Merge pull request #136 from pythonhealthdatascience/dev

amyheather · web-flow · commit 584471ade0f3 · 2025-12-02T12:14:42.000Z
Dev
diff --git a/CITATION.cff b/CITATION.cff
@@ -28,6 +28,10 @@ authors:
     email: a.l.harper@exeter.ac.uk
     affiliation: University of Exeter Business School
     orcid: https://orcid.org/0000-0001-5274-5037
+  - given-names: Fatemeh
+    family-names: Alidoost
+    affiliation: University of Exeter Business School
+    orcid: https://orcid.org/0009-0000-0252-560X
 repository-code: 'https://github.com/pythonhealthdatascience/des_rap_book'
 abstract: >-
   Step-by-step guide for building Python and R simulation
diff --git a/_quarto.yml b/_quarto.yml
@@ -65,6 +65,7 @@ website:
       - pages/verification_validation/verification_validation.qmd
       - pages/verification_validation/tests.qmd
       - pages/verification_validation/mathematical.qmd
+      - pages/verification_validation/quality_assurance.qmd
     - section: "Style & documentation"
       contents:
       - pages/style_docs/linting.qmd
diff --git a/index.qmd b/index.qmd
@@ -21,7 +21,7 @@ This practical guide shows you how to build **reproducible** discrete-event simu
 
 ![](pages/intro/rap_resources/rap.png)
 
-This resource is an output of **STARS**, a research project led by Associate Prof. **Tom Monks** [![ORCID](images/orcid.png)](https://orcid.org/0000-0003-2631-4481). The book is written by **Amy Heather** [![ORCID](images/orcid.png)](https://orcid.org/0000-0002-6596-3479) and reviewed by Prof. **Nav Mustafee** [![ORCID](images/orcid.png)](https://orcid.org/0000-0002-2204-8924), Dr. **Alison Harper** [![ORCID](images/orcid.png)](https://orcid.org/0000-0001-5274-5037), and Associate Prof. **Tom Monks** [![ORCID](images/orcid.png)](https://orcid.org/0000-0003-2631-4481). The STARS project is supported by the Medical Research Council [grant number MR/Z503915/1]. The listed researchers are associated with the **University of Exeter** Medical and Business Schools.
+This resource is an output of **STARS**, a research project led by Associate Prof. **Tom Monks** [![ORCID](images/orcid.png)](https://orcid.org/0000-0003-2631-4481). The book is written by **Amy Heather** [![ORCID](images/orcid.png)](https://orcid.org/0000-0002-6596-3479) and reviewed by Prof. **Nav Mustafee** [![ORCID](images/orcid.png)](https://orcid.org/0000-0002-2204-8924), Dr. **Alison Harper** [![ORCID](images/orcid.png)](https://orcid.org/0000-0001-5274-5037), Associate Prof. **Tom Monks** [![ORCID](images/orcid.png)](https://orcid.org/0000-0003-2631-4481), and **Fatemeh Alidoost** [![ORCID](images/orcid.png)](https://orcid.org/0009-0000-0252-560X). The STARS project is supported by the Medical Research Council [grant number MR/Z503915/1]. The listed researchers are associated with the **University of Exeter** Medical and Business Schools.
 
 > *Please **cite** us if you use this resource!*
 >
diff --git a/pages/_metadata.yml b/pages/_metadata.yml
@@ -0,0 +1,2 @@
+language:
+  title-block-published: "Page last modified"
diff --git a/pages/experiments/full_run.qmd b/pages/experiments/full_run.qmd
@@ -1,8 +1,6 @@
 ---
 title: Full run
 date: "2025-10-03T15:54:56+01:00"
-language:
-  title-block-published: "Page last modified"
 ---
 
 :::: {.pale-blue}
diff --git a/pages/experiments/scenarios.qmd b/pages/experiments/scenarios.qmd
@@ -2,8 +2,6 @@
 title: Scenario and sensitivity analysis
 bibliography: scenarios_resources/references.bib
 date: "2025-11-06T10:44:04+00:00"
-language:
-  title-block-published: "Page last modified"
 ---
 
 {{< include ../../scripts/_reticulate-setup.md >}}
diff --git a/pages/experiments/tables_figures.qmd b/pages/experiments/tables_figures.qmd
@@ -2,8 +2,6 @@
 title:  Tables and figures
 bibliography: scenarios_resources/references.bib
 date: "2025-10-24T10:55:25+01:00"
-language:
-  title-block-published: "Page last modified"
 ---
 
 {{< include ../../scripts/_reticulate-setup.md >}}
diff --git a/pages/further_info/conclusion.qmd b/pages/further_info/conclusion.qmd
@@ -1,8 +1,6 @@
 ---
 title: Conclusion
 date: "2025-11-05T11:44:20+00:00"
-language:
-  title-block-published: "Page last modified"
 ---
 
 <!-- Hide as no python-content or r-content blocks -->
diff --git a/pages/further_info/feedback.qmd b/pages/further_info/feedback.qmd
@@ -1,8 +1,6 @@
 ---
 title: Feedback
 date: "2025-10-24T14:38:09+01:00"
-language:
-  title-block-published: "Page last modified"
 ---
 
 <br>
@@ -34,13 +32,12 @@ All contributions are acknowledged in the README via the all-contributors system
 
 ## Contact information
 
-Prefer email instead? Reach out to the STARS team:
+Prefer email instead? Reach out to the STARS team - you can contact:
 
 * Amy Heather: [a.heather2@exeter.ac.uk](mailto:a.heather2@exeter.ac.uk)
 * Tom Monks: [t.m.w.monks@exeter.ac.uk](mailto:t.m.w.monks@exeter.ac.uk)
 * Alison Harper: [a.l.harper@exeter.ac.uk](mailto:a.l.harper@exeter.ac.uk)
 * Nav Mustafee: [n.mustafee@exeter.ac.uk](mailto:n.mustafee@exeter.ac.uk)
-* Andy Mayne: [andrew.mayne@somersetft.nhs.uk](mailto:andrew.mayne@somersetft.nhs.uk)
 
 This book is part of the **STARS (Sharing Tools and Artefacts for Reusable and Reproducible Simulations)** project, supported by the Medical Research Council.
 
diff --git a/pages/inputs/input_data.qmd b/pages/inputs/input_data.qmd
@@ -1,8 +1,6 @@
 ---
 title: Input data management
 date: "2025-10-13T15:40:55+01:00"
-language:
-  title-block-published: "Page last modified"
 ---
 
 <!-- Hide as no python-content or r-content blocks -->
diff --git a/pages/inputs/input_modelling.qmd b/pages/inputs/input_modelling.qmd
@@ -3,8 +3,6 @@ title: Input modelling
 output: html
 bibliography: input_modelling_resources/references.bib
 date: "2025-11-03T14:30:28+00:00"
-language:
-  title-block-published: "Page last modified"
 ---
 
 {{< include ../../scripts/_reticulate-setup.md >}}
diff --git a/pages/inputs/parameters_file.qmd b/pages/inputs/parameters_file.qmd
@@ -1,8 +1,6 @@
 ---
 title: Parameters from file
 date: "2025-11-06T10:43:42+00:00"
-language:
-  title-block-published: "Page last modified"
 ---
 
 {{< include ../../scripts/_reticulate-setup.md >}}
diff --git a/pages/inputs/parameters_script.qmd b/pages/inputs/parameters_script.qmd
@@ -1,8 +1,6 @@
 ---
 title: Parameters from script
 date: "2025-10-06T09:31:01+01:00"
-language:
-  title-block-published: "Page last modified"
 ---
 
 :::: {.pale-blue}
@@ -74,7 +72,7 @@ This makes it very difficult to change the values. Modellers might choose to...
 
 This involves manually changing parameter values in the script each time you want to run a new scenario. Problems with this approach include:
 
-* ❌ **Not a reproducible analytical pipeline**. Alot of manual intervention is required to re-run the model with different parameters.
+* ❌ **Not a reproducible analytical pipeline**. A lot of manual intervention is required to re-run the model with different parameters.
 * ❌ **Error-prone**. It would be easy to make mistakes or forget to update all relevant values.
 * ❌ **Parameters can get lost**. If you lost your notes or forget to record what you used, you won't know what values were used for past runs. 
 
diff --git a/pages/inputs/parameters_validation.qmd b/pages/inputs/parameters_validation.qmd
@@ -1,8 +1,6 @@
 ---
 title: Parameter validation
 date: "2025-11-03T10:48:30+00:00"
-language:
-  title-block-published: "Page last modified"
 ---
 
 {{< include ../../scripts/_reticulate-setup.md >}}
diff --git a/pages/intro/des.qmd b/pages/intro/des.qmd
@@ -2,8 +2,6 @@
 title: Discrete-event simulation (DES)
 bibliography: des_resources/references.bib
 date: "2025-10-23T16:24:23+01:00"
-language:
-  title-block-published: "Page last modified"
 ---
 
 <!-- Hide as no python-content or r-content blocks -->
diff --git a/pages/intro/examples.qmd b/pages/intro/examples.qmd
@@ -1,8 +1,6 @@
 ---
 title: Example conceptual models
 date: "2025-09-29T11:24:36+01:00"
-language:
-  title-block-published: "Page last modified"
 ---
 
 <!-- Hide as no python-content or r-content blocks -->
diff --git a/pages/intro/foss.qmd b/pages/intro/foss.qmd
@@ -1,8 +1,6 @@
 ---
 title: Open-source languages
 date: "2025-09-29T10:35:18+01:00"
-language:
-  title-block-published: "Page last modified"
 ---
 
 <!-- Hide as no python-content or r-content blocks -->
diff --git a/pages/intro/guidelines.qmd b/pages/intro/guidelines.qmd
@@ -4,8 +4,6 @@ format:
   html:
     css: guidelines_resources/guidelines_style.css
 date: "2025-10-23T14:21:39+01:00"
-language:
-  title-block-published: "Page last modified"
 ---
 
 <!-- Hide as no python-content or r-content blocks -->
diff --git a/pages/intro/rap.qmd b/pages/intro/rap.qmd
@@ -1,8 +1,6 @@
 ---
 title: Reproducibility and RAPs
 date: "2025-09-29T10:35:18+01:00"
-language:
-  title-block-published: "Page last modified"
 ---
 
 <!-- Hide as no python-content or r-content blocks -->
@@ -50,7 +48,7 @@ language:
 
 * ✅ **Time**. Even if you retain access to your code, failure to record exact parameters for every scenario or document the computational environment used, for example, could make the code non-reproducible when revisited, even if only a few months later. Troubleshooting non-reproducible code can be **time-consuming** or even **impossible** if required information is lost.
 
-Many of these advantages apply regardless fo whether code is shared publicly or remains proprietary.
+Many of these advantages apply regardless of whether code is shared publicly or remains proprietary.
 
 #### Advantages for others
 
diff --git a/pages/model/distributions.qmd b/pages/model/distributions.qmd
@@ -1,8 +1,6 @@
 ---
 title: Randomness
 date: "2025-11-05T14:14:21+00:00"
-language:
-  title-block-published: "Page last modified"
 ---
 
 {{< include ../../scripts/_reticulate-setup.md >}}
diff --git a/pages/model/logs.qmd b/pages/model/logs.qmd
@@ -3,8 +3,6 @@ title: Logging
 filters:
   - line-highlight
 date: "2025-11-03T10:48:30+00:00"
-language:
-  title-block-published: "Page last modified"
 ---
 
 {{< include ../../scripts/_reticulate-setup.md >}}
@@ -1371,6 +1369,10 @@ class Model:
             time_with_doctor = self.consult_dist.sample()
             yield self.env.timeout(time_with_doctor)
 
+            # Log end time
+            self.logger.log(msg=f"Patient {patient.patient_id} leaves.",
+                            sim_time=self.env.now)
+
     def run(self):
         """
         Run the simulation.
diff --git a/pages/model/logs_resources/python_log_example.log b/pages/model/logs_resources/python_log_example.log
@@ -19,16 +19,21 @@
 16.468: Patient 1 starts consultation.
 20.283: Patient 2 arrives.
 20.283: Patient 2 starts consultation.
+24.103: Patient 2 leaves.
+24.499: Patient 1 leaves.
 26.545: Patient 3 arrives.
 26.545: Patient 3 starts consultation.
 27.675: Patient 4 arrives.
 27.675: Patient 4 starts consultation.
 28.779: Patient 5 arrives.
 28.779: Patient 5 starts consultation.
+30.187: Patient 3 leaves.
+32.970: Patient 4 leaves.
 37.778: Patient 6 arrives.
 37.778: Patient 6 starts consultation.
 38.108: Patient 7 arrives.
 38.108: Patient 7 starts consultation.
 42.611: Patient 8 arrives.
 44.088: Patient 9 arrives.
+47.598: Patient 7 leaves.
 47.598: Patient 8 starts consultation.
diff --git a/pages/model/patients.qmd b/pages/model/patients.qmd
@@ -3,8 +3,6 @@ title: Entity generation
 filters:
   - line-highlight
 date: "2025-11-05T14:48:51+00:00"
-language:
-  title-block-published: "Page last modified"
 ---
 
 {{< include ../../scripts/_reticulate-setup.md >}}
diff --git a/pages/model/process.qmd b/pages/model/process.qmd
@@ -3,8 +3,6 @@ title: Entity processing
 filters:
   - line-highlight
 date: "2025-10-16T11:08:48+01:00"
-language:
-  title-block-published: "Page last modified"
 ---
 
 {{< include ../../scripts/_reticulate-setup.md >}}
diff --git a/pages/output_analysis/length_warmup.qmd b/pages/output_analysis/length_warmup.qmd
@@ -4,8 +4,6 @@ filters:
   - line-highlight
 bibliography: length_warmup_resources/references.bib
 date: "2025-11-05T11:21:31+00:00"
-language:
-  title-block-published: "Page last modified"
 ---
 
 {{< include ../../scripts/_reticulate-setup.md >}}
diff --git a/pages/output_analysis/n_reps.qmd b/pages/output_analysis/n_reps.qmd
@@ -3,8 +3,6 @@ title: Number of replications
 filters:
   - line-highlight
 date: "2025-11-05T11:32:15+00:00"
-language:
-  title-block-published: "Page last modified"
 ---
 
 {{< include ../../scripts/_reticulate-setup.md >}}
@@ -82,7 +80,7 @@ library(tidyr)
 
 When running your simulation model, each replication will give a slightly different result because of randomness. To get a reliable estimate of any performance measure (such as average waiting time), you run the simulation multiple times and take the average across all these runs.
 
-**How many replications should you run?** If you run **too few**, your average could jump around alot with varying seeds, making your result unstable and unreliable. If you run **too many**, it will take a long time and use more computing resources than needed. To find a sensible balance, we can use the **confidence interval method**.
+**How many replications should you run?** If you run **too few**, your average could jump around a lot with varying seeds, making your result unstable and unreliable. If you run **too many**, it will take a long time and use more computing resources than needed. To find a sensible balance, we can use the **confidence interval method**.
 
 Choice of an appropriate number of replications forms part of your model experimentation validation (see [verification and validation](../verification_validation/verification_validation.qmd#experimentation-validation) page).
 
diff --git a/pages/output_analysis/outputs.qmd b/pages/output_analysis/outputs.qmd
@@ -3,8 +3,6 @@ title: Performance measures
 filters:
   - line-highlight
 date: "2025-11-05T11:21:31+00:00"
-language:
-  title-block-published: "Page last modified"
 ---
 
 {{< include ../../scripts/_reticulate-setup.md >}}
diff --git a/pages/output_analysis/parallel.qmd b/pages/output_analysis/parallel.qmd
@@ -3,8 +3,6 @@ title: Parallel processing
 filters:
   - line-highlight
 date: "2025-11-05T11:21:31+00:00"
-language:
-  title-block-published: "Page last modified"
 ---
 
 {{< include ../../scripts/_reticulate-setup.md >}}
diff --git a/pages/output_analysis/replications.qmd b/pages/output_analysis/replications.qmd
@@ -3,8 +3,6 @@ title: Replications
 filters:
   - line-highlight
 date: "2025-11-05T11:21:31+00:00"
-language:
-  title-block-published: "Page last modified"
 ---
 
 {{< include ../../scripts/_reticulate-setup.md >}}
diff --git a/pages/output_analysis/warmup.qmd b/pages/output_analysis/warmup.qmd
@@ -3,8 +3,6 @@ title: Initialisation bias
 filters:
   - line-highlight
 date: "2025-11-03T10:48:30+00:00"
-language:
-  title-block-published: "Page last modified"
 ---
 
 {{< include ../../scripts/_reticulate-setup.md >}}
diff --git a/pages/project/stars.qmd b/pages/project/stars.qmd
@@ -1,8 +1,6 @@
 ---
 title: STARS
 date: "2025-10-24T10:55:46+01:00"
-language:
-  title-block-published: "Page last modified"
 ---
 
 <!-- Hide as no python-content or r-content blocks -->
diff --git a/pages/setup/code_structure.qmd b/pages/setup/code_structure.qmd
@@ -1,8 +1,6 @@
 ---
 title: Code organisation
 date: "2025-09-30T14:35:31+01:00"
-language:
-  title-block-published: "Page last modified"
 ---
 
 {{< include ../../scripts/_reticulate-setup.md >}}
diff --git a/pages/setup/environment.qmd b/pages/setup/environment.qmd
@@ -4,8 +4,6 @@ format:
   html:
     css: ../../styles/wrap_code.css
 date: "2025-11-06T10:01:59+00:00"
-language:
-  title-block-published: "Page last modified"
 ---
 
 :::: {.pale-blue}
diff --git a/pages/setup/package.qmd b/pages/setup/package.qmd
@@ -1,8 +1,6 @@
 ---
 title: Structuring as a package
 date: "2025-11-06T10:26:08+00:00"
-language:
-  title-block-published: "Page last modified"
 ---
 
 ::: {.pale-blue}
diff --git a/pages/setup/version.qmd b/pages/setup/version.qmd
@@ -1,8 +1,6 @@
 ---
 title: Version control
 date: "2025-09-29T10:35:18+01:00"
-language:
-  title-block-published: "Page last modified"
 ---
 
 ::: {.pale-blue}
diff --git a/pages/sharing/archive.qmd b/pages/sharing/archive.qmd
@@ -1,8 +1,6 @@
 ---
 title: Sharing and archiving
 date: "2025-11-03T09:11:34+00:00"
-language:
-  title-block-published: "Page last modified"
 ---
 
 ::: {.pale-blue}
diff --git a/pages/sharing/changelog.qmd b/pages/sharing/changelog.qmd
@@ -1,8 +1,6 @@
 ---
 title: Changelog
 date: "2025-09-29T10:35:18+01:00"
-language:
-  title-block-published: "Page last modified"
 ---
 
 ::: {.pale-blue}
diff --git a/pages/sharing/citation.qmd b/pages/sharing/citation.qmd
diff --git a/pages/sharing/licence.qmd b/pages/sharing/licence.qmd
diff --git a/pages/sharing/peer_review.qmd b/pages/sharing/peer_review.qmd
diff --git a/pages/style_docs/docstrings.qmd b/pages/style_docs/docstrings.qmd
diff --git a/pages/style_docs/documentation.qmd b/pages/style_docs/documentation.qmd
diff --git a/pages/style_docs/github_actions.qmd b/pages/style_docs/github_actions.qmd
diff --git a/pages/style_docs/linting.qmd b/pages/style_docs/linting.qmd
diff --git a/pages/verification_validation/mathematical.qmd b/pages/verification_validation/mathematical.qmd
diff --git a/pages/verification_validation/quality_assurance.qmd b/pages/verification_validation/quality_assurance.qmd
diff --git a/pages/verification_validation/quality_assurance_resources/qa.png b/pages/verification_validation/quality_assurance_resources/qa.png
diff --git a/pages/verification_validation/quality_assurance_resources/qa.svg b/pages/verification_validation/quality_assurance_resources/qa.svg
diff --git a/pages/verification_validation/tests.qmd b/pages/verification_validation/tests.qmd
diff --git a/pages/verification_validation/verification_validation.qmd b/pages/verification_validation/verification_validation.qmd

Original file line number	Diff line number	Diff line change
`@@ -21,7 +21,7 @@ This practical guide shows you how to build reproducible discrete-event simu`
`21`	`21`
`22`	`22`	`![](pages/intro/rap_resources/rap.png)`
`23`	`23`
`24`		-This resource is an output of STARS, a research project led by Associate Prof. Tom Monks [![ORCID](images/orcid.png)](https://orcid.org/0000-0003-2631-4481). The book is written by Amy Heather [![ORCID](images/orcid.png)](https://orcid.org/0000-0002-6596-3479) and reviewed by Prof. Nav Mustafee [![ORCID](images/orcid.png)](https://orcid.org/0000-0002-2204-8924), Dr. Alison Harper [![ORCID](images/orcid.png)](https://orcid.org/0000-0001-5274-5037), and Associate Prof. Tom Monks [![ORCID](images/orcid.png)](https://orcid.org/0000-0003-2631-4481). The STARS project is supported by the Medical Research Council [grant number MR/Z503915/1]. The listed researchers are associated with the University of Exeter Medical and Business Schools.
	`24`	+This resource is an output of STARS, a research project led by Associate Prof. Tom Monks [![ORCID](images/orcid.png)](https://orcid.org/0000-0003-2631-4481). The book is written by Amy Heather [![ORCID](images/orcid.png)](https://orcid.org/0000-0002-6596-3479) and reviewed by Prof. Nav Mustafee [![ORCID](images/orcid.png)](https://orcid.org/0000-0002-2204-8924), Dr. Alison Harper [![ORCID](images/orcid.png)](https://orcid.org/0000-0001-5274-5037), Associate Prof. Tom Monks [![ORCID](images/orcid.png)](https://orcid.org/0000-0003-2631-4481), and Fatemeh Alidoost [![ORCID](images/orcid.png)](https://orcid.org/0009-0000-0252-560X). The STARS project is supported by the Medical Research Council [grant number MR/Z503915/1]. The listed researchers are associated with the University of Exeter Medical and Business Schools.
`25`	`25`
`26`	`26`	`> Please cite* us if you use this resource!*`
`27`	`27`	`>`
Original file line number	Diff line number	Diff line change
`@@ -0,0 +1,2 @@`
	`1`	`+language:`
	`2`	`+ title-block-published: "Page last modified"`