Package: treespace 1.1.4.3

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]

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treespace.pdf |treespace.html✨
treespace/json (API)
NEWS

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

Peer review:

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

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

On CRAN:

cpp

7.38 score 27 stars 63 scripts 306 downloads 7 mentions 22 exports 146 dependencies

Last updated 1 years agofrom:47393c7993. Checks:OK: 7 NOTE: 2. Indexed: no.

TargetResultDate
Doc / VignettesOKDec 02 2024
R-4.5-win-x86_64NOTEDec 02 2024
R-4.5-linux-x86_64NOTEDec 02 2024
R-4.4-win-x86_64OKDec 02 2024
R-4.4-mac-x86_64OKDec 02 2024
R-4.4-mac-aarch64OKDec 02 2024
R-4.3-win-x86_64OKDec 02 2024
R-4.3-mac-x86_64OKDec 02 2024
R-4.3-mac-aarch64OKDec 02 2024

Exports:.render.server.infofindGrovesfindMRCIslinearMrcamakeCollapsedTreemedTreemultiDistplotGrovesplotGrovesD3plotTreeDiffrefTreeDistrelatedTreeDistsimulateIndTreetipDifftipsMRCAdepthstreeConcordancetreeDisttreespacetreespaceServertreeVecwiwMedTreewiwTreeDist

Dependencies:ade4adegenetadegraphicsapeaskpassbase64encbbmlebdsmatrixbootbslibcachemcellrangercliclusterclusterGenerationcodacodetoolscolorspacecombinatcommonmarkcpp11crayoncrosstalkcurldata.tabledeldirDEoptimdigestdistorydoParalleldotCall64dplyrDTellipseevaluateexpmfansifarverfastmapfieldsfontawesomeforeachfsgenericsggplot2gluegoogleVisgtablehighrhmshtmltoolshtmlwidgetshttpuvhttrigraphinterpisobanditeratorsjpegjquerylibjsonliteKernSmoothknitrlabelinglamWlaterlatticelatticeExtralazyevallifecycleLuminescencemagrittrmapsmarkdownMASSMatrixmatrixStatsmclustmemoisemgcvmimeminpack.lmmnormtmunsellmvtnormnlmenumDerivopenssloptimParallelpermutephangornphytoolspillarpixmappkgconfigplyrpngprettyunitsprogresspromisesquadprogR6rappdirsRCarbRColorBrewerRcppRcppArmadilloRcppEigenRcppParallelreadxlrematchreshape2rglrhandsontablerlangRLumShinyrmarkdownsassscalesscatterD3scatterplot3dsegmentedseqinrshapeshinyshinyBSshinydashboardsourcetoolsspspamstringistringrsystibbletidyselecttinytexutf8vctrsveganviridisLitewithrxfunXMLxtableyamlzoo

Comparing trees by tip label categories

Michelle Kendall

Rendered fromtipCategories.Rmdusingknitr::rmarkdownon Dec 02 2024.

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

Exploration of landscapes of phylogenetic trees

Thibaut Jombart, Michelle Kendall

Rendered fromintroduction.Rmdusingknitr::rmarkdownon Dec 02 2024.

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

treespace worked example: Dengue trees

Michelle Kendall, Thibaut Jombart

Rendered fromDengueVignette.Rmdusingknitr::rmarkdownon Dec 02 2024.

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

treespace worked example: Transmission trees

Michelle Kendall

Rendered fromTransmissionTreesVignette.Rmdusingknitr::rmarkdownon Dec 02 2024.

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