_pkgdown.yml

url: https://williamgearty.com/deeptime/
template:
  bootstrap: 5
  bootswatch: flatly
  bslib:
    navbar-padding-y: 8px
  includes:
    in_header: |
       <!-- Google tag (gtag.js) -->
       <script async src="https://www.googletagmanager.com/gtag/js?id=G-B48C68KGQJ"></script>
       <script>
         window.dataLayer = window.dataLayer || [];
         function gtag(){dataLayer.push(arguments);}
         gtag('js', new Date());

         gtag('config', 'G-B48C68KGQJ');
       </script>

figures:
  dev: grDevices::png

development:
  mode: auto

authors:
  William Gearty:
    href: https://williamgearty.com

articles:
- title: Articles
  navbar: ~
  contents:
  - coord_geo
  - phylogenies
  - coord
  - traits
  - time
  - geo
  - ggarrange2

reference:
- title: Adding geological timescales to plots
  desc: >
    The original purpose of deeptime, `coord_geo()` adds a highly
    customizable timescale to any `{ggplot2}` plot. Other functions now supplement
    it to aid in the visualization of data over long time scales.
  contents:
  - coord_geo
  - scale_color_geo
  - get_scale_data
  - guide_geo

- subtitle: Built-in interval data
  desc: >
    deeptime includes a selection of built-in interval data from the
    most up-to-date Geological Time Scale. These dataframes include name,
    max age, min age, abbreviation, and color columns.
  contents:
  - eons
  - eras
  - periods
  - epochs
  - stages

- subtitle: Deprecated functions
  desc: >
    The following function(s) represent early iterations of what is
    now `coord_geo()`. These function(s) still work but are considered
    "deprecated". They will be removed in a future version of deeptime, and
    users are strongly encouraged to use `coord_geo()` instead, which has more
    features and is still under active development.
  contents:
  - gggeo_scale

- title: Adding geological timescales to phylogenies
  desc: >
    These functions can be used to add timescales specifically to phylogenies
    that are plotted with [ggtree](https://www.bioconductor.org/packages/ggtree).
  contents:
  - coord_geo
  - coord_geo_radial
  - coord_geo_polar
  - scale_color_geo
  - get_scale_data
  - guide_geo

- subtitle: Adding text labels to phylogenies
  desc: >
    When using deeptime coordinate systems, this geom may work better than geoms
    from ggtree.
  contents:
  - geom_text_phylo

- title: Transforming coordinate systems
  desc: >
    These functions can be used to modify the way that your data is plotted
    by `{ggplot2}`.
  contents:
  - coord_trans_flip
  - coord_trans_xy

- title: Plotting trait data
  desc: >
    These functions can be used for visualizing species trait data.
  contents:
  - geom_phylomorpho
  - disparity_through_time
  - panel.disparity
  - coord_trans_xy

- title: Plotting temporal data
  desc: >
    These functions can be used for visualizing categorical temporal data.
  contents:
  - geom_points_range
  - stat_points_range
  - facet_grid_color
  - facet_wrap_color
  - facet_nested_color
  - facet_nested_wrap_color

- title: Plotting geologic data
  desc: >
    These functions can be used for visualizing geologic/stratigraphic data.
  contents:
  - grid.pattern_geo
  - geo_pattern
  - scale_fill_geopattern

- title: Combining and arranging plots
  desc: >
    These functions can be used to combine and arrange plots into
    publishable-quality figures.
  contents:
  - ggarrange2
  - gtable_frame2