Issue #398: Make documentation consistent across models (#447)

epinowcast · Nov 19, 2024 · 153b4cc · 153b4cc
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commit 153b4cc
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Showing 24 changed files with 75 additions and 40 deletions.
diff --git a/R/epidist.R b/R/epidist.R
@@ -1,6 +1,6 @@
 #' Fit epidemiological delay distributions using a `brms` interface
 #'
-#' @param data A `data.frame` containing line list data.
+#' @param data An object with class corresponding to an implemented model.
 #' @param formula An object of class [stats::formula] or [brms::brmsformula]
 #' (or one that can be coerced to those classes). A symbolic description of the
 #' model to be fitted. A formula must be provided for the distributional

diff --git a/R/latent_model.R b/R/latent_model.R
@@ -1,12 +1,16 @@
 #' Convert an object to an `epidist_latent_model` object
 #'
-#' @param data A `data.frame` containing line list data
+#' @param data An object to be converted to the class `epidist_latent_model`
 #' @family latent_model
 #' @export
 as_epidist_latent_model <- function(data) {
   UseMethod("as_epidist_latent_model")
 }
 
+
+#' The latent model method for `epidist_linelist_data` objects
+#'
+#' @param data An `epidist_linelist_data` object
 #' @method as_epidist_latent_model epidist_linelist_data
 #' @family latent_model
 #' @autoglobal
@@ -33,7 +37,7 @@ as_epidist_latent_model.epidist_linelist_data <- function(data) {
 
 #' Class constructor for `epidist_latent_model` objects
 #'
-#' @param data A data.frame to convert
+#' @param data An object to be set with the class `epidist_latent_model`
 #' @returns An object of class `epidist_latent_model`
 #' @family latent_model
 #' @export
@@ -44,7 +48,7 @@ new_epidist_latent_model <- function(data) {
 
 #' Check if data has the `epidist_latent_model` class
 #'
-#' @param data A `data.frame` containing line list data
+#' @param data An object
 #' @family latent_model
 #' @export
 is_epidist_latent_model <- function(data) {
@@ -93,9 +97,8 @@ epidist_family_model.epidist_latent_model <- function(
 
 #' Define the model-specific component of an `epidist` custom formula
 #'
-#' @param data A `data.frame` containing line list data
-#' @param formula As produced by [brms::brmsformula()]
-#' @param ... ...
+#' @inheritParams epidist_formula_model
+#' @param ... Additional arguments passed to method.
 #' @method epidist_formula_model epidist_latent_model
 #' @family latent_model
 #' @export

diff --git a/R/naive_model.R b/R/naive_model.R
@@ -1,6 +1,6 @@
 #' Prepare naive model to pass through to `brms`
 #'
-#' @param data A `data.frame` containing line list data
+#' @param data An object to be converted to the class `epidist_naive_model`
 #' @family naive_model
 #' @export
 as_epidist_naive_model <- function(data) {
@@ -27,7 +27,7 @@ as_epidist_naive_model.epidist_linelist_data <- function(data) {
 
 #' Class constructor for `epidist_naive_model` objects
 #'
-#' @param data A data.frame to convert
+#' @param data An object to be set with the class `epidist_naive_model`
 #' @returns An object of class `epidist_naive_model`
 #' @family naive_model
 #' @export
@@ -36,6 +36,15 @@ new_epidist_naive_model <- function(data) {
   return(data)
 }
 
+#' Check if data has the `epidist_naive_model` class
+#'
+#' @param data An object
+#' @family naive_model
+#' @export
+is_epidist_naive_model <- function(data) {
+  inherits(data, "epidist_naive_model")
+}
+
 #' @method assert_epidist epidist_naive_model
 #' @family naive_model
 #' @export
@@ -44,12 +53,3 @@ assert_epidist.epidist_naive_model <- function(data, ...) {
   assert_names(names(data), must.include = "delay")
   assert_numeric(data$delay, lower = 0)
 }
-
-#' Check if data has the `epidist_naive_model` class
-#'
-#' @param data A `data.frame` containing line list data
-#' @family naive_model
-#' @export
-is_epidist_naive_model <- function(data) {
-  inherits(data, "epidist_naive_model")
-}
diff --git a/man/as_epidist_latent_model.Rd b/man/as_epidist_latent_model.Rd
diff --git a/man/as_epidist_latent_model.epidist_linelist_data.Rd b/man/as_epidist_latent_model.epidist_linelist_data.Rd
diff --git a/man/as_epidist_naive_model.Rd b/man/as_epidist_naive_model.Rd
diff --git a/man/epidist.Rd b/man/epidist.Rd
diff --git a/man/epidist.default.Rd b/man/epidist.default.Rd
diff --git a/man/epidist_family.Rd b/man/epidist_family.Rd
diff --git a/man/epidist_family_model.Rd b/man/epidist_family_model.Rd
diff --git a/man/epidist_family_model.default.Rd b/man/epidist_family_model.default.Rd
diff --git a/man/epidist_family_model.epidist_latent_model.Rd b/man/epidist_family_model.epidist_latent_model.Rd
diff --git a/man/epidist_formula.Rd b/man/epidist_formula.Rd
diff --git a/man/epidist_formula_model.default.Rd b/man/epidist_formula_model.default.Rd
diff --git a/man/epidist_formula_model.epidist_latent_model.Rd b/man/epidist_formula_model.epidist_latent_model.Rd
diff --git a/man/epidist_model_prior.Rd b/man/epidist_model_prior.Rd
diff --git a/man/epidist_model_prior.default.Rd b/man/epidist_model_prior.default.Rd
diff --git a/man/epidist_prior.Rd b/man/epidist_prior.Rd
diff --git a/man/epidist_stancode.Rd b/man/epidist_stancode.Rd
diff --git a/man/epidist_stancode.default.Rd b/man/epidist_stancode.default.Rd
diff --git a/man/is_epidist_latent_model.Rd b/man/is_epidist_latent_model.Rd
diff --git a/man/is_epidist_naive_model.Rd b/man/is_epidist_naive_model.Rd
diff --git a/man/new_epidist_latent_model.Rd b/man/new_epidist_latent_model.Rd
diff --git a/man/new_epidist_naive_model.Rd b/man/new_epidist_naive_model.Rd