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

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

## Documentation for package ‘INLA’ version 21.11.29

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Code demos. Use demo() to run them.
- Package NEWS.

## Help Pages

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