TML-package |
Tropical Machine Learning in R |
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.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.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 |
lf_labels |
Phylogenetic trees based on lung fish data |
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-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-plus tropical line segment between two points |
TLineSeg_min |
Construct a min-plus tropical line segment accor |
TML |
Tropical Machine Learning in R |
tree.to.vector |
Phylogenetic tree to vector |
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.logistic.regression |
Tropical Logistic Regression |
trop.tri.plot.w.pts |
Plotting PCA-derived tropical triangles |
tropical.Gaussian |
Tropical Gaussian sampling about a center of mass |
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 |
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 |
vector.to.equidistant.tree |
Vector to equidistant tree |