Tropical Geometry Tools for Machine Learning

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Documentation for package ‘TML’ version 2.3.0

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