tinyVAST 1.4.0

• Adding student distribution, borrowing/importing code from sdmTMB
• Changing deviance_explained to map off student DF at MLE to avoid negative values, in way that can be easily generalized.
• Changing deviance_explained to map off overdispersion for negbin1 and negbin2
• Changing deviance_explained to map of power parameter for tweedie distribution
• add testthat checks comparing tweedie and negbin2 deviance-explained for tinyVAST with mgcv package
• Add vignette for seasonal spatio-temporal index standardization, using Yellowtail flounder data from VAST demo

tinyVAST 1.3.0

• Adding add_vertex_covariates to associate mesh vertices with covariates (hean Anderson)
• Adding option for covariate-based anisotropy using vertex_formula, while also allowing geometric anisotropy.
• Adding option for barriers using triangle_formula which permits an offset for barrier covariates
• Adding spatial_cor to use sparse matrices to compute the correlation between a coord and pred coordinates, e.g. to visualize covariate-based anisotropy
• Fix make_eof_ram to work as intended for multivariate models, e.g., having a separate response map and shared indices across variables (previously had a shared response map and shared indices, i.e., collapsed to univariate model)
• Fix bug arising in predict when spatial_varying involved a column of newdata that was expecting a factor, but provided a character-vector. Now coercers to factors using the levels of the original data (same behavior as for formula)
• Export fit$rep$negloglik_i as log-likelihood for each datum, for use in calculating out-of-sample predictive score
• Turn off SE reporting during index calculations (as speedup), and allow SE reporting for mu_g in predict
• Fix bug arising in project when spatial_varying was specified
• Adding web-only vignette showing predator-expanded diet estimator using joint model of specific stomach contents and predator density
• Fix bug arising when using weights argument using family of delta_gamma or delta_lognormal, where this bug was introduced in release 1.2.0 (h/t Peri Gerson for identifying the issue)
• Add vignette showing project function
• Add a web-only vignette showing the sponge-coral-fish case study to illustrate spatial structural modelling

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.
• Fix bug which previously resulted in non-converged models, where including DSEM arrow “x<->x, 0, sd_xy” would improperly add another term “x <-> x, 0, V[x]” because it didn’t previously parse the whitespaces when detecting missing covariances (h/t Jon Reum for flagging the issue)

tinyVAST 1.1.1

• 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]’”

tinyVAST 1.1.0

• 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.

tinyVAST 1.0.1

• 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

tinyVAST 1.0.0

• 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

tinyVAST 0.7.1

• 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)

tinyVAST 0.7.0

• 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

tinyVAST 0.6.0

• 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

tinyVAST 0.5.0

• Adding vignette showing how to fit multiple data types in an SDM
• Adding deviance_explained and calculating this by default

tinyVAST 0.4.0

• Adding code for simulation residuals, and examples to vignettes

tinyVAST 0.3.0

• Adding sdmTMB as dependency, and importing family options from it
• Adding vignette for joint analysis of condition and density

tinyVAST 0.2.0

• Add option to specify covariance in SEM and DSEM notation

tinyVAST 0.1.0

• Initial public alpha release