API for sdmTMB
Spatial and Spatiotemporal SPDE-Based GLMMs with 'TMB'
| Global functions | |
|---|---|
| .has_delta_attr | Source code |
| .onLoad | Source code |
| .onUnload | Source code |
| .one_sample_posterior | Source code |
| Beta | Man page Source code |
| Effect.sdmTMB | Man page Source code |
| Families | Man page |
| add_barrier_mesh | Man page Source code |
| add_model_index | Source code |
| add_to_family | Source code |
| add_utm_columns | Man page Source code |
| barnames | Source code |
| binary_search_knots | Source code |
| cAIC | Man page Source code |
| cAIC.sdmTMB | Source code |
| censored_poisson | Man page Source code |
| check_and_parse_thresh_params | Source code |
| check_bounds | 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_sdmTMB_version | Source code |
| check_spatiotemporal_arg | Source code |
| check_time_class | Source code |
| check_valid_factor_levels | Source code |
| check_visreg | Source code |
| chunk_time | Source code |
| coef.sdmTMB | Man page Source code |
| confint.sdmTMB | Source code |
| create_cov_matrices | 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_poisson_link_gamma | Man page Source code |
| delta_poisson_link_lognormal | 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 |
| dnbinom1 | Source code |
| dogfish | Man page |
| dstudent | Source code |
| emm_basis.sdmTMB | Source code |
| emmeans.sdmTMB | Man page |
| expand_time | Source code |
| extractAIC.sdmTMB | Source code |
| extract_mcmc | Man page Source code |
| find_missing_time | Source code |
| fitted.sdmTMB | Source code |
| fixef.sdmTMB | Source code |
| flatten_cov_output | 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_censored_upper | 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_re_tidy_list | Source code |
| get_response | Source code |
| get_scale_factor | Source code |
| get_smooth_terms | Source code |
| get_spde_matrices | Source code |
| ggplot2_installed | Man page Source code |
| halfnormal | Man page Source code |
| has_no_random_effects | Source code |
| hbll_s_grid | Man page |
| inla_docs_log | Source code |
| insert_pars | Source code |
| is_delta | 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 |
| make_anisotropy_spde | Source code |
| make_barrier_spde | Source code |
| make_indices | Source code |
| make_mesh | Man page Source code |
| make_time_lu | Source code |
| make_year_i | Source code |
| map_all_params | Source code |
| map_kappa | Source code |
| model.frame.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 |
| normal | Man page 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 |
| 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_pc_matern | Man page Source code |
| plot_smooth | Man page Source code |
| pnbinom1 | Source code |
| predict.sdmTMB | Man page 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_one_model | Source code |
| print_other_parameters | Source code |
| print_range | Source code |
| print_smooth_effects | Source code |
| print_time_varying | Source code |
| project | Man page Source code |
| pt_ls | Source code |
| qcs_grid | Man page |
| qnbinom1 | Source code |
| qres_beta | Source code |
| qres_binomial | 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_pois | Source code |
| qres_student | Source code |
| qres_tweedie | Source code |
| ranef.sdmTMB | Source code |
| recover_data.sdmTMB | Source code |
| reexports | Man page |
| reinitialize | Source code |
| reload_model | Source code |
| remove_9000 | Source code |
| remove_s_and_t2 | Source code |
| replicate_df | Man page Source code |
| residuals.sdmTMB | Man page Source code |
| rmvnorm_prec | Source code |
| rnbinom1 | Source code |
| run_extra_optimization | Man page Source code |
| run_newton_loops | Source code |
| s2rPred | Source code |
| safe_deparse | Source code |
| sanity | Man page Source code |
| sdmTMB | Man page Source code |
| sdmTMB_cv | Man page Source code |
| sdmTMB_simulate | Man page Source code |
| sdmTMB_stacking | Man page Source code |
| sdmTMBcontrol | Man page Source code |
| sdmTMBpriors | Man page Source code |
| set_delta_model | Man page Source code |
| set_limits | Source code |
| set_par_value | Source code |
| simulate.sdmTMB | Man page Source code |
| spread_sims | Man page Source code |
| student | Man page Source code |
| summary.sdmTMB | Source code |
| terms.sdmTMB | Source code |
| tidy | Man page |
| tidy.sdmTMB | Man page Source code |
| tidy.sdmTMB_cv | Man page Source code |
| truncated_nbinom1 | Man page Source code |
| truncated_nbinom2 | Man page Source code |
| tweedie | Man page Source code |
| unmap | Source code |
| update.sdmTMB | 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 |
