Move to marginal model name and lint

R/marginal_model.R

@@ -0,0 +1,55 @@
+#' Prepare marginal model to pass through to `brms`
+#'
+#' @param data A `data.frame` containing line list data
+#' @family marginal_model
+#' @export
+as_epidist_marginal_model <- function(data) {
+  UseMethod("as_epidist_marginal_model")
+}
+
+#' The marginal model method for `epidist_linelist_data` objects
+#'
+#' @param data An `epidist_linelist_data` object
+#' @method as_epidist_marginal_model epidist_linelist_data
+#' @family marginal_model
+#' @autoglobal
+#' @export
+as_epidist_marginal_model.epidist_linelist_data <- function(data) {
+  assert_epidist(data)
+
+  data <- data |>
+    mutate(delay = .data$stime_lwr - .data$ptime_lwr)
+
+  data <- new_epidist_marginal_model(data)
+  assert_epidist(data)
+  return(data)
+}
+
+#' Class constructor for `epidist_marginal_model` objects
+#'
+#' @param data A data.frame to convert
+#' @returns An object of class `epidist_marginal_model`
+#' @family marginal_model
+#' @export
+new_epidist_marginal_model <- function(data) {
+  class(data) <- c("epidist_marginal_model", class(data))
+  return(data)
+}
+
+#' @method assert_epidist epidist_marginal_model
+#' @family marginal_model
+#' @export
+assert_epidist.epidist_marginal_model <- function(data, ...) {
+  assert_data_frame(data)
+  assert_names(names(data), must.include = "delay")
+  assert_numeric(data$delay, lower = 0)
+}
+
+#' Check if data has the `epidist_marginal_model` class
+#'
+#' @param data A `data.frame` containing line list data
+#' @family marginal_model
+#' @export
+is_epidist_marginal_model <- function(data) {
+  inherits(data, "epidist_marginal_model")
+}

_pkgdown.yml

@@ -65,6 +65,10 @@ reference:
   desc: Functions for fitting delay distribution models using `brms`
   contents:
   - has_concept("fit")
+- title: Marginal model
+  desc: Specific methods for the marginal model
+  contents:
+  - has_concept("marginal_model")
 - title: Latent model
   desc: Specific methods for the latent model
   contents:

vignettes/approx-inference.Rmd

@@ -99,7 +99,7 @@ library(purrr)
 library(tidyr)
 library(tibble)
 library(tidybayes)
-library(cmdstanr)
+library(cmdstanr) # nolint
 ```
 
 To access the approximate inference methods used in this vignette we will need to use the `cmdstanr` backend for `brms` (we generally recommend using this backend for fitting models). To do this, we first need to install CmdStan (see the README for more details). We can check we have everything we need as follows:

vignettes/ebola.Rmd

@@ -53,7 +53,7 @@ library(tidybayes)
 library(modelr)
 library(patchwork)
 library(lubridate)
-library(cmdstanr)
+library(cmdstanr) # nolint
 ```
 
 For users new to `epidist`, before reading this article we recommend beginning with the "[Getting started with `epidist`](http://epidist.epinowcast.org/articles/epidist.html)" vignette.