# Bayesian Latent Gaussian Modelling using INLA and Extensions

## Documentation for package ‘inlabru’ version 2.3.1

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

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

## -- A --

as.bru_options | Create or update an options objects

## -- B --

bincount | 1D LGCP bin count simulation and comparison with data
bru | Convenient model fitting using (iterated) INLA
bru_call_options | Additional bru options
bru_component | Latent model component construction
bru_component_list | Methods for inlabru component lists
bru_compute_linearisation | Compute inlabru model linearisation information
bru_compute_linearisation.bru_like | Compute inlabru model linearisation information
bru_compute_linearisation.bru_like_list | Compute inlabru model linearisation information
bru_compute_linearisation.bru_model | Compute inlabru model linearisation information
bru_compute_linearisation.component | Compute inlabru model linearisation information
bru_fill_missing | Fill in missing values in Spatial grids
bru_info | Methods for bru_info objects
bru_info.bru | Methods for bru_info objects
bru_info.character | Methods for bru_info objects
bru_log | inlabru log message methods
bru_log_active | inlabru log message methods
bru_log_get | inlabru log message methods
bru_log_message | inlabru log message methods
bru_log_reset | inlabru log message methods
bru_make_stack | Build an inla data stack from linearisation information
bru_make_stack.bru_like | Build an inla data stack from linearisation information
bru_make_stack.bru_like_list | Build an inla data stack from linearisation information
bru_mapper | Methods for 'bru_mapper' objects
bru_mapper.default | Methods for 'bru_mapper' objects
bru_mapper.inla.mesh | Methods for 'bru_mapper' objects
bru_mapper.inla.mesh.1d | Methods for 'bru_mapper' objects
bru_mapper_factor | Methods for 'bru_mapper' objects
bru_mapper_index | Methods for 'bru_mapper' objects
bru_mapper_linear | Methods for 'bru_mapper' objects
bru_mapper_methods | Implementation methods for mapper objects
bru_mapper_multi | Methods for 'bru_mapper' objects
bru_mapper_offset | Methods for 'bru_mapper' objects
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_rerun | Convenient model fitting using (iterated) INLA
bru_safe_inla | Load INLA safely for examples and tests
bru_standardise_names | Standardise inla hyperparameter names

## -- C --

component | Latent model component construction
component.character | Latent model component construction
component_list | Methods for inlabru component lists
component_list.formula | Methods for inlabru component lists
component_list.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.
cprod | Cross product of integration points

## -- D --

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

## -- E --

evaluate_A | Compute all A-matrices
evaluate_index | Compute all index values
expand_labels | Expand labels
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 --

fm_CRS | Create a coordinate reference system object
fm_crs_get_ellipsoid_radius | Handling CRS/WKT
fm_crs_get_lengthunit | Handling CRS/WKT
fm_crs_get_wkt | Handling CRS/WKT
fm_crs_is_geocent | Handling CRS/WKT
fm_crs_set_ellipsoid_radius | Handling CRS/WKT
fm_crs_set_lengthunit | Handling CRS/WKT
fm_crs_wkt | Handling CRS/WKT
fm_fallback_PROJ6 | PROJ6 detection
fm_has_PROJ6 | PROJ6 detection
fm_not_for_PROJ4 | PROJ6 detection
fm_not_for_PROJ6 | PROJ6 detection
fm_requires_PROJ6 | PROJ6 detection
fm_spTransform | Handle transformation of various inla objects according to coordinate reference systems of sp::CRS or INLA::inla.CRS class.
fm_spTransform.default | Handle transformation of various inla objects according to coordinate reference systems of sp::CRS or INLA::inla.CRS class.
fm_spTransform.inla.mesh | Handle transformation of various inla objects according to coordinate reference systems of sp::CRS or INLA::inla.CRS class.
fm_spTransform.inla.mesh.lattice | Handle transformation of various inla objects according to coordinate reference systems of sp::CRS or INLA::inla.CRS class.
fm_spTransform.inla.mesh.segment | Handle transformation of various inla objects according to coordinate reference systems of sp::CRS or INLA::inla.CRS class.
fm_spTransform.SpatialPoints | Handle transformation of various inla objects according to coordinate reference systems of sp::CRS or INLA::inla.CRS class.
fm_spTransform.SpatialPointsDataFrame | Handle transformation of various inla objects according to coordinate reference systems of sp::CRS or INLA::inla.CRS class.
fm_sp_get_crs | Extract CRS information
fm_wkt_as_wkt_tree | Internal WKT handling
fm_wkt_get_ellipsoid_radius | Handling CRS/WKT
fm_wkt_get_lengthunit | Handling CRS/WKT
fm_wkt_is_geocent | Handling CRS/WKT
fm_wkt_predef | Create a coordinate reference system object
fm_wkt_set_ellipsoid_radius | Handling CRS/WKT
fm_wkt_set_lengthunit | Handling CRS/WKT
fm_wkt_tree_as_wkt | Internal WKT handling
fm_wkt_tree_get_item | Internal WKT handling
fm_wkt_tree_set_item | Internal WKT handling
fm_wkt_unit_params | Handling CRS/WKT

## -- G --

generate | Generate samples from fitted bru models
generate.bru | Generate samples from fitted bru models
gg | ggplot2 geomes for inlabru related objects
gg.data.frame | Geom for data.frame
gg.inla.mesh | Geom for inla.mesh objects
gg.inla.mesh.1d | Geom for inla.mesh.1d objects
gg.matrix | Geom for matrix
gg.prediction | Geom for predictions
gg.RasterLayer | Geom for RasterLayer 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
globe | Plot a globe using rgl
glplot | Render Spatial* and inla.mesh objects using RGL
glplot.inla.mesh | Visualize SpatialPoints using RGL
glplot.SpatialLines | Visualize SpatialLines using RGL
glplot.SpatialPoints | Visualize SpatialPoints using RGL
gm | ggplot geom for spatial data
gmap | Plot a map using extend of a spatial object
gorillas | Gorilla nesting sites

## -- I --

ibm_amatrix | Methods for 'bru_mapper' objects
ibm_amatrix.bru_mapper_factor | Implementation methods for mapper objects
ibm_amatrix.bru_mapper_index | Implementation methods for mapper objects
ibm_amatrix.bru_mapper_inla_mesh_1d | Implementation methods for mapper objects
ibm_amatrix.bru_mapper_inla_mesh_2d | Implementation methods for mapper objects
ibm_amatrix.bru_mapper_linear | Implementation methods for mapper objects
ibm_amatrix.bru_mapper_multi | Implementation methods for mapper objects
ibm_amatrix.bru_mapper_offset | Implementation methods for mapper objects
ibm_amatrix.default | Implementation methods for mapper objects
ibm_n | Methods for 'bru_mapper' objects
ibm_n.bru_mapper_factor | Implementation methods for mapper objects
ibm_n.bru_mapper_inla_mesh_1d | Implementation methods for mapper objects
ibm_n.bru_mapper_inla_mesh_2d | Implementation methods for mapper objects
ibm_n.bru_mapper_linear | Implementation methods for mapper objects
ibm_n.bru_mapper_multi | Implementation methods for mapper objects
ibm_n.bru_mapper_offset | Implementation methods for mapper objects
ibm_n.default | Implementation methods for mapper objects
ibm_valid_input | Methods for 'bru_mapper' objects
ibm_valid_input.bru_mapper_index | Implementation methods for mapper objects
ibm_valid_input.bru_mapper_multi | Implementation methods for mapper objects
ibm_valid_input.default | Implementation methods for mapper objects
ibm_values | Methods for 'bru_mapper' objects
ibm_values.bru_mapper_factor | Implementation methods for mapper objects
ibm_values.bru_mapper_inla_mesh_1d | Implementation methods for mapper objects
ibm_values.bru_mapper_inla_mesh_2d | Implementation methods for mapper objects
ibm_values.bru_mapper_linear | Implementation methods for mapper objects
ibm_values.bru_mapper_multi | Implementation methods for mapper objects
ibm_values.bru_mapper_offset | Implementation methods for mapper objects
ibm_values.default | Implementation methods for mapper objects
iinla.getOption | Deprecated functions in inlabru
iinla.setOption | Deprecated functions in inlabru
init.tutorial | Deprecated functions in inlabru
inla.stack.mjoin | Join stacks intended to be run with different likelihoods
inlabru | inlabru
inlabru-deprecated | Deprecated functions in inlabru
int | Weighted summation (integration) of data frame subsets
ipoints | Generate integration points

## -- L --

lambda1_1D | 1-Dimensional Homogeneous Poisson example.
lambda2_1D | 1-Dimensional NonHomogeneous Poisson example.
lambda3_1D | 1-Dimensional NonHomogeneous Poisson example.
lgcp | Log Gaussian Cox process (LGCP) inference using INLA
like | Likelihood construction for usage with 'bru()'
like_list | Likelihood construction for usage with 'bru()'
like_list.bru_like | Likelihood construction for usage with 'bru()'
like_list.list | Likelihood construction for usage with 'bru()'

## -- M --

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

## -- N --

names.bru_mapper_multi | Implementation methods for mapper objects
names<-.bru_mapper_multi | Implementation methods for mapper objects

## -- P --

pixels | Generate 'SpatialPixels' covering an 'inla.mesh'
plot.bru | Plot method for posterior marginals estimated by bru
plot.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
print.summary_bru | Summary for an inlabru fit
print.summary_bru_info | Methods for bru_info objects
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 --

row_kron | Row-wise Kronecker products

## -- S --

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 object
spde.posterior | Posteriors of SPDE hyper parameters and Matern correlation or covariance function.
spoly | Convert a data.frame of boundary points into a SpatialPolgonsDataFrame
stransform | Coordinate transformation for spatial objects
summary.bru | Summary for an inlabru fit
summary.bru_info | Methods for bru_info objects
summary.bru_options | Print inlabru options
summary_bru | Deprecated functions in inlabru

## -- T --

toygroups | Simulated 1D animal group locations and group sizes

## -- V --

vertices | Vertices
vertices-method | Vertices
vertices.inla.mesh | Extract vertex locations from an 'inla.mesh'

## -- misc --

[.bru_like_list | Likelihood construction for usage with 'bru()'
[.bru_mapper_multi | Implementation methods for mapper objects
[.component_list | Methods for inlabru component lists