Tropical Geometry Tools for Machine Learning

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Documentation for package ‘TML’ version 0.1.0

Help Pages

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
draw.tpolytope Draw a 3-D tropical polytope
draw.tpolytope.3d Draw a 3-D tropical polytope
HAR.TLineSeg Uniformly sample from a max-plus tropical line segment
HAR.TLineSeg.Norm Gaussian-like Sampling on a max-plus tropical line segment
hyper3d_max 2D or 3D rendering of max-plus or min-plus tropical hyperplane
hyper3d_min 2D or 3D rendering of max-plus or min-plus tropical hyperplane
hyper_3D 2D or 3D rendering of max-plus or min-plus tropical hyperplane
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
package-TML Tropical Machine Learning in R
Points.TLineSeg Sample k equally spaced points on a max-plus tropical line segment
pre.pplot.pro Projections of points onto a tropical triangle
project_pi Project a point on the tropical projective torus onto a tropical polytope.
rounding Remove all tentacles from a tropical simplex
Sim_points Simulated points over the tropical projective torus
Sim_Trees1 Phylogenetic trees data simulated from the Coalescant model
Sim_Trees2 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-plus tropical line segment between two points
TLineSeg_min Construct a min-plus tropical line segment accor
TML Tropical Machine Learning in R
trop.dist Compute the tropical distance
trop.dist.hyp_max Calculate the tropical distance to a max-tropical hyperplane
trop.dist.hyp_min Calculate the tropical distance to a min-tropical hyperplane
trop.Gaussian.MH Gaussian-like sampling using Metropolis filter
trop.Gaussian.MH.square Gaussian-like sampling using Metropolis filter
trop.tri.plot.w.pts Plotting PCA-derived tropical triangles
tropical.Gaussian Tropical Gaussian sampling about a center of mass
tropical.Gaussian.MH Gaussian-like 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
TropicalPolytope.extrapolation.HAR Vertex HAR with extrapolation MCMC with uniform target distribution
TropicalPolytope.extrapolation.HAR_NORM Tropical Gaussian sampling about a center of mass
trop_bal.vert Calculate the minimum generating vertex set of a tropical ball
Trop_ball Visualize a Tropical ball in 2D or 3D
Trop_FW Calculate the tropical Fermat-Weber point
Trop_Volume Estimate the volume of a tropical polytope
trop_wi_dist Tropical within-cluster measure
Ultrametrics.HAR Hit-and-Run Sampler for the space of ultrametrics