bigGP: Distributed Gaussian Process Calculations
Version 0.1-6

Distributes Gaussian process calculations across nodes in a distributed memory setting, using Rmpi. The bigGP class provides high-level methods for maximum likelihood with normal data, prediction, calculation of uncertainty (i.e., posterior covariance calculations), and simulation of realizations. In addition, bigGP provides an API for basic matrix calculations with distributed covariance matrices, including Cholesky decomposition, back/forwardsolve, crossproduct, and matrix multiplication.

Browse man pages Browse package API and functions Browse package files

AuthorChristopher Paciorek [aut, cre], Benjamin Lipshitz [aut], Prabhat [ctb], Cari Kaufman [ctb], Tina Zhuo [ctb], Rollin Thomas [ctb]
Date of publication2015-07-08 13:49:56
MaintainerChristopher Paciorek <paciorek@stat.berkeley.edu>
LicenseGPL (>= 2)
Version0.1-6
URL http://www.jstatsoft.org/v63/i10/
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("bigGP")

Man pages

alloc: Create Object with its Own Memory
bigGP: Package for Calculations with Big Gaussian Processes
bigGP.exit: Exit bigGP Environment
bigGP.init: Initialize bigGP package
bigGP-meta: Information about the number and identities of the processes
calcD: Calculate Partition Factor
calcIJ: Calculate Slave Process Identifiers
collectDiagonal: Return the Diagonal of a Distributed Square Matrix to the...
collectRectangularMatrix: Return a Distributed Rectangular Matrix to the Master Process
collectTriangularMatrix: Return a Distributed Symmetric or Triangular Matrix to the...
collectVector: Return a Distributed Vector to the Master Process
distributedKrigeProblem-class: ReferenceClass for Distributed Components of the krigeProblem...
distributeVector: Distribute a Vector to the Slave Processes
getDistributedVectorLength: Find Length of Subset of Vector or Matrix Stored on Slave...
krigeProblem-class: Class '"krigeProblem"'
localAssign: Assign a New Name to an Object on Slave Process
localCalc: Local Calculation Functions
localCollectVector: Local Distribution and Collection Functions
localGetVectorIndices: Get Indices of Vector or Matrix Elements Stored on Slave...
localKrigeProblemConstructMean: Calculate Mean Vector or Covariance Matrix on Slave Process
localRm: Remove Objects on Slave Process
pull: Copy Object from Slave Processes to Master
push: Copy Object from Master to Slave Processes
remoteCalc: Return a Distributed Vector to the Master Process
remoteCalcChol: Calculate Distributed Cholesky Decomposition
remoteConstructRnormVector: Create Distributed Vector or Matrix of Random Normals
remoteCrossProdMatSelf: Distributed Crossproduct of a Rectangular Matrix with Itself
remoteCrossProdMatVec: Distributed Crossproduct of a Rectangular Matrix and a Vector
remoteForwardsolve: Solve a Distributed Triangular System
remoteGetIndices: Determine Indices of Vector or Matrix Elements Stored on all...
remoteLs: Remote List Objects
remoteMultChol: Distributed Multiplication of Lower Triangular Matrix and a...
remoteRm: Remote Remove Objects
SN2011fe: SN2011fe Supernova Dataset

Functions

.bigGP Man page
.bigGP.fill Man page
SN2011fe Man page
SN2011fe_covfunc Man page
SN2011fe_crosscovfunc Man page
SN2011fe_initialParams Man page
SN2011fe_meanfunc Man page
SN2011fe_mle Man page
SN2011fe_mle_subset Man page
SN2011fe_newdata Man page
SN2011fe_newdata_subset Man page
SN2011fe_predcovfunc Man page
SN2011fe_predmeanfunc Man page
SN2011fe_subset Man page
alloc Man page Source code
bigGP Man page
bigGP-meta Man page
bigGP-package Man page
bigGP.exit Man page Source code
bigGP.fill Source code
bigGP.init Man page Source code
bigGP.quit Man page Source code
calcD Man page Source code
calcH, krigeProblem-method Man page
calcIJ Man page Source code
calcLogDens, krigeProblem-method Man page
calcPostCov, krigeProblem-method Man page
collectDiagonal Man page Source code
collectRectangularMatrix Man page Source code
collectTriangularMatrix Man page Source code
collectVector Man page Source code
distributeVector Man page Source code
distributedKrigeProblem Man page
distributedKrigeProblem-class Man page
getDistributedRectangularMatrixLength Man page Source code
getDistributedTriangularMatrixLength Man page Source code
getDistributedVectorLength Man page Source code
initializeSlaveProblems, krigeProblem-method Man page
krigeProblem Man page
krigeProblem-class Man page
localAssign Man page Source code
localBacksolve Man page Source code
localCalc Man page Source code
localCalcChol Man page Source code
localCollectDiagonal Man page Source code
localCollectDiagonalTest Man page Source code
localCollectRectangularMatrix Man page Source code
localCollectRectangularMatrixTest Man page Source code
localCollectTriangularMatrix Man page Source code
localCollectTriangularMatrixTest Man page Source code
localCollectVector Man page Source code
localCollectVectorTest Man page Source code
localConstructRnormMatrix Man page Source code
localCrossProdMatSelf Man page Source code
localCrossProdMatSelfDiag Man page Source code
localCrossProdMatVec Man page Source code
localDistributeVector Man page Source code
localDistributeVectorTest Man page Source code
localForwardsolve Man page Source code
localGetRectangularMatrixIndices Man page Source code
localGetTriangularMatrixIndices Man page Source code
localGetVectorIndices Man page Source code
localKrigeProblemConstructCov Man page Source code
localKrigeProblemConstructMean Man page Source code
localMultChol Man page Source code
localPull Man page Source code
localPullTest Man page Source code
localRm Man page Source code
optimizeLogDens, krigeProblem-method Man page
predict, krigeProblem-method Man page
pull Man page Source code
push Man page Source code
remoteBacksolve Man page Source code
remoteCalc Man page Source code
remoteCalcChol Man page Source code
remoteConstructCov, krigeProblem-method Man page
remoteConstructMean, krigeProblem-method Man page
remoteConstructRnormMatrix Man page Source code
remoteConstructRnormVector Man page Source code
remoteCrossProdMatSelf Man page Source code
remoteCrossProdMatSelfDiag Man page Source code
remoteCrossProdMatVec Man page Source code
remoteForwardsolve Man page Source code
remoteGetIndices Man page Source code
remoteLs Man page Source code
remoteMultChol Man page Source code
remoteRm Man page Source code
setParams, krigeProblem-method Man page
show, krigeProblem-method Man page
simulateRealizations, krigeProblem-method Man page

Files

TODO
inst
inst/CITATION
configure.ac
src
src/collect.h
src/comm.h
src/lib.h
src/trmv.c
src/fulltrs.c
src/fulltrs.h
src/gemmrp.h
src/gemmrect.h
src/tssyrk.h
src/gemv.c
src/fulltrsl.h
src/trmmr.h
src/tstrsm.c
src/tssyrk.c
src/tstrsm.h
src/trsmr.h
src/gemvl.h
src/gemmr.c
src/zeropad.c
src/trmv.h
src/trsmr.c
src/gemmrp.c
src/syrk.h
src/lib.c
src/fullsyrkr.c
src/transform.c
src/trs.c
src/fulltrsmr.h
src/gemmrt.c
src/syrk.c
src/gemmrt.h
src/gemvr.c
src/gemm.c
src/zeropad.h
src/chol.h
src/fullgemvr.h
src/local.c
src/wrappers.c
src/fulltrsl.c
src/fulltrmmr.c
src/trsm.c
src/fulltrmmr.h
src/syrkr.c
src/collect.c
src/trsl.h
src/Makevars.in
src/syrkr.h
src/gemvr.h
src/fullsyrkr_diag.h
src/gemmr.h
src/local.h
src/comm.c
src/cholesky.h
src/gemv.h
src/trmmr.c
src/chol.c
src/fullgemmrect.h
src/fulltrsmr.c
src/transform.h
src/fullsyrkr.h
src/fullgemmrect.c
src/trsm.h
src/gemm.h
src/fullgemvr.c
src/gemmrect.c
src/gemvl.c
src/trs.h
src/trsl.c
src/fulltrmv.c
src/fulltrmv.h
src/cholesky.c
src/fullsyrkr_diag.c
NAMESPACE
demo
demo/00Index
demo/article-example.R
INSTALL
NEWS
data
data/SN2011fe.rda
data/datalist
R
R/collectDistribute.R
R/krigeProblem.R
R/distributedComputation.R
R/bigGP.R
R/auxil.R
README.md
MD5
README
DESCRIPTION
configure
man
man/calcIJ.Rd
man/localRm.Rd
man/remoteCalc.Rd
man/remoteCrossProdMatVec.Rd
man/localCalc.Rd
man/getDistributedVectorLength.Rd
man/remoteConstructRnormVector.Rd
man/bigGP.init.Rd
man/remoteGetIndices.Rd
man/SN2011fe.Rd
man/bigGP.exit.Rd
man/collectTriangularMatrix.Rd
man/remoteMultChol.Rd
man/remoteRm.Rd
man/distributedKrigeProblem-class.Rd
man/alloc.Rd
man/bigGP-meta.Rd
man/localAssign.Rd
man/collectDiagonal.Rd
man/remoteCalcChol.Rd
man/calcD.Rd
man/remoteForwardsolve.Rd
man/collectRectangularMatrix.Rd
man/bigGP.Rd
man/remoteCrossProdMatSelf.Rd
man/distributeVector.Rd
man/pull.Rd
man/localCollectVector.Rd
man/localGetVectorIndices.Rd
man/collectVector.Rd
man/krigeProblem-class.Rd
man/remoteLs.Rd
man/push.Rd
man/localKrigeProblemConstructMean.Rd
cleanup
tools
tools/ax_lapack.m4
tools/ax_blas.m4
tools/configure.alt
tools/configure.alt.ac
bigGP documentation built on May 19, 2017, 10:36 p.m.