From ecc47bfdc463bd91069399dbbb2e10b4b9daec01 Mon Sep 17 00:00:00 2001 From: Gregor Gorjanc Date: Wed, 28 Jan 2026 12:45:37 +0000 Subject: [PATCH] Add citation for tree seq to DESCRIPTION and other such files #46 --- README.md | 2 ++ RcppTskit/DESCRIPTION | 23 ++++++++++++----------- RcppTskit/R/RcppTskit-package.R | 4 +++- RcppTskit/inst/WORDLIST | 3 +++ RcppTskit/man/RcppTskit-package.Rd | 4 +++- RcppTskit/vignettes/references.bib | 6 ++++-- 6 files changed, 27 insertions(+), 15 deletions(-) diff --git a/README.md b/README.md index 5d0e4f5..2fab145 100644 --- a/README.md +++ b/README.md @@ -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) . 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 diff --git a/RcppTskit/DESCRIPTION b/RcppTskit/DESCRIPTION index f486320..edafc80 100644 --- a/RcppTskit/DESCRIPTION +++ b/RcppTskit/DESCRIPTION @@ -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 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 - . '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) . See also + 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 . '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 diff --git a/RcppTskit/R/RcppTskit-package.R b/RcppTskit/R/RcppTskit-package.R index 4876a8e..a14a4b8 100644 --- a/RcppTskit/R/RcppTskit-package.R +++ b/RcppTskit/R/RcppTskit-package.R @@ -3,7 +3,9 @@ #' @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) +#' . +#' 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 diff --git a/RcppTskit/inst/WORDLIST b/RcppTskit/inst/WORDLIST index 7de6c8c..bd296a7 100644 --- a/RcppTskit/inst/WORDLIST +++ b/RcppTskit/inst/WORDLIST @@ -1,11 +1,14 @@ +ARG ARGs ORCID Rcpp SLiM TreeSequence Tskit +doi etc finaliser +iyae kastore msprime tskit diff --git a/RcppTskit/man/RcppTskit-package.Rd b/RcppTskit/man/RcppTskit-package.Rd index 308d531..5510b60 100644 --- a/RcppTskit/man/RcppTskit-package.Rd +++ b/RcppTskit/man/RcppTskit-package.Rd @@ -8,7 +8,9 @@ \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) +. +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 diff --git a/RcppTskit/vignettes/references.bib b/RcppTskit/vignettes/references.bib index f39c3e2..ba2c07b 100644 --- a/RcppTskit/vignettes/references.bib +++ b/RcppTskit/vignettes/references.bib @@ -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, @@ -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} }