epiverse-trace / serofoi

Estimates the Force-of-Infection of a given pathogen from population based sero-prevalence studies
https://epiverse-trace.github.io/serofoi/
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zero foi truncated for some ages or years based on epi knowledge #192

Closed zmcucunuba closed 5 months ago

zmcucunuba commented 5 months ago

In the foi chunks, we need to incorporate something like a vector with zero-truncated values.

First example: HPV This is a sexually transmitted infection, so we should restrict FOI to 0 for ages before sexual debut.

Age Chunk Is_zero
1 1 yes
2 1 yes
3 … 1 yes
15 2 no

Second example: CHIK

Similarly, for time-varying models. An example of this is Chikungunya virus in the Americas. We have good evidence that it didn't circulate in the human population before 2010.

Year | Chunk | Is_zero

Year Chunk Is_zero
2000 1 yes
2001 1 yes
1 yes
2010 2 no

Tagging @ekamau ;)

zmcucunuba commented 5 months ago

This has been implemented in #190 in the function set_sero_model using the parameter foi_windows