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  "Title": "R We There Yet? Visualizing MCMC Convergence in Phylogenetics",
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  "Description": "Implements various tests, visualizations, and metrics for\ndiagnosing convergence of MCMC chains in phylogenetics.  It\nimplements and automates many of the functions of the AWTY\npackage in the R environment, as well as a host of other\nfunctions.  Warren, Geneva, and Lanfear (2017),\n<doi:10.1093/molbev/msw279>.",
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  "Date/Publication": "2025-03-27 01:04:22 UTC",
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    "makeplot.splitfreqs.cumulative",
    "makeplot.splitfreqs.sliding",
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    "slide.freq",
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    "topological.autocorr",
    "topological.pseudo.ess",
    "tree.dist.matrix",
    "treespace"
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        "analyze.rwty"
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    },
    {
      "page": "check.chains",
      "title": "Function for checking suitability of chains for rwty analyses, auto-generating labels, etc",
      "topics": [
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      ]
    },
    {
      "page": "clade.freq",
      "title": "Returns clade names and frequencies",
      "topics": [
        "clade.freq"
      ]
    },
    {
      "page": "combine.ptables",
      "title": "Function for merging p tables for multiple MCMC chains",
      "topics": [
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      ]
    },
    {
      "page": "cumulative.freq",
      "title": "Cumulative means of clade split frequencies.",
      "topics": [
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    },
    {
      "page": "estimate.autocorr.m",
      "title": "Calculate sampling interval based on exponential semivariogram model.",
      "topics": [
        "estimate.autocorr.m"
      ]
    },
    {
      "page": "fungus",
      "title": "MrBayes output from analysis of Hibbett et al. data",
      "topics": [
        "fungus"
      ]
    },
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      "title": "Load all matching files from a directory into a list of rwty.chain objects",
      "topics": [
        "load.multi"
      ]
    },
    {
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      "title": "Custom functions to load tree lists so that rwty can do basic processing on the way in.",
      "topics": [
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      ]
    },
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      "title": "Plot the Change in Split Frequencies (CSF) in sliding windows over the course of an MCMC.",
      "topics": [
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      ]
    },
    {
      "page": "makeplot.acsf.sliding",
      "title": "Plot the Chaing in Split Frequencies (CSF) in sliding windows over the course of an MCMC.",
      "topics": [
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      ]
    },
    {
      "page": "makeplot.all.params",
      "title": "Plotting all parameters",
      "topics": [
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      ]
    },
    {
      "page": "makeplot.asdsf",
      "title": "Plot the Standard Deviation of Split Frequencies over the course of an MCMC.",
      "topics": [
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      ]
    },
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      "title": "Make autocorrelation plots of tree topologies from MCMC analyses",
      "topics": [
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    {
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      "title": "Plotting parameters against each other",
      "topics": [
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      "title": "Plotting parameters",
      "topics": [
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    },
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      "title": "Plot the pseudo ESS of tree topologies from MCMC chains.",
      "topics": [
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    },
    {
      "page": "makeplot.splitfreq.matrix",
      "title": "Plots a matrix of split frequency comparisons between multiple MCMC chains.",
      "topics": [
        "makeplot.splitfreq.matrix"
      ]
    },
    {
      "page": "makeplot.splitfreqs.cumulative",
      "title": "Plot cumulative split frequencies over the course of an MCMC",
      "topics": [
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      ]
    },
    {
      "page": "makeplot.splitfreqs.sliding",
      "title": "Plot split frequencies in sliding windows over the course of an MCMC",
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      ]
    },
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      "title": "Plotting parameters",
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    },
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      "title": "Plot chains in treespace.",
      "topics": [
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      "title": "Rename clades for easy recall",
      "topics": [
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      "title": "Rename clades for easy recall",
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      "title": "Calculate data for autocorrelation plots of tree topologies from MCMC analyses",
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      "title": "Calculate the pseudo Effective Sample Size (ESS) of tree topologies",
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      "title": "Tree distance matrix calculation",
      "topics": [
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      "source": "plot-comparisons.Rmd",
      "filename": "plot-comparisons.html",
      "title": "Comparing RWTY plots: what am I looking at?",
      "author": "Dan Warren, Anthony Geneva, and Rob Lanfear",
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      "headings": [
        "RWTY produces a number of different plots and statistics for evaluating the performance of MCMC chains.  These plots can help to illustrate problems with convergence in idividual chains as well as explore differences between chains built from different sequence data.  Here we're going to explore some of these plots in detail, comparing well-behaved to poorly-behaved chains when appropriate.",
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        "Parameter plots",
        "Topology trace plots and histograms",
        "Split frequency plots",
        "Pairs plots",
        "Average Change in Split Frequency (ACSF) plots",
        "Treespace plots",
        "Autocorrelation plots",
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      "title": "RWTY (R We There Yet): An R package for examining convergence of Bayesian phylogenetic analyses",
      "author": "Dan Warren, Anthony Geneva, and Rob Lanfear",
      "engine": "knitr::rmarkdown",
      "headings": [
        "RWTY: R We There Yet?",
        "Plot comparisons - what does it all mean?",
        "Installation",
        "Installing from GitHub using devtools",
        "Install from zip file",
        "Setting the number of cores",
        "Interacting with RWTY",
        "load.trees()",
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        "analyze.rwty()",
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      ],
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      "modified": "2021-08-27 07:40:38",
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