R Observatory: Metrics for DDD version 5.2.5

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

DDD

5.2.5Package record

Diversity-Dependent Diversification

7packages dependsuggested by 1

12.7Kdownloads / year

–test coverage

13/13flavors OK

Overview

About

Maintained by Rampal S. EtienneCRAN page ↗Website ↗

Implements maximum likelihood and bootstrap methods based on the diversity-dependent birth-death process to test whether speciation or extinction are diversity-dependent, under various models including various types of key innovations. See Etienne et al. 2012, Proc. Roy. Soc. B 279: 1300-1309, DOI:10.1098/rspb.2011.1439, Etienne & Haegeman 2012, Am. Nat. 180: E75-E89, DOI:10.1086/667574, Etienne et al. 2016. Meth. Ecol. Evol. 7: 1092-1099, DOI:10.1111/2041-210X.12565 and Laudanno et al. 2021. Syst. Biol. 70: 389–407, DOI:10.1093/sysbio/syaa048. Also contains functions to simulate the diversity-dependent process.

Install

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

install.packages("DDD", 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-ddd

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-DDD

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-DDD

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: 6.1 min · r-devel-windows-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK12 OK2026-04-25
NOTE12 OK, 2 NOTE2026-04-22
ERROR11 OK, 2 NOTE, 1 ERROR2026-04-18

Show 1 earlier changeHide 1 earlier change

NOTE12 OK, 2 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 5.2.5

README· In the repository, left out of the releaseVignettesNoNEWSNoCitation fileNoWebsiteYes · pkgdown

Help pages: 30 (1 internal)includes a package overview page
Examples that run: 100%23 run in a plain check
Exported functions with examples: 82%
Documented parameters: 99%
Return-value docs: 100%
Help pages citing references: 67%

How these are measured

Downloads

12.7K

CRAN downloads in the past year

Rank #3,358 · ~35/day · ~1.1K/mo

Releases R versions

Daily download trend is not available in this view yet.

1K30 days

3.3K90 days

12.7K1 year

Compare downloads with other packages →

Also on589 r2u8 autocran121 c2d4u

How downloads are counted

Repository

rsetienne/ddd ↗Account: rsetienne

4Stars

3Forks

0Open issues

2Open PRs

0Releases

281Commits

8Commit identities

281 commits · Last activity 2026-05-04 · 0% stars, 30d

Responsiveness

How these are sampled

PRs merged (all time): 78%
Median days to close, 50 most recently updated closed issues: 68
Median days to close, 50 most recently updated closed PRs: 0

Stars over time

2025-01-08 · 42026-07-07 · 4

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/rsetienne/ddd 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 2026-05-04 · The repository has a site deploy workflow

pkgdown site last built 2026-05-04

Coverage (1)

Coverage reporting

Lint, format, editor (1)

RStudio project

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

Dependencies

Declared dependencies

15 external dependencies (excludes base and recommended)

Installing DDD adds 36 packages (20 with compiled code, 36 MB of source tarballs). Heaviest: BH 14 MB, igraph 4.8 MB, maps 2.2 MB.

Depends (1)

R >= 3.5.0

Imports (10)

deSolve ape phytools subplex DEoptim psoMatrixexpm SparseM Rcpp

LinkingTo (3)

Rcpp RcppEigen BH

Suggests (3)

testthat testit igraph

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

7direct

1indirect

Imports 7

Suggested by 1

Depends, Imports or LinkingTo, most downloaded first

treestats DAISIE PBD secsse nodeSub DAMOCLES SADISA

Suggests, most downloaded first

nLTT

How these are counted

Code & Tests

People & History

People (4)

Rampal S. Etienne

Author, Maintainer since 0.2 (2012)

Bart Haegeman

Author

Hanno Hildenbrandt

Contributor · added in 5.2.1

Giovanni Laudanno

Contributor · added in 5.2.1

Releases (50)

Pick two releases to compare their code metrics.

5.2.5Latest
record
2026-05-04 · current release · diff ↗
R
R 4.6.0 released · 2026-04-24
5.2.4
record
2025-11-28 · diff ↗
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
5.2.2
record
2023-07-11 · diff ↗
R
R 4.3.0 released · 2023-04-21
5.2.1
record
2023-02-22 · diff ↗
R
R 4.2.0 released · 2022-04-22
5.0
record
2021-07-19 · diff ↗
R
R 4.1.0 released · 2021-05-18
4.4.1
record
2021-01-14 · diff ↗
4.4
record
2020-06-03 · diff ↗
R
R 4.0.0 released · 2020-04-24
4.3
record
2020-04-01 · diff ↗
4.2
record
2020-02-10 · diff ↗

Show 50 earlier eventsHide 50 earlier events

4.1
record
2019-06-21 · diff ↗ ·
added 1 export
rng_respecting_sample
R
R 3.6.0 released · 2019-04-26
4.0
record
2019-04-22 · diff ↗ ·
added 1 export
td_sim
3.9
record
2019-03-19 · diff ↗
3.8.1
record
2019-03-12 · diff ↗ ·
removed 1 export
pattern:^[[:alpha:]]+

added 26 exports
L2brts, L2phylo, bd_ML, bd_loglik, brts2phylo, conv, dd_KI_ML, dd_KI_loglik, dd_KI_sim, dd_LR, dd_ML, dd_MS_ML, dd_MS_loglik, dd_MS_sim, dd_SR_ML, dd_SR_loglik, dd_SR_sim, dd_loglik, dd_sim, optimizer, phylo2L, roundn, sample2, simplex, transform_pars, untransform_pars
3.7
record
2018-04-24 · diff ↗
R
R 3.5.0 released · 2018-04-23
3.6
record
2018-02-07 · diff ↗
3.5
record
2017-10-01 · diff ↗
R
R 3.4.0 released · 2017-04-21
3.4
record
2017-02-24 · diff ↗
3.3
record
2016-11-07 · diff ↗
R
R 3.3.0 released · 2016-05-03
3.2
record
2016-02-09 · diff ↗
3.1
record
2016-01-19 · diff ↗
R
R 3.2.0 released · 2015-04-16
R
R 3.1.0 released · 2014-04-10
3.0.3
record
2013-10-18 · diff ↗
3.0.2
record
2013-08-23 · diff ↗
3.0.1
record
2013-05-14 · diff ↗
R
R 3.0.0 released · 2013-04-03
3.0.0
record
2013-03-25 · diff ↗
3.0
record
2015-11-13 · diff ↗
2.15.3
record
2012-11-29 · diff ↗
2.15.2
record
2012-10-26 · diff ↗
2.15.1
record
2012-06-08 · diff ↗
R
R 2.15.0 released · 2012-03-30
2.14.2
record
2012-02-09 · diff ↗
2.7
record
2015-03-20 · diff ↗
2.6
record
2014-12-18 · diff ↗
2.5
record
2014-05-26 · diff ↗
2.4
record
2013-10-23 · diff ↗
2.3
record
2013-10-01 · diff ↗
2.2
record
2013-08-24 · diff ↗
2.1
record
2013-05-15 · diff ↗
2.0
record
2013-05-03 · diff ↗
1.11
record
2013-03-25 · diff ↗
1.10
record
2013-03-05 · diff ↗
1.9
record
2012-11-29 · diff ↗
1.8
record
2012-11-16 · diff ↗
1.7
record
2012-10-26 · diff ↗
1.5
record
2012-10-02 · diff ↗
1.4
record
2012-09-24 · diff ↗
1.3
record
2012-09-14 · diff ↗
1.2
record
2012-06-28 · diff ↗
1.1
record
2012-04-26 · diff ↗
0.4
record
2012-02-08 · diff ↗
0.3
record
2012-02-04 · diff ↗
0.2
record
2012-01-31
R
R 2.14.0 released · 2011-10-31

Package metadata

First published: 2012-01-31
Total releases: 50 / 14 yrs
License: GPL-3 OSI
Minimum R: ≥ 3.5.0
Download size: 94 KB

Appears in task views

Phylogenetics

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("DDD")

Format

Etienne, R. S., Haegeman, B., Hildenbrandt, H., & Laudanno, G. (2026). DDD: Diversity-Dependent Diversification (Version 5.2.5) [Computer software]. https://doi.org/10.32614/CRAN.package.DDD

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 DDD version 5.2.5 [Data set]. HJJB, LLC. Data release v2026-10-18. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-18, which the citation names so these numbers can be found later. More on citing and the projects behind them.

Report a problem with this page →