Data

Tools

Indexes

Applications

Experiments

Open Source Science

https://github.com/alan-turing-institute/uatk-aspics

A new implementation of an epidimic microsimulation (based on https://github.com/Urban-Analytics/RAMP-UA)

https://github.com/alan-turing-institute/uatk-aspics

Science Score: 10.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ○
    codemeta.json file
  • ○
    .zenodo.json file
  • ○
    DOI references
  • ✓
    Academic publication links
    Links to: sciencedirect.com, zenodo.org
  • ○
    Academic email domains
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (11.5%) to scientific vocabulary
Last synced: 10 months ago · JSON representation

Repository

A new implementation of an epidimic microsimulation (based on https://github.com/Urban-Analytics/RAMP-UA)

Basic Info
  • Host: GitHub
  • Owner: alan-turing-institute
  • License: mit
  • Language: Jupyter Notebook
  • Default Branch: main
  • Homepage:
  • Size: 2.9 MB
Statistics
  • Stars: 4
  • Watchers: 3
  • Forks: 3
  • Open Issues: 5
  • Releases: 0
Created over 4 years ago · Last pushed over 3 years ago
Metadata Files
Readme License

README.md

Agent-based Simulation of ePIdemics at Country Scale (ASPICS) v0.1

DOI

The Agent-based Simulation of ePIdemics at Country Scale (ASPICS) models the spread of an epidemic within any area of England. It is an extension to the national level of an earlier model called DyME (Dynamic Microsimulation for epidemics), with improvements to some elements of the modelling and much faster runtimes. It is currently pre-calibrated to run a simulation of the COVID-19 virus.

Status

We aim for this repository to provide an easy-to-use code base for building similar research, but this is still in progress. File an issue if you're interested in building off this work.

  • [x] initialisation produces a snapshot for any study area
  • [x] basic simulation with the snapshot
  • [x] home-to-work commuting
  • [x] Tune model for BMI studies
  • [ ] calibration / validation
  • [ ] large-scale events

Lineage

The history of this project is as follows:

  1. DyME was originally written in R, then later converted to Python and OpenCL: https://github.com/Urban-Analytics/RAMP-UA
  2. The "ecosystem of digital twins" branch heavily refactored the code to support running in different study areas and added a new seeding and commuting modelling: https://github.com/Urban-Analytics/RAMP-UA/tree/Ecotwins-withCommuting
  3. The Python and OpenCL code for running the model was copied into this repository from https://github.com/dabreegster/RAMP-UA/commits/dcarlino_dev and further cleaned up

There are many contributors to the project through these different stages; the version control history can be seen on Github in the other repositories.

Owner

  • Name: The Alan Turing Institute
  • Login: alan-turing-institute
  • Kind: organization
  • Email: info@turing.ac.uk

The UK's national institute for data science and artificial intelligence.

GitHub Events

Total
Last Year

Issues and Pull Requests

Last synced: 10 months ago

All Time
  • Total issues: 16
  • Total pull requests: 12
  • Average time to close issues: 27 days
  • Average time to close pull requests: 8 days
  • Total issue authors: 4
  • Total pull request authors: 4
  • Average comments per issue: 1.88
  • Average comments per pull request: 1.67
  • Merged pull requests: 8
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 1
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 1
  • Pull request authors: 0
  • Average comments per issue: 0.0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • mfbenitezp (7)
  • dabreegster (6)
  • HSalat (2)
  • mhauru (1)
Pull Request Authors
  • mfbenitezp (5)
  • dabreegster (5)
  • griff-rees (1)
  • HSalat (1)
Top Labels
Issue Labels
Pull Request Labels

Dependencies

poetry.lock pypi
  • atomicwrites 1.4.0 develop
  • attrs 21.4.0 develop
  • black 22.3.0 develop
  • more-itertools 8.12.0 develop
  • mypy-extensions 0.4.3 develop
  • packaging 21.3 develop
  • pathspec 0.9.0 develop
  • pluggy 0.13.1 develop
  • py 1.11.0 develop
  • pyparsing 3.0.8 develop
  • pytest 5.4.3 develop
  • tomli 2.0.1 develop
  • wcwidth 0.2.5 develop
  • click 8.1.2
  • colorama 0.4.4
  • glfw 2.5.3
  • imgui 1.4.1
  • linetimer 0.1.5
  • numpy 1.22.3
  • pandas 1.4.2
  • platformdirs 2.5.1
  • protobuf 3.20.0
  • pyopencl 2022.1
  • pyopengl 3.1.6
  • python-dateutil 2.8.2
  • pytools 2022.1.3
  • pytz 2022.1
  • pyyaml 6.0
  • six 1.16.0
  • tqdm 4.64.0
  • typing-extensions 4.1.1
pyproject.toml pypi
  • black ^22.1.0 develop
  • pytest ^5.2 develop
  • PyOpenGL ^3.1.6
  • PyYAML ^6.0
  • click ^8.0.3
  • glfw ^2.4.0
  • imgui ^1.4.1
  • linetimer ^0.1.5
  • numpy ^1.22.3
  • pandas ^1.4
  • protobuf ^3.20.0
  • pyopencl ^2022.1
  • python ^3.8
  • tqdm ^4.62.3