diff --git a/README.md b/README.md index 1be0af9..7f93659 100644 --- a/README.md +++ b/README.md @@ -5,7 +5,9 @@ `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) . +described in Wong et al. (2024) , +while `tskit` project is described in +Jeffrey et al. (2026) . 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 4eadd41..83cc4c4 100644 --- a/RcppTskit/DESCRIPTION +++ b/RcppTskit/DESCRIPTION @@ -9,20 +9,21 @@ Authors@R: c( person("Tskit Developers", role = "cph", comment = "Authors of included tskit C library") ) -Description: '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) . 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' package to load and analyse tree sequences as described - at . '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. +Description: '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) , while `tskit` project is + described in Jeffrey et al. (2026) . + 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' package to load and analyse tree sequences as + described at . '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. 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 857cdbe..ac90bce 100644 --- a/RcppTskit/R/RcppTskit-package.R +++ b/RcppTskit/R/RcppTskit-package.R @@ -4,7 +4,8 @@ #' `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) -#' . +#' , while `tskit` project is +#' described in Jeffrey et al. (2026) . #' 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 diff --git a/RcppTskit/man/RcppTskit-package.Rd b/RcppTskit/man/RcppTskit-package.Rd index 23cf22e..e3c4656 100644 --- a/RcppTskit/man/RcppTskit-package.Rd +++ b/RcppTskit/man/RcppTskit-package.Rd @@ -9,7 +9,8 @@ `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) -. +, while `tskit` project is +described in Jeffrey et al. (2026) . 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 diff --git a/RcppTskit/vignettes/references.bib b/RcppTskit/vignettes/references.bib index ba2c07b..94feb19 100644 --- a/RcppTskit/vignettes/references.bib +++ b/RcppTskit/vignettes/references.bib @@ -38,15 +38,15 @@ @article{jeffrey2026population Bisschop, Gertjan and Deng, Yun and Ellerman, E Castedo and - Forest, Thomas and + Forest, B Thomas and Fritze, Halley and Goldstein, Daniel and Gorjanc, Gregor and Gower, Graham and Gravel, Simon and Guez, Jeremy and - Haller, Benjamin C. and - Kern, Andrew D. and + Haller, Benjamin C and + Kern, Andrew D and Kirk, Lloyd and Krukov, Ivan and Lee, Hanbin and @@ -55,23 +55,23 @@ @article{jeffrey2026population Osmond, Matthew M and Palmer, Duncan S and Pope, Nathaniel S and - Ragsdale, Aaron and + Ragsdale, Aaron P and Robertson, Duncan and Rodrigues, Murillo F and - Weiss, Clemens and + van Kemenade, Hugo and + Weiss, Clemens L and Wohns, Anthony Wilder and Zhan, Shing H and - Zhang, Brian and - van Kemenade, Hugo and - Aspbury, Maz and - Baya, Nik and + Zhang, Brian C and + Aspbury, Marianne and + Baya, Nikolas A and Belsare, Saurabh and Biddanda, Arjun and - Campuzano, Curro and + Campuzano Jiménez, Francisco and Gladstein, Ariella and Guo, Bing and Karthikeyan, Savita and - Kretzschumar, Warren W and + Kretzschmar, Warren W and Rebollo, Inés and Saunack, Kumar and Shemirani, Ruhollah and @@ -83,8 +83,10 @@ @article{jeffrey2026population Zhang, Ao and Ralph, Peter Kelleher, Jerome}, - journal = {TODO}, - year = {2026} + journal = {arXiv}, + year = {2026}, + doi = {10.48550/arXiv.2602.09649}, + url = {https://arxiv.org/abs/2602.09649} } @article{lewanski2024era,