Function reference • inlabru

Model construction and estimation

Functions for constructing models and performing estimation.

inlabru-package _PACKAGE inlabru: inlabru

bru() bru_rerun(): Convenient model fitting using (iterated) INLA

bru_options() as.bru_options() bru_options_default() bru_options_check() bru_options_get() bru_options_set() bru_options_reset(): Create or update an options objects

component(): Latent model component construction

component_eval(): Evaluate component values in predictor expressions

component_list() c(<component_list>) c(<component>) `[`(<component_list>): Methods for inlabru component lists

like() like_list() c(<bru_like>) c(<bru_like_list>) `[`(<bru_like_list>): Observation model construction for usage with bru()

lgcp(): Log Gaussian Cox process (LGCP) inference using INLA

Posterior evaluation

Functions for evaluating posterior properties.

generate(): Generate samples from fitted bru models

predict(<bru>): Prediction from fitted bru model

spde.posterior(): Posteriors of SPDE hyper parameters and Matern correlation or covariance function.

deltaIC(): Summarise DIC and WAIC from lgcp objects.

devel.cvmeasure(): Variance and correlations measures for prediction components

Optimization log information

Accessing the optimization text log, and plotting the optimization convergence.

bru_log() print(<bru_log>) as.character(<bru_log>) `[`(<bru_log>) c(<bru_log>) length(<bru_log>): Access methods for bru_log objects

bru_log_bookmark() bru_log_bookmarks(): Methods for bru_log bookmarks

bru_log_message(): Add a log message

bru_log_new(): Create a bru_log object

bru_log_offset() bru_log_index(): Position methods for bru_log objects

bru_log_reset(): Clear log contents

bru_convergence_plot(): Plot inlabru convergence diagnostics

bru_timings_plot(): Plot inlabru iteration timings

Mapper methods

Functions for bru_mapper handling.

bru_get_mapper() bru_get_mapper_safely(): Extract mapper information from INLA model component objects

bru_mapper() bru_mapper_define(): Constructors for bru_mapper objects

bru_mapper_aggregate() ibm_n(<bru_mapper_aggregate>) ibm_n_output(<bru_mapper_aggregate>) ibm_values(<bru_mapper_aggregate>) ibm_jacobian(<bru_mapper_aggregate>) ibm_eval(<bru_mapper_aggregate>): Mapper for aggregation

bru_mapper_collect() ibm_n(<bru_mapper_collect>) ibm_n_output(<bru_mapper_collect>) ibm_values(<bru_mapper_collect>) ibm_is_linear(<bru_mapper_collect>) ibm_jacobian(<bru_mapper_collect>) ibm_eval(<bru_mapper_collect>) ibm_linear(<bru_mapper_collect>) ibm_invalid_output(<bru_mapper_collect>) `[`(<bru_mapper_collect>) ibm_names(<bru_mapper_collect>) `ibm_names<-`(<bru_mapper_collect>): Mapper for concatenated variables

bru_mapper_const() ibm_n(<bru_mapper_const>) ibm_values(<bru_mapper_const>) ibm_jacobian(<bru_mapper_const>) ibm_eval(<bru_mapper_const>): Constant mapper

bru_mapper_factor() ibm_n(<bru_mapper_factor>) ibm_values(<bru_mapper_factor>) ibm_jacobian(<bru_mapper_factor>): Mapper for factor variables

bru_mapper(<fm_mesh_1d>) ibm_n(<bru_mapper_fm_mesh_1d>) ibm_values(<bru_mapper_fm_mesh_1d>) ibm_jacobian(<bru_mapper_fm_mesh_1d>) bru_mapper(<inla.mesh.1d>) ibm_n(<bru_mapper_inla_mesh_1d>) ibm_values(<bru_mapper_inla_mesh_1d>) ibm_jacobian(<bru_mapper_inla_mesh_1d>): Mapper for fm_mesh_1d

bru_mapper(<fm_mesh_2d>) ibm_n(<bru_mapper_fm_mesh_2d>) ibm_values(<bru_mapper_fm_mesh_2d>) ibm_jacobian(<bru_mapper_fm_mesh_2d>) bru_mapper(<inla.mesh>) ibm_n(<bru_mapper_inla_mesh_2d>) ibm_values(<bru_mapper_inla_mesh_2d>) ibm_jacobian(<bru_mapper_inla_mesh_2d>): Mapper for fm_mesh_2d

ibm_n() ibm_n_output() ibm_values() ibm_is_linear() ibm_jacobian() ibm_linear() ibm_simplify() ibm_eval() ibm_eval2() ibm_names() `ibm_names<-`() ibm_inla_subset() ibm_invalid_output(): Generic methods for bru_mapper objects

bru_mapper_harmonics() ibm_n(<bru_mapper_harmonics>) ibm_jacobian(<bru_mapper_harmonics>): Mapper for cos/sin functions

bru_mapper_index() ibm_invalid_output(<bru_mapper_index>) ibm_jacobian(<bru_mapper_index>): Mapper for indexed variables

bru_mapper_linear() ibm_n(<bru_mapper_linear>) ibm_values(<bru_mapper_linear>) ibm_jacobian(<bru_mapper_linear>): Mapper for a linear effect

bru_mapper_logsumexp() ibm_jacobian(<bru_mapper_logsumexp>) ibm_eval(<bru_mapper_logsumexp>): Mapper for log-sum-exp aggregation

bru_mapper_marginal() ibm_n(<bru_mapper_marginal>) ibm_n_output(<bru_mapper_marginal>) ibm_values(<bru_mapper_marginal>) ibm_jacobian(<bru_mapper_marginal>) ibm_eval(<bru_mapper_marginal>): Mapper for marginal distribution transformation

bru_mapper_matrix() ibm_n(<bru_mapper_matrix>) ibm_values(<bru_mapper_matrix>) ibm_jacobian(<bru_mapper_matrix>): Mapper for matrix multiplication

bru_mapper_mesh_B() ibm_n(<bru_mapper_mesh_B>) ibm_values(<bru_mapper_mesh_B>) ibm_jacobian(<bru_mapper_mesh_B>): Mapper for basis conversion

bru_mapper_multi() ibm_n(<bru_mapper_multi>) ibm_n_output(<bru_mapper_multi>) ibm_values(<bru_mapper_multi>) ibm_is_linear(<bru_mapper_multi>) ibm_jacobian(<bru_mapper_multi>) ibm_linear(<bru_mapper_multi>) ibm_eval(<bru_mapper_multi>) ibm_invalid_output(<bru_mapper_multi>) `[`(<bru_mapper_multi>) ibm_names(<bru_mapper_multi>) `ibm_names<-`(<bru_mapper_multi>): Mapper for tensor product domains

bru_mapper_pipe() ibm_n(<bru_mapper_pipe>) ibm_n_output(<bru_mapper_pipe>) ibm_values(<bru_mapper_pipe>) ibm_jacobian(<bru_mapper_pipe>) ibm_eval(<bru_mapper_pipe>) ibm_eval2(<bru_mapper_pipe>) ibm_simplify(<bru_mapper_pipe>): Mapper for linking several mappers in sequence

bru_mapper_scale() ibm_n(<bru_mapper_scale>) ibm_n_output(<bru_mapper_scale>) ibm_values(<bru_mapper_scale>) ibm_jacobian(<bru_mapper_scale>) ibm_eval(<bru_mapper_scale>): Mapper for element-wise scaling

bru_mapper_shift() ibm_n(<bru_mapper_shift>) ibm_n_output(<bru_mapper_shift>) ibm_values(<bru_mapper_shift>) ibm_jacobian(<bru_mapper_shift>) ibm_eval(<bru_mapper_shift>): Mapper for element-wise shifting

bru_mapper_taylor() ibm_n(<bru_mapper_taylor>) ibm_n_output(<bru_mapper_taylor>) ibm_values(<bru_mapper_taylor>) ibm_jacobian(<bru_mapper_taylor>) ibm_eval(<bru_mapper_taylor>): Mapper for linear Taylor approximations

c(<bru_mapper>) c(<bm_list>) `[`(<bm_list>): Methods for mapper lists

bru_forward_transformation() bru_inverse_transformation(): Transformation tools

Miscellaneous

Miscellaneous functions.

eval_spatial(): Evaluate spatial covariates

bru_fill_missing(): Fill in missing values in Spatial grids

point2count(): Convert a plot sample of points into one of counts.

sample.lgcp(): Sample from an inhomogeneous Poisson process

Plot helpers

Functions for helping build figures.

plot(<bru>): Plot method for posterior marginals estimated by bru

plot(<bru_prediction>) plot(<prediction>): Plot prediction using ggplot2

plotsample(): Create a plot sample.

globe(): Visualize a globe using RGL

gg(<RasterLayer>): Geom for RasterLayer objects

gg(): ggplot2 geomes for inlabru related objects

gg(<SpatRaster>): Geom wrapper for SpatRaster 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(<bru_prediction>) gg(<prediction>): Geom for predictions

gg(<data.frame>): Geom for data.frame

gg(<inla.mesh.1d>): Geom for inla.mesh.1d objects

gg(<inla.mesh>): Geom for inla.mesh objects

gg(<matrix>): Geom for matrix

gg(<sf>): Geom helper for sf objects

glplot(): Render objects using RGL

gm(): ggplot geom for spatial data

gmap(): Plot a map using extent of a spatial object

bincount(): 1D LGCP bin count simulation and comparison with data

Printing methods

Functions for printing.

summary(<bru_info>) print(<summary_bru_info>) bru_info(): Methods for bru_info objects

bru_log() print(<bru_log>) as.character(<bru_log>) `[`(<bru_log>) c(<bru_log>) length(<bru_log>): Access methods for bru_log objects

summary(<bru_mapper>) summary(<bru_mapper_multi>) summary(<bru_mapper_pipe>) summary(<bru_mapper_collect>) print(<summary_bru_mapper>) print(<bru_mapper>): mapper object summaries

summary(<bru>) print(<summary_bru>): Summary for an inlabru fit

summary(<bru_options>) print(<summary_bru_options>): Print inlabru options

Data objects

Data objects

Poisson1_1D: 1-Dimensional Homogeneous Poisson example.

Poisson2_1D: 1-Dimensional NonHomogeneous Poisson example.

Poisson3_1D: 1-Dimensional NonHomogeneous Poisson example.

gorillas gorillas: Gorilla nesting sites

gorillas_sf gorillas_sf gorillas_sf_gcov(): Gorilla nesting sites in sf format

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

robins_subset: robins_subset

seals_sp: Seal pups

shrimp: Blue and red shrimp in the Western Mediterranean Sea

toygroups: Simulated 1D animal group locations and group sizes

Internal helper functions

Helper functions for more low level operations.

evaluate_comp_lin(): Compute all component linearisations

evaluate_index(): Compute all index values

evaluate_inputs(): Compute all component inputs

expand_labels(): Expand labels

inla.stack.mjoin(): Join stacks intended to be run with different likelihoods

spatial.to.ppp(): Convert SpatialPoints and boundary polygon to spatstat ppp object

bru_make_stack(): Build an inla data stack from linearisation information

bru_summarise(): Summarise and annotate data

bru_standardise_names(): Standardise inla hyperparameter names

bru_safe_inla(): Load INLA safely for examples and tests

bru_safe_sp(): Check for potential sp version compatibility issues

bru_call_options(): Additional bru options

bru_compute_linearisation(): Compute inlabru model linearisation information

Re-exported fmesher functions

Functions that used to be part of inlabru but are now in the fmesher package, and re-exported by inlabru for backwards compatibility.

Deprecated methods

Deprecated methods

ipoints(): Generate integration points

pixels(): Generate SpatialPixels covering an inla.mesh

multiplot(): Multiple ggplots on a page.

spoly(): Convert a data.frame of boundary points into a SpatialPolgonsDataFrame

sline(): Convert data frame to SpatialLinesDataFrame