minor tweaks to package family org

R/assert_epidist.R

@@ -4,11 +4,13 @@
 #' @param ... Additional arguments
 #' @return NULL invisibly
 #' @export
+#' @family assert
 assert_epidist <- function(data, ...) {
   UseMethod("assert_epidist")
 }
 
 #' @export
+#' @family assert
 assert_epidist.default <- function(data, ...) {
   cli_abort(
     c(

R/direct_model.R

@@ -29,7 +29,7 @@ as_direct_model.epidist_linelist <- function(data) {
 #'
 #' @param data A data.frame to convert
 #' @returns An object of class `epidist_direct_model`
-#' @keywords internal
+#' @family direct_model
 #' @export
 new_epidist_direct_model <- function(data) {
   class(data) <- c("epidist_direct_model", class(data))
@@ -48,7 +48,7 @@ assert_epidist.epidist_direct_model <- function(data, ...) {
 #' Check if data has the `epidist_direct_model` class
 #'
 #' @param data A `data.frame` containing line list data
-#' @family latent_individual
+#' @family direct_model
 #' @export
 is_direct_model <- function(data) {
   inherits(data, "epidist_direct_model")

R/epidist_linelist.R

@@ -2,7 +2,7 @@
 #'
 #' @param data The data to convert
 #' @param ... Additional arguments passed to methods
-#' @family preprocess
+#' @family linelist
 #' @export
 as_epidist_linelist <- function(data, ...) {
   UseMethod("as_epidist_linelist")
@@ -18,6 +18,7 @@ as_epidist_linelist <- function(data, ...) {
 #' @param ... Additional columns to add to the epidist_linelist object
 #' @importFrom tibble tibble
 #' @importFrom dplyr bind_cols
+#' @family linelist
 #' @export
 as_epidist_linelist.default <- function(
   data, ptime_upr = NULL, stime_lwr = NULL, stime_upr = NULL,
@@ -53,7 +54,7 @@ as_epidist_linelist.default <- function(
 #' @param obs_date A string giving the column of `data` containing the
 #' observation time as a datetime.
 #' @param ... Additional arguments passed to methods
-#' @family preprocess
+#' @family linelist
 #' @importFrom dplyr bind_cols
 #' @export
 as_epidist_linelist.data.frame <- function(
@@ -101,7 +102,7 @@ as_epidist_linelist.data.frame <- function(
 #'
 #' @param data A data.frame to convert
 #' @returns An object of class `epidist_linelist`
-#' @keywords internal
+#' @family linelist
 #' @export
 new_epidist_linelist <- function(data) {
   class(data) <- c("epidist_linelist", class(data))
@@ -112,13 +113,16 @@ new_epidist_linelist <- function(data) {
 #'
 #' @inheritParams as_epidist_linelist
 #' @param ... Additional arguments
-#' @family preprocess
+#' @family linelist
 #' @export
 is_epidist_linelist <- function(data, ...) {
   inherits(data, "epidist_linelist")
 }
 
-#' @rdname assert_epidist
+#' Assert validity of `epidist_linelist` objects
+#'
+#' @method assert_epidist epidist_linelist
+#' @family linelist
 #' @export
 assert_epidist.epidist_linelist <- function(data, ...) {
   assert_data_frame(data)

R/latent_individual.R

@@ -35,7 +35,7 @@ as_latent_individual.epidist_linelist <- function(data) {
 #'
 #' @param data A data.frame to convert
 #' @returns An object of class `epidist_latent_individual`
-#' @keywords internal
+#' @family latent_individual
 #' @export
 new_epidist_latent_individual <- function(data) {
   class(data) <- c("epidist_latent_individual", class(data))

R/utils.R

@@ -8,7 +8,7 @@
 #' @return A character string containing the Stan code chunk of interest.
 #' @keywords internal
 .stan_chunk <- function(path) {
-  local_path <- system.file(paste0("stan/", path), package = "epidist")
+  local_path <- system.file("stan", path, package = "epidist")
   paste(readLines(local_path), collapse = "\n")
 }
 

_pkgdown.yml

@@ -37,14 +37,14 @@ reference:
   desc: Functions for observing data
   contents:
   - has_concept("observe")
-- title: Preprocess
-  desc: Functions for preprocessing data
+- title: Linelist data
+  desc: Functions for preparing linelist data
   contents:
-  - has_concept("preprocess")
-- title: Validation
-  desc: Functions used to check validity of package objects
+  - has_concept("linelist")
+- title: Assert validity of objects
+  desc: Functions used to assert the validity of package objects
   contents:
-  - has_concept("validate")
+  - has_concept("assert")
 - title: Family
   desc: Functions related to specifying custom `brms` families
   contents: