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
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treespace_1.1.4.4.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
treespace/json (API)
NEWS

# Install 'treespace' in R:
install.packages('treespace', repos = c('https://phylotastic.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

7.51 score 29 stars 79 scripts 256 downloads 7 mentions 22 exports 166 dependencies

Last updated from:b288c56d3d. Checks:13 OK. Indexed: no.

TargetResultTimeFilesSyslog
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linux-devel-x86_64OK289
source / vignettesOK344
linux-release-arm64OK280
linux-release-x86_64OK287
macos-release-arm64OK197
macos-release-x86_64OK329
macos-oldrel-arm64OK148
macos-oldrel-x86_64OK463
windows-develOK281
windows-releaseOK194
windows-oldrelOK208
wasm-releaseOK239

Exports:.render.server.infofindGrovesfindMRCIslinearMrcamakeCollapsedTreemedTreemultiDistplotGrovesplotGrovesD3plotTreeDiffrefTreeDistrelatedTreeDistsimulateIndTreetipDifftipsMRCAdepthstreeConcordancetreeDisttreespacetreespaceServertreeVecwiwMedTreewiwTreeDist

Dependencies:ade4adegenetadegraphicsapeaskpassbackportsbase64encbbmlebdsmatrixbootbslibcachemcellrangercheckmateclassclassIntcliclusterclusterGenerationcodacodetoolscombinatcommonmarkcpp11crayoncrosstalkcurldata.tableDBIdeldirDEoptimdigestdistorydoParalleldotCall64dplyrDTe1071ellipseevaluateexpmfarverfastmapfieldsfontawesomeforeachfsfuturefuture.applygenericsggplot2globalsgluegoogleVisgtablehighrhmshtmltoolshtmlwidgetshttpuvhttrigraphinterpisobanditeratorsjpegjquerylibjsonliteKernSmoothknitrlabelinglamWlaterlatticelatticeExtralazyevalleafletleaflet.providerslifecyclelistenvlitedownLuminescencemagrittrmapsmarkdownMASSMatrixmatrixStatsmclustmemoisemgcvmimeminpack.lmmnormtmvtnormnlmenumDerivopenssloptimParallelosqpotelparallellypermutephangornphytoolspillarpixmappkgconfigplyrpngprettyunitsprogressprogressrpromisesproxyR6rappdirsrasterRCarbRColorBrewerRcppRcppArmadilloRcppEigenRcppParallelreadxlrematchreshape2rglrhandsontablerlangRLumShinyrmarkdowns2S7sassscalesscatterD3scatterplot3dsegmentedseqinrsfshapeshinyshinyBSshinydashboardsourcetoolsspspamstringistringrsysterratibbletidyselecttinytexunitsutf8vctrsveganviridisLitewithrwkxfunXMLxtableyaml

Comparing trees by tip label categories

Michelle Kendall

Rendered fromtipCategories.Rmdusingknitr::rmarkdownon Jun 02 2026.

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

Exploration of landscapes of phylogenetic trees

Thibaut Jombart, Michelle Kendall

Rendered fromintroduction.Rmdusingknitr::rmarkdownon Jun 02 2026.

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

treespace worked example: Dengue trees

Michelle Kendall, Thibaut Jombart

Rendered fromDengueVignette.Rmdusingknitr::rmarkdownon Jun 02 2026.

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

treespace worked example: Transmission trees

Michelle Kendall

Rendered fromTransmissionTreesVignette.Rmdusingknitr::rmarkdownon Jun 02 2026.

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