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Overhaul residuals vignette ('article') https://pbs-assess.github.io/sdmTMB/articles/web_only/residual-checking.html including brief intros to randomized quantile residuals, simulation-based residuals, 'one-sample' residuals, and uniform vs. Gaussian residuals.

Add check if prediction coordinates appear outside of fitted coordinates. #285

Fix memory issue with Tweedie family on large datasets. #302

Add experimental option to return standard normal residuals from dharma_residuals().

Make simulate.sdmTMB() not include extra_time elements.

Improved re-initialization of saved fitted model objects in new sessions.

Fix important bug in simulate.sdmTMB() method for delta families where the positive linear predictor was only getting simulated for observations present in the fitted data.

Add new "mle-mvn" type to residuals.sdmTMB() and make it the default. This is a fast option for evaluating goodness of fit that should be better than the previous default. See the details section in ?residuals.sdmTMB for details. The previous default is now called "mvn-eb" but is not recommended.

Bring dharma_residuals() back over from sdmTMBextra to sdmTMB. Add a new option in the type argument ("mle-mvn") that should make the simulation residuals consistent with the expected distribution. See the same new documentation in ?residuals.sdmTMB. The examples in ?dharma_residuals illustrate suggested use.

Fix bug in sanity() where gradient checks were missing abs() such that large negative gradients weren't getting caught. #324

Return offset vector in fitted object as an element. Ensure any extra time rows of data in the data element of the fitted object do not include the extra time slices.

Add experimental residuals option "mle-mvn" where a single approximate posterior sample of the random effects is drawn and these are combined with the MLE fixed effects to produce residuals. This may become the default option.

Add the generalized gamma distribution (thanks to J.T. Thorson with additional work by J.C. Dunic.) See gengamma(). This distribution is still in a testing phase and is not recommended for applied use yet. #286

Detect possible issue with factor(time) in formula if same column name is used for time and extra_time is specified. #320

Improve sanity() check output when there are NA fixed effect standard errors.

Set intern = FALSE within index bias correction, which seems to be considerably faster when testing with most models.

Fix a bug likely introduced in July 2023 that caused issues when extra_time was specified. This is an important bug and models fit with extra_time between that date (if using the GitHub version) and v0.4.2.9004 (2024-02-24) should be checked against a current version of sdmTMB (v0.4.2.9005 or greater). On CRAN, this affected v0.4.0 (2023-10-20) to v0.4.2. Details:

• The essence of the bug was that extra_time works by padding the data with a fake row of data for every extra time element (using the first row of data as the template). This is supposed to then be omitted from the likelihood so it has no impact on model fitting beyond spacing time-series processes appropriately and setting up internal structures for forecasting. Unfortunately, a bug was introduced that caused these fake data (1 per extra time element) to be included in the likelihood.

Issue error if time column has NAs. #298 #299

Fix bug in get_cog(..., format = "wide") where the time column was hardcoded to "year" by accident.

Poisson-link delta models now use a type argument in delta_gamma() and delta_lognormal(). delta_poisson_link_gamma() and delta_poisson_link_lognormal() are deprecated. #290

Delta families can now pass links that are different from the default "logit" and "log". #290

Force rebuild of CRAN binaries to fix issue with breaking Matrix ABI change causing NaN gradient errors. #288 #287

Fix crash in if sdmTMB(..., do_index = TRUE) and extra_time supplied along with predict_args = list(newdata = ...) that lacked extra_time elements.

Allow get_index() to work with missing time elements.

Add the ability to pass a custom randomized quantile function qres_func to residuals.sdmTMB().

Add check for factor random intercept columns in newdata to avoid a crash. #278 #280

Improve warnings/errors around use of do_index = TRUE and get_index() if newdata = NULL. #276

Fix prediction with offset when newdata is NULL but offset is specified. #274

Fix prediction failure when both offset and nsim are provided and model includes extra_time. #273

Fix memory issues detected by CRAN 'Additional issues' clang-UBSAN, valgrind.

Fix a bug predicting on new data with a specified offset and extra_time. #270

Add warning around non-factor handling of the spatial_varying formula. #269

Add experimental set_delta_model() for plotting delta models with ggeffects::ggpredict() (GitHub version only until next CRAN version).

Move add_barrier_mesh() to sdmTMBextra to avoid final INLA dependency. https://github.com/pbs-assess/sdmTMBextra

Switch to using the new fmesher package for all mesh/SPDE calculations. INLA is no longer a dependency.

Switch to diagonal.penalty = FALSE in mgcv::smoothCon(). This changes the scale of the linear component of the smoother, but should result in the same model. https://github.com/glmmTMB/glmmTMB/issues/928#issuecomment-1642862066

Implement cross validation for delta models #239

Remove ELPD from cross validation output. Use sum_loglik instead. #235

Turn on Newton optimization by default. #182

print() now checks sanity() and issues a warning if there may be issues. #176

Poisson-link delta models and censored likelihood distributions have been made considerably more robust. #186

Standard errors are now available on SD parameters etc. in tidy() #240

Fix bug in print()/tidy() for delta-model positive model component sigma_E. A recently introduce bug was causing sigma_E for the 2nd model to be reported as the 1st model component sigma_E.

Add new anisotropy plotting function.

Add anisotropic range printing. #149 by @jdunic

Create the sdmTMBextra package to remove rstan/tmbstan helpers, which were causing memory sanitizer errors on CRAN. https://github.com/pbs-assess/sdmTMBextra

The following functions are affected:

• predict.sdmTMB() now takes mcmc_samples, which is output from sdmTMBextra::extract_mcmc().
• simulate.sdmTMB() now takes mcmc_samples, which is output from sdmTMBextra::extract_mcmc().
• residuals.sdmTMB() now takes mcmc_samples, which is output sdmTMBextra::predict_mle_mcmc(). This only affects residuals(..., type = "mle-mcmc").

Move dharma_residuals() to sdmTMBextra to reduce heavy dependencies.

See examples in the Bayesian and residuals vignettes or in the help files for those functions within sdmTMBextra.

Various fixes to pass CRAN checks. #158

Fix memory issue highlighted by Additional issues CRAN checks. #158

'offset' argument can now be a character value indicating a column name. This is the preferred way of using an offset with parallel cross validation. #165

Fix parallel cross validation when using an offset vector. #165

Add leave-future-out cross validation functionality. #156

Example data qcs_grid is no longer replicated by year to save package space. #158

Add message with tidy(fit, "ran_pars") about why SEs are NA.

Add anisotropy to print() #157

Fix predict(..., type = "response", se_fit = TRUE), which involves issuing a warning and sticking to link space. #140