whiskerplot: Whisker plots of parameter posterior distributions

In jagsUI: A Wrapper Around 'rjags' to Streamline 'JAGS' Analyses

Description

Displays whisker plots for specified parameters on the same plot, with a point at the mean value for the posterior distribution and whiskers extending to the specified quantiles of the distribution.

Usage

  whiskerplot(x, parameters, quantiles=c(0.025,0.975), zeroline=TRUE, ...)

Arguments

x	A jagsUI object
parameters	A vector of names (as characters) of parameters to include in the plot. Parameter names must match parameters included in the model. Calling non-scalar parameters without subsetting (e.g. alpha) will plot all values of alpha.
quantiles	A vector with two values specifying the quantile values (lower and upper).
zeroline	If TRUE, a horizontal line at zero is drawn on the plot.
...	Additional arguments passed to plot.default

Author(s)

Ken Kellner [e-mail].

Examples

  
#Analyze Longley economic data in JAGS
#Number employed as a function of GNP
#See ?jags for a more detailed example

#Get data
data(longley)
gnp <- longley$GNP
employed <- longley$Employed
n <- length(employed)
data <- list(gnp=gnp,employed=employed,n=n)

#Identify filepath of model file
modfile <- tempfile()

writeLines("
model{

  #Likelihood
  for (i in 1:n){ 

    employed[i] ~ dnorm(mu[i], tau)     
    mu[i] <- alpha + beta*gnp[i]

  }
    
  #Priors
  alpha ~ dnorm(0, 0.00001)
  beta ~ dnorm(0, 0.00001)
  sigma ~ dunif(0,1000)
  tau <- pow(sigma,-2)

}
", con=modfile)

#Set parameters to monitor
params <- c('alpha','beta','sigma','mu')

#Run analysis

out <- jags(data = data,
            inits = NULL,
            parameters.to.save = params,
            model.file = modfile,
            n.chains = 3,
            n.adapt = 100,
            n.iter = 1000,
            n.burnin = 500,
            n.thin = 2)

#Examine output summary

out

#Generate whisker plots

#Plot alpha

whiskerplot(out,parameters=c('alpha'))

#Plot all values of mu

whiskerplot(out,parameters='mu')

#Plot a subset of mu

whiskerplot(out,parameters=c('mu[1]','mu[7]'))

#Plot mu and alpha together

whiskerplot(out,parameters=c('mu','alpha'))

jagsUI documentation built on June 18, 2021, 5:08 p.m.