Man pages for pbs-assess/sdmTMB
Spatial and Spatiotemporal SPDE-Based GLMMs with 'TMB'
| add_barrier_mesh | Transform a mesh object into a mesh with correlation barriers |
| add_utm_columns | Add UTM coordinates to a data frame |
| cAIC | Calculate conditional AIC |
| coef.sdmTMB | Get fixed-effect coefficients |
| dharma_residuals | DHARMa residuals |
| Effect.sdmTMB | Calculate effects |
| emmeans.sdmTMB | Estimated marginal means with the 'emmeans' package with... |
| extract_mcmc | Extract MCMC samples from a model fit with 'tmbstan'. |
| families | Additional families |
| gather_sims | Extract parameter simulations from the joint precision matrix |
| get_index | Extract a relative biomass/abundance index, center of... |
| get_index_sims | Calculate a population index via simulation from the joint... |
| get_pars | Get TMB parameter list |
| ggplot2_installed | Check if ggplot2 installed |
| make_mesh | Construct an SPDE mesh for sdmTMB |
| plot_anisotropy | Plot anisotropy from an sdmTMB model |
| plot_pc_matern | Plot PC Matérn priors |
| plot_smooth | Plot a smooth term from an sdmTMB model |
| predict.sdmTMB | Predict from an sdmTMB model |
| priors | Prior distributions |
| project | Project from an 'sdmTMB' model using simulation |
| reexports | Objects exported from other packages |
| replicate_df | Replicate a prediction data frame over time |
| residuals.sdmTMB | Residuals method for sdmTMB models |
| run_extra_optimization | Run extra optimization on an already fitted object |
| sanity | Sanity check of an sdmTMB model |
| sdmTMB | Fit a spatial or spatiotemporal GLMM with TMB |
| sdmTMBcontrol | Optimization control options |
| sdmTMB_cv | Cross validation with sdmTMB models |
| sdmTMB_simulate | Simulate from a spatial/spatiotemporal model |
| sdmTMB_stacking | Perform stacking with log scores on 'sdmTMB_cv()' output |
| set_delta_model | Set delta model for 'ggeffects::ggpredict()' |
| simulate.sdmTMB | Simulate from a fitted sdmTMB model |
| surveydata | Example fish survey data |
| tidy.sdmTMB | Turn sdmTMB model output into a tidy data frame |
| visreg_delta | Plot sdmTMB models with the 'visreg' package |
