Rate multipliers and IgG count #260
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Great work, a few small suggestions here! mportantly, might you be able to run the case study on a different country (as NZ) instead of Gilraltar? The gibraltar results were generated as a comparison to CovidSim for our original paper (publication pending) and covidsim doesn't have waning immunity!
| Matrix in the form of a dataframe | ||
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| waning_matrix =\ |
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This all seems quite complicated - can you document the maths of this process in the wiki, and link it here?
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@abbie-evans Can you add this link to this docstring so users can find it easily?
python_examples/gibraltar_example/simulation_outputs/without_intervention/age_stratify.png
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…abm into waning-immunity
…abm into waning-immunity
Co-authored-by: Kit Gallagher <[email protected]>
Co-authored-by: Kit Gallagher <[email protected]>
| Matrix in the form of a dataframe | ||
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| """ | ||
| waning_matrix =\ |
There was a problem hiding this comment.
@abbie-evans Can you add this link to this docstring so users can find it easily?
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@abbie-evans @mghosh00 Can you revisit this - the PR description said that you have updated the wiki to include all new parameters, but a quick search of the plain text shows this is not complete. All parameters should be documented on the wiki, with sources and an explanation of what each parameter is. Edit: For structured parameters (such as nested lists) you should also explain the structure of the data object. |
Summary
We have added the
RateMultiplier(so that individuals with waning immunity have different transition probabilities between statuses), implemented these into a waning transition matrix, and added theIgGFOIMultiplier(so that the force of infection is lessened for waning individuals) classes. We have also sourced parameters for theIgGFOIMultiplierclass from this paper by Lumley et al. as explained in the updated Parameters section of the wiki.Further work
Some parameters for
RateMultiplierhave been sourced, but we still need to find more to complete all transitions between states.Checklist
All new functions have docstrings in the correct style
I've verified the complete docs build locally without errors
I've maintained 100% coverage (please mention any 'no cover' annotations explicitly)
I've unit-tested all new methods directly
Breaking change (fix or feature that would cause existing functionality to change)
I have read the CONTRIBUTING document.
My code follows the code style of this project.
I have updated the wiki with new parameters/model functionality
Closing issues
Closes #254 and #256