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("negenes-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('negenes')
> 
> assign(".oldSearch", search(), env = .CheckExEnv)
> assign(".oldNS", loadedNamespaces(), env = .CheckExEnv)
> cleanEx(); ..nameEx <- "Mtb80"
> 
> ### * Mtb80
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: Mtb80
> ### Title: Number of insertion sites in each gene in M tb CDC1551
> ### Aliases: Mtb80
> ### Keywords: datasets
> 
> ### ** Examples
> 
> ## Not run: data(Mtb80)
> ##D 
> ##D # simulate 44% of genes to be essential
> ##D essential <- rep(0,nrow(Mtb80))
> ##D essential[sample(1:nrow(Mtb80),ceiling(nrow(Mtb80)*0.44))] <- 1
> ##D 
> ##D # simulate 759 mutants
> ##D counts <- sim.mutants(Mtb80[,1], essential, Mtb80[,2], 759)
> ##D 
> ##D # run the Gibbs sampler
> ##D output <- negenes(Mtb80[,1], counts[,1], Mtb80[,2], counts[,2])
> ## End(Not run)
> 
> 
> 
> cleanEx(); ..nameEx <- "negenes"
> 
> ### * negenes
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: negenes
> ### Title: Estimate the number of essential genes in a genome
> ### Aliases: negenes
> ### Keywords: models
> 
> ### ** Examples
> 
> data(Mtb80)
> 
> # simulate 44% of genes to be essential
> essential <- rep(0,nrow(Mtb80))
> essential[sample(1:nrow(Mtb80),ceiling(nrow(Mtb80)*0.44))] <- 1
> 
> # simulate 759 mutants
> counts <- sim.mutants(Mtb80[,1], essential, Mtb80[,2], 759)
> 
> # run the Gibbs sampler without returning detailed output
> output <- negenes(Mtb80[,1], counts[,1], Mtb80[,2], counts[,2])
   0
  20
  40
  60
  80
 100
> 
> # run the Gibbs sampler, returning the detailed output
> output2 <- negenes(Mtb80[,1], counts[,1], Mtb80[,2], counts[,2], return=TRUE)
   0
  20
  40
  60
  80
 100
> 
> 
> 
> cleanEx(); ..nameEx <- "sim.mutants"
> 
> ### * sim.mutants
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: sim.mutants
> ### Title: Simulate data for a random transposon mutagenesis experiment
> ### Aliases: sim.mutants
> ### Keywords: datagen
> 
> ### ** Examples
> 
> ## Not run: data(Mtb80)
> ##D 
> ##D # simulate 44% of genes to be essential
> ##D essential <- rep(0,nrow(Mtb80))
> ##D essential[sample(1:nrow(Mtb80),ceiling(nrow(Mtb80)*0.44))] <- 1
> ##D 
> ##D # simulate 759 mutants
> ##D counts <- sim.mutants(Mtb80[,1], essential, Mtb80[,2], 759)
> ##D 
> ##D # run the Gibbs sampler
> ##D output <- negenes(Mtb80[,1], counts[,1], Mtb80[,2], counts[,2])
> ## End(Not run)
> 
> 
> 
> ### * <FOOTER>
> ###
> cat("Time elapsed: ", proc.time() - get("ptime", env = .CheckExEnv),"\n")
Time elapsed:  21.09 0.08 21.38 0 0 
> grDevices::dev.off()
null device 
          1 
> ###
> ### Local variables: ***
> ### mode: outline-minor ***
> ### outline-regexp: "\\(> \\)?### [*]+" ***
> ### End: ***
> quit('no')