Package: inlabru 2.12.0.9000

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:Finn Lindgren [aut, cre, cph], Fabian E. Bachl [aut, cph], David L. Borchers [ctb, dtc, cph], Daniel Simpson [ctb, cph], Lindesay Scott-Howard [ctb, dtc, cph], Seaton Andy [ctb], Suen Man Ho [ctb, cph], Roudier Pierre [ctb, cph], Meehan Tim [ctb, cph], Reddy Peddinenikalva Niharika [ctb, cph], Perepolkin Dmytro [ctb, cph]

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inlabru/json (API)
NEWS

# Install 'inlabru' in R:
install.packages('inlabru', repos = c('https://inlabru-org.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/inlabru-org/inlabru/issues

Datasets:
  • 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_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_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
  • 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

On CRAN:

12.54 score 90 stars 6 packages 854 scripts 1.7k downloads 130 exports 33 dependencies

Last updated 1 hours agofrom:f593e56368. Checks:OK: 6 NOTE: 1. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 21 2024
R-4.5-winOKNov 21 2024
R-4.5-linuxOKNov 21 2024
R-4.4-winOKNov 21 2024
R-4.4-macOKNov 21 2024
R-4.3-winNOTENov 21 2024
R-4.3-macOKNov 21 2024

Exports:add_mappersas.bru_optionsbincountbrubru_call_optionsbru_componentbru_component_listbru_compute_linearisationbru_convergence_plotbru_fill_missingbru_forward_transformationbru_get_mapperbru_get_mapper_safelybru_indexbru_infobru_inla.stack.mexpandbru_inla.stack.mjoinbru_inverse_transformationbru_like_control_familybru_like_inla_familybru_like_listbru_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_fmesherbru_mapper_harmonicsbru_mapper_indexbru_mapper_linearbru_mapper_logsumexpbru_mapper_marginalbru_mapper_matrixbru_mapper_mesh_Bbru_mapper_multibru_mapper_pipebru_mapper_repeatbru_mapper_scalebru_mapper_shiftbru_mapper_taylorbru_modelbru_obsbru_optionsbru_options_checkbru_options_defaultbru_options_getbru_options_resetbru_options_setbru_rerunbru_response_sizebru_safe_inlabru_safe_spbru_standardise_namesbru_summarisebru_timingsbru_timings_plotbru_usedbru_used_updatebru_used_varscomp_lin_evaldeltaICdevel.cvmeasureeval_spatialevaluate_comp_simpleevaluate_effect_multi_stateevaluate_effect_single_stateevaluate_modelevaluate_statefm_cprodfm_crsfm_intfm_pixelsfm_sp2segmentgenerateggglobeglplotgmapgorillas_sf_gcovgorillas_spibm_evalibm_eval2ibm_inla_subsetibm_invalid_outputibm_is_linearibm_jacobianibm_linearibm_nibm_n_outputibm_namesibm_names<-ibm_simplifyibm_valuesiinlaindex_evalinla_subset_evalinla.spde2.pcmatern_Binput_evallgcplikelike_listlocal_basic_fixed_effect_testdatalocal_basic_intercept_testdatalocal_bru_options_setlocal_bru_safe_inlalocal_bru_testthat_assignlocal_bru_testthat_setuplocal_bru_testthat_tolerancesmake_hierarchical_mesh_basismexdolphin_spmultiplotplotmarginal.inlaplotsamplepoint2countrow_kronsample.lgcpslinespatial.to.pppspde.posteriorspoly

Dependencies:classclassIntcliDBIdplyre1071fansifmeshergenericsglueKernSmoothlatticelifecyclemagrittrMASSMatrixMatrixModelspillarpkgconfigplyrproxyR6Rcpprlangs2sftibbletidyselectunitsutf8vctrswithrwk

Articles list

Rendered fromarticles.Rmdusingknitr::rmarkdownon Nov 21 2024.

Last update: 2023-10-29
Started: 2023-10-29

Defining model components

Andy Seaton

Rendered fromcomponent.Rmdusingknitr::rmarkdownon Nov 21 2024.

Last update: 2024-11-20
Started: 2022-10-17

Devel: Customised model components with the bru_mapper system

Rendered frombru_mapper.Rmdusingknitr::rmarkdownon Nov 21 2024.

Last update: 2024-11-15
Started: 2022-10-17

Iterative linearised INLA method

Finn Lindgren and Man Ho Suen

Rendered frommethod.Rmdusingknitr::rmarkdownon Nov 21 2024.

Last update: 2022-10-17
Started: 2020-11-26

Nonlinear model approximation

Rendered fromlinearapprox.Rmdusingknitr::rmarkdownon Nov 21 2024.

Last update: 2024-09-30
Started: 2021-01-08

Prediction scores

Finn Lindgren

Rendered fromprediction_scores.Rmdusingknitr::rmarkdownon Nov 21 2024.

Last update: 2023-08-31
Started: 2022-10-17

Readme and manuals

Help Manual

Help pageTopics
inlabruinlabru-package inlabru
1D LGCP bin count simulation and comparison with databincount
Methods for mapper listsbm_list c.bm_list c.bru_mapper [.bm_list
Convenient model fitting using (iterated) INLAbru bru_rerun print.bru
Latent model component constructionbru_component bru_component.character component
Evaluate component values in predictor expressionsbru_component_eval
Methods for inlabru component listsbru_component_list bru_component_list.formula bru_component_list.list c.component c.component_list component_list [.component_list
Plot inlabru convergence diagnosticsbru_convergence_plot
Fill in missing values in Spatial gridsbru_fill_missing
Extract mapper information from INLA model component objectsbru_get_mapper bru_get_mapper.inla.rgeneric bru_get_mapper.inla.spde bru_get_mapper_safely
Extract predictor index informationbru_index bru_index.bru bru_index.bru_like
Methods for bru_info objectsbru_info bru_info.bru bru_info.character print.bru_info print.summary_bru_info summary.bru_info
Access methods for 'bru_log' objectsas.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' bookmarksbru_log_bookmark bru_log_bookmarks
Add a log messagebru_log_message
Create a 'bru_log' objectbru_log_new
Position methods for 'bru_log' objectsbru_log_index bru_log_offset
Clear log contentsbru_log_reset
Constructors for 'bru_mapper' objectsbru_mapper bru_mapper_define
Mapper for aggregationbru_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 variablesbru_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 mapperbru_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 variablesbru_mapper_factor ibm_jacobian.bru_mapper_factor ibm_n.bru_mapper_factor ibm_values.bru_mapper_factor
Mapper for general 'fmesher' function space objectsbru_mapper_fmesher ibm_jacobian.bru_mapper_fmesher ibm_n.bru_mapper_fmesher ibm_values.bru_mapper_fmesher
Generic methods for bru_mapper objectsbru_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 functionsbru_mapper_harmonics ibm_jacobian.bru_mapper_harmonics ibm_n.bru_mapper_harmonics
Mapper for indexed variablesbru_mapper_index ibm_invalid_output.bru_mapper_index ibm_jacobian.bru_mapper_index
Mapper for a linear effectbru_mapper_linear ibm_jacobian.bru_mapper_linear ibm_n.bru_mapper_linear ibm_values.bru_mapper_linear
Mapper for log-sum-exp aggregationbru_mapper_logsumexp ibm_eval.bru_mapper_logsumexp ibm_jacobian.bru_mapper_logsumexp
Mapper for marginal distribution transformationbru_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 multiplicationbru_mapper_matrix ibm_jacobian.bru_mapper_matrix ibm_n.bru_mapper_matrix ibm_values.bru_mapper_matrix
Mapper for basis conversionbru_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 domainsbru_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 sequencebru_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 repeating a mapperbru_mapper_repeat ibm_eval.bru_mapper_repeat ibm_invalid_output.bru_mapper_repeat ibm_jacobian.bru_mapper_repeat ibm_linear.bru_mapper_repeat ibm_n.bru_mapper_repeat ibm_n_output.bru_mapper_repeat ibm_values.bru_mapper_repeat
Mapper for element-wise scalingbru_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 shiftingbru_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 approximationsbru_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 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 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
Observation model construction for usage with 'bru()'bru_like_list bru_like_list.bru_like bru_like_list.list bru_obs c.bru_like c.bru_like_list like like_list [.bru_like_list
Create or update an options objectsas.bru_options bru_options bru_options_check bru_options_default bru_options_get bru_options_reset bru_options_set
Response size queriesbru_response_size bru_response_size.bru bru_response_size.bru_info bru_response_size.bru_like bru_response_size.bru_like_list
Extract timing information from fitted bru objectbru_timings bru_timings.bru
Plot inlabru iteration timingsbru_timings_plot
Transformation toolsbru_forward_transformation bru_inverse_transformation bru_transformation
Summarise DIC and WAIC from 'lgcp' objects.deltaIC
Variance and correlations measures for prediction componentsdevel.cvmeasure
Evaluate spatial covariateseval_spatial eval_spatial.sf eval_spatial.SpatialGridDataFrame eval_spatial.SpatialPixelsDataFrame eval_spatial.SpatialPolygonsDataFrame eval_spatial.SpatRaster eval_spatial.stars
Generate samples from fitted bru modelsgenerate generate.bru
ggplot2 geomes for inlabru related objectsgg
Geom for predictionsgg.bru_prediction gg.prediction
Geom for data.framegg.data.frame
Geom for fm_mesh_1d objectsgg.fm_mesh_1d gg.inla.mesh.1d
Geom for fm_mesh_2d objectsgg.fm_mesh_2d gg.inla.mesh
Geom for matrixgg.matrix
Geom for RasterLayer objectsgg.RasterLayer
Geom helper for sf objectsgg.sf
Geom for SpatialGridDataFrame objectsgg.SpatialGridDataFrame
Geom for SpatialLines objectsgg.SpatialLines
Geom for SpatialPixels objectsgg.SpatialPixels
Geom for SpatialPixelsDataFrame objectsgg.SpatialPixelsDataFrame
Geom for SpatialPoints objectsgg.SpatialPoints
Geom for SpatialPolygons objectsgg.SpatialPolygons
Geom wrapper for SpatRaster objectsgg.SpatRaster
Visualize a globe using RGLglobe
Render objects using RGLglplot glplot.fm_mesh_2d glplot.inla.mesh glplot.SpatialLines glplot.SpatialPoints
Gorilla nesting sites in sf formatgorillas_sf gorillas_sf_gcov gorillas_sp
Log Gaussian Cox process (LGCP) inference using INLAlgcp
Pan-tropical spotted dolphins in the Gulf of Mexicomexdolphin_sf mexdolphin_sp
Marine renewables strategic environmental assessmentmrsea
Multiple ggplots on a page.multiplot
Plot method for posterior marginals estimated by bruplot.bru plotmarginal.inla
Plot prediction using ggplot2plot.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 modelpredict.bru
robins_subsetrobins_subset
Sample from an inhomogeneous Poisson processsample.lgcp
Blue and red shrimp in the Western Mediterranean Seashrimp
Posteriors of SPDE hyper parameters and Matern correlation or covariance function.spde.posterior
Summary for an inlabru fitprint.summary_bru summary.bru
Summary and print methods for observation modelsprint.bru_like print.bru_like_list print.summary_bru_like print.summary_bru_like_list summary.bru_like summary.bru_like_list
mapper object summariesprint.bru_mapper print.summary_bru_mapper summary.bru_mapper summary.bru_mapper_collect summary.bru_mapper_multi summary.bru_mapper_pipe summary.bru_mapper_repeat
Print inlabru optionsprint.summary_bru_options summary.bru_options
Simulated 1D animal group locations and group sizestoygroups
Simulated 2D point process datatoypoints