_pkgdown.yml

destination: ../docs/ggspectra
url: https://docs.r4photobiology.info/ggspectra/

template:
  bootstrap: 5

reference:
  - title: Package overview
    contents:
    - '`ggspectra-package`'
  - title: Plot basics
    desc: Function `ggplot()` is a generic method defined in package 'ggplot2', especialisations defined in package 'ggspectra' provide default `aes()` for spectral classes.
    contents:
    - ggplot
  - title: 'Layer: Geoms'
    desc: Geoms, short for geometric objects, describe the type of plot you will produce.
    contents:
    - geom_spct
  - title: 'Layer: Statistics'
    desc: It is often useful to summarize spectral data before plotting, and that is what these transformations do.
    contents:
    - stat_color
    - stat_find_qtys
    - stat_find_wls
    - stat_peaks
    - stat_label_peaks
    - stat_spikes
    - stat_wb_box
    - stat_wb_hbar
    - stat_wb_column
    - stat_wb_contribution
    - stat_wb_irrad
    - stat_wb_label
    - stat_wb_mean
    - stat_wb_relative
    - stat_wb_sirrad
    - stat_wb_total
    - stat_wl_strip
    - stat_wl_summary
  - title: Scales
    desc: Scales control the mapping between data and aesthetics. The scales defined in package 'ggspectra' are continuous scales with defaults suitable for spectral data.
    contents:
    - scale_x_wl_continuous
    - scale_x_wavenumber_continuous
    - scale_x_frequency_continuous
    - scale_x_energy_eV_continuous
    - scale_x_energy_J_continuous
    - scale_y_s.e.response_continuous
    - scale_y_s.e.irrad_continuous
    - scale_y_A_internal_continuous
    - scale_y_Tfr_internal_continuous
    - scale_y_Rfr_specular_continuous
    - scale_y_Afr_continuous
    - scale_y_cps_continuous
    - scale_y_counts_continuous
    - scale_y_multipliers_continuous
    - sec_axis_w_number
  - title: Automatic plot creation
    desc: Autoplot methods for spectra and a function for color-patch charts. They all return `gg` objects.
    contents:
    - autoplot.raw_spct
    - autoplot.calibration_spct
    - autoplot.cps_spct
    - autoplot.source_spct
    - autoplot.response_spct
    - autoplot.filter_spct
    - autoplot.reflector_spct
    - autoplot.object_spct
    - autoplot.generic_spct
    - autoplot.waveband
    - autotitle
    - set_annotations_default
    - color_chart
  - title: Helper functions
    desc: Formatters, International System of units, unit conversions.
    contents:
    - black_or_white
    - exponent2prefix
    - SI_pl_format
    - SI_tg_format
    - w_number
    - axis_labels
    - w_length_label
    - counts_label
    - cps_label
    - Rfr_label
    - A_label
    - Tfr_label
    - Afr_label
    - s.e.irrad_label
    - s.e.response_label
    - multipliers_label
    - multiplot
    - plot.generic_spct

navbar:
  structure:
    left:  [intro, reference, articles, tutorials, news]
    right: [search, github]
  components:
    intro:
      icon: fas fa-home fa-lg
      href: index.html
      aria-label: Home
    reference:
      text: Reference
      href: reference/index.html
    news:
      text: Changelog
      href: news/index.html
    articles:
      text: User Guide
      menu:
      - text: '0 The R for Photobiology Suite'
        href: articles/userguide0-r4p-introduction.html
      - text: '1 Grammar of Graphics'
        href: articles/userguide1-grammar.html
      - text: '2 Autoplot Methods'
        href: articles/userguide2-autoplot-methods.html
      - text: 'Article: Plotting transformed spectral data'
        href: articles/data-manipulation.html
      - text: 'Article: Animated plots of spectral data'
        href: articles/animated-plots.html
    tutorials:
      text: Resources
      menu:
      - text: Using R for Photobiology Blog
        href: https://www.r4photobiology.info/
      - text: R for Photobiology Suite documentation
        href: https://www.r4photobiology.info/package-status/
      - text: More on 'ggplot2'
        href: https://ggplot2.tidyverse.org/
      - text: Other 'ggplot2' extensions
        href: https://exts.ggplot2.tidyverse.org/
      - text: ------
      - text: Book 'Learn R - As a Language'
        href: https://www.learnr-book.info/
      - text: A handbook of methods
        href: https://doi.org/10.31885/9789521083631
      - text: Photobiological Sciences Online
        href: http://photobiology.info/