RcppTskit

0.2.0

'R' Access to the 'tskit C' API

0packages depend

1Kdownloads / year

21.1%test coverage

13/13checks pass

Overview

About

Maintained by Gregor GorjancFirst published 2026-02-271 releasesCRAN page ↗GitHub ↗

'Tskit' enables efficient storage, manipulation, and analysis of ancestral recombination graphs (ARGs) using succinct tree sequence encoding. The tree sequence encoding of an ARG is described in Wong et al. (2024) doi:10.1093/genetics/iyae100, while `tskit` project is described in Jeffrey et al. (2026) doi:10.48550/arXiv.2602.09649. See also https://tskit.dev for project news, documentation, and tutorials. 'Tskit' provides 'Python', 'C', and 'Rust' application programming interfaces (APIs). The 'Python' API can be called from 'R' via the 'reticulate' package to load and analyse tree sequences as described at https://tskit.dev/tutorials/tskitr.html. 'RcppTskit' provides 'R' access to the 'tskit C' API for cases where the 'reticulate' option is not optimal; for example, high-performance or low-level work with tree sequences. Currently, 'RcppTskit' provides a limited set of 'R' functions because the 'Python' API and 'reticulate' already covers most needs.

Install

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

install.packages("RcppTskit", 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("HighlanderLab/RcppTskit")

Development version from HighlanderLab/RcppTskit. 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-rcpptskit

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-RcppTskit

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-RcppTskit

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

Health

CRAN checks

13OK

Slowest check: 4.3 min · r-oldrel-macos-x86_64

Code health

Yes

Tests · ratio 1.08

21.1%

Coverage · measured lines

100%

Documentation · exports

Dependencies · direct

Check history

OK2026-04-25
12 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
WARNING2026-04-22
13 OK · 0 NOTE · 1 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-18
12 OK · 0 NOTE · 1 WARNING · 1 ERROR · 0 FAILURE
WARNING2026-04-09
13 OK · 0 NOTE · 1 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-03-26
12 OK · 0 NOTE · 1 WARNING · 1 ERROR · 0 FAILURE

Show 1 earlier snapshots

WARNING2026-03-10
13 OK · 0 NOTE · 1 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMENoVignettesNopkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 70%
Documented parameters: 100%
Return-value docs: 78%
References docs: 0%

Downloads

CRAN downloads in the past year

Rank #21,230 · ~3/day · ~86/mo

Releases R versions

Daily download trend is not available in this view yet.

17830 days

57090 days

1K1 year

Compare downloads with other packages →

Also on159 r2u8 autocran

Repository

GitHub ↗ highlanderlab/rcpptskit

3Stars

5Forks

30Open issues

1Open PRs

0Releases

144Commits

4Contributors

144 commits · Last activity 2026-04-10

Repository practices

Upstream repositoryBeta

3 development-tooling and community-health practices detected across 3 families in the upstream repository

Checks run against github.com/highlanderlab/rcpptskit on 2026-07-19.

Continuous integration (1)

GitHub Actions

Automation and maintenance (1)

pre-commit

Git structural (1)

Submodules

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

Dependencies

Declared dependencies

9 external dependencies (excludes base and recommended)

Depends (1)

R >= 4.0.0

Imports (4)

methodsR6 Rcpp reticulate

LinkingTo (1)

Rcpp

Suggests (5)

covr knitr quarto spelling testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Code Composition

C 30,035 (84%)R 2,663 (7%)Rd 1,428 (4%)C++ 1,131 (3%)Vignettes 415 (1%)Other 146 (0%)

Code characteristics

Object systems

R62

Cyclomatic complexity: 1.0 median / 8 max
Test cases: 12 / 1.08 per code line

Test coverage

Line coverage

21%

Expression

20.5%

Tests / Examples

21.1% / 20% ex

Functions

1063 8 exported

Complexity

1.6 avg / 8 max

Call network

1063 nodes / 1910 edges

Call graph

Open call graph →

Loading call graph…

Lowest coverage

1063 functions

Function	Cyclo	Coverage
check_tskit_py exp	4	100%
get_tskit_py exp	8	100%
tc_py_to_r exp	1	100%
ts_py_to_r exp	1	100%
load_args_to_options	3	100%
tc_ptr_print	2	100%

People & History

People (2)

Maintainer (1)

Gregor Gorjanc

Author, Maintainer, Copyright holder

Authors (1)

Gregor Gorjanc

Author, Maintainer, Copyright holder

Gregor Gorjanc

Author, Maintainer, Copyright holder

Tskit Developers

Package Timeline

1 release. R releases are shown for context.

R
R 4.6.0 released · 2026-04-24
0.2.0Latest
2026-03-10 · current release
R
R 4.5.0 released · 2025-04-11

Package metadata

First published: 2026-02-27
Total releases: 1 / 1 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 4.0.0
Download size: 266 KB
Installed size: not tracked yet
With dependencies: not tracked yet

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