style(lint): linting

Author: amyheather

NAMESPACE

@@ -2,8 +2,11 @@
 
 export(add_patient_generator)
 export(check_all_param_names)
+export(check_all_positive)
+export(check_nonneg_integer)
 export(check_param_names)
 export(check_param_values)
+export(check_positive_integer)
 export(check_prob_vector)
 export(check_run_number)
 export(create_asu_arrivals)
@@ -15,6 +18,7 @@ export(create_rehab_arrivals)
 export(create_rehab_los)
 export(create_rehab_routing)
 export(create_rehab_trajectory)
+export(filter_warmup)
 export(get_occupancy_stats)
 export(model)
 export(runner)

R/filter_warmup.R

@@ -15,8 +15,8 @@ filter_warmup <- function(result, warm_up_period) {
       group_by(.data[["name"]]) |>
       filter(all(.data[["start_time"]] >= warm_up_period)) |>
       ungroup()
-    result[["occupancy"]] <- result[["occupancy"]] |>
-      filter(time >= warm_up_period)
+    result[["occupancy"]] <- filter(result[["occupancy"]],
+                                    time >= warm_up_period)
   }
-  return(result)
+  result
 }

R/model.R

@@ -1,5 +1,5 @@
 # To avoid package build warning (name in expand.grid())
-utils::globalVariables(c("time"))
+utils::globalVariables("time")
 
 #' Run simulation.
 #'

R/validate_model_inputs.R

@@ -117,7 +117,7 @@ check_prob_vector <- function(vec, name) {
   if (!is.numeric(vec)) {
     stop('Routing vector "', name, '" must be numeric.', call. = FALSE)
   }
-  if (any(vec < 0 | vec > 1)) {
+  if (any(vec < 0L | vec > 1L)) {
     stop('All values in routing vector "', name, '" must be between 0 and 1.',
          call. = FALSE)
   }
@@ -128,54 +128,88 @@ check_prob_vector <- function(vec, name) {
 }
 
 
-#' Validate parameter values.
+#' Check if a value is a positive integer
 #'
-#' Ensure that specific parameters are positive numbers, or non-negative
-#' integers, and that probability vectors are in [0, 1] and sum to 1 (within
-#' tolerance).
+#' Throws an error if the value is not a positive integer (> 0).
 #'
-#' @param param List containing parameters for the simulation.
+#' @param x The value to check.
+#' @param name The name of the parameter (for error messages).
 #'
-#' @return Throws an error if any specified parameter value is invalid.
+#' @return None. Throws an error if the check fails.
 #' @export
 
-check_param_values <- function(param) {
-
-  # Check that number of runs is positive integer
-  if (
-    !is.null("number_of_runs") &&
-    "number_of_runs" <= 0L &&
-    "number_of_runs" %% 1L == 0L
-  ) {
-    stop('The parameter "number_of_runs" must be integer greater than 0.',
-         call. = FALSE)
+check_positive_integer <- function(x, name) {
+  if (is.null(x) || x <= 0L || x %% 1L != 0L) {
+    stop(
+      sprintf('The parameter "%s" must be an integer greater than 0.', name),
+      call. = FALSE
+    )
   }
+}
 
-  # Check that listed parameters are not negative (i.e. must be 0+)
-  non_neg <- c("asu_arrivals", "rehab_arrivals", "asu_los", "rehab_los")
-  for (sub in non_neg) {
-    if (!is.null(param[[sub]])) {
-      vals <- unlist(param[[sub]])
-      if (any(vals <= 0L)) {
-        stop('All values in "', sub, '" must be greater than 0.', call. = FALSE)
-      }
-    }
+#' Check if all values are positive
+#'
+#' Throws an error if any value in the input is not positive (> 0).
+#'
+#' @param x The vector or list of values to check.
+#' @param name The name of the parameter (for error messages).
+#'
+#' @return None. Throws an error if the check fails.
+#' @export
+
+check_all_positive <- function(x, name) {
+  if (!is.null(x) && any(unlist(x) <= 0L)) {
+    stop(
+      sprintf('All values in "%s" must be greater than 0.', name),
+      call. = FALSE
+    )
   }
+}
 
-  # Check that listed parameters are non-negative integers
-  n_list <- c("warm_up_period", "data_collection_period")
-  for (n in n_list) {
-    if (param[[n]] < 0L || param[[n]] %% 1L != 0L) {
-      stop('The parameter "', n,
-           '" must be an integer greater than or equal to 0.', call. = FALSE)
-    }
+#' Check if a value is a non-negative integer
+#'
+#' Throws an error if the value is not a non-negative integer (>= 0).
+#'
+#' @param x The value to check.
+#' @param name The name of the parameter (for error messages).
+#'
+#' @return None. Throws an error if the check fails.
+#' @export
+
+check_nonneg_integer <- function(x, name) {
+  if (is.null(x) || x < 0L || x %% 1L != 0L) {
+    stop(
+      sprintf('The parameter "%s" must be an integer >= 0.', name),
+      call. = FALSE
+    )
   }
+}
+
+#' Validate parameter values
+#'
+#' Ensures that specific parameters are positive numbers, non-negative integers,
+#' and that probability vectors are in [0, 1] and sum to 1 (within tolerance).
+#'
+#' @param param List containing parameters for the simulation.
+#'
+#' @return None. Throws an error if any specified parameter value is invalid.
+#' @export
+
+check_param_values <- function(param) {
+  check_positive_integer(param[["number_of_runs"]], "number_of_runs")
+
+  lapply(c("asu_arrivals", "rehab_arrivals", "asu_los", "rehab_los"),
+         function(nm) check_all_positive(param[[nm]], nm))
+
+  lapply(c("warm_up_period", "data_collection_period"),
+         function(nm) check_nonneg_integer(param[[nm]], nm))
 
-  # Check that listed parameters are between 0 and 1 and sum to 1 (+- 0.01)
   for (routing in c("asu_routing", "rehab_routing")) {
-    for (name in names(param[[routing]])) {
-      vec <- unlist(param[[routing]][[name]], use.names = FALSE)
-      check_prob_vector(vec, paste0(routing, "$", name))
+    if (!is.null(param[[routing]])) {
+      lapply(names(param[[routing]]), function(name) {
+        vec <- unlist(param[[routing]][[name]], use.names = FALSE)
+        check_prob_vector(vec, paste0(routing, "$", name))
+      })
     }
   }
 }

man/check_all_positive.Rd

@@ -302,14 +302,14 @@ make_delay_table <- function(
 
     # Extract and filter base and scenario data
     base_df <- base[[unit_name]] |>
-      filter(beds %in% unit_beds) |>
-      select(beds, .data[["prob_delay"]], .data[["1_in_n_delay"]]) |>
+      filter(.data[["beds"]] %in% unit_beds) |>
+      select(.data[["beds"]], .data[["prob_delay"]], .data[["1_in_n_delay"]]) |>
       rename_with(~paste0(., "_", base_name),
                   c("prob_delay", "1_in_n_delay"))
 
     scenario_df <- scenario[[unit_name]] |>
-      filter(beds %in% unit_beds) |>
-      select(beds, .data[["prob_delay"]], .data[["1_in_n_delay"]]) |>
+      filter(.data[["beds"]] %in% unit_beds) |>
+      select(.data[["beds"]], .data[["prob_delay"]], .data[["1_in_n_delay"]]) |>
       rename_with(~paste0(., "_", scenario_name),
                   c("prob_delay", "1_in_n_delay"))
 
@@ -325,7 +325,7 @@ make_delay_table <- function(
 
   # Combine and return
   bind_rows(asu_table, rehab_table) |>
-    arrange(unit, beds)
+    arrange(unit, .data[["beds"]])
 }
 ```