Add citation for tree seq to DESCRIPTION and other such files #46

Author: gregorgorjanc

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) <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

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 <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

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)
+#' <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

RcppTskit/inst/WORDLIST

@@ -1,11 +1,14 @@
+ARG
 ARGs
 ORCID
 Rcpp
 SLiM
 TreeSequence
 Tskit
+doi
 etc
 finaliser
+iyae
 kastore
 msprime
 tskit

RcppTskit/man/RcppTskit-package.Rd

@@ -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}
 }