Package: inlabru 2.11.1
Finn Lindgren
inlabru:Bayesian Latent Gaussian Modelling using INLA and Extensions
Facilitates spatial and general latent Gaussian modeling using integrated nested Laplace approximation via the INLA package (<https://www.r-inla.org>). Additionally, extends the GAM-like model class to more general nonlinear predictor expressions, and implements a log Gaussian Cox process likelihood for modeling univariate and spatial point processes based on ecological survey data. Model components are specified with general inputs and mapping methods to the latent variables, and the predictors are specified via general R expressions, with separate expressions for each observation likelihood model in multi-likelihood models. A prediction method based on fast Monte Carlo sampling allows posterior prediction of general expressions of the latent variables. Ecology-focused introduction in Bachl, Lindgren, Borchers, and Illian (2019) <doi:10.1111/2041-210X.13168>.
Authors:
inlabru_2.11.1.tar.gz
inlabru_2.11.1.tar.gz(r-4.5-noble)inlabru_2.11.1.tar.gz(r-4.4-noble)
inlabru_2.11.1.tgz(r-4.4-emscripten)inlabru_2.11.1.tgz(r-4.3-emscripten)
inlabru.pdf |inlabru.html✨
inlabru/json (API)
NEWS
| # Installinlabru in R: |
| install.packages('inlabru',repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/inlabru-org/inlabru/issues
- 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.
- 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.
- gorillas - Gorilla nesting sites
- gorillas_sf - Gorilla nesting sites in sf format
- lambda1_1D - 1-Dimensional Homogeneous Poisson example.
- lambda2_1D - 1-Dimensional NonHomogeneous Poisson example.
- lambda3_1D - 1-Dimensional NonHomogeneous Poisson example.
- 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
- pts1 - 1-Dimensional Homogeneous Poisson example.
- pts2 - 1-Dimensional NonHomogeneous Poisson example.
- pts3 - 1-Dimensional NonHomogeneous Poisson example.
- robins_subset - Robins_subset
- seals_sp - Seal pups
- 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
Last updated 4 days agofrom:4bc5da1e51
Exports:add_mappersas.bru_optionsbincountbrubru_call_optionsbru_compute_linearisationbru_convergence_plotbru_fill_missingbru_forward_transformationbru_get_mapperbru_get_mapper_safelybru_infobru_inla.stack.mexpandbru_inla.stack.mjoinbru_int_polygonbru_inverse_transformationbru_like_control_familybru_like_inla_familybru_logbru_log_bookmarkbru_log_bookmarksbru_log_indexbru_log_messagebru_log_newbru_log_offsetbru_log_resetbru_make_stackbru_mapperbru_mapper_aggregatebru_mapper_collectbru_mapper_constbru_mapper_definebru_mapper_factorbru_mapper_harmonicsbru_mapper_indexbru_mapper_linearbru_mapper_logsumexpbru_mapper_marginalbru_mapper_matrixbru_mapper_mesh_Bbru_mapper_multibru_mapper_offsetbru_mapper_pipebru_mapper_scalebru_mapper_shiftbru_mapper_taylorbru_modelbru_optionsbru_options_checkbru_options_defaultbru_options_getbru_options_resetbru_options_setbru_rerunbru_safe_inlabru_safe_spbru_standardise_namesbru_summarisebru_timingsbru_timings_plotbru_usedbru_used_updatebru_used_varscomp_lin_evalcomponentcomponent_listdeltaICdevel.cvmeasureeval_spatialevaluate_comp_simpleevaluate_effect_multi_stateevaluate_effect_single_stateevaluate_modelevaluate_statefm_as_fmfm_as_inla_meshfm_as_inla_mesh_segmentfm_as_lattice_2dfm_as_mesh_1dfm_as_mesh_2dfm_as_segmfm_as_sfcfm_as_sp_crsfm_centroidsfm_containsfm_cprodfm_crsfm_CRSfm_CRS_as_listfm_crs_get_ellipsoid_radiusfm_crs_get_lengthunitfm_crs_get_wktfm_crs_is_geocentfm_crs_is_identicalfm_crs_obliquefm_crs_oblique<-fm_crs_set_ellipsoid_radiusfm_crs_set_lengthunitfm_CRSargsfm_CRSargs_as_listfm_ellipsoid_radiusfm_ellipsoid_radius<-fm_evaluatefm_evaluatorfm_evaluator_latticefm_has_PROJ6fm_identical_CRSfm_intfm_int_multi_samplerfm_is_withinfm_lattice_2dfm_length_unitfm_length_unit<-fm_list_as_CRSfm_mesh_1dfm_mesh_2dfm_pixelsfm_proj4stringfm_segmfm_sp_get_crsfm_sp2segmentfm_spTransformfm_store_pointsfm_transformfm_verticesfm_wktfm_wkt_as_wkt_treefm_wkt_get_ellipsoid_radiusfm_wkt_get_lengthunitfm_wkt_is_geocentfm_wkt_predeffm_wkt_set_ellipsoid_radiusfm_wkt_set_lengthunitfm_wkt_tree_as_wktfm_wkt_tree_get_itemfm_wkt_tree_set_itemfm_wkt_unit_paramsgenerateggglobeglplotgmgmapgorillas_sf_gcovibm_evalibm_eval2ibm_inla_subsetibm_invalid_outputibm_is_linearibm_jacobianibm_linearibm_nibm_n_outputibm_namesibm_names<-ibm_simplifyibm_valuesiinlaindex_evalinla_subset_evalinla.spde2.pcmatern_Binput_evalis.insidelgcplikelike_listlocal_basic_fixed_effect_testdatalocal_basic_intercept_testdatalocal_bru_options_setlocal_bru_safe_inlalocal_bru_testthat_assignlocal_bru_testthat_setuplocal_bru_testthat_toleranceslocal_mrsea_convertmake_hierarchical_mesh_basismultiplotplotmarginal.inlaplotsamplepoint2countrow_kronsample.lgcpslinespatial.to.pppspde.posteriorspolyvertices.inla.mesh
Dependencies:classclassIntcliDBIdplyre1071fansifmeshergenericsglueKernSmoothlatticelifecyclemagrittrMASSMatrixMatrixModelspillarpkgconfigplyrproxyR6Rcpprlangs2sfspterratibbletidyselectunitsutf8vctrswithrwk
Articles list
Rendered fromarticles.Rmdusingknitr::rmarkdownon Jul 02 2024.Last update: 2023-12-21
Started: 2023-12-21
Defining model components
Rendered fromcomponent.Rmdusingknitr::rmarkdownon Jul 02 2024.Last update: 2024-07-02
Started: 2022-10-24
Devel: Customised model components with the bru_mapper system
Rendered frombru_mapper.Rmdusingknitr::rmarkdownon Jul 02 2024.Last update: 2023-10-29
Started: 2022-10-24
Iterative linearised INLA method
Rendered frommethod.Rmdusingknitr::rmarkdownon Jul 02 2024.Last update: 2022-10-24
Started: 2021-03-16
Nonlinear model approximation
Rendered fromlinearapprox.Rmdusingknitr::rmarkdownon Jul 02 2024.Last update: 2022-10-24
Started: 2021-03-16
Prediction scores
Rendered fromprediction_scores.Rmdusingknitr::rmarkdownon Jul 02 2024.Last update: 2023-10-29
Started: 2022-10-24
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| inlabru | inlabru-package inlabru |
| 1D LGCP bin count simulation and comparison with data | bincount |
| Methods for mapper lists | bm_list c.bm_list c.bru_mapper [.bm_list |
| Convenient model fitting using (iterated) INLA | bru bru_rerun |
| Additional bru options | bru_call_options |
| Compute inlabru model linearisation information | bru_compute_linearisation bru_compute_linearisation.bru_like bru_compute_linearisation.bru_like_list bru_compute_linearisation.bru_model bru_compute_linearisation.component |
| Plot inlabru convergence diagnostics | bru_convergence_plot |
| Fill in missing values in Spatial grids | bru_fill_missing |
| Transformation tools | bru_forward_transformation bru_inverse_transformation bru_transformation |
| Extract mapper information from INLA model component objects | bru_get_mapper bru_get_mapper.inla.rgeneric bru_get_mapper.inla.spde bru_get_mapper_safely |
| Access methods for 'bru_log' objects | as.character.bru_log bru_log bru_log.bru bru_log.bru_log bru_log.character bru_log.iinla c.bru_log length.bru_log print.bru_log [.bru_log |
| Methods for 'bru_log' bookmarks | bru_log_bookmark bru_log_bookmarks |
| Add a log message | bru_log_message |
| Create a 'bru_log' object | bru_log_new |
| Position methods for 'bru_log' objects | bru_log_index bru_log_offset |
| Clear log contents | bru_log_reset |
| Constructors for 'bru_mapper' objects | bru_mapper bru_mapper_define |
| Mapper for aggregation | bru_mapper_aggregate ibm_eval.bru_mapper_aggregate ibm_jacobian.bru_mapper_aggregate ibm_n.bru_mapper_aggregate ibm_n_output.bru_mapper_aggregate ibm_values.bru_mapper_aggregate |
| Mapper for concatenated variables | bru_mapper_collect ibm_eval.bru_mapper_collect ibm_invalid_output.bru_mapper_collect ibm_is_linear.bru_mapper_collect ibm_jacobian.bru_mapper_collect ibm_linear.bru_mapper_collect ibm_n.bru_mapper_collect ibm_names.bru_mapper_collect ibm_names<-.bru_mapper_collect ibm_n_output.bru_mapper_collect ibm_values.bru_mapper_collect [.bru_mapper_collect |
| Constant mapper | bru_mapper_const ibm_eval.bru_mapper_const ibm_jacobian.bru_mapper_const ibm_n.bru_mapper_const ibm_values.bru_mapper_const |
| Mapper for factor variables | bru_mapper_factor ibm_jacobian.bru_mapper_factor ibm_n.bru_mapper_factor ibm_values.bru_mapper_factor |
| Generic methods for bru_mapper objects | bru_mapper_generics ibm_eval ibm_eval.default ibm_eval2 ibm_eval2.default ibm_inla_subset ibm_inla_subset.default ibm_invalid_output ibm_invalid_output.default ibm_is_linear ibm_is_linear.default ibm_jacobian ibm_jacobian.default ibm_linear ibm_linear.default ibm_n ibm_n.default ibm_names ibm_names.default ibm_names<- ibm_n_output ibm_n_output.default ibm_simplify ibm_simplify.default ibm_values ibm_values.default |
| Mapper for cos/sin functions | bru_mapper_harmonics ibm_jacobian.bru_mapper_harmonics ibm_n.bru_mapper_harmonics |
| Mapper for indexed variables | bru_mapper_index ibm_invalid_output.bru_mapper_index ibm_jacobian.bru_mapper_index |
| Mapper for a linear effect | bru_mapper_linear ibm_jacobian.bru_mapper_linear ibm_n.bru_mapper_linear ibm_values.bru_mapper_linear |
| Mapper for log-sum-exp aggregation | bru_mapper_logsumexp ibm_eval.bru_mapper_logsumexp ibm_jacobian.bru_mapper_logsumexp |
| Mapper for marginal distribution transformation | bru_mapper_marginal ibm_eval.bru_mapper_marginal ibm_jacobian.bru_mapper_marginal ibm_n.bru_mapper_marginal ibm_n_output.bru_mapper_marginal ibm_values.bru_mapper_marginal |
| Mapper for matrix multiplication | bru_mapper_matrix ibm_jacobian.bru_mapper_matrix ibm_n.bru_mapper_matrix ibm_values.bru_mapper_matrix |
| Mapper for basis conversion | bru_mapper_mesh_B ibm_jacobian.bru_mapper_mesh_B ibm_n.bru_mapper_mesh_B ibm_values.bru_mapper_mesh_B |
| Mapper for tensor product domains | bru_mapper_multi ibm_eval.bru_mapper_multi ibm_invalid_output.bru_mapper_multi ibm_is_linear.bru_mapper_multi ibm_jacobian.bru_mapper_multi ibm_linear.bru_mapper_multi ibm_n.bru_mapper_multi ibm_names.bru_mapper_multi ibm_names<-.bru_mapper_multi ibm_n_output.bru_mapper_multi ibm_values.bru_mapper_multi [.bru_mapper_multi |
| Mapper for linking several mappers in sequence | bru_mapper_pipe ibm_eval.bru_mapper_pipe ibm_eval2.bru_mapper_pipe ibm_jacobian.bru_mapper_pipe ibm_n.bru_mapper_pipe ibm_n_output.bru_mapper_pipe ibm_simplify.bru_mapper_pipe ibm_values.bru_mapper_pipe |
| Mapper for element-wise scaling | bru_mapper_scale ibm_eval.bru_mapper_scale ibm_jacobian.bru_mapper_scale ibm_n.bru_mapper_scale ibm_n_output.bru_mapper_scale ibm_values.bru_mapper_scale |
| Mapper for element-wise shifting | bru_mapper_shift ibm_eval.bru_mapper_shift ibm_jacobian.bru_mapper_shift ibm_n.bru_mapper_shift ibm_n_output.bru_mapper_shift ibm_values.bru_mapper_shift |
| Mapper for linear Taylor approximations | bru_mapper_taylor ibm_eval.bru_mapper_taylor ibm_jacobian.bru_mapper_taylor ibm_n.bru_mapper_taylor ibm_n_output.bru_mapper_taylor ibm_values.bru_mapper_taylor |
| Mapper for 'fm_mesh_1d' | bru_mapper.fm_mesh_1d bru_mapper.inla.mesh.1d ibm_jacobian.bru_mapper_fm_mesh_1d ibm_jacobian.bru_mapper_inla_mesh_1d ibm_n.bru_mapper_fm_mesh_1d ibm_n.bru_mapper_inla_mesh_1d ibm_values.bru_mapper_fm_mesh_1d ibm_values.bru_mapper_inla_mesh_1d |
| Mapper for 'fm_mesh_2d' | bru_mapper.fm_mesh_2d bru_mapper.inla.mesh ibm_jacobian.bru_mapper_fm_mesh_2d ibm_jacobian.bru_mapper_inla_mesh_2d ibm_n.bru_mapper_fm_mesh_2d ibm_n.bru_mapper_inla_mesh_2d ibm_values.bru_mapper_fm_mesh_2d ibm_values.bru_mapper_inla_mesh_2d |
| Create or update an options objects | as.bru_options bru_options bru_options_check bru_options_default bru_options_get bru_options_reset bru_options_set |
| Load INLA safely for examples and tests | bru_safe_inla |
| Check for potential 'sp' version compatibility issues | bru_safe_sp |
| Standardise inla hyperparameter names | bru_standardise_names |
| Summarise and annotate data | bru_summarise |
| Extract timing information from fitted bru object | bru_timings bru_timings.bru |
| Plot inlabru iteration timings | bru_timings_plot |
| Latent model component construction | bru_component component component.character |
| Evaluate component values in predictor expressions | component_eval |
| Methods for inlabru component lists | bru_component_list c.component c.component_list component_list component_list.formula component_list.list [.component_list |
| Summarise DIC and WAIC from 'lgcp' objects. | deltaIC |
| Variance and correlations measures for prediction components | devel.cvmeasure |
| Evaluate spatial covariates | eval_spatial eval_spatial.sf eval_spatial.SpatialGridDataFrame eval_spatial.SpatialPixelsDataFrame eval_spatial.SpatialPolygonsDataFrame eval_spatial.SpatRaster eval_spatial.stars |
| Compute all component linearisations | evaluate_comp_lin |
| Compute all index values | evaluate_index |
| Compute all component inputs | evaluate_inputs |
| Expand labels | expand_labels |
| Generate samples from fitted bru models | generate generate.bru |
| ggplot2 geomes for inlabru related objects | gg |
| Geom for predictions | gg.bru_prediction gg.prediction |
| Geom for data.frame | gg.data.frame |
| Geom for fm_mesh_1d objects | gg.fm_mesh_1d gg.inla.mesh.1d |
| Geom for inla.mesh objects | gg.fm_mesh_2d gg.inla.mesh |
| Geom for matrix | gg.matrix |
| Geom for RasterLayer objects | gg.RasterLayer |
| Geom helper for sf objects | gg.sf |
| Geom for SpatialGridDataFrame objects | gg.SpatialGridDataFrame |
| Geom for SpatialLines objects | gg.SpatialLines |
| Geom for SpatialPixels objects | gg.SpatialPixels |
| Geom for SpatialPixelsDataFrame objects | gg.SpatialPixelsDataFrame |
| Geom for SpatialPoints objects | gg.SpatialPoints |
| Geom for SpatialPolygons objects | gg.SpatialPolygons |
| Geom wrapper for SpatRaster objects | gg.SpatRaster |
| Visualize a globe using RGL | globe |
| Render objects using RGL | glplot glplot.fm_mesh_2d glplot.inla.mesh glplot.SpatialLines glplot.SpatialPoints |
| ggplot geom for spatial data | gm |
| Plot a map using extent of a spatial object | gmap |
| Gorilla nesting sites | gorillas |
| Gorilla nesting sites in sf format | gorillas_sf gorillas_sf_gcov |
| Log Gaussian Cox process (LGCP) inference using INLA | lgcp |
| Observation model construction for usage with 'bru()' | c.bru_like c.bru_like_list like like_list like_list.bru_like like_list.list [.bru_like_list |
| Pan-tropical spotted dolphins in the Gulf of Mexico | mexdolphin |
| Pan-tropical spotted dolphins in the Gulf of Mexico | mexdolphin_sf |
| Marine renewables strategic environmental assessment | mrsea |
| Multiple ggplots on a page. | multiplot |
| Plot method for posterior marginals estimated by bru | plot.bru plotmarginal.inla |
| Plot prediction using ggplot2 | plot.bru_prediction plot.prediction |
| Create a plot sample. | plotsample |
| Convert a plot sample of points into one of counts. | point2count |
| 1-Dimensional Homogeneous Poisson example. | countdata1 E_nc1 lambda1_1D Poisson1_1D pts1 |
| 1-Dimensional NonHomogeneous Poisson example. | countdata2 cov2_1D E_nc2 lambda2_1D Poisson2_1D pts2 |
| 1-Dimensional NonHomogeneous Poisson example. | countdata3a countdata3b E_nc3a E_nc3b lambda3_1D Poisson3_1D pts3 |
| Prediction from fitted bru model | predict.bru |
| robins_subset | robins_subset |
| Sample from an inhomogeneous Poisson process | sample.lgcp |
| Seal pups | seals seals_sp |
| Blue and red shrimp in the Western Mediterranean Sea | shrimp |
| Convert data frame to SpatialLinesDataFrame | sline |
| Convert SpatialPoints and boundary polygon to spatstat ppp object | spatial.to.ppp |
| Posteriors of SPDE hyper parameters and Matern correlation or covariance function. | spde.posterior |
| Convert a data.frame of boundary points into a SpatialPolgonsDataFrame | spoly |
| Summary for an inlabru fit | print.summary_bru summary.bru |
| Methods for bru_info objects | bru_info bru_info.bru bru_info.character print.summary_bru_info summary.bru_info |
| mapper object summaries | print.bru_mapper print.summary_bru_mapper summary.bru_mapper summary.bru_mapper_collect summary.bru_mapper_multi summary.bru_mapper_pipe |
| Print inlabru options | print.summary_bru_options summary.bru_options |
| Simulated 1D animal group locations and group sizes | toygroups |
| Simulated 2D point process data | toypoints |
