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  "Title": "Analysis of Evolutionary Diversification",
  "Version": "2.0.11",
  "Date": "2023-02-17",
  "Author": "Luke Harmon, Matthew Pennell, Chad Brock, Joseph Brown, Wendell\nChallenger, Jon Eastman, Rich FitzJohn, Rich Glor, Gene Hunt,\nLiam Revell, Graham Slater, Josef Uyeda, Jason Weir and CRAN\nteam (corrections in 2022)",
  "Maintainer": "Luke Harmon <lukeh@uidaho.edu>",
  "Description": "Methods for fitting macroevolutionary models to\nphylogenetic trees Pennell (2014)\n<doi:10.1093/bioinformatics/btu181>.",
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    "calibrate.mecca",
    "calibrate.rjmcmc",
    "cherries",
    "congruify.phylo",
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    "crown.p",
    "dcount",
    "deltaTree",
    "disparity",
    "dlunif",
    "drop.extinct",
    "drop.random",
    "dtpois",
    "dtt",
    "edgelabels.auteur",
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    "ess",
    "ex.jumpsimulator",
    "ex.ratesimulator",
    "ex.traitgram",
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    "fitContinuous",
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    "fitDiscrete",
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    "getAncStates",
    "glomogram.phylo",
    "hash.node",
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    "heights",
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    "ic.sigma",
    "is.constrained",
    "is.extinct",
    "is.phylo",
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    "kappaTree",
    "lambdaTree",
    "linearchangeTree",
    "Linnaean",
    "load.rjmcmc",
    "lookup.phylo",
    "make.bm.relaxed",
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    "mecca",
    "medusa",
    "mkn.lik",
    "name.check",
    "nh.test",
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    "ouTree",
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    "phylo.lookup",
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    "rate.estimate",
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    "sim.bdtree",
    "sim.char",
    "sim.mecca",
    "span.phylo",
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    "startingpt.mecca",
    "stem.limits",
    "stem.p",
    "tip.disparity",
    "tips",
    "to.auteur",
    "to.coda",
    "treedata",
    "tworateTree",
    "uniqueMultiPhylo",
    "white.mkn",
    "write.pathd8",
    "write.r8s",
    "write.treePL"
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      "title": "example datasets",
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      "file": "amphibia.rda",
      "class": [
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      ],
      "fields": [],
      "table": true,
      "tojson": false
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      "name": "caniformia",
      "title": "example datasets",
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      "file": "caniformia.rda",
      "class": [
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      "table": false,
      "tojson": false
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      "file": "carnivores.rda",
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      "table": false,
      "tojson": false
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      "title": "example datasets",
      "object": "caudata",
      "file": "caudata.rda",
      "class": [
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      ],
      "fields": [],
      "table": false,
      "tojson": false
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      "name": "chelonia",
      "title": "example datasets",
      "object": "chelonia",
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      "class": [
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      ],
      "fields": [],
      "table": false,
      "tojson": false
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      "name": "geospiza",
      "title": "example datasets",
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      "class": [
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      "table": false,
      "tojson": false
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      "title": "example datasets",
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      "file": "primates.rda",
      "class": [
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      "fields": [],
      "table": false,
      "tojson": false
    },
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      "title": "example datasets",
      "object": "whales",
      "file": "whales.rda",
      "class": [
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      "table": false,
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      "page": "geiger-package",
      "title": "GEIGER",
      "topics": [
        "geiger-package",
        "geiger"
      ]
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    {
      "page": "aicm",
      "title": "Akaike's Information Criterion for MCMC samples (AICM)",
      "topics": [
        "aicm"
      ]
    },
    {
      "page": "aicw",
      "title": "determining Akaike weights",
      "topics": [
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      ]
    },
    {
      "page": "aov.phylo",
      "title": "phylogenetic ANOVA and MANOVA",
      "topics": [
        "aov.phylo"
      ]
    },
    {
      "page": "bd.ms",
      "title": "estimate net diversification rate",
      "topics": [
        "bd.km",
        "bd.ms",
        "crown.limits",
        "crown.p",
        "stem.limits",
        "stem.p"
      ]
    },
    {
      "page": "calibrate.mecca",
      "title": "calibrating MECCA",
      "topics": [
        "calibrate.mecca"
      ]
    },
    {
      "page": "calibrate.rjmcmc",
      "title": "initialize proposal width",
      "topics": [
        "calibrate.rjmcmc"
      ]
    },
    {
      "page": "congruify.phylo",
      "title": "ultrametricization of trees from a supplied timetree",
      "topics": [
        "congruify.phylo"
      ]
    },
    {
      "page": "dcount",
      "title": "prior densities for truncated discrete random variable",
      "topics": [
        "dcount"
      ]
    },
    {
      "page": "drop.extinct",
      "title": "prune specified taxa from a phylogenetic tree",
      "topics": [
        "drop.extinct",
        "drop.random",
        "is.extinct"
      ]
    },
    {
      "page": "dtt",
      "title": "disparity-through-time",
      "topics": [
        "disparity",
        "dtt"
      ]
    },
    {
      "page": "fitContinuous",
      "title": "Model fitting for continuous comparative data",
      "topics": [
        "fitContinuous"
      ]
    },
    {
      "page": "fitContinuousMCMC",
      "title": "Fit models of continuous trait evolution to comparative data using MCMC",
      "topics": [
        "fitContinuousMCMC"
      ]
    },
    {
      "page": "fitDiscrete",
      "title": "Model fitting for discrete comparative data",
      "topics": [
        "as.Qmatrix.gfit",
        "fitDiscrete"
      ]
    },
    {
      "page": "gbresolve",
      "title": "NCBI taxonomy",
      "topics": [
        "gbcontain",
        "gbresolve",
        "gbresolve.phylo"
      ]
    },
    {
      "page": "geiger-data",
      "title": "example datasets",
      "topics": [
        "amphibia",
        "caniformia",
        "carnivores",
        "caudata",
        "chelonia",
        "geospiza",
        "primates",
        "whales"
      ]
    },
    {
      "page": "geiger-defunct",
      "title": "deprecated functions in GEIGER",
      "topics": [
        "area.between.curves",
        "BDsim",
        "birthdeath.tree",
        "calibrate.proposalwidth",
        "compare.rates",
        "deltaTree",
        "disp.calc",
        "dtt.full",
        "exponentialchangeTree",
        "get.simulation.matrix",
        "getAncStates",
        "ic.sigma",
        "intercalate.samples",
        "kappaTree",
        "lambdaTree",
        "linearchangeTree",
        "node.leaves",
        "node.sons",
        "ouTree",
        "phy.anova",
        "phy.manova",
        "pool.rjmcmcsamples",
        "prune.extinct.taxa",
        "prune.random.taxa",
        "rate.estimate",
        "rescaleTree",
        "runMedusa",
        "shifts.plot",
        "speciationalTree",
        "tip.disparity",
        "tracer",
        "transform.phylo",
        "tworateTree",
        "vmat"
      ]
    },
    {
      "page": "geiger-examples",
      "title": "internal geiger functions",
      "topics": [
        "ex.jumpsimulator",
        "ex.ratesimulator",
        "ex.traitgram"
      ]
    },
    {
      "page": "geiger-internal",
      "title": "internal geiger functions",
      "topics": [
        "argn",
        "argn.bm",
        "argn.default",
        "argn.mkn",
        "argn<-",
        "argn<-.bm",
        "as.phylo.hphylo",
        "bf",
        "bm.lik",
        "cherries",
        "coef.gfit",
        "coef.gfits",
        "constrain",
        "constrain.k",
        "constrain.m",
        "dlunif",
        "drop.tip",
        "dtpois",
        "edgelabels.auteur",
        "edges.phylo",
        "ess",
        "exemplar.phylo",
        "fitDiversification",
        "fitSplitModel",
        "gbresolve.default",
        "gbtaxdump",
        "gen",
        "getBD",
        "getDiversificationModel",
        "getFullSplitModel",
        "hash.node",
        "hashes.phylo",
        "hashes.rjmcmc",
        "hdr",
        "heights",
        "heights.multiPhylo",
        "heights.phylo",
        "hme",
        "is.constrained",
        "is.phylo",
        "is.root",
        "kendallmoran.rate",
        "likfx.bm",
        "Linnaean",
        "load",
        "logLik.gfit",
        "logLik.gfits",
        "make.bm.relaxed",
        "mkn.lik",
        "PATHd8.phylo",
        "plot.auteurMCMC",
        "plot.auteurMCMCMC",
        "plot.rjmcmc",
        "plot.rjmcmc.list",
        "plotDiversificationSurface",
        "print.auteurRAW",
        "print.bayesfactor",
        "print.bm",
        "print.constraint.m",
        "print.glnL",
        "print.gprior",
        "print.mcmc.list",
        "print.mkn",
        "print.rbm",
        "print.rjmcmc",
        "print.rjmcmcmc",
        "print.taxdump",
        "print.transformer",
        "resplitEdgeMatrixGeiger",
        "root.phylo",
        "sem",
        "sim.mecca",
        "span.phylo",
        "splitEdgeMatrixGeiger",
        "ultrametricize.phylo",
        "unique.phylo",
        "uniqueMultiPhylo",
        "white.mkn",
        "write.pathd8",
        "write.r8s",
        "write.treePL"
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    },
    {
      "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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