Changelog • tinyVAST

tinyVAST 1.2.0

Adding a new spatial domain using sf::st_make_grid
Adding option for geometric anisotropy when using sf::st_make_grid
Fix bug in deviance for lognormal distribution in delta models (h/t Sean Anderson for finding it)
Change family = “binomial” to use weights as number of Binomial trials N
Fix deviance_explained to work with non-default weights argument
Add fit$internal$packageVersion to allow predict, cAIC etc to check and throw error if there’s a package inconsistency between object and installed package
Add conditional_gmrf to do conditional simulations from a GMRF
Add project to project tinyVAST forward in time
Eliminate ... argument to tinyVAST so that it’s obvious if an argument is mis-named.

CRAN release: 2025-05-07

Adding option for geometric anisotropy when using the SPDE method
For some reason, the CPP edits also address an error message during devtools::check_win_devel “array subscript ’const __m128i[0]’ is partly outside array bounds of ‘unsigned char [12]’”

CRAN release: 2025-05-03

Adding term_covariance to calculate the covariance among variables for SEM term, or covariance among variables-and-lags for DSEM terms
Adding Restricted Spatial Regression estimator for covariates alphaprime_j and alphaprime2_j to fit$rep output.
Adding methods to allow use of cv to calculate crossvalidation skill
Add bias.correct option to predict (but still no flag for SEs for anything except p_i)
Switch sample_variable from using obj$env$MC to obj$env$spHess(random=TRUE) which seems more stable as dependency
Add functionality for te and ti splines, although they remain poorly tested
Add error check to sfnetwork_mesh to detect if the stream network is not ordered as a tree
Improve stream network vignette to use matrix notation for joint precision, and modify simulate_sfnetwork to use that
Change tinyVAST.cpp to use matrix notation constructor and fix bug in previous constructor where the covariance between first and second nodes was not right
Expand test-sfnetworks.R integrated test to confirm that matrix-notation precision constructor is identical to the inverse of Ornstein-Uhlenbeck covariance as intended.

CRAN release: 2025-03-21

Modify examples for simulate.tinyVAST and sample_variable to try to avoid terminal output giving error in valgrind check
Add ivector_minus_one function to satisfy clang-UBSAN
Swap GMRF(Q).Quadform(x) to x.matrix().transpose() * (Q * x.matrix()) to avoid calculating log-determinant of Q in the smoothers penalty, to avoid valgrind errors
Add tinyVASTcontrol option that suppresses nlminb warning messages by default, which are typically not informative to casual users

CRAN release: 2025-03-13

Adding nbinom1 and nbinom2 families
Simplify argument names, by changing sem to space_term, dsem to spacetime_term and spatial_graph to spatial_domain, and eliminating delta_ in the names for arguments to delta_options
Add time_term to allow time-variable interaction (e.g., AR1 intercepts)
Adding overview and model-description vignettes
Add simulate S3 generic

Fixed bug (wrong output) when using predict(fit, what="mu_g") and a Poisson-linked delta model
Fixed bug (cryptic error message) when using integrate_output
Add cAIC (but disabling EDF calculation for now)

Adding option for spatially-varying-coefficient (SVC) models
Add error-check for when data has a factor with extra levels, which conflicted with the logic of adding all origdata levels to newdata when calling predict, and hence caused an uniformative error previously

Change integrate_output interface by splitting W_gz and V_gz into four vectors area, type, covariate, and weighting_index to simplify documentations and improve naming
Fix bug where cloglog and logit links were not previously implemented for use in predict and integrate_output