R: Tropical Geometry Tools for Machine Learning

# Tropical Geometry Tools for Machine Learning

## Documentation for package ‘TML’ version 2.3.0

- DESCRIPTION file
- Package README

## Help Pages

bw.nn | Nearest neighbor bandwidth calculation
cluster.ratio_HC | Ratio of within and between tropical measures for tropical hierarchical clusters
cluster.ratio_KM | Ratio of within and between tropical measures for k-means clusters
convert.to.tree | Create a phylogenetic tree from an ultrametric
draw.thyper | 2D or 3D rendering of max-plus or min-plus tropical hyperplane
draw.tpolytope | Draw a 2-D or 3-D tropical polytope
draw.tpolytope.2d | Draw a 2-D or 3-D tropical polytope
draw.tpolytope.3d | Draw a 2-D or 3-D tropical polytope
FWpoint.num.w.reg | Modified Fermat-Weber point numerical solver for ultrametrics
FWpoint.numerical | Fermat-Weber point numerical solver
HAR.TLineSeg | Uniformly sample from a max-plus tropical line segment
HAR.TLineSeg.centroid | Gaussian-like Sampling on a max- or min-plus tropical line segment
hyper_3D | 2D or 3D rendering of max-plus or min-plus tropical hyperplane
lung_fish | Phylogenetic trees based on lung fish data
max_ins.ball | Calculate the center point and radius of the maximum inscribed ball for a tropical simplex
min_enc.ball | Calculate a minimum enclosing ball for a tropical polytope
normaliz.polytope | Normalize a point or set of points in the tropical projective torus
normaliz.tree | Normalize a phylogenetic tree
normaliz.ultrametrics | Normalize a point or set of points in the tropical projective torus
normaliz.vector | Normalize a point or set of points in the tropical projective torus
normaliz.vectors | Normalize a point or set of points in the tropical projective torus
normalize | Normalize a point or set of points in the tropical projective torus
over_bet_HC | Tropical cluster betweeness measure for each cluster in a set of hierarchical clusters
over_bet_KM | Tropical cluster betweeness measure for a each of a set of k-means derived set of clusters
Points.TLineSeg | Sample k equally spaced points on a max- or min-plus tropical line segment
pre.pplot.pro | Projections of points onto a tropical triangle
prob.class | Estimated probability for binary class assignment
project.pi | Project a point on the tropical projective torus onto a tropical polytope
pw.trop.dist | Constructs the dissimilarity matrix for a set of ultrametrics
rounding | Remove all tentacles from a tropical simplex
sigmoid | Sigmoid function
Sim_points | Simulated points over the tropical projective torus
Sim_Trees1 | Six data sets of phylogenetic trees data simulated from the Coalescant model.
Sim_Trees1025 | Six data sets of phylogenetic trees data simulated from the Coalescant model.
Sim_Trees105 | Six data sets of phylogenetic trees data simulated from the Coalescant model.
Sim_Trees11 | Six data sets of phylogenetic trees data simulated from the Coalescant model.
Sim_Trees110 | Six data sets of phylogenetic trees data simulated from the Coalescant model.
Sim_Trees12 | Six data sets of phylogenetic trees data simulated from the Coalescant model.
Sim_Trees15 | Six data sets of phylogenetic trees data simulated from the Coalescant model.
Sim_Trees2 | Six data sets of phylogenetic trees data simulated from the Coalescant model.
Sim_Trees2025 | Six data sets of phylogenetic trees data simulated from the Coalescant model.
Sim_Trees205 | Six data sets of phylogenetic trees data simulated from the Coalescant model.
Sim_Trees21 | Six data sets of phylogenetic trees data simulated from the Coalescant model.
Sim_Trees210 | Six data sets of phylogenetic trees data simulated from the Coalescant model.
Sim_Trees22 | Six data sets of phylogenetic trees data simulated from the Coalescant model.
Sim_Trees25 | Six data sets of phylogenetic trees data simulated from the Coalescant model.
tdets | Calculate the tropical determinant of a square matrix.
TKmeans | K-means clustering over the tropical projective torus
TLineSeg | Construct a max- or min-plus tropical line segment between two points
TML | Tropical Machine Learning in R
tree.to.vector | Phylogenetic tree to vector
trop.bal.all_vert | Calculate the minimum or entire generating vertex set of a tropical ball using a max- or min-plus algebra
trop.bal.vert | Calculate the minimum or entire generating vertex set of a tropical ball using a max- or min-plus algebra
trop.centroid.MH | Centroid-based sampling using Metropolis filter
trop.centroid.MH.square | Centroid-based sampling using Metropolis filter
trop.dist | Compute the tropical distance
trop.FW | Calculate the tropical Fermat-Weber point
trop.hyper.dist | Calculate the tropical distance to a max-tropical hyperplane
trop.logistic.regression | Tropical Logistic Regression
trop.tri.plot.w.pts | Plotting PCA-derived tropical triangles
trop.Volume | Estimate the volume of a tropical polytope
tropical.centroid | Tropical centroid-based sampling about a center of mass
tropical.centroid.MH | Centroid-based sampling using Metropolis filter
Tropical.HC.AGNES | Agglomerative (AGNES) tropical hierarchical clustering
tropical.KDE | Tropical Kernel Density Estimation of Phylogenetic Trees
tropical.PCA | Tropical principal component analysis (PCA) on over tropical projective torus
tropical.PCA.Polytope | Tropical principal component analysis (PCA) on over tropical projective torus
Trop_ball | Visualize a Tropical ball in 2D or 3D
trop_wi_dist | Tropical within-cluster measure
Ultrametrics.HAR | Hit-and-Run Sampler for the space of ultrametrics
VE.HAR | Vertex HAR with extrapolation (VHE) MCMC with uniform target distribution
VE.HAR.centroid | Tropical centroid-based sampling about a center of mass
vector.to.equidistant.tree | Vector to equidistant tree