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Changelog

Source: NEWS.md

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

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