Data Analysis Tools over Space of Phylogenetic Trees Using Tropical Geometry

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Documentation for package ‘Rtropical’ version 1.2.1

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

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