Adding tags and other documentation such that pkgdown site is working

R/ltcad.R

@@ -1,4 +1,5 @@
 #' @method epidist_prepare epidist_ltcad
+#' @family ltcad
 #' @export
 epidist_prepare.epidist_ltcad <- function(data) {
   data <- data.table::as.data.table(data)
@@ -22,6 +23,7 @@ epidist_prepare.epidist_ltcad <- function(data) {
 }
 
 #' @method epidist_stancode epidist_ltcad
+#' @family ltcad
 #' @export
 epidist_stancode.epidist_ltcad <- function(data, family = "lognormal") {
   stanvars_version <- epidist_version_stanvar()
@@ -72,6 +74,7 @@ epidist_stancode.epidist_ltcad <- function(data, family = "lognormal") {
 }
 
 #' @method epidist_priors epidist_ltcad
+#' @family ltcad
 #' @export
 epidist_priors.epidist_ltcad <- function(data) {
   return(NULL)
@@ -83,6 +86,7 @@ epidist_priors.epidist_ltcad <- function(data) {
 #' @param sigma Formula for the delay standard deviation. Defaults to intercept
 #' only.
 #' @method epidist_formula epidist_ltcad
+#' @family ltcad
 #' @export
 epidist_formula.epidist_ltcad <- function(data, delay_central = ~ 1,
                                           sigma = ~ 1) {
@@ -97,6 +101,7 @@ epidist_formula.epidist_ltcad <- function(data, delay_central = ~ 1,
 }
 
 #' @method epidist_family epidist_ltcad
+#' @family ltcad
 #' @export
 epidist_family.epidist_ltcad <- function(data) {
   brms::custom_family(
@@ -112,6 +117,7 @@ epidist_family.epidist_ltcad <- function(data) {
 }
 
 #' @method epidist epidist_ltcad
+#' @family ltcad
 #' @export
 epidist.epidist_ltcad <- function(data, formula = epidist_formula(data),
                                   family = epidist_family(data),

R/methods.R

@@ -1,7 +1,8 @@
 #' Prepare data for modelling
 #'
-#' @param data A dataframe to be used for modelling
+#' @param data A dataframe to be used for modelling.
 #' @rdname epidist_prepare
+#' @family methods
 #' @export
 epidist_prepare <- function(data, ...) {
   UseMethod("epidist_prepare")
@@ -11,10 +12,11 @@ epidist_prepare <- function(data, ...) {
 #'
 #' @param model Character string, model type to prepare to use.
 #' Supported options are "ltcad".
-#' @param ... Additional arguments passed to model specific epidist_prepare
+#' @param ... Additional arguments passed to model specific `epidist_prepare`
 #' functions
 #' @rdname epidist_prepare
 #' @method epidist_prepare default
+#' @family methods
 #' @export
 epidist_prepare.default <- function(data, model, ...) {
   model <- match.arg(model, choices = c("ltcad"))
@@ -24,53 +26,58 @@ epidist_prepare.default <- function(data, model, ...) {
 
 #' Define a model specific formula
 #' 
-#' @export
-#' @inheritParams epidist_priors
+#' @inheritParams epidist_prepare
 #' @param ... Additional arguments for method.
+#' @family methods
+#' @export
 epidist_formula <- function(data, ...) {
   UseMethod("epidist_formula")
 }
 
 #' Define model specific family
 #' 
-#' @export
-#' @inheritParams epidist_priors
+#' @inheritParams epidist_prepare
 #' @param ... Additional arguments for method.
+#' @family methods
+#' @export
 epidist_family <- function(data, ...) {
   UseMethod("epidist_family")
 }
 
 #' Define model specific priors
 #' 
-#' @export
-#' @inheritParams epidist
+#' @inheritParams epidist_prepare
 #' @param ... Additional arguments for method.
 #' @rdname epidist_priors
+#' @family methods
+#' @export
 epidist_priors <- function(data, ...) {
   UseMethod("epidist_priors")
 }
 
 #' Define model specific stancode
 #' 
-#' @export
-#' @inheritParams epidist_priors
+#' @inheritParams epidist_prepare
 #' @param ... Additional arguments for method.
 #' @rdname id_stancode
+#' @family methods
+#' @export
 epidist_stancode <- function(data, ...) {
   UseMethod("epidist_stancode")
 }
 
 #' Interface using `brms`
 #'
-#' @param data ...
-#' @param formula ... 
+#' @param formula A formula as defined using [epidist_formula()]
 #' @param family ...
 #' @param priors ...
 #' @param custom_stancode ...
 #' @param fn Likely `brms::brm`. Also possible to be `brms::make_stancode` or
 #' `brms::make_standata`.
+#' @inheritParams epidist_prepare
 #' @param ... Additional arguments for method.
+#' @family methods
 #' @export
 epidist <- function(data, formula, family, priors, custom_stancode, fn, ...) {
   UseMethod("epidist")
-}
+}

R/utils.R

@@ -3,6 +3,7 @@
 #' @param path The path within the "stan" folder of the installed epidist
 #' package to the Stan code chunk of interest.
 #' @return A character string containing the Stan code chunk of interest.
+#' @family utils
 #' @export
 epidist_stan_chunk <- function(path) {
   local_path <- system.file(paste0("stan/", path), package = "epidist")
@@ -13,6 +14,8 @@ epidist_stan_chunk <- function(path) {
 #'
 #' @return A brms stanvar chunk containing the package version used to build
 #' the Stan code.
+#' @family utils
+#' @export
 epidist_version_stanvar <- function() {
   version <- utils::packageVersion("epidist")
   comment <- paste0("// code chunks used from epidist ", version, "\n")

_pkgdown.yml

@@ -24,10 +24,14 @@ reference:
   desc: Functions for observing data
   contents:
   - has_concept("observe")
-- title: Model
+- title: Methods
   desc: Functions for estimating epidemiological delays
   contents:
-  - has_concept("model")
+  - has_concept("methods")
+- title: Latent truncation censoring adjusted delay model
+  desc: Model-specific functions
+  contents:
+  - has_concept("ltcad")
 - title: Postprocess
   desc: Functions for postprocessing model output
   contents:
@@ -40,3 +44,6 @@ reference:
   desc: Data included with the package
   contents:
   - has_concept("data")
+- title: Utility functions
+  contents:
+  - has_concept("utils")