{
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  "Title": "Pre- And Postprocessing of Morphological Data from Relaxed Clock\nBayesian Phylogenetics",
  "Description": "Performs automated morphological character partitioning\nfor phylogenetic analyses and analyze macroevolutionary\nparameter outputs from clock (time-calibrated) Bayesian\ninference analyses, following concepts introduced by Simões and\nPierce (2021) <doi:10.1038/s41559-021-01532-x>.",
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  "Repository": "https://tiago-simoes.r-universe.dev",
  "Date/Publication": "2025-08-27 14:14:33 UTC",
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  "Author": "Tiago Simoes [cre, aut] (ORCID:\n<https://orcid.org/0000-0003-4716-649X>),\nNoah Greifer [aut] (ORCID: <https://orcid.org/0000-0003-3067-7154>),\nJoelle Barido-Sottani [aut] (ORCID:\n<https://orcid.org/0000-0002-5220-5468>),\nStephanie Pierce [aut] (ORCID: <https://orcid.org/0000-0003-0717-1841>)",
  "Maintainer": "Tiago Simoes <trsimoes87@gmail.com>",
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    "clockrate_reg_plot",
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    "cluster_to_nexus",
    "combine_log",
    "drop.dummy.beast",
    "drop.dummy.mb",
    "FBD_dens_plot",
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    "FBD_summary",
    "FBD_tests1",
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    "get_pwt_rates_BEAST2",
    "get_pwt_rates_MrBayes",
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    "make_clusters",
    "offset.to.dummy",
    "offset.to.dummy.metadata",
    "plot_back_rates",
    "plot_treerates_sgn",
    "write_partitioned_alignments",
    "write_partitioned_alignments2",
    "write.beast.treedata"
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      "title": "A morphological phylogenetic data matrix",
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        "Glyptolepis",
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        "Gyroptychius",
        "Osteolepis",
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        "Medoevia",
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        "Ectosteorhachis",
        "Beelarongia",
        "Canowindra",
        "Koharalepis",
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        "Spodichthys",
        "Tristichopterus",
        "Eusthenopteron",
        "Jarvikina",
        "Platycephalichthys",
        "Cabonnichthys",
        "Mandageria",
        "Eusthenodon",
        "Hongyu",
        "Bruehnopteron",
        "Tinirau",
        "Panderichthys",
        "Elpistostege",
        "Tiktaalik",
        "Parmastega",
        "Ventastega",
        "Acanthostega",
        "Ichthyostega",
        "Tulerpeton"
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      "rows": 178,
      "table": true,
      "tojson": true
    },
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      "file": "post_trees.rda",
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        "TH",
        "TL",
        "prop_ancfossil",
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        "net_speciation_1",
        "net_speciation_2",
        "net_speciation_3",
        "net_speciation_4",
        "relative_extinction_1",
        "relative_extinction_2",
        "relative_extinction_3",
        "relative_extinction_4",
        "relative_fossilization_1",
        "relative_fossilization_2",
        "relative_fossilization_3",
        "relative_fossilization_4",
        "tk02var",
        "clockrate"
      ],
      "rows": 10000,
      "table": true,
      "tojson": true
    },
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      "name": "posterior3p",
      "title": "Posterior parameter samples (3 clock partions)",
      "object": "posterior3p",
      "file": "posterior3p.rda",
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      ],
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        "prop_ancfossil.all.",
        "sigma.1.",
        "sigma.2.",
        "sigma.3.",
        "m.1.",
        "m.2.",
        "m.3.",
        "net_speciation_1.all.",
        "net_speciation_2.all.",
        "net_speciation_3.all.",
        "net_speciation_4.all.",
        "relative_extinction_1.all.",
        "relative_extinction_2.all.",
        "relative_extinction_3.all.",
        "relative_extinction_4.all.",
        "relative_fossilization_1.all.",
        "relative_fossilization_2.all.",
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        "tk02var.2.",
        "tk02var.3.",
        "clockrate.all."
      ],
      "rows": 10000,
      "table": true,
      "tojson": true
    },
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      "title": "Mean clock rates by node and clade (single clock)",
      "object": "RateTable_Means_1p_Clades",
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      "class": [
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        "nodes",
        "rates"
      ],
      "rows": 79,
      "table": true,
      "tojson": true
    },
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      "name": "RateTable_Means_3p_Clades",
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        "rates2",
        "rates3"
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      "table": true,
      "tojson": true
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      "name": "tree_clock2",
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      "object": "tree_clock2",
      "file": "tree_clock2.rda",
      "class": [
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      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "tree1p",
      "title": "Phylogenetic tree with a single clock partition",
      "object": "tree1p",
      "file": "tree1p.rda",
      "class": [
        "treedata"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "tree3p",
      "title": "Phylogenetic tree with 3 clock partitions",
      "object": "tree3p",
      "file": "tree3p.rda",
      "class": [
        "treedata"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    }
  ],
  "_help": [
    {
      "page": "characters",
      "title": "A morphological phylogenetic data matrix",
      "topics": [
        "characters"
      ]
    },
    {
      "page": "clade_membership",
      "title": "Designate clade membership for each tip for downstream analyses summarizing rates for each clade",
      "topics": [
        "clade_membership"
      ]
    },
    {
      "page": "clock_reshape",
      "title": "Convert clock rate tables from wide to long format",
      "topics": [
        "clock_reshape"
      ]
    },
    {
      "page": "clockrate_dens_plot",
      "title": "Plot clock rate distributions",
      "topics": [
        "clockrate_dens_plot"
      ]
    },
    {
      "page": "clockrate_reg_plot",
      "title": "Plot regression lines between sets of rates",
      "topics": [
        "clockrate_reg_plot"
      ]
    },
    {
      "page": "clockrate_summary",
      "title": "Compute rate summary statistics across clades and clocks",
      "topics": [
        "clockrate_summary"
      ]
    },
    {
      "page": "cluster_to_nexus",
      "title": "Export character partitions to a Nexus file",
      "topics": [
        "cluster_to_nexus"
      ]
    },
    {
      "page": "combine_log",
      "title": "Combine and filter (.p) log files from Mr.Bayes, BEAST2 and MCMCTREE",
      "topics": [
        "combine_log"
      ]
    },
    {
      "page": "drop.dummy.beast",
      "title": "Remove dummy tip from beast summary trees, accounting for metadata on the tips",
      "topics": [
        "drop.dummy.beast"
      ]
    },
    {
      "page": "drop.dummy.mb",
      "title": "Remove dummy tip from Mr. Bayes summary trees, accounting for metadata on the tips",
      "topics": [
        "drop.dummy.mb"
      ]
    },
    {
      "page": "FBD_dens_plot",
      "title": "Density plots for each FBD parameter",
      "topics": [
        "FBD_dens_plot"
      ]
    },
    {
      "page": "FBD_normality_plot",
      "title": "Inspect FBD parameter distributions visually",
      "topics": [
        "FBD_normality_plot"
      ]
    },
    {
      "page": "FBD_reshape",
      "title": "Convert an FBD posterior parameter table from wide to long format",
      "topics": [
        "FBD_reshape"
      ]
    },
    {
      "page": "FBD_summary",
      "title": "Summarize FBD posterior parameter estimates",
      "topics": [
        "FBD_summary"
      ]
    },
    {
      "page": "FBD_tests1",
      "title": "Test assumptions of normality and homoscedasticity for FBD posterior parameters",
      "topics": [
        "FBD_tests1"
      ]
    },
    {
      "page": "FBD_tests2",
      "title": "Test for differences in FBD parameter values",
      "topics": [
        "FBD_tests2"
      ]
    },
    {
      "page": "get_clockrate_table_BEAST2",
      "title": "Extract evolutionary rates from Bayesian clock trees produced by BEAST2",
      "topics": [
        "get_clockrate_table_BEAST2"
      ]
    },
    {
      "page": "get_clockrate_table_MrBayes",
      "title": "Extract evolutionary rates from a Bayesian clock tree produced by Mr. Bayes",
      "topics": [
        "get_clockrate_table_MrBayes"
      ]
    },
    {
      "page": "get_gower_dist",
      "title": "Compute Gower distances between characters",
      "topics": [
        "get_gower_dist"
      ]
    },
    {
      "page": "get_pwt_rates_BEAST2",
      "title": "Conduct pairwise t-tests between node rates and clock base rates from a BEAST2 output.",
      "topics": [
        "get_pwt_rates_BEAST2"
      ]
    },
    {
      "page": "get_pwt_rates_MrBayes",
      "title": "Conduct pairwise t-tests between node rates and clock base rate from a Mr.Bayes output.",
      "topics": [
        "get_pwt_rates_MrBayes"
      ]
    },
    {
      "page": "get_sil_widths",
      "title": "Calculate silhouette widths index for various numbers of partitions",
      "topics": [
        "get_sil_widths",
        "plot.sil_width_df"
      ]
    },
    {
      "page": "make_clusters",
      "title": "Estimate and plot character partitions",
      "topics": [
        "make_clusters",
        "plot.cluster_df"
      ]
    },
    {
      "page": "offset.to.dummy",
      "title": "Convert trees produced by a BEAST2 FBD analysis with offset to trees with correct ages.",
      "topics": [
        "offset.to.dummy"
      ]
    },
    {
      "page": "offset.to.dummy.metadata",
      "title": "Convert trees produced by a BEAST2 FBD analysis with offset to trees with correct ages, accounting for possible metadata on the tips.",
      "topics": [
        "offset.to.dummy.metadata"
      ]
    },
    {
      "page": "plot_back_rates",
      "title": "Plots distribution of background rates extracted from posterior log files.",
      "topics": [
        "plot_back_rates"
      ]
    },
    {
      "page": "plot_treerates_sgn",
      "title": "Plot Bayesian evolutionary tree with rate thresholds for selection mode",
      "topics": [
        "plot_treerates_sgn"
      ]
    },
    {
      "page": "post_trees",
      "title": "Multiple phylogenetic clock trees",
      "topics": [
        "post_trees"
      ]
    },
    {
      "page": "posterior1p",
      "title": "Posterior parameter samples (single clock)",
      "topics": [
        "posterior1p"
      ]
    },
    {
      "page": "posterior3p",
      "title": "Posterior parameter samples (3 clock partions)",
      "topics": [
        "posterior3p"
      ]
    },
    {
      "page": "RateTable_Means_1p_Clades",
      "title": "Mean clock rates by node and clade (single clock)",
      "topics": [
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    },
    {
      "page": "RateTable_Means_3p_Clades",
      "title": "Mean clock rates by node and clade (3 clock partitions)",
      "topics": [
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    {
      "page": "tree_clock1",
      "title": "BEAST2 phylogenetic tree with clock rates from partition 1",
      "topics": [
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    {
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      "title": "BEAST2 phylogenetic tree with clock rates from partition 2",
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      "title": "Phylogenetic tree with a single clock partition",
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      "page": "write_partitioned_alignments",
      "title": "Write character partitions as separate Nexus files (for use in BEAUti)",
      "topics": [
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    },
    {
      "page": "write_partitioned_alignments2",
      "title": "Write alignment partitions as separate alignment files for various data types",
      "topics": [
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    },
    {
      "page": "write.beast.treedata",
      "title": "Export multiple treedata objects (S4 class tree files) to BEAST NEXUS file",
      "topics": [
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        "0. Set your BEAST2 analysis to log multiple clocks",
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        "1. Import posterior log file",
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      "title": "Evolutionary Rates & Selection Mode (Mr.Bayes)",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Evolutionary Rates Statistics and Plots",
        "1. Get rates from the clock tree and create a rate table",
        "2. Export the rate table and plot tree with node values",
        "Plot tree node labels to customize clade names",
        "3. Import rate table with custom clade memberships",
        "4. Get summary stats for each clade/clock partition",
        "5. Plot rates by clock partition and clade",
        "6. Rate linear models",
        "ADDENDUM: Example using rates from single clock analysis (no partitioning)",
        "Selection Mode",
        "1. Import combined log file from all runs.",
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      "headings": [
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        "Types of morphological data",
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