Changes in version 1.6.0 - Adding nearest-neighbors Gaussian Process option - Add tinyVASTcontrol(tmb_random) argument to allow exploration of penalized likelihood - Modifying tinyVASTcontrol(tmb_par) to allow users to supply a partial list of starting values, e.g., to provide values for semi-variance parameters when changing model resolution. - Add development$optimizer argument for using optim(method="L-BFGS-B") or TMB::newton, which is necessary when using penalized likelihood with >40,000 random effects. And removing tinyVASTcontrol option for suppress_optim_warnings (making it always TRUE) - Adding Makevar -DTMBAD_INDEX_TYPE=uint64_t to allow GetTape for RTMB manipulation - Change SAR using areal_model for spatial_domain to (1) eliminate row-standardization (which messed up the areal interpretation), and (2) defining an informative start for kappa to start with a value that avoids numerical under/overflow; - Adding argument block to integrate_output to allow calculating multiple derived quantities using a single call (to avoid extra MakeADFun calls) Changes in version 1.5.1 (2026-04-14) - Fix bug, where previous versions where not simulating measurement errors for delta-models using obj$simulate(). h\t github ilar-cloud for reporting on issue-402 Changes in version 1.5.0 (2026-03-23) - Add starting value log_kappa when using SPDE method, using SD of X and Y coordinates and converting to equivalent kappa - Fix bug in project for logical class in empty vectors - Add development options to explore hess-compress option (and commenting out incomplete Cholesky for now) - Add sanity function to check for evidence of non-convergence - Improve detection of sf class for areal models Changes in version 1.4.0 (2025-12-20) - 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 Changes in version 1.3.0 (2025-09-13) - Adding add_vertex_covariates to associate mesh vertices with covariates (h\t Sean 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 Changes in version 1.2.0 (2025-07-19) - 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) Changes in version 1.1.1 (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]'" Changes in version 1.1.0 (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. Changes in version 1.0.1 (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 Changes in version 1.0.0 (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 Changes in version 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) Changes in version 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 Changes in version 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 Changes in version 0.5.0 - Adding vignette showing how to fit multiple data types in an SDM - Adding deviance_explained and calculating this by default Changes in version 0.4.0 - Adding code for simulation residuals, and examples to vignettes Changes in version 0.3.0 - Adding sdmTMB as dependency, and importing family options from it - Adding vignette for joint analysis of condition and density Changes in version 0.2.0 - Add option to specify covariance in SEM and DSEM notation Changes in version 0.1.0 - Initial public alpha release