Calculate a credible set for the posterior distribution on the Beta hyperparameters.

Description

This function accepts a distribution calculated with pprob.dist and calculates a credible set of the specified level for the hyperparameters. If the credible set includes the value (1,1) the sample is likely to be uniform.

Usage

  cred.set(dist,delta=NULL,level=0.95)

Arguments

Details

The cred.set function calculates a credible set of the specified level based on the distribution calculated with pprob.dist. The grid size, delta, should match the grid size from the call to pprob.dist. The result is a matrix of the same size as dist which indicates whether each point is in the credible set.

Value

Author(s)

Jeffrey T. Leek jleek@jhsph.edu

References

J.T. Leek and J.D. Storey, "The Joint Null Distribution of Multiple Hypothesis Tests."

See Also

dks, dks.pvalue, pprob.dist,cred.set

Examples

  ## Load data
  data(dksdata) 

  ## Calculate the posterior distribution
  dist1 <- pprob.dist(P[,1])

  delta = 0.1
  ## Calculate a 95% credible set
  cred1 <- cred.set(dist1,delta=0.1)

  ## Plot the posterior and the credible set
  
  alpha <- seq(0.1,10,by=delta)
  beta <- seq(0.1,10,by=delta)

  par(mfrow=c(1,2))
  image(log10(alpha),log10(beta),dist1,xaxt="n",yaxt="n",xlab="Alpha",ylab="Beta")
  axis(1,at=c(-2,-1,0,1,2),labels=c("10^-2","10^-1","10^0","10^1","10^2"))
  axis(2,at=c(-2,-1,0,1,2),labels=c("10^-2","10^-1","10^0","10^1","10^2"))
  points(0,0,col="blue",cex=1,pch=19)	

  image(log10(alpha),log10(beta),cred1$cred,xaxt="n",yaxt="n",xlab="Alpha",ylab="Beta")
  axis(1,at=c(-2,-1,0,1,2),labels=c("10^-2","10^-1","10^0","10^1","10^2"))
  axis(2,at=c(-2,-1,0,1,2),labels=c("10^-2","10^-1","10^0","10^1","10^2"))
  points(0,0,col="blue",cex=1,pch=19)	

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(dks)
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/dks/cred.set.Rd_%03d_medium.png", width=480, height=480)
> ### Name: cred.set
> ### Title: Calculate a credible set for the posterior distribution on the
> ###   Beta hyperparameters.
> ### Aliases: cred.set
> ### Keywords: misc
> 
> ### ** Examples
> 
>   ## Load data
>   data(dksdata) 
> 
>   ## Calculate the posterior distribution
>   dist1 <- pprob.dist(P[,1])
> 
>   delta = 0.1
>   ## Calculate a 95% credible set
>   cred1 <- cred.set(dist1,delta=0.1)
> 
>   ## Plot the posterior and the credible set
>   
>   alpha <- seq(0.1,10,by=delta)
>   beta <- seq(0.1,10,by=delta)
> 
>   par(mfrow=c(1,2))
>   image(log10(alpha),log10(beta),dist1,xaxt="n",yaxt="n",xlab="Alpha",ylab="Beta")
>   axis(1,at=c(-2,-1,0,1,2),labels=c("10^-2","10^-1","10^0","10^1","10^2"))
>   axis(2,at=c(-2,-1,0,1,2),labels=c("10^-2","10^-1","10^0","10^1","10^2"))
>   points(0,0,col="blue",cex=1,pch=19)	
> 
>   image(log10(alpha),log10(beta),cred1$cred,xaxt="n",yaxt="n",xlab="Alpha",ylab="Beta")
>   axis(1,at=c(-2,-1,0,1,2),labels=c("10^-2","10^-1","10^0","10^1","10^2"))
>   axis(2,at=c(-2,-1,0,1,2),labels=c("10^-2","10^-1","10^0","10^1","10^2"))
>   points(0,0,col="blue",cex=1,pch=19)	
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>