Package index
-
inlabru-package
inlabru
- inlabru
-
bru()
bru_rerun()
print(<bru>)
- Convenient model fitting using (iterated) INLA
-
bru_obs()
like()
bru_obs_list()
c(<bru_obs>)
c(<bru_obs_list>)
`[`(<bru_obs_list>)
like_list()
bru_like_list()
- Observation model construction for usage with
bru()
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bru_options()
as.bru_options()
bru_options_default()
bru_options_check()
bru_options_get()
bru_options_set()
bru_options_reset()
bru_options_set_local()
- Create or update an options objects
-
bru_comp()
bru_component()
- Latent model component construction
-
bru_comp_eval()
- Evaluate component values in predictor expressions
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bru_comp_list()
c(<bru_comp_list>)
c(<bru_comp>)
`[`(<bru_comp_list>)
- Methods for inlabru component lists
-
lgcp()
- Log Gaussian Cox process (LGCP) inference using INLA
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bru_response_size()
- Response size queries
-
bru_index()
experimental - Extract predictor index information
-
generate()
- Generate samples from fitted bru models
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predict(<bru>)
- Prediction from fitted bru model
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spde.posterior()
- Posteriors of SPDE hyper parameters and Matern correlation or covariance function.
-
deltaIC()
- Summarise DIC and WAIC from
lgcp
objects.
-
devel.cvmeasure()
- Variance and correlations measures for prediction components
Optimization log information
Accessing the optimization text log, and plotting the optimization convergence.
-
bru_log()
format(<bru_log>)
print(<bru_log>)
as.character(<bru_log>)
`[`(<bru_log>)
c(<bru_log>)
length(<bru_log>)
- Access methods for
bru_log
objects
-
bru_log_bookmark()
bru_log_bookmarks()
- Methods for
bru_log
bookmarks
-
bru_log_message()
bru_log_abort()
bru_log_warn()
- Add a log message
-
bru_log_new()
- Create a
bru_log
object
-
bru_log_offset()
bru_log_index()
- Position methods for
bru_log
objects
-
bru_log_reset()
- Clear log contents
-
bru_convergence_plot()
- Plot inlabru convergence diagnostics
-
bru_timings()
- Extract timing information from fitted bru object
-
bru_timings_plot()
- Plot inlabru iteration timings
-
bru_get_mapper()
bru_get_mapper_safely()
- Extract mapper information from INLA model component objects
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bm_aggregate()
bru_mapper_aggregate()
ibm_n(<bm_aggregate>)
ibm_n_output(<bm_aggregate>)
ibm_values(<bm_aggregate>)
ibm_jacobian(<bm_aggregate>)
ibm_eval(<bm_aggregate>)
- Mapper for aggregation
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bm_collect()
bru_mapper_collect()
ibm_n(<bm_collect>)
ibm_n_output(<bm_collect>)
ibm_values(<bm_collect>)
ibm_is_linear(<bm_collect>)
ibm_jacobian(<bm_collect>)
ibm_eval(<bm_collect>)
ibm_linear(<bm_collect>)
ibm_invalid_output(<bm_collect>)
`[`(<bm_collect>)
`[`(<bru_mapper_collect>)
ibm_names(<bm_collect>)
`ibm_names<-`(<bm_collect>)
`ibm_names<-`(<bru_mapper_collect>)
- Mapper for concatenated variables
-
bm_const()
bru_mapper_const()
ibm_n(<bm_const>)
ibm_values(<bm_const>)
ibm_jacobian(<bm_const>)
ibm_eval(<bm_const>)
- Constant mapper
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bm_factor()
bru_mapper_factor()
ibm_n(<bm_factor>)
ibm_values(<bm_factor>)
ibm_jacobian(<bm_factor>)
- Mapper for factor variables
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bru_mapper(<fm_mesh_1d>)
ibm_n(<bm_fm_mesh_1d>)
ibm_values(<bm_fm_mesh_1d>)
ibm_jacobian(<bm_fm_mesh_1d>)
ibm_n(<bm_inla_mesh_1d>)
ibm_values(<bm_inla_mesh_1d>)
ibm_jacobian(<bm_inla_mesh_1d>)
- Mapper for
fm_mesh_1d
-
bru_mapper(<fm_mesh_2d>)
ibm_n(<bm_fm_mesh_2d>)
ibm_values(<bm_fm_mesh_2d>)
ibm_jacobian(<bm_fm_mesh_2d>)
ibm_n(<bm_inla_mesh_2d>)
ibm_values(<bm_inla_mesh_2d>)
ibm_jacobian(<bm_inla_mesh_2d>)
- Mapper for
fm_mesh_2d
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bm_fmesher()
bru_mapper_fmesher()
ibm_n(<bm_fmesher>)
ibm_values(<bm_fmesher>)
ibm_jacobian(<bm_fmesher>)
- Mapper for general
fmesher
function space objects
-
bm_harmonics()
bru_mapper_harmonics()
ibm_n(<bm_harmonics>)
ibm_jacobian(<bm_harmonics>)
- Mapper for cos/sin functions
-
bm_index()
bru_mapper_index()
ibm_invalid_output(<bm_index>)
ibm_jacobian(<bm_index>)
- Mapper for indexed variables
-
bm_linear()
bru_mapper_linear()
ibm_n(<bm_linear>)
ibm_values(<bm_linear>)
ibm_jacobian(<bm_linear>)
- Mapper for a linear effect
-
bm_logsumexp()
bru_mapper_logsumexp()
ibm_jacobian(<bm_logsumexp>)
ibm_eval(<bm_logsumexp>)
- Mapper for log-sum-exp aggregation
-
bm_marginal()
bru_mapper_marginal()
ibm_n(<bm_marginal>)
ibm_n_output(<bm_marginal>)
ibm_values(<bm_marginal>)
ibm_jacobian(<bm_marginal>)
ibm_eval(<bm_marginal>)
- Mapper for marginal distribution transformation
-
bm_matrix()
bru_mapper_matrix()
ibm_n(<bm_matrix>)
ibm_values(<bm_matrix>)
ibm_jacobian(<bm_matrix>)
- Mapper for matrix multiplication
-
bm_mesh_B()
bru_mapper_mesh_B()
ibm_n(<bm_mesh_B>)
ibm_values(<bm_mesh_B>)
ibm_jacobian(<bm_mesh_B>)
- Mapper for basis conversion
-
bm_multi()
bru_mapper_multi()
ibm_n(<bm_multi>)
ibm_n_output(<bm_multi>)
ibm_values(<bm_multi>)
ibm_is_linear(<bm_multi>)
ibm_jacobian(<bm_multi>)
ibm_linear(<bm_multi>)
ibm_eval(<bm_multi>)
ibm_invalid_output(<bm_multi>)
`[`(<bm_multi>)
`[`(<bru_mapper_multi>)
ibm_names(<bm_multi>)
`ibm_names<-`(<bm_multi>)
`ibm_names<-`(<bru_mapper_multi>)
- Mapper for tensor product domains
-
bm_pipe()
bru_mapper_pipe()
ibm_n(<bm_pipe>)
ibm_n_output(<bm_pipe>)
ibm_values(<bm_pipe>)
ibm_jacobian(<bm_pipe>)
ibm_eval(<bm_pipe>)
ibm_eval2(<bm_pipe>)
ibm_simplify(<bm_pipe>)
- Mapper for linking several mappers in sequence
-
bm_repeat()
bru_mapper_repeat()
ibm_n(<bm_repeat>)
ibm_n_output(<bm_repeat>)
ibm_values(<bm_repeat>)
ibm_jacobian(<bm_repeat>)
ibm_eval(<bm_repeat>)
ibm_linear(<bm_repeat>)
ibm_invalid_output(<bm_repeat>)
- Mapper for repeating a mapper
-
bm_scale()
bru_mapper_scale()
ibm_n(<bm_scale>)
ibm_n_output(<bm_scale>)
ibm_values(<bm_scale>)
ibm_jacobian(<bm_scale>)
ibm_eval(<bm_scale>)
- Mapper for element-wise scaling
-
bm_shift()
bru_mapper_shift()
ibm_n(<bm_shift>)
ibm_n_output(<bm_shift>)
ibm_values(<bm_shift>)
ibm_jacobian(<bm_shift>)
ibm_eval(<bm_shift>)
- Mapper for element-wise shifting
-
bm_sum()
bru_mapper_sum()
ibm_n(<bm_sum>)
ibm_n_output(<bm_sum>)
ibm_values(<bm_sum>)
ibm_is_linear(<bm_sum>)
ibm_jacobian(<bm_sum>)
ibm_eval(<bm_sum>)
ibm_linear(<bm_sum>)
ibm_invalid_output(<bm_sum>)
`[`(<bm_sum>)
`[`(<bru_mapper_sum>)
ibm_names(<bm_sum>)
`ibm_names<-`(<bm_sum>)
`ibm_names<-`(<bru_mapper_sum>)
- Mapper for adding multiple mappers
-
bm_taylor()
bru_mapper_taylor()
ibm_n(<bm_taylor>)
ibm_n_output(<bm_taylor>)
ibm_values(<bm_taylor>)
ibm_jacobian(<bm_taylor>)
ibm_eval(<bm_taylor>)
- Mapper for linear Taylor approximations
-
bru_mapper()
bru_mapper_define()
- Constructors for
bru_mapper
objects
-
ibm_n()
ibm_n_output()
ibm_values()
ibm_is_linear()
ibm_jacobian()
ibm_linear()
ibm_simplify()
ibm_eval()
ibm_eval2()
ibm_names()
`ibm_names<-`()
ibm_inla_subset()
ibm_invalid_output()
- Generic methods for bru_mapper objects
-
as_bm_list()
c(<bru_mapper>)
c(<bm_list>)
`[`(<bm_list>)
ibm_linear(<bm_list>)
ibm_simplify(<bm_list>)
- Methods for mapper lists
-
ibm_linear(<bru_model>)
ibm_linear(<bru_comp_list>)
ibm_linear(<bru_comp>)
ibm_simplify(<bru_model>)
ibm_simplify(<bru_comp>)
ibm_simplify(<bru_comp_list>)
- Mapper methods for model objects
-
as_bru_mapper()
- Methods for mapper extraction
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bru_forward_transformation()
bru_inverse_transformation()
- Transformation tools
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eval_spatial()
- Evaluate spatial covariates
-
bru_fill_missing()
- Fill in missing values in Spatial grids
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point2count()
- Convert a plot sample of points into one of counts.
-
sample.lgcp()
- Sample from an inhomogeneous Poisson process
-
plot(<bru>)
plotmarginal.inla()
- Plot method for posterior marginals estimated by bru
-
plot(<bru_prediction>)
plot(<prediction>)
- Plot prediction using ggplot2
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plotsample()
- Create a plot sample.
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globe()
- Visualize a globe using RGL
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gg(<RasterLayer>)
- Geom for RasterLayer objects
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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
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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
-
gg(<bru_prediction>)
gg(<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 fm_mesh_2d objects
-
gg(<matrix>)
- Geom for matrix
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gg(<sf>)
- Geom helper for sf objects
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glplot()
- Render objects using RGL
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bincount()
- 1D LGCP bin count simulation and comparison with data
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format(<bru_mapper>)
summary(<bru_mapper>)
format(<bm_multi>)
format(<bm_pipe>)
format(<bm_collect>)
format(<bm_sum>)
format(<bm_repeat>)
print(<summary_bru_mapper>)
print(<bru_mapper>)
- mapper object summaries
-
bru()
bru_rerun()
print(<bru>)
- Convenient model fitting using (iterated) INLA
-
bru_info()
summary(<bru_info>)
print(<summary_bru_info>)
print(<bru_info>)
- Methods for bru_info objects
-
bru_log()
format(<bru_log>)
print(<bru_log>)
as.character(<bru_log>)
`[`(<bru_log>)
c(<bru_log>)
length(<bru_log>)
- Access methods for
bru_log
objects
-
summary(<bru_obs>)
summary(<bru_obs_list>)
print(<summary_bru_obs>)
print(<summary_bru_obs_list>)
print(<bru_obs>)
print(<bru_obs_list>)
- Summary and print methods for observation models
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summary(<bru>)
print(<summary_bru>)
- Summary for an inlabru fit
-
summary(<bru_options>)
print(<summary_bru_options>)
- Print inlabru options
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Poisson1_1D
- 1-Dimensional Homogeneous Poisson example.
-
Poisson2_1D
- 1-Dimensional NonHomogeneous Poisson example.
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Poisson3_1D
- 1-Dimensional NonHomogeneous Poisson example.
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gorillas_sf
gorillas_sf_gcov()
gorillas_sp()
- Gorilla nesting sites in sf format
-
mexdolphin_sf
mexdolphin_sp()
- Pan-tropical spotted dolphins in the Gulf of Mexico
-
mrsea
- Marine renewables strategic environmental assessment
-
robins_subset
- robins_subset
-
shrimp
- Blue and red shrimp in the Western Mediterranean Sea
-
toygroups
- Simulated 1D animal group locations and group sizes
-
toypoints
- Simulated 2D point process data
-
evaluate_effect_single_state()
- Evaluate a component effect
-
evaluate_index()
- Compute all index values
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evaluate_inputs()
- Compute all component inputs
-
evaluate_model()
evaluate_state()
- Evaluate or sample from a posterior result given a model and locations
-
evaluate_predictor()
- Evaluate component effects or expressions
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expand_labels()
- Expand labels
-
bru_inla.stack.mjoin()
- Join stacks intended to be run with different likelihoods
-
spatial.to.ppp()
- Convert SpatialPoints and boundary polygon to spatstat ppp object
-
bru_make_stack()
- Build an inla data stack from linearisation information
-
bru_summarise()
- Summarise and annotate data
-
bru_standardise_names()
- Standardise inla hyperparameter names
-
bru_safe_inla()
- Load INLA safely for examples and tests
-
bru_safe_sp()
- Check for potential
sp
version compatibility issues
-
bru_call_options()
- Additional bru options
-
bru_compute_linearisation()
- Compute inlabru model linearisation information
-
bru_is_additive()
- Check for predictor expression additivity
-
multiplot()
deprecated - Multiple ggplots on a page.