Man pages for inlabru
Bayesian Latent Gaussian Modelling using INLA and Extensions
| add_mappers | Add component input/latent mappers |
| as_bru_comp | Conversion methods for 'bru_comp' and 'bru_comp_list' objects |
| as_bru_mapper | Methods for mapper extraction |
| as_bru_obs | Conversion methods for 'bru_obs' and 'bru_obs_list' objects |
| augment.bru | Augment a bru model fit with fitted values |
| bincount | 1D LGCP bin count simulation and comparison with data |
| bm_aggregate | Mapper for aggregation |
| bm_collect | Mapper for concatenated variables |
| bm_const | Constant mapper |
| bm_expr | Mapper for general expressions |
| bm_factor | Mapper for factor variables |
| bm_fmesher | Mapper for general 'fmesher' function space objects |
| bm_fm_mesh_1d | Mapper for 'fm_mesh_1d' |
| bm_fm_mesh_old | Deprecated methods |
| bm_harmonics | Mapper for cos/sin functions |
| bm_index | Mapper for indexed variables |
| bm_linear | Mapper for a linear effect |
| bm_list | Methods for mapper lists |
| bm_logitaverage | Mapper for logit-sum-inverse-logit aggregation |
| bm_logsumexp | Mapper for log-sum-exp aggregation |
| bm_marginal | Mapper for marginal distribution transformation |
| bm_matrix | Mapper for matrix multiplication |
| bm_multi | Mapper for tensor product domains |
| bm_pipe | Mapper for linking several mappers in sequence |
| bm_reparam | Mapper for reparameterising mapper states |
| bm_repeat | Mapper for repeating a mapper |
| bm_repeat_indexing | Re-indexing matrix for repeated mappers |
| bm_scale | Mapper for element-wise scaling |
| bm_shift | Mapper for element-wise shifting |
| bm_sum | Mapper for adding multiple mappers |
| bm_summary | mapper object summaries |
| bm_taylor | Mapper for linear Taylor approximations |
| bru | Convenient model fitting using (iterated) INLA |
| bru_block_gcpo | Extract block-averaged GCPO scores from one or more fitted... |
| bru_call_options | Additional bru options |
| bru_comp | Latent model component construction |
| bru_comp_env_extra | Get/set component environment data |
| bru_comp_eval | Evaluate component values in predictor expressions |
| bru_comp_list | Methods for inlabru component lists |
| bru_compute_linearisation | Compute inlabru model linearisation information |
| bru_convergence_plot | Plot inlabru convergence diagnostics |
| bru_data_mask | Create inlabru data mask |
| bru_env_get | Get access to the internal environment |
| bru_eval | Evaluate or sample from a posterior result given a model and... |
| bru_eval_fun | Obtain bru component evaluation functions |
| bru_eval_in_data_context | Evaluate expressions in data contexts |
| bru_fill_missing | Fill in missing values in Spatial grids |
| bru_formula_to_bru_obs_code | Convert components to R code |
| bru_gcpo_table | Compare block-averaged GCPO scores across multiple fitted bru... |
| bru_get_mapper | Extract mapper information from INLA model component objects |
| bru_index | Extract predictor or component index information |
| bru_info | Methods for bru_info objects |
| bru_inla_formula | Extract INLA formula |
| bru_inla.stack.mexpand | Backwards compatibility to handle mexpand for INLA <=... |
| bru_inla.stack.mjoin | Join stacks intended to be run with different likelihoods |
| bru_input | Store and evaluate component inputs |
| bru_input_text | Extract input definitions as text |
| bru_is_additive | Check for predictor expression additivity |
| bru_is_linear | Check for predictor linearity |
| bru_is_rowwise | Check for predictor rowwise evaluability |
| bru_log | Access methods for 'bru_log' objects |
| bru_log_bookmark | Methods for 'bru_log' bookmarks |
| bru_log_message | Add a log message |
| bru_log_offset | Position methods for 'bru_log' objects |
| bru_log_reset | Clear log contents |
| bru_make_stack | Build an inla data stack from linearisation information |
| bru_mapper | Constructors for 'bru_mapper' objects |
| bru_mapper_generics | Generic methods for bru_mapper objects |
| bru_model | Create an inlabru model object from model components |
| bru_model_mapper_methods | Mapper methods for model objects |
| bru_names | Extract standardised names from a bru or inla result object |
| bru_obs | Observation model construction for 'bru()' |
| bru_obs_gcpo | Utility functions for bru observation model GCPO |
| bru_obs_methods | Utility functions for bru observation model objects |
| bru_obs_print | Summary and print methods for observation models |
| bru_options | Create or update an options objects |
| bru_pred_expr | Predictor expression handler object |
| bru_response_size | Response size queries |
| bru_safe_inla | Load INLA safely for examples and tests |
| bru_safe_sp | Check for potential 'sp' version compatibility issues |
| bru_safe_terra | Check for potential 'terra' installation issues |
| bru_set_missing | Set missing values in observation models |
| bru_standardise_names | Standardise inla hyperparameter names |
| bru_state | Extract model state properties or samples |
| bru_summarise | Summarise and annotate data |
| bru_timings | Extract timing information from fitted bru object |
| bru_timings_plot | Plot inlabru iteration timings |
| bru_transformation | Transformation tools |
| bru_used | List components used in a model |
| bru_used_update | Update used_component information objects |
| bru_used_vars | Extract basic variable names from expression |
| cv_hex | Hexagon tiling of region |
| cv_partition | Grid partitioning |
| deltaIC | Summarise DIC from 'lgcp' estimates. |
| devel.cvmeasure | Variance and correlations measures for prediction components |
| eval_spatial | Evaluate spatial covariates |
| evaluate_effect | Evaluate a component effect |
| evaluate_model | Evaluate or sample from a posterior result given a model and... |
| evaluate_predictor | Evaluate component effects or expressions |
| expand_labels | Expand labels |
| extract_property | Extract a summary property from all results of an inla result |
| generate | Sampling based on bru posteriors |
| gg | ggplot2 geomes for inlabru related objects |
| gg.bru_prediction | Geom for predictions |
| gg.fm_mesh_1d | Geom for fm_mesh_1d objects |
| gg.fm_mesh_2d | Geom for fm_mesh_2d objects |
| gg.matrix | Geom for matrix |
| gg.RasterLayer | Geom for RasterLayer objects |
| gg.sf | Geom helper for sf objects |
| gg.Spatial | Geoms for sp Spatial objects |
| gg.SpatRaster | Geom wrapper for SpatRaster objects |
| glance.bru | Glance at a bru model fit |
| glplot | Render objects using RGL |
| gorillas | Deprecated alias for sp version of the gorillas dataset |
| gorillas_sf | Gorilla nesting sites in sf format |
| ibm_as_taylor | Compute a mapper linearisation |
| ibm_eval | Evaluate a mapping |
| ibm_eval2 | Evaluate a mapper and its Jacobian |
| ibm_eval_methods | Specific 'ibm_eval' method implementations |
| ibm_inla_subset | Find index subset of INLA visible states |
| ibm_input | Interface between 'bru_input' and 'bru_mapper' |
| ibm_invalid_output | Detect invalid input to a mapper |
| ibm_is_linear | Check if a mapper is linear/affine |
| ibm_is_rowwise | Check if a mapper is rowwise |
| ibm_jacobian | Jacobian of a mapper |
| ibm_n | Size of the latent vector of a mapping |
| ibm_names | Names of submapper |
| ibm_n_output | Output size of a mapping |
| ibm_simplify | Simplify a mapper |
| ibm_values | Value vector for a mapping |
| iinla | Iterated INLA |
| inlabru-deprecated | Deprecated functions in inlabru |
| inlabru_group_cv_block_conversion | Convert node-block indices into groups of node indices |
| inlabru-package | inlabru |
| inla_subset_eval | Obtain inla index subset information |
| lgcp | Log Gaussian Cox process (LGCP) inference using INLA |
| lgcp_IC | Information criteria for point processes |
| local_testthat | Unit test helpers |
| materncov.bands | Matern correlation or covariance function approximate... |
| mexdolphin | Deprecated alias for sp version of the mexdolphin dataset |
| mexdolphin_sf | Pan-tropical spotted dolphins in the Gulf of Mexico |
| mrsea | Marine renewables strategic environmental assessment |
| multiplot | Multiple ggplots on a page. |
| new_bru_log | Create a 'bru_log' object |
| new_bru_used | Store information about used components |
| parse_inclusion | Parse inclusion of component labels in a predictor expression |
| pcmatern_B | Make hierarchical mesh basis functions |
| plot.bru | Plot method for posterior marginals estimated by bru |
| plotsample | Create a plot sample. |
| point2count | Convert a plot sample of points into one of counts. |
| Poisson1_1D | 1-Dimensional Homogeneous Poisson example. |
| Poisson2_1D | 1-Dimensional NonHomogeneous Poisson example. |
| Poisson3_1D | 1-Dimensional NonHomogeneous Poisson example. |
| predict | Prediction from fitted bru model |
| reexports | Objects exported from other packages |
| robins_subset | robins_subset |
| sample.lgcp | Sample from an inhomogeneous Poisson process |
| shrimp | Blue and red shrimp in the Western Mediterranean Sea |
| sline | Convert data frame to SpatialLinesDataFrame |
| spatial.to.ppp | Convert SpatialPoints and boundary polygon to spatstat ppp... |
| spde.posterior | Posteriors of SPDE hyper parameters and Matern correlation or... |
| spoly | Convert a data.frame of boundary points into a... |
| summary.bru_comp | Summarise components |
| summary.bru_input | Summarise component inputs |
| summary.bru_options | Print inlabru options |
| tidy.bru | Extract a bru model fit into a tidy tibble |
| toygroups | Simulated 1D animal group locations and group sizes |
| toypoints | Simulated 2D point process data |
