R Observatory: Metrics for GUILDS version 1.4.7

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

GUILDS

1.4.7

Implementation of Sampling Formulas for the Unified Neutral Model of Biodiversity and Biogeography, with or without Guild Structure

1packages depend

17.2Kdownloads / year

96.6%test coverage

13/13flavors OK

Overview

About

Maintained by Thijs JanzenCRAN page ↗GitHub ↗Issues ↗

A collection of sampling formulas for the unified neutral model of biogeography and biodiversity. Alongside the sampling formulas, it includes methods to perform maximum likelihood optimization of the sampling formulas, methods to generate data given the neutral model, and methods to estimate the expected species abundance distribution. Sampling formulas included in the GUILDS package are the Etienne Sampling Formula (Etienne 2005), the guild sampling formula, where guilds are assumed to differ in dispersal ability (Janzen et al. 2015), and the guilds sampling formula conditioned on guild size (Janzen et al. 2015).

Install

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

install.packages("GUILDS", 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("thijsjanzen/GUILDS")

Development version from thijsjanzen/GUILDS. 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-guilds

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-GUILDS

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-GUILDS

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: 4.0 min · r-devel-windows-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK14 OK2026-04-22
ERROR13 OK, 1 ERROR2026-04-18
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.4.7

READMEYes · 342 wordsVignettesYes · 1 · dynamicNEWSNoCitation fileYes · cites a publication

Help pages: 15 (1 internal)includes a package overview page
Examples that run: 92%12 run in a plain check · 1 never run
Exported functions with examples: 93%
Documented parameters: 100%
Return-value docs: 86%
Help pages citing references: 47%

Vignettes (1)

Walkthrough HTML

How these are measured

Downloads

17.2K

CRAN downloads in the past year

Rank #3,172 · ~47/day · ~1.4K/mo

Releases R versions

Daily download trend is not available in this view yet.

1.7K30 days

3.8K90 days

17.2K1 year

Compare downloads with other packages →

Also on597 r2u8 autocran6.3K conda_forge250 bioconda

How downloads are counted

Repository

thijsjanzen/guilds ↗Account: thijsjanzen

3Stars

1Forks

0Open issues

1Open PRs

1Releases

168Commits

3Commit identities

168 commits · Last activity 2025-03-13

Responsiveness

How these are sampled

PRs merged (all time): 100%
Median days to close, 50 most recently updated closed issues: 1
Median days to close, 50 most recently updated closed PRs: 0

Stars over time

2025-07-13 · 32026-07-07 · 3

How these are measured

PracticesBeta

7 development-tooling and community-health practices detected across 4 families in the upstream repository

Checks run against github.com/thijsjanzen/guilds on 2026-10-11.

Continuous integration (2)

GitHub ActionsR CMD check workflow

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

Docs source (3)

pkgdown

GitHub Pages site last deployed 2025-03-13 · The repository has a site deploy workflow

Coverage (1)

Coverage reporting

Lint, format, editor (1)

RStudio project

How this is detected·Detection ruleset v3 (2026-09-26)

Dependencies

Declared dependencies

7 external dependencies (excludes base and recommended)

Installing GUILDS adds 3 packages (2 with compiled code, 4.3 MB of source tarballs). Heaviest: nloptr 2.1 MB, Rcpp 1.8 MB, pracma 389 KB.

Depends (0)

none

Imports (3)

nloptr pracma Rcpp

LinkingTo (1)

Rcpp

Suggests (3)

knitr rmarkdown testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

1direct

11indirect

Imports 1

Depends, Imports or LinkingTo, most downloaded first

sads

How these are counted

Code & Tests

People & History

People (4)

Thijs Janzen

Author, Maintainer since 1.0 (2014)

Jerome Chave

Contributor · added in 1.3

Bart Haegeman

Contributor · added in 1.3

Franck Jabot

Contributor · added in 1.3

Releases (11)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
R
R 4.5.0 released · 2025-04-11
1.4.7Latest
record
2025-03-11 · current release · diff ↗
R
R 4.4.0 released · 2024-04-24
1.4.6
record
2023-08-21 · diff ↗
R
R 4.3.0 released · 2023-04-21
R
R 4.2.0 released · 2022-04-22
1.4.5
record
2022-03-24 · diff ↗
1.4.4
record
2022-03-16 · diff ↗
1.4.1
record
2022-02-25 · diff ↗
1.4
record
2022-02-24 · diff ↗ ·
removed 1 export
simplex
R
R 4.1.0 released · 2021-05-18
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

Show 8 earlier eventsHide 8 earlier events

1.3
record
2016-09-26 · diff ↗ ·
removed 1 export
pattern:^[[:alpha:]]+

added 15 exports
generate.ESF, generate.Guilds, generate.Guilds.Cond, expected.SAD.Guilds.Conditional, expected.SAD.Guilds, expected.SAD, logLikelihood.ESF, logLikelihood.Guilds, logLikelihood.Guilds.Conditional, maxLikelihood.ESF, maxLikelihood.Guilds, maxLikelihood.Guilds.Conditional, preston_plot, calcKDA, simplex
R
R 3.3.0 released · 2016-05-03
1.2.1
record
2015-04-21 · diff ↗
R
R 3.2.0 released · 2015-04-16
1.2
record
2014-09-07 · diff ↗
1.1
record
2014-09-06 · diff ↗
1.0
record
2014-09-05
R
R 3.1.0 released · 2014-04-10

Package metadata

First published: 2014-09-05
Total releases: 11 / 12 yrs
License: GPL-2 OSI
Download size: 91 KB

Cite

Cite this package

Run in R for the authors' entry:

citation("GUILDS")

The package provides a citation file, so citation() returns the authors' own entry.

It points to 10.1016/j.jtbi.2015.03.018.

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 GUILDS version 1.4.7 [Data set]. HJJB, LLC. Data release v2026-10-17. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-17, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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