Package: treespace 1.1.4.4

Michelle Kendall

treespace: Statistical Exploration of Landscapes of Phylogenetic Trees

Tools for the exploration of distributions of phylogenetic trees. This package includes a 'shiny' interface which can be started from R using treespaceServer(). For further details see Jombart et al. (2017) <doi:10.1111/1755-0998.12676>.

Authors:Thibaut Jombart [aut], Michelle Kendall [aut, cre], Jacob Almagro-Garcia [aut], Caroline Colijn [aut]

treespace_1.1.4.4.tar.gz
treespace_1.1.4.4.zip(r-4.7)treespace_1.1.4.4.zip(r-4.6)treespace_1.1.4.4.zip(r-4.5)
treespace_1.1.4.4.tgz(r-4.6-x86_64)treespace_1.1.4.4.tgz(r-4.6-arm64)treespace_1.1.4.4.tgz(r-4.5-x86_64)treespace_1.1.4.4.tgz(r-4.5-arm64)
treespace_1.1.4.4.tar.gz(r-4.7-arm64)treespace_1.1.4.4.tar.gz(r-4.7-x86_64)treespace_1.1.4.4.tar.gz(r-4.6-arm64)treespace_1.1.4.4.tar.gz(r-4.6-x86_64)
treespace_1.1.4.4.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
treespace/json (API)

# Install 'treespace' in R:
install.packages('treespace', repos = c('https://thibautjombart.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/thibautjombart/treespace/issues

Uses libs:
  • c++– GNU Standard C++ Library v3
Datasets:

On CRAN:

Conda:

cpp

7.53 score 29 stars 83 scripts 395 downloads 7 mentions 22 exports 159 dependencies

Last updated from:b288c56d3d. Checks:13 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-arm64OK261
linux-devel-x86_64OK272
source / vignettesOK352
linux-release-arm64OK282
linux-release-x86_64OK244
macos-release-arm64OK162
macos-release-x86_64OK574
macos-oldrel-arm64OK142
macos-oldrel-x86_64OK402
windows-develOK260
windows-releaseOK244
windows-oldrelOK232
wasm-releaseOK207

Exports:.render.server.infofindGrovesfindMRCIslinearMrcamakeCollapsedTreemedTreemultiDistplotGrovesplotGrovesD3plotTreeDiffrefTreeDistrelatedTreeDistsimulateIndTreetipDifftipsMRCAdepthstreeConcordancetreeDisttreespacetreespaceServertreeVecwiwMedTreewiwTreeDist

Dependencies:ade4adegenetadegraphicsapeaskpassbase64encbbmlebdsmatrixbootbslibcachemcellrangerclassclassIntcliclusterclusterGenerationcodacodetoolscombinatcommonmarkcpp11crayoncrosstalkcurldata.tableDBIdeldirDEoptimdigestdistorydoParalleldotCall64dplyrDTe1071ellipseevaluateexpmfarverfastmapfastmatchfieldsfontawesomeforeachfsgenericsggplot2gluegoogleVisgtablehighrhmshtmltoolshtmlwidgetshttpuvhttrigraphinterpisobanditeratorsjpegjquerylibjsonliteKernSmoothknitrlabelinglamWlaterlatticelatticeExtralazyevalleafletleaflet.providerslifecyclelitedownLuminescencemagrittrmapsmarkdownMASSMatrixmatrixStatsmclustmemoisemgcvmimeminpack.lmmnormtmvtnormnlmenumDerivopenssloptimParallelotelpermutephangornphytoolspillarpixmappkgconfigplyrpngprettyunitsprogresspromisesproxyquadprogR6rappdirsrasterRCarbRColorBrewerRcppRcppArmadilloRcppEigenRcppParallelreadxlrematchreshape2rglrhandsontablerlangRLumShinyrmarkdowns2S7sassscalesscatterD3scatterplot3dsegmentedseqinrsfshapeshinyshinyBSshinydashboardsourcetoolsspspamstringistringrsysterratibbletidyselecttinytexunitsutf8vctrsveganviridisLitewithrwkxfunXMLxtableyaml

Exploration of landscapes of phylogenetic trees
Installing treespace | Content overview | Exploring trees with treespace | Identifying clusters of trees | treespaceServer: a web application for treespace | Finding median trees | Emphasising the placement of certain tips or clades | Method: characterising a tree by a vector | References | Authors / Contributors
Rendered fromintroduction.Rmdusingknitr::rmarkdown

Last update: 2023-03-29
Started: 2017-03-13

treespace worked example: Transmission trees
Examples | Comparing three simple trees | Comparing many trees using an MDS plot | Median trees
Rendered fromTransmissionTreesVignette.Rmdusingknitr::rmarkdown

Last update: 2021-03-23
Started: 2017-03-13

treespace worked example: Dengue trees
Loading treespace and data: | Creating neighbour-joining and maximum likelihood trees: | Using treespace to compare trees | treespace analysis | Using treespace to analyse the BEAST trees in more detail: | References
Rendered fromDengueVignette.Rmdusingknitr::rmarkdown

Last update: 2020-11-13
Started: 2017-03-13

Comparing trees by tip label categories
Related tree distance | Concordance
Rendered fromtipCategories.Rmdusingknitr::rmarkdown

Last update: 2020-10-08
Started: 2018-01-16