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
Rtropical_1.2.1.zip(r-4.7-any)Rtropical_1.2.1.zip(r-4.6-any)Rtropical_1.2.1.zip(r-4.5-any)
Rtropical_1.2.1.tgz(r-4.6-any)Rtropical_1.2.1.tgz(r-4.5-any)
Rtropical_1.2.1.tar.gz(r-4.7-any)Rtropical_1.2.1.tar.gz(r-4.6-any)
Rtropical_1.2.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
Rtropical/json (API)

# 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:

4.00 score 6 scripts 277 downloads 20 exports 87 dependencies

Last updated from:6713304282. Checks:9 OK. Indexed: yes.

Target	Result	Time
linux-devel-x86_64	OK	357
source / vignettes	OK	412
linux-release-x86_64	OK	339
macos-release-arm64	OK	305
macos-oldrel-arm64	OK	241
windows-devel	OK	204
windows-release	OK	191
windows-oldrel	OK	201
wasm-release	OK	140

Exports:as.matrix.multiPhylo as.vector.phylo coef.cv.tropsvm coef.tropsvm cv.tropsvm linsp_to_poly plot.troppca predict.cv.tropsvm predict.tropsvm read.nexus.to.data.matrix read.tree.to.data.matrix summary.cv.tropsvm tropdet tropFW troppca.linsp troppca.linsp2poly troppca.poly tropproj.linsp tropproj.poly tropsvm

Dependencies:ape caret class cli clock codetools cpp11 data.table diagram digest dplyr e1071 farver fastmatch foreach future future.apply generics ggplot2 globals glue gmp gower gtable hardhat igraph ipred isoband iterators KernSmooth labeling latex2exp lattice lava lifecycle listenv lpSolve lpSolveAPI lubridate magrittr MASS Matrix ModelMetrics nlme nnet numDeriv parallelly phangorn pillar pkgconfig plyr pROC prodlim progressr proxy purrr quadprog R6 RColorBrewer Rcpp RcppAlgos RcppArmadillo RcppParallel recipes reshape2 Rfast rlang rpart S7 scales shape sparsevctrs SQUAREM stringi stringr survival tibble tidyr tidyselect timechange timeDate tzdb utf8 vctrs viridisLite withr zigg

The Rtropical package

Tropical SVM | Tropical PCA | Tropical Fermat-weber Point

Rendered fromusage.Rmdusingknitr::rmarkdown

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

Help page	Topics
Simulated Tree Data with Different Proximity Parameter Value	all_trees
Apicomplexa gene trees sample data set.	apicomplexa
Vectorize a Set of Phylognetic Trees	as.matrix.multiPhylo
Vectorize a Phylogenetic Tree	as.vector.phylo
Extract Optimal Tropical Hyperplane from a cv.tropsvm object	coef.cv.tropsvm
Extract Optimal Tropical Hyperplane from a tropsvm object	coef.tropsvm
Cross-Validation for Tropical Support Vector Machines	cv.tropsvm
Coelacanths genome and transcriptome data	lungfish
Plot the Tropical Principal Components with Data Projections	plot.troppca
Predict Method for Tropical Support Vector Machines based on Cross-Validation	predict.cv.tropsvm
Predict Method for Tropical Support Vector Machines	predict.tropsvm
Read NEXUS-formatted trees from two categories into a data matrix	read.nexus.to.data.matrix
Read Newick-formatted trees in two categories into a data matrix	read.tree.to.data.matrix
Simulated Tree Data	sim_trees
Summarize an Analysis of Cross-Validated Tropical Support Vector Machine	summary.cv.tropsvm
Tropical Determinant of a Matrix	tropdet
Tropical Fermat-Weber Point	tropFW
Tropical Principal Component Analysis by Tropical Linear Space	troppca.linsp
Tropical Principal Component Analysis by Polytope Converted from Linear Space	troppca.linsp2poly
Tropical Principal Component Analysis by Tropical Polytope	troppca.poly
Projection on Tropical Linear Space	tropproj.linsp
Projection on Tropical Polytope	tropproj.poly
Tropical Support Vector Machines	tropsvm

Package: Rtropical 1.2.1

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

Citation

Development and contributors

Readme and manuals

Help Manual

Usage by other packages (reverse dependencies)