_pkgdown.yml

url: https://nerc-ceh.github.io/jsdmstan/
template:
  bootstrap: 5
  bslib:
    bg: "#fff"
    fg: "#292C2F"
    primary: "#0483A4"
    secondary: "#EAEFEC"
    success: "#37a635"
    info: "#34b8c7"
    warning: "#F49633"
    base_font: {google: "Montserrat"}
    heading_font: {google: "Montserrat"}
    code_font: {google: "Roboto Mono"}
reference:
- title: Simulate data
  desc: Simulate data according to the jsdm model structures
- contents:
  - jsdm_sim_data
  - sim_helpers
- title: Model
  desc: Run jsdmstan models
- contents:
  - stan_jsdm
  - stan_gllvm
  - stan_mglmm
  - update.jsdmStanFit
- title: Set-up functions
  desc: >
    Functions used to set up the prior structure (used in both data simulation
    and model fitting) and the Stan code used within model fitting
- contents:
  - jsdm_stancode
  - jsdm_prior
- title: Summaries
  desc: >
    Extract useful quantities from the model objects. This includes overall
    summaries of model parameters and model diagnostics.
- contents:
  - extract
  - loo.jsdmStanFit
  - jsdmstan-extractors
  - loo
  - print.jsdmStanFit
  - summary.jsdmStanFit
  - print.jsdmStanFamily
- title: Graphical summaries
  desc: >
    Plots of various model parameters, including jSDM specific summary plots as
    well as more general model summaries
- contents:
  - corrplot
  - envplot
  - ordiplot
  - mcmc_plot.jsdmStanFit
  - plot.jsdmStanFit
- title: Posterior prediction
  desc: >
    Extract posterior distributions and predict from them, including graphical
    posterior checks
- contents:
  - starts_with("posterior_")
  - pp_check.jsdmStanFit
  - multi_pp_check
  - jsdm_statsummary
- title: Other
  desc: Objects and classes used within jsdmstan
- contents:
  - jsdmStanFit
  - jsdmStanFamily
  - jsdmstan-package
  - has_keyword("datasets")