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Changelog

Source: NEWS.md

tinyVAST 1.3.0

CRAN release: 2025-09-13

  • 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

CRAN release: 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)

tinyVAST 1.1.1

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]’”

tinyVAST 1.1.0

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.

tinyVAST 1.0.1

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

tinyVAST 1.0.0

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

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