feat(parameters): add parameters for the stroke model (in functions, but otherwise similar to https://github.com/pythonhealthdatascience/pydesrap_stroke/simulation/parameters.py)

Author: amyheather

R/parameters.R

@@ -0,0 +1,229 @@
+#' Acute Stroke Unit (ASU) arrival intervals (days).
+#'
+#' For example, a value of 1.2 means a new admission every 1.2 days.
+#'
+#' @param stroke Numeric. Mean days between stroke patient arrivals.
+#' @param tia Numeric. Mean days between transient ischaemic attack (TIA)
+#' patient arrivals.
+#' @param neuro Numeric. Mean days between complex neurological patient
+#' arrivals.
+#' @param other Numeric. Mean days between other patient arrivals.
+#'
+#' @return A named list of arrival intervals for ASU.
+create_asu_arrivals <- function(
+    stroke = 1.2, tia = 9.3, neuro = 3.6, other = 3.2
+) {
+  list(
+    stroke = stroke,
+    tia = tia,
+    neuro = neuro,
+    other = other
+  )
+}
+
+#' Rehabilitation unit arrival intervals (days).
+#'
+#' For example, a value of 21.8 means a new admission every 21.8 days.
+#'
+#' @param stroke Numeric. Mean days between stroke patient arrivals.
+#' @param neuro Numeric. Mean days between complex neurological patient
+#' arrivals.
+#' @param other Numeric. Mean days between other patient arrivals.
+#'
+#' @return A named list of arrival intervals for rehabilitation unit.
+create_rehab_arrivals <- function(
+    stroke = 21.8, neuro = 31.7, other = 28.6
+) {
+  list(
+    stroke = stroke,
+    neuro = neuro,
+    other = other
+  )
+}
+
+#' Acute Stroke Unit (ASU) length of stay (LOS) distributions (days).
+#'
+#' Mean and standard deviation (SD) of LOS in days in the ASU.
+#'
+#' @param stroke_noesd_mean Numeric. Mean LOS for stroke patients without early
+#' supported discharged (ESD).
+#' @param stroke_noesd_sd Numeric. SD LOS for stroke patients without ESD.
+#' @param stroke_esd_mean Numeric. Mean LOS for stroke patients with ESD.
+#' @param stroke_esd_sd Numeric. SD LOS for stroke patients with ESD.
+#' @param stroke_mortality_mean Numeric. Mean LOS for stroke patients who pass
+#' away.
+#' @param stroke_mortality_sd Numeric. SD LOS for stroke patients who pass
+#' away.
+#' @param tia_mean Numeric. Mean LOS for transient ischemic attack (TIA)
+#' patients.
+#' @param tia_sd Numeric. SD LOS for TIA patients.
+#' @param neuro_mean Numeric. Mean LOS for complex neurological patients
+#' @param neuro_sd Numeric. SD LOS for complex neurological patients
+#' @param other_mean Numeric. Mean LOS for other patients.
+#' @param other_sd Numeric. SD LOS for other patients.
+#'
+#' @return A named list of LOS distributions for ASU.
+create_asu_los <- function(
+    stroke_noesd_mean = 7.4, stroke_noesd_sd = 8.61,
+    stroke_esd_mean = 4.6, stroke_esd_sd = 4.8,
+    stroke_mortality_mean = 7.0, stroke_mortality_sd = 8.7,
+    tia_mean = 1.8, tia_sd = 2.3,
+    neuro_mean = 4.0, neuro_sd = 5.0,
+    other_mean = 3.8, other_sd = 5.2
+) {
+  list(
+    stroke_noesd = list(mean = stroke_noesd_mean, sd = stroke_noesd_sd),
+    stroke_esd = list(mean = stroke_esd_mean, sd = stroke_esd_sd),
+    stroke_mortality = list(mean = stroke_mortality_mean, sd = stroke_mortality_sd),
+    tia = list(mean = tia_mean, sd = tia_sd),
+    neuro = list(mean = neuro_mean, sd = neuro_sd),
+    other = list(mean = other_mean, sd = other_sd)
+  )
+}
+
+#' Rehabilitation unit length of stay (LOS) distributions (days).
+#'
+#' @param stroke_noesd_mean Numeric. Mean LOS for stroke patients without early
+#' supported discharged (ESD).
+#' @param stroke_noesd_sd Numeric. SD LOS for stroke patients without ESD.
+#' @param stroke_esd_mean Numeric. Mean LOS for stroke patients with ESD.
+#' @param stroke_esd_sd Numeric. SD LOS for stroke patients with ESD.
+#' @param tia_mean Numeric. Mean LOS for transient ischemic attack (TIA)
+#' patients.
+#' @param tia_sd Numeric. SD LOS for TIA patients.
+#' @param neuro_mean Numeric. Mean LOS for complex neurological patients
+#' @param neuro_sd Numeric. SD LOS for complex neurological patients
+#' @param other_mean Numeric. Mean LOS for other patients.
+#' @param other_sd Numeric. SD LOS for other patients.
+#'
+#' @return A named list of LOS distributions for rehabilitation unit.
+create_rehab_los <- function(
+    stroke_noesd_mean = 28.4, stroke_noesd_sd = 27.2,
+    stroke_esd_mean = 30.3, stroke_esd_sd = 23.1,
+    tia_mean = 18.7, tia_sd = 23.5,
+    neuro_mean = 27.6, neuro_sd = 28.4,
+    other_mean = 16.1, other_sd = 14.1
+) {
+  list(
+    stroke_noesd = list(mean = stroke_noesd_mean, sd = stroke_noesd_sd),
+    stroke_esd = list(mean = stroke_esd_mean, sd = stroke_esd_sd),
+    tia = list(mean = tia_mean, sd = tia_sd),
+    neuro = list(mean = neuro_mean, sd = neuro_sd),
+    other = list(mean = other_mean, sd = other_sd)
+  )
+}
+
+#' ASU routing probabilities.
+#'
+#' Probabilities of each patient type being transferred from the acute
+#' stroke unit (ASU) to other destinations.
+#'
+#' @param stroke_rehab Numeric. Probability stroke patient to rehab.
+#' @param stroke_esd Numeric. Probability stroke patient to early supported
+#' discharge (ESD) services.
+#' @param stroke_other Numeric. Probability stroke patient to other
+#' destinations (e.g., own home, care home, mortality).
+#' @param tia_rehab Numeric. Probability transient ischemic attack (TIA)
+#' patient to rehab.
+#' @param tia_esd Numeric. Probability TIA patient to ESD.
+#' @param tia_other Numeric. Probability TIA patient to other.
+#' @param neuro_rehab Numeric. Probability complex neurological patient to
+#' rehab.
+#' @param neuro_esd Numeric. Probability complex neurological patient to ESD.
+#' @param neuro_other Numeric. Probability complex neurological patient to
+#' other.
+#' @param other_rehab Numeric. Probability other patient to rehab.
+#' @param other_esd Numeric. Probability other patient to ESD.
+#' @param other_other Numeric. Probability other patient to other.
+#'
+#' @return A named list of routing probabilities for ASU.
+create_asu_routing <- function(
+    stroke_rehab = 0.24, stroke_esd = 0.13, stroke_other = 0.63,
+    tia_rehab = 0.01, tia_esd = 0.01, tia_other = 0.98,
+    neuro_rehab = 0.11, neuro_esd = 0.05, neuro_other = 0.84,
+    other_rehab = 0.05, other_esd = 0.10, other_other = 0.85
+) {
+  list(
+    stroke = list(rehab = stroke_rehab, esd = stroke_esd, other = stroke_other),
+    tia = list(rehab = tia_rehab, esd = tia_esd, other = tia_other),
+    neuro = list(rehab = neuro_rehab, esd = neuro_esd, other = neuro_other),
+    other = list(rehab = other_rehab, esd = other_esd, other = other_other)
+  )
+}
+
+#' Rehabilitation unit routing probabilities.
+#'
+#' Probabilities of each patient type being transferred from the rehabilitation
+#' unit to other destinations.
+#'
+#' @param stroke_esd Numeric. Probability stroke patient to early supported
+#' discharge (ESD) services.
+#' @param stroke_other Numeric. Probability stroke patient to other
+#' destinations (e.g., own home, care home, mortality).
+#' @param tia_esd Numeric. Probability transient ischemic attack (TIA) patient
+#' to ESD.
+#' @param tia_other Numeric. Probability TIA patient to other.
+#' @param neuro_esd Numeric. Probability complex neurological patient to ESD.
+#' @param neuro_other Numeric. Probability complex neurological patient to
+#' other.
+#' @param other_esd Numeric. Probability other patient to ESD.
+#' @param other_other Numeric. Probability other patient to other.
+#'
+#' @return A named list of routing probabilities for rehabilitation unit.
+create_rehab_routing <- function(
+    stroke_esd = 0.40, stroke_other = 0.60,
+    tia_esd = 0, tia_other = 1,
+    neuro_esd = 0.09, neuro_other = 0.91,
+    other_esd = 0.13, other_other = 0.88
+) {
+  list(
+    stroke = list(esd = stroke_esd, other = stroke_other),
+    tia = list(esd = tia_esd, other = tia_other),
+    neuro = list(esd = neuro_esd, other = neuro_other),
+    other = list(esd = other_esd, other = other_other)
+  )
+}
+
+#' Generate complete parameter list for simulation.
+#'
+#' @param asu_arrivals List. Acute stroke unit (ASU) arrival intervals.
+#' @param rehab_arrivals List. Rehabilitation unit arrival intervals.
+#' @param asu_los List. ASU length of stay (LOS) distributions.
+#' @param rehab_los List. Rehabilitation unit LOS distributions.
+#' @param asu_routing List. ASU routing probabilities.
+#' @param rehab_routing List. Rehabilitation unit routing probabilities.
+#' @param warm_up_period Integer. Length of warm-up period (days).
+#' @param data_collection_period Integer. Length of data collection period
+#' (days).
+#' @param number_of_runs Integer. Number of simulation runs.
+#' @param audit_interval Numeric. Audit interval (days).
+#' @param cores Integer. Number of CPU cores to use.
+#'
+#' @return A named list of all simulation parameters.
+create_parameters <- function(
+    asu_arrivals = create_asu_arrivals(),
+    rehab_arrivals = create_rehab_arrivals(),
+    asu_los = create_asu_los(),
+    rehab_los = create_rehab_los(),
+    asu_routing = create_asu_routing(),
+    rehab_routing = create_rehab_routing(),
+    warm_up_period = 365 * 3,
+    data_collection_period = 365 * 5,
+    number_of_runs = 150,
+    audit_interval = 1,
+    cores = 1
+) {
+  list(
+    asu_arrivals = asu_arrivals,
+    rehab_arrivals = rehab_arrivals,
+    asu_los = asu_los,
+    rehab_los = rehab_los,
+    asu_routing = asu_routing,
+    rehab_routing = rehab_routing,
+    warm_up_period = warm_up_period,
+    data_collection_period = data_collection_period,
+    number_of_runs = number_of_runs,
+    audit_interval = audit_interval,
+    cores = cores
+  )
+}