sp.name <- "cb"                 # *** CHANGE HERE
degfree <- 10 			# *** CHANGE HERE
Nreps <- 399			# *** CHANGE HERE	
options(echo=F)
#
# INSTRUCTIONS FOR BATCH PROCESS:
#
# This file is called bootstrap.in.  It is *not* an Splus function,
# but is a file kept in the working directory of Splus.  
# Note: designed for Splus v3.4 for UNIX: I don't know whether (or how)
# this works on other systems.  
#
# RUNNING THE JOB:
# 	1) Edit in this file the name of the species data frame (sp.name),
#	   the degrees of freedom (degfree), and the number of 
#	   bootstrap replicates required (Nreps):
#	   these three lines are marked with the note 
#	   *** CHANGE HERE.
#          It is best to choose Nreps to be (say) 499, 399, 299, 199, etc
#	   for later calculation of confidence intervals.
#	2) The output file will be called sp.bootind.Nreps.df, 
#	   where "sp" is replaced by the species code (e.g. cb), 
# 	   "Nreps" is replaced by the number of replicates (e.g. 399), 
# 	   and "df" is replaced by the degrees of freedom for the fit
# 	   (e.g. 10).
#	3) *Outside* of Splus, type the batch command:
# 	   Splus BATCH bootstrap.in sp.bootind.Nreps.df
#	   where sp, Nreps, and df have been changed accordingly.
# 	   (e.g. Splus BATCH bootstrap.in cb.bootind.399.10).
#	   Monitor progress via the output file sp.bootind.Nreps.df;
#	   the whole computation could take several hours.  
# 	4) When the program has finished, start Splus and view the
#	   resulting matrix of bootstrapped indices, which has name
# 	   sp.bootind.Nreps.df in Splus (sp, Nreps, df as appropriate).
# 	5) No harm in starting Splus sessions or anything else while
# 	   the BATCH program is running, but note that running this
# 	   BATCH program will automatically obliterate any previous Splus
# 	   objects called sp.bootind.Nreps.df or tmp.index.matrix. 
#          (Also see the last line of this file, in the rm(...) statement,
#          to see the names of all other objects that will be
#          obliterated.)
#          So *be very careful* that sp.name, or degfree, or Nreps, has 
# 	   been edited at the top before this function is next applied,
#          otherwise all results from the previous application will be
#          obliterated.  Killing the batch process at any time during its
#          execution will prevent this from happening, but once the batch
#          process is finished, the previous objects are lost. 
#
# NOTE:
# 
# If the bootstrap crashes or has to be terminated, all of the results 
# up to the point of termination are preserved in the output file 
# sp.bootind.Nreps.df, (i.e. cb.bootind.399.10 or whatever). 
#
# To salvage the results from this file in the event of early termination:
# 	1) edit out everything up to and including the line marked "EDIT
#		OUT EVERYTHING UP TO HERE";
# 	2) at the Splus command line, type (e.g.)
#  sp.bootind.crash <- as.matrix(read.table("sp.bootind.Nreps.df",header=T))
#	        where sp, Nreps, and df are replaced as appropriate. 
# 	3) edit out everything beyond the line at bottom of file marked
# 		"EDIT OUT EVERYTHING BEYOND HERE"
# 	4) the results so far are probably also in Splus object 
#   	   tmp.index.matrix, but check them against the output file and
# 	   be cautious because this object is overwritten every time 
#	   the batch process is started. 
#
# 
	sps <- eval(parse(text=sp.name))
        if(length(sps$count[is.na(sps$count)]) > 0) stop(
                        "no missing data allowed")
# start bootstrap loop:
        assign("sps", sps, frame = 1)
        assign("degfree", degfree, frame = 1)
	cat("\n\nEDIT OUT EVERYTHING UP TO HERE \n\n")
	cat("rep", paste("yr", 1:length(unique(sps$year)), sep=""), "\n")
        replicate.func <- function(i)
        {
                rep.indices <- bootstrap.func(sps, defree = degfree)
		cat(paste("rep", i, sep=""), format(rep.indices, digits=8), 
			"\n") 
		rep.indices
        }
	tmp.index.matrix <- vector("list", Nreps) #
# tmp.index.matrix will store the results but be removed as soon as the
# full set is transferred to an object with the correct name.
        For(i = 1:Nreps, tmp.index.matrix = replicate.func(i))
	cat("\n\nEDIT OUT EVERYTHING BEYOND HERE \n\n")
	resmat.name <- paste(sp.name, "bootind", Nreps, degfree, sep=".")
	tmp.index.matrix <- matrix(unlist(tmp.index.matrix), byrow = T,
		nrow = Nreps)
	assign(resmat.name, tmp.index.matrix)
	cat("Bootstrapping complete : now start Splus session to find matrix of results: \n",resmat.name, ".\n")
	rm(tmp.index.matrix, sps, replicate.func, i, resmat.name, degfree,
	sp.name, Nreps)