Merge pull request #8 from pythonhealthdatascience/dev

Dev

Author: amyheather

.gitignore

@@ -39,9 +39,6 @@ vignettes/*.pdf
 # R Environment Variables
 .Renviron
 
-# pkgdown site
-docs/
-
 # translation temp files
 po/*~
 

CITATION.cff

@@ -20,4 +20,4 @@ abstract: >-
   Reproducible analytical pipeline (RAP) for R discrete-event simulation (DES)
   implementing the Stroke Capacity Planning Model from Monks et al. 2016.
 version: 0.1.0
-date-released: '2025-06-30'
+date-released: '2025-07-11'

NEWS.md

@@ -2,3 +2,11 @@
 # Stroke capacity planning model: R DES RAP 0.1.0
 
 🌱 First release of the R stroke model.
+
+## New features
+
+* Implementation of the stroke model in R as a package (`R/`).
+* Reproduction of paper results (`rmarkdown/analysis.Rmd`).
+* Other RMarkdown files to generate results for tests, demonstrate logging, and how parameters can be loaded from a csv (`rmarkdown/`).
+* Back, functional and unit tests (`tests/`).
+* Other features include continuous integration (tests and linting), checklists, R environment, and other metadata.

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)

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)
         )

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),

README.md

@@ -56,16 +56,45 @@ renv::snapshot()
 
 The simulation code is in the `R/` folder as a local package. There are files executing the model and analysing the results in `rmarkdown/`.
 
-To run the model with base parameters once or with replications:
+**Install the local package:**
 
 ```{.r}
-# TODO
+devtools::install()  # Needed if running in parallel
+devtools::load_all()  # Sufficient if running sequentially
+
+library(simulation)
+```
+
+**Run a single simulation:**
+
+```{.r}
+param <- create_parameters(number_of_runs = 1L)
+single_results <- runner(param = param)
 ```
 
-Example altering the model parameters:
+**Run multiple replications:**
 
 ```{.r}
-# TODO
+param <- create_parameters(number_of_runs = 5L)
+single_results <- runner(param = param)
+```
+
+**Run all analyses (from command line):**
+
+```{.r}
+bash run_rmarkdown.sh
+```
+
+**Run tests:**
+
+```{.r}
+devtools::test()
+```
+
+**Lint code:**
+
+```{.r}
+lintr::lint_dir()
 ```
 
 ### Generating the results from the article
@@ -87,23 +116,27 @@ To generate these, simply execute `rmarkdown/analysis.Rmd`.
 
 Original:
 
+![](docs/article/fig1.png)
+
 From this repository:
 
-**TODO**
+![](outputs/figure1_asu.png)
 
 **Figure 3**
 
 Original:
 
+![](docs/article/fig3.png)
+
 From this repository:
 
-**TODO**
+![](outputs/figure3_asu.png)
 
 <br>
 
 ## Run time and machine specification
 
-The run time for this analysis (`notebooks/analysis.Rm`) is **TODO** seconds. This was on an Intel Core i7-12700H, 32GB RAM, Ubuntu 24.04.1.
+The run time for this analysis (`notebooks/analysis.Rmd`) is **1m 38s** seconds. This was on an Intel Core i7-12700H, 32GB RAM, Ubuntu 24.04.1.
 
 The other notebooks generate results for tests and illustrate other functionality (e.g. importing parameters from csv, running with logs), and these just take a second or two.