Bayesian Latent Gaussian Modelling using INLA and Extensions

Documentation for package ‘inlabru’ version 2.11.1

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inlabru

-- A --

as.bru_options	Create or update an options objects
as.character.bru_log	Access methods for 'bru_log' objects

-- B --

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_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_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_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_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_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.inla.mesh	Mapper for 'fm_mesh_2d'
bru_mapper.inla.mesh.1d	Mapper for 'fm_mesh_1d'
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_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_taylor	Mapper for linear Taylor approximations
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_safe_sp	Check for potential 'sp' version compatibility issues
bru_standardise_names	Standardise inla hyperparameter names
bru_summarise	Summarise and annotate data
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_like	Observation model construction for usage with 'bru()'
c.bru_like_list	Observation model construction for usage with 'bru()'
c.bru_log	Access methods for 'bru_log' objects
c.bru_mapper	Methods for mapper lists
c.component	Methods for inlabru component lists
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.

-- D --

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

-- E --

evaluate_comp_lin	Compute all component linearisations
evaluate_index	Compute all index values
evaluate_inputs	Compute all component inputs
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
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.

-- 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 inla.mesh objects
gg.inla.mesh	Geom for inla.mesh objects
gg.inla.mesh.1d	Geom for fm_mesh_1d 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.inla.mesh	Render objects using RGL
glplot.SpatialLines	Render objects using RGL
glplot.SpatialPoints	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
gorillas_sf_gcov	Gorilla nesting sites in sf format

-- I --

ibm_eval	Generic methods for bru_mapper objects
ibm_eval.bru_mapper_aggregate	Mapper for aggregation
ibm_eval.bru_mapper_collect	Mapper for concatenated variables
ibm_eval.bru_mapper_const	Constant mapper
ibm_eval.bru_mapper_logsumexp	Mapper for log-sum-exp aggregation
ibm_eval.bru_mapper_marginal	Mapper for marginal distribution transformation
ibm_eval.bru_mapper_multi	Mapper for tensor product domains
ibm_eval.bru_mapper_pipe	Mapper for linking several mappers in sequence
ibm_eval.bru_mapper_scale	Mapper for element-wise scaling
ibm_eval.bru_mapper_shift	Mapper for element-wise shifting
ibm_eval.bru_mapper_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.bru_mapper_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.bru_mapper_collect	Mapper for concatenated variables
ibm_invalid_output.bru_mapper_index	Mapper for indexed variables
ibm_invalid_output.bru_mapper_multi	Mapper for tensor product domains
ibm_invalid_output.default	Generic methods for bru_mapper objects
ibm_is_linear	Generic methods for bru_mapper objects
ibm_is_linear.bru_mapper_collect	Mapper for concatenated variables
ibm_is_linear.bru_mapper_multi	Mapper for tensor product domains
ibm_is_linear.default	Generic methods for bru_mapper objects
ibm_jacobian	Generic methods for bru_mapper objects
ibm_jacobian.bru_mapper_aggregate	Mapper for aggregation
ibm_jacobian.bru_mapper_collect	Mapper for concatenated variables
ibm_jacobian.bru_mapper_const	Constant mapper
ibm_jacobian.bru_mapper_factor	Mapper for factor variables
ibm_jacobian.bru_mapper_fm_mesh_1d	Mapper for 'fm_mesh_1d'
ibm_jacobian.bru_mapper_fm_mesh_2d	Mapper for 'fm_mesh_2d'
ibm_jacobian.bru_mapper_harmonics	Mapper for cos/sin functions
ibm_jacobian.bru_mapper_index	Mapper for indexed variables
ibm_jacobian.bru_mapper_inla_mesh_1d	Mapper for 'fm_mesh_1d'
ibm_jacobian.bru_mapper_inla_mesh_2d	Mapper for 'fm_mesh_2d'
ibm_jacobian.bru_mapper_linear	Mapper for a linear effect
ibm_jacobian.bru_mapper_logsumexp	Mapper for log-sum-exp aggregation
ibm_jacobian.bru_mapper_marginal	Mapper for marginal distribution transformation
ibm_jacobian.bru_mapper_matrix	Mapper for matrix multiplication
ibm_jacobian.bru_mapper_mesh_B	Mapper for basis conversion
ibm_jacobian.bru_mapper_multi	Mapper for tensor product domains
ibm_jacobian.bru_mapper_pipe	Mapper for linking several mappers in sequence
ibm_jacobian.bru_mapper_scale	Mapper for element-wise scaling
ibm_jacobian.bru_mapper_shift	Mapper for element-wise shifting
ibm_jacobian.bru_mapper_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.bru_mapper_collect	Mapper for concatenated variables
ibm_linear.bru_mapper_multi	Mapper for tensor product domains
ibm_linear.default	Generic methods for bru_mapper objects
ibm_n	Generic methods for bru_mapper objects
ibm_n.bru_mapper_aggregate	Mapper for aggregation
ibm_n.bru_mapper_collect	Mapper for concatenated variables
ibm_n.bru_mapper_const	Constant mapper
ibm_n.bru_mapper_factor	Mapper for factor variables
ibm_n.bru_mapper_fm_mesh_1d	Mapper for 'fm_mesh_1d'
ibm_n.bru_mapper_fm_mesh_2d	Mapper for 'fm_mesh_2d'
ibm_n.bru_mapper_harmonics	Mapper for cos/sin functions
ibm_n.bru_mapper_inla_mesh_1d	Mapper for 'fm_mesh_1d'
ibm_n.bru_mapper_inla_mesh_2d	Mapper for 'fm_mesh_2d'
ibm_n.bru_mapper_linear	Mapper for a linear effect
ibm_n.bru_mapper_marginal	Mapper for marginal distribution transformation
ibm_n.bru_mapper_matrix	Mapper for matrix multiplication
ibm_n.bru_mapper_mesh_B	Mapper for basis conversion
ibm_n.bru_mapper_multi	Mapper for tensor product domains
ibm_n.bru_mapper_pipe	Mapper for linking several mappers in sequence
ibm_n.bru_mapper_scale	Mapper for element-wise scaling
ibm_n.bru_mapper_shift	Mapper for element-wise shifting
ibm_n.bru_mapper_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.bru_mapper_collect	Mapper for concatenated variables
ibm_names.bru_mapper_multi	Mapper for tensor product domains
ibm_names.default	Generic methods for bru_mapper objects
ibm_names<-	Generic methods for bru_mapper objects
ibm_names<-.bru_mapper_collect	Mapper for concatenated variables
ibm_names<-.bru_mapper_multi	Mapper for tensor product domains
ibm_n_output	Generic methods for bru_mapper objects
ibm_n_output.bru_mapper_aggregate	Mapper for aggregation
ibm_n_output.bru_mapper_collect	Mapper for concatenated variables
ibm_n_output.bru_mapper_marginal	Mapper for marginal distribution transformation
ibm_n_output.bru_mapper_multi	Mapper for tensor product domains
ibm_n_output.bru_mapper_pipe	Mapper for linking several mappers in sequence
ibm_n_output.bru_mapper_scale	Mapper for element-wise scaling
ibm_n_output.bru_mapper_shift	Mapper for element-wise shifting
ibm_n_output.bru_mapper_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.bru_mapper_pipe	Mapper for linking several mappers in sequence
ibm_simplify.default	Generic methods for bru_mapper objects
ibm_values	Generic methods for bru_mapper objects
ibm_values.bru_mapper_aggregate	Mapper for aggregation
ibm_values.bru_mapper_collect	Mapper for concatenated variables
ibm_values.bru_mapper_const	Constant mapper
ibm_values.bru_mapper_factor	Mapper for factor variables
ibm_values.bru_mapper_fm_mesh_1d	Mapper for 'fm_mesh_1d'
ibm_values.bru_mapper_fm_mesh_2d	Mapper for 'fm_mesh_2d'
ibm_values.bru_mapper_inla_mesh_1d	Mapper for 'fm_mesh_1d'
ibm_values.bru_mapper_inla_mesh_2d	Mapper for 'fm_mesh_2d'
ibm_values.bru_mapper_linear	Mapper for a linear effect
ibm_values.bru_mapper_marginal	Mapper for marginal distribution transformation
ibm_values.bru_mapper_matrix	Mapper for matrix multiplication
ibm_values.bru_mapper_mesh_B	Mapper for basis conversion
ibm_values.bru_mapper_multi	Mapper for tensor product domains
ibm_values.bru_mapper_pipe	Mapper for linking several mappers in sequence
ibm_values.bru_mapper_scale	Mapper for element-wise scaling
ibm_values.bru_mapper_shift	Mapper for element-wise shifting
ibm_values.bru_mapper_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()'
like_list.bru_like	Observation model construction for usage with 'bru()'
like_list.list	Observation model construction for usage with 'bru()'

-- M --

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.

-- 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.bru_log	Access methods for 'bru_log' objects
print.bru_mapper	mapper object summaries
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_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

-- S --

sample.lgcp	Sample from an inhomogeneous Poisson process
seals	Seal pups
seals_sp	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
summary.bru	Summary for an inlabru fit
summary.bru_info	Methods for bru_info objects
summary.bru_mapper	mapper object summaries
summary.bru_mapper_collect	mapper object summaries
summary.bru_mapper_multi	mapper object summaries
summary.bru_mapper_pipe	mapper object summaries
summary.bru_options	Print inlabru options

-- T --

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

-- misc --

[.bm_list	Methods for mapper lists
[.bru_like_list	Observation model construction for usage with 'bru()'
[.bru_log	Access methods for 'bru_log' objects
[.bru_mapper_collect	Mapper for concatenated variables
[.bru_mapper_multi	Mapper for tensor product domains
[.component_list	Methods for inlabru component lists