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rSPDE package

rSPDE rSPDE-package
Rational approximations of fractional SPDEs.

rSPDE models

rspde.matern()
Matern rSPDE model object for INLA
rspde.metric_graph()
Matern rSPDE model object for metric graphs in INLA
rspde.spacetime()
Space-Time Random Fields via SPDE Approximation
rspde.anistropic2d()
Rational approximations of stationary anisotropic Gaussian Matern random fields
rspde.matern1d()
Matern rSPDE model object for INLA
matern.operators()
Rational approximations of stationary Gaussian Matern random fields
matern2d.operators()
Rational approximations of stationary anisotropic Gaussian Matern random fields
spde.matern.operators()
Rational approximations of non-stationary Gaussian SPDE Matern random fields
fractional.operators()
Rational approximations of fractional operators
matern.rational()
Rational approximation of the Matern fields on intervals and metric graphs
spacetime.operators()
Space-time random fields

Linear mixed-effects models

rspde_lme()
rSPDE linear mixed effects models
predict(<rspde_lme>)
Prediction of a mixed effects regression model on a metric graph.
summary(<rspde_lme>)
Summary Method for rspde_lme Objects.
glance(<rspde_lme>)
Glance at an rspde_lme object
augment(<rspde_lme>)
Augment data with information from a rspde_lme object

Intrinsic models

intrinsic.matern.operators()
Covariance-based approximations of intrinsic fields
variogram.intrinsic.spde()
Variogram of intrinsic SPDE model
rspde.intrinsic.matern()
Intrinsic Matern rSPDE model object for INLA
simulate(<intrinsicCBrSPDEobj>)
Simulation of a fractional intrinsic SPDE using the covariance-based rational SPDE approximation

Log-likelihood

rSPDE.matern.loglike()
Object-based log-likelihood function for latent Gaussian fractional SPDE model using the rational approximations
rSPDE.loglike()
Object-based log-likelihood function for latent Gaussian fractional SPDE model
spde.matern.loglike()
Parameter-based log-likelihood for a latent Gaussian Matern SPDE model using a rational SPDE approximation
rSPDE.construct.matern.loglike()
Constructor of Matern loglikelihood functions.
construct.spde.matern.loglike()
Constructor of Matern loglikelihood functions for non-stationary models.

Computation of precision matrices

rspde.matern.precision()
Precision matrix of the covariance-based rational approximation of stationary Gaussian Matern random fields
rspde.matern.precision.integer()
Precision matrix of stationary Gaussian Matern random fields with integer covariance exponent

Methods for rSPDE, CBrSPDE and spacetime objects

predict(<rSPDEobj>)
Prediction of a fractional SPDE using a rational SPDE approximation
simulate(<rSPDEobj>)
Simulation of a fractional SPDE using a rational SPDE approximation
summary(<rSPDEobj>) print(<summary.rSPDEobj>) print(<rSPDEobj>)
Summarise rSPDE objects
update(<rSPDEobj>)
Update parameters of rSPDEobj objects
predict(<CBrSPDEobj>)
Prediction of a fractional SPDE using the covariance-based rational SPDE approximation
simulate(<CBrSPDEobj>)
Simulation of a fractional SPDE using the covariance-based rational SPDE approximation
summary(<CBrSPDEobj>) print(<summary.CBrSPDEobj>) print(<CBrSPDEobj>)
Summarise CBrSPDE objects
update(<CBrSPDEobj>)
Update parameters of CBrSPDEobj objects
precision()
Get the precision matrix of CBrSPDEobj objects
predict(<CBrSPDEobj2d>)
Prediction of an anisotropic Whittle-Matern field
simulate(<CBrSPDEobj2d>)
Simulation of a fractional SPDE using the covariance-based rational SPDE approximation
summary(<CBrSPDEobj2d>) print(<summary.CBrSPDEobj2d>) print(<CBrSPDEobj2d>)
Summarise CBrSPDEobj2d objects
update(<CBrSPDEobj2d>)
Update parameters of CBrSPDEobj2d objects
precision(<CBrSPDEobj2d>)
Get the precision matrix of CBrSPDEobj2d objects
simulate(<rSPDEobj1d>)
Simulation of a Matern field using a rational SPDE approximation
summary(<rSPDEobj1d>) print(<summary.rSPDEobj1d>) print(<rSPDEobj1d>)
Summarise rSPDE objects without FEM
update(<rSPDEobj1d>)
Update parameters of rSPDEobj1d objects
precision(<rSPDEobj1d>)
Get the precision matrix of rSPDEobj1d objects
precision(<spacetimeobj>)
Get the precision matrix of spacetimeobj objects
predict(<spacetimeobj>)
Prediction of a space-time SPDE
simulate(<spacetimeobj>)
Simulation of space-time models
update(<spacetimeobj>)
Update parameters of spacetimeobj objects
summary(<spacetimeobj>) print(<summary.spacetimeobj>) print(<spacetimeobj>)
Summarise spacetime objects

Functions and methods for R-INLA rSPDE objects

rspde.make.A()
Observation/prediction matrices for rSPDE models.
spde.make.A()
Observation/prediction matrices for rSPDE models with integer smoothness.
rspde.make.index()
rSPDE model index vector generation
graph_data_rspde()
Data extraction from metric graphs for 'rSPDE' models
rspde.mesh.project() rspde.mesh.projector()
Calculate a lattice projection to/from an inla.mesh for rSPDE objects
rspde.result()
rSPDE result extraction from INLA estimation results
summary(<rspde_result>)
Summary for posteriors of field parameters for an inla_rspde model from a rspde_result object
precision(<inla_rspde>)
Get the precision matrix of inla_rspde objects
gg_df()
Data frame for result objects from R-INLA fitted models to be used in ggplot2
gg_df(<rspde_result>)
Data frame for rspde_result objects to be used in ggplot2

Functions and methods for rSPDE interface for inlabru

cross_validation()
Perform cross-validation on a list of fitted models.
group_predict()
Perform prediction on a testing set based on a training set
predict(<inla_rspde_matern1d>)
Predict method for 'inlabru' stationary Matern 1d models
bru_get_mapper.inla_rspde() ibm_n.bru_mapper_inla_rspde() ibm_values.bru_mapper_inla_rspde() ibm_jacobian.bru_mapper_inla_rspde()
rSPDE inlabru mapper
bru_get_mapper.inla_rspde_spacetime()
rSPDE space time inlabru mapper
bru_get_mapper.inla_rspde_anisotropic2d()
rSPDE anisotropic inlabru mapper
bru_get_mapper.inla_rspde_matern1d() ibm_n.bru_mapper_inla_rspde_matern1d() ibm_values.bru_mapper_inla_rspde_matern1d() ibm_jacobian.bru_mapper_inla_rspde_matern1d()
rSPDE stationary inlabru mapper
rSPDE.A1d()
Observation matrix for finite element discretization on R
rSPDE.fem1d()
Finite element calculations for problems on R
rSPDE.fem2d()
Finite element calculations for problems in 2D
rSPDE.Ast()
Observation matrix for space-time models

Auxiliary functions

create_train_test_indices()
Create train and test splits to be used in the cross_validation function
get.initial.values.rSPDE()
Initial values for log-likelihood optimization in rSPDE models with a latent stationary Gaussian Matern model
require.nowarnings()
Warnings free loading of add-on packages
matern.covariance()
The Matern covariance function
matern.rational.cov()
Rational approximation of the Matern covariance
folded.matern.covariance.1d()
The 1d folded Matern covariance function
folded.matern.covariance.2d()
The 2d folded Matern covariance function
rspde.matern.precision.opt()
Optimized precision matrix of the covariance-based rational approximation
rspde.matern.precision.integer.opt()
Optimized precision matrix of stationary Gaussian Matern random fields with integer covariance exponent
`rational.order<-`()
Changing the order of the rational approximation
`rational.type<-`()
Changing the type of the rational approximation
rational.order()
Get the order of rational approximation.
rational.type()
Get type of rational approximation.
transform_parameters_anisotropic()
Transform Anisotropic SPDE Model Parameters to Original Scale
transform_parameters_spacetime()
Transform Spacetime SPDE Model Parameters to Original Scale

Operator operations