chore(docstrings): change from `` to \code{} in docstrings, and add full stops

Author: amyheather

R/add_patient_generator.R

@@ -14,8 +14,8 @@
 #' one of: "stroke", "tia", "neuro", or "other". Determines which arrival rate
 #' parameter is used.
 #' @param param Nested list containing simulation parameters. Must have
-#' structure `param$<unit>_arrivals$<patient_type>` containing numeric
-#' arrival intervals (e.g., `param$asu_arrivals$stroke = 10`).
+#' structure \code{param$<unit>_arrivals$<patient_type>} containing numeric
+#' arrival intervals (e.g., \code{param$asu_arrivals$stroke = 10}).
 #'
 #' @importFrom simmer add_generator
 #' @importFrom stats rexp

R/create_rehab_trajectory.R

@@ -1,11 +1,12 @@
-#' Create rehab patient trajectory
+#' Create rehab patient trajectory.
 #'
 #' @param patient_type Character string specifying patient category. Must be
 #' one of: "stroke", "tia", "neuro", or "other". Determines which arrival rate
 #' parameter is used.
 #' @param param Nested list containing simulation parameters. Must have
-#' structure `param$rehab_routing$<patient_type>` containing the probability of
-#' routing to each destination (e.g.`param$rehab_routing$stroke$esd = 0.40`).
+#' structure \code{param$rehab_routing$<patient_type>} containing the
+#' probability of routing to each destination (e.g.
+#' \code{param$rehab_routing$stroke$esd = 0.40}).
 #'
 #' @importFrom simmer trajectory
 #'

R/model.R

@@ -3,7 +3,7 @@
 #' @param run_number Integer representing index of current simulation run.
 #' @param param Named list of model parameters.
 #' @param set_seed Whether to set seed within the model function (which we
-#' may not wish to do if being set elsewhere - such as done in runner()).
+#' may not wish to do if being set elsewhere - such as done in \code{runner()}).
 #' Default is TRUE.
 #'
 #' @importFrom simmer get_attribute get_mon_arrivals get_mon_resources
@@ -19,19 +19,30 @@ model <- function(run_number, param, set_seed = TRUE) {
     set.seed(run_number)
   }
 
+  # Transform LOS parameters to lognormal scale
+  param[["asu_los_lnorm"]] <- transform_to_lnorm(param[["asu_los"]])
+  param[["rehab_los_lnorm"]] <- transform_to_lnorm(param[["rehab_los"]])
+
   # Create simmer environment
   env <- simmer("simulation", verbose = TRUE)
 
   # Add ASU and rehab direct admission patient generators
   for (unit in c("asu", "rehab")) {
     for (patient_type in names(param[[paste0(unit, "_arrivals")]])) {
+
+      # Create patient trajectory
+      traj <- if (unit == "asu") {
+        create_asu_trajectory(
+          env = env, patient_type = patient_type, param = param
+        )
+      } else {
+        create_rehab_trajectory(patient_type, param)
+      }
+
+      # Add patient generator using the created trajectory
       env <- add_patient_generator(
         env = env,
-        # Get trajectory given unit and patient type
-        trajectory = (
-          if (unit == "asu") create_asu_trajectory(patient_type, param)
-          else create_rehab_trajectory(patient_type, param)
-        ),
+        trajectory = traj,
         unit = unit,
         patient_type = patient_type,
         param = param

R/sample_routing.R

@@ -1,14 +1,15 @@
-#' Sample a destination based on probabilities
+#' Sample a destination based on probabilities.
 #'
 #' Randomly selects a destination from a list, where each destination has an
 #' associated probability. The destination is returned as a numeric index, as
-#' `simmer::set_attribute()` requires a numeric or function.
+#' \code{simmer::set_attribute()} requires a numeric or function.
 #'
 #' @param prob_list Named list. The names are destination labels (character),
 #' and the values are their corresponding probabilities (numeric, non-negative,
 #' sum to 1).
 #'
-#' @return An integer. The index of the selected destination within `prob_list`.
+#' @return An integer. The index of the selected destination within
+#' \code{prob_list}.
 #' @export
 
 sample_routing <- function(prob_list) {