refactor(process_replications): change to more informative name get_run_results() + lint + rerun (off charge so slower)

amyheather · amyheather · commit 0cd9403e8f32 · 2025-03-04T15:53:53.000Z
diff --git a/NAMESPACE b/NAMESPACE
@@ -1,9 +1,9 @@
 # Generated by roxygen2: do not edit by hand
 
 export(confidence_interval_method)
+export(get_run_results)
 export(model)
 export(parameters)
-export(process_replications)
 export(run_scenarios)
 export(runner)
 export(valid_inputs)
@@ -36,6 +36,7 @@ importFrom(simmer,add_generator)
 importFrom(simmer,add_resource)
 importFrom(simmer,get_mon_arrivals)
 importFrom(simmer,get_mon_resources)
+importFrom(simmer,now)
 importFrom(simmer,release)
 importFrom(simmer,run)
 importFrom(simmer,seize)
diff --git a/R/choose_replications.R b/R/choose_replications.R
@@ -21,7 +21,7 @@ confidence_interval_method <- function(replications, desired_precision, metric,
   # Run model for specified number of replications
   param <- parameters(number_of_runs = replications)
   raw_results <- runner(param)
-  results <- process_replications(raw_results)
+  results <- get_run_results(raw_results)
 
   # If mean of metric is less than 1, multiply by 100
   if (mean(results[[metric]]) < 1L) {
diff --git a/R/get_run_results.R b/R/get_run_results.R
@@ -1,4 +1,4 @@
-#' Process results from each replication.
+#' Get results from each replication.
 #'
 #' For each replication (there can be one or many), calculate the: (1) number
 #' of arrivals, (2) mean wait time for each resource, (3) mean activity time
@@ -22,14 +22,14 @@
 #' @importFrom dplyr group_by summarise n_distinct mutate lead full_join
 #' @importFrom purrr reduce
 #' @importFrom rlang .data
-#' @importFrom simmer get_mon_resources get_mon_arrivals
+#' @importFrom simmer get_mon_resources get_mon_arrivals now
 #' @importFrom tidyr pivot_wider drop_na
 #' @importFrom tidyselect any_of
 #'
 #' @return Tibble with results from each replication.
 #' @export
 
-process_replications <- function(results) {
+get_run_results <- function(results) {
 
   # Remove patients who were still waiting and had not completed
   results[["arrivals"]] <- results[["arrivals"]] %>%
diff --git a/R/runner.R b/R/runner.R
@@ -36,7 +36,7 @@ runner <- function(param) {
 
   # Combine the results from multiple replications into just two dataframes
   if (param[["number_of_runs"]] == 1L) {
-    results <- results[[1]]
+    results <- results[[1L]]
   } else {
     all_arrivals <- do.call(
       rbind, lapply(results, function(x) x[["arrivals"]])
diff --git a/R/scenarios.R b/R/scenarios.R
@@ -42,7 +42,7 @@ run_scenarios <- function(scenarios, base_list) {
 
     # Run replications for the current scenario and process results
     raw_results <- runner(param)
-    scenario_result <- process_replications(raw_results)
+    scenario_result <- get_run_results(raw_results)
 
     # Append scenario parameters to the results
     scenario_result[["scenario"]] <- index
diff --git a/man/get_run_results.Rd b/man/get_run_results.Rd
diff --git a/outputs/cores1.png b/outputs/cores1.png
diff --git a/outputs/cores2.png b/outputs/cores2.png
diff --git a/rmarkdown/analysis.Rmd b/rmarkdown/analysis.Rmd
@@ -23,7 +23,6 @@ The run time is provided at the end of the notebook.
 Install the latest version of the local simulation package.
 
 ```{r}
-# devtools::install()
 devtools::load_all()
 ```
 
@@ -66,7 +65,7 @@ raw_results <- runner(param = parameters())
 Process results and save to `.csv`.
 
 ```{r}
-run_results <- process_replications(raw_results)
+run_results <- get_run_results(raw_results)
 head(run_results)
 
 write.csv(run_results, file.path(output_dir, "base_run_results.csv"))
diff --git a/rmarkdown/analysis.md b/rmarkdown/analysis.md
@@ -37,7 +37,6 @@ The run time is provided at the end of the notebook.
 Install the latest version of the local simulation package.
 
 ``` r
-# devtools::install()
 devtools::load_all()
 ```
 
@@ -82,7 +81,7 @@ raw_results <- runner(param = parameters())
 Process results and save to `.csv`.
 
 ``` r
-run_results <- process_replications(raw_results)
+run_results <- get_run_results(raw_results)
 head(run_results)
 ```
 
@@ -348,7 +347,7 @@ print(table_latex)
 ```
 
     ## % latex table generated in R 4.4.1 by xtable 1.8-4 package
-    ## % Tue Mar  4 15:30:46 2025
+    ## % Tue Mar  4 15:50:08 2025
     ## \begin{table}[ht]
     ## \centering
     ## \begin{tabular}{rrllll}
@@ -574,7 +573,7 @@ print(sensitivity_table_latex)
 ```
 
     ## % latex table generated in R 4.4.1 by xtable 1.8-4 package
-    ## % Tue Mar  4 15:30:53 2025
+    ## % Tue Mar  4 15:50:24 2025
     ## \begin{table}[ht]
     ## \centering
     ## \begin{tabular}{rrl}
@@ -615,12 +614,19 @@ tail(result[["arrivals"]])
 ```
 
     ##           name start_time end_time activity_time resource replication
-    ## 160 patient156   77.59569       NA            NA    nurse           0
-    ## 161 patient109   53.05827       NA            NA    nurse           0
-    ## 162 patient157   77.98085       NA            NA    nurse           0
-    ## 163 patient158   78.34954       NA            NA    nurse           0
-    ## 164  patient64   34.31794       NA            NA    nurse           0
-    ## 165 patient159   78.37804       NA            NA    nurse           0
+    ## 160 patient148   74.24750       NA            NA    nurse           0
+    ## 161 patient151   75.76834       NA            NA    nurse           0
+    ## 162 patient153   76.74319       NA            NA    nurse           0
+    ## 163 patient159   78.37804       NA            NA    nurse           0
+    ## 164  patient43   20.56980       NA            NA    nurse           0
+    ## 165 patient160   78.41585       NA            NA    nurse           0
+    ##     q_time_unseen
+    ## 160      5.752504
+    ## 161      4.231663
+    ## 162      3.256809
+    ## 163      1.621961
+    ## 164     59.430201
+    ## 165      1.584149
 
 ## Example run with logs
 
@@ -863,6 +869,34 @@ verbose_run[["arrivals"]]
     ## 25 patient26 99.0189155        NA            NA    nurse           0
     ## 26 patient24 84.4587897        NA            NA    nurse           0
     ## 27 patient23 82.4020925        NA            NA    nurse           0
+    ##    q_time_unseen
+    ## 1             NA
+    ## 2             NA
+    ## 3             NA
+    ## 4             NA
+    ## 5             NA
+    ## 6             NA
+    ## 7             NA
+    ## 8             NA
+    ## 9             NA
+    ## 10            NA
+    ## 11            NA
+    ## 12            NA
+    ## 13            NA
+    ## 14            NA
+    ## 15            NA
+    ## 16            NA
+    ## 17            NA
+    ## 18            NA
+    ## 19            NA
+    ## 20            NA
+    ## 21            NA
+    ## 22            NA
+    ## 23            NA
+    ## 24            NA
+    ## 25     0.9810845
+    ## 26    15.5412103
+    ## 27    17.5979075
 
 ## Calculate run time
 
@@ -877,4 +911,4 @@ seconds <- as.integer(runtime %% 60L)
 print(sprintf("Notebook run time: %dm %ds", minutes, seconds))
 ```
 
-    ## [1] "Notebook run time: 0m 19s"
+    ## [1] "Notebook run time: 0m 43s"
diff --git a/rmarkdown/choosing_cores.Rmd b/rmarkdown/choosing_cores.Rmd
@@ -19,7 +19,6 @@ The run time is provided at the end of the notebook.
 Install the latest version of the local simulation package.
 
 ```{r}
-# devtools::install()
 devtools::load_all()
 ```
 
@@ -32,7 +31,6 @@ library(dplyr)
 library(ggplot2)
 library(knitr)
 library(simulation)
-library(tidyr)
 
 options(data.table.summarise.inform = FALSE)
 options(dplyr.summarise.inform = FALSE)
diff --git a/rmarkdown/choosing_cores.md b/rmarkdown/choosing_cores.md
@@ -26,7 +26,6 @@ The run time is provided at the end of the notebook.
 Install the latest version of the local simulation package.
 
 ``` r
-# devtools::install()
 devtools::load_all()
 ```
 
@@ -63,17 +62,7 @@ library(dplyr)
 library(ggplot2)
 library(knitr)
 library(simulation)
-library(tidyr)
-```
-
-    ## 
-    ## Attaching package: 'tidyr'
-
-    ## The following object is masked from 'package:testthat':
-    ## 
-    ##     matches
 
-``` r
 options(data.table.summarise.inform = FALSE)
 options(dplyr.summarise.inform = FALSE)
 # nolint end
@@ -196,4 +185,4 @@ seconds <- as.integer(runtime %% 60L)
 print(sprintf("Notebook run time: %dm %ds", minutes, seconds))
 ```
 
-    ## [1] "Notebook run time: 1m 14s"
+    ## [1] "Notebook run time: 2m 9s"
diff --git a/rmarkdown/choosing_replications.Rmd b/rmarkdown/choosing_replications.Rmd
@@ -19,7 +19,6 @@ The run time is provided at the end of the notebook.
 Install the latest version of the local simulation package.
 
 ```{r}
-# devtools::install()
 devtools::load_all()
 ```
 
@@ -29,7 +28,6 @@ Load required packages.
 # nolint start: undesirable_function_linter.
 library(data.table)
 library(dplyr)
-library(ggplot2)
 library(knitr)
 library(simulation)
 library(tidyr)
diff --git a/rmarkdown/choosing_replications.md b/rmarkdown/choosing_replications.md
@@ -26,7 +26,6 @@ The run time is provided at the end of the notebook.
 Install the latest version of the local simulation package.
 
 ``` r
-# devtools::install()
 devtools::load_all()
 ```
 
@@ -60,7 +59,6 @@ library(dplyr)
     ##     intersect, setdiff, setequal, union
 
 ``` r
-library(ggplot2)
 library(knitr)
 library(simulation)
 library(tidyr)
@@ -215,4 +213,4 @@ seconds <- as.integer(runtime %% 60L)
 print(sprintf("Notebook run time: %dm %ds", minutes, seconds))
 ```
 
-    ## [1] "Notebook run time: 0m 2s"
+    ## [1] "Notebook run time: 0m 5s"
diff --git a/rmarkdown/generate_exp_results.Rmd b/rmarkdown/generate_exp_results.Rmd
@@ -19,7 +19,6 @@ The run time is provided at the end of this notebook.
 Install the latest version of the local simulation package.
 
 ```{r}
-# devtools::install()
 devtools::load_all()
 ```
 
@@ -62,7 +61,7 @@ raw_results <- runner(param)
 
 ```{r}
 # Process results
-results <- process_replications(raw_results)
+results <- get_run_results(raw_results)
 
 # Preview
 head(results)
diff --git a/rmarkdown/generate_exp_results.md b/rmarkdown/generate_exp_results.md
@@ -24,7 +24,6 @@ The run time is provided at the end of this notebook.
 Install the latest version of the local simulation package.
 
 ``` r
-# devtools::install()
 devtools::load_all()
 ```
 
@@ -69,7 +68,7 @@ raw_results <- runner(param)
 
 ``` r
 # Process results
-results <- process_replications(raw_results)
+results <- get_run_results(raw_results)
 
 # Preview
 head(results)
diff --git a/tests/testthat/test-backtest.R b/tests/testthat/test-backtest.R
@@ -16,7 +16,7 @@ test_that("results from a new run match those previously generated", {
 
   # Run the replications then get the monitored arrivals and resources
   raw_results <- runner(param)
-  results <- as.data.frame(process_replications(raw_results))
+  results <- as.data.frame(get_run_results(raw_results))
 
   # Import the expected results
   exp_results <- read.csv(test_path("testdata", "results.csv"))
diff --git a/tests/testthat/test-functionaltest.R b/tests/testthat/test-functionaltest.R
