{
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  "Package": "paleoDiv",
  "Title": "Extracting and Visualizing Paleobiodiversity",
  "Version": "0.4.12",
  "Authors@R": "person(\"Darius\", \"Nau\", , \"dariusnau@gmx.at\", role = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0009-0000-4343-6830\"))",
  "Description": "Contains various tools for conveniently downloading and\nediting taxon-specific datasets from the Paleobiology Database\n<https://paleobiodb.org>, extracting information on abundance,\ntemporal distribution of subtaxa and taxonomic diversity\nthrough deep time, and visualizing these data in relation to\nphylogeny and stratigraphy.",
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  "Author": "Darius Nau [aut, cre] (ORCID:\n<https://orcid.org/0009-0000-4343-6830>)",
  "Maintainer": "Darius Nau <dariusnau@gmx.at>",
  "Config/pak/sysreqs": "libicu-dev",
  "Repository": "https://theropod1.r-universe.dev",
  "Date/Publication": "2026-05-27 19:34:57 UTC",
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    "abdistr_",
    "add.alpha",
    "convert.sptab",
    "darken",
    "div.gg",
    "divdistr_",
    "divdistr_int",
    "ggcol",
    "jitterp",
    "mk.sptab",
    "multijitter",
    "occ.cleanup",
    "pdb",
    "pdb.autodiv",
    "pdb.diff",
    "pdb.union",
    "phylo.spindles",
    "redraw.phylo",
    "rmean",
    "rmeana",
    "stax.sel",
    "synonymize",
    "tree.age.combine",
    "tree.ages",
    "tree.ages.spp",
    "ts.periods",
    "ts.stages",
    "tsconv",
    "viol",
    "violins"
  ],
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    {
      "name": "ages_archosauria",
      "title": "ages_archosauria",
      "object": "ages_archosauria",
      "class": [
        "matrix",
        "array"
      ],
      "fields": [
        "FAD",
        "LAD"
      ],
      "rows": 13,
      "table": true,
      "tojson": true
    },
    {
      "name": "archosauria",
      "title": "archosauria",
      "object": "archosauria",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "diversity_table",
      "title": "diversity_table",
      "object": "diversity_table",
      "class": [
        "data.frame"
      ],
      "fields": [
        "x_orig",
        "x",
        "Sauropodomorpha",
        "Ceratopsia",
        "Ornithopoda",
        "Coelurosauria",
        "Allosauroidea",
        "Megalosauroidea",
        "Neoceratosauria",
        "Pachycephalosauria",
        "Stegosauria",
        "Ankylosauria",
        "Coelophysoidea",
        "Pterosauria",
        "Crocodylomorpha"
      ],
      "rows": 94,
      "table": true,
      "tojson": true
    },
    {
      "name": "tree_archosauria",
      "title": "tree_archosauria",
      "object": "tree_archosauria",
      "class": [
        "phylo"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    }
  ],
  "_help": [
    {
      "page": "ab.gg",
      "title": "Make a data.frame() that can be used to plot diversity data with density plots, e.g. in ggplot2",
      "topics": [
        "ab.gg"
      ]
    },
    {
      "page": "abdistr_",
      "title": "Count number of entries in occurrence or collection data.frame for specific points in geological time",
      "topics": [
        "abdistr_"
      ]
    },
    {
      "page": "add.alpha",
      "title": "Add transparency to any color",
      "topics": [
        "add.alpha"
      ]
    },
    {
      "page": "ages_archosauria",
      "title": "ages_archosauria",
      "topics": [
        "ages_archosauria"
      ]
    },
    {
      "page": "archosauria",
      "title": "archosauria",
      "topics": [
        "archosauria"
      ]
    },
    {
      "page": "convert.sptab",
      "title": "Convert geological ages in taxon-range tables as constructed by mk.sptab() for plotting alongside a time-calibrated phylogeny.",
      "topics": [
        "convert.sptab"
      ]
    },
    {
      "page": "darken",
      "title": "Darken or lighten colors by adding/subtracting to or hsv channel values",
      "topics": [
        "darken"
      ]
    },
    {
      "page": "div.gg",
      "title": "Make a data.frame() that can be used to plot diversity data with density plots, e.g. in ggplot2",
      "topics": [
        "div.gg"
      ]
    },
    {
      "page": "divdistr_",
      "title": "Calculate total range-through taxon richness for any point in time based on a taxon-range table",
      "topics": [
        "divdistr_"
      ]
    },
    {
      "page": "divdistr_int",
      "title": "Count number of taxon records overlapping a specific time interval.",
      "topics": [
        "divdistr_int"
      ]
    },
    {
      "page": "diversity_table",
      "title": "diversity_table",
      "topics": [
        "diversity_table"
      ]
    },
    {
      "page": "ggcol",
      "title": "Replicate the standard color scheme from ggplot2",
      "topics": [
        "ggcol"
      ]
    },
    {
      "page": "jitterp",
      "title": "plot data as a jitter-plot",
      "topics": [
        "jitterp"
      ]
    },
    {
      "page": "mk.sptab",
      "title": "Generate a taxon-range table based on an occurrence dataset.",
      "topics": [
        "mk.sptab"
      ]
    },
    {
      "page": "multijitter",
      "title": "Wrapper around jitterp that plots multiple jitter plots on the same plotting device (analogous to violins())",
      "topics": [
        "multijitter"
      ]
    },
    {
      "page": "occ.cleanup",
      "title": "Clean up occurrence dataset by removing double whitespaces and commonly used character combinations in the identified name that will result in more than one factor level per identified taxon.",
      "topics": [
        "occ.cleanup"
      ]
    },
    {
      "page": "pdb",
      "title": "Download data from the paleobiology database.",
      "topics": [
        "pdb"
      ]
    },
    {
      "page": "pdb.autodiv",
      "title": "A wrapper around pdb(), occ.cleanup() and mk.sptab() to automatically download and clean occurrence data from the paleobiology database and build species-level taxon-range tables for multiple taxa in one step.",
      "topics": [
        "pdb.autodiv"
      ]
    },
    {
      "page": "pdb.diff",
      "title": "Subtract one occurrence data.frame from another, for disentangling overlapping taxonomies or quantifying stem-lineage diversity.",
      "topics": [
        "pdb.diff"
      ]
    },
    {
      "page": "pdb.union",
      "title": "Form the union of two occurrence data.frames or remove duplicates from occurrence data.frame. Useful if parts of a clade are not included in the downloaded dataset and need to be added separately.",
      "topics": [
        "pdb.union"
      ]
    },
    {
      "page": "phylo.spindles",
      "title": "Plots a phylogenetic tree with spindle-diagrams, optimized for showing taxonomic diversity.",
      "topics": [
        "phylo.spindles"
      ]
    },
    {
      "page": "redraw.phylo",
      "title": "Redraw the lines of a phylogenetic tree.",
      "topics": [
        "redraw.phylo"
      ]
    },
    {
      "page": "rmean",
      "title": "Calculate a rolling mean for a vector x.",
      "topics": [
        "rmean"
      ]
    },
    {
      "page": "rmeana",
      "title": "Calculate a rolling mean based on distance within a second variable.",
      "topics": [
        "rmeana"
      ]
    },
    {
      "page": "stax.sel",
      "title": "Extract subsets of an occurrence data.frame.",
      "topics": [
        "stax.sel"
      ]
    },
    {
      "page": "synonymize",
      "title": "Combine selected entries in a taxon-range table to remove duplicates",
      "topics": [
        "synonymize"
      ]
    },
    {
      "page": "tree_archosauria",
      "title": "tree_archosauria",
      "topics": [
        "tree_archosauria"
      ]
    },
    {
      "page": "tree.age.combine",
      "title": "Combine two calibration matrixes and fill in NA values in one with values from another",
      "topics": [
        "tree.age.combine"
      ]
    },
    {
      "page": "tree.ages",
      "title": "Automatically build matrix for time-calibration of phylogenetic trees using occurrence data.",
      "topics": [
        "tree.ages"
      ]
    },
    {
      "page": "tree.ages.spp",
      "title": "Automatically build matrix for time-calibration of phylogenetic trees using occurrence data.",
      "topics": [
        "tree.ages.spp"
      ]
    },
    {
      "page": "ts.periods",
      "title": "Add a horizontal, period-level phanerozoic timescale to any plot, especially calibrated phylogenies plotted with ape.",
      "topics": [
        "ts.periods"
      ]
    },
    {
      "page": "ts.stages",
      "title": "Add a horizontal, stage-level phanerozoic timescale to any plot, especially calibrated phylogenies plotted with ape.",
      "topics": [
        "ts.stages"
      ]
    },
    {
      "page": "tsconv",
      "title": "Convert geological ages for accurate plotting alongside a calibrated phylogeny",
      "topics": [
        "tsconv"
      ]
    },
    {
      "page": "viol",
      "title": "Generate a violin plot",
      "topics": [
        "viol"
      ]
    },
    {
      "page": "violins",
      "title": "Wrapper around viol() to conveniently plot multiple violins on a single plot, analogous to the behavior of boxplot()",
      "topics": [
        "violins"
      ]
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    "cli",
    "digest",
    "glue",
    "lattice",
    "lifecycle",
    "magrittr",
    "nlme",
    "Rcpp",
    "rlang",
    "stringi",
    "stringr",
    "vctrs"
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      "source": "Paleobiodiversity_analysis.Rmd",
      "filename": "Paleobiodiversity_analysis.html",
      "title": "Paleobiodiversity Analysis",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Basic Workflow of the paleoDiv Package",
        "Editing Datasets and Generating Taxon-Range Tables",
        "Using PaleobioDB Data to Estimate and Plot Diversity and Abundance",
        "Plotting Spindle Diagrams with or without Phylogeny",
        "Important parameters for phylo.spindles include:"
      ],
      "created": "2024-03-07 09:50:05",
      "modified": "2025-03-23 20:32:04",
      "commits": 4
    }
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