Package: RcppTskit 0.3.0
Gregor Gorjanc
RcppTskit: 'R' Access to the 'tskit C' API
'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 functions because the 'Python' API and 'reticulate' already cover most needs. The provided `RcppTskit R` API mirrors the `tskit Python` API, while the `RcppTskit C++` API mirrors the `tskit C` API.
Authors:
RcppTskit_0.3.0.tar.gz
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RcppTskit.pdf |RcppTskit.html✨
RcppTskit/json (API)
NEWS
| # Install 'RcppTskit' in R: |
| install.packages('RcppTskit', repos = c('https://highlanderlab.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/highlanderlab/rcpptskit/issues
Last updated from:16d5be2c11. Checks:13 OK. Indexed: yes.
| Target | Result | Time | Files | Log |
|---|---|---|---|---|
| linux-devel-arm64 | OK | 164 | ||
| linux-devel-x86_64 | OK | 157 | ||
| source / vignettes | OK | 333 | ||
| linux-release-arm64 | OK | 159 | ||
| linux-release-x86_64 | OK | 165 | ||
| macos-devel-arm64 | OK | 168 | ||
| macos-devel-x86_64 | OK | 369 | ||
| macos-release-arm64 | OK | 136 | ||
| macos-release-x86_64 | OK | 230 | ||
| windows-devel | OK | 173 | ||
| windows-release | OK | 194 | ||
| windows-oldrel | OK | 190 | ||
| wasm-release | OK | 141 |
Exports:check_tskit_pyget_tskit_pykastore_versionTableCollectiontc_loadtc_py_to_rtc_readTreeSequencets_loadts_py_to_rts_readtskit_version
Dependencies:bitbit64herejsonlitelatticeMatrixpngR6rappdirsRcppRcppTOMLreticulaterlangrprojrootwithr
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Get the reticulate 'tskit' Python module | check_tskit_py get_tskit_py |
| Report the version of installed kastore C API | kastore_version |
| Table collection R6 class (TableCollection) | TableCollection |
| Load a table collection from a file | tc_load tc_read |
| Transfer a table collection from reticulate Python to R | tc_py_to_r |
| Succinct tree sequence R6 class (TreeSequence) | TreeSequence |
| Load a tree sequence from a file | ts_load ts_read |
| Transfer a tree sequence from reticulate Python to R | ts_py_to_r |
| Report the version of installed 'tskit' C API | tskit_version |
