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  "Package": "mvMORPH",
  "Type": "Package",
  "Title": "Multivariate Comparative Tools for Fitting Evolutionary Models\nto Morphometric Data",
  "Version": "1.2.2",
  "Date": "2024-08-28",
  "Authors@R": "c(person(given = \"Julien\",\nfamily = \"Clavel\",\nrole = c(\"aut\", \"cre\"),\nemail = \"julien.clavel@hotmail.fr\"),\nperson(given = c(\"with\", \"contributions\", \"from\", \"Aaron\"),\nfamily = \"King\",\nrole = \"aut\"),\nperson(given = \"Emmanuel\",\nfamily = \"Paradis\",\nrole = \"aut\"))",
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  "Description": "Fits multivariate (Brownian Motion, Early Burst, ACDC,\nOrnstein-Uhlenbeck and Shifts) models of continuous traits\nevolution on trees and time series. 'mvMORPH' also proposes\nhigh-dimensional multivariate comparative tools (linear models\nusing Generalized Least Squares and multivariate tests) based\non penalized likelihood.  See Clavel et al. (2015)\n<DOI:10.1111/2041-210X.12420>, Clavel et al. (2019)\n<DOI:10.1093/sysbio/syy045>, and Clavel & Morlon (2020)\n<DOI:10.1093/sysbio/syaa010>.",
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  "Repository": "https://phylotastic.r-universe.dev",
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    "ancestral",
    "dfaShape",
    "effectsize",
    "EIC",
    "estim",
    "GIC",
    "halflife",
    "LRT",
    "manova.gls",
    "mapping.asr",
    "mv.Precalc",
    "mvBM",
    "mvEB",
    "mvgls",
    "mvgls.dfa",
    "mvgls.pca",
    "mvLL",
    "mvols",
    "mvOU",
    "mvOUTS",
    "mvqqplot",
    "mvRWTS",
    "mvSHIFT",
    "mvSIM",
    "pairwise.contrasts",
    "pairwise.glh",
    "pcaShape",
    "pruning",
    "stationary"
  ],
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    {
      "name": "phyllostomid",
      "title": "Phylogeny and trait data for a sample of Phyllostomid bats",
      "object": "phyllostomid",
      "file": "phyllostomid.rda",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    }
  ],
  "_help": [
    {
      "page": "mvMORPH-package",
      "title": "Multivariate Comparative Methods for Fitting Evolutionary Models to Morphometric Data",
      "topics": [
        "mvMORPH-package",
        "mvMORPH"
      ]
    },
    {
      "page": "aicw",
      "title": "Akaike weights",
      "topics": [
        "aicw"
      ]
    },
    {
      "page": "ancestral",
      "title": "Estimation of traits ancestral states.",
      "topics": [
        "ancestral"
      ]
    },
    {
      "page": "coef.mvgls",
      "title": "Extract multivariate gls (or ols) model coefficients",
      "topics": [
        "coef.mvgls"
      ]
    },
    {
      "page": "dfaShape",
      "title": "Projection of 2D and 3D shapes (from geometric morphometric datasets) on Discriminant axes",
      "topics": [
        "dfaShape"
      ]
    },
    {
      "page": "effectsize",
      "title": "Multivariate measure of association/effect size for objects of class \"manova.gls\"",
      "topics": [
        "effectsize"
      ]
    },
    {
      "page": "EIC",
      "title": "Extended Information Criterion (EIC) to compare models fit with 'mvgls' (or 'mvols') by Maximum Likelihood (ML) or Penalized Likelihood (PL)",
      "topics": [
        "EIC"
      ]
    },
    {
      "page": "estim",
      "title": "Ancestral states reconstructions and missing value imputation with phylogenetic/time-series models",
      "topics": [
        "estim"
      ]
    },
    {
      "page": "fitted.mvgls",
      "title": "Extract multivariate gls (or ols) model fitted values",
      "topics": [
        "fitted.mvgls"
      ]
    },
    {
      "page": "GIC",
      "title": "Generalized Information Criterion (GIC) to compare models fit with 'mvgls' (or 'mvols') by Maximum Likelihood (ML) or Penalized Likelihood (PL)",
      "topics": [
        "GIC"
      ]
    },
    {
      "page": "halflife",
      "title": "The phylogenetic half-life for an Ornstein-Uhlenbeck process",
      "topics": [
        "halflife"
      ]
    },
    {
      "page": "LRT",
      "title": "Likelihood Ratio Test",
      "topics": [
        "LRT"
      ]
    },
    {
      "page": "manova.gls",
      "title": "Multivariate Analysis of Variance",
      "topics": [
        "manova.gls"
      ]
    },
    {
      "page": "mv.Precalc",
      "title": "Model parameterization for the various mvMORPH functions",
      "topics": [
        "mv.Precalc"
      ]
    },
    {
      "page": "mvBM",
      "title": "Multivariate Brownian Motion models of continuous traits evolution",
      "topics": [
        "mvBM"
      ]
    },
    {
      "page": "mvEB",
      "title": "Multivariate Early Burst model of continuous traits evolution",
      "topics": [
        "mvEB"
      ]
    },
    {
      "page": "mvgls",
      "title": "Fit linear model using Generalized Least Squares to multivariate (high-dimensional) data sets",
      "topics": [
        "mvgls"
      ]
    },
    {
      "page": "mvgls.dfa",
      "title": "Discriminant Function Analysis (DFA) - also called Linear Discriminant Analysis (LDA) or Canonical Variate Analysis (CVA) - based on multivariate GLS (or OLS) model fit",
      "topics": [
        "mvgls.dfa"
      ]
    },
    {
      "page": "mvgls.pca",
      "title": "Principal Component Analysis (PCA) based on GLS (or OLS) estimate of the traits variance-covariance matrix (possibly regularized)",
      "topics": [
        "mvgls.pca"
      ]
    },
    {
      "page": "mvLL",
      "title": "Multivariate (and univariate) algorithms for log-likelihood estimation of arbitrary covariance matrix/trees",
      "topics": [
        "mvLL"
      ]
    },
    {
      "page": "mvols",
      "title": "Fit linear model using Ordinary Least Squares to multivariate (high-dimensional) data sets",
      "topics": [
        "mvols"
      ]
    },
    {
      "page": "mvOU",
      "title": "Multivariate Ornstein-Uhlenbeck model of continuous traits evolution",
      "topics": [
        "mvOU"
      ]
    },
    {
      "page": "mvOUTS",
      "title": "Multivariate continuous trait evolution for a stationary time series (Ornstein-Uhlenbeck model)",
      "topics": [
        "mvOUTS"
      ]
    },
    {
      "page": "mvqqplot",
      "title": "Quantile-Quantile plots for multivariate models fit with 'mvgls' or 'mvols'",
      "topics": [
        "mvqqplot"
      ]
    },
    {
      "page": "mvRWTS",
      "title": "Multivariate Brownian motion / Random Walk model of continuous traits evolution on time series",
      "topics": [
        "mvRWTS"
      ]
    },
    {
      "page": "mvSHIFT",
      "title": "Multivariate change in mode of continuous trait evolution",
      "topics": [
        "mvSHIFT"
      ]
    },
    {
      "page": "mvSIM",
      "title": "Simulation of (multivariate) continuous traits on a phylogeny",
      "topics": [
        "mvSIM"
      ]
    },
    {
      "page": "pairwise.contrasts",
      "title": "Pairwise contrasts",
      "topics": [
        "pairwise.contrasts"
      ]
    },
    {
      "page": "pairwise.glh",
      "title": "Pairwise multivariate tests between levels of a factor",
      "topics": [
        "pairwise.glh"
      ]
    },
    {
      "page": "pcaShape",
      "title": "Projection of 2D and 3D shapes (from geometric morphometric datasets) on Principal Component Axes (PCA)",
      "topics": [
        "pcaShape"
      ]
    },
    {
      "page": "phyllostomid",
      "title": "Phylogeny and trait data for a sample of Phyllostomid bats",
      "topics": [
        "phyllostomid"
      ]
    },
    {
      "page": "predict.mvgls",
      "title": "Predictions from (multivariate) gls or ols model fit",
      "topics": [
        "predict.mvgls"
      ]
    },
    {
      "page": "predict.mvgls.dfa",
      "title": "Predictions from Discriminant analysis conducted with a mvgls model fit",
      "topics": [
        "predict.mvgls.dfa"
      ]
    },
    {
      "page": "pruning",
      "title": "Pruning algorithm to compute the square root of the phylogenetic covariance matrix and its determinant.",
      "topics": [
        "pruning"
      ]
    },
    {
      "page": "residuals.mvgls",
      "title": "Extract gls (or ols) model residuals",
      "topics": [
        "residuals.mvgls"
      ]
    },
    {
      "page": "stationary",
      "title": "The stationary variance of an Ornstein-Uhlenbeck process",
      "topics": [
        "stationary"
      ]
    },
    {
      "page": "vcov.mvgls",
      "title": "Calculate variance-covariance matrix for a fitted object of class 'mvgls'",
      "topics": [
        "vcov.mvgls"
      ]
    }
  ],
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  ],
  "_vignettes": [
    {
      "source": "How_to_use_mvMORPH.Rmd",
      "filename": "How_to_use_mvMORPH.html",
      "title": "How to use mvMORPH?",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Trees and Time series",
        "Phylogenetic trees",
        "Time series",
        "Data and Errors",
        "Simulating data",
        "Optimization methods",
        "Likelihood computation methods",
        "error                          -                    X                   X                    X                     X                   X",
        "Multivariate GLS models and High-Dimensional datasets",
        "Model comparison",
        "Treatment of the root",
        "Ancestral state and primary optimum",
        "Multiple phylogenetic means",
        "Directional trends",
        "Constraints",
        "Overview of the various constraint parameterizations in mvMORPH",
        "\"User-defined\" constraints",
        "The \"param\" list",
        "The \"decomp\" and \"decompSigma\" options",
        "the \"vcv\" argument",
        "Functions",
        "The loglikelihood function",
        "The matrix parameterization functions",
        "Fossil data",
        "Overview of the functions",
        "Imputing missing values",
        "Ancestral state reconstructions",
        "Tweak mvMORPH",
        "Make your own model!",
        "Reuse of the returned log-likelihood functions",
        "Bayesian mcmc"
      ],
      "created": "2016-06-06 12:37:55",
      "modified": "2023-03-13 01:01:09",
      "commits": 16
    },
    {
      "source": "tutorial_mvMORPH.Rmd",
      "filename": "tutorial_mvMORPH.html",
      "title": "mvMORPH: an R package for fitting multivariate evolutionary models",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Example 1: Models with distinct selective regimes",
        "Type I          0.213        0.22",
        "Example 2: Tests for evolutionary correlations between two species groups",
        "References:"
      ],
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      "modified": "2016-10-13 11:53:50",
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