_pkgdown.yml

url: https://inlabru-org.github.io/inlabru/

template:
  bootswatch: cosmo
  bootstrap: 5
  math-rendering: "katex"

navbar:
  structure:
    left: [home, intro, reference, general-articles, lgcp-articles, technical-articles, news]
    right: [search, github]
  components:
    general-articles:
      text: General examples
      menu:
      - text: Basic examples
      - text: Random field models in 1D
        href: articles/random_fields.html
      - text: Spatial random field models in 2D
        href: articles/random_fields_2d.html
      - text: Publications
        href: articles/publications.html
      - text: ---
      - text: Concepts
      - text: Defining a model component
        href: articles/component.html
      - text: ---
      - text: Special models and techniques
      - text: Spatially varying coefficient models
        href: articles/svc.html
      - text: ZIP and ZAP count models (zero-inflation)
        href: articles/zip_zap_models.html
      - text: Computing posterior prediction scores
        href: articles/prediction_scores.html
      - text: ---
      - text: Full articles list
        href: articles/articles.html
    lgcp-articles:
      text: Point processes
      menu:
      - text: Point process examples
      - text: LGCPs - An example in one dimension
        href: articles/1d_lgcp.html
      - text: LGCPs - An example in two dimensions (sf version)
        href: articles/2d_lgcp.html
      - text: LGCPs - An example in two dimensions (sp version)
        href: articles/2d_lgcp_sp.html
      - text: LGCPs - Spatial covariates
        href: articles/2d_lgcp_covars.html
      - text: LGCPs - Distance sampling
        href: articles/2d_lgcp_distancesampling.html
      - text: LGCPs - Plot sampling
        href: articles/2d_lgcp_plotsampling.html
      - text: LGCPs - Multiple likelihoods
        href: articles/2d_lgcp_multilikelihood.html
      - text: LGCPs - An example in space and time
        href: articles/2d_lgcp_spatiotemporal.html
      - text: LGCPs - Residuals (sf version)
        href: articles/2d_lgcp_residuals_sf.html
      - text: LGCPs - Residuals (sp version)
        href: articles/2d_lgcp_residuals.html
      - text: LGCPs - Distance sampling and per-transect covariates (work in progress)
        href: articles/2d_lgcp_per_transect_covars.html
    technical-articles:
      text: Technical articles
      menu:
      - text: Mapper techniques
      - text: Customised model component with the bru_mapper system
        href: articles/bru_mapper.html
      - text: Converting inla.spde.make.A calls to the bru_mapper system
        href: articles/mesh_mapping.html
      - text: ---
      - text: Theory and technical documentation
      - text: Installation of INLA and inlabru with Apptainer on HPC
        href: articles/Apptainer.html
      - text: The iterative linearised inlabru method
        href: articles/method.html
      - text: A nonlinear model approximation example
        href: articles/linearapprox.html
      - text: Code internal flow diagrams for model evaluation
        href: articles/devel_flow.html
      - text: Class and method information tables
        href: articles/classes.html

redirects:
  - ["articles/web/Apptainer.html", "articles/Apptainer.html"]
  - ["articles/web/publications.html", "articles/publications.html"]
  - ["articles/web/2d_lgcp_multilikelihood.html", "articles/2d_lgcp_multilikelihood.html"]
  - ["articles/web/2d_lgcp_spatiotemporal.html", "articles/2d_lgcp_spatiotemporal.html"]
  - ["articles/web/2d_lgcp.html", "articles/2d_lgcp.html"]
  - ["articles/web/2d_lgcp_sf.html", "articles/2d_lgcp_sf.html"]
  - ["articles/web/1d_lgcp.html", "articles/1d_lgcp_.html"]
  - ["articles/web/2d_lgcp_plotsampling.html", "articles/2d_lgcp_plotsampling.html"]
  - ["articles/web/2d_lgcp_distancesampling.html", "articles/2d_lgcp_distancesampling.html"]
  - ["articles/web/2d_lgcp_covars.html", "articles/2d_lgcp_covars.html"]
  - ["articles/web/2d_lgcp_residuals_sf.html", "articles/2d_lgcp_residuals_sf.html"]
  - ["articles/web/2d_lgcp_residuals.html", "articles/2d_lgcp_residuals.html"]
  - ["articles/web/random_fields.html", "articles/random_fields.html"]
  - ["articles/web/mesh_mapping.html", "articles/mesh_mapping.html"]
  - ["articles/web/devel_flow.html", "articles/devel_flow.html"]
  - ["articles/web/svc.html", "articles/svc.html"]
  - ["articles/web/random_fields_2d.html", "articles/random_fields_2d.html"]
  - ["articles/2d_lgcp_sf.html", "articles/2d_lgcp.html"]
  - ["articles/components_vignette.html", "articles/component.html"]

reference:
- title: "Model construction and estimation"
  desc: "Functions for constructing models and performing estimation."
  contents:
  - matches("^inlabru-package$")
  - matches("^bru$")
  - matches("^bru_obs$")
  - matches("^bru_rerun$")
  - matches("^bru_options$")
  - starts_with("bru_comp")
  - starts_with("bru_input")
  - starts_with("lgcp")
  - starts_with("bru_response_size")
  - starts_with("bru_set_missing")
  - starts_with("bru_index")
  - starts_with("like")
- title: "Posterior evaluation"
  desc: "Functions for evaluating posterior properties."
  contents:
  - starts_with("bru_names")
  - starts_with("generate")
  - starts_with("predict")
  - starts_with("spde.posterior")
  - starts_with("deltaIC")
  - starts_with("devel.cvmeasure")
- title: "Optimization log information"
  desc: "Accessing the optimization text log, and plotting the optimization convergence."
  contents:
  - starts_with("bru_log")
  - starts_with("bru_convergence_plot")
  - starts_with("bru_timings")
- title: "Object/property extraction/queries"
  desc: "Functions for extracting or querying properties of objects."
  contents:
  - starts_with("as_bru_")
  - starts_with("as_bru_obs")
  - starts_with("as_bru_obs_list")
  - starts_with("as_bru_comp_list")
  - starts_with("bru_is_")
  - starts_with("bru_is_linear")
  - starts_with("bru_is_additive")
  - starts_with("bru_is_rowwise")
- title: "Mapper methods"
  desc: "Functions for `bru_mapper` handling."
- subtitle: "Low level and wrapper methods"
  contents:
  - starts_with("bru_get_mapper")
  - matches("^bru_mapper$")
- subtitle: "Constructor methods"
  contents:
  - starts_with("bm_")
- subtitle: "Evaluator methods"
  contents:
  - matches("^bru_mapper_generics$")
  - starts_with("ibm_")
- subtitle: "Conversion and helper methods"
  contents:
  - starts_with("as_bru_mapper")
  - starts_with("as_bm_list")
  - starts_with("bru_forward_transformation")
- title: "Miscellaneous"
  desc: "Miscellaneous functions."
  contents:
  - starts_with("eval_spatial")
  - starts_with("bru_fill_missing")
  - starts_with("point2count")
  - starts_with("sample.lgcp")
- title: "Plot helpers"
  desc: "Functions for helping build figures."
  contents:
  - starts_with("plot")
  - starts_with("globe")
  - starts_with("gg")
  - starts_with("glplot")
  - starts_with("gm")
  - starts_with("gmap")
  - starts_with("bincount")
- title: "Printing methods"
  desc: "Functions for printing."
  contents:
  - starts_with("print")
  - starts_with("summary")
- title: "Data objects"
  desc: "Data objects"
  contents:
  - matches("Poisson1_")
  - matches("Poisson2_")
  - matches("Poisson3_")
  - matches("gorillas")
  - matches("gorillas_sf")
  - matches("mexdolphin")
  - matches("mrsea")
  - matches("robins_subset")
  - matches("shrimp")
  - matches("toygroups")
  - matches("toypoints")
- title: "Internal helper functions"
  desc: "Helper functions for more low level operations."
  contents:
  - starts_with("evaluate_", internal = TRUE)
  - starts_with("expand_labels", internal = TRUE)
  - starts_with("bru_inla.stack.mjoin", internal = TRUE)
  - starts_with("spatial.to.ppp", internal = TRUE)
  - starts_with("bru_make_stack", internal = TRUE)
  - starts_with("bru_summarise", internal = TRUE)
  - starts_with("bru_standardise_names", internal = TRUE)
  - starts_with("bru_safe_inla", internal = TRUE)
  - starts_with("bru_safe_sp", internal = TRUE)
  - starts_with("bru_call_options", internal = TRUE)
  - starts_with("bru_compute_linearisation", internal = TRUE)
  - starts_with("bru_is_additive", internal = TRUE)
- title: "Deprecated methods"
  desc: "Deprecated methods"
  contents:
  - matches("ipoints")
  - matches("pixels")
  - matches("multiplot")
  - matches("spoly")
  - matches("sline")
#- title: "Other functions"
#  desc: "Other functions"
#  contents:
#  - matches("")