Updated NMG model

An updated NMG model for the COVID-19 pandemic in South Africa was released today and can be found at https://nmg-covid-19.sctechnology.co.za/. The model for the first time includes a herd immunity parameter that must be entered by the user. This parameter represents the percentage of the population that will be infected when the virus stops spreading in the population. A herd immunity parameter of 30% is used as the default in this updated model to reflect the experience of past pandemics. This reduces the forecast for total deaths at 61 600 for the pandemic in South Africa.  I discuss this change in more detail in an earlier blog that can be found at https://modellingcovid-19.blogspot.com/2020/05/herd-immunity-will-be-reached-sooner.html.

The NMG model is released with a web tool that allows the user to vary the input parameters.  A screenshot of the web tool is set out below:


The two key input parameters for the model are the reproduction number and the herd immunity parameter.  These parameters can be changed using the sliders above the first graph.  The outputs from the model are shown in the first graph, and the user can select from six output fields.

The model is calibrated for the confirmed cases and deaths reported to 10 May 2020, and the fit of the model to this experience is shown in the two smaller line graphs.  The shape of the model curve (determined by the reproduction number) is set using the confirmed cases experience, and the extent of under-reporting (of symptomatic lives) is set using the deaths reported experience.  The fit is updated each week using the experience reported to the previous Sunday.

The model can be run for South Africa as a whole or for each province separately.  The model is fit for an individual province by varying the seed values (day 1 values) for the exposed and symptomatic unreported lives only.  The shape of the model curve (determined by the reproduction number) is retained at the level fit to the experience for South Africa as a whole. 

Finally, there is a link to the NMG report that describes the workings of the model and a download button that allows the user to download key output fields for the model given the input parameters selected.

it would be great to get feedback on the web tool..


13 May 2020

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