styler::style_pkg()

ThomUK · Dec 10, 2023 · b219f9d · b219f9d
1 parent 699c165
commit b219f9d
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Showing 5 changed files with 65 additions and 72 deletions.
diff --git a/R/app_config.R b/R/app_config.R
@@ -23,18 +23,17 @@ app_sys <- function(...) {
 #'
 #' @noRd
 get_golem_config <- function(
-  value,
-  config = Sys.getenv(
-    "GOLEM_CONFIG_ACTIVE",
-    Sys.getenv(
-      "R_CONFIG_ACTIVE",
-      "default"
-    )
-  ),
-  use_parent = TRUE,
-  # Modify this if your config file is somewhere else
-  file = app_sys("golem-config.yml")
-) {
+    value,
+    config = Sys.getenv(
+      "GOLEM_CONFIG_ACTIVE",
+      Sys.getenv(
+        "R_CONFIG_ACTIVE",
+        "default"
+      )
+    ),
+    use_parent = TRUE,
+    # Modify this if your config file is somewhere else
+    file = app_sys("golem-config.yml")) {
   config::get(
     value = value,
     config = config,

diff --git a/R/mod_assumptions.R b/R/mod_assumptions.R
@@ -4,10 +4,10 @@
 #'
 #' @param id,input,output,session Internal parameters for {shiny}.
 #'
-#' @noRd 
+#' @noRd
 #'
-#' @importFrom shiny NS tagList 
-mod_assumptions_ui <- function(id){
+#' @importFrom shiny NS tagList
+mod_assumptions_ui <- function(id) {
   ns <- NS(id)
   tagList(
     HTML("<p>The code for this project is open-source, and is on <a href='https://github.com/ThomUK/DESPatientPathway' target='_blank'>GitHub.</a></p>"),
@@ -16,7 +16,7 @@ mod_assumptions_ui <- function(id){
         width = 12,
         p("This model is in development.  It is not yet ready to be used for planning.  Some of the issues to be resolved are detailed below."),
         HTML(
-            "<ul>
+          "<ul>
               <li>Is the main queue appearing in the right place?  Is the typical real waiting list post referral and pre OP appointment, or is it post OP appt and pre-admission.</li>
               <li>How to model the queue between OP appt and hospital admission?</li>
               <li>Appointment non-attendance is not yet modelled.  Attendance is assumed to be 100%.</li>
@@ -29,19 +29,18 @@ mod_assumptions_ui <- function(id){
     ),
   )
 }
-    
+
 #' assumptions Server Functions
 #'
-#' @noRd 
-mod_assumptions_server <- function(id){
-  moduleServer( id, function(input, output, session){
+#' @noRd
+mod_assumptions_server <- function(id) {
+  moduleServer(id, function(input, output, session) {
     ns <- session$ns
-
   })
 }
-    
+
 ## To be copied in the UI
 # mod_assumptions_ui("assumptions_1")
-    
+
 ## To be copied in the server
 # mod_assumptions_server("assumptions_1")
diff --git a/R/mod_simulation.R b/R/mod_simulation.R
@@ -7,7 +7,7 @@
 #' @noRd
 #'
 #' @importFrom shiny NS tagList
-mod_simulation_ui <- function(id){
+mod_simulation_ui <- function(id) {
   ns <- NS(id)
   tagList(
     shinyjs::useShinyjs(),
@@ -47,7 +47,7 @@ mod_simulation_ui <- function(id){
           sliderInput(NS(id, "numPatBacklogSize"), "Number of existing patients in the OP clinic backlog", value = 500, min = 0, max = 5000),
           sliderInput(NS(id, "numPatReferralRate"), "Number of new patient referrals (monthly)", value = 100, min = 0, max = 1000),
           sliderInput(NS(id, "numOPOutcomeFup"), "OP outcome: Book followup (%)", value = 25, min = 0, max = 100),
-          sliderInput(NS(id, "numOPOutcomeAdmit"), "OP outcome: Admit (%)", value = 10 , min = 0, max = 100),
+          sliderInput(NS(id, "numOPOutcomeAdmit"), "OP outcome: Admit (%)", value = 10, min = 0, max = 100),
           uiOutput(NS(id, "OPOutcomeDischarge")), # a shinyjs output
           sliderInput(NS(id, "numPreOpLos"), "Average pre-operative length of stay (hours)", value = 6, min = 0, max = 36),
           sliderInput(NS(id, "numPostOpLos"), "Average post-operative length of stay (days)", value = 3, min = 0, max = 42, step = 0.1),
@@ -64,7 +64,8 @@ mod_simulation_ui <- function(id){
       ),
       column(1)
     ),
-    column(12,
+    column(
+      12,
       hr(),
       plotOutput(NS(id, "queuePlot")),
       hr(),
@@ -82,25 +83,27 @@ mod_simulation_ui <- function(id){
 #' simulation Server Functions
 #'
 #' @noRd
-mod_simulation_server <- function(id){
-  moduleServer( id, function(input, output, session){
+mod_simulation_server <- function(id) {
+  moduleServer(id, function(input, output, session) {
     ns <- session$ns
 
     #### REACTIVITY ####
     # display a disabled input for the discharge rate (which depends on followup and admit rates)
-    output$OPOutcomeDischarge = renderUI({
-      shinyjs::disabled(sliderInput(inputId = "OPOutcomeDischarge", label = "OP outcome: Discharge (%)",
-                                    min = 0, max = 100, value = max(0, (100 - input$numOPOutcomeFup - input$numOPOutcomeAdmit))))
+    output$OPOutcomeDischarge <- renderUI({
+      shinyjs::disabled(sliderInput(
+        inputId = "OPOutcomeDischarge", label = "OP outcome: Discharge (%)",
+        min = 0, max = 100, value = max(0, (100 - input$numOPOutcomeFup - input$numOPOutcomeAdmit))
+      ))
     })
 
     # handle the cases where discharge rate is already zero
-    observeEvent(input$numOPOutcomeFup,  {
-      if(input$numOPOutcomeFup + input$numOPOutcomeAdmit > 100){
+    observeEvent(input$numOPOutcomeFup, {
+      if (input$numOPOutcomeFup + input$numOPOutcomeAdmit > 100) {
         updateSliderInput(session = session, inputId = "numOPOutcomeAdmit", value = 100 - input$numOPOutcomeFup)
       }
     })
-    observeEvent(input$numOPOutcomeAdmit,  {
-      if(input$numOPOutcomeFup + input$numOPOutcomeAdmit > 100){
+    observeEvent(input$numOPOutcomeAdmit, {
+      if (input$numOPOutcomeFup + input$numOPOutcomeAdmit > 100) {
         updateSliderInput(session = session, inputId = "numOPOutcomeFup", value = 100 - input$numOPOutcomeAdmit)
       }
     })
@@ -165,11 +168,10 @@ mod_simulation_server <- function(id){
         B->F;
 
       }
-      ")
-    )
+      "
+    ))
 
     observeEvent(input$updateButton, {
-
       # it's most convenient to use library calls while prototyping
       # may remove later
       library(simmer)
@@ -193,7 +195,7 @@ mod_simulation_server <- function(id){
       # make a plot
       output$queuePlot <- renderPlot(
         plot(sim_resources, metric = "usage", items = "queue", steps = TRUE) +
-          scale_x_continuous(name = "Days", labels = scales::number_format(scale = 1/60/24)) + # format labels to represent days
+          scale_x_continuous(name = "Days", labels = scales::number_format(scale = 1 / 60 / 24)) + # format labels to represent days
           labs(
             title = "Queue size",
             y = "Number of patients"
@@ -203,9 +205,9 @@ mod_simulation_server <- function(id){
       )
       output$serverPlot <- renderPlot(
         plot(sim_resources, metric = "usage", items = "server", steps = TRUE) +
-          scale_x_continuous(name = "Days", labels = scales::number_format(scale = 1/60/24)) + # format labels to represent days
-            scale_color_manual(values = "lightgreen") +
-            labs(
+          scale_x_continuous(name = "Days", labels = scales::number_format(scale = 1 / 60 / 24)) + # format labels to represent days
+          scale_color_manual(values = "lightgreen") +
+          labs(
             subtitle = "Dotted line = max capacity, Solid line = actual usage",
             y = "Used"
           ) +
@@ -224,10 +226,7 @@ mod_simulation_server <- function(id){
       output$trajectoryPlot <- DiagrammeR::renderGrViz(
         plot(patient, verbose = TRUE)
       )
-
-
     })
-
   })
 }
 

diff --git a/R/run_app.R b/R/run_app.R
@@ -8,12 +8,11 @@
 #' @importFrom shiny shinyApp
 #' @importFrom golem with_golem_options
 run_app <- function(
-  onStart = NULL,
-  options = list(),
-  enableBookmarking = "url",
-  uiPattern = "/",
-  ...
-) {
+    onStart = NULL,
+    options = list(),
+    enableBookmarking = "url",
+    uiPattern = "/",
+    ...) {
   with_golem_options(
     app = shinyApp(
       ui = app_ui,

diff --git a/R/run_sim.R b/R/run_sim.R
@@ -6,8 +6,7 @@
 #' @export
 #' @noRd
 #'
-run_sim <- function(model_config){
-
+run_sim <- function(model_config) {
   # read the model config to a short variable name
   mc <- model_config()
 
@@ -18,37 +17,37 @@ run_sim <- function(model_config){
   # patient arrivals
   rate <- mc$pat_referral_rate * 12 / 365 / 24 / 60 # monthly -> annual, then calculate patients per minute
   dist_patient_arrival <- function() rexp(1, rate)
-  #dist_patient_arrival()
+  # dist_patient_arrival()
 
   # initial backlog of patients
   dist_starting_backlog <- at(rep(0, mc$pat_backlog_size))
-  #dist_starting_backlog()
+  # dist_starting_backlog()
 
   dist_pre_op_ward_los <- function() rexp(1, 1 / (60 * mc$pre_op_los)) # x60 = hours
-  #dist_pre_op_ward_los()
+  # dist_pre_op_ward_los()
 
   dist_operating_time <- function() rexp(1, 1 / mc$theatre_proc_length) # minutes
-  #dist_operating_time()
+  # dist_operating_time()
 
   dist_post_op_ward_los <- function() rexp(1, 1 / (60 * 24 * mc$post_op_los)) # 60x24 = days
-  #dist_post_op_ward_los()
+  # dist_post_op_ward_los()
 
   # OP outcoming result. 1 = admit to wl, 2 = OP followup, 3 = discharged
   op_disch_rate <- (100 - mc$op_admit_rate - mc$op_fup_rate)
 
   dist_op_outcome <- function() sample(1:3, 1, FALSE, c(mc$op_admit_rate, mc$op_fup_rate, op_disch_rate))
-  #dist_op_outcome()
+  # dist_op_outcome()
 
   # create some schedules to close resources overnight
   op_clinic_schedule <- schedule(
-    c(60*8, 60*16),
+    c(60 * 8, 60 * 16),
     c(1, 0),
-    period = 60*24
+    period = 60 * 24
   )
   theatre_schedule <- schedule(
-    c(60*8, 60*16),
+    c(60 * 8, 60 * 16),
     c(1, 0),
-    period = 60*24
+    period = 60 * 24
   )
 
   # create the patient pathway branches
@@ -63,20 +62,17 @@ run_sim <- function(model_config){
 
   branch_admit <- trajectory("admit for treatment") |>
     set_attribute("admitted_for_treatment", 1) |>
-
     # take a pre-op bed
     set_attribute("moved_to_pre_op_bed", 1) |>
     seize("Bed") |>
     timeout(dist_pre_op_ward_los) |>
     release("Bed") |>
-
     # operate
     set_attribute("moved_to_theatre", 1) |>
     seize("Theatre") |>
     timeout(dist_operating_time) |>
     release("Theatre") |>
     log_("Im recovering") |>
-
     # take a recovery ward bed
     set_attribute("moved_to_post_op_bed", 1) |>
     seize("Bed") |>
@@ -93,12 +89,13 @@ run_sim <- function(model_config){
     seize("OP Clinic", 1, tag = "op_clinic") |>
     timeout(function() rnorm(1, mean = mc$op_clinic_length, sd = 6)) |>
     release("OP Clinic", 1) |>
-
     # branch into admission and discharge
-    branch(dist_op_outcome, FALSE,
-           branch_admit,
-           branch_followup_later,
-           branch_discharge_from_op)
+    branch(
+      dist_op_outcome, FALSE,
+      branch_admit,
+      branch_followup_later,
+      branch_discharge_from_op
+    )
 
 
   sim <- env |>
@@ -108,7 +105,7 @@ run_sim <- function(model_config){
     add_generator("backlog patient", patient, dist_starting_backlog, mon = 2) |>
     add_generator("new patient", patient, dist_patient_arrival, mon = 2)
 
-  env |> run(60*24*7 * mc$forecast_length) # 60 * 24 * 7 = 1 week
+  env |> run(60 * 24 * 7 * mc$forecast_length) # 60 * 24 * 7 = 1 week
 
   res <- list(
     sim = sim,