Generate a local pkgdown site for this package

Run `pkgdown::build_site()` to generate the site in `./docs/`.

.Rbuildignore

@@ -8,3 +8,6 @@
 ^test.*.R$
 ^vignettes/articles$
 .gitlab-ci.yml
+^_pkgdown\.yml$
+^docs$
+^pkgdown$

_pkgdown.yml

+url: ~
+template:
+  bootstrap: 5
+
+articles:
+- title: Articles
+  navbar: ~
+  contents:
+  - articles/model-description
+  - evidence-for-parameter-values
+  - rbc-steady-state
+  - sensitivity-analyses
+  - uninfected-rbc-loss
+  - increased-macrophages
+
+reference:
+- title: "Running model simulations"
+  desc: >
+    Functions that run model simulations.
+  contents:
+    - run_spleenrbc
+- title: "Model parameters"
+  desc: >
+    Functions that define baseline parameters and calculate the values of
+    steady-state parameters (i.e., in the absence of a malaria infection).
+  contents:
+  - ends_with("_parameters")
+  - retic_steady_state
+  - reticulocyte_prod
+- title: "Model state"
+  desc: >
+    Functions that create and update the model state.
+  contents:
+    - initial_spleenrbc_state
+    - step_spleenrbc_model
+    - run_spleenrbc_model
+    - resolve_negative_rbcs
+- title: "Model outputs"
+  desc: >
+    Functions that record key outputs and calculate derived quantities.
+  contents:
+    - individual_results
+    - infection_flows_and_loss
+    - calculate_irbc_ratio
+    - credible_intervals
+    - rbc_counts_to_haemoglobin
+    - prepare_spleenrbc_snapshot
+- title: "Sensitivity analysis"
+  desc: >
+    Functions that define the sensitivity analysis simulations.
+  contents:
+  - lhs_distributions
+  - sample_parameters
+- title: "Package data"
+  desc: >
+    Baseline parameter values and clinical data.
+  contents:
+    - parameters_pf
+    - parameters_pv
+    - rbc_steady_state
+    - splenectomised
+    - hhs_asymp
+- title: "Rate functions"
+  desc: >
+    Functions that calculate the value of rate parameters.
+  contents:
+    - starts_with("alpha_")
+    - beta
+    - starts_with("delta_")
+    - erythropoiesis
+    - starts_with("lambda_")
+    - starts_with("rho")
+    - zeta

vignettes/articles/model-description.Rmd

@@ -27,6 +27,8 @@ linkcolor: blue
 bibliography: ["references.bib"]
 csl: journal-of-theoretical-biology.csl
 link-citations: true
+pkgdown:
+  as_is: true
 ---
 
 <!-- Define LaTeX commands for custom notation -->

vignettes/introduction.Rmd → vignettes/spleenrbc.Rmd

 ---
-title: "Introduction: an overview of the model"
+title: "Introduction to spleenrbc"
 output:
   rmarkdown::html_vignette:
     code_folding: show
 vignette: >
-  %\VignetteIndexEntry{Introduction: an overview of the model}
+  %\VignetteIndexEntry{Introduction to spleenrbc}
   %\VignetteEngine{knitr::rmarkdown}
   %\VignetteEncoding{UTF-8}
 ---