Package: Rtropical 1.2.1

Rtropical: Data Analysis Tools over Space of Phylogenetic Trees Using Tropical Geometry

Process phylogenetic trees with tropical support vector machine and principal component analysis defined with tropical geometry. Details about tropical support vector machine are available in : Tang, X., Wang, H. & Yoshida, R. (2020) <arxiv:2003.00677>. Details about tropical principle component analysis are available in : Page, R., Yoshida, R. & Zhang L. (2020) <doi:10.1093/bioinformatics/btaa564> and Yoshida, R., Zhang, L. & Zhang, X. (2019) <doi:10.1007/s11538-018-0493-4>.

Authors:Houjie Wang [aut, cre], Kaizhang Wang [aut], Grady Weyenberg [aut], Xiaoxian Tang [aut], Ruriko Yoshida [aut]

Rtropical_1.2.1.tar.gz
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Rtropical.pdf |Rtropical.html✨
Rtropical/json (API)
NEWS

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

Bug tracker:https://github.com/houjiewang/rtropical/issues

Datasets:
  • all_trees - Simulated Tree Data with Different Proximity Parameter Value
  • apicomplexa - Apicomplexa gene trees sample data set.
  • lungfish - Coelacanths genome and transcriptome data
  • sim_trees - Simulated Tree Data

On CRAN:

Conda:

4.00 score 5 scripts 149 downloads 20 exports 90 dependencies

Last updated 3 years agofrom:6713304282. Checks:9 OK. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKMar 23 2025
R-4.5-winOKMar 23 2025
R-4.5-macOKMar 23 2025
R-4.5-linuxOKMar 23 2025
R-4.4-winOKMar 23 2025
R-4.4-macOKMar 23 2025
R-4.4-linuxOKMar 23 2025
R-4.3-winOKMar 23 2025
R-4.3-macOKMar 23 2025

Exports:as.matrix.multiPhyloas.vector.phylocoef.cv.tropsvmcoef.tropsvmcv.tropsvmlinsp_to_polyplot.troppcapredict.cv.tropsvmpredict.tropsvmread.nexus.to.data.matrixread.tree.to.data.matrixsummary.cv.tropsvmtropdettropFWtroppca.linsptroppca.linsp2polytroppca.polytropproj.linsptropproj.polytropsvm

Dependencies:apecaretclasscliclockcodetoolscolorspacecpp11data.tablediagramdigestdplyre1071fansifarverfastmatchforeachfuturefuture.applygenericsggplot2globalsgluegmpgowergtablehardhatigraphipredisobanditeratorsKernSmoothlabelinglatex2explatticelavalifecyclelistenvlpSolvelpSolveAPIlubridatemagrittrMASSMatrixmgcvModelMetricsmunsellnlmennetnumDerivparallellyphangornpillarpkgconfigplyrpROCprodlimprogressrproxypurrrquadprogR6RColorBrewerRcppRcppAlgosRcppArmadilloRcppParallelrecipesreshape2RfastrlangrpartscalesshapesparsevctrsSQUAREMstringistringrsurvivaltibbletidyrtidyselecttimechangetimeDatetzdbutf8vctrsviridisLitewithrzigg

The Rtropical package

Rendered fromusage.Rmdusingknitr::rmarkdownon Mar 23 2025.

Last update: 2021-09-15
Started: 2021-06-30