Full Bayesian Analysis of Latent Gaussian Models using Integrated Nested Laplace Approximations


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Documentation for package ‘INLA’ version 21.11.22

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A B C D E F G H I J K L M N O P Q R S T V W Z misc

INLA-package Integrated Nested Laplace Approximation

-- A --

agaussian Aggregate Gaussian into an equivalent observation
aggregate.gaussian Aggregate Gaussian into an equivalent observation
ar.dpacf Utility functions for the PC prior for a an AR(p) model
ar.pacf2acf Convert between parameterizations for the AR(p) model
ar.pacf2phi Convert between parameterizations for the AR(p) model
ar.phi2acf Convert between parameterizations for the AR(p) model
ar.phi2pacf Convert between parameterizations for the AR(p) model
ar.rpacf Utility functions for the PC prior for a an AR(p) model
as.inla.mdata Create an mdata-object for INLA
as.inla.mesh.segment Convert 'sp' curve objects to 'inla.mesh.segment' objects.
as.inla.mesh.segment.Line Convert 'sp' curve objects to 'inla.mesh.segment' objects.
as.inla.mesh.segment.Lines Convert 'sp' curve objects to 'inla.mesh.segment' objects.
as.inla.mesh.segment.Polygon Convert 'sp' curve objects to 'inla.mesh.segment' objects.
as.inla.mesh.segment.Polygons Convert 'sp' curve objects to 'inla.mesh.segment' objects.
as.inla.mesh.segment.SpatialLines Convert 'sp' curve objects to 'inla.mesh.segment' objects.
as.inla.mesh.segment.SpatialLinesDataFrame Convert 'sp' curve objects to 'inla.mesh.segment' objects.
as.inla.mesh.segment.SpatialPoints Convert 'sp' curve objects to 'inla.mesh.segment' objects.
as.inla.mesh.segment.SpatialPointsDataFrame Convert 'sp' curve objects to 'inla.mesh.segment' objects.
as.inla.mesh.segment.SpatialPolygons Convert 'sp' curve objects to 'inla.mesh.segment' objects.
as.inla.mesh.segment.SpatialPolygonsDataFrame Convert 'sp' curve objects to 'inla.mesh.segment' objects.
as.inla.surv Create a Survival Object for INLA

-- B --

barrier Functions for defining the Barrier models
barrier Functions for defining the Barrier models
barrier.fem Functions for defining the Barrier models
barrier.fem Functions for defining the Barrier models
barrier.pcmatern Functions for defining the Barrier models
barrier.pcmatern Functions for defining the Barrier models
barrier.polygon Functions for defining the Barrier models
barrier.polygon Functions for defining the Barrier models
barrier.q Functions for defining the Barrier models
barrier.q Functions for defining the Barrier models
binary.install Install alternative binary builds
BivMetaAnalysis Bivariate Meta Analysis

-- C --

Cancer ~~ data name/kind ... ~~
cbind.data.frames Convert a Cox proportional hazard model into Poisson regression
changelog inla.changelog
collect.results Collect results from a inla-call
compare.results Compare INLA and MCMC results
control.bgev.default Control variables in control.bgev.default
control.bgev.default.default Control variables in control.bgev.default
control.compute Control variables in control.compute
control.compute.default Control variables in control.compute
control.expert Control variables in control.expert
control.expert.default Control variables in control.expert
control.family Control variables in control.family
control.family.default Control variables in control.family
control.fixed Control variables in control.fixed
control.fixed.default Control variables in control.fixed
control.group Control variables in control.group
control.group.default Control variables in control.group
control.hazard Control variables in control.hazard
control.hazard.default Control variables in control.hazard
control.inla Control variables in control.inla
control.inla.default Control variables in control.inla
control.lincomb Control variables in control.lincomb
control.lincomb.default Control variables in control.lincomb
control.link Control variables in control.link
control.link.default Control variables in control.link
control.lp.scale Control variables in control.lp.scale
control.lp.scale.default Control variables in control.lp.scale
control.mix Control variables in control.mix
control.mix.default Control variables in control.mix
control.mode Control variables in control.mode
control.mode.default Control variables in control.mode
control.pardiso.default Control variables in control.pardiso.default
control.pardiso.default.default Control variables in control.pardiso.default
control.predictor Control variables in control.predictor
control.predictor.default Control variables in control.predictor
control.results Control variables in control.results
control.results.default Control variables in control.results
control.update Control variables in control.update
control.update.default Control variables in control.update
cormat.dim2p Utility functions for the PC prior for a correlation matrix
cormat.dtheta Utility functions for the PC prior for a correlation matrix
cormat.p2dim Utility functions for the PC prior for a correlation matrix
cormat.permute Utility functions for the PC prior for a correlation matrix
cormat.R2r Utility functions for the PC prior for a correlation matrix
cormat.r2R Utility functions for the PC prior for a correlation matrix
cormat.R2theta Utility functions for the PC prior for a correlation matrix
cormat.r2theta Utility functions for the PC prior for a correlation matrix
cormat.rtheta Utility functions for the PC prior for a correlation matrix
cormat.theta2R Utility functions for the PC prior for a correlation matrix
cormat.theta2r Utility functions for the PC prior for a correlation matrix
coxph Convert a Cox proportional hazard model into Poisson regression
cpo.inla Improved estimates for the CPO/PIT-values
crs_wkt Handling CRS/WKT
cut Group-wise model criticism using node-splitting

-- D --

debug.graph Debug a graph-file
dmarginal Functions which operates on marginals
Drivers Time series with seasonal effect

-- E --

emarginal Functions which operates on marginals
Epil Repeated measures on Poisson counts
extract.groups Extract tagged boundary/internal segments.
extract.groups.inla.mesh.segment Extract tagged boundary/internal segments.

-- F --

f Define general Gaussian models in the INLA formula
fgn Return the coefficients in the 3-component AR(1) mixture representing FGN(H)

-- G --

geobugs2inla INLA utility functions
Germany Disease Mapping
get.inlaEnv Return the internal environment used by INLA
graph2matrix Construct a neighbour-matrix from a 'graph'

-- H --

hpdmarginal Functions which operates on marginals
hyperpar.inla Improved estimates for the hyperparameters
hyperpar.sample Produce samples from the approximated joint posterior for the hyperparameters
hyperpar.sampler Produce samples from the approximated joint posterior for the hyperparameters

-- I --

idx Convert indexes
iidkd.sample Provide samples from the 'iidkd' component (experimental)
INLA Integrated Nested Laplace Approximation
inla Bayesian analysis of structured additive models
inla-class inla estimation object class
inla.1djmarginal Sample, transform and evaluate from a joint marginal approximation
inla.agaussian Aggregate Gaussian into an equivalent observation
inla.ar.pacf2acf Convert between parameterizations for the AR(p) model
inla.ar.pacf2phi Convert between parameterizations for the AR(p) model
inla.ar.phi2acf Convert between parameterizations for the AR(p) model
inla.ar.phi2pacf Convert between parameterizations for the AR(p) model
inla.as.CRS.list Show expanded CRS arguments
inla.as.CRSargs.list Show expanded CRS arguments
inla.as.dgTMatrix Convert a matrix or sparse matrix into the sparse formate used by INLA
inla.as.list.CRS Show expanded CRS arguments
inla.as.list.CRSargs Show expanded CRS arguments
inla.as.sparse Convert a matrix or sparse matrix into the sparse formate used by INLA
inla.as.wkt.wkt_tree Internal WKT handling
inla.as.wkt_tree.wkt Internal WKT handling
inla.barrier Functions for defining the Barrier models
inla.barrier Functions for defining the Barrier models
inla.barrier.fem Functions for defining the Barrier models
inla.barrier.fem Functions for defining the Barrier models
inla.barrier.pcmatern Functions for defining the Barrier models
inla.barrier.pcmatern Functions for defining the Barrier models
inla.barrier.polygon Functions for defining the Barrier models
inla.barrier.polygon Functions for defining the Barrier models
inla.barrier.q Functions for defining the Barrier models
inla.barrier.q Functions for defining the Barrier models
inla.binary.install Install alternative binary builds
inla.changelog inla.changelog
inla.changes inla.changelog
inla.collect.results Collect results from a inla-call
inla.compare.results Compare INLA and MCMC results
inla.contour.segment Constraint segments for inla.mesh Constructs 'inla.mesh.segment' objects that can be used to specify boundary and interior constraint edges in calls to 'inla.mesh()'.
inla.control.bgev.default Control variables in control.bgev.default
inla.control.compute Control variables in control.compute
inla.control.expert Control variables in control.expert
inla.control.family Control variables in control.family
inla.control.fixed Control variables in control.fixed
inla.control.group Control variables in control.group
inla.control.hazard Control variables in control.hazard
inla.control.inla Control variables in control.inla
inla.control.lincomb Control variables in control.lincomb
inla.control.link Control variables in control.link
inla.control.lp.scale Control variables in control.lp.scale
inla.control.mix Control variables in control.mix
inla.control.mode Control variables in control.mode
inla.control.pardiso.default Control variables in control.pardiso.default
inla.control.predictor Control variables in control.predictor
inla.control.results Control variables in control.results
inla.control.update Control variables in control.update
inla.coxph Convert a Cox proportional hazard model into Poisson regression
inla.cpo Improved estimates for the CPO/PIT-values
inla.CRS Create a coordinate reference system object
inla.CRSargs Show expanded CRS arguments
inla.crs_get_ellipsoid_radius Handling CRS/WKT
inla.crs_get_lengthunit Handling CRS/WKT
inla.crs_get_wkt Handling CRS/WKT
inla.crs_is_geocent Handling CRS/WKT
inla.crs_set_ellipsoid_radius Handling CRS/WKT
inla.crs_set_lengthunit Handling CRS/WKT
inla.cut Group-wise model criticism using node-splitting
inla.debug.graph Debug a graph-file
inla.delaunay Low level function for high-quality triangulations
inla.dev.new Opens a new device
inla.diameter Diameter of a point set
inla.diameter.default Diameter of a point set
inla.diameter.inla.mesh Diameter of a point set
inla.diameter.inla.mesh.1d Diameter of a point set
inla.diameter.inla.mesh.lattice Diameter of a point set
inla.diameter.inla.mesh.segment Diameter of a point set
inla.dmarginal Functions which operates on marginals
inla.doc View documentation
inla.emarginal Functions which operates on marginals
inla.extract.el Extract elements by matching name from container objects.
inla.extract.el.data.frame Extract elements by matching name from container objects.
inla.extract.el.list Extract elements by matching name from container objects.
inla.extract.el.matrix Extract elements by matching name from container objects.
inla.fallback_PROJ6 PROJ6 detection
inla.fgn Return the coefficients in the 3-component AR(1) mixture representing FGN(H)
inla.fmesher.smorg Compute various mesh related quantities.
inla.generate.colors Generate text RGB color specifications.
inla.geobugs2inla INLA utility functions
inla.get.inlaEnv Return the internal environment used by INLA
inla.getOption Set and get global options for INLA
inla.graph Read and write a graph-object
inla.graph2matrix Construct a neighbour-matrix from a 'graph'
inla.group Group or cluster covariates
inla.has_PROJ6 PROJ6 detection
inla.hpdmarginal Functions which operates on marginals
inla.hyperpar Improved estimates for the hyperparameters
inla.hyperpar.sample Produce samples from the approximated joint posterior for the hyperparameters
inla.hyperpar.sampler Produce samples from the approximated joint posterior for the hyperparameters
inla.identical.CRS Test CRS and inla.CRS for equality
inla.idx Convert indexes
inla.iidkd.sample Provide samples from the 'iidkd' component (experimental)
inla.inla.doc View documentation
inla.joint.marginal Sample, transform and evaluate from a joint marginal approximation
inla.joint.marginal.eval Sample, transform and evaluate from a joint marginal approximation
inla.jp.define Joint-prior models
inla.knmodels Spacetime interaction models
inla.knmodels.sample Spacetime interaction models sampler function
inla.ks.plot Kolmogorov-Smirnov Test Plots
inla.lattice2node Functions to define mapping between a lattice and nodes
inla.lattice2node.mapping Functions to define mapping between a lattice and nodes
inla.link Link functions in INLA
inla.link.cauchit Link functions in INLA
inla.link.cloglog Link functions in INLA
inla.link.identity Link functions in INLA
inla.link.invalid Link functions in INLA
inla.link.invcauchit Link functions in INLA
inla.link.invcloglog Link functions in INLA
inla.link.inverse Link functions in INLA
inla.link.invidentity Link functions in INLA
inla.link.invinvalid Link functions in INLA
inla.link.invinverse Link functions in INLA
inla.link.invlog Link functions in INLA
inla.link.invlogit Link functions in INLA
inla.link.invloglog Link functions in INLA
inla.link.invneglog Link functions in INLA
inla.link.invprobit Link functions in INLA
inla.link.invqpoisson Link functions in INLA
inla.link.invrobit Link functions in INLA
inla.link.invsn Link functions in INLA
inla.link.invtan Link functions in INLA
inla.link.log Link functions in INLA
inla.link.logit Link functions in INLA
inla.link.loglog Link functions in INLA
inla.link.neglog Link functions in INLA
inla.link.probit Link functions in INLA
inla.link.robit Link functions in INLA
inla.link.sn Link functions in INLA
inla.link.tan Link functions in INLA
inla.list.models List available model components, likelihoods, priors, etc
inla.load Load or source a file
inla.make.lincomb Create linear combinations
inla.make.lincombs Create linear combinations
inla.marginal Functions which operates on marginals
inla.matern.cov Numerical evaluation of Matern and related covariance functions.
inla.matern.cov.s2 Numerical evaluation of Matern and related covariance functions.
inla.matern.cov.s2.unstable Numerical evaluation of Matern and related covariance functions.
inla.matrix2vector Functions to define mapping between a lattice and nodes
inla.mdata Create an mdata-object for INLA
inla.merge Merge a mixture of 'inla'-objects
inla.mesh Low level function for high-quality triangulations
inla.mesh.1d Function space definition objects for 1D SPDE models.
inla.mesh.1d.A Mapping matrix for 1D meshes
inla.mesh.1d.bary Mapping matrix for 1D meshes
inla.mesh.1d.fem Function space definition objects for 1D SPDE models.
inla.mesh.1d.fem Finite element matrices
inla.mesh.2d High-quality triangulations
inla.mesh.assessment Interactive mesh building and diagnostics
inla.mesh.assessment Interactive mesh building and diagnostics
inla.mesh.basis Basis functions for inla.mesh
inla.mesh.boundary Constraint segment extraction for inla.mesh
inla.mesh.components Compute connected mesh subsets
inla.mesh.components Compute connected mesh subsets
inla.mesh.create Low level function for high-quality triangulations
inla.mesh.deriv Directional derivative matrices for functions on meshes.
inla.mesh.fem Finite element matrices
inla.mesh.interior Constraint segment extraction for inla.mesh
inla.mesh.lattice Lattice grids for inla.mesh
inla.mesh.map Coordinate mappings for 'inla.mesh' projections.
inla.mesh.map.lim Coordinate mappings for 'inla.mesh' projections.
inla.mesh.project Methods for projecting to/from an inla.mesh
inla.mesh.project.inla.mesh Methods for projecting to/from an inla.mesh
inla.mesh.project.inla.mesh.1d Methods for projecting to/from an inla.mesh
inla.mesh.project.inla.mesh.projector Methods for projecting to/from an inla.mesh
inla.mesh.projector Methods for projecting to/from an inla.mesh
inla.mesh.projector.inla.mesh Methods for projecting to/from an inla.mesh
inla.mesh.projector.inla.mesh.1d Methods for projecting to/from an inla.mesh
inla.mesh.query High-quality triangulations
inla.mesh.segment Constraint segments for inla.mesh Constructs 'inla.mesh.segment' objects that can be used to specify boundary and interior constraint edges in calls to 'inla.mesh()'.
inla.mesh.segment.default Constraint segments for inla.mesh Constructs 'inla.mesh.segment' objects that can be used to specify boundary and interior constraint edges in calls to 'inla.mesh()'.
inla.mesh.segment.inla.mesh.segment Constraint segments for inla.mesh Constructs 'inla.mesh.segment' objects that can be used to specify boundary and interior constraint edges in calls to 'inla.mesh()'.
inla.mmarginal Functions which operates on marginals
inla.models Valid models in INLA
inla.nmix.fitted Estimate posterior distributions of fitted lambda values
inla.nmix.lambda.fitted Estimate posterior distributions of fitted lambda values
inla.node2lattice Functions to define mapping between a lattice and nodes
inla.node2lattice.mapping Functions to define mapping between a lattice and nodes
inla.nonconvex.hull Nonconvex set extensions.
inla.nonconvex.hull.basic Nonconvex set extensions.
inla.not_for_PROJ4 PROJ6 detection
inla.not_for_PROJ6 PROJ6 detection
inla.option Set and get global options for INLA
inla.options Set and get global options for INLA
inla.over_sp_mesh Check which mesh triangles are inside a polygon
inla.pardiso PARDISO support in R-INLA
inla.pardiso.check PARDISO support in R-INLA
inla.pc.alphaw Utility functions for the PC prior for the 'alpha' parameter in the Weibull likelihood
inla.pc.ar Utility functions for the PC prior for a an AR(p) model
inla.pc.ar.dpacf Utility functions for the PC prior for a an AR(p) model
inla.pc.ar.rpacf Utility functions for the PC prior for a an AR(p) model
inla.pc.cor0 Utility functions for the PC prior for correlation in AR(1)
inla.pc.cor1 Utility functions for the PC prior for correlation in AR(1)
inla.pc.cormat Utility functions for the PC prior for a correlation matrix
inla.pc.cormat.dim2p Utility functions for the PC prior for a correlation matrix
inla.pc.cormat.dtheta Utility functions for the PC prior for a correlation matrix
inla.pc.cormat.p2dim Utility functions for the PC prior for a correlation matrix
inla.pc.cormat.permute Utility functions for the PC prior for a correlation matrix
inla.pc.cormat.R2r Utility functions for the PC prior for a correlation matrix
inla.pc.cormat.r2R Utility functions for the PC prior for a correlation matrix
inla.pc.cormat.R2theta Utility functions for the PC prior for a correlation matrix
inla.pc.cormat.r2theta Utility functions for the PC prior for a correlation matrix
inla.pc.cormat.rtheta Utility functions for the PC prior for a correlation matrix
inla.pc.cormat.theta2R Utility functions for the PC prior for a correlation matrix
inla.pc.cormat.theta2r Utility functions for the PC prior for a correlation matrix
inla.pc.dalphaw Utility functions for the PC prior for the 'alpha' parameter in the Weibull likelihood
inla.pc.dcor0 Utility functions for the PC prior for correlation in AR(1)
inla.pc.dcor1 Utility functions for the PC prior for correlation in AR(1)
inla.pc.ddof PC-prior for dof in a standarized Student-t
inla.pc.dgamma Utility functions for the PC prior for 'Gamma(1/a, 1/a)'
inla.pc.dgammacount Utility functions for the PC prior for the 'gammacount' likelihood
inla.pc.dgevtail Utility functions for the PC prior for the 'tail' parameter in the GEV likelihood
inla.pc.dof PC-prior for dof in a standarized Student-t
inla.pc.dprec Utility functions for the PC prior for the precision
inla.pc.dsn Utility functions for the PC prior for 'skewness' in the skew-normal linkfunction and likelihood
inla.pc.gamma Utility functions for the PC prior for 'Gamma(1/a, 1/a)'
inla.pc.gammacount Utility functions for the PC prior for the 'gammacount' likelihood
inla.pc.gevtail Utility functions for the PC prior for the 'tail' parameter in the GEV likelihood
inla.pc.multvar Multivariate PC priors
inla.pc.multvar.h.default Multivariate PC priors
inla.pc.multvar.simplex Multivariate PC priors
inla.pc.multvar.simplex.d Multivariate PC priors
inla.pc.multvar.simplex.r Multivariate PC priors
inla.pc.multvar.sphere Multivariate PC priors
inla.pc.multvar.sphere.d Multivariate PC priors
inla.pc.multvar.sphere.r Multivariate PC priors
inla.pc.palphaw Utility functions for the PC prior for the 'alpha' parameter in the Weibull likelihood
inla.pc.pcor0 Utility functions for the PC prior for correlation in AR(1)
inla.pc.pcor1 Utility functions for the PC prior for correlation in AR(1)
inla.pc.pgamma Utility functions for the PC prior for 'Gamma(1/a, 1/a)'
inla.pc.pgammacount Utility functions for the PC prior for the 'gammacount' likelihood
inla.pc.pgevtail Utility functions for the PC prior for the 'tail' parameter in the GEV likelihood
inla.pc.pprec Utility functions for the PC prior for the precision
inla.pc.prec Utility functions for the PC prior for the precision
inla.pc.psn Utility functions for the PC prior for 'skewness' in the skew-normal linkfunction and likelihood
inla.pc.qalphaw Utility functions for the PC prior for the 'alpha' parameter in the Weibull likelihood
inla.pc.qcor0 Utility functions for the PC prior for correlation in AR(1)
inla.pc.qcor1 Utility functions for the PC prior for correlation in AR(1)
inla.pc.qgamma Utility functions for the PC prior for 'Gamma(1/a, 1/a)'
inla.pc.qgammacount Utility functions for the PC prior for the 'gammacount' likelihood
inla.pc.qgevtail Utility functions for the PC prior for the 'tail' parameter in the GEV likelihood
inla.pc.qprec Utility functions for the PC prior for the precision
inla.pc.qsn Utility functions for the PC prior for 'skewness' in the skew-normal linkfunction and likelihood
inla.pc.ralphaw Utility functions for the PC prior for the 'alpha' parameter in the Weibull likelihood
inla.pc.rcor0 Utility functions for the PC prior for correlation in AR(1)
inla.pc.rcor1 Utility functions for the PC prior for correlation in AR(1)
inla.pc.rgamma Utility functions for the PC prior for 'Gamma(1/a, 1/a)'
inla.pc.rgammacount Utility functions for the PC prior for the 'gammacount' likelihood
inla.pc.rgevtail Utility functions for the PC prior for the 'tail' parameter in the GEV likelihood
inla.pc.rprec Utility functions for the PC prior for the precision
inla.pc.rsn Utility functions for the PC prior for 'skewness' in the skew-normal linkfunction and likelihood
inla.pc.sn Utility functions for the PC prior for 'skewness' in the skew-normal linkfunction and likelihood
inla.pc.t PC-prior for dof in a standarized Student-t
inla.plot Default INLA plotting
inla.pmarginal Functions which operates on marginals
inla.posterior.sample Generate samples, and functions thereof, from an approximated posterior of a fitted model
inla.posterior.sample.eval Generate samples, and functions thereof, from an approximated posterior of a fitted model
inla.priors.used Print priors used
inla.prune Prune the INLA-package
inla.q Control and view a remote inla-queue
inla.qdel Control and view a remote inla-queue
inla.qget Control and view a remote inla-queue
inla.qinv Computes (parts of) the inverse of a SPD sparse matrix
inla.qlog Control and view a remote inla-queue
inla.qmarginal Functions which operates on marginals
inla.qnuke Control and view a remote inla-queue
inla.qreordering Compute the reordering using the GMRFLib implementation
inla.qsample Generate samples from a GMRF using the GMRFLib implementation
inla.qsolve Solves linear SPD systems
inla.qstat Control and view a remote inla-queue
inla.rbind.data.frames Convert a Cox proportional hazard model into Poisson regression
inla.read.graph Read and write a graph-object
inla.remote Setup remote computing
inla.reorderings Reorderings methods for sparse matrices
inla.requires_PROJ6 PROJ6 detection
inla.rerun Rerun an analysis
inla.rgeneric.ar1.model rgeneric models
inla.rgeneric.define rgeneric models
inla.rgeneric.iid.model rgeneric models
inla.rgeneric.q rgeneric models
inla.rgeneric.wrapper rgeneric models
inla.rjmarginal Sample, transform and evaluate from a joint marginal approximation
inla.rjmarginal.eval Sample, transform and evaluate from a joint marginal approximation
inla.rmarginal Functions which operates on marginals
inla.row.kron Row-wise Kronecker products
inla.scale.model Scale an intrinsic GMRF model
inla.set.control.bgev.default.default Control variables in control.bgev.default
inla.set.control.compute.default Control variables in control.compute
inla.set.control.expert.default Control variables in control.expert
inla.set.control.family.default Control variables in control.family
inla.set.control.fixed.default Control variables in control.fixed
inla.set.control.group.default Control variables in control.group
inla.set.control.hazard.default Control variables in control.hazard
inla.set.control.inla.default Control variables in control.inla
inla.set.control.lincomb.default Control variables in control.lincomb
inla.set.control.link.default Control variables in control.link
inla.set.control.lp.scale.default Control variables in control.lp.scale
inla.set.control.mix.default Control variables in control.mix
inla.set.control.mode.default Control variables in control.mode
inla.set.control.pardiso.default.default Control variables in control.pardiso.default
inla.set.control.predictor.default Control variables in control.predictor
inla.set.control.results.default Control variables in control.results
inla.set.control.update.default Control variables in control.update
inla.setOption Set and get global options for INLA
inla.simplify.curve Recursive curve simplification.
inla.smarginal Functions which operates on marginals
inla.sp2segment Convert 'sp' curve objects to 'inla.mesh.segment' objects.
inla.spde.make.A Observation/prediction matrices for mesh models.
inla.spde.make.block.A Observation matrices for mesh models.
inla.spde.make.index SPDE model index vector generation
inla.spde.models List SPDE models supported by inla.spde objects
inla.spde.precision Precision matrices for SPDE models Calculates the precision matrix for given parameter values based on an 'inla.spde' model object.
inla.spde.precision.inla.spde1 Precision matrices for SPDE models Calculates the precision matrix for given parameter values based on an 'inla.spde' model object.
inla.spde.precision.inla.spde2 Precision matrices for SPDE models Calculates the precision matrix for given parameter values based on an 'inla.spde' model object.
inla.spde.result SPDE result extraction from INLA estimation results
inla.spde.result.inla.spde1 SPDE result extraction from INLA estimation results
inla.spde.result.inla.spde2 SPDE result extraction from INLA estimation results
inla.spde.sample Sample from SPDE models
inla.spde.sample.default Sample from SPDE models
inla.spde.sample.inla.spde Sample from SPDE models
inla.spde1 Old SPDE model objects for INLA
inla.spde1.create Old SPDE model objects for INLA
inla.spde1.imatern Old SPDE model objects for INLA
inla.spde1.matern Old SPDE model objects for INLA
inla.spde1.matern.osc Old SPDE model objects for INLA
inla.spde1.models List SPDE models supported by inla.spde objects
inla.spde1.precision Precision matrices for SPDE models Calculates the precision matrix for given parameter values based on an 'inla.spde' model object.
inla.spde1.result SPDE result extraction from INLA estimation results
inla.spde2 Generic spde2 model creation.
inla.spde2.generic Generic spde2 model creation.
inla.spde2.matern Matern SPDE model object for INLA
inla.spde2.matern.sd.basis Approximate variance-compensating basis functions
inla.spde2.models List SPDE models supported by inla.spde objects
inla.spde2.pcmatern Matern SPDE model object with PC prior for INLA
inla.spde2.precision Precision matrices for SPDE models Calculates the precision matrix for given parameter values based on an 'inla.spde' model object.
inla.spde2.result SPDE result extraction from INLA estimation results
inla.spde2.theta2phi0 Generic spde2 model creation.
inla.spde2.theta2phi0 Matern SPDE model object for INLA
inla.spde2.theta2phi1 Generic spde2 model creation.
inla.spde2.theta2phi1 Matern SPDE model object for INLA
inla.spde2.theta2phi2 Generic spde2 model creation.
inla.spde2.theta2phi2 Matern SPDE model object for INLA
inla.spTransform Wrapper method for 'sp::spTransform'
inla.spTransform.default Wrapper method for 'sp::spTransform'
inla.spTransform.inla.mesh Wrapper method for 'sp::spTransform'
inla.spTransform.inla.mesh.lattice Wrapper method for 'sp::spTransform'
inla.spTransform.inla.mesh.segment Wrapper method for 'sp::spTransform'
inla.spTransform.SpatialPoints Wrapper method for 'sp::spTransform'
inla.spTransform.SpatialPointsDataFrame Wrapper method for 'sp::spTransform'
inla.spy Construct a neighbour-matrix from a 'graph'
inla.sp_get_crs Extract CRS information
inla.ssh.copy.id Setup remote computing
inla.stack Data stacking for advanced INLA models
inla.stack.A Data stacking for advanced INLA models
inla.stack.compress Data stacking for advanced INLA models
inla.stack.data Data stacking for advanced INLA models
inla.stack.index Data stacking for advanced INLA models
inla.stack.join Data stacking for advanced INLA models
inla.stack.LHS Data stacking for advanced INLA models
inla.stack.remove.unused Data stacking for advanced INLA models
inla.stack.RHS Data stacking for advanced INLA models
inla.stack.sum Data stacking for advanced INLA models
inla.surv Create a Survival Object for INLA
inla.tjmarginal Sample, transform and evaluate from a joint marginal approximation
inla.tmarginal Functions which operates on marginals
inla.update Upgrade the INLA-package
inla.upgrade Upgrade the INLA-package
inla.vector2matrix Functions to define mapping between a lattice and nodes
inla.version Show the version of the INLA-package
inla.wkt_get_ellipsoid_radius Handling CRS/WKT
inla.wkt_get_lengthunit Handling CRS/WKT
inla.wkt_is_geocent Handling CRS/WKT
inla.wkt_predef Create a coordinate reference system object
inla.wkt_set_ellipsoid_radius Handling CRS/WKT
inla.wkt_set_lengthunit Handling CRS/WKT
inla.wkt_tree_get_item Internal WKT handling
inla.wkt_tree_set_item Internal WKT handling
inla.wkt_unit_params Handling CRS/WKT
inla.write.graph Read and write a graph-object
inla.zmarginal Functions which operates on marginals
is.inla.mdata Create an mdata-object for INLA
is.inla.surv Create a Survival Object for INLA

-- J --

joint.marginal Sample, transform and evaluate from a joint marginal approximation
joint.marginal.eval Sample, transform and evaluate from a joint marginal approximation
jp Joint-prior models
jp.define Joint-prior models

-- K --

Kidney Kidney infection data
knmodels Spacetime interaction models
ks.plot Kolmogorov-Smirnov Test Plots

-- L --

lattice2node Functions to define mapping between a lattice and nodes
lattice2node.mapping Functions to define mapping between a lattice and nodes
Leuk The Leukemia data
Leukemia The Leukemia data
lines.inla.mesh.segment Draw 'inla.mesh.segment' objects.
link Link functions in INLA
list.models List available model components, likelihoods, priors, etc

-- M --

make.lincomb Create linear combinations
make.lincombs Create linear combinations
marginal Functions which operates on marginals
matrix2vector Functions to define mapping between a lattice and nodes
merge.inla Merge a mixture of 'inla'-objects
meshbuilder Interactive mesh building and diagnostics
mmarginal Functions which operates on marginals
Munich The Munich rent data

-- N --

NewEngland The New England map
nmix.lambda.fitted Estimate posterior distributions of fitted lambda values
node2lattice Functions to define mapping between a lattice and nodes
node2lattice.mapping Functions to define mapping between a lattice and nodes
nwEngland The New England map

-- O --

Oral ~~ data name/kind ... ~~

-- P --

pacf2acf Convert between parameterizations for the AR(p) model
pacf2phi Convert between parameterizations for the AR(p) model
param2.matern.orig Parameter settings for 'inla.spde2.matern' models.
pc.alphaw Utility functions for the PC prior for the 'alpha' parameter in the Weibull likelihood
pc.cor0 Utility functions for the PC prior for correlation in AR(1)
pc.cor1 Utility functions for the PC prior for correlation in AR(1)
pc.dalphaw Utility functions for the PC prior for the 'alpha' parameter in the Weibull likelihood
pc.dcor0 Utility functions for the PC prior for correlation in AR(1)
pc.dcor1 Utility functions for the PC prior for correlation in AR(1)
pc.ddof PC-prior for dof in a standarized Student-t
pc.dgamma Utility functions for the PC prior for 'Gamma(1/a, 1/a)'
pc.dgammacount Utility functions for the PC prior for the 'gammacount' likelihood
pc.dgevtail Utility functions for the PC prior for the 'tail' parameter in the GEV likelihood
pc.dof PC-prior for dof in a standarized Student-t
pc.dprec Utility functions for the PC prior for the precision
pc.dsn Utility functions for the PC prior for 'skewness' in the skew-normal linkfunction and likelihood
pc.gamma Utility functions for the PC prior for 'Gamma(1/a, 1/a)'
pc.gammacount Utility functions for the PC prior for the 'gammacount' likelihood
pc.gevtail Utility functions for the PC prior for the 'tail' parameter in the GEV likelihood
pc.multvar Multivariate PC priors
pc.multvar.h.default Multivariate PC priors
pc.multvar.simplex Multivariate PC priors
pc.multvar.simplex.d Multivariate PC priors
pc.multvar.simplex.r Multivariate PC priors
pc.multvar.sphere Multivariate PC priors
pc.multvar.sphere.d Multivariate PC priors
pc.multvar.sphere.r Multivariate PC priors
pc.palphaw Utility functions for the PC prior for the 'alpha' parameter in the Weibull likelihood
pc.pcor0 Utility functions for the PC prior for correlation in AR(1)
pc.pcor1 Utility functions for the PC prior for correlation in AR(1)
pc.pgamma Utility functions for the PC prior for 'Gamma(1/a, 1/a)'
pc.pgammacount Utility functions for the PC prior for the 'gammacount' likelihood
pc.pgevtail Utility functions for the PC prior for the 'tail' parameter in the GEV likelihood
pc.pprec Utility functions for the PC prior for the precision
pc.prec Utility functions for the PC prior for the precision
pc.psn Utility functions for the PC prior for 'skewness' in the skew-normal linkfunction and likelihood
pc.qalphaw Utility functions for the PC prior for the 'alpha' parameter in the Weibull likelihood
pc.qcor0 Utility functions for the PC prior for correlation in AR(1)
pc.qcor1 Utility functions for the PC prior for correlation in AR(1)
pc.qgamma Utility functions for the PC prior for 'Gamma(1/a, 1/a)'
pc.qgammacount Utility functions for the PC prior for the 'gammacount' likelihood
pc.qgevtail Utility functions for the PC prior for the 'tail' parameter in the GEV likelihood
pc.qprec Utility functions for the PC prior for the precision
pc.qsn Utility functions for the PC prior for 'skewness' in the skew-normal linkfunction and likelihood
pc.ralphaw Utility functions for the PC prior for the 'alpha' parameter in the Weibull likelihood
pc.rcor0 Utility functions for the PC prior for correlation in AR(1)
pc.rcor1 Utility functions for the PC prior for correlation in AR(1)
pc.rgamma Utility functions for the PC prior for 'Gamma(1/a, 1/a)'
pc.rgammacount Utility functions for the PC prior for the 'gammacount' likelihood
pc.rgevtail Utility functions for the PC prior for the 'tail' parameter in the GEV likelihood
pc.rprec Utility functions for the PC prior for the precision
pc.rsn Utility functions for the PC prior for 'skewness' in the skew-normal linkfunction and likelihood
pc.sn Utility functions for the PC prior for 'skewness' in the skew-normal linkfunction and likelihood
pc.t PC-prior for dof in a standarized Student-t
phi2acf Convert between parameterizations for the AR(p) model
phi2pacf Convert between parameterizations for the AR(p) model
plot.CRS Plot CRS and inla.CRS objects
plot.inla Default INLA plotting
plot.inla.CRS Plot CRS and inla.CRS objects
plot.inla.graph Read and write a graph-object
plot.inla.mesh Draw a triangulation mesh object
plot.inla.surv Create a Survival Object for INLA
plot.inla.trimesh Low level triangulation mesh plotting
pmarginal Functions which operates on marginals
posterior.sample Generate samples, and functions thereof, from an approximated posterior of a fitted model
posterior.sample.eval Generate samples, and functions thereof, from an approximated posterior of a fitted model
PRborder The PRborder data
print.inla Print a INLA fit
print.inla.graph.summary Read and write a graph-object
print.inla.mdata Create an mdata-object for INLA
print.inla.q Control and view a remote inla-queue
print.inla.surv Create a Survival Object for INLA
print.summary.inla Summary for a INLA fit
print.summary.inla.mesh Summarizing triangular mesh objects
priors.used Print priors used
PRprec The PRprec data
prune Prune the INLA-package

-- Q --

qinv Computes (parts of) the inverse of a SPD sparse matrix
qmarginal Functions which operates on marginals
qreordering Compute the reordering using the GMRFLib implementation
qsample Generate samples from a GMRF using the GMRFLib implementation
qsolve Solves linear SPD systems

-- R --

read.graph Read and write a graph-object
reorderings Reorderings methods for sparse matrices
rerun Rerun an analysis
rgeneric rgeneric models
rgeneric.ar1.model rgeneric models
rgeneric.define rgeneric models
rgeneric.iid.model rgeneric models
rgeneric.q rgeneric models
rgeneric.wrapper rgeneric models
rjmarginal Sample, transform and evaluate from a joint marginal approximation
rjmarginal.eval Sample, transform and evaluate from a joint marginal approximation
rmarginal Functions which operates on marginals

-- S --

Salm Extra-Poisson variation in dose-response study
scale.model Scale an intrinsic GMRF model
Scotland Conditional Autoregressive (CAR) model for disease mapping
Seeds Factorial design
set.control.bgev.default.default Control variables in control.bgev.default
set.control.compute.default Control variables in control.compute
set.control.expert.default Control variables in control.expert
set.control.family.default Control variables in control.family
set.control.fixed.default Control variables in control.fixed
set.control.group.default Control variables in control.group
set.control.hazard.default Control variables in control.hazard
set.control.inla.default Control variables in control.inla
set.control.lincomb.default Control variables in control.lincomb
set.control.link.default Control variables in control.link
set.control.lp.scale.default Control variables in control.lp.scale
set.control.mix.default Control variables in control.mix
set.control.mode.default Control variables in control.mode
set.control.pardiso.default.default Control variables in control.pardiso.default
set.control.predictor.default Control variables in control.predictor
set.control.results.default Control variables in control.results
set.control.update.default Control variables in control.update
smarginal Functions which operates on marginals
SPDEtoy toy simulated data set for the SPDE tutorial
spy Construct a neighbour-matrix from a 'graph'
ssh.copy.id Setup remote computing
summary.inla Summary for a INLA fit
summary.inla.graph Read and write a graph-object
summary.inla.mesh Summarizing triangular mesh objects
summary.inla.q Control and view a remote inla-queue
summary.surv.inla Summary for a INLA fit
Surg Surgical: Institutional ranking
SurvSim Survival data

-- T --

tjmarginal Sample, transform and evaluate from a joint marginal approximation
Tokyo Binomial time series

-- V --

vector2matrix Functions to define mapping between a lattice and nodes
version Show the version of the INLA-package

-- W --

write.graph Read and write a graph-object

-- Z --

Zambia Semiparametric regression
zmarginal Functions which operates on marginals

-- misc --

1djmarginal Sample, transform and evaluate from a joint marginal approximation