refactor(load+strokenoesd): remove redundant library(simulation) when using load_all(), and change stroke_noesd to stroke_no_esd to match python

amyheather · amyheather · commit d6d6ba59ac03 · 2025-07-11T11:50:56.000+01:00
diff --git a/R/create_asu_trajectory.R b/R/create_asu_trajectory.R
@@ -55,7 +55,7 @@ create_asu_trajectory <- function(env, patient_type, param) {
         los_params <- switch(
           dest,
           esd = param[["asu_los_lnorm"]][["stroke_esd"]],
-          rehab = param[["asu_los_lnorm"]][["stroke_noesd"]],
+          rehab = param[["asu_los_lnorm"]][["stroke_no_esd"]],
           other = param[["asu_los_lnorm"]][["stroke_mortality"]],
           stop("Stroke post-asu destination '", dest, "' invalid",
                call. = FALSE)
diff --git a/R/create_rehab_trajectory.R b/R/create_rehab_trajectory.R
@@ -55,7 +55,7 @@ create_rehab_trajectory <- function(env, patient_type, param) {
         los_params <- switch(
           dest,
           esd = param[["rehab_los_lnorm"]][["stroke_esd"]],
-          other = param[["rehab_los_lnorm"]][["stroke_noesd"]],
+          other = param[["rehab_los_lnorm"]][["stroke_no_esd"]],
           stop("Stroke post-rehab destination '", dest, "' invalid",
                call. = FALSE)
         )
diff --git a/R/parameters.R b/R/parameters.R
@@ -40,9 +40,9 @@ create_rehab_arrivals <- function(
 #'
 #' Mean and standard deviation (SD) of LOS in days in the ASU.
 #'
-#' @param stroke_noesd_mean Numeric. Mean LOS for stroke patients without early
+#' @param stroke_no_esd_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_no_esd_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
@@ -61,15 +61,15 @@ create_rehab_arrivals <- function(
 #' @export
 
 create_asu_los <- function(
-  stroke_noesd_mean = 7.4, stroke_noesd_sd = 8.61,
+  stroke_no_esd_mean = 7.4, stroke_no_esd_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_no_esd = list(mean = stroke_no_esd_mean, sd = stroke_no_esd_sd),
     stroke_esd = list(mean = stroke_esd_mean, sd = stroke_esd_sd),
     stroke_mortality = list(mean = stroke_mortality_mean,
                             sd = stroke_mortality_sd),
@@ -81,9 +81,9 @@ create_asu_los <- function(
 
 #' Rehabilitation unit length of stay (LOS) distributions (days).
 #'
-#' @param stroke_noesd_mean Numeric. Mean LOS for stroke patients without early
+#' @param stroke_no_esd_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_no_esd_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)
@@ -98,14 +98,14 @@ create_asu_los <- function(
 #' @export
 
 create_rehab_los <- function(
-  stroke_noesd_mean = 28.4, stroke_noesd_sd = 27.2,
+  stroke_no_esd_mean = 28.4, stroke_no_esd_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_no_esd = list(mean = stroke_no_esd_mean, sd = stroke_no_esd_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),
diff --git a/README.md b/README.md
@@ -59,7 +59,9 @@ The simulation code is in the `R/` folder as a local package. There are files ex
 **Install the local package:**
 
 ```{.r}
-devtools::install()
+devtools::install()  # Needed if running in parallel
+devtools::load_all()  # Sufficient if running sequentially
+
 library(simulation)
 ```
 
diff --git a/inputs/data_dictionary.md b/inputs/data_dictionary.md
@@ -0,0 +1,9 @@
+# Data dictionary for `parameters.csv`
+
+| Column | Data type | Description | Possible values |
+| - | - | - | - |
+| unit | str | Hospital unit | `asu`: Acute Stroke Unit<br>`rehab`: Rehabilitation Unit (post-acute recovery care) |
+| parameter | str | Type of operational metric | `iat`: Inter-arrival time (time between patient admissions)<br>`los`: Length of stay (duration from admission to discharge)<br>`routing`: Transition probability between care pathways  |
+| type | str | Patient classification or care transition path | **For `iat`/`los`:**<br>`stroke`: Stroke patients<br>`stroke_esd`: Stroke patients transferred to Early Supported Discharge<br>`stroke_no_esd`: Stroke patients not transferred to Early Supported Discharge<br>`tia`: Transient Ischemic Attack patients<br>`neuro`: Complex neurological patients<br>`other`: Other patient types<br><br>**For `routing`:**<br>`[diagnosis]_rehab`: Probability of transferring to rehabilitation unit<br>`[diagnosis]_esd`: Probability of Early Supported Discharge<br>`[diagnosis]_other`: Probability of other discharge pathways |
+| mean | float | **For `iat`:** Mean days between admissions<br>**For `los`:** Mean days in unit<br>**For `routing`:** Probability (0-1 scale) | - |
+| sd | float | Standard deviation of the mean | - |
diff --git a/inputs/parameters.csv b/inputs/parameters.csv
@@ -0,0 +1,38 @@
+unit,parameter,type,mean,sd
+asu,iat,stroke,1.2,NA
+asu,iat,tia,9.3,NA
+asu,iat,neuro,3.6,NA
+asu,iat,other,3.2,NA
+rehab,iat,stroke,21.8,NA
+rehab,iat,neuro,31.7,NA
+rehab,iat,other,28.6,NA
+asu,los,stroke_no_esd,7.4,8.61
+asu,los,stroke_esd,4.6,4.8
+asu,los,tia,1.8,2.3
+asu,los,neuro,4,5
+asu,los,other,3.8,5.2
+rehab,los,stroke_no_esd,28.4,27.2
+rehab,los,stroke_esd,30.3,2un3.1
+rehab,los,tia,18.7,23.5
+rehab,los,neuro,27.6,28.4
+rehab,los,other,16.1,14.1
+asu,routing,stroke_rehab,0.24,NA
+asu,routing,stroke_esd,0.13,NA
+asu,routing,stroke_other,0.63,NA
+asu,routing,tia_rehab,0.01,NA
+asu,routing,tia_esd,0.01,NA
+asu,routing,tia_other,0.98,NA
+asu,routing,neuro_rehab,0.11,NA
+asu,routing,neuro_esd,0.05,NA
+asu,routing,neuro_other,0.84,NA
+asu,routing,other_rehab,0.05,NA
+asu,routing,other_esd,0.1,NA
+asu,routing,other_other,0.85,NA
+rehab,routing,stroke_esd,0.4,NA
+rehab,routing,stroke_other,0.6,NA
+rehab,routing,tia_esd,0,NA
+rehab,routing,tia_other,1,NA
+rehab,routing,neuro_esd,0.09,NA
+rehab,routing,neuro_other,0.91,NA
+rehab,routing,other_esd,0.13,NA
+rehab,routing,other_other,0.88,NA
diff --git a/man/create_asu_los.Rd b/man/create_asu_los.Rd
diff --git a/man/create_rehab_los.Rd b/man/create_rehab_los.Rd
diff --git a/outputs/log_example.log b/outputs/log_example.log
@@ -1,8 +1,8 @@
 Parameters:
 asu_arrivals=list(stroke = 1.2, tia = 9.3, neuro = 3.6, other = 3.2);
  rehab_arrivals=list(stroke = 3, neuro = 31.7, other = 28.6);
- asu_los=list(stroke_noesd = list(mean = 7.4, sd = 8.61), stroke_esd = list(mean = 4.6, sd = 4.8), stroke_mortality = list(mean = 7, sd = 8.7), tia = list(mean = 1.8, sd = 2.3), neuro = list(mean = 4, sd = 5), other = list(mean = 3.8, sd = 5.2));
- rehab_los=list(stroke_noesd = list(mean = 28.4, sd = 27.2), stroke_esd = list(mean = 30.3, sd = 23.1), tia = list(mean = 18.7, sd = 23.5), neuro = list(mean = 27.6, sd = 28.4), other = list(mean = 16.1, sd = 14.1));
+ asu_los=list(stroke_no_esd = list(mean = 7.4, sd = 8.61), stroke_esd = list(mean = 4.6, sd = 4.8), stroke_mortality = list(mean = 7, sd = 8.7), tia = list(mean = 1.8, sd = 2.3), neuro = list(mean = 4, sd = 5), other = list(mean = 3.8, sd = 5.2));
+ rehab_los=list(stroke_no_esd = list(mean = 28.4, sd = 27.2), stroke_esd = list(mean = 30.3, sd = 23.1), tia = list(mean = 18.7, sd = 23.5), neuro = list(mean = 27.6, sd = 28.4), other = list(mean = 16.1, sd = 14.1));
  asu_routing=list(stroke = list(rehab = 0.24, esd = 0.13, other = 0.63), tia = list(rehab = 0.01, esd = 0.01, other = 0.98), neuro = list(rehab = 0.11, esd = 0.05, other = 0.84), other = list(rehab = 0.05, esd = 0.1, other = 0.85));
  rehab_routing=list(stroke = list(esd = 0.4, other = 0.6), tia = list(esd = 0, other = 1), neuro = list(esd = 0.09, other = 0.91), other = list(esd = 0.13, other = 0.88));
  warm_up_period=3;
@@ -14,8 +14,8 @@ asu_arrivals=list(stroke = 1.2, tia = 9.3, neuro = 3.6, other = 3.2);
  log_to_file=TRUE;
  file_path=../outputs/log_example.log;
  verbose=TRUE;
- asu_los_lnorm=list(stroke_noesd = list(meanlog = 1.57347219029677, sdlog = 0.925211121759084), stroke_esd = list(meanlog = 1.15775021244827, sdlog = 0.858261138636461), stroke_mortality = list(meanlog = 1.47890496960638, sdlog = 0.966442113578391), tia = list(meanlog = 0.103778649052444, sdlog = 0.983878057331979), neuro = list(meanlog = 0.915802688887627, sdlog = 0.970042960112864), other = list(meanlog = 0.807396441784017, sdlog = 1.02723378541433));
- rehab_los_lnorm=list(stroke_noesd = list(meanlog = 3.02093582638726, sdlog = 0.806787851643665), stroke_esd = list(meanlog = 3.18205014379696, sdlog = 0.676901128257839), tia = list(meanlog = 2.45477304821951, sdlog = 0.973396605337238), neuro = list(meanlog = 2.95675141458562, sdlog = 0.849781569743057), other = list(meanlog = 2.49418211833932, sdlog = 0.754502688730926))
+ asu_los_lnorm=list(stroke_no_esd = list(meanlog = 1.57347219029677, sdlog = 0.925211121759084), stroke_esd = list(meanlog = 1.15775021244827, sdlog = 0.858261138636461), stroke_mortality = list(meanlog = 1.47890496960638, sdlog = 0.966442113578391), tia = list(meanlog = 0.103778649052444, sdlog = 0.983878057331979), neuro = list(meanlog = 0.915802688887627, sdlog = 0.970042960112864), other = list(meanlog = 0.807396441784017, sdlog = 1.02723378541433));
+ rehab_los_lnorm=list(stroke_no_esd = list(meanlog = 3.02093582638726, sdlog = 0.806787851643665), stroke_esd = list(meanlog = 3.18205014379696, sdlog = 0.676901128257839), tia = list(meanlog = 2.45477304821951, sdlog = 0.973396605337238), neuro = list(meanlog = 2.95675141458562, sdlog = 0.849781569743057), other = list(meanlog = 2.49418211833932, sdlog = 0.754502688730926))
 Log:
 0.865903: asu_other0: 🚶 Arrived at ASU
 0.865903: asu_other0: 🎯 Planned ASU -> 3 (other)
diff --git a/rmarkdown/analysis.md b/rmarkdown/analysis.md
@@ -70,11 +70,12 @@ devtools::install(upgrade = "never")
     ##    checking DESCRIPTION meta-information ...  ✔  checking DESCRIPTION meta-information
     ##   ─  checking for LF line-endings in source and make files and shell scripts
     ##   ─  checking for empty or unneeded directories
+    ##    Removed empty directory ‘simulation/tests/testthat/_snaps’
     ##    Omitted ‘LazyData’ from DESCRIPTION
     ##   ─  building ‘simulation_0.1.0.tar.gz’
     ##      
     ## Running /opt/R/4.4.1/lib/R/bin/R CMD INSTALL \
-    ##   /tmp/RtmpH3Tbtm/simulation_0.1.0.tar.gz --install-tests 
+    ##   /tmp/Rtmpz9aafi/simulation_0.1.0.tar.gz --install-tests 
     ## * installing to library ‘/home/amy/.cache/R/renv/library/rdesrap_stroke-34041c45/linux-ubuntu-noble/R-4.4/x86_64-pc-linux-gnu’
     ## * installing *source* package ‘simulation’ ...
     ## ** using staged installation
@@ -1048,4 +1049,4 @@ seconds <- as.integer(runtime %% 60L)
 cat(sprintf("Notebook run time: %dm %ds", minutes, seconds))
 ```
 
-    ## Notebook run time: 1m 38s
+    ## Notebook run time: 2m 33s
diff --git a/rmarkdown/generate_exp_results.Rmd b/rmarkdown/generate_exp_results.Rmd
@@ -27,7 +27,6 @@ Load required packages.
 ```{r setup}
 # nolint start: undesirable_function_linter.
 library(dplyr)
-library(simulation)
 # nolint end
 ```
 
diff --git a/rmarkdown/generate_exp_results.md b/rmarkdown/generate_exp_results.md
@@ -1,7 +1,7 @@
 Generate expected results
 ================
 Amy Heather
-2025-07-10
+2025-07-11
 
 - [Set-up](#set-up)
 - [Base case](#base-case)
@@ -54,7 +54,6 @@ library(dplyr)
     ##     intersect, setdiff, setequal, union
 
 ``` r
-library(simulation)
 # nolint end
 ```
 
@@ -103,11 +102,11 @@ print(param)
     ## 
     ## 
     ## $asu_los
-    ## $asu_los$stroke_noesd
-    ## $asu_los$stroke_noesd$mean
+    ## $asu_los$stroke_no_esd
+    ## $asu_los$stroke_no_esd$mean
     ## [1] 7.4
     ## 
-    ## $asu_los$stroke_noesd$sd
+    ## $asu_los$stroke_no_esd$sd
     ## [1] 8.61
     ## 
     ## 
@@ -153,11 +152,11 @@ print(param)
     ## 
     ## 
     ## $rehab_los
-    ## $rehab_los$stroke_noesd
-    ## $rehab_los$stroke_noesd$mean
+    ## $rehab_los$stroke_no_esd
+    ## $rehab_los$stroke_no_esd$mean
     ## [1] 28.4
     ## 
-    ## $rehab_los$stroke_noesd$sd
+    ## $rehab_los$stroke_no_esd$sd
     ## [1] 27.2
     ## 
     ## 
@@ -389,4 +388,4 @@ seconds <- as.integer(runtime %% 60L)
 cat(sprintf("Notebook run time: %dm %ds", minutes, seconds))
 ```
 
-    ## Notebook run time: 0m 1s
+    ## Notebook run time: 0m 3s
diff --git a/rmarkdown/logs.md b/rmarkdown/logs.md
diff --git a/tests/testthat/test-functionaltest.R b/tests/testthat/test-functionaltest.R

Original file line number	Diff line number	Diff line change
`@@ -55,7 +55,7 @@ create_rehab_trajectory <- function(env, patient_type, param) {`
`55`	`55`	`los_params <- switch(`
`56`	`56`	`dest,`
`57`	`57`	`esd = param[["rehab_los_lnorm"]][["stroke_esd"]],`
`58`		`- other = param[["rehab_los_lnorm"]][["stroke_noesd"]],`
	`58`	`+ other = param[["rehab_los_lnorm"]][["stroke_no_esd"]],`
`59`	`59`	`stop("Stroke post-rehab destination '", dest, "' invalid",`
`60`	`60`	`call. = FALSE)`
`61`	`61`	`)`