Merge pull request #98 from pythonhealthdatascience/dev

Dev

Author: amyheather

.all-contributorsrc

@@ -0,0 +1,4 @@
+{
+  "projectName": "des_rap_book",
+  "projectOwner": "pythonhealthdatascience"
+}

.flake8

@@ -6,6 +6,7 @@ per-file-ignores =
     parameters_file.py: E402,F811,E0102
     parameters_validation.py: F821
     replications.py: F401,F811,F821
+    pages/output_analysis/n_reps.py: E0602,F401,F821,W0611
     pages/output_analysis/outputs_resources/*.py:E261,E262,F821
     pages/output_analysis/replications_resources/*.py:E261,E262,F821
     pages/inputs/parameters_validation_resources/ParamClass.py: C0103

README.md

@@ -7,6 +7,7 @@
 ![Code licence](https://img.shields.io/badge/🛡️_Code_licence-MIT-8a00c2?style=for-the-badge&labelColor=gray)
 ![Text licence](https://img.shields.io/badge/🛡️_Text_licence-CC--BY--SA--4.0-b100cd?style=for-the-badge&labelColor=gray)
 [![ORCID](https://img.shields.io/badge/ORCID_Amy_Heather-0000--0002--6596--3479-A6CE39?style=for-the-badge&logo=orcid&logoColor=white)](https://orcid.org/0000-0002-6596-3479)
+[![All Contributors](https://img.shields.io/github/all-contributors/pythonhealthdatascience/des_rap_book?color=ee8449&style=for-the-badge)](#contributors)
 
 </div>
 
@@ -174,4 +175,17 @@ pre-commit install
 
 ## Funding
 
-This project is supported by the Medical Research Council [grant number [MR/Z503915/1](https://gtr.ukri.org/projects?ref=MR%2FZ503915%2F1)].
+This project is supported by the Medical Research Council [grant number [MR/Z503915/1](https://gtr.ukri.org/projects?ref=MR%2FZ503915%2F1)].
+
+<br>
+
+## Contributors
+
+<!-- ALL-CONTRIBUTORS-LIST:START - Do not remove or modify this section -->
+<!-- prettier-ignore-start -->
+<!-- markdownlint-disable -->
+
+<!-- markdownlint-restore -->
+<!-- prettier-ignore-end -->
+
+<!-- ALL-CONTRIBUTORS-LIST:END -->

_quarto.yml

@@ -55,7 +55,8 @@ website:
     - section: "Experimentation"
       contents:
       - pages/experiments/scenarios.qmd
-      - pages/experiments/sensitivity.qmd
+      - pages/experiments/tables_figures.qmd
+      - pages/experiments/full_run.qmd
     - section: "Verification & validation"
       contents:
       - pages/verification_validation/logs.qmd
@@ -67,10 +68,6 @@ website:
       - pages/style_docs/docstrings.qmd
       - pages/style_docs/documentation.qmd
       - pages/style_docs/github_actions.qmd
-    - section: "Reports & manuscripts"
-      contents:
-      - pages/reports/tables_figures.qmd
-      - pages/reports/full_run.qmd
     - section: "Collaboration & sharing"
       contents:
       - pages/sharing/peer_review.qmd

pages/experiments/full_run.qmd

@@ -0,0 +1,98 @@
+---
+title: ❌ Full run
+---
+
+:::: {.pale-blue}
+
+**Learning objectives:**
+
+* TODO
+
+**Relevant reproducibility guidelines:**
+
+* STARS Reproducibility Recommendations (⭐): Ensure model parameters are correct.
+* NHS Levels of RAP (🥈): Outputs are produced by code with minimal manual intervention.
+
+**Pre-reading:**
+
+TODO
+
+**Required packages:**
+
+TODO
+
+::::
+
+## Explore the example models
+
+<div class="h3-tight"></div>
+
+### Nurse visit simulation
+
+:::: {.python-content}
+
+{{< include ../../html/pydesrapmms.html >}}
+
+::: {.blue-table}
+| | |
+| - | - |
+| **Key files** | |
+| **What to look for?** | |
+| **Why it matters?** | |
+: {tbl-colwidths="[20,80]"}
+:::
+
+::::
+
+:::: {.r-content}
+
+{{< include ../../html/rdesrapmms.html >}}
+
+::: {.blue-table}
+| | |
+| - | - |
+| **Key files** | |
+| **What to look for?** | |
+| **Why it matters?** | |
+: {tbl-colwidths="[20,80]"}
+:::
+
+::::
+
+### Stroke pathway simulation
+
+:::: {.python-content}
+
+{{< include ../../html/pydesrapstroke.html >}}
+
+::: {.blue-table}
+| | |
+| - | - |
+| **Key files** | |
+| **What to look for?** | |
+| **Why it matters?** | |
+: {tbl-colwidths="[20,80]"}
+:::
+
+::::
+
+:::: {.r-content}
+
+{{< include ../../html/rdesrapstroke.html >}}
+
+::: {.blue-table}
+| | |
+| - | - |
+| **Key files** | |
+| **What to look for?** | |
+| **Why it matters?** | |
+: {tbl-colwidths="[20,80]"}
+:::
+
+::::
+
+## Test yourself
+
+<!--TODO-->
+
+<br><br>