_pkgdown.yml

url: https://tiago-simoes.github.io/EvoPhylo/

template:
  bootstrap: 5

reference:
- title: Functions
- subtitle: Character partitioning
  desc: >
    See `vignette("char-part")` for a complete workflow that uses these functions to
    conduct automated morphological character partitioning as a pre-processing step
    for clock (time-calibrated) Bayesian phylogenetic analysis of morphological data
    using the programs Mr. Bayes or BEAST2.
- contents:
  - get_gower_dist
  - get_sil_widths
  - make_clusters
  - cluster_to_nexus
  - write_partitioned_alignments
- subtitle: Evolutionary rates & selection mode (MrBayes)
  desc: >
    See `vignette("rates-selection_MrBayes")` for a complete workflow that uses these functions
    to extract evolutionary rate parameters estimated from relaxed clock Bayesian
    inference analyses produced by the program Mr. Bayes and use evolutionary rate
    based inference of selection mode (or strength) adapted to clock-based rates.
- contents:
  - get_clockrate_table_MrBayes
  - clockrate_dens_plot
  - clockrate_reg_plot
  - clockrate_summary
  - combine_log
  - clock_reshape
  - plot_back_rates
  - get_pwt_rates_MrBayes
  - plot_treerates_sgn
- subtitle: Evolutionary rates & selection mode (BEAST2)
  desc: >
    See `vignette("rates-selection_BEAST2")` for a complete workflow that uses these functions
    to extract evolutionary rate parameters estimated from relaxed clock Bayesian
    inference analyses produced by the program BEAST2 and use evolutionary rate
    based inference of selection mode (or strength) adapted to clock-based rates.
- contents:
  - get_clockrate_table_BEAST2
  - clockrate_dens_plot
  - clockrate_reg_plot
  - clockrate_summary
  - clock_reshape
  - plot_back_rates
  - get_pwt_rates_BEAST2
  - plot_treerates_sgn
- subtitle: Analyzing FBD parameters
  desc: >
    See `vignette("fbd-params")` for a complete workflow that uses these functions
    to extract FBD parameters estimated from relaxed
    clock Bayesian inference analyses produced by Mr. Bayes and BEAST2.
- contents:
  - combine_log
  - FBD_dens_plot
  - FBD_normality_plot
  - FBD_reshape
  - FBD_summary
  - FBD_tests1
  - FBD_tests2
- subtitle: Analyzing Trees With Offsets
  desc: >
    See `vignette("offset_handling")` for a complete workflow that uses these functions
    to summarize trees with offsets (with fossil species only) as produced by the SA package in BEAST2.
- contents:
  - drop.dummy.beast
  - drop.dummy.mb
  - offset.to.dummy
  - offset.to.dummy.metadata
  - write.beast.treedata
- title: Datasets
- contents:
  - has_keyword("datasets")

articles:
- title: ~
  navbar: ~
  contents:
  - data_treatment
  - char-part
  - rates-selection_MrBayes
  - rates-selection_BEAST2
  - fbd-params
  - offset_handling