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Spectrum confidence interval

Late answer, but maybe still helpful (if I am correct this question is 
still unanswered on R-help):
Cl?ment Poirier wrote:
This is not supported in plot.spec (the plot method for spec objects), 
since handled in the else part after
   if (ci <= 0 || !is.numeric(x$df) || log == "no")
Type
  plot.spec

In the code for that function, you will find the function definition of 
spec.ci() which calculates the confidence intervals. Just define that 
function in your workspace and you can go on and add lines to your plot now.

Best wishes,
Uwe Ligges