Bayesian Latent Gaussian Modelling using INLA and Extensions


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Documentation for package ‘inlabru’ version 2.5.2

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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_forward_transformation Transformation tools
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_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_collect 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_matrix 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 --

c.component_list Methods for inlabru component lists
component Latent model component construction
component.character Latent model component construction
component_eval Evaluate component values in predictor expressions
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_collect Implementation methods for 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_matrix 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_inla_subset Methods for 'bru_mapper' objects
ibm_inla_subset.default Methods for 'bru_mapper' objects
ibm_n Methods for 'bru_mapper' objects
ibm_n.bru_mapper_collect Implementation methods for 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_matrix 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_collect Implementation methods for 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_collect Implementation methods for 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_matrix 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_collect Implementation methods for mapper objects
names.bru_mapper_multi Implementation methods for mapper objects
names<-.bru_mapper_collect 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_collect Implementation methods for mapper objects
[.bru_mapper_multi Implementation methods for mapper objects
[.component_list Methods for inlabru component lists