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  "Title": "Analysis of Evolutionary Diversification",
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  "Description": "Methods for fitting macroevolutionary models to\nphylogenetic trees Pennell (2014)\n<doi:10.1093/bioinformatics/btu181>.",
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      "table": false,
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      "page": "geiger-package",
      "title": "GEIGER",
      "topics": [
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        "geiger"
      ]
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      "page": "aicm",
      "title": "Akaike's Information Criterion for MCMC samples (AICM)",
      "topics": [
        "aicm"
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    {
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      "title": "determining Akaike weights",
      "topics": [
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    {
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      "title": "phylogenetic ANOVA and MANOVA",
      "topics": [
        "aov.phylo"
      ]
    },
    {
      "page": "bd.ms",
      "title": "estimate net diversification rate",
      "topics": [
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        "bd.ms",
        "crown.limits",
        "crown.p",
        "stem.limits",
        "stem.p"
      ]
    },
    {
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      "title": "calibrating MECCA",
      "topics": [
        "calibrate.mecca"
      ]
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    {
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      "title": "initialize proposal width",
      "topics": [
        "calibrate.rjmcmc"
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      "title": "ultrametricization of trees from a supplied timetree",
      "topics": [
        "congruify.phylo"
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      "topics": [
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    },
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      "title": "prune specified taxa from a phylogenetic tree",
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        "is.extinct"
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        "dtt"
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      "title": "Model fitting for continuous comparative data",
      "topics": [
        "fitContinuous"
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    {
      "page": "fitContinuousMCMC",
      "title": "Fit models of continuous trait evolution to comparative data using MCMC",
      "topics": [
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      "page": "fitDiscrete",
      "title": "Model fitting for discrete comparative data",
      "topics": [
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        "fitDiscrete"
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      "title": "NCBI taxonomy",
      "topics": [
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        "gbresolve",
        "gbresolve.phylo"
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      "page": "geiger-data",
      "title": "example datasets",
      "topics": [
        "amphibia",
        "caniformia",
        "carnivores",
        "caudata",
        "chelonia",
        "geospiza",
        "primates",
        "whales"
      ]
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    {
      "page": "geiger-defunct",
      "title": "deprecated functions in GEIGER",
      "topics": [
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        "BDsim",
        "birthdeath.tree",
        "calibrate.proposalwidth",
        "compare.rates",
        "deltaTree",
        "disp.calc",
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        "geiger-defunct",
        "get.simulation.matrix",
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        "pool.rjmcmcsamples",
        "prune.extinct.taxa",
        "prune.random.taxa",
        "rate.estimate",
        "rescaleTree",
        "runMedusa",
        "shifts.plot",
        "speciationalTree",
        "tip.disparity",
        "tracer",
        "transform.phylo",
        "tworateTree",
        "vmat"
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    {
      "page": "geiger-examples",
      "title": "internal geiger functions",
      "topics": [
        "ex.jumpsimulator",
        "ex.ratesimulator",
        "ex.traitgram"
      ]
    },
    {
      "page": "load.rjmcmc",
      "title": "posterior samples from single or multiple MCMC runs",
      "topics": [
        "load.rjmcmc"
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    },
    {
      "page": "make.gbm",
      "title": "tailor reversible-jump Markov chain Monte Carlo sampling",
      "topics": [
        "make.gbm"
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    },
    {
      "page": "mecca",
      "title": "running a MECCA analysis",
      "topics": [
        "mecca"
      ]
    },
    {
      "page": "medusa",
      "title": "MEDUSA: modeling evolutionary diversification using stepwise AIC",
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