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BiologicalRecordsCentre / sparta

Species Presence/Absence R Trends Analyses
http://biologicalrecordscentre.github.io/sparta/index.html
MIT License
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Harmonizing the parameter names in BUGS wrt literature #78

Open drnickisaac opened 6 years ago

drnickisaac commented 6 years ago

Presently, the state model year effect are referred to as "a" in the BUGS code but "b" in the literature. This is very confusing because the detection model year effect is referred to as "a" in teh literature (but alpha.p in the BUGS code. I'd like to rename the "a" terms in getModelFile.R as "b". I'd like @GPowney and @CharlieOuthwaite to identify what downstream impacts this would have. Do you ever use the "a" parameters from the BUGS output?

AugustT commented 5 years ago

I can foresee that changing all these names could cause all sorts of problems. This doesn't mean we shouldn't do it, just be careful when we do.

galinajonsson commented 5 years ago

Changing the parameter names ("a" to "b" + "alpha.p" to "a") will NOT affect: plot.occDet() as this function uses the occupancy parameter outputs (referred to as "psi.fs")

AugustT commented 5 years ago

This might effect the initial values function getInitialValues and get getParameters - Check these

galinajonsson commented 5 years ago

Below are the lines of occDetFunc that will need to be changed if the terms are renamed:

https://github.com/BiologicalRecordsCentre/sparta/blob/46e9d8bef799fee3d781f8ce4695f2a66c33da1f/R/occDetFunc.r#L454-L459

galinajonsson commented 5 years ago

There is nothing to change for getBugsData or getInitValues.

For getModelFile:

For getObsModel: