R Observatory: Metrics for cladoRcpp version 0.15.1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

cladoRcpp

0.15.1Package record

C++ Implementations of Phylogenetic Cladogenesis Calculations

1packages depend

9.2Kdownloads / year

–test coverage

13/13flavors OK

Overview

About

Maintained by Nicholas J. MatzkeCRAN page ↗Website ↗

Various cladogenesis-related calculations that are slow in pure R are implemented in C++ with Rcpp. These include the calculation of the probability of various scenarios for the inheritance of geographic range at the divergence events on a phylogenetic tree, and other calculations necessary for models which are not continuous-time markov chains (CTMC), but where change instead occurs instantaneously at speciation events. Typically these models must assess the probability of every possible combination of (ancestor state, left descendent state, right descendent state). This means that there are up to (# of states)^3 combinations to investigate, and in biogeographical models, there can easily be hundreds of states, so calculation time becomes an issue. C++ implementation plus clever tricks (many combinations can be eliminated a priori) can greatly speed the computation time over naive R implementations. CITATION INFO: This package is the result of my Ph.D. research, please cite the package if you use it! Type: citation(package="cladoRcpp") to get the citation information.

Install

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

install.packages("cladoRcpp", 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-cladorcpp

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-cladoRcpp

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-cladoRcpp

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: 2.8 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 0.15.1

READMENoVignettesNoNEWSYes · 0% structuredCitation fileYes · computed when R runs itWebsiteYes

Help pages: 17includes a package overview page
Examples that run: 100%17 run in a plain check
Exported functions with examples: 100%
Documented parameters: 95%
Return-value docs: 100%
Help pages citing references: 18%

How these are measured

Downloads

9.2K

CRAN downloads in the past year

Rank #4,155 · ~25/day · ~765/mo

Releases R versions

Daily download trend is not available in this view yet.

83230 days

2.1K90 days

9.2K1 year

Compare downloads with other packages →

Also on435 r2u10 autocran103 c2d4u

How downloads are counted

Dependencies

Declared dependencies

3 external dependencies (excludes base and recommended)

Installing cladoRcpp adds 2 packages (2 with compiled code, 2.8 MB of source tarballs). Heaviest: Rcpp 1.8 MB, RcppArmadillo 1.0 MB.

Depends (0)

none

Imports (1)

Rcpp

LinkingTo (2)

Rcpp RcppArmadillo

Suggests (0)

none

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

1direct

0indirect

Imports 1

Depends, Imports or LinkingTo, most downloaded first

deepSTRAPP

How these are counted

Code & Tests

People & History

People (1)

Nicholas J. Matzke

Listed in earlier versions (2)

U.C. Berkeley

no longer listed · 0.1

Dept. of Integrative Biology

no longer listed · 0.1

Releases (7)

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
R
R 4.4.0 released · 2024-04-24
R
R 4.3.0 released · 2023-04-21
R
R 4.2.0 released · 2022-04-22
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
0.15.1Latest
record
2018-11-21 · current release · diff ↗
0.15
record
2018-10-09 · diff ↗ ·
removed 1 export
pattern:^[[:alpha:]]+

added 16 exports
Rcpp_combn_zerostart, areas_list_to_states_list_old, numstates_from_numareas, rcpp_areas_list_to_states_list, rcpp_calc_anclikes_sp, rcpp_calc_anclikes_sp_COOprobs, rcpp_calc_anclikes_sp_COOweights_faster, rcpp_calc_anclikes_sp_prebyte, rcpp_calc_anclikes_sp_rowsums, rcpp_calc_anclikes_sp_using_COOprobs, rcpp_calc_rowsums_for_COOweights_columnar, rcpp_calc_splitlikes_using_COOweights_columnar, rcpp_convolve, rcpp_mult2probvect, rcpp_states_list_to_DEmat, strsplit3
R
R 3.5.0 released · 2018-04-23
R
R 3.4.0 released · 2017-04-21
R
R 3.3.0 released · 2016-05-03
R
R 3.2.0 released · 2015-04-16
0.14.4
record
2014-05-18 · diff ↗
R
R 3.1.0 released · 2014-04-10

Show 5 earlier eventsHide 5 earlier events

0.14.2
record
2013-07-15 · diff ↗
0.14
record
2013-06-23 · diff ↗
0.11
record
2013-04-11 · diff ↗
0.1
record
2013-04-04
R
R 3.0.0 released · 2013-04-03

Package metadata

First published: 2013-04-04
Total releases: 7 / 13 yrs
License: GPL (>= 2) OSI
Download size: 62 KB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("cladoRcpp")

The package provides a citation file that builds its entry when R runs it. Run citation() to see it.

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 cladoRcpp version 0.15.1 [Data set]. HJJB, LLC. Data release v2026-10-20. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-20, 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 →