Function reference • inlabru

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