Bayesian Spike and Slab Hierarchical Models

Documentation for package ‘BayesSpike’ version 0.500

DESCRIPTION file.

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A B C D E F G H I K L M N O P Q R S T W Y misc

-- A --

AFDBayesSpike	BayesSpikeFromAutoDiallel, converting BayesDiallel, "FullDiallelAnalyze" object to use of BayesSpike algorithm
AllTauPriors	MT the loaded properties of Onii loaded in group of Tauii parameters.
AutomaticQuantiles	Marginal Posterior Quantiles of Draws
automaticQuantiles	Marginal Posterior Quantiles of Draws
automaticquantiles	Marginal Posterior Quantiles of Draws

-- B --

BayeSpikeCL	BayesSpikeCpp 'Rcpp' Module Class
BayesSpike	BayesSpike package
BayesSpikeCL	BayesSpikeCpp 'Rcpp' Module Class
bayesspikecl	BayesSpikeCpp 'Rcpp' Module Class
BayesSpikeCpp	BayesSpikeCpp 'Rcpp' Module Class
BayesspikeCpp	BayesSpikeCpp 'Rcpp' Module Class
bayesspikecpp	BayesSpikeCpp 'Rcpp' Module Class
BayesSpikeFromAutoDiallel	BayesSpikeFromAutoDiallel, converting BayesDiallel, "FullDiallelAnalyze" object to use of BayesSpike algorithm
BayesSpikeR5	BayesSpikeR5 'ReferenceClasses' Reference Class
BayesspikeR5	BayesSpikeR5 'ReferenceClasses' Reference Class
bayesspiker5	BayesSpikeR5 'ReferenceClasses' Reference Class
BayesSpikeRegression	BayesSpikeRegression algorithm
BetaHPDLongQuantiles	Marginal Posterior Quantiles of Draws
BetaHPDQuantiles	Marginal Posterior Quantiles of Draws
BetaHpdQuantiles	Marginal Posterior Quantiles of Draws
Betahpdquantiles	Marginal Posterior Quantiles of Draws
betaHPDQuantiles	Marginal Posterior Quantiles of Draws
betaHpdQuantiles	Marginal Posterior Quantiles of Draws
BetaHPDUnshrinkQuantiles	Marginal Posterior Quantiles of Draws
BetaHPDUnshrunkQuantiles	Marginal Posterior Quantiles of Draws
BetaQuantiles	Marginal Posterior Quantiles of Draws
betaQuantiles	Marginal Posterior Quantiles of Draws
BetaSymmetricConfidenceMatrix	Marginal Posterior Quantiles of Draws
BetaSymmetricLongConfidenceMatrix	Marginal Posterior Quantiles of Draws
BetaSymmetricLongQuantiles	Marginal Posterior Quantiles of Draws
BetaSymmetricQuantiles	Marginal Posterior Quantiles of Draws
BetasymmetricQuantiles	Marginal Posterior Quantiles of Draws
betaSymmetricQuantiles	Marginal Posterior Quantiles of Draws
BetaSymmetricUnshrinkQuantiles	Marginal Posterior Quantiles of Draws
betaSymmetricUnshrinkQuantiles	Marginal Posterior Quantiles of Draws
BetaSymmetricUnshrunkQuantiles	Marginal Posterior Quantiles of Draws
betaSymmetricUnshrunkQuantiles	Marginal Posterior Quantiles of Draws
BSCPP	BayesSpikeCpp 'Rcpp' Module Class
BSCpp	BayesSpikeCpp 'Rcpp' Module Class
bscpp	BayesSpikeCpp 'Rcpp' Module Class

-- C --

CimplteteTime	Time Recordings for algorithm timing
Coda	Coda MCMC chains.
coda	Coda MCMC chains.
CodaList	Coda MCMC chains.
codaList	Coda MCMC chains.
codalist	Coda MCMC chains.
CodaTable	Coda MCMC chains.
codaTable	Coda MCMC chains.
CompleteTime	Time Recordings for algorithm timing
ConfidenceQuantiles	Marginal Posterior Quantiles of Draws
confidencequantiles	Marginal Posterior Quantiles of Draws
CurrentPostProbCodaBuffer	BayesSpikeCpp 'Rcpp' Module Class
CurrentTauPriors	MT the loaded properties of Onii loaded in group of Tauii parameters.

-- D --

DefaultFileDir	Hard Drive storage space
defaultfiledir	Hard Drive storage space
dfTNoise	Noise distribution
DoEEProbSort	Equi-Energy Sampling for Bayes Spike
DoLogitNonePostPreProb	Marginal Posterior Quantiles of Draws
DoLogitPostProb	Marginal Posterior Quantiles of Draws
DoLogitPreProb	Marginal Posterior Quantiles of Draws
DoRecord	Coda MCMC chains.
Dorecord	Coda MCMC chains.
doRecord	Coda MCMC chains.
dorecord	Coda MCMC chains.

-- E --

EE-Sampling	Equi-Energy Sampling for Bayes Spike
EEMergeEvery	Equi-Energy Sampling for Bayes Spike
EEProbSortWidth	Equi-Energy Sampling for Bayes Spike
EEsampling	Equi-Energy Sampling for Bayes Spike
Eesampling	Equi-Energy Sampling for Bayes Spike
eesampling	Equi-Energy Sampling for Bayes Spike

-- F --

FileDir	Hard Drive storage space
filedir	Hard Drive storage space
FileName	Hard Drive storage space
fileName	Hard Drive storage space
filename	Hard Drive storage space
FullDiallel	Create HappyR Object

-- G --

GenerateProbCodaList

BayesSpikeCpp 'Rcpp' Module Class

-- H --

HPDQuantiles

Marginal Posterior Quantiles of Draws

-- I --

InitiateTime	Time Recordings for algorithm timing
initiatetime	Time Recordings for algorithm timing

-- K --

KeepPosteriorQuantiles	Marginal Posterior Quantiles of Draws
KeepposteriorQuantiles	Marginal Posterior Quantiles of Draws
Keepposteriorquantiles	Marginal Posterior Quantiles of Draws
keepPosteriorQuantiles	Marginal Posterior Quantiles of Draws
keepposteriorquantiles	Marginal Posterior Quantiles of Draws
KeepPostQuantiles	Marginal Posterior Quantiles of Draws
keepPostQuantiles	Marginal Posterior Quantiles of Draws
KeepQuantiles	Marginal Posterior Quantiles of Draws
keepquantiles	Marginal Posterior Quantiles of Draws

-- L --

LengthPostProb	BayesSpikeCpp 'Rcpp' Module Class
LengthPostProbCodaBuffer	BayesSpikeCpp 'Rcpp' Module Class
logit	Logit Regression algorithm
LogitRegression	Logit Regression algorithm
logitRegression	Logit Regression algorithm
LongList	Subset, disk-loaded Coda MCMC chains.
longlist	Subset, disk-loaded Coda MCMC chains.

-- M --

Mt	MT the loaded properties of Onii loaded in group of Tauii parameters.
Mt	MT the loaded properties of Onii loaded in group of Tauii parameters.
mt	MT the loaded properties of Onii loaded in group of Tauii parameters.
mt	MT the loaded properties of Onii loaded in group of Tauii parameters.
MTOnii	MT the loaded properties of Onii loaded in group of Tauii parameters.
MTOnii	MT the loaded properties of Onii loaded in group of Tauii parameters.

-- N --

NewPostProbWrite	BayesSpikeCpp 'Rcpp' Module Class
NewWrite	Hard Drive storage space
newwrite	Hard Drive storage space

-- O --

oniiMT	MT the loaded properties of Onii loaded in group of Tauii parameters.
oniiMT	MT the loaded properties of Onii loaded in group of Tauii parameters.
onpia	Prior for activation
OnPiD	Prior for activation

-- P --

PiA	Prior for activation
PiACodaList	Subset, disk-loaded Coda MCMC chains.
PiAHPDQuantiles	Marginal Posterior Quantiles of Draws
PiAHpdQuantiles	Marginal Posterior Quantiles of Draws
PiAhpdquantiles	Marginal Posterior Quantiles of Draws
piAHpdQuantiles	Marginal Posterior Quantiles of Draws
piaHPDQuantiles	Marginal Posterior Quantiles of Draws
PiAPrior	Prior for activation
PiAQuantiles	Marginal Posterior Quantiles of Draws
piAQuantiles	Marginal Posterior Quantiles of Draws
PiASymmetricQuantiles	Marginal Posterior Quantiles of Draws
piASymmetricQuantiles	Marginal Posterior Quantiles of Draws
piasymmetricQuantiles	Marginal Posterior Quantiles of Draws
PiD	Prior for activation
PiPrior	Prior for activation
piprior	Prior for activation
PostBufferFile	BayesSpikeCpp 'Rcpp' Module Class
PosteriorCodaList	Subset, disk-loaded Coda MCMC chains.
PosteriorProbabilityCodaList	Subset, disk-loaded Coda MCMC chains.
PostProbBuffer	BayesSpikeCpp 'Rcpp' Module Class
PostProbCoda	BayesSpikeCpp 'Rcpp' Module Class
PostProbCodaBuffer	BayesSpikeCpp 'Rcpp' Module Class
PostProbCodaList	BayesSpikeCpp 'Rcpp' Module Class
PostProbCodaList	Subset, disk-loaded Coda MCMC chains.
ProbCodaList	BayesSpikeCpp 'Rcpp' Module Class
ProbCodaList	Subset, disk-loaded Coda MCMC chains.
probit	Logit Regression algorithm
ProbitRegression	Logit Regression algorithm
probitRegression	Logit Regression algorithm

-- Q --

Quantiles	Marginal Posterior Quantiles of Draws
quantiles	Marginal Posterior Quantiles of Draws
QuantilesBeta	Marginal Posterior Quantiles of Draws
QuantilesPiA	Marginal Posterior Quantiles of Draws
QuantilesSigma	Marginal Posterior Quantiles of Draws
QuantilesTau	Marginal Posterior Quantiles of Draws

-- R --

RandomTruncNorm	Random Truncated Distribution Draws
RandomTruncT	Random Truncated Distribution Draws
ReLoad	BayesSpike package
Reload	BayesSpike package
reload	BayesSpike package
ReturnSubCodaFromFiles	Load in Coda from compressed files
ReturnSubCodaFromfiles	Load in Coda from compressed files
ReturnSubCodafromfiles	Load in Coda from compressed files
ReturnSubcodafromfiles	Load in Coda from compressed files
Robit	Logit Regression algorithm
robit	Logit Regression algorithm
RobitRegression	Logit Regression algorithm
robitRegression	Logit Regression algorithm
rTruncNorm	Random Truncated Distribution Draws
rtruncnorm	Random Truncated Distribution Draws
rTruncT	Random Truncated Distribution Draws
rtrunct	Random Truncated Distribution Draws
RTT	Random Truncated Distribution Draws
rTT	Random Truncated Distribution Draws

-- S --

Save	BayesSpike package
save	BayesSpike package
SaveDir	Hard Drive storage space
savedir	Hard Drive storage space
SecondInitiateTime	Time Recordings for algorithm timing
secondinitiatetime	Time Recordings for algorithm timing
secondinitieatetime	Time Recordings for algorithm timing
SetupSaveDir	Hard Drive storage space
SetupSaveFile	Hard Drive storage space
SigCodaList	Subset, disk-loaded Coda MCMC chains.
SigHPDQuantiles	Marginal Posterior Quantiles of Draws
SighpdQuantiles	Marginal Posterior Quantiles of Draws
Sigma	Noise distribution
sigma	Noise distribution
SigmaCodaList	Subset, disk-loaded Coda MCMC chains.
SigmaHPDQuantiles	Marginal Posterior Quantiles of Draws
SigmaHpdQuantiles	Marginal Posterior Quantiles of Draws
Sigmahpdquantiles	Marginal Posterior Quantiles of Draws
sigmaHPDQuantiles	Marginal Posterior Quantiles of Draws
SigmaPrior	Noise distribution
sigmaPrior	Noise distribution
sigmaprior	Noise distribution
sigmaQuantiles	Marginal Posterior Quantiles of Draws
SigmaSymmetricQuantiles	Marginal Posterior Quantiles of Draws
SigmasymmetricQuantiles	Marginal Posterior Quantiles of Draws
sigmaSymmetricQuantiles	Marginal Posterior Quantiles of Draws
SigSymmetricQuantiles	Marginal Posterior Quantiles of Draws
sigSymmetricQuantiles	Marginal Posterior Quantiles of Draws
SSave	BayesSpike package
Ssave	BayesSpike package
ssave	BayesSpike package
SubcodaList	Subset, disk-loaded Coda MCMC chains.
SubCodaLongList	Subset, disk-loaded Coda MCMC chains.
subcodalonglist	Subset, disk-loaded Coda MCMC chains.
SubSetCoords	Subset, disk-loaded Coda MCMC chains.
SubsetCoords	Subset, disk-loaded Coda MCMC chains.
SubSetTau	Subset, disk-loaded Coda MCMC chains.
subsettau	Subset, disk-loaded Coda MCMC chains.
SymmetricQuantiles	Marginal Posterior Quantiles of Draws

-- T --

TauCodaList	Subset, disk-loaded Coda MCMC chains.
tauFixed	Prior for "fixed", individual Beta coefficients
taufixed	Prior for "fixed", individual Beta coefficients
TauHPDQuantiles	Marginal Posterior Quantiles of Draws
TauHpdQuantiles	Marginal Posterior Quantiles of Draws
Tauhpdquantiles	Marginal Posterior Quantiles of Draws
tauHPDQuantiles	Marginal Posterior Quantiles of Draws
tauHpdQuantiles	Marginal Posterior Quantiles of Draws
TauOniiPrior	MT the loaded properties of Onii loaded in group of Tauii parameters.
TauOniiPrior	MT the loaded properties of Onii loaded in group of Tauii parameters.
TauQuantiles	Marginal Posterior Quantiles of Draws
tauQuantiles	Marginal Posterior Quantiles of Draws
TauSymmetricQuantiles	Marginal Posterior Quantiles of Draws
TausymmetricQuantiles	Marginal Posterior Quantiles of Draws
tauSymmetricQuantiles	Marginal Posterior Quantiles of Draws
TBSR5	BayesSpikeR5 'ReferenceClasses' Reference Class
TBSr5	BayesSpikeR5 'ReferenceClasses' Reference Class
tbsr5	BayesSpikeR5 'ReferenceClasses' Reference Class
TemperatureList	Equi-Energy Sampling for Bayes Spike
TypeFixedPrior	Prior for "fixed", individual Beta coefficients
typefixedprior	Prior for "fixed", individual Beta coefficients

-- W --

WeightCodaList

Subset, disk-loaded Coda MCMC chains.

-- Y --

YCodaList

Subset, disk-loaded Coda MCMC chains.

-- misc --

.DefaultFileDir	Hard Drive storage space
.SigmaCodaList	Subset, disk-loaded Coda MCMC chains.
.SubSetCoords	Subset, disk-loaded Coda MCMC chains.
.SubSetTau	Subset, disk-loaded Coda MCMC chains.
.SubsetTau	Subset, disk-loaded Coda MCMC chains.
.TauCodaList	Subset, disk-loaded Coda MCMC chains.