Package: BayesNSGP 0.1.2

BayesNSGP: Bayesian Analysis of Non-Stationary Gaussian Process Models

Enables off-the-shelf functionality for fully Bayesian, nonstationary Gaussian process modeling. The approach to nonstationary modeling involves a closed-form, convolution-based covariance function with spatially-varying parameters; these parameter processes can be specified either deterministically (using covariates or basis functions) or stochastically (using approximate Gaussian processes). Stationary Gaussian processes are a special case of our methodology, and we furthermore implement approximate Gaussian process inference to account for very large spatial data sets (Finley, et al (2017) <arxiv:1702.00434v2>). Bayesian inference is carried out using Markov chain Monte Carlo methods via the 'nimble' package, and posterior prediction for the Gaussian process at unobserved locations is provided as a post-processing step.

Authors:Daniel Turek, Mark Risser

BayesNSGP_0.1.2.tar.gz
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BayesNSGP.pdf |BayesNSGP.html
BayesNSGP/json (API)

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

Peer review:

On CRAN:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

1.00 score 1 stars 5 scripts 227 downloads 29 exports 48 dependencies

Last updated 3 years agofrom:2fe1901919. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 17 2024
R-4.5-winOKNov 17 2024
R-4.5-linuxOKNov 17 2024
R-4.4-winOKNov 17 2024
R-4.4-macOKNov 17 2024
R-4.3-winOKNov 17 2024
R-4.3-macOKNov 17 2024

Exports:calcQFcalculateAD_nscalculateU_nsconditionLatentObsdetermineNeighborsdmnorm_nngpdmnorm_sgvinverseEigenmatern_corrnimble_sparse_cholnimble_sparse_crossprodnimble_sparse_solvenimble_sparse_tcrossprodnsCorrnsCrosscorrnsCrossdistnsCrossdist3dnsDistnsDist3dnsgpModelnsgpPredictorderCoordinatesMMDR_sparse_cholR_sparse_crossprodR_sparse_solveR_sparse_tcrossprodrmnorm_nngprmnorm_sgvsgvSetup

Dependencies:clicodacolorspacecpp11DBIdplyrfansifarverFNNgenericsggplot2gluegtableigraphisobandlabelinglatticelifecyclelpSolvemagrittrMASSMatrixmgcvminqamitoolsmunsellnimblenlmenumDerivpillarpkgconfigpracmaproxyR6RColorBrewerRcppRcppArmadillorlangscalesStatMatchsurveysurvivaltibbletidyselectutf8vctrsviridisLitewithr

Readme and manuals

Help Manual

Help pageTopics
Calculate the Gaussian quadratic form for the NNGP approximationcalcQF
Calculate A and D matrices for the NNGP approximationcalculateAD_ns
Calculate the (sparse) matrix UcalculateU_ns
Assign conditioning sets for the SGV approximationconditionLatentObs
Determine the k-nearest neighbors for each spatial coordinate.determineNeighbors
Function for the evaluating the NNGP approximate density.dmnorm_nngp
Function for the evaluating the SGV approximate density.dmnorm_sgv
Calculate covariance elements based on eigendecomposition componentsinverseEigen
Calculate a stationary Matern correlation matrixmatern_corr
nimble_sparse_cholnimble_sparse_chol
nimble_sparse_crossprodnimble_sparse_crossprod
nimble_sparse_solvenimble_sparse_solve
nimble_sparse_tcrossprodnimble_sparse_tcrossprod
Calculate a nonstationary Matern correlation matrixnsCorr
Calculate a nonstationary Matern cross-correlation matrixnsCrosscorr
Calculate coordinate-specific cross-distance matricesnsCrossdist
Calculate coordinate-specific cross-distance matrices, only for nearest neighbors and store in an arraynsCrossdist3d
Calculate coordinate-specific distance matricesnsDist
Calculate coordinate-specific distance matrices, only for nearest neighbors and store in an arraynsDist3d
NIMBLE code for a generic nonstationary GP modelnsgpModel
Posterior prediction for the NSGPnsgpPredict
Order coordinates according to a maximum-minimum distance criterion.orderCoordinatesMMD
R_sparse_cholR_sparse_chol
nimble_sparse_crossprodR_sparse_crossprod
nimble_sparse_solveR_sparse_solve
nimble_sparse_tcrossprodR_sparse_tcrossprod
Function for the evaluating the NNGP approximate density.rmnorm_nngp
Function for the evaluating the SGV approximate density.rmnorm_sgv
One-time setup wrapper function for the SGV approximationsgvSetup