Update residual-checking.Rmd

pbs-assess / sdmTMB

:earth_americas: An R package for spatial and spatiotemporal GLMMs with TMB

https://pbs-assess.github.io/sdmTMB/

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Update residual-checking.Rmd #268

Open ericward-noaa opened 10 months ago

ericward-noaa commented 10 months ago

Added diagnostics for delta/presence-absence models: AUC, TSS

TSS addition motivated by discussion here: https://github.com/pbs-assess/sdmTMB/issues/84

It'd be easy to turn the TSS code into a function if it's more broadly useful

seananderson commented 10 months ago

Thanks - can you add pROC to .github/workflows/pkgdown.yaml in the extra packages for web-only vignettes? And maybe remove the extra spaces in roc <- pROC::roc( actual_values, plogis(pred$est) )?

I'm trying to decide if this fits with the residual checking vignette given it doesn't involve residuals. Would the cross-validation vignette be a more natural place maybe adding a quick example of AUC on the cross-validation predictions?

ericward-noaa commented 10 months ago

Deleted the spaces
I was hoping to avoid another dependency on pROC, so I made both the chunks that used it not evaluated (only 1 was off before, hence the warning)
I can go either way on using this here or in the cross validation. I think there's lots of examples of people using AUC on train or test data