sdmTMB
Spatial and Spatiotemporal SPDE-Based GLMMs with 'TMB'

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596
Source code
154
Man pages
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sdmTMB: Spatial and Spatiotemporal SPDE-Based GLMMs with 'TMB'
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API for sdmTMB
Spatial and Spatiotemporal SPDE-Based GLMMs with 'TMB'

Global functions
.align_sf_crs Source code
.append_nonlocal_coef_columns Source code
.apply_design Source code
.as_dgC Source code
.as_general_dgC Source code
.as_sf_polygons Source code
.as_tmb_family_data Source code
.build_nonlocal_tmb_data Source code
.build_vertex_time_covariates Source code
.censored_direct_init Source code
.censored_upper_arg Source code
.check_family_capability Source code
.check_no_missing_covariates Source code
.classify_binomial_like_numeric_rows Source code
.compile_family_spec Source code
.complete_model_rows Source code
.compute_nonlocal_term_values Source code
.covariate_model_frame Source code
.extract_nonlocal_term_exprs Source code
.family_metadata Source code
.family_parameter_values Source code
.family_spec_build_response Source code
.family_spec_combine_simulated Source code
.family_spec_component Source code
.family_spec_component_active Source code
.family_spec_component_prediction_output Source code
.family_spec_component_value Source code
.family_spec_has_two_components Source code
.family_spec_is_multi_family Source code
.family_spec_observed_response Source code
.family_spec_prediction_link_name Source code
.family_spec_process_response Source code
.family_spec_response_family_id Source code
.family_spec_row_family_id Source code
.family_spec_slot_length Source code
.family_spec_validate_response Source code
.formula_list Source code
.get_delta_model Source code
.get_model_frame_rows Source code
.has_delta_attr Source code
.is_named_family_list Source code
.is_poisson_link_delta_model Source code
.is_whole_number Source code
.make_design Source code
.make_family_param_slots Source code
.map_family_codes Source code
.map_family_parameters Source code
.nl_plot_context Source code
.nl_plot_df Source code
.nl_plot_extract_kappas Source code
.nl_plot_extract_mesh Source code
.nl_plot_ggplot Source code
.nl_plot_locations Source code
.nl_plot_resolve_time Source code
.nl_plot_time_panels Source code
.nonlocal_log_kappaS_bounds Source code
.nonlocal_log_kappaS_start Source code
.nonlocal_predict_colnames Source code
.nonlocal_prediction_requires_full_time Source code
.nonlocal_start_code Source code
.nonlocal_term_only Source code
.nonlocal_time_indexed Source code
.nonlocal_time_indexed_from_object Source code
.nonlocal_uses_external_grid Source code
.normalize_areal_W Source code
.normalize_censored_trials Source code
.object_family_spec Source code
.object_has_two_components Source code
.object_is_delta Source code
.object_par Source code
.onLoad Source code
.onUnload Source code
.one_sample_posterior Source code
.parse_nonlocal_formula Source code
.poisson_link_delta_mu_from_eta Source code
.posterior_re_sampler Source code
.prepare_family_response Source code
.prepare_index_input Source code
.prepare_nonlocal_grid_inputs Source code
.process_binomial_like_rows Source code
.process_binomial_response Source code
.project_nonlocal_vertex_time Source code
.resolve_areal_space_column Source code
.resolve_link_pred Source code
.response_linkinv Source code
.saved_phi Source code
.sf_areal_adjacency_matrix Source code
.sf_unit_names Source code
.solve_nonlocal_vertex_time Source code
.subset_by_na_action Source code
.subset_mesh_rows Source code
.subset_rows Source code
.tidy_multi_family_param_rows Source code
.tidy_rsr_effects Source code
.validate_areal_matrix_structure Source code
.validate_areal_matrix_values Source code
.validate_areal_row_sums Source code
.validate_derived_link Source code
.validate_distribution_column Source code
.validate_family_spec Source code
.validate_family_spec_list Source code
.validate_multi_family_scope Source code
.validate_nonlocal_terms Source code
Beta Man page Source code
Effect.sdmTMB Man page Source code
Families Man page
add_model_index Source code
add_to_family Source code
add_utm_columns Man page Source code
aniso_ranges_to_df Source code
apply_inverse_link Source code
areal_projection_matrix Source code
backend_sdmTMB Source code
barnames Source code
betabinomial Man page Source code
binary_search_knots Source code
cAIC Man page Source code
cAIC.sdmTMB Source code
calculate_anisotropy_components Source code
call_fn_name Source code
censored_betabinomial Man page Source code
censored_binomial Man page Source code
censored_nbinom1 Man page Source code
censored_nbinom2 Man page Source code
censored_poisson Man page Source code
check_and_collapse_spatial_fields Source code
check_and_parse_thresh_params Source code
check_bounds Source code
check_censored_betabinomial Source code
check_for_H Source code
check_irregalar_time Source code
check_model_arg Source code
check_offset Source code
check_overdisp Source code
check_project_sims_var Source code
check_sdmTMB_version Source code
check_spatiotemporal_arg Source code
check_time_class Source code
check_valid_factor_levels Source code
chunk_time Source code
coef.sdmTMB Man page Source code
compare_deviance Man page Source code
confint.sdmTMB Source code
create_cov_matrices Source code
custom_prior_spec Source code
cv_control Source code
cv_integrated_loglik Source code
cv_param_sampler Source code
cv_to_waywiser Man page Source code
delta_beta Man page Source code
delta_gamma Man page Source code
delta_gamma_mix Man page Source code
delta_gengamma Man page Source code
delta_lognormal Man page Source code
delta_lognormal_mix Man page Source code
delta_truncated_nbinom1 Man page Source code
delta_truncated_nbinom2 Man page Source code
deviance.sdmTMB Source code
df.residual.sdmTMB Source code
dharma_residuals Man page Source code
diffusion Man page Source code
dnbinom1 Source code
dogfish Man page
domain_n_s Source code
domain_obs_index Source code
domain_pred_index Source code
dstudent Source code
dummy_sparse_1x1 Source code
dummy_spde Source code
dummy_spde_aniso Source code
dummy_spde_barrier Source code
elpd.sdmTMB_cv Man page Source code
emm_basis.sdmTMB Source code
emmeans.sdmTMB Man page
expand_time Source code
extractAIC.sdmTMB Source code
extract_call_name Source code
extract_project_sims Source code
find_missing_time Source code
finish_generic Source code
fit_first_phase Source code
fit_hessian_fixed Source code
fitted.sdmTMB Source code
fixef.sdmTMB Source code
flatten_cov_output Source code
flatten_prior_element Source code
flatten_prior_elements Source code
gamma_cv Man page Source code
gamma_mix Man page Source code
gather_sims Man page Source code
gengamma Man page Source code
get_anisotropic_ranges Source code
get_censored_upper Man page Source code
get_cog Man page Source code
get_convergence_diagnostics Source code
get_crs Man page Source code
get_eao Man page Source code
get_fitted_time Source code
get_generic Source code
get_index Man page Source code
get_index_sims Man page Source code
get_index_split Man page Source code
get_kappa_map Source code
get_pars Man page Source code
get_prior_densities Man page Source code
get_prior_parameters Man page Source code
get_range_edge Man page Source code
get_re_tidy_list Source code
get_response Source code
get_scale_factor Source code
get_smooth_terms Source code
get_spde_matrices Source code
get_weighted_average Man page Source code
ggplot2_installed Man page Source code
halfnormal Man page Source code
has_no_random_effects Source code
hbll_s_grid Man page
index_report Source code
index_sdreport Source code
inla_docs_log Source code
insert_pars Source code
is_areal_domain Source code
is_areal_fit Source code
is_car_fit Source code
is_delta Source code
is_visreg_call Source code
joint_precision_report Source code
ll_binomial Source code
ll_gamma Source code
ll_gaussian Source code
ll_lognormal Source code
ll_nbinom1 Source code
ll_nbinom2 Source code
ll_sdmTMB Source code
ll_student Source code
ll_tweedie Source code
log1mexp Source code
logLik.sdmTMB Source code
log_sum_exp Source code
lognormal Man page Source code
lognormal_mix Man page Source code
lognormal_prior Man page Source code
make_anisotropy_spde Source code
make_areal_domain Man page Source code
make_barrier_spde Source code
make_category_svc Man page Source code
make_indices Source code
make_mesh Man page Source code
make_sdmTMB_adfun Source code
make_time_lu Source code
make_year_i Source code
make_zero_one_map Man page Source code
map_all_params Source code
map_kappa Source code
maybe_suppress_warnings Source code
model.frame.sdmTMB Source code
model.matrix.sdmTMB Source code
move_proj_to_tmbdat Source code
mround Source code
mvnormal Man page Source code
named_list Source code
nbinom1 Man page Source code
nbinom2 Man page Source code
nbinom2_mix Man page Source code
nobs.sdmTMB Source code
nonlocal_terms Man page
normal Man page Source code
normalize_bar_only_formula Source code
ohio_df Man page
ohio_sf Man page
ordbeta Man page Source code
ordbeta_cutpoints Source code
par_df Source code
par_message Source code
parse_formula Source code
parse_smoothers Source code
parse_spatial_arg Source code
parse_threshold_formula Source code
pbbinom Source code
pc_matern Man page Source code
pcod Man page
pcod_2011 Man page
pcod_mesh_2011 Man page
pgengamma Source code
plot.sdmTMBmesh Man page Source code
plot_anisotropy Man page Source code
plot_anisotropy2 Man page Source code
plot_nonlocal_covariate Man page Source code
plot_nonlocal_kernel Man page Source code
plot_pc_matern Man page Source code
plot_smooth Man page Source code
pnbinom1 Source code
predict.sdmTMB Man page Source code
predict_check_newdata Source code
predict_components Source code
predict_design_matrix Source code
predict_design_matrix_legacy Source code
predict_disp_matrix Source code
predict_draw_reports Source code
predict_draws Source code
predict_est Source code
predict_fitted_term_reports Source code
predict_fixed_matrices Source code
predict_iid_re_matrices Source code
predict_nonlocal_cols Source code
predict_nonlocal_field Source code
predict_objective Source code
predict_offset Source code
predict_prepare Source code
predict_report_only Source code
predict_request Source code
predict_return Source code
predict_sdmTMB Source code
predict_select Source code
predict_spatial_index Source code
predict_svc_matrix Source code
predict_terms Source code
predict_tv_matrix Source code
predict_visreg Source code
prepare_spatial_domain Source code
print.sdmTMB Source code
print.sdmTMB_cv Source code
print_anisotropy Source code
print_footer Source code
print_header Source code
print_iid_re Source code
print_int_slope_re Source code
print_main_effects Source code
print_model_info Source code
print_multi_family_summary Source code
print_one_model Source code
print_other_parameters Source code
print_range Source code
print_smooth_effects Source code
print_time_varying Source code
prior_parlist Source code
project Man page Source code
project_apply_future_re Source code
project_conditional_draws Source code
project_historical_draws Source code
project_historical_re_indices Source code
project_joint_draws Source code
project_replace_parameter Source code
project_sd_report Source code
project_time_extension Source code
pt_ls Source code
ptruncated_nbinom1 Source code
ptruncated_nbinom2 Source code
qcs_grid Man page
qnbinom1 Source code
qres_beta Source code
qres_betabinomial Source code
qres_binomial Source code
qres_censored_betabinomial Source code
qres_censored_binomial Source code
qres_censored_nb Source code
qres_censored_nbinom1 Source code
qres_censored_nbinom2 Source code
qres_gamma Source code
qres_gamma_mix Source code
qres_gaussian Source code
qres_gengamma Source code
qres_lognormal Source code
qres_lognormal_mix Source code
qres_nbinom1 Source code
qres_nbinom2 Source code
qres_nbinom2_mix Source code
qres_ordbeta Source code
qres_pois Source code
qres_student Source code
qres_truncated_nbinom1 Source code
qres_truncated_nbinom2 Source code
qres_tweedie Source code
ranef.sdmTMB Source code
recover_data.sdmTMB Source code
reexports Man page
refit_censored_betabinomial Source code
reinitialize Source code
reload_model Source code
remake_tmb_obj Source code
remove_s_and_t2 Source code
replicate_df Man page Source code
residuals.sdmTMB Man page Source code
rmvnorm_chol Source code
rmvnorm_prec Source code
rnbinom1 Source code
rtmb_aniso_H Source code
rtmb_aniso_bases Source code
rtmb_areal Source code
rtmb_as_vector Source code
rtmb_betabinom_shapes Source code
rtmb_censpois_devresid Source code
rtmb_censpois_logprob Source code
rtmb_censpois_logprob_value Source code
rtmb_check_custom_priors Source code
rtmb_code_name Source code
rtmb_combined_projection Source code
rtmb_component_mean Source code
rtmb_count_logsum Source code
rtmb_custom_log_density Source code
rtmb_custom_terms Source code
rtmb_dbetabinom Source code
rtmb_dcensbetabinom Source code
rtmb_dcensbinom Source code
rtmb_dcenscount Source code
rtmb_dcensnb Source code
rtmb_dcenspois Source code
rtmb_derived_indices Source code
rtmb_dgengamma Source code
rtmb_diffusion_inputs Source code
rtmb_diffusion_scales Source code
rtmb_diffusion_terms Source code
rtmb_digamma_diff Source code
rtmb_dordbeta Source code
rtmb_evaluate Source code
rtmb_family_inputs Source code
rtmb_gengamma_devresid Source code
rtmb_gengamma_log_theta Source code
rtmb_gengamma_qw Source code
rtmb_gmrf Source code
rtmb_gmrf_scale Source code
rtmb_ifelse_positive Source code
rtmb_iid_effects Source code
rtmb_inv_pow_diff Source code
rtmb_inverse_link Source code
rtmb_latent_effects Source code
rtmb_lbetabinom Source code
rtmb_lgamma_diff Source code
rtmb_linear_predictor Source code
rtmb_linear_predictors Source code
rtmb_link Source code
rtmb_log_field_sd Source code
rtmb_logit_inverse_link Source code
rtmb_make_objective Source code
rtmb_mixture Source code
rtmb_mixture_projection Source code
rtmb_nb_deviance Source code
rtmb_nbinom1_deviance Source code
rtmb_objective Source code
rtmb_obs_family Source code
rtmb_obs_groups Source code
rtmb_obs_state Source code
rtmb_observations Source code
rtmb_pc_matern Source code
rtmb_pick Source code
rtmb_precision Source code
rtmb_precision_inputs Source code
rtmb_prepare Source code
rtmb_prior_inputs Source code
rtmb_prior_nll Source code
rtmb_product Source code
rtmb_re_groups Source code
rtmb_report Source code
rtmb_report_values Source code
rtmb_rgmrf Source code
rtmb_rhs_solve Source code
rtmb_row_inputs Source code
rtmb_smooth_effects Source code
rtmb_smooth_index Source code
rtmb_spatiotemporal_field Source code
rtmb_station_values Source code
rtmb_threshold Source code
rtmb_time_varying Source code
rtmb_transform Source code
rtmb_trigamma_diff Source code
rtmb_truncated_nb Source code
rtmb_validate Source code
rtmb_value Source code
run_extra_optimization Man page Source code
run_newton_loops Source code
run_nlminb_loops Source code
s2rPred Source code
sanity Man page Source code
sdmTMB Man page Source code
sdmTMB_cv Man page Source code
sdmTMB_simulate Man page
sdmTMB_stacking Man page Source code
sdmTMBcontrol Man page Source code
sdmTMBpriors Man page Source code
sdreport_sdmTMB Source code
set_delta_model Man page Source code
set_limits Source code
set_par_value Source code
sigma.sdmTMB Man page Source code
simulate.sdmTMB Man page Source code
simulate_new Man page Source code
spread_sims Man page Source code
student Man page Source code
summary.sdmTMB Source code
sync_last_par_best Source code
termnames Source code
terms.sdmTMB Source code
tidy Man page
tidy.sdmTMB Man page Source code
tidy.sdmTMB_cv Man page Source code
time_lag Man page Source code
truncated_nbinom1 Man page Source code
truncated_nbinom2 Man page Source code
try_newton_step Source code
tweedie Man page Source code
unmap Source code
update.sdmTMB Man page Source code
vcov.sdmTMB Source code
visreg2d_delta Man page Source code
visreg_delta Man page Source code
wcvi_grid Man page
yelloweye Man page
sdmTMB documentation built on Oct. 17, 2026, 1:07 a.m.

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