Here is how I did this:
fnam=file.path("directory path")
filist=list.files(fnam, recursive=TRUE, pattern="wav")
filist1=paste(fnam, "/", filist, sep="")
nfiles=length(filist1)
test_rms=c("Full File Path", "RMS-L","RMS-R")
for (i in 1:nfiles){
inname=filist1[i]
ywave=readWave(inname)
L=ywave@left
R=ywave@right
test_rms = rbind(test_rms, c(inname, rms(L), rms(R)))
}
The code for RMS can be replaced with whatever process you need to preform. I will say that the code failed to run through my entire directory, as I had may sub-directories. At least two deep from the path I specified. This code went one level in, and read everything in that directory, even wav files in further sub-directories. I think this script just can handle two directories out.