Adding alternative tree metrics

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: treespace
 Title: Statistical Exploration of Landscapes of Phylogenetic Trees
-Date: 2019-12-05
+Date: 2020-07-29
 Version: 1.1.3.2
 Authors@R: c(TJ = person("Thibaut", "Jombart", email="thibautjombart@gmail.com", role = "aut", comment = c(ORCID = "0000-0003-2226-8692")),
  	     MK = person("Michelle", "Kendall", email="michelle.kendall@bdi.ox.ac.uk", role = c("aut", "cre"), comment = c(ORCID = "0000-0001-7344-7071")),
@@ -14,7 +14,7 @@ Description: Tools for the exploration of distributions of phylogenetic trees.
 Depends: R (>= 3.4.0), ape, ade4
 Imports: adegenet, adegraphics, adephylo, combinat, compiler, distory,
         fields, htmlwidgets, MASS, methods, parallel, phangorn, phytools, Rcpp,
-        rgl, RLumShiny, scatterD3, shiny, shinyBS, utils
+        rgl, RLumShiny, scatterD3, shiny, shinyBS, TreeDist, utils
 LinkingTo: Rcpp
 Suggests: ggplot2, igraph, knitr, pander, RColorBrewer, reshape2,
         rmarkdown, testthat
@@ -24,7 +24,8 @@ Collate: RcppExports.R metrics.R medTree.R treespace.R findGroves.R
         plotGroves.R plotTreeDiff.R servers.R transmissionTrees.R
         data.R makeCollapsedTree.R relatedTreeDist.R simulateIndTree.R
         tipsMRCAdepths.R treeConcordance.R
-RoxygenNote: 7.0.2
+Encoding: UTF-8
+RoxygenNote: 7.1.1
 VignetteBuilder: knitr
 URL: https://cran.r-project.org/package=treespace,
         https://github.com/thibautjombart/treespace

NAMESPACE

@@ -29,6 +29,10 @@ import(shiny)
 importFrom(MASS,Shepard)
 importFrom(RLumShiny,jscolorInput)
 importFrom(Rcpp,evalCpp)
+importFrom(TreeDist,ClusteringInfoDistance)
+importFrom(TreeDist,MatchingSplitDistance)
+importFrom(TreeDist,MatchingSplitInfoDistance)
+importFrom(TreeDist,PhylogeneticInfoDistance)
 importFrom(ade4,cailliez)
 importFrom(ade4,dudi.pco)
 importFrom(ade4,is.euclid)

R/treespace.R

@@ -14,6 +14,10 @@
 #' \item \code{wRF} the weighted Robinson Foulds metric using \code{wRF.dist} from package \code{phangorn} (considers the trees unrooted)
 #' \item \code{nNodes} the Steel & Penny tip-tip path difference metric, (topological, ignoring branch lengths), using \code{path.dist} from package \code{phangorn} (considers the trees unrooted)
 #' \item \code{patristic} the Steel & Penny tip-tip path difference metric, using branch lengths, calling \code{path.dist} from package \code{phangorn} (considers the trees unrooted)
+#' \item \code{CID} the clustering information difference metric, calling \code{ClusteringInformationDistance()} from package \pkg{TreeDist} (considers the trees unrooted)
+#' \item \code{PID} the phylogenetic information difference metric, calling \code{PhylogeneticInformationDistance()} from package \pkg{TreeDist} (considers the trees unrooted)
+#' \item \code{MS} the matching splits distance, calling \code{MatchingSplitsDistance()} from package \pkg{TreeDist} (considers the trees unrooted)
+#' \item \code{MSID} the matching splits information difference metric, calling \code{ClusteringInformationDistance()} from package \pkg{TreeDist} (considers the trees unrooted)
 #' \item \code{Abouheif}: performs Abouheif's test, inherited from \code{distTips} in \code{adephylo}. See Pavoine et al. (2008) and \code{adephylo}.
 #' \item \code{sumDD}: sum of direct descendants of all nodes on the path, related to Abouheif's test, inherited from \code{distTips} in \code{adephylo}.
 #' }
@@ -36,6 +40,8 @@
 #' @importFrom phangorn RF.dist
 #' @importFrom phangorn wRF.dist
 #' @importFrom parallel mcmapply
+#' @importFrom TreeDist ClusteringInfoDistance MatchingSplitDistance
+#'  MatchingSplitInfoDistance PhylogeneticInfoDistance
 #'
 #' @examples
 #'
@@ -47,6 +53,15 @@
 #' res <- treespace(x, nf=3)
 #' table.paint(as.matrix(res$D))
 #' scatter(res$pco)
+#' 
+#' ## Consider trees rooted:
+#' rootedtrees <- structure(lapply(x, function (tr){
+#'   tr$edge.length <- NULL
+#'   TreeTools::AddTip(tr, where=0)
+#' }), class='multiPhylo')
+#' rootedres <- treespace(rootedtrees,nf=3)
+#' table.paint(as.matrix(rootedres$D))
+#' scatter(rootedres$pco)
 #'
 #' data(woodmiceTrees)
 #' woodmiceDists <- treespace(woodmiceTrees,nf=3)
@@ -67,6 +82,27 @@
 #' }
 #' }
 #'
+#' @encoding UTF-8
+#' @references 
+#' Bogdanowicz D, Giaro K (2012). “Matching split distance for unrooted binary
+#' phylogenetic trees.” IEEE/ACM Transactions on Computational Biology and 
+#' Bioinformatics, 9(1), 150–160. doi: 10.1109/TCBB.2011.48.
+#' 
+#' Kendall M, Colijn C (2016). “Mapping phylogenetic trees to reveal distinct
+#' patterns of evolution.” Molecular Biology and Evolution, 33(10), 2735--2743.
+#' doi: 10.1093/molbev/msw124 
+#' 
+#' Robinson DF, Foulds LR (1981). “Comparison of phylogenetic trees.” 
+#' Mathematical Biosciences, 53(1-2), 131–147. 
+#' doi: 10.1016/0025-5564(81)90043-2.
+#' 
+#' Smith MR (2020). “Information theoretic Generalized Robinson-Foulds metrics 
+#' for comparing phylogenetic trees.” Bioinformatics, in production. 
+#' doi: 10.1093/bioinformatics/btaa614.
+#'
+#' Steel, M. A., & Penny, D. (1993). Distributions of tree comparison 
+#' metrics—some new results. Systematic Biology, 42 (2), 126–141.
+#' doi: 10.1093/sysbio/42.2.126
 #'
 #' @export
 treespace <- function(x, method="treeVec", nf=NULL, lambda=0, return.tree.vectors=FALSE, processors=1, ...){
@@ -144,6 +180,18 @@ treespace <- function(x, method="treeVec", nf=NULL, lambda=0, return.tree.vector
         D <- ade4::cailliez(D, print=FALSE)
       }
     }
+    else if (method == 'CID') {
+      D <- as.dist(ClusteringInfoDistance(x))
+    }
+    else if (method == 'PID') {
+      D <- as.dist(PhylogeneticInfoDistance(x))
+    }
+    else if (method == 'MS') {
+      D <- as.dist(MatchingSplitDistance(x))
+    }
+    else if (method == 'MSID') {
+      D <- as.dist(MatchingSplitInfoDistance(x))
+    }
 
     ## restore labels
     attr(D,"Labels") <- lab
@@ -154,10 +202,10 @@ treespace <- function(x, method="treeVec", nf=NULL, lambda=0, return.tree.vector
 
     ## BUILD RESULT AND RETURN ##
     if (return.tree.vectors==TRUE) {
-    out <- list(D=D, pco=pco, vectors=df)
+      out <- list(D=D, pco=pco, vectors=df)
     }
     else {
-    out <- list(D=D, pco=pco)
+      out <- list(D=D, pco=pco)
     }
     return(out)
 } # end treespace

vignettes/tipCategories.Rmd

@@ -1,5 +1,5 @@
 ---
-title: "Comparing trees by tip label categories"
+title: "treespace worked example: comparing by tip categories"
 author: "Michelle Kendall"
 date: "`r Sys.Date()`"
 output: rmarkdown::html_vignette