Package: treespace 1.1.4.3
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:
treespace_1.1.4.3.tar.gz
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treespace_1.1.4.3.tgz(r-4.4-x86_64)treespace_1.1.4.3.tgz(r-4.4-arm64)treespace_1.1.4.3.tgz(r-4.3-x86_64)treespace_1.1.4.3.tgz(r-4.3-arm64)
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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')) |
Bug tracker:https://github.com/thibautjombart/treespace/issues
- DengueBEASTMCC - Dengue fever BEAST MCC tree
- DengueSeqs - Dengue fever sequences
- DengueTrees - BEAST analysis of Dengue fever
- fluTrees - BEAST analysis of seasonal influenza
- woodmiceTrees - Bootstrap trees from woodmouse dataset
Last updated 1 years agofrom:47393c7993. Checks:OK: 7 NOTE: 2. Indexed: no.
Target | Result | Date |
---|---|---|
Doc / Vignettes | OK | Sep 03 2024 |
R-4.5-win-x86_64 | NOTE | Sep 03 2024 |
R-4.5-linux-x86_64 | NOTE | Sep 03 2024 |
R-4.4-win-x86_64 | OK | Sep 03 2024 |
R-4.4-mac-x86_64 | OK | Sep 03 2024 |
R-4.4-mac-aarch64 | OK | Sep 03 2024 |
R-4.3-win-x86_64 | OK | Sep 03 2024 |
R-4.3-mac-x86_64 | OK | Sep 03 2024 |
R-4.3-mac-aarch64 | OK | Sep 03 2024 |
Exports:.render.server.infofindGrovesfindMRCIslinearMrcamakeCollapsedTreemedTreemultiDistplotGrovesplotGrovesD3plotTreeDiffrefTreeDistrelatedTreeDistsimulateIndTreetipDifftipsMRCAdepthstreeConcordancetreeDisttreespacetreespaceServertreeVecwiwMedTreewiwTreeDist
Dependencies:ade4adegenetadegraphicsapeaskpassbase64encbbmlebdsmatrixbootbslibcachemcellrangercliclusterclusterGenerationcodacodetoolscolorspacecombinatcommonmarkcpp11crayoncrosstalkcurldata.tabledeldirDEoptimdigestdistorydoParalleldotCall64dplyrDTellipseevaluateexpmfansifarverfastmapfastmatchfieldsfontawesomeforeachfsgenericsggplot2ggseqlogogluegoogleVisgtablehighrhmshtmltoolshtmlwidgetshttpuvhttrigraphinterpisobanditeratorsjpegjquerylibjsonliteKernSmoothknitrlabelinglamWlaterlatticelatticeExtralazyevallifecycleLuminescencemagrittrmapsmarkdownMASSMatrixmatrixStatsmclustmemoisemgcvmimeminpack.lmmnormtmunsellmvtnormnlmenumDerivopenssloptimParallelpermutephangornphytoolspillarpixmappkgconfigplyrpngprettyunitsprogresspromisesquadprogR6rappdirsRCarbRColorBrewerRcppRcppArmadilloRcppEigenRcppParallelreadxlrematchreshape2rglrhandsontablerlangRLumShinyrmarkdownsassscalesscatterD3scatterplot3dsegmentedseqinrshapeshinyshinyBSshinydashboardsourcetoolsspspamstringistringrsystibbletidyselecttinytexutf8vctrsveganviridisLitewithrxfunXMLxtableyamlzoo
Comparing trees by tip label categories
Rendered fromtipCategories.Rmd
usingknitr::rmarkdown
on Sep 03 2024.Last update: 2020-10-08
Started: 2018-01-16
Exploration of landscapes of phylogenetic trees
Rendered fromintroduction.Rmd
usingknitr::rmarkdown
on Sep 03 2024.Last update: 2023-03-29
Started: 2017-03-13
treespace worked example: Dengue trees
Rendered fromDengueVignette.Rmd
usingknitr::rmarkdown
on Sep 03 2024.Last update: 2020-11-13
Started: 2017-03-13
treespace worked example: Transmission trees
Rendered fromTransmissionTreesVignette.Rmd
usingknitr::rmarkdown
on Sep 03 2024.Last update: 2021-03-23
Started: 2017-03-13