As discussed at ACEFA launch, we should be explicit in the docs about whether time-varying proportions are applied at the date of infection, or the date of observation. Given that might depend on the observation model and how the proportion was defined by the user, we should probably make it an option.
To have the proportion timeseries apply to infection dates, we would do:
expected <- convolution_matrix %*% (infections * proportion)
To have the timeseries apply to observation dates we would do:
expected <- (convolution_matrix %*% infections) * proportion
We currently don't have the parentheses which I think evaluates like the second one. I also think this should probably be the default, especially for things like DoW.
As discussed at ACEFA launch, we should be explicit in the docs about whether time-varying proportions are applied at the date of infection, or the date of observation. Given that might depend on the observation model and how the proportion was defined by the user, we should probably make it an option.
To have the proportion timeseries apply to infection dates, we would do:
To have the timeseries apply to observation dates we would do:
We currently don't have the parentheses which I think evaluates like the second one. I also think this should probably be the default, especially for things like DoW.