sourceR: Fits a Non-Parametric Bayesian Source Attribution Model
Version 1.0.1

Implements a non-parametric source attribution model to attribute cases of disease to sources in Bayesian framework with source and type effects. Type effects are clustered using a Dirichlet Process. Multiple times and locations are supported.

Browse man pages Browse package API and functions Browse package files

AuthorPoppy Miller [aut, cre, cph], Chris Jewell [aut], Jonathan Marshall [ctb], Nigel French [ctb]
Date of publication2017-05-09 07:15:38 UTC
MaintainerPoppy Miller <p.miller@lancaster.ac.uk>
LicenseGPL-3
Version1.0.1
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("sourceR")

Man pages

AdaptiveDirMRW: AdaptiveDirMRW
AdaptiveLogDirMRW: AdaptiveLogDirMRW
AdaptiveMultiMRW: AdaptiveMultiMRW
Alpha: Constructs alpha prior
Alpha_: Alpha prior hyperparameter class
campy: Human cases of campylobacteriosis and numbers of source...
DataNode: DataNode
DirichletNode: DirichletNode
DirichletProcessNode: DirichletProcessNode
DPModel_impl: Builds the source attribution model. Is not intended to be...
FormulaNode: FormulaNode
GammaNode: GammaNode
HaldDP: Builds a HaldDP source attribution model
Node: Node
PoisGammaDPUpdate: PoisGammaDPUpdate
PoissonNode: PoissonNode
Prev: Constructs prevalence data
Q: Constructs initial values for q
sim_SA: Simulated data: Human cases of campylobacteriosis and numbers...
sliceTensor: Slices a tensorA::tensor
sourceR: sourceR: A package for fitting Bayesian non-parametric source...
StochasticNode: StochasticNode
X: Constructs source data
Y: Constructs disease count data

Functions

AdaptiveDirMRW Man page
AdaptiveLogDirMRW Man page
AdaptiveMultiMRW Man page
Alpha Man page Source code
Alpha_ Man page
DPModel_impl Man page
DataNode Man page
DirichletNode Man page
DirichletProcessNode Man page
FormulaNode Man page
GammaNode Man page
HaldDP Man page Source code
Node Man page
PoisGammaDPUpdate Man page
PoissonNode Man page
Prev Man page Source code
Q Man page Source code
StochasticNode Man page
X Man page Source code
Y Man page Source code
are_colours Source code
arrayextend Source code
campy Man page
check_alphavalue_CI Source code
ci_SPIn Source code
ci_chenShao Source code
ci_percentiles Source code
clusterHeatMap Source code
dequeue Source code
dequeue.queue Source code
enqueue Source code
enqueue.queue Source code
getOnlineCov Source code
getStats Source code
isFiniteInteger Source code
isFiniteLogical Source code
isFinitePositive Source code
isFinitePositiveInteger Source code
isProb Source code
makeOnlineCov Source code
print.queue Source code
queue Source code
resetStats Source code
sim_SA Man page
sliceTensor Man page Source code
sourceR Man page
sourceR-package Man page
summary.queue Source code
updateOnlineCov Source code

Files

inst
inst/doc
inst/doc/sourceR.ltx
inst/doc/sourceR.pdf
tests
tests/testthat.R
tests/testthat
tests/testthat/testHaldDP.R
tests/testthat/testCI.R
tests/testthat/testQ.R
tests/testthat/haldDPres1.rds
tests/testthat/haldDPres3.rds
tests/testthat/haldDPres2.rds
tests/testthat/testHaldDPTimeLoc.R
tests/testthat/haldDPFlat.rds
tests/testthat/testDP.R
tests/testthat/dataX.rds
tests/testthat/testMHUpdaters.R
tests/testthat/haldDPdataStrct.rds
tests/testthat/haldDPpriorInit.rds
tests/testthat/testData.R
tests/testthat/testDirichletNode.R
tests/testthat/haldDPlambdaj.rds
tests/testthat/haldDPres4.rds
NAMESPACE
data
data/campy.rda
data/sim_SA.rda
R
R/utils.R
R/campy.R
R/onlineCov.R
R/queue.R
R/model.R
R/sourceR.R
R/credibleIntervals.R
R/data.R
R/node.R
R/posterior.R
R/sim_SA.R
R/interface.R
R/heatmap.R
R/mcmc.R
R/acceptance.R
vignettes
vignettes/Fig3.pdf
vignettes/sourceR.ltx
vignettes/Fig4.pdf
vignettes/Fig1.pdf
vignettes/Fig2.pdf
MD5
build
build/vignette.rds
DESCRIPTION
man
man/AdaptiveDirMRW.Rd
man/sourceR.Rd
man/campy.Rd
man/StochasticNode.Rd
man/PoisGammaDPUpdate.Rd
man/sliceTensor.Rd
man/Q.Rd
man/PoissonNode.Rd
man/DPModel_impl.Rd
man/Alpha.Rd
man/DirichletNode.Rd
man/HaldDP.Rd
man/FormulaNode.Rd
man/Alpha_.Rd
man/AdaptiveLogDirMRW.Rd
man/GammaNode.Rd
man/DataNode.Rd
man/Prev.Rd
man/DirichletProcessNode.Rd
man/X.Rd
man/Y.Rd
man/AdaptiveMultiMRW.Rd
man/sim_SA.Rd
man/Node.Rd
sourceR documentation built on May 20, 2017, 4:43 a.m.