agesocial: Country-specific social contacts and demography #303
adamkucharski
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Would be interested to hear thoughts from @sbfnk @finlaycampbell @nicholasdavies @kieshaprem @njtierney |
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Matrices from Prem et al. are packaged in contactdata. Is any functionality you need not available there? |
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Description
Epidemic scenario models often need country-specific demography and data on age-stratified social mixing, particularly if implemented as interactive dashboards where users select a country. In Epiverse package vignettes, contact matrices are currently pulled from available data in {socialmixr}. Alternatively, synethic matrices can be generated with packages like conmat.
However, other model implementations, such as covidm shiny app and simex have backend functions that import demography and projected contact matrices for a range of countries from Prem et al or contactdata that align with model structure (e.g. number of age classes), as well as pulling from alternative sources where available.
Given these are so commonly used, it could make sense to modularise this particular functionality for matrix-model alignment so that could be called by the various scenario models out there – either as a small package or a contribution to the above ones.
Typical end-users
Users of epidemics, finalsize, simulist, odin, seir etc.
Key potential collaborators
Maintainers of simex, socialmixr, conmat, contactdata
Inputs
Social mixing data and demographic statistics
Outputs
Age-specific social mixing matrix and demography vector
Imports
simex and covidm_shiny2 include the underlying data files, but would probably not be best suited as dependencies – instead, they could use this modularised functionality.
Used by
finalsize
epidemics
seir
Related projects
Usage
Additional comments
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