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:

4.00 score 5 scripts 163 downloads 20 exports 90 dependencies

Last updated 3 years agofrom:6713304282. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 23 2024
R-4.5-winOKNov 23 2024
R-4.5-linuxOKNov 23 2024
R-4.4-winOKNov 23 2024
R-4.4-macOKNov 23 2024
R-4.3-winOKNov 23 2024
R-4.3-macOKNov 23 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 Nov 23 2024.

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