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  "Package": "mvSLOUCH",
  "Type": "Package",
  "Title": "Multivariate Stochastic Linear Ornstein-Uhlenbeck Models for\nPhylogenetic Comparative Hypotheses",
  "Version": "2.7.7",
  "Date": "2025-07-24",
  "Authors@R": "c(person(family=\"Bartoszek\",given=\"Krzysztof\",role=c(\"cre\",\"aut\"),email=\"krzbar@protonmail.ch\"),\nperson(family=\"Clarke\", given=\"John\", email=\"j.clarke.paleo@gmail.com\",role=c(\"ctb\")),\nperson(family=\"Fuentes-Gonzalez\", given=\"Jesualdo\", email=\"jafuentesgonzalez@ua.edu\",role=c(\"ctb\")),\nperson(family=\"Pienaar\", given=\"Jason\", email=\"jason.pienaar@ua.edu\",role=c(\"ctb\")))",
  "Maintainer": "Krzysztof Bartoszek <krzbar@protonmail.ch>",
  "Description": "Fits multivariate Ornstein-Uhlenbeck types of models to\ncontinues trait data from species related by a common\nevolutionary history. See K. Bartoszek, J, Pienaar, P. Mostad,\nS. Andersson, T. F. Hansen (2012)\n<doi:10.1016/j.jtbi.2012.08.005> and K. Bartoszek, and J.\nTredgett Clarke, J. Fuentes-Gonzalez, V. Mitov, J. Pienaar, M.\nPiwczynski, R. Puchalka, K. Spalik, K. L. Voje (2024)\n<doi:10.1111/2041-210X.14376>. The suggested PCMBaseCpp package\n(which significantly speeds up the likelihood calculations) can\nbe obtained from <https://github.com/venelin/PCMBaseCpp/>.",
  "License": "GPL (>= 2) | file LICENCE",
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    "simulate_clustered_phylogeny",
    "simulBMProcPhylTree",
    "simulMVSLOUCHProcPhylTree",
    "simulOUCHProcPhylTree",
    "SummarizeBM",
    "SummarizeMVSLOUCH",
    "SummarizeOUCH"
  ],
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    {
      "page": "mvSLOUCH-package",
      "title": "Multivariate Ornstein-Uhlenbeck type stochastic differential equation models for phylogenetic comparative data.",
      "topics": [
        "mvSLOUCH-package",
        "mvSLOUCH"
      ]
    },
    {
      "page": "BrownianMotionModel",
      "title": "Estimate parameters under a Brownian motion model of evolution",
      "topics": [
        "BrownianMotionModel"
      ]
    },
    {
      "page": "drawPhylProcess",
      "title": "Plots the realization of a process evolving on a phylogenetic tree",
      "topics": [
        "drawPhylProcess"
      ]
    },
    {
      "page": "estimate.evolutionary.model",
      "title": "Wrapper function to find best (out of BM, OU, OUOU, OUBM) fitting evolutionary model and estimate its parameters.",
      "topics": [
        "estimate.evolutionary.model"
      ]
    },
    {
      "page": "fitch.mvsl",
      "title": "Unordered Fitch parsimony reconstruction of discrete character states",
      "topics": [
        "fitch.mvsl"
      ]
    },
    {
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      "title": "Generate a list of model setups for the function 'estimate.evolutionary.model'.",
      "topics": [
        "generate.model.setups"
      ]
    },
    {
      "page": "mvslouchModel",
      "title": "Estimate parameters under a (multivariate) OUBM model of evolution",
      "topics": [
        "mvslouchModel"
      ]
    },
    {
      "page": "OU_phylreg",
      "title": "Performs a phylogenetic regression under a given OU model of evolution",
      "topics": [
        "OU_phylreg"
      ]
    },
    {
      "page": "OU_RSS",
      "title": "Calculates the RSS under a (multivariate) phylogenetic OU model of evolution",
      "topics": [
        "OU_RSS"
      ]
    },
    {
      "page": "OU_xVz",
      "title": "Performs a vector matrix vector multiplcation under a (multivariate) phylogenetic OU model of evolution",
      "topics": [
        "OU_xVz"
      ]
    },
    {
      "page": "ouchModel",
      "title": "Estimate parameters under a (multivariate) OU model of evolution",
      "topics": [
        "ouchModel"
      ]
    },
    {
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      "title": "Parametric bootstrap for confidence intervals",
      "topics": [
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    },
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      "title": "Simulate data on a phylogeny under a (multivariate) OU model",
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      ]
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      "title": "Summarize parameters estimated under a Brownian motion model",
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      "title": "Summarize parameters estimated under a (multivariate) OU motion model",
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