Function reference
-
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()
bru_mapper_mesh_B()
- 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>)
ibm_n(<bru_mapper_mesh_B>)
ibm_values(<bru_mapper_mesh_B>)
ibm_jacobian(<bru_mapper_mesh_B>)
- 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_safe_sp()
- Check for potential
sp
version compatibility issues
-
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
-
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_int()
- Multi-domain integration
-
fm_pixels()
- Generate lattice points covering a 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
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gg(<SpatRaster>)
- Geom wrapper for SpatRaster objects
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gg(<SpatialGridDataFrame>)
- Geom for SpatialGridDataFrame objects
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gg(<SpatialLines>)
- Geom for SpatialLines objects
-
gg(<SpatialPixels>)
- Geom for SpatialPixels objects
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gg(<SpatialPixelsDataFrame>)
- Geom for SpatialPixelsDataFrame objects
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gg(<SpatialPoints>)
- Geom for SpatialPoints objects
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gg(<SpatialPolygons>)
- Geom for SpatialPolygons objects
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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
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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-package
_PACKAGE
inlabru
- inlabru
-
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 aninla.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