# Bayesian Latent Gaussian Modelling using INLA and Extensions

## Documentation for package ‘inlabru’ version 2.13.0

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

A B C D E F G I L M P R S T misc

inlabru-package | inlabru

## -- A --

as.bru_options | Create or update an options objects
as.character.bru_log | Access methods for 'bru_log' objects
as_bm_list | Methods for mapper lists
as_bm_list.bm_list | Methods for mapper lists
as_bm_list.bru_comp_list | Methods for mapper lists
as_bm_list.list | Methods for mapper lists
as_bru_mapper | Methods for mapper extraction
as_bru_mapper.bru_comp | Methods for mapper extraction
as_bru_mapper.bru_mapper | Methods for mapper extraction
as_bru_mapper.bru_subcomp | Methods for mapper extraction

## -- B --

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_factor | Mapper for factor variables
bm_fmesher | Mapper for general 'fmesher' function space objects
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_logsumexp | Mapper for log-sum-exp aggregation
bm_marginal | Mapper for marginal distribution transformation
bm_matrix | Mapper for matrix multiplication
bm_mesh_B | Mapper for basis conversion
bm_multi | Mapper for tensor product domains
bm_pipe | Mapper for linking several mappers in sequence
bm_repeat | Mapper for repeating a mapper
bm_scale | Mapper for element-wise scaling
bm_shift | Mapper for element-wise shifting
bm_sum | Mapper for adding multiple mappers
bm_taylor | Mapper for linear Taylor approximations
bru | Convenient model fitting using (iterated) INLA
bru_comp | Latent model component construction
bru_comp.character | Latent model component construction
bru_component | Latent model component construction
bru_component_eval | Evaluate component values in predictor expressions
bru_component_list | Methods for inlabru component lists
bru_comp_eval | Evaluate component values in predictor expressions
bru_comp_list | Methods for inlabru component lists
bru_comp_list.formula | Methods for inlabru component lists
bru_comp_list.list | Methods for inlabru component lists
bru_convergence_plot | Plot inlabru convergence diagnostics
bru_fill_missing | Fill in missing values in Spatial grids
bru_forward_transformation | Transformation tools
bru_get_mapper | Extract mapper information from INLA model component objects
bru_get_mapper.inla.rgeneric | Extract mapper information from INLA model component objects
bru_get_mapper.inla.spde | Extract mapper information from INLA model component objects
bru_get_mapper_safely | Extract mapper information from INLA model component objects
bru_info | Methods for bru_info objects
bru_info.bru | Methods for bru_info objects
bru_info.character | Methods for bru_info objects
bru_inverse_transformation | Transformation tools
bru_like_list | Observation model construction for usage with 'bru()'
bru_log | Access methods for 'bru_log' objects
bru_log.bru | Access methods for 'bru_log' objects
bru_log.bru_log | Access methods for 'bru_log' objects
bru_log.character | Access methods for 'bru_log' objects
bru_log.iinla | Access methods for 'bru_log' objects
bru_log_abort | Add a log message
bru_log_bookmark | Methods for 'bru_log' bookmarks
bru_log_bookmarks | Methods for 'bru_log' bookmarks
bru_log_index | Position methods for 'bru_log' objects
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_log_warn | Add a log message
bru_mapper | Constructors for 'bru_mapper' objects
bru_mapper.fm_mesh_1d | Mapper for 'fm_mesh_1d'
bru_mapper.fm_mesh_2d | Mapper for 'fm_mesh_2d'
bru_mapper_aggregate | Mapper for aggregation
bru_mapper_collect | Mapper for concatenated variables
bru_mapper_const | Constant mapper
bru_mapper_define | Constructors for 'bru_mapper' objects
bru_mapper_factor | Mapper for factor variables
bru_mapper_fmesher | Mapper for general 'fmesher' function space objects
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_repeat | Mapper for repeating a mapper
bru_mapper_scale | Mapper for element-wise scaling
bru_mapper_shift | Mapper for element-wise shifting
bru_mapper_sum | Mapper for adding multiple mappers
bru_mapper_taylor | Mapper for linear Taylor approximations
bru_model_mapper_methods | Mapper methods for model objects
bru_obs | Observation model construction for usage with 'bru()'
bru_obs_list | Observation model construction for usage with 'bru()'
bru_obs_list.bru_obs_list | Observation model construction for usage with 'bru()'
bru_obs_list.list | Observation model construction for usage with 'bru()'
bru_options | Create or update an options objects
bru_options_check | Create or update an options objects
bru_options_default | Create or update an options objects
bru_options_get | Create or update an options objects
bru_options_reset | Create or update an options objects
bru_options_set | Create or update an options objects
bru_options_set_local | Create or update an options objects
bru_rerun | Convenient model fitting using (iterated) INLA
bru_response_size | Response size queries
bru_response_size.bru | Response size queries
bru_response_size.bru_info | Response size queries
bru_response_size.bru_obs | Response size queries
bru_response_size.bru_obs_list | Response size queries
bru_response_size.default | Response size queries
bru_response_size.inla.surv | Response size queries
bru_set_missing | Set missing values in observation models
bru_set_missing.bru | Set missing values in observation models
bru_set_missing.bru_obs | Set missing values in observation models
bru_set_missing.bru_obs_list | Set missing values in observation models
bru_timings | Extract timing information from fitted bru object
bru_timings.bru | Extract timing information from fitted bru object
bru_timings_plot | Plot inlabru iteration timings
bru_transformation | Transformation tools

## -- C --

c.bm_list | Methods for mapper lists
c.bru_comp | Methods for inlabru component lists
c.bru_comp_list | Methods for inlabru component lists
c.bru_log | Access methods for 'bru_log' objects
c.bru_mapper | Methods for mapper lists
c.bru_obs | Observation model construction for usage with 'bru()'
c.bru_obs_list | Observation model construction for usage with 'bru()'
component | Latent model component construction
component_list | Methods for inlabru component lists
countdata1 | 1-Dimensional Homogeneous Poisson example.
countdata2 | 1-Dimensional NonHomogeneous Poisson example.
countdata3a | 1-Dimensional NonHomogeneous Poisson example.
countdata3b | 1-Dimensional NonHomogeneous Poisson example.
cov2_1D | 1-Dimensional NonHomogeneous Poisson example.

## -- D --

deltaIC | Summarise DIC and WAIC from 'lgcp' objects.
devel.cvmeasure | Variance and correlations measures for prediction components

## -- E --

eval_spatial | Evaluate spatial covariates
eval_spatial.sf | Evaluate spatial covariates
eval_spatial.SpatialGridDataFrame | Evaluate spatial covariates
eval_spatial.SpatialPixelsDataFrame | Evaluate spatial covariates
eval_spatial.SpatialPolygonsDataFrame | Evaluate spatial covariates
eval_spatial.SpatRaster | Evaluate spatial covariates
eval_spatial.stars | Evaluate spatial covariates
E_nc1 | 1-Dimensional Homogeneous Poisson example.
E_nc2 | 1-Dimensional NonHomogeneous Poisson example.
E_nc3a | 1-Dimensional NonHomogeneous Poisson example.
E_nc3b | 1-Dimensional NonHomogeneous Poisson example.

## -- F --

format.bm_collect | mapper object summaries
format.bm_list | mapper object summaries
format.bm_multi | mapper object summaries
format.bm_pipe | mapper object summaries
format.bm_repeat | mapper object summaries
format.bm_sum | mapper object summaries
format.bru_log | Access methods for 'bru_log' objects
format.bru_mapper | mapper object summaries

## -- G --

generate | Generate samples from fitted bru models
generate.bru | 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 fm_mesh_2d objects
gg.matrix | Geom for matrix
gg.prediction | Geom for predictions
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
glplot.fm_mesh_2d | Render objects using RGL
glplot.SpatialLines | Render objects using RGL
glplot.SpatialPoints | Render objects using RGL
gorillas_sf | Gorilla nesting sites in sf format
gorillas_sf_gcov | Gorilla nesting sites in sf format
gorillas_sp | Gorilla nesting sites in sf format

## -- I --

ibm_eval | Generic methods for bru_mapper objects
ibm_eval.bm_aggregate | Mapper for aggregation
ibm_eval.bm_collect | Mapper for concatenated variables
ibm_eval.bm_const | Constant mapper
ibm_eval.bm_logsumexp | Mapper for log-sum-exp aggregation
ibm_eval.bm_marginal | Mapper for marginal distribution transformation
ibm_eval.bm_multi | Mapper for tensor product domains
ibm_eval.bm_pipe | Mapper for linking several mappers in sequence
ibm_eval.bm_repeat | Mapper for repeating a mapper
ibm_eval.bm_scale | Mapper for element-wise scaling
ibm_eval.bm_shift | Mapper for element-wise shifting
ibm_eval.bm_sum | Mapper for adding multiple mappers
ibm_eval.bm_taylor | Mapper for linear Taylor approximations
ibm_eval.default | Generic methods for bru_mapper objects
ibm_eval2 | Generic methods for bru_mapper objects
ibm_eval2.bm_pipe | Mapper for linking several mappers in sequence
ibm_eval2.default | Generic methods for bru_mapper objects
ibm_inla_subset | Generic methods for bru_mapper objects
ibm_inla_subset.default | Generic methods for bru_mapper objects
ibm_invalid_output | Generic methods for bru_mapper objects
ibm_invalid_output.bm_collect | Mapper for concatenated variables
ibm_invalid_output.bm_index | Mapper for indexed variables
ibm_invalid_output.bm_multi | Mapper for tensor product domains
ibm_invalid_output.bm_repeat | Mapper for repeating a mapper
ibm_invalid_output.bm_sum | Mapper for adding multiple mappers
ibm_invalid_output.default | Generic methods for bru_mapper objects
ibm_is_linear | Generic methods for bru_mapper objects
ibm_is_linear.bm_collect | Mapper for concatenated variables
ibm_is_linear.bm_multi | Mapper for tensor product domains
ibm_is_linear.bm_sum | Mapper for adding multiple mappers
ibm_is_linear.default | Generic methods for bru_mapper objects
ibm_jacobian | Generic methods for bru_mapper objects
ibm_jacobian.bm_aggregate | Mapper for aggregation
ibm_jacobian.bm_collect | Mapper for concatenated variables
ibm_jacobian.bm_const | Constant mapper
ibm_jacobian.bm_factor | Mapper for factor variables
ibm_jacobian.bm_fmesher | Mapper for general 'fmesher' function space objects
ibm_jacobian.bm_fm_mesh_1d | Mapper for 'fm_mesh_1d'
ibm_jacobian.bm_fm_mesh_2d | Mapper for 'fm_mesh_2d'
ibm_jacobian.bm_harmonics | Mapper for cos/sin functions
ibm_jacobian.bm_index | Mapper for indexed variables
ibm_jacobian.bm_inla_mesh_1d | Mapper for 'fm_mesh_1d'
ibm_jacobian.bm_inla_mesh_2d | Mapper for 'fm_mesh_2d'
ibm_jacobian.bm_linear | Mapper for a linear effect
ibm_jacobian.bm_logsumexp | Mapper for log-sum-exp aggregation
ibm_jacobian.bm_marginal | Mapper for marginal distribution transformation
ibm_jacobian.bm_matrix | Mapper for matrix multiplication
ibm_jacobian.bm_mesh_B | Mapper for basis conversion
ibm_jacobian.bm_multi | Mapper for tensor product domains
ibm_jacobian.bm_pipe | Mapper for linking several mappers in sequence
ibm_jacobian.bm_repeat | Mapper for repeating a mapper
ibm_jacobian.bm_scale | Mapper for element-wise scaling
ibm_jacobian.bm_shift | Mapper for element-wise shifting
ibm_jacobian.bm_sum | Mapper for adding multiple mappers
ibm_jacobian.bm_taylor | Mapper for linear Taylor approximations
ibm_jacobian.default | Generic methods for bru_mapper objects
ibm_linear | Generic methods for bru_mapper objects
ibm_linear.bm_collect | Mapper for concatenated variables
ibm_linear.bm_list | Methods for mapper lists
ibm_linear.bm_multi | Mapper for tensor product domains
ibm_linear.bm_repeat | Mapper for repeating a mapper
ibm_linear.bm_sum | Mapper for adding multiple mappers
ibm_linear.bru_comp | Mapper methods for model objects
ibm_linear.bru_comp_list | Mapper methods for model objects
ibm_linear.bru_model | Mapper methods for model objects
ibm_linear.default | Generic methods for bru_mapper objects
ibm_n | Generic methods for bru_mapper objects
ibm_n.bm_aggregate | Mapper for aggregation
ibm_n.bm_collect | Mapper for concatenated variables
ibm_n.bm_const | Constant mapper
ibm_n.bm_factor | Mapper for factor variables
ibm_n.bm_fmesher | Mapper for general 'fmesher' function space objects
ibm_n.bm_fm_mesh_1d | Mapper for 'fm_mesh_1d'
ibm_n.bm_fm_mesh_2d | Mapper for 'fm_mesh_2d'
ibm_n.bm_harmonics | Mapper for cos/sin functions
ibm_n.bm_inla_mesh_1d | Mapper for 'fm_mesh_1d'
ibm_n.bm_inla_mesh_2d | Mapper for 'fm_mesh_2d'
ibm_n.bm_linear | Mapper for a linear effect
ibm_n.bm_marginal | Mapper for marginal distribution transformation
ibm_n.bm_matrix | Mapper for matrix multiplication
ibm_n.bm_mesh_B | Mapper for basis conversion
ibm_n.bm_multi | Mapper for tensor product domains
ibm_n.bm_pipe | Mapper for linking several mappers in sequence
ibm_n.bm_repeat | Mapper for repeating a mapper
ibm_n.bm_scale | Mapper for element-wise scaling
ibm_n.bm_shift | Mapper for element-wise shifting
ibm_n.bm_sum | Mapper for adding multiple mappers
ibm_n.bm_taylor | Mapper for linear Taylor approximations
ibm_n.default | Generic methods for bru_mapper objects
ibm_names | Generic methods for bru_mapper objects
ibm_names.bm_collect | Mapper for concatenated variables
ibm_names.bm_multi | Mapper for tensor product domains
ibm_names.bm_sum | Mapper for adding multiple mappers
ibm_names.default | Generic methods for bru_mapper objects
ibm_names<- | Generic methods for bru_mapper objects
ibm_names<-.bm_collect | Mapper for concatenated variables
ibm_names<-.bm_multi | Mapper for tensor product domains
ibm_names<-.bm_sum | Mapper for adding multiple mappers
ibm_names<-.bru_mapper_collect | Mapper for concatenated variables
ibm_names<-.bru_mapper_multi | Mapper for tensor product domains
ibm_names<-.bru_mapper_sum | Mapper for adding multiple mappers
ibm_n_output | Generic methods for bru_mapper objects
ibm_n_output.bm_aggregate | Mapper for aggregation
ibm_n_output.bm_collect | Mapper for concatenated variables
ibm_n_output.bm_marginal | Mapper for marginal distribution transformation
ibm_n_output.bm_multi | Mapper for tensor product domains
ibm_n_output.bm_pipe | Mapper for linking several mappers in sequence
ibm_n_output.bm_repeat | Mapper for repeating a mapper
ibm_n_output.bm_scale | Mapper for element-wise scaling
ibm_n_output.bm_shift | Mapper for element-wise shifting
ibm_n_output.bm_sum | Mapper for adding multiple mappers
ibm_n_output.bm_taylor | Mapper for linear Taylor approximations
ibm_n_output.default | Generic methods for bru_mapper objects
ibm_simplify | Generic methods for bru_mapper objects
ibm_simplify.bm_list | Methods for mapper lists
ibm_simplify.bm_pipe | Mapper for linking several mappers in sequence
ibm_simplify.bru_comp | Mapper methods for model objects
ibm_simplify.bru_comp_list | Mapper methods for model objects
ibm_simplify.bru_model | Mapper methods for model objects
ibm_simplify.default | Generic methods for bru_mapper objects
ibm_values | Generic methods for bru_mapper objects
ibm_values.bm_aggregate | Mapper for aggregation
ibm_values.bm_collect | Mapper for concatenated variables
ibm_values.bm_const | Constant mapper
ibm_values.bm_factor | Mapper for factor variables
ibm_values.bm_fmesher | Mapper for general 'fmesher' function space objects
ibm_values.bm_fm_mesh_1d | Mapper for 'fm_mesh_1d'
ibm_values.bm_fm_mesh_2d | Mapper for 'fm_mesh_2d'
ibm_values.bm_inla_mesh_1d | Mapper for 'fm_mesh_1d'
ibm_values.bm_inla_mesh_2d | Mapper for 'fm_mesh_2d'
ibm_values.bm_linear | Mapper for a linear effect
ibm_values.bm_marginal | Mapper for marginal distribution transformation
ibm_values.bm_matrix | Mapper for matrix multiplication
ibm_values.bm_mesh_B | Mapper for basis conversion
ibm_values.bm_multi | Mapper for tensor product domains
ibm_values.bm_pipe | Mapper for linking several mappers in sequence
ibm_values.bm_repeat | Mapper for repeating a mapper
ibm_values.bm_scale | Mapper for element-wise scaling
ibm_values.bm_shift | Mapper for element-wise shifting
ibm_values.bm_sum | Mapper for adding multiple mappers
ibm_values.bm_taylor | Mapper for linear Taylor approximations
ibm_values.default | Generic methods for bru_mapper objects
inlabru | inlabru

## -- L --

lambda1_1D | 1-Dimensional Homogeneous Poisson example.
lambda2_1D | 1-Dimensional NonHomogeneous Poisson example.
lambda3_1D | 1-Dimensional NonHomogeneous Poisson example.
length.bru_log | Access methods for 'bru_log' objects
lgcp | Log Gaussian Cox process (LGCP) inference using INLA
like | Observation model construction for usage with 'bru()'
like_list | Observation model construction for usage with 'bru()'

## -- M --

mexdolphin_sf | Pan-tropical spotted dolphins in the Gulf of Mexico
mexdolphin_sp | Pan-tropical spotted dolphins in the Gulf of Mexico
mrsea | Marine renewables strategic environmental assessment
multiplot | Multiple ggplots on a page.

## -- P --

plot.bru | Plot method for posterior marginals estimated by bru
plot.bru_prediction | Plot prediction using ggplot2
plot.prediction | Plot prediction using ggplot2
plotmarginal.inla | 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.bru | Prediction from fitted bru model
print.bm_list | mapper object summaries
print.bru | Convenient model fitting using (iterated) INLA
print.bru_info | Methods for bru_info objects
print.bru_log | Access methods for 'bru_log' objects
print.bru_mapper | mapper object summaries
print.bru_obs | Summary and print methods for observation models
print.bru_obs_list | Summary and print methods for observation models
print.summary_bru | Summary for an inlabru fit
print.summary_bru_info | Methods for bru_info objects
print.summary_bru_mapper | mapper object summaries
print.summary_bru_obs | Summary and print methods for observation models
print.summary_bru_obs_list | Summary and print methods for observation models
print.summary_bru_options | Print inlabru options
pts1 | 1-Dimensional Homogeneous Poisson example.
pts2 | 1-Dimensional NonHomogeneous Poisson example.
pts3 | 1-Dimensional NonHomogeneous Poisson example.

## -- R --

robins_subset | robins_subset

## -- S --

sample.lgcp | Sample from an inhomogeneous Poisson process
shrimp | Blue and red shrimp in the Western Mediterranean Sea
spde.posterior | Posteriors of SPDE hyper parameters and Matern correlation or covariance function.
summary.bru | Summary for an inlabru fit
summary.bru_info | Methods for bru_info objects
summary.bru_mapper | mapper object summaries
summary.bru_obs | Summary and print methods for observation models
summary.bru_obs_list | Summary and print methods for observation models
summary.bru_options | Print inlabru options

## -- T --

toygroups | Simulated 1D animal group locations and group sizes
toypoints | Simulated 2D point process data

## -- misc --

[.bm_collect | Mapper for concatenated variables
[.bm_list | Methods for mapper lists
[.bm_multi | Mapper for tensor product domains
[.bm_sum | Mapper for adding multiple mappers
[.bru_comp_list | Methods for inlabru component lists
[.bru_log | Access methods for 'bru_log' objects
[.bru_mapper_collect | Mapper for concatenated variables
[.bru_mapper_multi | Mapper for tensor product domains
[.bru_mapper_sum | Mapper for adding multiple mappers
[.bru_obs_list | Observation model construction for usage with 'bru()'