (1)

R >= 2.10

Imports (4)

apemethodsrlang tidytree

LinkingTo (0)

none

Suggests (10)

paleotree knitr rmarkdown devtools TreeSim treeio ggtree ggfun ggplot2 ggrepel

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

2direct

0indirect

Imports 2

Suggested by 2

Depends, Imports or LinkingTo, most downloaded first

FossilSimShiny MorphSim

Suggests, most downloaded first

admtools StratPal

How these are counted

Code & Tests

People & History

People (5)

Joëlle Barido-Sottani

Author, Maintainer, Copyright holder · added in 2.4.4

Joseph O'Reilly

Author, Copyright holder · added in 2.4.4

Walker Pett

Author, Copyright holder

Ugnė Stolz

Author, Copyright holder · added in 2.4.0

Rachel Warnock

Author, Copyright holder

Maintainer since 2.0.0 (2018)

Listed in earlier versions (1)

Joelle Barido-Sottani

no longer listed · 2.0.0 to 2.4.3

Releases (13)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
2.4.4Latest
record
2026-02-26 · current release · diff ↗
2.4.3
record
2025-11-06 · diff ↗
2.4.2
record
2025-10-28 · diff ↗
R
R 4.5.0 released · 2025-04-11
2.4.1
record
2024-10-02 · diff ↗
2.4.0
record
2024-09-05 · diff ↗ ·
added 2 exports
fbdrange, get_fbdrange_from_file
2.3.3
record
2024-04-29 · diff ↗
R
R 4.4.0 released · 2024-04-24
2.3.2
record
2023-10-05 · diff ↗
R
R 4.3.0 released · 2023-04-21
2.3.1
record
2022-07-19 · diff ↗
R
R 4.2.0 released · 2022-04-22
2.3.0
record
2022-04-19 · diff ↗
R
R 4.1.0 released · 2021-05-18
2.2.0
record
2021-04-05 · diff ↗ ·
added 1 export
reconstructed.tree.fossils.objects

Show 6 earlier eventsHide 6 earlier events

R
R 4.0.0 released · 2020-04-24
R
R 3.6.0 released · 2019-04-26
2.1.1
record
2019-02-21 · diff ↗
2.1.0
record
2018-11-16 · diff ↗ ·
added 14 exports
fossils.to.BEAST.constraints, fossils.to.BEAST.start.tree, get.tip.descs, place.fossils, prune.fossil.tips, rangeplot.asymmetric, remove.stem.fossils, remove.stem.lineages, species.end, species.start, subsample.fossils.oldest, subsample.fossils.oldest.and.youngest, subsample.fossils.uniform, subsample.fossils.youngest
2.0.0
record
2018-07-28
R
R 3.5.0 released · 2018-04-23

Package metadata

First published: 2018-07-28
Total releases: 13 / 8 yrs
License: GPL-3 OSI
Minimum R: ≥ 2.10
Download size: 1.2 MB

Appears in task views

Paleontology Phylogenetics

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("FossilSim")

Format

Barido-Sottani, J., O'Reilly, J., Pett, W., Stolz, U., & Warnock, R. (2026). FossilSim: Simulation and Plots for Fossil and Taxonomy Data (Version 2.4.4) [Computer software]. https://doi.org/10.32614/CRAN.package.FossilSim

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 FossilSim version 2.4.4 [Data set]. HJJB, LLC. Data release v2026-10-25. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-25, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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