Sean Anderson

Here's a start based on the last report in rough order of importance. - [x] anisotropy with delta models - [x] sdmTMB_simulate() with IID or AR1 or RW fields -...

Release sdmTMB 0.1.0

1

First release: * [x] `usethis::use_cran_comments()` * [x] Update (aspirational) install instructions in README * [x] Proofread `Title:` and `Description:` * [x] Check that all exported functions have `@return` and `@examples`...

Only apply range part of PC matern prior once if range is shared

1

See this issue for more details: https://github.com/pbs-assess/sdmTMB/issues/95 The TMB code is there, it's just a matter of only applying the range part once if needed.

Update delta-model vignette to use new built-in delta functionality

4

Might as well still keep the illustration of fitting them independently as well. Include showing how to use `simulate()`, `residuals()`, `predict()`, `tidy()`, etc. while picking a model or using both...

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'...

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...

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...

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

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`.

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...