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Patch to remove dependency on adephylo as requested by CRAN
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A patch which - hopefully only temporarily, while adephylo is fixed - removes "Abouheif" and "sumDD" as available metrics in the function treespace.
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MichelleKendall committed Sep 7, 2023
1 parent c93acc3 commit 47393c7
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8 changes: 4 additions & 4 deletions DESCRIPTION
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Package: treespace
Title: Statistical Exploration of Landscapes of Phylogenetic Trees
Date: 2023-04-03
Version: 1.1.4.2
Date: 2023-09-07
Version: 1.1.4.3
Authors@R: c(TJ = person("Thibaut", "Jombart", email="[email protected]", role = "aut", comment = c(ORCID = "0000-0003-2226-8692")),
MK = person("Michelle", "Kendall", email="[email protected]", role = c("aut", "cre"), comment = c(ORCID = "0000-0001-7344-7071")),
JAG = person("Jacob", "Almagro-Garcia", role = "aut", comment = c(ORCID = "0000-0002-0595-7333")),
Expand All @@ -11,12 +11,12 @@ Description: Tools for the exploration of distributions of phylogenetic trees.
treespaceServer().
For further details see Jombart et al. (2017) <DOI:10.1111/1755-0998.12676>.
Depends: R (>= 3.4.0), ape, ade4
Imports: adegenet, adegraphics, adephylo, combinat, compiler, distory,
Imports: adegenet, adegraphics, combinat, compiler, distory,
fields, htmlwidgets, MASS, methods, parallel, phangorn, phytools, Rcpp,
rgl, RLumShiny, scatterD3, shiny, shinyBS, utils
LinkingTo: Rcpp
Suggests: ggplot2, igraph, knitr, pander, RColorBrewer, reshape2,
rmarkdown, testthat
rmarkdown, sf, testthat
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
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1 change: 0 additions & 1 deletion NAMESPACE
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Expand Up @@ -42,7 +42,6 @@ importFrom(adegraphics,insert)
importFrom(adegraphics,s.class)
importFrom(adegraphics,s.label)
importFrom(adegraphics,s1d.barchart)
importFrom(adephylo,distTips)
importFrom(combinat,combn)
importFrom(combinat,combn2)
importFrom(compiler,cmpfun)
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5 changes: 5 additions & 0 deletions NEWS.md
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treespace v1.1.4.3
==================

Patch to remove dependency on the `adephylo` package as required by CRAN - hopefully only temporarily.

treespace v1.1.4.2
==================

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52 changes: 0 additions & 52 deletions R/clusters.R~

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19 changes: 0 additions & 19 deletions R/data.R~

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2 changes: 1 addition & 1 deletion R/servers.R
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Expand Up @@ -18,7 +18,7 @@
#' @importFrom adegraphics s1d.barchart
#' @importFrom adegraphics s.class
#' @importFrom adegraphics s.label
#' @importFrom adephylo distTips
#@importFrom adephylo distTips
#' @importFrom distory dist.multiPhylo
#' @importFrom fields rdist
#' @importFrom htmlwidgets saveWidget
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7 changes: 4 additions & 3 deletions R/treespace.R
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Expand Up @@ -28,7 +28,7 @@
#'
#' @import ape
#' @importFrom ade4 dudi.pco cailliez is.euclid
#' @importFrom adephylo distTips
#@importFrom adephylo distTips
#' @importFrom distory dist.multiPhylo
#' @importFrom fields rdist
#' @importFrom phangorn KF.dist
Expand Down Expand Up @@ -108,9 +108,10 @@ treespace <- function(x, method="treeVec", nf=NULL, lambda=0, return.tree.vector
D <- as.dist(rdist(df))
}
else if(method %in% c("Abouheif","sumDD")){
df <- t(mcmapply(adephylo::distTips, x, method=method, MoreArgs=dots, mc.cores=processors))
stop("Unfortunately, the methods of Abouheif and sumDD for summarising the tree as a vector are currently unavailable because of an issue with the package adephylo, on which they depend. Please select another method.")
#df <- t(mcmapply(adephylo::distTips, x, method=method, MoreArgs=dots, mc.cores=processors))
## get pairwise Euclidean distances ##
D <- as.dist(rdist(df))
#D <- as.dist(rdist(df))
}
else if(method=="patristic"){
D <- path.dist(x, use.weight=TRUE)
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