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'))

Peer review:

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:

20 exports 0.83 score 90 dependencies 5 scripts 166 downloads

Last updated 2 years agofrom:6713304282. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKAug 25 2024
R-4.5-winOKAug 25 2024
R-4.5-linuxOKAug 25 2024
R-4.4-winOKAug 25 2024
R-4.4-macOKAug 25 2024
R-4.3-winOKAug 25 2024
R-4.3-macOKAug 25 2024

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.applygenericsggplot2globalsgluegmpgowergtablehardhatigraphipredisobanditeratorsKernSmoothlabelinglatex2explatticelavalifecyclelistenvlpSolvelpSolveAPIlubridatemagrittrMASSMatrixmgcvModelMetricsmunsellnlmennetnumDerivparallellyphangornpillarpkgconfigplyrpROCprodlimprogressrproxypurrrquadprogR6RColorBrewerRcppRcppAlgosRcppArmadilloRcppGSLRcppParallelRcppZigguratrecipesreshape2RfastrlangrpartscalesshapeSQUAREMstringistringrsurvivaltibbletidyrtidyselecttimechangetimeDatetzdbutf8vctrsviridisLitewithr

The Rtropical package

Rendered fromusage.Rmdusingknitr::rmarkdownon Aug 25 2024.

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