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add_vertex_covariates to associate mesh vertices
with covariates (hean Anderson)vertex_formula, while also allowing geometric
anisotropy.triangle_formula which
permits an offset for barrier covariatesspatial_cor to use sparse matrices to compute
the correlation between a coord and pred
coordinates, e.g. to visualize covariate-based anisotropymake_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)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)fit$rep$negloglik_i as log-likelihood for each
datum, for use in calculating out-of-sample predictive scoremu_g in predictproject when
spatial_varying was specifiedweights 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)project functionsf::st_make_gridsf::st_make_gridweights as number of
Binomial trials Ndeviance_explained to work with non-default
weights argumentfit$internal$packageVersion to allow
predict, cAIC etc to check and throw error if
there’s a package inconsistency between object and installed
packageconditional_gmrf to do conditional simulations from
a GMRFproject to project tinyVAST forward in time... argument to tinyVAST so that
it’s obvious if an argument is mis-named.devtools::check_win_devel “array subscript ’const
__m128i[0]’ is partly outside array bounds of ‘unsigned char [12]’”term_covariance to calculate the covariance
among variables for SEM term, or covariance among variables-and-lags for
DSEM termsalphaprime_j and alphaprime2_j to
fit$rep output.cv to calculate
crossvalidation skillbias.correct option to predict (but still no flag
for SEs for anything except p_i)sample_variable from using
obj$env$MC to obj$env$spHess(random=TRUE)
which seems more stable as dependencyte and ti splines,
although they remain poorly testedsfnetwork_mesh to detect if the
stream network is not ordered as a treesimulate_sfnetwork to use thattinyVAST.cpp to use matrix notation constructor
and fix bug in previous constructor where the covariance between first
and second nodes was not righttest-sfnetworks.R integrated test to confirm
that matrix-notation precision constructor is identical to the inverse
of Ornstein-Uhlenbeck covariance as intended.simulate.tinyVAST and
sample_variable to try to avoid terminal output giving
error in valgrind checkivector_minus_one function to satisfy
clang-UBSANGMRF(Q).Quadform(x) to
x.matrix().transpose() * (Q * x.matrix()) to avoid
calculating log-determinant of Q in the smoothers penalty,
to avoid valgrind errorssem to
space_term, dsem to
spacetime_term and spatial_graph to
spatial_domain, and eliminating delta_ in the
names for arguments to delta_optionstime_term to allow time-variable interaction (e.g.,
AR1 intercepts)simulate S3 genericpredict(fit, what="mu_g") and a Poisson-linked delta
modelintegrate_outputcAIC (but disabling EDF calculation for now)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
previouslyintegrate_output interface by splitting
W_gz and V_gz into four vectors
area, type, covariate, and
weighting_index to simplify documentations and improve
namingpredict and
integrate_outputdeviance_explained and calculating this by
defaultsdmTMB as dependency, and importing family
options from itThese binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
Health stats visible at Monitor.