# Example for Jags-Ymet-Xnom2grp-MrobustHet.R
#-------------------------------------------------------------------------------
# Optional generic preliminaries:
#graphics.off() # This closes all of R's graphics windows.
#rm(list=ls()) # Careful! This clears all of R's memory!
JagsYmetXnom2grpMrobustHet <- function()
{
out <- list()
oldClass(out) <- "JagsYmetXnom2grpMrobustHet"
return(out)
}
mod <- JagsYmetXnom2grpMrobustHet()
#-------------------------------------------------------------------------------
# Load The data file
myDataFrame = read.csv(system.file("data", "ShohatOphirKAMH2012dataReduced.csv", package = "dbda"))
#yName="Score"
#xName="Group"
#fileNameRoot = "TwoGroupIQrobustHet-"
fileNameRoot = NULL
#RopeMuDiff=c(-0.5,0.5) ; RopeSdDiff=c(-0.5,0.5) ; RopeEff=c(-0.1,0.1)
# myDataFrame = read.csv( file="ShohatOphirKAMH2012dataReduced.csv" )
xName="Group"
yName="PreferenceIndex"
#fileNameRoot="ShohatOphirKAMH2012data-PI-"
RopeMuDiff=c(-0.1,0.1) ; RopeSdDiff=c(-0.1,0.1) ; RopeEff=c(-0.1,0.1)
# myDataFrame = read.csv( file="ShohatOphirKAMH2012dataReduced.csv" )
# xName="Group"
# yName="GrandTotal"
# fileNameRoot="ShohatOphirKAMH2012data-GT-"
# RopeMuDiff=c(-0.1,0.1) ; RopeSdDiff=c(-0.1,0.1) ; RopeEff=c(-0.1,0.1)
# myDataFrame = read.csv( file="RatLives.csv" )
# xName="Group"
# yName="DaysLive"
# fileNameRoot = "RatLives-"
# RopeMuDiff=c(-10,10) ; RopeSdDiff=c(-10,10) ; RopeEff=c(-0.1,0.1)
# myDataFrame = read.csv( file="RatLives.csv" )
# xName="Group"
# myDataFrame = cbind( myDataFrame , DaysLiveSq = myDataFrame$DaysLive^2 )
# yName="DaysLiveSq"
# fileNameRoot = "RatLives-DaySq-"
# RopeMuDiff=c(-100,100) ; RopeSdDiff=c(-100,100) ; RopeEff=c(-0.1,0.1)
graphFileType = "eps"
#-------------------------------------------------------------------------------
# Load the relevant model into R's working memory:
#source("Jags-Ymet-Xnom2grp-MrobustHet.R")
#-------------------------------------------------------------------------------
# Generate the MCMC chain:
mcmcCoda = genMCMC(mod, datFrm=myDataFrame , yName=yName , xName=xName ,
numSavedSteps=50000 , saveName=fileNameRoot )
#-------------------------------------------------------------------------------
# Display diagnostics of chain, for specified parameters:
parameterNames = varnames(mcmcCoda) # get all parameter names
for ( parName in parameterNames ) {
diagMCMC( codaObject=mcmcCoda , parName=parName ,
saveName=fileNameRoot , saveType=graphFileType )
}
#-------------------------------------------------------------------------------
# Get summary statistics of chain:
summaryInfo = smryMCMC(mod, mcmcCoda , RopeMuDiff=RopeMuDiff ,
RopeSdDiff=RopeSdDiff , RopeEff=RopeEff ,
saveName=fileNameRoot )
show(summaryInfo)
# Display posterior information:
plotMCMC(mod, mcmcCoda , datFrm=myDataFrame , yName=yName , xName=xName ,
RopeMuDiff=RopeMuDiff , RopeSdDiff=RopeSdDiff , RopeEff=RopeEff ,
pairsPlot=TRUE , saveName=fileNameRoot , saveType=graphFileType )
#-------------------------------------------------------------------------------
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