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Merged
merged 28 commits into from
Feb 27, 2025
Merged

Amy #29

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85c15d9
fix(model): add error handling for results processing when there are …
amyheather Feb 11, 2025
3526aa1
tests(functional): add tests for extreme IAT, NaN, and sampled times
amyheather Feb 11, 2025
d40ead2
fix(exponential): add error handling for invalid mean
amyheather Feb 11, 2025
903be4a
tests(unit): add test for invalid exponential inputs
amyheather Feb 11, 2025
143d73c
refactor(choosing): split choosing parameters notebooks into three se…
amyheather Feb 12, 2025
1ee39a2
feat(replications): add automated method for rep number from sim-tools
amyheather Feb 12, 2025
ce122bc
style(replications): docstrings and linting
amyheather Feb 13, 2025
0a6b022
fix(summary_stats): no stdev/ci for n<3
amyheather Feb 13, 2025
91fa439
feat(replications): streamline confidence_interval_methods so complem…
amyheather Feb 13, 2025
7e1be58
fix/test(replications): wrote some tests, and made some adjustments t…
amyheather Feb 13, 2025
ce30a42
chore(replications): reran notebook to go with last commit
amyheather Feb 13, 2025
023219b
fix(replications): fixed confidence_interval_method and add test
amyheather Feb 13, 2025
1bb6cf4
tests(replication): add back tests for the replications.py objects
amyheather Feb 13, 2025
fe42a2d
refactor(replications): simplify OnlineStatistics
amyheather Feb 13, 2025
cf5efb4
refactor(replications): convert ReplicationsAlgorithm to check multip…
amyheather Feb 14, 2025
79839b9
tests(replications): add more unit tests
amyheather Feb 14, 2025
fd74877
feat(replications): convert maual methods to check multiple metrics
amyheather Feb 14, 2025
06a86c5
fix(replications): prevent bonus rep after limit hit
amyheather Feb 14, 2025
130aa77
tests(replications): update backtest data to multiple metrics
amyheather Feb 14, 2025
e6ee752
chore(general): linting, docstrings, standardisation, rerun, etc.
amyheather Feb 14, 2025
31cd660
feat(replications): add explanation of OnlineStatistics and Replicati…
amyheather Feb 14, 2025
842bbe5
fix(replications): ReplicationsAlgorithm now can run initial replicat…
amyheather Feb 26, 2025
7e4ca18
tests(replication): add test related to recent fix - that algorithm o…
amyheather Feb 26, 2025
bf81ec2
chore(docs): minor corrections to replications.py docstring and hsma_…
amyheather Feb 26, 2025
be7988a
tests(replication): add test for ReplicationsAlgorithm when initial r…
amyheather Feb 26, 2025
5df7a0c
docs(replications): add explanation of ReplicationsAlgorithm
amyheather Feb 27, 2025
183df48
tests(model): add extreme nurses test
amyheather Feb 27, 2025
9dff66e
chore(linting): lint replications.py
amyheather Feb 27, 2025
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18 changes: 9 additions & 9 deletions README.md
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Expand Up @@ -32,8 +32,6 @@ Table of contents:

## 📌  Introduction

<!--TODO: Add links to STARS, relevant publication, and https://github.com/pythonhealthdatascience/rap_des/ -->

This repository provides a template for building discrete-event simulation (DES) models in Python.

😊 **Simple:** Easy-to-follow code structure using [SimPy](https://simpy.readthedocs.io/en/latest/). Implements a simple M/M/s queueing model in which patients arrive, wait to see a nurse, have a consultation with the nurse and then leave. Follows a modular structure: uses object-oriented programming, with the simulation implemented through classes.
Expand All @@ -43,7 +41,7 @@ This repository provides a template for building discrete-event simulation (DES)
* ["Levels of RAP" framework](https://nhsdigital.github.io/rap-community-of-practice/introduction_to_RAP/levels_of_RAP/) from the NHS RAP Community of Practice (`docs/nhs_rap.md`).
* Recommendations from [Heather et al. 2025](https://doi.org/10.48550/arXiv.2501.13137) "*On the reproducibility of discrete-event simulation studies in health research: an empirical study using open models*" (`docs/heather_2025.md`).

🚀 **Extendable:** This template adapts from Sammi Rosser and Dan Chalk (2024) ["HSMA - the little book of DES"](https://github.com/hsma-programme/hsma6_des_book). The book includes additional advanced features that can be used to extend the model in this template, including:
🚀 **Extendable:** This template is partly adapted from Sammi Rosser and Dan Chalk (2024) ["HSMA - the little book of DES"](https://github.com/hsma-programme/hsma6_des_book). The book includes additional advanced features that can be used to extend the model in this template, including:

* Multiple activities
* Branching paths
Expand Down Expand Up @@ -247,10 +245,12 @@ repo/
The overall run time will vary depending on how the template model is used. A few example implementations are provided in `notebooks/` and the run times for these were:

* `analysis.ipynb` - 23s
* `choosing_parameters.ipynb` - 22s
* `choosing_cores.ipynb` - 21s
* `choosing_replications.ipynb` - 11s
* `choosing_warmup.ipynb` - 2s
* `generate_exp_results.ipynb` - 0s

<!--TODO: Add test times -->
<!--TODO: Update run times -->

These times were obtained on an Intel Core i7-12700H with 32GB RAM running Ubuntu 24.04.1 Linux.

Expand All @@ -268,10 +268,10 @@ You can also cite the GitHub repository:

Researcher details:

| Contributor | Role | ORCID | GitHub |
| --- | --- | --- | --- |
| Amy Heather | Author | [![ORCID: Heather](https://img.shields.io/badge/ORCID-0000--0002--6596--3479-brightgreen)](https://orcid.org/0000-0002-6596-3479) | https://github.com/amyheather |
| Tom Monks | Code review | [![ORCID: Monks](https://img.shields.io/badge/ORCID-0000--0003--2631--4481-brightgreen)](https://orcid.org/0000-0003-2631-4481) | https://github.com/TomMonks |
| Contributor | ORCID | GitHub |
| --- | --- | --- |
| Amy Heather | [![ORCID: Heather](https://img.shields.io/badge/ORCID-0000--0002--6596--3479-brightgreen)](https://orcid.org/0000-0002-6596-3479) | https://github.com/amyheather |
| Tom Monks | [![ORCID: Monks](https://img.shields.io/badge/ORCID-0000--0003--2631--4481-brightgreen)](https://orcid.org/0000-0003-2631-4481) | https://github.com/TomMonks |

<br>

Expand Down
2 changes: 1 addition & 1 deletion docs/hsma_changes.md
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@@ -1,6 +1,6 @@
# Changes from the HSMA model

This template model is adapted from Sammi Rosser and Dan Chalk (2024) HSMA - the little book of DES (https://github.com/hsma-programme/hsma6_des_book) (MIT Licence). It also uses an exponentional distribution class from Monks (2021) sim-tools: fundamental tools to support the simulation process in python (https://github.com/TomMonks/sim-tools) (MIT Licence).
This template model is based on a few sources - including: Sammi Rosser and Dan Chalk (2024) HSMA - the little book of DES (https://github.com/hsma-programme/hsma6_des_book) (MIT Licence).

This page explains some of the differences between the models in the HSMA book, and this template.

Expand Down
411 changes: 411 additions & 0 deletions images/replications_algorithm.drawio
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145 changes: 145 additions & 0 deletions images/replications_statistics.drawio
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