R Observatory: Metrics for DAISIE version 5.0.2

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

DAISIE

5.0.2

Dynamical Assembly of Islands by Speciation, Immigration and Extinction

2packages depend

3.6Kdownloads / year

–test coverage

13/13checks pass

Overview

About

Maintained by Rampal S. EtienneFirst published 2015-05-2114 releasesCRAN page ↗GitHub ↗

Simulates and computes the (maximum) likelihood of a dynamical model of island biota assembly through speciation, immigration and extinction. See Valente et al. (2015) doi:10.1111/ele.12461.

Install

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

install.packages("DAISIE", 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("rsetienne/DAISIE")

Development version from rsetienne/DAISIE. 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-daisie

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-DAISIE

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-DAISIE

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

Health

CRAN checks

13OK

Slowest check: 20.1 min · r-devel-windows-x86_64

Code health

Yes

Tests · ratio 0.59

not tracked

Coverage

100%

Documentation · exports

15

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
OK2026-04-25
12 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-04-22
11 OK · 3 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-18
10 OK · 3 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE

Show 1 earlier snapshots

NOTE2026-03-10
11 OK · 3 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMENoVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 96%
Documented parameters: 92%
Return-value docs: 100%
References docs: 24%

Downloads

3.6K

CRAN downloads in the past year

Rank #8,126 · ~10/day · ~303/mo

Releases R versions

Daily download trend is not available in this view yet.

40730 days

1.1K90 days

3.6K1 year

Compare downloads with other packages →

Also on485 r2u25 autocran53 c2d4u

Repository

GitHub ↗ rsetienne/daisie

10Stars

11Forks

21Open issues

0Open PRs

25Releases

2,859Commits

19Contributors

License GPL-3.0 · 2,859 commits · Last activity 2026-08-07 · 0% stars, 30d

Stars over time

2023-04-25 · 92026-07-07 · 10

Repository practices

Upstream repositoryBeta

5 development-tooling and community-health practices detected across 5 families in the upstream repository

Checks run against github.com/rsetienne/daisie on 2026-08-16.

Continuous integration (1)

GitHub Actions

Reproducibility and dev environment (1)

data-raw/

Research and citation (1)

Zenodo

Lint, format, editor (1)

RStudio project

Show all practices

Coverage (1)

.covrignore

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

Dependencies

Declared dependencies

30 external dependencies (excludes base and recommended)

Depends (1)

R >= 4.2.0

Imports (15)

DDD deSolve doParallel foreachgraphicsmagrittrMatrixparallelpracma Rcppstatssubplex tensor testitutils

LinkingTo (3)

Rcpp RcppEigen BH

Suggests (17)

ape covr dplyr future future.apply ggplot2 ggtree (>= 3.0.0)gridExtra knitr phytools pnd purrr rmarkdown testthat tibble tidytree tidyr

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

2direct

0indirect

DAISIEprep nLTT

Code & Tests

Datasets

People & History

People (15)

Maintainer (1)

Rampal S. Etienne

Author, Maintainer · added in 1.0.1

Authors (10)

Rampal S. Etienne

Author, Maintainer · added in 1.0.1

Richèl J.C. Bilderbeek

Author · added in 3.0.0

Ornela Dehayem Nanwou

Author · added in 4.6.0

Bart Haegeman

Author · added in 3.0.0

Hanno Hildenbrandt

Author · added in 4.2.0

Joshua W. Lambert

Author · added in 3.0.1

Albert B. Phillimore

Author · added in 3.0.0

Pedro Santos Neves

Author · added in 4.3.1

Luis Valente

Author · added in 3.0.0

Shu Xie

Author · added in 3.0.0

Contributors (5)

Torsten Hauffe

Contributor · added in 3.0.0

Thijs Janzen

Contributor · added in 5.0.2

Nadiah Kristensen

Contributor · added in 3.0.0

Giovanni Laudanno

Contributor · added in 3.0.0

Raphael Scherrer

Contributor · added in 3.0.0

Listed in earlier versions (7)

Rampal S. Etienne & Luis M. Valente

no longer listed · 1.0

Luis M. Valente & Albert B. Phillimore

no longer listed · 1.0.1

Albert B. Phillimore & Bart Haegenan

no longer listed · 1.0.2

Luis M. Valente

no longer listed · 1.0.2 to 1.4

Albert B. Phillimore & Bart Haegeman

no longer listed · 1.2 to 1.4

Joshua Lambert

no longer listed · 3.0.0

Pedro Neves

no longer listed · 3.0.0 to 4.2.0

Package Timeline

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

5.0.2Latest
2026-07-31 · current release · diff ↗
R
R 4.6.0 released · 2026-04-24
4.6.0
2025-06-01 · diff ↗
R
R 4.5.0 released · 2025-04-11
4.5.0
2025-02-05 · diff ↗
R
R 4.4.0 released · 2024-04-24
4.4.1
2023-10-22 · diff ↗
R
R 4.3.0 released · 2023-04-21
4.4.0
2023-04-03 · diff ↗
unarchivedReturned to CRAN
2023-04-03
archivedRemoved from CRAN
2023-03-01
issues were not corrected in time
4.3.1
2023-02-13 · diff ↗
4.2.0
2022-06-02 · diff ↗
R
R 4.2.0 released · 2022-04-22
R
R 4.1.0 released · 2021-05-18
3.0.1
2020-08-26 · diff ↗

Show 12 earlier events

3.0.0
2020-08-14 · diff ↗
R
R 4.0.0 released · 2020-04-24
R
R 3.6.0 released · 2019-04-26
R
R 3.5.0 released · 2018-04-23
R
R 3.4.0 released · 2017-04-21
1.4
2017-04-13 · diff ↗
1.2
2016-11-14 · diff ↗
R
R 3.3.0 released · 2016-05-03
1.0.2
2015-09-29 · diff ↗
1.0.1
2015-06-03 · diff ↗
1.0
2015-05-21
R
R 3.2.0 released · 2015-04-16

Package metadata

First published: 2015-05-21
Total releases: 14 / 11 yrs
License: GPL (>= 3) | file LICENSE OSI
Minimum R: ≥ 4.2.0
Bundled data: 592 KB / 17 files
Download size: 1.2 MB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("DAISIE")

Format

Etienne, R. S., Bilderbeek, R. J. C., Dehayem Nanwou, O., Haegeman, B., Hauffe, T., Hildenbrandt, H., Janzen, T., Kristensen, N., Lambert, J. W., Laudanno, G., Phillimore, A. B., Santos Neves, P., Scherrer, R., Valente, L., & Xie, S. (2026). DAISIE: Dynamical Assembly of Islands by Speciation, Immigration and Extinction (Version 5.0.2) [Computer software]. https://doi.org/10.32614/CRAN.package.DAISIE

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 DAISIE version 5.0.2 [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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