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  "Title": "Simulation and Plots for Fossil and Taxonomy Data",
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  "_exports": [
    "as.fossils",
    "as.taxonomy",
    "beast.fbd.format",
    "count.fossils",
    "count.fossils.binned",
    "fbdrange",
    "fossils",
    "fossils.to.BEAST.constraints",
    "fossils.to.BEAST.start.tree",
    "fossils.to.paleotree.record",
    "fossils.to.pyrate",
    "get_fbdrange_from_file",
    "get.tip.descs",
    "is.fossils",
    "is.taxonomy",
    "paleotree.record.to.fossils",
    "place.fossils",
    "prune.fossil.tips",
    "prune.SAtree.to.ranges",
    "rangeplot.asymmetric",
    "reconcile.fossils.taxonomy",
    "reconstructed.tree.fossils.objects",
    "remove.stem.fossils",
    "remove.stem.lineages",
    "sampled.tree.from.combined",
    "SAtree",
    "SAtree.from.fossils",
    "sim.anagenetic.species",
    "sim.cryptic.species",
    "sim.extant.samples",
    "sim.fbd.age",
    "sim.fbd.rateshift.taxa",
    "sim.fbd.taxa",
    "sim.fossils.environment",
    "sim.fossils.intervals",
    "sim.fossils.poisson",
    "sim.gradient",
    "sim.interval.ages",
    "sim.taxonomy",
    "sim.tip.samples",
    "sim.trait.values",
    "species.end",
    "species.start",
    "subsample.fossils.oldest",
    "subsample.fossils.oldest.and.youngest",
    "subsample.fossils.uniform",
    "subsample.fossils.youngest",
    "taxonomy",
    "tree.max"
  ],
  "_help": [
    {
      "page": "beast.fbd.format",
      "title": "Transforms a tree and fossils into a tree in Newick format which can be read by BEAST2.",
      "topics": [
        "beast.fbd.format"
      ]
    },
    {
      "page": "count.fossils",
      "title": "Count the total number of fossils",
      "topics": [
        "count.fossils"
      ]
    },
    {
      "page": "count.fossils.binned",
      "title": "Count the total number of fossils per interval",
      "topics": [
        "count.fossils.binned"
      ]
    },
    {
      "page": "fbdrange",
      "title": "Creates an fbdrange object from provided tree and data",
      "topics": [
        "fbdrange"
      ]
    },
    {
      "page": "fossils",
      "title": "Fossils object",
      "topics": [
        "as.fossils",
        "fossils",
        "is.fossils"
      ]
    },
    {
      "page": "fossils.to.BEAST.constraints",
      "title": "Create a set of BEAST2 constraints to construct a DPPDIV style fixed extant topology FBD analysis in BEAST2.6",
      "topics": [
        "fossils.to.BEAST.constraints"
      ]
    },
    {
      "page": "fossils.to.BEAST.start.tree",
      "title": "Create a suitable starting tree for a DPPDIV style FBD analysis in BEAST2",
      "topics": [
        "fossils.to.BEAST.start.tree"
      ]
    },
    {
      "page": "fossils.to.paleotree.record",
      "title": "Transforms a fossils dataframe and either taxonomy or tree into a fossilRecordSimulation object from package paleotree.",
      "topics": [
        "fossils.to.paleotree.record"
      ]
    },
    {
      "page": "fossils.to.pyrate",
      "title": "Generate output in the format used by the program PyRate",
      "topics": [
        "fossils.to.pyrate"
      ]
    },
    {
      "page": "FossilSim",
      "title": "FossilSim: A package for simulating and plotting fossil and taxonomy data",
      "topics": [
        "FossilSim-package",
        "FossilSim"
      ]
    },
    {
      "page": "get_fbdrange_from_file",
      "title": "Import fbdrange object from file",
      "topics": [
        "get_fbdrange_from_file"
      ]
    },
    {
      "page": "get.tip.descs",
      "title": "Obtain the tips that define each clade in a tree",
      "topics": [
        "get.tip.descs"
      ]
    },
    {
      "page": "paleotree.record.to.fossils",
      "title": "Transforms a fossilRecordSimulation object from package paleotree to a tree and taxonomy and fossils objects.",
      "topics": [
        "paleotree.record.to.fossils"
      ]
    },
    {
      "page": "place.fossils",
      "title": "Place fossil samples from one tree in another tree, i.e. find the ancestral node for each fossil sample in one tree.",
      "topics": [
        "place.fossils"
      ]
    },
    {
      "page": "plot.fbdrange",
      "title": "Plot oriented tree with stratigraphic ranges",
      "topics": [
        "plot.fbdrange"
      ]
    },
    {
      "page": "plot.fossils",
      "title": "Plot simulated fossils",
      "topics": [
        "plot.fossils"
      ]
    },
    {
      "page": "plot.taxonomy",
      "title": "Plot simulated taxonomy",
      "topics": [
        "plot.taxonomy"
      ]
    },
    {
      "page": "prune.fossil.tips",
      "title": "Remove fossil lineages from a tree",
      "topics": [
        "prune.fossil.tips"
      ]
    },
    {
      "page": "prune.SAtree.to.ranges",
      "title": "Removes all intermediate fossils from a combined tree and labels the first and last fossils of each lineage.",
      "topics": [
        "prune.SAtree.to.ranges"
      ]
    },
    {
      "page": "rangeplot.asymmetric",
      "title": "Make an asymmetric stratigraphic range plot from a tree object of class phylo",
      "topics": [
        "rangeplot.asymmetric"
      ]
    },
    {
      "page": "reconcile.fossils.taxonomy",
      "title": "Reconcile existing fossil and taxonomy objects",
      "topics": [
        "reconcile.fossils.taxonomy"
      ]
    },
    {
      "page": "reconstructed.tree.fossils.objects",
      "title": "Returns tree and fossil objects that you can use to plot the reconstructed tree.",
      "topics": [
        "reconstructed.tree.fossils.objects"
      ]
    },
    {
      "page": "remove.stem.fossils",
      "title": "Remove fossil samples that occur in the stem",
      "topics": [
        "remove.stem.fossils"
      ]
    },
    {
      "page": "remove.stem.lineages",
      "title": "Remove stem lineages from a tree.",
      "topics": [
        "remove.stem.lineages"
      ]
    },
    {
      "page": "sampled.tree.from.combined",
      "title": "Removes all unsampled lineages from a combined tree. Extinct tips are only sampled if they are fossils. With default settings all extant tips are sampled.",
      "topics": [
        "sampled.tree.from.combined"
      ]
    },
    {
      "page": "SAtree",
      "title": "Tree with sampled ancestors represented as zero-length edges",
      "topics": [
        "SAtree"
      ]
    },
    {
      "page": "SAtree.from.fossils",
      "title": "Transforms a tree and fossils dataframe to a combined SA tree.",
      "topics": [
        "SAtree.from.fossils"
      ]
    },
    {
      "page": "sim.anagenetic.species",
      "title": "Simulate anagenetic species on a taxonomy object",
      "topics": [
        "sim.anagenetic.species"
      ]
    },
    {
      "page": "sim.cryptic.species",
      "title": "Simulate cryptic species on a taxonomy object",
      "topics": [
        "sim.cryptic.species"
      ]
    },
    {
      "page": "sim.extant.samples",
      "title": "Include extant samples in the fossil object, with optional rho sampling.",
      "topics": [
        "sim.extant.samples"
      ]
    },
    {
      "page": "sim.fbd.age",
      "title": "sim.fbd.age: Simulating fossilized birth-death trees of a fixed age.",
      "topics": [
        "sim.fbd.age"
      ]
    },
    {
      "page": "sim.fbd.rateshift.taxa",
      "title": "sim.fbd.rateshift.taxa: Simulating fossilized birth death trees incorporating rate shifts.",
      "topics": [
        "sim.fbd.rateshift.taxa"
      ]
    },
    {
      "page": "sim.fbd.taxa",
      "title": "sim.fbd.taxa: Simulating fossilized birth-death trees on a fixed number of extant taxa.",
      "topics": [
        "sim.fbd.taxa"
      ]
    },
    {
      "page": "sim.fossils.environment",
      "title": "Simulate fossils under an environment-dependent model of preservation (Holland, 1995)",
      "topics": [
        "sim.fossils.environment"
      ]
    },
    {
      "page": "sim.fossils.intervals",
      "title": "Simulate fossils under a non-uniform model of preservation for a given set of consecutive time intervals",
      "topics": [
        "sim.fossils.intervals"
      ]
    },
    {
      "page": "sim.fossils.poisson",
      "title": "Simulate fossils under a Poisson sampling model",
      "topics": [
        "sim.fossils.poisson"
      ]
    },
    {
      "page": "sim.gradient",
      "title": "Simulate an environmental gradient",
      "topics": [
        "sim.gradient"
      ]
    },
    {
      "page": "sim.interval.ages",
      "title": "Reassign fossil ages to user-specified stratigraphic intervals",
      "topics": [
        "sim.interval.ages"
      ]
    },
    {
      "page": "sim.taxonomy",
      "title": "Simulate taxonomy",
      "topics": [
        "sim.taxonomy"
      ]
    },
    {
      "page": "sim.tip.samples",
      "title": "Include extant and extinct tip samples in the fossil object, with optional rho sampling.",
      "topics": [
        "sim.tip.samples"
      ]
    },
    {
      "page": "sim.trait.values",
      "title": "Simulate trait values with variation across lineages",
      "topics": [
        "sim.trait.values"
      ]
    },
    {
      "page": "species.end",
      "title": "Find a species' end (i.e extinction) time from a taxonomy object",
      "topics": [
        "species.end"
      ]
    },
    {
      "page": "species.start",
      "title": "Find a species' start (i.e speciation) time from a taxonomy object",
      "topics": [
        "species.start"
      ]
    },
    {
      "page": "subsample.fossils.oldest",
      "title": "Obtain a subsample of fossil occurrences containing the oldest fossil sample in each node of the tree.",
      "topics": [
        "subsample.fossils.oldest"
      ]
    },
    {
      "page": "subsample.fossils.oldest.and.youngest",
      "title": "Obtain a subsample of fossil occurrences containing the oldest and youngest fossil sample found at each node of the tree.",
      "topics": [
        "subsample.fossils.oldest.and.youngest"
      ]
    },
    {
      "page": "subsample.fossils.uniform",
      "title": "Obtain a uniform random sample of fossil occurrences.",
      "topics": [
        "subsample.fossils.uniform"
      ]
    },
    {
      "page": "subsample.fossils.youngest",
      "title": "Obtain a subsample of fossil occurrences containing the youngest fossil sample in each node of the tree.",
      "topics": [
        "subsample.fossils.youngest"
      ]
    },
    {
      "page": "summary.taxonomy",
      "title": "Display taxonomy object",
      "topics": [
        "summary.taxonomy"
      ]
    },
    {
      "page": "taxonomy",
      "title": "Taxonomy object",
      "topics": [
        "as.taxonomy",
        "is.taxonomy",
        "taxonomy"
      ]
    },
    {
      "page": "tree.max",
      "title": "Find the maximum age in a phylo object (root age or origin time)",
      "topics": [
        "tree.max"
      ]
    }
  ],
  "_readme": "https://github.com/fossilsim/fossilsim/raw/HEAD/README.md",
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  "_vignettes": [
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      "source": "paleotree.Rmd",
      "filename": "paleotree.html",
      "title": "Converting from and to paleotree format",
      "author": "Joelle Barido-Sottani",
      "engine": "knitr::rmarkdown",
      "headings": [
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