Make workflow showing how to use other POLYMOD-alike contact data sources (contact surveys) with conmat

[njtierney]

Add to the vignette "Using other data sources"

Potentially add a new class of data that helps define a contact survey.

[njtierney]

For example, there are existing surveys listed in socialmixr, which get the social contact surveys that can then be used - see https://zenodo.org/communities/social_contact_data?q=&l=list&p=1&s=10&sort=newest

Some other TODOs on this topic:

• Use another survey from somewhere in Europe (a comparison point for POLYMOD)
• Another survey country from a country that has a different contact pattern to POLYMOD, e.g., Zambia, Indonesia, Singapore.
• Fit models using POLYMOD, POLYMOD-alike, and other country.
• Use those fitted models to then predict (create a contact matrix) to a country like Australia, and see how the contact matrices are different across different contact surveys. So we are keeping the "newdata" part of the prediction the same, and changing the models that are used.

Some notes about communication of this

• We step between model fitting and model prediction a lot in this, so it will be important to make it as clear as we can how those processes are different
• Potentially pre-compute the different models from the different surveys.
• Discuss some rules/heuristics on how to choose a contact survey that will might be best for your country/population
• It will be important to discuss and explain to people why using models that are build on contact surveys that are quite different to their country (different meaning different contact/social patterns within a country).
• For example, using a model fit using the POLYMOD contact survey, which is based in Europe, on a multi generational population like Singapore, will probably give you quite different results to using a contact survey from Singapore. (see the paper,"Apparent structural changes in contact patterns during COVID-19 were driven by survey design and long-term demographic trends" for a discussion on this problem: https://arxiv.org/abs/2406.01639)

[njtierney]

To understand how POLYMOD data was transformed:

conmat/R/get_polymod_contact_data.R

Line 40 in 419c9ba

get_polymod_contact_data <- function(setting = c("all", "home", "work", "school", "other"),

[chitrams]

As of Monday, 25 Nov at 12:00

Next actions

• Incorporate the code into vignette to show how the different population structures impact the resulting contact matrix
  • But also put functions used back into the package (see Adding more contact surveys to conmat #175)
• Perhaps create flowchart of process so easier to grasp for users? To clearly distinguish between model fitting and model prediction throughout the process
• Finalise draft of other-data-sources.Rmd vignette

Questions

• Why are NGMs in the other-data-sources.Rmd vignette? Perhaps they would be better in another vignette of their own?
• What did Nick mean by "Potentially add a new class of data that helps define a contact survey."? Is this the same as Adding more contact surveys to conmat #175?

[chitrams]

Flowchart to add to vignette: