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

# Data Analysis Tools over Space of Phylogenetic Trees Using Tropical Geometry

## Documentation for package ‘Rtropical’ version 1.2.1

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## 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