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Merged
gregorgorjanc merged 1 commit into from
Jan 28, 2026
Merged

Add citation for tree seq to DESCRIPTION and other such files #50

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2 changes: 2 additions & 0 deletions README.md
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Expand Up @@ -4,6 +4,8 @@

`Tskit` enables performant 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>.
See 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` R package to
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23 changes: 12 additions & 11 deletions RcppTskit/DESCRIPTION
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Expand Up @@ -11,17 +11,18 @@ Authors@R: c(
)
Description: 'Tskit' enables performant storage, manipulation, and
analysis of ancestral recombination graphs (ARGs) using succinct tree
sequence encoding. See <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' R package to seamlessly load and
analyse a tree sequence as described at
<https://tskit.dev/tutorials/tskitr.html>. 'RcppTskit' provides R
access to the 'tskit' C API for use cases where the 'reticulate'
option is not optimal. For example, for high-performance and low-level
work with tree sequences. Currently, 'RcppTskit' provides a limited
number of R functions due to the availability of extensive Python API
and the 'reticulate' option.
sequence encoding. The tree sequence encoding of an ARG is described
in Wong et al. (2024) <doi:10.1093/genetics/iyae100>. 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' R package to seamlessly load and analyse a tree sequence
as described at <https://tskit.dev/tutorials/tskitr.html>. 'RcppTskit'
provides R access to the 'tskit' C API for use cases where the
'reticulate' option is not optimal. For example, for high-performance
and low-level work with tree sequences. Currently, 'RcppTskit'
provides a limited number of R functions due to the availability of
extensive Python API and the 'reticulate' option.
License: MIT + file LICENSE
URL: https://github.com/HighlanderLab/RcppTskit
BugReports: https://github.com/HighlanderLab/RcppTskit/issues
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4 changes: 3 additions & 1 deletion RcppTskit/R/RcppTskit-package.R
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#' @description
#' `Tskit` enables performant storage, manipulation, and analysis of
#' ancestral recombination graphs (ARGs) using succinct tree sequence encoding.
#' See https://tskit.dev for project news, documentation, and tutorials.
#' The tree sequence encoding of an ARG is described in Wong et al. (2024)
#' <doi:10.1093/genetics/iyae100>.
#' 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` R package to
#' seamlessly load and analyse a tree sequence as described at
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3 changes: 3 additions & 0 deletions RcppTskit/inst/WORDLIST
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@@ -1,11 +1,14 @@
ARG
ARGs
ORCID
Rcpp
SLiM
TreeSequence
Tskit
doi
etc
finaliser
iyae
kastore
msprime
tskit
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4 changes: 3 additions & 1 deletion RcppTskit/man/RcppTskit-package.Rd
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6 changes: 4 additions & 2 deletions RcppTskit/vignettes/references.bib
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Expand Up @@ -8,7 +8,8 @@ @article{brandt2024promise
journal = {Genome Biology and Evolution},
year = {2024},
pages = {evae005},
doi = {10.1093/gbe/evae005}
doi = {10.1093/gbe/evae005},
url = {https://doi.org/10.1093/gbe/evae005}
}

@manual{eddelbuettel2026rcpp,
Expand Down Expand Up @@ -138,5 +139,6 @@ @article{wong2024general
pages = {iyae100},
year = {2024},
month = {07},
doi = {10.1093/genetics/iyae100}
doi = {10.1093/genetics/iyae100},
url = {https://doi.org/10.1093/genetics/iyae100}
}
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