feat(stroke): Clear out repository, and amend key files to be relevant to stroke (CITATION, DESCRIPTION, NEWS, README)

Author: amyheather

CITATION.cff

@@ -3,7 +3,7 @@
 
 cff-version: 1.2.0
 title: >-
-  R DES RAP Template
+  Stroke capacity planning model: R DES RAP
 message: >-
   If you use this software, please cite it using the
   metadata from this file.
@@ -15,9 +15,9 @@ authors:
     affiliation: University of Exeter
     orcid: 'https://orcid.org/0000-0002-6596-3479'
 repository-code: >-
-  https://github.com/pythonhealthdatascience/rdesrap_mms
+  https://github.com/pythonhealthdatascience/rdesrap_stroke
 abstract: >-
-  A template for creating discrete-event simulation (DES) models in R
-  within a reproducible analytical pipeline (RAP).
-version: 0.4.0
-date-released: '2025-06-04'
+  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'

DESCRIPTION

@@ -9,36 +9,17 @@ Authors@R: c(
       role = c("aut", "cre")
     )
   )
-URL: https://github.com/pythonhealthdatascience/rdesrap_mms
-Description: Template reproducible analytical pipeline (RAP) for simple R
-    discrete-event simulation (DES) model.
+URL: https://github.com/pythonhealthdatascience/rdesrap_stroke
+Description: Reproducible analytical pipeline (RAP) for R discrete-event
+  simulation (DES) implementing the Stroke Capacity Planning Model from Monks
+  et al. 2016.
 License: MIT + file LICENSE
 Encoding: UTF-8
 LazyData: true
 RoxygenNote: 7.3.2
 Imports:
-    simmer,
-    magrittr,
-    dplyr,
-    purrr,
-    rlang,
-    tidyr,
-    tidyselect,
-    future,
-    future.apply,
-    ggplot2,
-    tibble,
-    gridExtra,
-    R6
+    simmer
 Suggests:
     testthat (>= 3.0.0),
-    patrick,
-    lintr,
-    devtools,
-    xtable,
-    data.table,
-    mockery,
-    fitdistrplus,
-    lubridate,
-    plotly
+    lintr
 Config/testthat/edition: 3

NAMESPACE

@@ -1,77 +1,4 @@
-# R DES RAP Template 0.4.0
 
-Major changes include: addition of two new metrics (queue length and patients in service); input modelling; and synthetic data. Also, enabled solutions below the defined initial replications for the replications algorithm.
+# Stroke capacity planning model: R DES RAP 0.1.0
 
-## New features
-
-* Add synthetic data and explanation in `README`.
-* Add `input_modelling.Rmd`.
-* Add unit tests for `find_position()`.
-* Add mock paper with figures mentioned in `.Rmd`/`README`.
-* Add `CITATION`.
-* Add printing of parameters when running model.
-* Add two new metrics: queue length and patients in service.
-
-## Bug fixes
-
-* Add `find_position()` which allows us to find a solution below the initial replications set when using `ReplicationsAlgorithm`.
-
-## Other changes
-
-* Changed desired precision when choosing replications to 0.1.
-* Made `README` simpler/clearer, so it focuses on describing the repository, rather than on being a template.
-* Add `fitdistrplus`, `lubridate` and `plotly`, and updated some packages.
-* Set `renv` snapshot type to implicit (was previously all).
-* In `choosing_cores.Rmd`, set `devtools::install(upgrade = "never")` (else would try to update packages).
-* GitHub action runs tests on latest mac, windows and ubuntu (but not on development or old ubuntu anymore).
-
-# R DES RAP Template 0.3.0
-
-Major changes include addition of functions/classes for choosing the warm-up length and number of replications. Other changes include tests, possibility to override seeds in runner, a bug fix for the mean wait time and serve length, code refactoring, and others.
-
-## New features
-
-* Add file explaining how `set_attributes()` changes results (`using_set_attributes.Rmd`).
-* Add functions for choosing warm-up length (`choose_warmup`) and an example file (`choosing_warmup.Rmd`).
-* Add some extra checks in functional tests using the unseen metrics.
-* Add classes/functions for automated choice of the number of replications (`choose_replications.R`) and an example file explaining these (`choosing_replications.Rmd`), along with tests for these (`test-backtest-replications.R`, `test-functionaltest-replications.R`, `test-unittest-replications.R`).
-* Add options in `runner()` to override future.seed and use the run numbers as seeds (allowing consistency with `model()`) (and add test using it).
-* Add unit test for parallel processing.
-
-## Bug fixes
-
-* Corrected calculation of mean wait and serve length (previously dropped all arrivals NA for `end_time` - now bases on `wait_time`, and so includes people who are midway through appointment at end of simulation).
-
-## Other changes
-
-* Split calculations from `get_run_results()` into seperate functions for simplicity, and to make them reusable for other purposes.
-* Simplified calculation of utilisation (same output, simpler code).
-* Add example of calculating overall results table to `analysis.Rmd`.
-* Add "how does model work" and "acknowledgements" sections to README.
-
-# R DES RAP Template 0.2.0
-
-Warm-up period, "unseen" metrics and tests. Note that the alteration to record service duration altered the order of random number generation, so results now differ from before.
-
-## New features
-
-* Add warm-up period (`filter_warmup()`).
-* Add measurement of when service starts and its duration during the model run (`set_attribute("nurse_serve_start", ...` and `set_attribute("nurse_serve_length", ...`).
-* Add count and wait time for unseen patients in the run results.
-* Add tests for warm-up, unseen metrics, and logs.
-* Add `arrivals` and `resources` to base case back test.
-
-## Bug fixes
-
-* Include all patients in the run results `arrivals` count (and not only those who completed the service).
-* Include patients partway through service in the `mean_waiting_time` and `mean_service_time` (and not only those who completed the service).
-* Use `devtools::install()` in `choosing_cores.Rmd` (required to get updated package for parallel processing).
-
-## Other changes
-
-* Simplify scenario back test.
-* Add DOI and Zenodo citation to README.
-
-# R DES RAP Template 0.1.0
-
-🌱 First release of the R DES template.
+🌱 First release of the R stroke model.