sdmTMB

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Add vignette on residuals / diagnostics

1

Specifically thinking about spatial and spatial residuals and updating plots in `vista`. Will work on this soon. Could be standalone or folded into other vignettes

ericward-noaa

Add and document ggeffects ggpredict support

6

Moving discussion here to its own thread. - `ggeffects::ggeffect()` (marginal effects based on the fixed effect covariance matrix, doesn't work for splines or breakpoints) was already working in the 'dev'...

seananderson

Add vignette on forecasting

6

jindivero

Add unit testing against VAST

3

Will have to be outside the usual testthat folder (for now in a folder in `inst`?) or skipped in all but local runs, which might be ideal assuming it doesn't...

seananderson

Make predict work with newdata not expanded by time

1

In cases where newdata is the same for all time slices and is large, it would save memory and speed (faster MakeADFun call) if newdata didn't have to be expanded...

seananderson

even when type = "link"

ecophilina

ecophilina

Make vignette on modelling presence-only data

7

Base it off of @ericward-noaa 's example: https://pbs-assess.github.io/sdmTMB-teaching/noaa-psaw-2022/06-presence-only.html#1 https://github.com/pbs-assess/sdmTMB-teaching/blob/main/noaa-psaw-2022/06-presence-only.Rmd

seananderson

Inspiration in VAST: https://github.com/James-Thorson-NOAA/VAST/blob/7a9a3f7b84227fb41ab027ea3312df13c2035ff6/R/project_model.R Can probably build this off `sdmTMB_simulate()`. Requires extending the parameter object and re-running MakeADFun, then simulate. Faster than if done during fitting with `extra_time`.

seananderson

Add tmbstan examples, vignette, and predict function

1

Probably needs a prediction helper function to pass the posterior samples through the `obj$report()` function as is done in the predict function for the joint precision matrix simulation. Should also...

seananderson