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TML

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Install

install.packages('TML')

Version

2.3.0

License

MIT + file LICENSE

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3

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Maintainer

David Barnhill

Last Published

July 29th, 2024

Functions in TML (2.3.0)

VE.HAR

Vertex HAR with extrapolation (VHE) MCMC with uniform target distribution
Ultrametrics.HAR

Hit-and-Run Sampler for the space of ultrametrics
min_enc.ball

Calculate a minimum enclosing ball for a tropical polytope
normaliz.tree

Normalize a phylogenetic tree
TML-package

TML: Tropical Geometry Tools for Machine Learning
pre.pplot.pro

Projections of points onto a tropical triangle
over_bet_KM

Tropical cluster betweeness measure for a each of a set of k-means derived set of clusters
trop.FW

Calculate the tropical Fermat-Weber point
max_ins.ball

Calculate the center point and radius of the maximum inscribed ball for a tropical simplex
tree.to.vector

Phylogenetic tree to vector
lung_fish

Phylogenetic trees based on lung fish data
TML

Tropical Machine Learning in R
draw.tpolytope

Draw a 2-D or 3-D tropical polytope
Trop_ball

Visualize a Tropical ball in 2D or 3D
Tropical.HC.AGNES

Agglomerative (AGNES) tropical hierarchical clustering
cluster.ratio_KM

Ratio of within and between tropical measures for k-means clusters
rounding

Remove all tentacles from a tropical simplex
tropical.centroid

Tropical centroid-based sampling about a center of mass
pw.trop.dist

Constructs the dissimilarity matrix for a set of ultrametrics
sigmoid

Sigmoid function
vector.to.equidistant.tree

Vector to equidistant tree
prob.class

Estimated probability for binary class assignment
tropical.KDE

Tropical Kernel Density Estimation of Phylogenetic Trees
project.pi

Project a point on the tropical projective torus onto a tropical polytope
tropical.PCA

Tropical principal component analysis (PCA) on over tropical projective torus
convert.to.tree

Create a phylogenetic tree from an ultrametric
tdets

Calculate the tropical determinant of a square matrix.
over_bet_HC

Tropical cluster betweeness measure for each cluster in a set of hierarchical clusters
normalize

Normalize a point or set of points in the tropical projective torus
trop.tri.plot.w.pts

Plotting PCA-derived tropical triangles
trop_wi_dist

Tropical within-cluster measure
tropical.centroid.MH

Centroid-based sampling using Metropolis filter
hyper_3D

2D or 3D rendering of max-plus or min-plus tropical hyperplane
trop.bal.vert

Calculate the minimum or entire generating vertex set of a tropical ball using a max- or min-plus algebra
trop.dist

Compute the tropical distance
trop.hyper.dist

Calculate the tropical distance to a max-tropical hyperplane
trop.Volume

Estimate the volume of a tropical polytope
trop.logistic.regression

Tropical Logistic Regression
Points.TLineSeg

Sample k equally spaced points on a max- or min-plus tropical line segment
FWpoint.numerical

Fermat-Weber point numerical solver
Sim_Trees1

Six data sets of phylogenetic trees data simulated from the Coalescant model.
TKmeans

K-means clustering over the tropical projective torus
FWpoint.num.w.reg

Modified Fermat-Weber point numerical solver for ultrametrics
HAR.TLineSeg.centroid

Gaussian-like Sampling on a max- or min-plus tropical line segment
HAR.TLineSeg

Uniformly sample from a max-plus tropical line segment
TLineSeg

Construct a max- or min-plus tropical line segment between two points
bw.nn

Nearest neighbor bandwidth calculation
cluster.ratio_HC

Ratio of within and between tropical measures for tropical hierarchical clusters
Sim_points

Simulated points over the tropical projective torus
Sim_Trees2

Six data sets of phylogenetic trees data simulated from the Coalescant model.