tlomodel

Epidemiology modelling framework for the Thanzi la Onse project

https://github.com/ucl/tlomodel

Science Score: 75.0%

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

  • CITATION.cff file
    Found CITATION.cff file
  • codemeta.json file
    Found codemeta.json file
  • .zenodo.json file
    Found .zenodo.json file
  • DOI references
    Found 3 DOI reference(s) in README
  • Academic publication links
    Links to: zenodo.org
  • Academic email domains
  • Institutional organization owner
    Organization ucl has institutional domain (www.ucl.ac.uk)
  • JOSS paper metadata
  • Scientific vocabulary similarity
    Low similarity (10.6%) to scientific vocabulary

Keywords

epidemiology health-economic-evaluation healthcare-systems individual-based-modelling simulation-modeling
Last synced: 6 months ago · JSON representation ·

Repository

Epidemiology modelling framework for the Thanzi la Onse project

Basic Info
  • Host: GitHub
  • Owner: UCL
  • License: mit
  • Language: Python
  • Default Branch: master
  • Homepage: https://www.tlomodel.org/
  • Size: 159 MB
Statistics
  • Stars: 28
  • Watchers: 6
  • Forks: 15
  • Open Issues: 249
  • Releases: 0
Topics
epidemiology health-economic-evaluation healthcare-systems individual-based-modelling simulation-modeling
Created almost 8 years ago · Last pushed 6 months ago
Metadata Files
Readme Contributing License Citation

README.md

Thanzi la Onse

Thanzi la Onse model

License DOI Tests status Checks status Documentation status

The Thanzi la Onse model (TLOmodel) is a part of the Thanzi la Onse (Health for All) Collaboration. Our fundamental aim is to develop the use of epidemiological and economic science to effect a step-change in the way that health priorities are addressed through policy interventions in low-income countries. We are doing this by developing a model that represents explicitly the generation of health gains in a population, which can be used to examine the effect of resource allocation, management and clinical practice, in order to contribute to informing decision-making.

Project team

TLOmodel is developed in a collaboration between:

It benefits from a close partnership between this team and the Ministry of Health, Malawi.

A full list of contributors is available in the documentation.

Acknowledgements

This work has been funded by grants from Wellcome, GCRF and UKRI.

Owner

  • Name: University College London
  • Login: UCL
  • Kind: organization
  • Email: rc-softdev@ucl.ac.uk

Citation (CITATION.cff)

# Author list automatically generated from contributors.yaml by running
#     python src/scripts/automation/update_citation.py
# Any manual updates to author list here may be overwritten
cff-version: 1.2.0
title: The Thanzi La Onse Model
doi: 10.5281/zenodo.10144015
message: If you use this software, please cite it using the metadata from this file.
type: software
authors:
- given-names: Timothy
  family-names: Hallett
  orcid: https://orcid.org/0000-0002-9681-0424
  affiliation: Imperial College London
  website: https://www.imperial.ac.uk/people/timothy.hallett
- given-names: Andrew
  family-names: Phillips
  orcid: https://orcid.org/0000-0003-2384-4807
  affiliation: University College London
  website: https://profiles.ucl.ac.uk/5430
- given-names: Asif
  family-names: Tamuri
  orcid: https://orcid.org/0000-0001-6633-3789
  affiliation: University College London
  website: https://www.homepages.ucl.ac.uk/~ucbtaut/
- given-names: Tim
  family-names: Colbourn
  orcid: https://orcid.org/0000-0002-6917-6552
  affiliation: University College London
  website: https://profiles.ucl.ac.uk/3084
- given-names: Joseph
  family-names: Collins
  orcid: https://orcid.org/0000-0003-4801-7218
  affiliation: University College London
  website: https://profiles.ucl.ac.uk/70734
- given-names: Iwona
  family-names: Hawryluk
  orcid: https://orcid.org/0000-0001-6919-4366
  affiliation: Imperial College London
  website: https://www.imperial.ac.uk/people/i.hawryluk19
- given-names: Britta
  family-names: Jewell
  orcid: https://orcid.org/0000-0003-4275-8509
  website: https://www.imperial.ac.uk/people/b.jewell
- given-names: Ines
  family-names: Li Lin
  orcid: https://orcid.org/0000-0002-1945-3208
  affiliation: University College London
- given-names: Tara
  family-names: Mangal
  orcid: https://orcid.org/0000-0001-9222-8632
  affiliation: Imperial College London
  website: https://www.imperial.ac.uk/people/t.mangal
- given-names: Robbie
  family-names: Manning-Smith
  orcid: https://orcid.org/0000-0002-9457-2821
  affiliation: University College London
- given-names: Sakshi
  family-names: Mohan
  orcid: https://orcid.org/0000-0002-1268-1769
  affiliation: University of York
  website: https://www.york.ac.uk/che/staff/research/sakshi-mohan/
- given-names: Wingston
  family-names: Ng'ambi
  orcid: https://orcid.org/0000-0003-3967-905X
  affiliation: Kamuzu University of Health Sciences
  website: https://www.linkedin.com/in/wingston-ng-ambi-7950707b
- given-names: Bingling
  family-names: She
  orcid: https://orcid.org/0000-0001-5976-8987
  affiliation: Imperial College London
  website: https://www.imperial.ac.uk/people/b.she
- given-names: Matthew
  family-names: Gillman
- given-names: Mosè
  family-names: Giordano
  orcid: https://orcid.org/0000-0002-7218-2873
  affiliation: University College London
  website: https://giordano.github.io/
- given-names: Matthew
  family-names: Graham
  orcid: https://orcid.org/0000-0001-9104-7960
  affiliation: University College London
  website: https://matt-graham.github.io
- given-names: Emmanuel
  family-names: Mnjowe
  affiliation: Kamuzu University of Health Sciences
  website: https://www.linkedin.com/in/emmanuel-mnjowe-067481162
- given-names: Stefan
  family-names: Piatek
  orcid: https://orcid.org/0000-0002-3028-5292
  affiliation: University College London
  website: https://profiles.ucl.ac.uk/67238
- given-names: Jonathan
  family-names: Cooper
  orcid: https://orcid.org/0000-0001-6009-3542
  affiliation: University College London
  website: https://profiles.ucl.ac.uk/59377
- given-names: Dimitra
  family-names: Salmanidou
  orcid: https://orcid.org/0000-0002-2147-0787
  affiliation: University College London
  website: https://www.researchgate.net/profile/Dimitra-Salmanidou
- given-names: William
  family-names: Graham
  orcid: https://orcid.org/0000-0003-0058-263X
  affiliation: University College London
  website: https://willgraham01.github.io/
- given-names: Margherita
  family-names: Molaro
  orcid: https://orcid.org/0000-0002-1841-4274
  affiliation: Imperial College London
- given-names: Eva
  family-names: Janoušková
  orcid: https://orcid.org/0000-0002-4104-0119
  affiliation: University College London
  website: https://profiles.ucl.ac.uk/90260
- given-names: Rachel
  family-names: Murray-Watson
  affiliation: Imperial College London
  orcid: https://orcid.org/0000-0001-9079-5975
repository-code: https://github.com/UCL/TLOmodel
url: https://tlomodel.org
abstract: Our fundamental aim is to develop the use of epidemiological and economic
  science to effect a step-change in the way that health priorities are addressed
  through policy interventions in low-income countries. We are doing this by developing
  a model that represents explicitly the generation of health gains in a population,
  which can be used to examine the effect of resource allocation, management and clinical
  practice, in order to contribute to informing decision-making.
keywords:
- Epidemiology
- Healthcare Systems
- Health-Economics
- Simulation Modelling
- Individual-based Modelling
license: MIT

GitHub Events

Total
  • Fork event: 11
  • Create event: 143
  • Release event: 3
  • Issues event: 113
  • Watch event: 14
  • Delete event: 258
  • Member event: 4
  • Issue comment event: 502
  • Push event: 1,354
  • Gollum event: 37
  • Pull request event: 190
  • Pull request review event: 372
  • Pull request review comment event: 388
Last Year
  • Fork event: 11
  • Create event: 143
  • Release event: 3
  • Issues event: 113
  • Watch event: 14
  • Delete event: 258
  • Member event: 4
  • Issue comment event: 502
  • Push event: 1,354
  • Gollum event: 37
  • Pull request event: 190
  • Pull request review event: 372
  • Pull request review comment event: 388

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 197
  • Total pull requests: 352
  • Average time to close issues: 12 months
  • Average time to close pull requests: about 2 months
  • Total issue authors: 22
  • Total pull request authors: 25
  • Average comments per issue: 2.19
  • Average comments per pull request: 2.55
  • Merged pull requests: 197
  • Bot issues: 0
  • Bot pull requests: 8
Past Year
  • Issues: 66
  • Pull requests: 133
  • Average time to close issues: 13 days
  • Average time to close pull requests: 11 days
  • Issue authors: 16
  • Pull request authors: 17
  • Average comments per issue: 0.86
  • Average comments per pull request: 1.11
  • Merged pull requests: 68
  • Bot issues: 0
  • Bot pull requests: 5
Top Authors
Issue Authors
  • tbhallett (50)
  • tamuri (30)
  • matt-graham (25)
  • EvaJanouskova (16)
  • mmsuarezcosta (12)
  • mnjowe (9)
  • joehcollins (9)
  • tdm32 (8)
  • marghe-molaro (7)
  • stefpiatek (5)
  • thewati (4)
  • jonc125 (4)
  • sakshimohan (4)
  • BinglingICL (3)
  • willGraham01 (3)
Pull Request Authors
  • tbhallett (60)
  • matt-graham (46)
  • tamuri (37)
  • tdm32 (29)
  • marghe-molaro (23)
  • willGraham01 (21)
  • EvaJanouskova (20)
  • joehcollins (19)
  • mnjowe (18)
  • sakshimohan (11)
  • RachelMurray-Watson (9)
  • stefpiatek (8)
  • dependabot[bot] (8)
  • andrew-phillips-1 (7)
  • thewati (7)
Top Labels
Issue Labels
framework (23) epi (17) enhancement (16) bug (15) performance (8) website (6) gh-actions (6) azure-batch (6) documentation (5) module (3) tests (3) question (3) good-for-new-starter (1) warning (1) dependencies (1)
Pull Request Labels
epi (8) dependencies (8) framework (6) bug (4) gh-actions (3) enhancement (2) github_actions (2) question (2) duplicate (1) health-econ (1) website (1) documentation (1) module (1)

Dependencies

.github/workflows/comment-triggered-ci.yml actions
.github/workflows/run-on-comment.yml actions
  • actions/checkout v3 composite
  • actions/github-script v6 composite
  • peter-murray/workflow-application-token-action e8782d687a306fb13d733244d0f2a50e272d3752 composite
deploy/Dockerfile docker
  • python 3.8-slim-buster build
docs/requirements.txt pypi
  • sphinx >=1.3
  • sphinx-rtd-theme *
requirements/base.txt pypi
  • adal ==1.2.6
  • azure-batch ==10.0.0
  • azure-common ==1.1.26
  • azure-core ==1.11.0
  • azure-identity ==1.5.0
  • azure-keyvault ==4.1.0
  • azure-keyvault-certificates ==4.2.1
  • azure-keyvault-keys ==4.3.1
  • azure-keyvault-secrets ==4.2.0
  • azure-storage-file-share ==12.4.1
  • certifi ==2020.12.5
  • cffi ==1.14.5
  • chardet ==4.0.0
  • click ==7.1.2
  • cryptography ==3.4.6
  • cycler ==0.10.0
  • et-xmlfile ==1.0.1
  • gitdb ==4.0.5
  • gitpython ==3.1.13
  • idna ==2.10
  • isodate ==0.6.0
  • jdcal ==1.4.1
  • kiwisolver ==1.3.1
  • matplotlib ==3.3.4
  • msal ==1.9.0
  • msal-extensions ==0.3.0
  • msrest ==0.6.21
  • msrestazure ==0.6.4
  • numpy ==1.20.1
  • oauthlib ==3.1.0
  • openpyxl ==3.0.6
  • pandas ==1.2.2
  • pillow ==8.1.0
  • portalocker ==1.7.1
  • pycparser ==2.20
  • pyjwt ==2.0.1
  • pyparsing ==2.4.7
  • pyshp ==2.3.0
  • python-dateutil ==2.8.1
  • pytz ==2021.1
  • requests ==2.25.1
  • requests-oauthlib ==1.3.0
  • scipy ==1.6.1
  • six ==1.15.0
  • smmap ==3.0.5
  • squarify ==0.4.3
  • urllib3 ==1.26.3
requirements/dev.txt pypi
  • adal ==1.2.6 development
  • appdirs ==1.4.4 development
  • attrs ==20.3.0 development
  • azure-batch ==10.0.0 development
  • azure-common ==1.1.26 development
  • azure-core ==1.11.0 development
  • azure-identity ==1.5.0 development
  • azure-keyvault ==4.1.0 development
  • azure-keyvault-certificates ==4.2.1 development
  • azure-keyvault-keys ==4.3.1 development
  • azure-keyvault-secrets ==4.2.0 development
  • azure-storage-file-share ==12.4.1 development
  • certifi ==2020.12.5 development
  • cffi ==1.14.5 development
  • chardet ==4.0.0 development
  • click ==7.1.2 development
  • cryptography ==3.4.6 development
  • cycler ==0.10.0 development
  • distlib ==0.3.1 development
  • et-xmlfile ==1.0.1 development
  • filelock ==3.0.12 development
  • gitdb ==4.0.5 development
  • gitpython ==3.1.13 development
  • idna ==2.10 development
  • iniconfig ==1.1.1 development
  • isodate ==0.6.0 development
  • jdcal ==1.4.1 development
  • kiwisolver ==1.3.1 development
  • matplotlib ==3.3.4 development
  • msal ==1.9.0 development
  • msal-extensions ==0.3.0 development
  • msrest ==0.6.21 development
  • msrestazure ==0.6.4 development
  • numpy ==1.20.1 development
  • oauthlib ==3.1.0 development
  • openpyxl ==3.0.6 development
  • packaging ==20.9 development
  • pandas ==1.2.2 development
  • pillow ==8.1.0 development
  • pip-tools ==5.5.0 development
  • pluggy ==0.13.1 development
  • portalocker ==1.7.1 development
  • py ==1.10.0 development
  • pycparser ==2.20 development
  • pyjwt ==2.0.1 development
  • pyparsing ==2.4.7 development
  • pyshp ==2.1.3 development
  • pytest ==6.2.2 development
  • python-dateutil ==2.8.1 development
  • pytz ==2021.1 development
  • requests ==2.25.1 development
  • requests-oauthlib ==1.3.0 development
  • scipy ==1.6.1 development
  • six ==1.15.0 development
  • smmap ==3.0.5 development
  • squarify ==0.4.3 development
  • toml ==0.10.2 development
  • tox ==3.22.0 development
  • urllib3 ==1.26.3 development
  • virtualenv ==20.4.2 development
.github/workflows/run-profiling.yaml actions
  • actions/checkout v3 composite
  • actions/download-artifact v3 composite
  • actions/upload-artifact v3 composite
  • dmnemec/copy_file_to_another_repo_action v1.1.1 composite
  • peter-evans/repository-dispatch v2 composite
.github/workflows/calibration.yaml actions
.github/workflows/checks.yml actions
  • actions/cache v3 composite
  • actions/checkout v4 composite
  • actions/setup-python v5 composite
.github/workflows/docs.yml actions
  • actions/cache v3 composite
  • actions/checkout v4 composite
  • actions/setup-python v5 composite
.github/workflows/tests.yml actions
  • actions/checkout v4 composite
pyproject.toml pypi
  • GitPython *
  • azure-batch *
  • azure-identity *
  • azure-keyvault *
  • azure-storage-file-share *
  • click *
  • matplotlib *
  • numpy *
  • openpyxl ==3.1.0
  • pandas ~=2.0.0
  • pyshp *
  • scipy *
  • squarify *