Merge branch 'master' into rhub.yaml

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: TreeDist
 Type: Package
 Title: Calculate and Map Distances Between Phylogenetic Trees
-Version: 2.7.0
+Version: 2.7.0.9000
 Authors@R: c(person("Martin R.", "Smith",
                     email = "[email protected]", 
                     role = c("aut", "cre", "cph", "prg"), 
@@ -93,5 +93,5 @@ ByteCompile: true
 Encoding: UTF-8
 Language: en-GB
 X-schema.org-keywords: phylogenetics, tree-distance
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.1
 Roxygen: list(markdown = TRUE)

NEWS.md

@@ -1,3 +1,7 @@
+# TreeDist 2.7.0.9000 (development)
+
+- Fix dead links in documentation
+
 # TreeDist 2.7.0 (2023-10-25)
 
 - Fix calculation error in `StrainCol()`.

R/TreeDist-package.R

@@ -98,15 +98,15 @@
 #' 
 #' Other R packages implementing tree distance functions include:
 #'   
-#'   * [ape](http://ape-package.ird.fr/):
+#'   * [ape](https://emmanuelparadis.github.io/):
 #'     - `cophenetic.phylo()`: Cophenetic distance
 #'     - `dist.topo()`: Path (topological) distance, Robinson–Foulds distance.
 #'   * [phangorn](https://cran.r-project.org/package=phangorn)
 #'     - `treedist()`: Path, Robinson–Foulds and approximate SPR distances.
 #'   * [Quartet](https://ms609.github.io/Quartet/): Triplet and Quartet distances, 
 #'   using the tqDist algorithm.
 #'   * [TBRDist](https://ms609.github.io/TBRDist/): TBR and SPR distances on 
-#'   unrooted trees, using the 'uspr; C library.
+#'   unrooted trees, using the 'uspr' C library.
 #'   * [distory](https://cran.r-project.org/package=distory) (unmaintained): 
 #'     Geodesic distance
 #' 

R/lap.R

@@ -1,8 +1,7 @@
 #' Solve linear assignment problem using LAPJV
 #'
 #' Use the algorithm of \insertCite{Jonker1987;textual}{TreeDist} to solve the 
-#' [Linear Sum Assignment Problem](
-#' http://www.assignmentproblems.com/doc/LSAPIntroduction.pdf).
+#' Linear Sum Assignment Problem (LSAP).
 #' 
 #' The Linear Assignment Problem seeks to match each row of a matrix with a 
 #' column, such that the cost of the matching is minimized.

R/tree_distance_info.R

@@ -94,18 +94,25 @@
 #' To balance memory demands and runtime with flexibility, these functions are
 #' implemented for trees with up to 2048 leaves.
 #' To analyse trees with up to 8192 leaves, you will need to a modified version
-#' of \pkg{TreeTools}.
-#' First uninstall \pkg{TreeDist} and \pkg{TreeTools} using `remove.packages()`.
-#' Then use `devtools::install_github("ms609/TreeTools", ref = "more-leaves")`
-#' to install the modified \pkg{TreeTools} package.
-#' Finally, install \pkg{TreeDist} using
-#'`devtools::install_github("ms609/TreeDist")`.
+#' of the package:
+#' `install.packages("BigTreeDist", repos = "https://ms609.github.io/packages/")`
+#' Use `library("BigTreeDist")` *instead* of `library("TreeDist")` to load
+#' the modified package – or prefix functions with the package name, e.g.
+#' `BigTreeDist::TreeDistance()`.
+#' 
+#' As an alternative download method,
+#' uninstall \pkg{TreeDist} and \pkg{TreeTools} using
+#' `remove.packages()`, then use
+#'  `devtools::install_github("ms609/TreeTools", ref = "more-leaves")`
+#' to install the modified \pkg{TreeTools} package; then, 
+#' install \pkg{TreeDist} using
+#' `devtools::install_github("ms609/TreeDist", ref = "more-leaves")`.
 #' (\pkg{TreeDist} will need building from source _after_ the modified 
 #' \pkg{TreeTools} package has been installed, as its code links to values
 #' set in the TreeTools source code.)
 #' 
 #' Trees with over 8192 leaves require further modification of the source code,
-#' which the maintainer will attempt on demand; please [comment on GitHub](
+#' which the maintainer plans to attempt in the future; please [comment on GitHub](
 #' https://github.com/ms609/TreeTools/issues/141) if you would find this useful.
 #' 
 #' @template tree12ListParams

codemeta.json

@@ -8,13 +8,13 @@
   "codeRepository": "https://github.com/ms609/TreeDist/",
   "issueTracker": "https://github.com/ms609/TreeDist/issues/",
   "license": "https://spdx.org/licenses/GPL-3.0",
-  "version": "2.7.0",
+  "version": "2.7.0.9000",
   "programmingLanguage": {
     "@type": "ComputerLanguage",
     "name": "R",
     "url": "https://r-project.org"
   },
-  "runtimePlatform": "R version 4.3.1 (2023-06-16)",
+  "runtimePlatform": "R version 4.3.2 (2023-10-31)",
   "provider": {
     "@id": "https://cran.r-project.org",
     "@type": "Organization",
@@ -500,7 +500,7 @@
     "SystemRequirements": "C++17"
   },
   "keywords": ["phylogenetics", "tree-distance"],
-  "fileSize": "1447.959KB",
+  "fileSize": "1448.6KB",
   "citation": [
     {
       "@type": "ScholarlyArticle",
@@ -567,7 +567,7 @@
           "email": "[email protected]"
         }
       ],
-      "name": "TreeDist: Distances between Phylogenetic Trees. R package version 2.7.0",
+      "name": "TreeDist: Distances between Phylogenetic Trees. R package version 2.7.0.9000",
       "identifier": "10.5281/zenodo.3528124",
       "@id": "https://doi.org/10.5281/zenodo.3528124",
       "sameAs": "https://doi.org/10.5281/zenodo.3528124",

inst/WORDLIST

@@ -26,6 +26,7 @@ Kawa
 KendallColijn
 LAPJV
 Leeuwen
+LSAP
 MASTInfo
 MASTSize
 MDS