gadgetplots/_pkgdown.yml at master · gadget-framework/gadgetplots · GitHub

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template:
  bootstrap: 5

reference:

- title: Model overviews
  desc: >
    The `make_html()` function generates a
    [single html file](https://gadget-framework.github.io/gadgetplots/articles/make_html_output.html)
    out of `gadgetutils::g3_fit()` output that contains key model diagnostics.
    The `gadget_plots()` function saves a set of diagnostics plots into
    a folder.
  contents:
  - make_html
  - gadget_plots

- title: Plotting functions
  desc: >
    The package produces plots in four categories:

      1) `plot_*()` functions plot gadget model **output** generated
      using `gadgetutils::g3_fit()`. These functions have a generic
      shorthand, the `plot()`, with `param` argument specifying the
      type of plot.

      2) `dplot_*()` functions plot gadget model **input data** generated
      using [mfdb](https://github.com/gadget-framework/mfdb),
      `gadgetutils::g3_data()` or `gadgetutils::add_g3_attributes()`
      functions.

      3) the `g3d_plot()` function plots **data directly** from a gadget
      model object.

      4) `g3plot_*` functions plot gadget **suitability (selectivity)
      functions**.

- title: The `plot_*` for `g3_fit` output
  desc: >
    These functions make the plots typically used in asssessment
    and model diagnostics. Some of the functions have `return_data`
    argument, which can be used to quickly grab associated data for
    further analyses, custom plots and tables.
- subtitle: General
  contents:
  - plot.gadget.fit
  - plot_annual
- subtitle: Age-related
  contents:
  - plot_adist
  - plot_ageclass
  - plot_agecomp
  - plot_agelength
  - plot_growth
- subtitle: Stock status
  contents:
  - plot_biomass
  - plot_ssb
  - plot_rec
  - plot_sr
  - plot_si
- subtitle: Catches and fleets
  contents:
  - plot_catch
  - plot_f
  - plot_hr
  - plot_suitability
- subtitle: Distributions
  contents:
  - plot_catchdist
  - plot_ldist
  - plot_stockcomp
  - plot_stockdist
- subtitle: Parameters and fit
  contents:
  - plot_likelihood
  - plot_param
  - plot_resid
  - plot_weight
- subtitle: Model diagnostics
  desc: >
    These functions require a list of gadget.fit objects generated
    using the `gadgetutils::g3_jitter()`, `gadgetutils::g3_leaveout()`,
    and `gadgetutils::g3_retro()` functions.
  contents:
  - plot_jitter
  - plot_leaveout
  - plot_retro

- title: The `dplot_*` for gadget input data
  desc: >
    These functions plot gadget input data attempting to highlight
    attributes, which guide the model fitting, but are often difficult to notice
    otherwise.
  contents:
  - dplot_adist
  - dplot_aldist
  - dplot_ldist
  - dplot_sexr
  - dplot_stockdist
  - dplot_catch

- title: The `g3d_plot` for gadget model objects
  desc: >
    The `g3d_plot()` function plots all observational data passed into a TMB or
    R gadget model.
  contents:
  - g3d_plot

- title: The `g3plot_*` for suitability functions
  desc: >
    These plot gadget suitability functions, which can be difficult to comprehend
    without visualizing. The model parameters can be extracted from a gadget.fit
    object or typed in manually.
  contents:
  - g3plot_andersen
  - g3plot_exponentiall50

- title: Example data
  desc: >
    Datasets to demonstrate plot functions.
  contents:
  - fit
  - aldist_example
  - ldist_example
  - sexratio_example
  - stockdist_example
  - example_catches

navbar:
 components:
   articles:
      text: Articles
      menu:
      - text: make_html output
        href: articles/make_html_output.html