Man pages for inlabru-org/inlabru
Bayesian Latent Gaussian Modelling using INLA and Extensions
| add_mappers | Add component input/latent mappers |
| bincount | 1D LGCP bin count simulation and comparison with data |
| bm_list | Methods for mapper lists |
| bru | Convenient model fitting using (iterated) INLA |
| bru_call_options | Additional bru options |
| bru_compute_linearisation | Compute inlabru model linearisation information |
| bru_convergence_plot | Plot inlabru convergence diagnostics |
| bru_env_get | Get access to the internal environment |
| bru_fill_missing | Fill in missing values in Spatial grids |
| bru_get_mapper | Extract mapper information from INLA model component objects |
| bru_info | Methods for bru_info objects |
| bru_int_polygon | Integration points for polygons inside an inla.mesh |
| bru_like_methods | Utility functions for bru likelihood objects |
| 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_new | Create a 'bru_log' object |
| 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_aggregate | Mapper for aggregation |
| bru_mapper_collect | Mapper for concatenated variables |
| bru_mapper_const | Constant mapper |
| bru_mapper_factor | Mapper for factor variables |
| bru_mapper_fm_mesh_1d | Mapper for 'fm_mesh_1d' |
| bru_mapper_fm_mesh_2d | Mapper for 'fm_mesh_2d' |
| bru_mapper_generics | Generic methods for bru_mapper objects |
| bru_mapper_harmonics | Mapper for cos/sin functions |
| bru_mapper_index | Mapper for indexed variables |
| bru_mapper_linear | Mapper for a linear effect |
| bru_mapper_logsumexp | Mapper for log-sum-exp aggregation |
| bru_mapper_marginal | Mapper for marginal distribution transformation |
| bru_mapper_matrix | Mapper for matrix multiplication |
| bru_mapper_mesh_B | Mapper for basis conversion |
| bru_mapper_multi | Mapper for tensor product domains |
| bru_mapper_pipe | Mapper for linking several mappers in sequence |
| bru_mapper_scale | Mapper for element-wise scaling |
| bru_mapper_shift | Mapper for element-wise shifting |
| bru_mapper_summary | mapper object summaries |
| bru_mapper_taylor | Mapper for linear Taylor approximations |
| bru_model | Create an inlabru model object from model components |
| bru_options | Create or update an options objects |
| bru_safe_inla | Load INLA safely for examples and tests |
| bru_safe_sp | Check for potential 'sp' version compatibility issues |
| bru_standardise_names | Standardise inla hyperparameter names |
| bru_summarise | Summarise and annotate data |
| 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 |
| code.components | Convert components to R code |
| comp_lin_eval | Construct component linearisations |
| component | Latent model component construction |
| component_eval | Evaluate component values in predictor expressions |
| component_list | Methods for inlabru component lists |
| cprod | (Blockwise) cross product of integration points |
| deltaIC | Summarise DIC and WAIC from 'lgcp' objects. |
| devel.cvmeasure | Variance and correlations measures for prediction components |
| eval_in_data_context | Evaluate expressions in the data context |
| eval_spatial | Evaluate spatial covariates |
| evaluate_comp_lin | Compute all component linearisations |
| evaluate_comp_simple | Compute simplified component mappings |
| evaluate_comp_simple_list_subsetting | Subsetting of comp_simple_list objects, retaining class |
| evaluate_effect | Evaluate a component effect |
| evaluate_index | Compute all index values |
| evaluate_inputs | Compute all component inputs |
| 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 | Generate samples from fitted bru models |
| gg | ggplot2 geomes for inlabru related objects |
| gg.bru_prediction | Geom for predictions |
| gg.data.frame | Geom for data.frame |
| gg.fm_mesh_1d | Geom for fm_mesh_1d objects |
| gg.fm_mesh_2d | Geom for inla.mesh objects |
| gg.matrix | Geom for matrix |
| gg.RasterLayer | Geom for RasterLayer objects |
| gg.sf | Geom helper for sf objects |
| gg.SpatialGridDataFrame | Geom for SpatialGridDataFrame objects |
| gg.SpatialLines | Geom for SpatialLines objects |
| gg.SpatialPixels | Geom for SpatialPixels objects |
| gg.SpatialPixelsDataFrame | Geom for SpatialPixelsDataFrame objects |
| gg.SpatialPoints | Geom for SpatialPoints objects |
| gg.SpatialPolygons | Geom for SpatialPolygons objects |
| gg.SpatRaster | Geom wrapper for SpatRaster objects |
| globe | Visualize a globe using RGL |
| glplot | Render objects using RGL |
| gm | ggplot geom for spatial data |
| gmap | Plot a map using extent of a spatial object |
| gorillas | Gorilla nesting sites |
| gorillas_sf | Gorilla nesting sites in sf format |
| iinla | Iterated INLA |
| index_eval | Obtain indices |
| inlabru-deprecated | Deprecated functions in inlabru |
| inlabru-package | inlabru |
| inla.stack.mjoin | Join stacks intended to be run with different likelihoods |
| inla_subset_eval | Obtain inla index subset information |
| input_eval | Obtain component inputs |
| integration_weight_aggregation | Aggregate integration weights onto mesh nodes |
| ipoints | Generate integration points |
| lgcp | Log Gaussian Cox process (LGCP) inference using INLA |
| like | Observation model construction for usage with 'bru()' |
| local_testthat | Unit test helpers |
| materncov.bands | Matern correlation or covariance function approximate... |
| mexdolphin | Pan-tropical spotted dolphins in the Gulf of Mexico |
| mexdolphin_sf | Pan-tropical spotted dolphins in the Gulf of Mexico |
| mrsea | Marine renewables strategic environmental assessment |
| multiplot | Multiple ggplots on a page. |
| parse_inclusion | Parse inclusion of component labels in a predictor expression |
| pcmatern_B | Make hierarchical mesh basis functions |
| pixels | Generate 'SpatialPixels' covering an 'inla.mesh' |
| plot.bru | Plot method for posterior marginals estimated by bru |
| plot.bru_prediction | Plot prediction using ggplot2 |
| 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.bru | Prediction from fitted bru model |
| reexports | Objects exported from other packages |
| robins_subset | robins_subset |
| row_kron | Row-wise Kronecker products |
| sample.lgcp | Sample from an inhomogeneous Poisson process |
| seals | Seal pups |
| 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 | Summary for an inlabru fit |
| summary.bru_options | Print inlabru options |
| summary.component | Summarise components |
| toygroups | Simulated 1D animal group locations and group sizes |
| toypoints | Simulated 2D point process data |
