From 2d1ba57385a00c141d47908e953bb87d1af5d46e Mon Sep 17 00:00:00 2001 From: "Martin R. Smith" <1695515+ms609@users.noreply.github.com> Date: Fri, 5 Jan 2024 13:17:05 +0000 Subject: [PATCH 1/7] Simplify download using /packages --- R/tree_distance_info.R | 21 ++++++++++++++------- man/TreeDistance.Rd | 21 ++++++++++++++------- 2 files changed, 28 insertions(+), 14 deletions(-) diff --git a/R/tree_distance_info.R b/R/tree_distance_info.R index 95d7d1b9..183515dd 100644 --- a/R/tree_distance_info.R +++ b/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 diff --git a/man/TreeDistance.Rd b/man/TreeDistance.Rd index 4f2c28d0..b64730ad 100644 --- a/man/TreeDistance.Rd +++ b/man/TreeDistance.Rd @@ -230,18 +230,25 @@ to be "correct", use \code{normalize = SplitwiseInfo(trueTree)} (SPI, MSI) or 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 \code{remove.packages()}. -Then use \code{devtools::install_github("ms609/TreeTools", ref = "more-leaves")} -to install the modified \pkg{TreeTools} package. -Finally, install \pkg{TreeDist} using -\code{devtools::install_github("ms609/TreeDist")}. +of the package: +\code{install.packages("BigTreeDist", repos = "https://ms609.github.io/packages/")} +Use \code{library("BigTreeDist")} \emph{instead} of \code{library("TreeDist")} to load +the modified package – or prefix functions with the package name, e.g. +\code{BigTreeDist::TreeDistance()}. + +As an alternative download method, +uninstall \pkg{TreeDist} and \pkg{TreeTools} using +\code{remove.packages()}, then use +\code{devtools::install_github("ms609/TreeTools", ref = "more-leaves")} +to install the modified \pkg{TreeTools} package; then, +install \pkg{TreeDist} using +\code{devtools::install_github("ms609/TreeDist", ref = "more-leaves")}. (\pkg{TreeDist} will need building from source \emph{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 \href{https://github.com/ms609/TreeTools/issues/141}{comment on GitHub} if you would find this useful. +which the maintainer plans to attempt in the future; please \href{https://github.com/ms609/TreeTools/issues/141}{comment on GitHub} if you would find this useful. } \examples{ From 9be7dba7d76c165633dc94a87855f592f34f04ba Mon Sep 17 00:00:00 2001 From: "Martin R. Smith" <1695515+ms609@users.noreply.github.com> Date: Thu, 8 Feb 2024 10:31:27 +0000 Subject: [PATCH 2/7] Update ape URL --- R/TreeDist-package.R | 4 ++-- man/TreeDist-package.Rd | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/R/TreeDist-package.R b/R/TreeDist-package.R index b1a1b4c7..5446f97d 100644 --- a/R/TreeDist-package.R +++ b/R/TreeDist-package.R @@ -98,7 +98,7 @@ #' #' 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) @@ -106,7 +106,7 @@ #' * [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 #' diff --git a/man/TreeDist-package.Rd b/man/TreeDist-package.Rd index 59a89b1f..0cdc1ab5 100644 --- a/man/TreeDist-package.Rd +++ b/man/TreeDist-package.Rd @@ -114,7 +114,7 @@ R using \code{vignette(package = "TreeDist")}. Other R packages implementing tree distance functions include: \itemize{ -\item \href{http://ape-package.ird.fr/}{ape}: +\item \href{https://emmanuelparadis.github.io/}{ape}: \itemize{ \item \code{cophenetic.phylo()}: Cophenetic distance \item \code{dist.topo()}: Path (topological) distance, Robinson–Foulds distance. @@ -126,7 +126,7 @@ Other R packages implementing tree distance functions include: \item \href{https://ms609.github.io/Quartet/}{Quartet}: Triplet and Quartet distances, using the tqDist algorithm. \item \href{https://ms609.github.io/TBRDist/}{TBRDist}: TBR and SPR distances on -unrooted trees, using the 'uspr; C library. +unrooted trees, using the 'uspr' C library. \item \href{https://cran.r-project.org/package=distory}{distory} (unmaintained): Geodesic distance } From 9c93d59cd915690bb5bac3a74760c6d1baa89e0f Mon Sep 17 00:00:00 2001 From: "Martin R. Smith" <1695515+ms609@users.noreply.github.com> Date: Thu, 8 Feb 2024 10:33:25 +0000 Subject: [PATCH 3/7] Remove dead link http://www.assignmentproblems.com/doc/LSAPIntroduction.pdf is no more --- R/lap.R | 3 +-- man/LAPJV.Rd | 2 +- 2 files changed, 2 insertions(+), 3 deletions(-) diff --git a/R/lap.R b/R/lap.R index 6182ed63..1359cc95 100644 --- a/R/lap.R +++ b/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. diff --git a/man/LAPJV.Rd b/man/LAPJV.Rd index 561d0032..552f175d 100644 --- a/man/LAPJV.Rd +++ b/man/LAPJV.Rd @@ -16,7 +16,7 @@ and \code{matching}, the columns matched to each row of the matrix in turn. } \description{ Use the algorithm of \insertCite{Jonker1987;textual}{TreeDist} to solve the -\href{http://www.assignmentproblems.com/doc/LSAPIntroduction.pdf}{Linear Sum Assignment Problem}. +Linear Sum Assignment Problem (LSAP). } \details{ The Linear Assignment Problem seeks to match each row of a matrix with a From 2c18789925d5044f2d1000f30f366bcc4d4fa77d Mon Sep 17 00:00:00 2001 From: "Martin R. Smith" <1695515+ms609@users.noreply.github.com> Date: Thu, 8 Feb 2024 10:35:35 +0000 Subject: [PATCH 4/7] v2.7.0.9000 --- DESCRIPTION | 2 +- NEWS.md | 4 ++++ 2 files changed, 5 insertions(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index b4bf508b..70ce1aea 100644 --- a/DESCRIPTION +++ b/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 = "martin.smith@durham.ac.uk", role = c("aut", "cre", "cph", "prg"), diff --git a/NEWS.md b/NEWS.md index 3672de2d..81ffcde8 100644 --- a/NEWS.md +++ b/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()`. From ec36b97ade814487b88a1d4f2662f89ca8fc3e09 Mon Sep 17 00:00:00 2001 From: GitHub Actions Date: Thu, 8 Feb 2024 10:43:31 +0000 Subject: [PATCH 5/7] Update codemeta.json --- codemeta.json | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/codemeta.json b/codemeta.json index 3fc9262f..ae5af073 100644 --- a/codemeta.json +++ b/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": "martin.smith@durham.ac.uk" } ], - "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", From 59685dc4eed2bf44edb7bee00ca7d15a54ca9da5 Mon Sep 17 00:00:00 2001 From: "Martin R. Smith" <1695515+ms609@users.noreply.github.com> Date: Thu, 15 Feb 2024 13:25:14 +0000 Subject: [PATCH 6/7] LSAP --- inst/WORDLIST | 1 + 1 file changed, 1 insertion(+) diff --git a/inst/WORDLIST b/inst/WORDLIST index c2f593e3..f0a8b7cf 100644 --- a/inst/WORDLIST +++ b/inst/WORDLIST @@ -26,6 +26,7 @@ Kawa KendallColijn LAPJV Leeuwen +LSAP MASTInfo MASTSize MDS From 2772e24fe8fe5149867d10422372a84f08feb715 Mon Sep 17 00:00:00 2001 From: "Martin R. Smith" <1695515+ms609@users.noreply.github.com> Date: Fri, 23 Feb 2024 14:56:28 +0000 Subject: [PATCH 7/7] Roxygen 7.3.1 --- DESCRIPTION | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index 70ce1aea..b4790f17 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -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)