Package: TML 2.3.0

TML: Tropical Geometry Tools for Machine Learning

Suite of tropical geometric tools for use in machine learning applications. These methods may be summarized in the following references: Yoshida, et al. (2022) <arxiv:2209.15045>, Barnhill et al. (2023) <arxiv:2303.02539>, Barnhill and Yoshida (2023) <doi:10.3390/math11153433>, Aliatimis et al. (2023) <arxiv:2306.08796>, Yoshida et al. (2022) <arxiv:2206.04206>, and Yoshida et al. (2019) <doi:10.1007/s11538-018-0493-4>.

Authors:David Barnhill [aut, cre], Ruriko Yoshida [aut], Georgios Aliatimis [aut], Keiji Miura [aut]

TML_2.3.0.tar.gz
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TML.pdf |TML.html✨
TML/json (API)

# Install 'TML' in R:
install.packages('TML', repos = c('https://barnhilldave.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/barnhilldave/tml/issues

Datasets:
  • 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_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.
  • Sim_points - Simulated points over the tropical projective torus
  • lung_fish - Phylogenetic trees based on lung fish data

On CRAN:

50 exports 2 stars 1.41 score 76 dependencies 1 scripts 329 downloads

Last updated 2 months agofrom:d34974055e. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKAug 28 2024
R-4.5-winOKAug 28 2024
R-4.5-linuxOKAug 28 2024
R-4.4-winOKAug 28 2024
R-4.4-macOKAug 28 2024
R-4.3-winOKAug 28 2024
R-4.3-macOKAug 28 2024

Exports:bw.nncluster.ratio_HCcluster.ratio_KMconvert.to.treedraw.thyperdraw.tpolytope.2ddraw.tpolytope.3dFWpoint.num.w.regFWpoint.numericalHAR.TLineSegHAR.TLineSeg.centroidmax_ins.ballmin_enc.ballnormaliz.polytopenormaliz.treenormaliz.ultrametricsnormaliz.vectornormaliz.vectorsover_bet_HCover_bet_KMPoints.TLineSegpre.pplot.proprob.classproject.pipw.trop.distroundingsigmoidtdetsTKmeansTLineSegtree.to.vectorTrop_balltrop_wi_disttrop.bal.all_verttrop.bal.verttrop.centroid.MHtrop.centroid.MH.squaretrop.disttrop.FWtrop.hyper.disttrop.logistic.regressiontrop.tri.plot.w.ptstrop.VolumeTropical.HC.AGNEStropical.KDEtropical.PCA.PolytopeUltrametrics.HARVE.HARVE.HAR.centroidvector.to.equidistant.tree

Dependencies:apebase64encbitopsbslibcachemcaToolscliclusterclusterGenerationcodacodetoolscombinatcpp11DEoptimdigestdoParallelevaluateexpmfastmapfastmatchfontawesomeforeachfsgenericsgluegmpgplotsgtoolshighrhtmltoolshtmlwidgetsigraphiteratorsjquerylibjsonliteKernSmoothknitrlatticelifecyclelpSolvelpSolveAPImagrittrmapsMASSMatrixmemoisemimemiscToolsmnormtnlmenumDerivoptimParallelphangornphytoolspkgconfigquadprogR6rappdirsrcddRcppRcppAlgosRcppArmadilloRcppGSLRcppParallelRcppZigguratRfastrglrlangrmarkdownROCRsassscatterplot3dtinytexvctrsxfunyaml

Readme and manuals

Help Manual

Help pageTopics
Nearest neighbor bandwidth calculationbw.nn
Ratio of within and between tropical measures for tropical hierarchical clusterscluster.ratio_HC
Ratio of within and between tropical measures for k-means clusterscluster.ratio_KM
Create a phylogenetic tree from an ultrametricconvert.to.tree
Draw a 2-D or 3-D tropical polytopedraw.tpolytope draw.tpolytope.2d draw.tpolytope.3d
Modified Fermat-Weber point numerical solver for ultrametricsFWpoint.num.w.reg
Fermat-Weber point numerical solverFWpoint.numerical
Uniformly sample from a max-plus tropical line segmentHAR.TLineSeg
Gaussian-like Sampling on a max- or min-plus tropical line segmentHAR.TLineSeg.centroid
2D or 3D rendering of max-plus or min-plus tropical hyperplanedraw.thyper hyper_3D
Phylogenetic trees based on lung fish datalung_fish
Calculate the center point and radius of the maximum inscribed ball for a tropical simplexmax_ins.ball
Calculate a minimum enclosing ball for a tropical polytopemin_enc.ball
Normalize a phylogenetic treenormaliz.tree
Normalize a point or set of points in the tropical projective torusnormaliz.polytope normaliz.ultrametrics normaliz.vector normaliz.vectors normalize
Tropical cluster betweeness measure for each cluster in a set of hierarchical clustersover_bet_HC
Tropical cluster betweeness measure for a each of a set of k-means derived set of clustersover_bet_KM
Sample k equally spaced points on a max- or min-plus tropical line segmentPoints.TLineSeg
Projections of points onto a tropical trianglepre.pplot.pro
Estimated probability for binary class assignmentprob.class
Project a point on the tropical projective torus onto a tropical polytopeproject.pi
Constructs the dissimilarity matrix for a set of ultrametricspw.trop.dist
Remove all tentacles from a tropical simplexrounding
Sigmoid functionsigmoid
Simulated points over the tropical projective torusSim_points
Six data sets of phylogenetic trees data simulated from the Coalescant model.Sim_Trees1 Sim_Trees1025 Sim_Trees105 Sim_Trees11 Sim_Trees110 Sim_Trees12 Sim_Trees15
Six data sets of phylogenetic trees data simulated from the Coalescant model.Sim_Trees2 Sim_Trees2025 Sim_Trees205 Sim_Trees21 Sim_Trees210 Sim_Trees22 Sim_Trees25
Calculate the tropical determinant of a square matrix.tdets
K-means clustering over the tropical projective torusTKmeans
Construct a max- or min-plus tropical line segment between two pointsTLineSeg
Tropical Machine Learning in RTML
Phylogenetic tree to vectortree.to.vector
Visualize a Tropical ball in 2D or 3DTrop_ball
Tropical within-cluster measuretrop_wi_dist
Calculate the minimum or entire generating vertex set of a tropical ball using a max- or min-plus algebratrop.bal.all_vert trop.bal.vert
Compute the tropical distancetrop.dist
Calculate the tropical Fermat-Weber pointtrop.FW
Calculate the tropical distance to a max-tropical hyperplanetrop.hyper.dist
Tropical Logistic Regressiontrop.logistic.regression
Plotting PCA-derived tropical trianglestrop.tri.plot.w.pts
Estimate the volume of a tropical polytopetrop.Volume
Tropical centroid-based sampling about a center of masstropical.centroid VE.HAR.centroid
Centroid-based sampling using Metropolis filtertrop.centroid.MH trop.centroid.MH.square tropical.centroid.MH
Agglomerative (AGNES) tropical hierarchical clusteringTropical.HC.AGNES
Tropical Kernel Density Estimation of Phylogenetic Treestropical.KDE
Tropical principal component analysis (PCA) on over tropical projective torustropical.PCA tropical.PCA.Polytope
Hit-and-Run Sampler for the space of ultrametricsUltrametrics.HAR
Vertex HAR with extrapolation (VHE) MCMC with uniform target distributionVE.HAR
Vector to equidistant treevector.to.equidistant.tree