{
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  "Package": "TML",
  "Type": "Package",
  "Title": "Tropical Geometry Tools for Machine Learning",
  "Version": "2.3.0",
  "Authors@R": "c(person('David', 'Barnhill', email='david.barnhill@nps.edu',role = c('aut','cre'), comment = c(ORCID = \"0009-0006-2781-7434\")),person('Ruriko', 'Yoshida', role = c('aut')),person('Georgios','Aliatimis',role=c('aut')),person('Keiji','Miura',role=c('aut')))",
  "Description": "Suite of tropical geometric tools for use in machine\nlearning applications. These methods may be summarized in the\nfollowing references: Yoshida, et al. (2022)\n<arxiv:2209.15045>, Barnhill et al. (2023) <arxiv:2303.02539>,\nBarnhill and Yoshida (2023) <doi:10.3390/math11153433>,\nAliatimis et al. (2023) <arXiv:2306.08796>, Yoshida et al.\n(2022) <arXiv:2206.04206>, and Yoshida et al. (2019)\n<doi:10.1007/s11538-018-0493-4>.",
  "License": "MIT + file LICENSE",
  "Maintainer": "David Barnhill <david.barnhill@nps.edu>",
  "URL": "https://github.com/barnhilldave/TML",
  "BugReports": "https://github.com/barnhilldave/TML/issues",
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  "Repository": "https://barnhilldave.r-universe.dev",
  "Date/Publication": "2024-07-29 13:58:12 UTC",
  "RemoteUrl": "https://github.com/barnhilldave/tml",
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  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-09-17 08:07:05 UTC",
    "User": "root"
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  "Author": "David Barnhill [aut, cre] (ORCID:\n<https://orcid.org/0009-0006-2781-7434>),\nRuriko Yoshida [aut],\nGeorgios Aliatimis [aut],\nKeiji Miura [aut]",
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  "_created": "2026-09-17T08:07:05.000Z",
  "_published": "2026-09-17T08:33:11.961Z",
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    "cluster.ratio_HC",
    "cluster.ratio_KM",
    "convert.to.tree",
    "draw.thyper",
    "draw.tpolytope.2d",
    "draw.tpolytope.3d",
    "FWpoint.num.w.reg",
    "FWpoint.numerical",
    "HAR.TLineSeg",
    "HAR.TLineSeg.centroid",
    "max_ins.ball",
    "min_enc.ball",
    "normaliz.polytope",
    "normaliz.tree",
    "normaliz.ultrametrics",
    "normaliz.vector",
    "normaliz.vectors",
    "over_bet_HC",
    "over_bet_KM",
    "Points.TLineSeg",
    "pre.pplot.pro",
    "prob.class",
    "project.pi",
    "pw.trop.dist",
    "rounding",
    "sigmoid",
    "tdets",
    "TKmeans",
    "TLineSeg",
    "tree.to.vector",
    "Trop_ball",
    "trop_wi_dist",
    "trop.bal.all_vert",
    "trop.bal.vert",
    "trop.centroid.MH",
    "trop.centroid.MH.square",
    "trop.dist",
    "trop.FW",
    "trop.hyper.dist",
    "trop.logistic.regression",
    "trop.tri.plot.w.pts",
    "trop.Volume",
    "Tropical.HC.AGNES",
    "tropical.KDE",
    "tropical.PCA.Polytope",
    "Ultrametrics.HAR",
    "VE.HAR",
    "VE.HAR.centroid",
    "vector.to.equidistant.tree"
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    {
      "name": "lung_fish",
      "title": "Phylogenetic trees based on lung fish data",
      "object": "lung_fish",
      "class": [
        "matrix",
        "array"
      ],
      "fields": [
        "Callorhinc-Danio",
        "Callorhinc-Gallus",
        "Callorhinc-Homo",
        "Callorhinc-Latimeria",
        "Callorhinc-Leucoraja",
        "Callorhinc-Lungfish",
        "Callorhinc-Scyliorhin",
        "Callorhinc-Takifugu",
        "Callorhinc-Xenopus",
        "Danio-Gallus",
        "Danio-Homo",
        "Danio-Latimeria",
        "Danio-Leucoraja",
        "Danio-Lungfish",
        "Danio-Scyliorhin",
        "Danio-Takifugu",
        "Danio-Xenopus",
        "Gallus-Homo",
        "Gallus-Latimeria",
        "Gallus-Leucoraja",
        "Gallus-Lungfish",
        "Gallus-Scyliorhin",
        "Gallus-Takifugu",
        "Gallus-Xenopus",
        "Homo-Latimeria",
        "Homo-Leucoraja",
        "Homo-Lungfish",
        "Homo-Scyliorhin",
        "Homo-Takifugu",
        "Homo-Xenopus",
        "Latimeria-Leucoraja",
        "Latimeria-Lungfish",
        "Latimeria-Scyliorhin",
        "Latimeria-Takifugu",
        "Latimeria-Xenopus",
        "Leucoraja-Lungfish",
        "Leucoraja-Scyliorhin",
        "Leucoraja-Takifugu",
        "Leucoraja-Xenopus",
        "Lungfish-Scyliorhin",
        "Lungfish-Takifugu",
        "Lungfish-Xenopus",
        "Scyliorhin-Takifugu",
        "Scyliorhin-Xenopus",
        "Takifugu-Xenopus"
      ],
      "rows": 1290,
      "table": true,
      "tojson": true
    },
    {
      "name": "Sim_points",
      "title": "Simulated points over the tropical projective torus",
      "object": "Sim_points",
      "class": [
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        "array"
      ],
      "fields": [],
      "rows": 150,
      "table": true,
      "tojson": true
    },
    {
      "name": "Sim_Trees1025",
      "title": "Six data sets of phylogenetic trees data simulated from the Coalescant model.",
      "object": "Sim_Trees1",
      "class": [
        "matrix",
        "array"
      ],
      "fields": [],
      "rows": 1000,
      "table": true,
      "tojson": true
    },
    {
      "name": "Sim_Trees105",
      "title": "Six data sets of phylogenetic trees data simulated from the Coalescant model.",
      "object": "Sim_Trees1",
      "class": [
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        "array"
      ],
      "fields": [],
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      "table": true,
      "tojson": true
    },
    {
      "name": "Sim_Trees11",
      "title": "Six data sets of phylogenetic trees data simulated from the Coalescant model.",
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      "fields": [],
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    {
      "name": "Sim_Trees110",
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    },
    {
      "name": "Sim_Trees12",
      "title": "Six data sets of phylogenetic trees data simulated from the Coalescant model.",
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      "table": true,
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    {
      "name": "Sim_Trees15",
      "title": "Six data sets of phylogenetic trees data simulated from the Coalescant model.",
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      "table": true,
      "tojson": true
    },
    {
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      "title": "Six data sets of phylogenetic trees data simulated from the Coalescant model.",
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      "title": "Six data sets of phylogenetic trees data simulated from the Coalescant model.",
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    },
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      "name": "Sim_Trees21",
      "title": "Six data sets of phylogenetic trees data simulated from the Coalescant model.",
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    },
    {
      "name": "Sim_Trees210",
      "title": "Six data sets of phylogenetic trees data simulated from the Coalescant model.",
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    {
      "name": "Sim_Trees22",
      "title": "Six data sets of phylogenetic trees data simulated from the Coalescant model.",
      "object": "Sim_Trees2",
      "class": [
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        "array"
      ],
      "fields": [],
      "rows": 1000,
      "table": true,
      "tojson": true
    },
    {
      "name": "Sim_Trees25",
      "title": "Six data sets of phylogenetic trees data simulated from the Coalescant model.",
      "object": "Sim_Trees2",
      "class": [
        "matrix",
        "array"
      ],
      "fields": [],
      "rows": 1000,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "bw.nn",
      "title": "Nearest neighbor bandwidth calculation",
      "topics": [
        "bw.nn"
      ]
    },
    {
      "page": "cluster.ratio_HC",
      "title": "Ratio of within and between tropical measures for tropical hierarchical clusters",
      "topics": [
        "cluster.ratio_HC"
      ]
    },
    {
      "page": "cluster.ratio_KM",
      "title": "Ratio of within and between tropical measures for k-means clusters",
      "topics": [
        "cluster.ratio_KM"
      ]
    },
    {
      "page": "convert.to.tree",
      "title": "Create a phylogenetic tree from an ultrametric",
      "topics": [
        "convert.to.tree"
      ]
    },
    {
      "page": "draw.tpolytope",
      "title": "Draw a 2-D or 3-D tropical polytope",
      "topics": [
        "draw.tpolytope",
        "draw.tpolytope.2d",
        "draw.tpolytope.3d"
      ]
    },
    {
      "page": "FWpoint.regularization",
      "title": "Modified Fermat-Weber point numerical solver for ultrametrics",
      "topics": [
        "FWpoint.num.w.reg"
      ]
    },
    {
      "page": "FWpoint.numerical",
      "title": "Fermat-Weber point numerical solver",
      "topics": [
        "FWpoint.numerical"
      ]
    },
    {
      "page": "HAR.TLineSeg",
      "title": "Uniformly sample from a max-plus tropical line segment",
      "topics": [
        "HAR.TLineSeg"
      ]
    },
    {
      "page": "HAR.TLineSeg.centroid",
      "title": "Gaussian-like Sampling on a max- or min-plus tropical line segment",
      "topics": [
        "HAR.TLineSeg.centroid"
      ]
    },
    {
      "page": "draw_thyper",
      "title": "2D or 3D rendering of max-plus or min-plus tropical hyperplane",
      "topics": [
        "draw.thyper",
        "hyper_3D"
      ]
    },
    {
      "page": "Lung_Fish",
      "title": "Phylogenetic trees based on lung fish data",
      "topics": [
        "lung_fish"
      ]
    },
    {
      "page": "max_ins.ball",
      "title": "Calculate the center point and radius of the maximum inscribed ball for a tropical simplex",
      "topics": [
        "max_ins.ball"
      ]
    },
    {
      "page": "min_enc.ball",
      "title": "Calculate a minimum enclosing ball for a tropical polytope",
      "topics": [
        "min_enc.ball"
      ]
    },
    {
      "page": "normaliz.tree",
      "title": "Normalize a phylogenetic tree",
      "topics": [
        "normaliz.tree"
      ]
    },
    {
      "page": "normalize",
      "title": "Normalize a point or set of points in the tropical projective torus",
      "topics": [
        "normaliz.polytope",
        "normaliz.ultrametrics",
        "normaliz.vector",
        "normaliz.vectors",
        "normalize"
      ]
    },
    {
      "page": "over_bet_HC",
      "title": "Tropical cluster betweeness measure for each cluster in a set of hierarchical clusters",
      "topics": [
        "over_bet_HC"
      ]
    },
    {
      "page": "over_bet_KM",
      "title": "Tropical cluster betweeness measure for a each of a set of k-means derived set of clusters",
      "topics": [
        "over_bet_KM"
      ]
    },
    {
      "page": "Points.TLineSeg",
      "title": "Sample k equally spaced points on a max- or min-plus tropical line segment",
      "topics": [
        "Points.TLineSeg"
      ]
    },
    {
      "page": "pre.pplot.pro",
      "title": "Projections of points onto a tropical triangle",
      "topics": [
        "pre.pplot.pro"
      ]
    },
    {
      "page": "prob.class",
      "title": "Estimated probability for binary class assignment",
      "topics": [
        "prob.class"
      ]
    },
    {
      "page": "project.pi",
      "title": "Project a point on the tropical projective torus onto a tropical polytope",
      "topics": [
        "project.pi"
      ]
    },
    {
      "page": "pw.trop.dist",
      "title": "Constructs the dissimilarity matrix for a set of ultrametrics",
      "topics": [
        "pw.trop.dist"
      ]
    },
    {
      "page": "rounding",
      "title": "Remove all tentacles from a tropical simplex",
      "topics": [
        "rounding"
      ]
    },
    {
      "page": "sigmoid",
      "title": "Sigmoid function",
      "topics": [
        "sigmoid"
      ]
    },
    {
      "page": "Sim_points",
      "title": "Simulated points over the tropical projective torus",
      "topics": [
        "Sim_points"
      ]
    },
    {
      "page": "Sim_Trees1",
      "title": "Six data sets of phylogenetic trees data simulated from the Coalescant model.",
      "topics": [
        "Sim_Trees1",
        "Sim_Trees1025",
        "Sim_Trees105",
        "Sim_Trees11",
        "Sim_Trees110",
        "Sim_Trees12",
        "Sim_Trees15"
      ]
    },
    {
      "page": "Sim_Trees2",
      "title": "Six data sets of phylogenetic trees data simulated from the Coalescant model.",
      "topics": [
        "Sim_Trees2",
        "Sim_Trees2025",
        "Sim_Trees205",
        "Sim_Trees21",
        "Sim_Trees210",
        "Sim_Trees22",
        "Sim_Trees25"
      ]
    },
    {
      "page": "tdets",
      "title": "Calculate the tropical determinant of a square matrix.",
      "topics": [
        "tdets"
      ]
    },
    {
      "page": "TKmeans",
      "title": "K-means clustering over the tropical projective torus",
      "topics": [
        "TKmeans"
      ]
    },
    {
      "page": "TLineSeg",
      "title": "Construct a max- or min-plus tropical line segment between two points",
      "topics": [
        "TLineSeg"
      ]
    },
    {
      "page": "TML",
      "title": "Tropical Machine Learning in R",
      "topics": [
        "TML"
      ]
    },
    {
      "page": "tree.to.vector",
      "title": "Phylogenetic tree to vector",
      "topics": [
        "tree.to.vector"
      ]
    },
    {
      "page": "Trop_ball",
      "title": "Visualize a Tropical ball in 2D or 3D",
      "topics": [
        "Trop_ball"
      ]
    },
    {
      "page": "trop_wi_dist",
      "title": "Tropical within-cluster measure",
      "topics": [
        "trop_wi_dist"
      ]
    },
    {
      "page": "tropical.ball.verts",
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