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PhilipMostert / PointedSDMs_Workshop

Workshop material for the PointedSDMs R package
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Marwah's comments of the PointedSDMs Workshop slides #4

Open marwah83 opened 1 week ago

marwah83 commented 1 week ago

In slides 2 1) what is the spatial effect? in specify spatial code? 2)  \lambda(s) = exp{\eta(s)}, : is eta(s) a Gaussian process? 3) Gaussian random field is it the joint distribution of the locations, which has normal(0,sigma)

In Slides 3 1) is the spatial field is just the Gaussian random field? 2) in slide Multispecies model structure: please organize the points in a meaningful way ( I could not understand it) 3)in slide Multispecies: Spatial field structure: a) what is independent spatial effect? b) what is common spatial effect(field)? c) what do you mean by copied spatial effect?

how the above(a,b,c) related to the slide Spatial field structure?

In slides 4 how the Spatial Effect Structures slide related to what is in slides 3 about the Spatial field structure?

PhilipMostert commented 1 week ago
  1. The spatial effect is included in the model to account for unmeasured covariates and potential spatial autocorrelation.
  2. eta(s) is the linear predictor of the process model, which includes spatial covariates and the spatial effect.
  3. Same as in 1. -- the GRF is assumed to be 0 mean with a Matérn covariance function.
  4. Yes, we were quite loose with terminology.
  5. Independent -- one spatial field per species
  6. Common -- one field for all species
  7. Copied -- using R-INLA's copy feature (ie term copied across different linear predictors, scaled by the beta term)
  8. Independent probably means "copy", common field means "shared", replicate means one field per species, but with shared hyperparameters (the maths describing the format of the spatial effects is in tutorial 3).
PhilipMostert commented 1 week ago

Hope that these answer your questions, I think it's also a good idea to play around the vignette 3 to see what these different settings mean with an actual example.