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Mismatch between alpha_sd default in docs and in code #861

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zsusswein opened this issue Nov 20, 2024 · 1 comment · Fixed by #862
Closed

Mismatch between alpha_sd default in docs and in code #861

zsusswein opened this issue Nov 20, 2024 · 1 comment · Fixed by #862

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@zsusswein
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zsusswein commented Nov 20, 2024

Summary:
The docs list a prior of 0.05

EpiNow2/R/opts.R

Lines 461 to 463 in e9cb977

#' @param alpha_sd Numeric, defaults to 0.05. The standard deviation of the
#' magnitude parameter of the Gaussian process kernel. Can be tuned to adjust
#' how far alpha is allowed to deviate form its prior mean (`alpha_mean`).

and the code has a prior of 0.01

alpha_sd = 0.01,

Description:

Looks like this came from #856

EpiNow2 Version:
main


I'll open a PR to fix.

As an aside, I'd be very interested in seeing a vignette from #855. Our team at CFA are extensive users of EpiNow2. In our work, we turn the default alpha_sd prior down to 0.0075 and usually jump to adjusting the lengthscale prior in the case of divergences. We need to do more testing on both of those choices and would love guidance from the EpiNow2 team.

@jamesmbaazam
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Thanks for spotting this @zsusswein. Your PR is welcomed.

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2 participants