R Observatory: Metrics for DAISIEprep version 1.0.1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

DAISIEprep

1.0.1Package record

Extracts Phylogenetic Island Community Data from Phylogenetic Trees

0packages depend

3.1Kdownloads / year

–test coverage

13/13flavors OK

Overview

About

Maintained by Joshua W. LambertCRAN page ↗GitHub ↗Website ↗Issues ↗

Extracts colonisation and branching times of island species to be used for analysis in the R package 'DAISIE'. It uses phylogenetic and endemicity data to extract the separate island colonists and store them.

Changes in 1.0.1

A patch release to due to testing errors occurring since {ggplot2} v4.0.0 was released. Tests using

plot_phylod() which depends on {ggtree} and thus {ggplot2} are temporarily

skipped due to errors on R devel to prevent the package becoming archived,

and will be fixed shortly in another patch release.

This release also updates the package maintainer email.

NEW FEATURES

New DAISIE FAQ vignette (@Neves-P & @luislvalente, #55 & #56).

MINOR IMPROVEMENTS

Updated test-coverage.yaml GitHub actions workflow.

BUG FIXES

None

DEPRECATED AND DEFUNCT

Show all changes in 1.0.1Hide the rest of the changes in 1.0.1

None

From NEWS.md in the release

Install

R (CRAN)pak (dev)Ubuntu (r2u)

install.packages("DAISIEprep", 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("joshwlambert/DAISIEprep")

Development version from joshwlambert/DAISIEprep. 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-daisieprep

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

Health

CRAN checks

13OK

CRAN check page ↗

Slowest check: 6.2 min · r-oldrel-windows-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 1.0.1

READMEYes · 496 wordsVignettesYes · 6 · dynamicNEWSYes · 100% structured · mentions 1.0.1Citation fileNoWebsiteYes · pkgdown

The repository also keeps web-only articles.

Help pages: 82 (8 internal)includes a package overview page
Examples that run: 100%39 run in a plain check
Exported functions with examples: 71%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 0%

Vignettes (6)

DAISIE FAQs HTML
DAISIEprep Tutorial HTML
Extracting species with multiple tips in the phylogeny HTML
Forcing non-endemic singletons: solutions and limitations HTML
Performance HTML
Sensitivity HTML

How these are measured

Downloads

3.1K

CRAN downloads in the past year

Rank #14,232 · ~8/day · ~254/mo

Releases R versions

Daily download trend is not available in this view yet.

25630 days

84290 days

3.1K1 year

Compare downloads with other packages →

Also on112 r2u

How downloads are counted

Repository

joshwlambert/daisieprep ↗Account: joshwlambert

6Stars

4Forks

5Open issues

1Open PRs

12Releases

474Commits

5Commit identities

phylogeneticsisland-biogeographydata-sciencer

License file reads as GPL-3.0 · 474 commits · Last activity 2026-05-15 · Default branch at 1.0.1.9000, ahead of CRAN 1.0.1 (checked 2026-10-25)

Responsiveness

How these are sampled

PRs merged (all time): 96%
Median days to close, 50 most recently updated closed issues: 48
Median days to close, 50 most recently updated closed PRs: 0

Stars over time

2023-02-22 · 62026-07-07 · 6

How these are measured

PracticesBeta

13 development-tooling and community-health practices detected across 8 families in the upstream repository

Checks run against github.com/joshwlambert/daisieprep on 2026-10-25.

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 (2)

Code of conductContributing guide

Docs source (3)

pkgdown

GitHub Pages site last deployed 2026-05-15 · The repository has a site deploy workflow

pkgdown site last built 2026-05-15

Coverage (1)

Coverage reporting

Show all practicesHide 4 practices

Reproducibility and dev environment (1)

data-raw/

CRAN release process (2)

cran-comments.mdrevdep/

Research and citation (1)

Zenodo

Lint, format, editor (1)

RStudio project

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

Dependencies

Declared dependencies

18 external dependencies (excludes base and recommended)

Installing DAISIEprep adds 87 packages (50 with compiled code, 78 MB of source tarballs). Heaviest: BH 14 MB, stringi 11 MB, ggplot2 6.0 MB. 1 more not on CRAN is not measured.

Depends (1)

R >= 4.0

Imports (10)

methodsape phylobase ggplot2 scales ggtree DAISIE castor tibble rlang

LinkingTo (0)

none

Suggests (9)

testthat knitr rmarkdown covr diversitree corHMM tidyr dplyr ggimage

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

How these are counted

Code & Tests

Datasets

People & History

People (5)

Joshua W. Lambert

Author, Maintainer since 0.3.2 (2023)

Author

Author

Author

Author

Releases (4)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
1.0.1Latest
record
2025-10-31 · current release · diff ↗
R
R 4.5.0 released · 2025-04-11
1.0.0
record
2024-12-18 · diff ↗
R
R 4.4.0 released · 2024-04-24
0.4.0
record
2024-04-02 · diff ↗
0.3.2
record
2023-04-25
R
R 4.3.0 released · 2023-04-21

Package metadata

First published: 2023-04-25
Total releases: 4 / 3 yrs
License: GPL (>= 3) OSI
Minimum R: ≥ 4.0
Bundled data: 39 KB / 17 files
Download size: 2.0 MB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("DAISIEprep")

Format

Lambert, J. W., Pannetier, T., Roeble, L., Santos Neves, P., & Valente, L. (2025). DAISIEprep: Extracts Phylogenetic Island Community Data from Phylogenetic Trees (Version 1.0.1) [Computer software]. https://doi.org/10.32614/CRAN.package.DAISIEprep

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 DAISIEprep version 1.0.1 [Data set]. HJJB, LLC. Data release v2026-10-26. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-26, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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