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All functions

Poisson1_1D
1-Dimensional Homogeneous Poisson example.
Poisson2_1D
1-Dimensional NonHomogeneous Poisson example.
Poisson3_1D
1-Dimensional NonHomogeneous Poisson example.
bincount()
1D LGCP bin count simulation and comparison with data
c(<bru_mapper>) c(<bm_list>) `[`(<bm_list>)
Methods for mapper lists
bru() bru_rerun()
Convenient model fitting using (iterated) INLA
bru_call_options()
Additional bru options
bru_compute_linearisation()
Compute inlabru model linearisation information
bru_convergence_plot()
Plot inlabru convergence diagnostics
bru_fill_missing()
Fill in missing values in Spatial grids
bru_get_mapper() bru_get_mapper_safely()
Extract mapper information from INLA model component objects
summary(<bru_info>) print(<summary_bru_info>) bru_info()
Methods for bru_info objects
bru_log_reset() bru_log_get() bru_log_message() bru_log() bru_log_active()
inlabru log message methods
bru_make_stack()
Build an inla data stack from linearisation information
bru_mapper() bru_mapper_define() bru_mapper_index() bru_mapper_taylor() bru_mapper_linear() bru_mapper_matrix() bru_mapper_factor() bru_mapper_const() bru_mapper_scale() bru_mapper_aggregate() bru_mapper_logsumexp() bru_mapper_pipe() bru_mapper_multi() bru_mapper_collect() bru_mapper_harmonics()
Constructors for bru_mapper objects
ibm_n() ibm_n_output() ibm_values() ibm_amatrix() ibm_is_linear() ibm_jacobian() ibm_linear() ibm_eval() ibm_names() `ibm_names<-`() ibm_inla_subset() ibm_invalid_output()
Generic methods for bru_mapper objects
ibm_n(<bru_mapper_inla_mesh_2d>) ibm_values(<bru_mapper_inla_mesh_2d>) ibm_jacobian(<bru_mapper_inla_mesh_2d>) ibm_n(<bru_mapper_inla_mesh_1d>) ibm_values(<bru_mapper_inla_mesh_1d>) ibm_jacobian(<bru_mapper_inla_mesh_1d>) ibm_invalid_output(<bru_mapper_index>) ibm_jacobian(<bru_mapper_index>) 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>) ibm_n(<bru_mapper_linear>) ibm_values(<bru_mapper_linear>) ibm_jacobian(<bru_mapper_linear>) ibm_n(<bru_mapper_matrix>) ibm_values(<bru_mapper_matrix>) ibm_jacobian(<bru_mapper_matrix>) ibm_n(<bru_mapper_factor>) ibm_values(<bru_mapper_factor>) ibm_jacobian(<bru_mapper_factor>) ibm_n(<bru_mapper_const>) ibm_values(<bru_mapper_const>) ibm_jacobian(<bru_mapper_const>) ibm_eval(<bru_mapper_const>) ibm_n(<bru_mapper_scale>) ibm_n_output(<bru_mapper_scale>) ibm_values(<bru_mapper_scale>) ibm_jacobian(<bru_mapper_scale>) ibm_linear(<bru_mapper_scale>) ibm_eval(<bru_mapper_scale>) 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>) ibm_linear(<bru_mapper_aggregate>) ibm_jacobian(<bru_mapper_logsumexp>) ibm_eval(<bru_mapper_logsumexp>) ibm_linear(<bru_mapper_logsumexp>) ibm_n(<bru_mapper_pipe>) ibm_n_output(<bru_mapper_pipe>) ibm_values(<bru_mapper_pipe>) ibm_jacobian(<bru_mapper_pipe>) ibm_linear(<bru_mapper_pipe>) ibm_eval(<bru_mapper_pipe>) 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>) 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>) ibm_n(<bru_mapper_harmonics>) ibm_jacobian(<bru_mapper_harmonics>)
Methods for bru_mapper objects
summary(<bru_mapper>) summary(<bru_mapper_multi>) summary(<bru_mapper_pipe>) summary(<bru_mapper_collect>) print(<summary_bru_mapper>)
mapper object summaries
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
bru_safe_inla()
Load INLA safely for examples and tests
bru_standardise_names()
Standardise inla hyperparameter names
bru_summarise()
Summarise and annotate data
bru_forward_transformation() bru_inverse_transformation()
Transformation tools
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
cprod()
Cross product of integration points
deltaIC()
Summarise DIC and WAIC from lgcp objects.
devel.cvmeasure()
Variance and correlations measures for prediction components
eval_spatial()
Evaluate spatial covariates
evaluate_comp_lin()
Compute all component linearisations
evaluate_index()
Compute all index values
evaluate_inputs()
Compute all component inputs
expand_labels()
Expand labels
fm_CRS()
Create a coordinate reference system object
fm_as_sp_crs() fm_as_sfc() fm_as_inla_mesh_segment() fm_as_inla_mesh() fm_sp2segment()
Coercion methods to and from meshes
fm_crs() fm_crs_oblique() `fm_crs_oblique<-`() print(<fm_crs>) st_crs(<fm_crs>) `$`(<fm_crs>) fm_wkt_predef()
Obtain coordinate reference system object
fm_wkt_is_geocent() fm_crs_is_geocent() fm_wkt_get_ellipsoid_radius() fm_crs_get_ellipsoid_radius() fm_ellipsoid_radius() fm_wkt_set_ellipsoid_radius() `fm_ellipsoid_radius<-`() fm_crs_set_ellipsoid_radius() fm_wkt_unit_params() fm_wkt_get_lengthunit() fm_wkt_set_lengthunit() fm_crs_get_lengthunit() fm_crs_set_lengthunit() fm_length_unit() `fm_length_unit<-`() fm_wkt() fm_crs_get_wkt()
Handling CRS/WKT
fm_evaluate() fm_evaluator() fm_evaluator_inla_mesh() fm_evaluator_inla_mesh_1d() fm_evaluator_lattice()
Methods for projecting to/from an inla.mesh
fm_transform()
Object coordinate transformation
generate()
Generate samples from fitted bru models
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(<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(<prediction>)
Geom for predictions
globe()
Plot a globe using rgl
glplot()
Render Spatial* and inla.mesh objects using RGL
glplot(<SpatialLines>)
Visualize SpatialLines using RGL
glplot(<SpatialPoints>)
Visualize SpatialPoints using RGL
glplot(<inla.mesh>)
Visualize SpatialPoints using RGL
gm()
ggplot geom for spatial data
gmap()
Plot a map using extent of a spatial object
gorillas
Gorilla nesting sites
inla.stack.mjoin()
Join stacks intended to be run with different likelihoods
stransform() init.tutorial() fm_has_PROJ6() fm_not_for_PROJ6() fm_not_for_PROJ4() fm_fallback_PROJ6() fm_requires_PROJ6() fm_sp_get_crs() fm_spTransform() ibm_valid_input() ibm_amatrix(<bru_mapper_inla_mesh_2d>) ibm_amatrix(<bru_mapper_inla_mesh_1d>) ibm_amatrix(<bru_mapper_index>) ibm_amatrix(<bru_mapper_linear>) ibm_amatrix(<bru_mapper_matrix>) ibm_amatrix(<bru_mapper_factor>) bru_mapper_offset() ibm_n(<bru_mapper_offset>) ibm_values(<bru_mapper_offset>) ibm_amatrix(<bru_mapper_offset>) ibm_amatrix(<bru_mapper_multi>) ibm_amatrix(<bru_mapper_collect>) eval_SpatialDF()
Deprecated functions in inlabru
inlabru
inlabru
int()
Weighted summation (integration) of data frame subsets
ipoints()
Generate integration points
lgcp()
Log Gaussian Cox process (LGCP) inference using INLA
like() like_list() `[`(<bru_like_list>)
Likelihood construction for usage with bru()
mexdolphin
Pan-tropical spotted dolphins in the Gulf of Mexico
mrsea
Marine renewables strategic environmental assessment
multiplot()
Multiple ggplots on a page.
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.
predict(<bru>)
Prediction from fitted bru model
robins_subset
robins_subset
row_kron()
Row-wise Kronecker products
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
st_check_dim()
Check for "XYZ", "XYM" and "XYZM" sfg classes
st_check_polygon()
Check sfg polygon satisfies standards for POLYGON simple features
st_signed_area()
Calculate signed area for polygon
summary(<bru>) print(<summary_bru>)
Summary for an inlabru fit
summary(<bru_options>) print(<summary_bru_options>)
Print inlabru options
toygroups
Simulated 1D animal group locations and group sizes
vertices.inla.mesh()
Extract vertex locations from an inla.mesh
fm_wkt_as_wkt_tree() fm_wkt_tree_as_wkt() fm_wkt_tree_get_item() fm_wkt_tree_set_item()
Internal WKT handling