R : Copyright 2005, The R Foundation for Statistical Computing
Version 2.1.1  (2005-06-20), ISBN 3-900051-07-0

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> ### * <HEADER>
> ###
> attach(NULL, name = "CheckExEnv")
> assign(".CheckExEnv", as.environment(2), pos = length(search())) # base
> ## add some hooks to label plot pages for base and grid graphics
> setHook("plot.new", ".newplot.hook")
> setHook("persp", ".newplot.hook")
> setHook("grid.newpage", ".gridplot.hook")
> 
> assign("cleanEx",
+        function(env = .GlobalEnv) {
+ 	   rm(list = ls(envir = env, all.names = TRUE), envir = env)
+            RNGkind("default", "default")
+ 	   set.seed(1)
+    	   options(warn = 1)
+ 	   delayedAssign("T", stop("T used instead of TRUE"),
+ 		  assign.env = .CheckExEnv)
+ 	   delayedAssign("F", stop("F used instead of FALSE"),
+ 		  assign.env = .CheckExEnv)
+ 	   sch <- search()
+ 	   newitems <- sch[! sch %in% .oldSearch]
+ 	   for(item in rev(newitems))
+                eval(substitute(detach(item), list(item=item)))
+ 	   missitems <- .oldSearch[! .oldSearch %in% sch]
+ 	   if(length(missitems))
+ 	       warning("items ", paste(missitems, collapse=", "),
+ 		       " have been removed from the search path")
+        },
+        env = .CheckExEnv)
> assign("..nameEx", "__{must remake R-ex/*.R}__", env = .CheckExEnv) # for now
> assign("ptime", proc.time(), env = .CheckExEnv)
> grDevices::postscript("ppc-Examples.ps")
> assign("par.postscript", graphics::par(no.readonly = TRUE), env = .CheckExEnv)
> options(contrasts = c(unordered = "contr.treatment", ordered = "contr.poly"))
> options(warn = 1)    
> library('ppc')
> 
> assign(".oldSearch", search(), env = .CheckExEnv)
> assign(".oldNS", loadedNamespaces(), env = .CheckExEnv)
> cleanEx(); ..nameEx <- "ppc.cv"
> 
> ### * ppc.cv
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: ppc.cv
> ### Title: Cross-validation for PPC analysis
> ### Aliases: ppc.cv
> 
> 
> ### ** Examples
> 
> ## for a complete worked example of this function in a PPC analysis  see
> ##  http://www-stat.stanford.edu/~tibs/PPC/Rdist/Rscript.rawdata
> 
> 
> 
> cleanEx(); ..nameEx <- "ppc.fdr"
> 
> ### * ppc.fdr
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: ppc.fdr
> ### Title: Function to estimate False Discovery rates for peaks in PPC
> ###   analysis
> ### Aliases: ppc.fdr
> 
> 
> ### ** Examples
> 
> ## for a complete worked example of this function in a PPC analysis  see
> ##  http://www-stat.stanford.edu/~tibs/PPC/Rdist/Rscript.rawdata
> 
> 
> 
> cleanEx(); ..nameEx <- "ppc.find.splits"
> 
> ### * ppc.find.splits
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: ppc.find.splits
> ### Title: Function to find best discriminating split points for training
> ###   data in mass spec
> ### Aliases: ppc.find.splits
> 
> 
> ### ** Examples
> 
> ## for a complete worked example of this function in a PPC analysis  see
> ##  http://www-stat.stanford.edu/~tibs/PPC/Rdist/Rscript.rawdata
> 
> 
> 
> cleanEx(); ..nameEx <- "ppc.make.centroid.list"
> 
> ### * ppc.make.centroid.list
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: ppc.make.centroid.list
> ### Title: Function to make a list of peak centroids, from a set of peaks
> ###   from different spectra
> ### Aliases: ppc.make.centroid.list
> 
> 
> ### ** Examples
> 
> ## for a complete worked example of this function in a PPC analysis  see
> ##  http://www-stat.stanford.edu/~tibs/PPC/Rdist/Rscript.rawdata
> 
> 
> 
> cleanEx(); ..nameEx <- "ppc.make.peaklist"
> 
> ### * ppc.make.peaklist
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: ppc.make.peaklist
> ### Title: Function to extract peaks from raw mass spec data
> ### Aliases: ppc.make.peaklist
> 
> 
> ### ** Examples
> 
> ## for a complete worked example of this function in a PPC analysis  see
> ##  http://www-stat.stanford.edu/~tibs/PPC/Rdist/Rscript.rawdata
> 
> 
> 
> cleanEx(); ..nameEx <- "ppc.peak.summary"
> 
> ### * ppc.peak.summary
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: ppc.peak.summary
> ### Title: Produce summary of peaks from PPC analysis
> ### Aliases: ppc.peak.summary
> 
> 
> ### ** Examples
> 
> ## for a complete worked example of this function in a PPC analysis  see
> ##  http://www-stat.stanford.edu/~tibs/PPC/Rdist/Rscript.rawdata
> 
> 
> 
> cleanEx(); ..nameEx <- "ppc.peaks"
> 
> ### * ppc.peaks
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: ppc.peaks
> ### Title: Find local maxima
> ### Aliases: ppc.peaks
> 
> 
> ### ** Examples
> 
> x<-rnorm(1000)
> a<-ppc.peaks(x, .02)
> 
> 
> 
> cleanEx(); ..nameEx <- "ppc.plot.hist"
> 
> ### * ppc.plot.hist
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: ppc.plot.hist
> ### Title: Plot peak histograms from PPC analysis
> ### Aliases: ppc.plot.hist
> 
> 
> ### ** Examples
> 
> ## for a complete worked example of this function in a PPC analysis  see
> ##  http://www-stat.stanford.edu/~tibs/PPC/Rscript.rawdata
> 
> 
> 
> cleanEx(); ..nameEx <- "ppc.plotcv"
> 
> ### * ppc.plotcv
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: ppc.plotcv
> ### Title: Function to plot CV curves from PPC analysis
> ### Aliases: ppc.plotcv
> 
> 
> ### ** Examples
> 
> ## for a complete worked example of this function in a PPC analysis  see
> ##  http://www-stat.stanford.edu/~tibs/PPC/Rdist/Rscript.rawdata
> 
> 
> 
> cleanEx(); ..nameEx <- "ppc.plotcvprob"
> 
> ### * ppc.plotcvprob
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: ppc.plotcvprob
> ### Title: Function to plot CV probabilities from PPC analysis
> ### Aliases: ppc.plotcvprob
> 
> 
> ### ** Examples
> 
> ## for a complete worked example of this function in a PPC analysis  see
> ##  http://www-stat.stanford.edu/~tibs/PPC/Rdist/Rscript.rawdata
> 
> 
> 
> cleanEx(); ..nameEx <- "ppc.plotfdr"
> 
> ### * ppc.plotfdr
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: ppc.plotfdr
> ### Title: Function to plot FDR results from PPC analysis
> ### Aliases: ppc.plotfdr
> 
> 
> ### ** Examples
> 
> ## for a complete worked example of this function in a PPC analysis  see
> ##  http://www-stat.stanford.edu/~tibs/PPC/Rdist/Rscript.rawdata
> 
> 
> 
> cleanEx(); ..nameEx <- "ppc.predict"
> 
> ### * ppc.predict
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: ppc.predict
> ### Title: Function to do test set prediction for the PPC method
> ### Aliases: ppc.predict
> 
> 
> ### ** Examples
> 
> ## for a complete worked example of this function in a PPC analysis  see
> ##  http://www-stat.stanford.edu/~tibs/PPC/Rdist/Rscript.rawdata
> 
> 
> 
> cleanEx(); ..nameEx <- "ppc.predict.peaks"
> 
> ### * ppc.predict.peaks
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: ppc.predict.peaks
> ### Title: A function to find centroid peaks, in a list of individual peaks
> ### Aliases: ppc.predict.peaks
> 
> 
> ### ** Examples
> 
> ## for a complete worked example of this function in a PPC analysis  see
> ##  http://www-stat.stanford.edu/~tibs/PPC/Rdist/Rscript.rawdata
> 
> 
> 
> cleanEx(); ..nameEx <- "ppc.predict.peaks1"
> 
> ### * ppc.predict.peaks1
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: ppc.predict.peaks1
> ### Title: A function to find centroid peaks, in a list of individual peaks
> ###   from one spectrum
> ### Aliases: ppc.predict.peaks1
> 
> 
> ### ** Examples
> 
> ## for a complete worked example of this function in a PPC analysis  see
> ##  http://www-stat.stanford.edu/~tibs/PPC/Rdist/Rscript.rawdata
> 
> 
> 
> cleanEx(); ..nameEx <- "ppc.predict1"
> 
> ### * ppc.predict1
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: ppc.predict1
> ### Title: Function to do a single test set prediction for the PPC method
> ### Aliases: ppc.predict1
> 
> 
> ### ** Examples
> 
> ## for a complete worked example of this function in a PPC analysis  see
> ##  http://www-stat.stanford.edu/~tibs/PPC/Rdist/Rscript.rawdata
> 
> 
> 
> cleanEx(); ..nameEx <- "ppc.read.peaks.batch"
> 
> ### * ppc.read.peaks.batch
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: ppc.read.peaks.batch
> ### Title: Read in mass spec peak data, with batches
> ### Aliases: ppc.read.peaks.batch
> 
> 
> ### ** Examples
> 
> ## for a complete worked example of this function in a PPC analysis  see
> ##  http://www-stat.stanford.edu/~tibs/PPC/Rdist/Rscript.peakdata
> 
> 
> 
> cleanEx(); ..nameEx <- "ppc.read.peaks.nobatch"
> 
> ### * ppc.read.peaks.nobatch
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: ppc.read.peaks.nobatch
> ### Title: Read in mass spec peak data, without batches
> ### Aliases: ppc.read.peaks.nobatch
> 
> 
> ### ** Examples
> 
> ## for a complete worked example of this function in a PPC analysis  see
> ##  http://www-stat.stanford.edu/~tibs/PPC/Rdist/Rscript.peakdata
> 
> 
> 
> cleanEx(); ..nameEx <- "ppc.read.raw.batch"
> 
> ### * ppc.read.raw.batch
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: ppc.read.raw.batch
> ### Title: A function to read in raw protein mass spec data, with batches
> ### Aliases: ppc.read.raw.batch
> 
> 
> ### ** Examples
> 
> ## for a complete worked example of this function in a PPC analysis  see
> ##  http://www-stat.stanford.edu/~tibs/PPC/Rdist/Rscript.rawdata
> 
> 
> 
> cleanEx(); ..nameEx <- "ppc.read.raw.nobatch"
> 
> ### * ppc.read.raw.nobatch
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: ppc.read.raw.nobatch
> ### Title: A function to read in raw protein mass spec data, with no
> ###   batches
> ### Aliases: ppc.read.raw.nobatch
> 
> 
> ### ** Examples
> 
> ## for a complete worked example of this function in a PPC analysis  see
> ##  http://www-stat.stanford.edu/~tibs/PPC/Rdist/Rscript.rawdata
> 
> 
> 
> cleanEx(); ..nameEx <- "ppc.remove.beforeslash.and.suffix"
> 
> ### * ppc.remove.beforeslash.and.suffix
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: ppc.remove.beforeslash.and.suffix
> ### Title: Remove characters efore a slash and at end
> ### Aliases: ppc.remove.beforeslash.and.suffix
> 
> 
> ### ** Examples
> 
> ## for a complete worked example of this function in a PPC analysis  see
> ##  http://www-stat.stanford.edu/~tibs/PPC/Rdist/Rscript.rawdata
> 
> 
> 
> cleanEx(); ..nameEx <- "ppc.remove.suffix"
> 
> ### * ppc.remove.suffix
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: ppc.remove.suffix
> ### Title: Function to remove the suffix from a file name
> ### Aliases: ppc.remove.suffix
> 
> 
> ### ** Examples
> 
> ## for a complete worked example of this function in a PPC analysis  see
> ##  http://www-stat.stanford.edu/~tibs/PPC/Rdist/Rscript.rawdata
> 
> 
> 
> cleanEx(); ..nameEx <- "ppc.subset.and.reshape"
> 
> ### * ppc.subset.and.reshape
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: ppc.subset.and.reshape
> ### Title: Function to subset and reshape raw mass spec data
> ### Aliases: ppc.subset.and.reshape
> 
> 
> ### ** Examples
> 
> ## for a complete worked example of this function in a PPC analysis  see
> ##  http://www-stat.stanford.edu/~tibs/PPC/Rdist/Rscript.rawdata
> 
> 
> 
> cleanEx(); ..nameEx <- "ppc.subset.and.reshape.peakdata"
> 
> ### * ppc.subset.and.reshape.peakdata
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: ppc.subset.and.reshape.peakdata
> ### Title: Function to subset and reshape mass spec peak data
> ### Aliases: ppc.subset.and.reshape.peakdata
> 
> 
> ### ** Examples
> 
> ## for a complete worked example of this function in a PPC analysis  see
> ##  http://www-stat.stanford.edu/~tibs/PPC/Rdist/Rscript.peakdata
> 
> 
> 
> ### * <FOOTER>
> ###
> cat("Time elapsed: ", proc.time() - get("ptime", env = .CheckExEnv),"\n")
Time elapsed:  0.1 0 0.11 0 0 
> grDevices::dev.off()
null device 
          1 
> ###
> ### Local variables: ***
> ### mode: outline-minor ***
> ### outline-regexp: "\\(> \\)?### [*]+" ***
> ### End: ***
> quit('no')