1 # COVID-19 CovidSim Model
3 This is the COVID-19 CovidSim microsimulation model developed by the MRC Centre
4 for Global Infectious Disease Analysis hosted at Imperial College, London.
6 CovidSim models the transmission dynamics and severity of COVID-19 infections
7 throughout a spatially and socially structured population over time. It enables
8 modelling of how intervention policies and healthcare provision affect the
9 spread of COVID-19. With parameter changes, it can be used to model other
10 respiratory viruses, such as influenza.
14 :warning: This code is released with no support.
16 :warning: This model is in active development and so parameter name and
17 behaviours, and output file formats will change without notice.
19 :warning: The model is stochastic. Multiple runs with different seeds should be
20 undertaken to see average behaviour. This can now be done easily with the `/NR`
21 command line parameter. The model code behaves deterministically if run with the
22 same number of threads enabled and run with the same random number seends.
24 :warning: As with any mathematical model, it is easy to misconfigure inputs and
25 therefore get meaningless outputs. The Imperial College COVID-19 team only
26 endorses outputs it has itself generated.
30 This model is in active development and subject to significant code changes
33 - Enable modelling of more geographies
35 - Enable modelling of different intervention scenarios
41 The model is written in C++ and runs on Windows and Linux-based systems.
43 Running the model for the whole of the UK requires approximately 20GB of RAM.
44 Other regions will require different amounts of memory (some up to 256GB).
46 It is strongly recommended to build the model with OpenMP support enabled to
47 improve performance on multi-core processors. 24 to 32 core Xeon systems give
48 optimal performance for large (e.g. UK, US) populations.
50 See [build.md](./docs/build.md) for detailed build instructions.
54 From within your build directory do:
58 # If you want more progress indication
64 *IMPORTANT*: The test scripts use test data only are not runs reflective of
65 real-world situations.
69 The directory [data](./data) contains sample data.
71 The Python script [run_sample.py](./data/run_sample.py) demonstrates how to
72 invoke CovidSim to use this data. See the [sample README](./data/README.md) for
73 details on how to run the samples.
77 Model documentation can be found in the [docs](./docs) directory. Of
78 particular interest are:
80 - [Model Overview](./docs/model-overview.md)
81 - [Model Glossary](./docs/model-glossary.md)
82 - [Model Inputs and Outputs](./docs/inputs-and-outputs.md)
83 - [Interventions description](./docs/intervention-description.md)
84 - [R Scripts for Output Visualisation](./docs/inputs-and-outputs.md#r-summary-visualisations)
86 Given the entire Imperial College team is working full-time on the COVID-19
87 response, documentation is currently sparse. More documentation and sample files
88 will be added as time permits. In the coming few weeks this will include a much
89 more extensive set of input files to model strategies for exiting lockdown.
93 The following papers are relevant to the model. Please note that some of them
94 may require a subscription.
96 - <https://www.imperial.ac.uk/media/imperial-college/medicine/sph/ide/gida-fellowships/Imperial-College-COVID19-NPI-modelling-16-03-2020.pdf>
97 - <https://www.nature.com/articles/nature04795>
98 - <https://www.nature.com/articles/nature04017>
99 - <https://www.pnas.org/content/105/12/4639.short>
101 ## Copyright and Licensing
103 The source code for CovidSim is licensed under the GPLv3, see
104 [LICENSE.md](LICENSE.md).
106 It is Copyright Imperial College of Science, Technology and Medicine. The
107 lead developers are Neil Ferguson, Gemma Nedjati-Giliani and Daniel Laydon.
109 Additional contributions for open-sourcing made by Imperial College of
110 Science, Technology and Medicine, GitHub Inc, and John Carmack are copyright
113 Licensing details for material from other projects may be found in
114 [NOTICE.md](NOTICE.md). In summary:
116 CovidSim includes code modified from
117 [RANLIB](https://people.sc.fsu.edu/~jburkardt/c_src/ranlib/ranlib.html) which
118 is licensed under the LGPLv3.
120 Sample data in the repository has been derived from the following sources:
122 WorldPop (www.worldpop.org - School of Geography and Environmental Science,
123 University of Southampton; Department of Geography and Geosciences, University
124 of Louisville; Departement de Geographie, Universite de Namur) and Center for
125 International Earth Science Information Network (CIESIN), Columbia University
126 (2018). Global High Resolution Population Denominators Project - Funded by The
127 Bill and Melinda Gates Foundation (OPP1134076).
128 <https://dx.doi.org/10.5258/SOTON/WP00647>
130 WorldPop is licensed under the Creative Commons Attribution 4.0 International
131 License (CC BY 4.0). The text of the license can be found at:
132 <https://creativecommons.org/licenses/by/4.0/legalcode>
136 Due to time pressure on the development team, we are unable to provide user
137 support at this time.
139 If you find issues with the code please raise them in our
140 [Issue Tracker](https://github.com/mrc-ide/covid-sim/issues).
142 This repository has a code of conduct which is detailed in
143 [the code of conduct](./CODE_OF_CONDUCT.md). When raising an issue in this
144 repository you agree to abide by the code of conduct.