Package: inlabru 2.14.1.9005

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], Andy Seaton [ctb], Man Ho Suen [ctb, cph], Pierre Roudier [ctb, cph], Tim Meehan [ctb, cph], Niharika Reddy Peddinenikalva [ctb, cph], Dmytro Perepolkin [ctb, cph], Novica Nakov [ctb], Hans Montcho [ctb, cph]

inlabru_2.14.1.9005.tar.gz
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manual.pdf |manual.html✨
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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'))

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

Pkgdown/docs site:https://inlabru-org.github.io

Uses libs:
  • c++– GNU Standard C++ Library v3
Datasets:
  • 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.
  • 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.
  • 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:

Conda:

cpp

13.48 score 126 stars 7 packages 1.2k scripts 3.9k downloads 190 exports 33 dependencies

Last updated from:fbcae8e394. Checks:13 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-arm64OK254
linux-devel-x86_64OK253
source / vignettesOK320
linux-release-arm64OK286
linux-release-x86_64OK272
macos-release-arm64OK225
macos-release-x86_64OK419
macos-oldrel-arm64OK159
macos-oldrel-x86_64OK359
windows-develOK226
windows-releaseOK265
windows-oldrelOK229
wasm-releaseOK178

Exports:add_mappersas_bm_listas_bru_compas_bru_comp_listas_bru_infoas_bru_mapperas_bru_obsas_bru_obs_listas.bru_optionsbincountbm_aggregatebm_autodetectbm_collectbm_constbm_factorbm_fmesherbm_harmonicsbm_indexbm_linearbm_logitaveragebm_logsumexpbm_marginalbm_matrixbm_mesh_Bbm_multibm_pipebm_reparambm_repeatbm_repeat_indexingbm_repeat_indexing_matrixbm_scalebm_shiftbm_sumbm_taylorbrubru_block_gcpobru_call_optionsbru_compbru_comp_envbru_comp_env_extrabru_comp_env_extra<-bru_comp_env<-bru_comp_listbru_compute_linearisationbru_convergence_plotbru_eval_in_data_contextbru_fill_missingbru_forward_transformationbru_gcpo_tablebru_get_mapperbru_get_mapper_safelybru_indexbru_infobru_inla_formulabru_inla.stack.mexpandbru_inla.stack.mjoinbru_inputbru_input_textbru_inverse_transformationbru_is_additivebru_is_linearbru_is_rowwisebru_like_listbru_logbru_log_abortbru_log_bookmarkbru_log_bookmarksbru_log_indexbru_log_messagebru_log_newbru_log_offsetbru_log_resetbru_log_warnbru_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_sumbru_mapper_taylorbru_modelbru_namesbru_obsbru_obs_control_familybru_obs_control_gcpobru_obs_inla_familybru_obs_listbru_optionsbru_options_checkbru_options_defaultbru_options_getbru_options_resetbru_options_setbru_options_set_localbru_pred_exprbru_rerunbru_response_sizebru_safe_inlabru_safe_spbru_safe_terrabru_set_missingbru_set_missing<-bru_standardise_namesbru_summarisebru_timingsbru_timings_plotbru_usedbru_used_updatebru_used_varscv_hexcv_partitiondelta_ICdeltaICdevel.cvmeasureeval_spatialevaluate_effect_single_stateevaluate_modelevaluate_stategenerateggglobeglplotgmapgorillas_sf_gcovgorillas_spibm_evalibm_eval2ibm_inla_subsetibm_input_availableibm_input_getibm_input_newibm_input_setibm_invalid_outputibm_is_linearibm_is_rowwiseibm_jacobianibm_linearibm_nibm_n_outputibm_namesibm_names<-ibm_simplifyibm_valuesiinlaindex_evalinla_subset_evalinla.spde2.pcmatern_Binput_evallgcplgcp_IClikelike_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_basismaterncov.bandsmexdolphin_spmultiplotnew_bru_inputnew_bru_pred_exprnew_bru_usedplotmarginal.inlaplotsamplepoint2countrow_kronsample.lgcpslinespatial.to.pppspde.posteriorspoly

Dependencies:classclassIntcliDBIdplyre1071fmeshergenericsglueKernSmoothlatticelifecyclemagrittrMASSMatrixMatrixModelspillarpkgconfigproxyR6Rcpprlangs2sfspsplancstibbletidyselectunitsutf8vctrswithrwk

Articles list

Rendered fromarticles.Rmdusingknitr::rmarkdownon Jun 02 2026.

Last update: 2025-12-12
Started: 2023-10-29

Classes and methods

Rendered fromclasses.Rmdusingknitr::rmarkdownon Jun 02 2026.

Last update: 2025-10-02
Started: 2025-10-01

Defining model components

Andy Seaton

Rendered fromcomponent.Rmdusingknitr::rmarkdownon Jun 02 2026.

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

Devel: Customised model components with the bru_mapper system

Rendered frombru_mapper.Rmdusingknitr::rmarkdownon Jun 02 2026.

Last update: 2025-12-12
Started: 2022-10-17

Iterative linearised INLA method

Finn Lindgren and Man Ho Suen

Rendered frommethod.Rmdusingknitr::rmarkdownon Jun 02 2026.

Last update: 2025-12-12
Started: 2020-11-26

Nonlinear model approximation

Rendered fromlinearapprox.Rmdusingknitr::rmarkdownon Jun 02 2026.

Last update: 2026-04-14
Started: 2021-01-08

Prediction scores

Finn Lindgren

Rendered fromprediction_scores.Rmdusingknitr::rmarkdownon Jun 02 2026.

Last update: 2025-12-02
Started: 2022-10-17

Readme and manuals

Help Manual

Help pageTopics
inlabruinlabru-package inlabru
Conversion methods for 'bru_comp' and 'bru_comp_list' objectsas_bru_comp as_bru_comp.bru_comp as_bru_comp_list as_bru_comp_list.bru as_bru_comp_list.bru_comp as_bru_comp_list.bru_comp_list as_bru_comp_list.bru_info as_bru_comp_list.bru_model as_bru_comp_list.formula as_bru_comp_list.list
Methods for mapper extractionas_bru_mapper as_bru_mapper.bru_comp as_bru_mapper.bru_mapper as_bru_mapper.bru_subcomp
Conversion methods for 'bru_obs' and 'bru_obs_list' objectsas_bru_obs as_bru_obs.bru_obs as_bru_obs_list as_bru_obs_list.bru as_bru_obs_list.bru_info as_bru_obs_list.bru_model as_bru_obs_list.bru_obs as_bru_obs_list.bru_obs_list as_bru_obs_list.list
Augment a bru model fit with fitted valuesaugment.bru
1D LGCP bin count simulation and comparison with databincount
Mapper for aggregationbm_aggregate bru_mapper_aggregate
Mapper for concatenated variablesbm_collect bru_mapper_collect [.bm_collect [.bru_mapper_collect
Constant mapperbm_const bru_mapper_const
Mapper for factor variablesbm_factor bru_mapper_factor
Mapper for 'fm_mesh_1d'bm_fm_mesh_1d bru_mapper.fm_mesh_1d
Mapper for general 'fmesher' function space objectsbm_fmesher bru_mapper.fm_mesh_2d bru_mapper_fmesher
Mapper for cos/sin functionsbm_harmonics bru_mapper_harmonics
Mapper for indexed variablesbm_index bru_mapper_index
Mapper for a linear effectbm_linear bru_mapper_linear
Methods for mapper listsas_bm_list as_bm_list.bm_list as_bm_list.bru_comp_list as_bm_list.list bm_list c.bm_list c.bru_mapper [.bm_list
Mapper for logit-sum-inverse-logit aggregationbm_logitaverage
Mapper for log-sum-exp aggregationbm_logsumexp bru_mapper_logsumexp
Mapper for marginal distribution transformationbm_marginal bru_mapper_marginal
Mapper for matrix multiplicationbm_matrix bru_mapper_matrix
Mapper for tensor product domainsbm_multi bru_mapper_multi [.bm_multi [.bru_mapper_multi
Mapper for linking several mappers in sequencebm_pipe bru_mapper_pipe
Mapper for reparameterising mapper statesbm_reparam
Mapper for repeating a mapperbm_repeat bru_mapper_repeat
Mapper for element-wise scalingbm_scale bru_mapper_scale
Mapper for element-wise shiftingbm_shift bru_mapper_shift
Mapper for adding multiple mappersbm_sum bru_mapper_sum [.bm_sum [.bru_mapper_sum
Mapper for linear Taylor approximationsbm_taylor bru_mapper_taylor
Convenient model fitting using (iterated) INLAbru bru_rerun print.bru print.summary_bru summary.bru
Extract block-averaged GCPO scores from one or more fitted bru modelsbru_block_gcpo
Latent model component constructionbru_comp bru_comp.character bru_component component
Get/set component environment databru_comp_env bru_comp_env<- bru_comp_env_extra bru_comp_env_extra<-
Evaluate component values in predictor expressionsbru_component_eval bru_comp_eval
Methods for inlabru component listsbru_component_list bru_comp_list bru_comp_list.bru_comp bru_comp_list.bru_comp_list bru_comp_list.formula bru_comp_list.list c.bru_comp c.bru_comp_list component_list [.bru_comp_list
Plot inlabru convergence diagnosticsbru_convergence_plot
Fill in missing values in Spatial gridsbru_fill_missing
Compare block-averaged GCPO scores across multiple fitted bru modelsbru_gcpo_table
Extract mapper information from INLA model component objectsbru_get_mapper bru_get_mapper.inla.cgeneric bru_get_mapper.inla.rgeneric bru_get_mapper.inla.spde bru_get_mapper.inla_model_reparam bru_get_mapper_safely
Extract predictor or component index informationbru_index bru_index.bru bru_index.bru_comp bru_index.bru_comp_list bru_index.bru_info bru_index.bru_model bru_index.bru_obs bru_index.bru_obs_list index_eval
Methods for bru_info objectsas_bru_info as_bru_info.bru as_bru_info.bru_info bru_info bru_info.bru bru_info.character print.bru_info print.summary_bru_info summary.bru_info
Store and evaluate component inputsbru_input bru_input.bm_collect bru_input.bm_multi bru_input.bm_pipe bru_input.bm_repeat bru_input.bm_sum bru_input.bru_comp bru_input.bru_comp_list bru_input.bru_input bru_input.bru_mapper bru_input.bru_model bru_input.bru_obs bru_input.bru_obs_list new_bru_input
Check for predictor expression additivitybru_is_additive bru_is_additive.bru_obs bru_is_additive.bru_obs_list bru_is_additive.bru_pred_expr bru_is_additive.character bru_is_additive.expression bru_is_additive.formula
Check for predictor linearitybru_is_linear bru_is_linear.bru bru_is_linear.bru_comp bru_is_linear.bru_comp_list bru_is_linear.bru_info bru_is_linear.bru_mapper bru_is_linear.bru_model bru_is_linear.bru_obs bru_is_linear.bru_obs_list bru_is_linear.bru_pred_expr
Check for predictor rowwise evaluabilitybru_is_rowwise bru_is_rowwise.bru_comp bru_is_rowwise.bru_comp_list bru_is_rowwise.bru_mapper bru_is_rowwise.bru_obs bru_is_rowwise.bru_obs_list bru_is_rowwise.bru_pred_expr
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 format.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_abort bru_log_message bru_log_warn
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
Generic methods for bru_mapper objectsbru_mapper_generics
Mapper methods for model objectsbru_model_mapper_methods ibm_linear.bm_list ibm_linear.bru_comp_list ibm_linear.bru_model ibm_simplify.bm_list ibm_simplify.bru_comp ibm_simplify.bru_comp_list ibm_simplify.bru_model
Extract standardised names from a bru or inla result objectbru_names bru_names.bru bru_names.inla
Observation model construction for usage with 'bru()'bru_like_list bru_obs bru_obs_list bru_obs_list.bru_obs bru_obs_list.bru_obs_list bru_obs_list.list c.bru_obs c.bru_obs_list like like_list [.bru_obs_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 bru_options_set_local
Response size queriesbru_response_size bru_response_size.bru bru_response_size.bru_info bru_response_size.bru_obs bru_response_size.bru_obs_list bru_response_size.default bru_response_size.inla.surv bru_response_size.list
Set missing values in observation modelsbru_set_missing bru_set_missing.bru bru_set_missing.bru_info bru_set_missing.bru_obs bru_set_missing.bru_obs_list bru_set_missing.data.frame bru_set_missing.default bru_set_missing.inla.surv bru_set_missing<-
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 from 'lgcp' estimates.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
Summarise component inputsformat.bru_input print.bru_input summary.bru_input
mapper object summariesformat.bm_collect format.bm_list format.bm_multi format.bm_pipe format.bm_reparam format.bm_repeat format.bm_sum format.bru_mapper print.bm_list print.bru_mapper print.summary_bru_mapper summary.bru_mapper
Generate samples from fitted bru modelsgenerate generate.bru
ggplot2 geomes for inlabru related objectsgg
Geom for predictionsgg.bru_prediction gg.data.frame gg.prediction plot.bru_prediction plot.prediction
Geom for fm_mesh_1d objectsgg.fm_mesh_1d
Geom for fm_mesh_2d objectsgg.fm_mesh_2d
Geom for matrixgg.matrix
Geom for RasterLayer objectsgg.RasterLayer
Geom helper for sf objectsgg.sf
Geoms for sp Spatial objectsgg.Spatial gg.SpatialGridDataFrame gg.SpatialLines gg.SpatialPixels gg.SpatialPixelsDataFrame gg.SpatialPoints gg.SpatialPolygons
Geom wrapper for SpatRaster objectsgg.SpatRaster
Glance at a bru model fitglance.bru
Render objects using RGLglobe glplot glplot.fm_mesh_2d glplot.SpatialLines glplot.SpatialPoints
Gorilla nesting sites in sf formatgorillas_sf gorillas_sf_gcov gorillas_sp
Evaluate a mappingibm_eval ibm_eval.bm_aggregate ibm_eval.bm_collect ibm_eval.bm_const ibm_eval.bm_logitaverage ibm_eval.bm_logsumexp ibm_eval.bm_marginal ibm_eval.bm_multi ibm_eval.bm_pipe ibm_eval.bm_reparam ibm_eval.bm_repeat ibm_eval.bm_scale ibm_eval.bm_shift ibm_eval.bm_sum ibm_eval.bm_taylor ibm_eval.default
Evaluate a mapper and its Jacobianibm_eval2 ibm_eval2.bm_pipe ibm_eval2.default
Find index subset of INLA visible statesibm_inla_subset ibm_inla_subset.default
Interface between 'bru_input' and 'bru_mapper'bm_autodetect ibm_input ibm_input_available ibm_input_get ibm_input_new ibm_input_set
Detect invalid input to a mapperibm_invalid_output ibm_invalid_output.bm_collect ibm_invalid_output.bm_index ibm_invalid_output.bm_multi ibm_invalid_output.bm_repeat ibm_invalid_output.bm_sum ibm_invalid_output.default
Check if a mapper is linear/affineibm_is_linear ibm_is_linear.bm_collect ibm_is_linear.bm_multi ibm_is_linear.bm_sum ibm_is_linear.default
Check if a mapper is rowwiseibm_is_rowwise ibm_is_rowwise.default
Jacobian of a mapperibm_jacobian ibm_jacobian.bm_aggregate ibm_jacobian.bm_collect ibm_jacobian.bm_const ibm_jacobian.bm_factor ibm_jacobian.bm_fmesher ibm_jacobian.bm_fm_mesh_1d ibm_jacobian.bm_harmonics ibm_jacobian.bm_index ibm_jacobian.bm_linear ibm_jacobian.bm_logitaverage ibm_jacobian.bm_logsumexp ibm_jacobian.bm_marginal ibm_jacobian.bm_matrix ibm_jacobian.bm_multi ibm_jacobian.bm_pipe ibm_jacobian.bm_reparam ibm_jacobian.bm_repeat ibm_jacobian.bm_scale ibm_jacobian.bm_shift ibm_jacobian.bm_sum ibm_jacobian.bm_taylor ibm_jacobian.default
Compute a mapper linearisationibm_linear ibm_linear.bm_collect ibm_linear.bm_multi ibm_linear.bm_repeat ibm_linear.bm_sum ibm_linear.bru_comp ibm_linear.default
Size of the latent vector of a mappingibm_n ibm_n.bm_aggregate ibm_n.bm_collect ibm_n.bm_const ibm_n.bm_factor ibm_n.bm_fmesher ibm_n.bm_fm_mesh_1d ibm_n.bm_harmonics ibm_n.bm_linear ibm_n.bm_marginal ibm_n.bm_matrix ibm_n.bm_multi ibm_n.bm_pipe ibm_n.bm_reparam ibm_n.bm_repeat ibm_n.bm_scale ibm_n.bm_shift ibm_n.bm_sum ibm_n.bm_taylor ibm_n.default
Output size of a mappingibm_n_output ibm_n_output.bm_aggregate ibm_n_output.bm_collect ibm_n_output.bm_marginal ibm_n_output.bm_multi ibm_n_output.bm_pipe ibm_n_output.bm_reparam ibm_n_output.bm_repeat ibm_n_output.bm_scale ibm_n_output.bm_shift ibm_n_output.bm_sum ibm_n_output.bm_taylor ibm_n_output.default
Names of submapperibm_names ibm_names.bm_collect ibm_names.bm_multi ibm_names.bm_sum ibm_names.default ibm_names<- ibm_names<-.bm_collect ibm_names<-.bm_multi ibm_names<-.bm_sum ibm_names<-.bru_mapper_collect ibm_names<-.bru_mapper_multi ibm_names<-.bru_mapper_sum
Simplify a mapperibm_simplify ibm_simplify.bm_pipe ibm_simplify.default
Value vector for a mappingibm_values ibm_values.bm_aggregate ibm_values.bm_collect ibm_values.bm_const ibm_values.bm_factor ibm_values.bm_fmesher ibm_values.bm_fm_mesh_1d ibm_values.bm_linear ibm_values.bm_marginal ibm_values.bm_matrix ibm_values.bm_multi ibm_values.bm_pipe ibm_values.bm_reparam ibm_values.bm_repeat ibm_values.bm_scale ibm_values.bm_shift ibm_values.bm_sum ibm_values.bm_taylor ibm_values.default
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
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 and print methods for observation modelsprint.bru_obs print.bru_obs_list print.summary_bru_obs print.summary_bru_obs_list summary.bru_obs summary.bru_obs_list
Print inlabru optionsprint.summary_bru_options summary.bru_options
Tidy a bru model fittidy.bru
Simulated 1D animal group locations and group sizestoygroups
Simulated 2D point process datatoypoints