irreg.outer.boot.func <- function(sp, defree = 10, Nrep = 399, indexfile)
{
# irreg.outer.boot.func: 
# Modification of outer.boot.func to deal with data taken at irregular 
# time points, but for indices to be evaluated at integer time points. 
# Only difference from outer.boot.func is the call to irreg.bootstrap.func
# instead of bootstrap.func.
# 
# Blurb for outer.boot.func follows:
# Calls the function bootstrap.func that will compute a 
# bootstrap resample, fit the GAM and find the indices.
# 
# NOTE: the BATCH file bootstrap.in  probably requires less memory than
# this function and is probably preferable. 
# 
# sp is the dataframe with columns headed "site", "year", "count", 
# and no missing values. 
# Nrep is number of bootstrap replicates; defree is degrees of freedom
# for the GAM fit.  Indexfile is the name of a file in the working
# directory (see below): it should be in quotes (" ").  
# 
# Example:
#   cb.bootind.399.10 <- outer.boot.func(cb, 10, 399, "cb.bootind.399.10")
# 
# NOTE:
# The file indexfile is a safeguard against premature termination of the
# bootstrap routine: all results are written to this file as the 
# function proceeds.  If the program crashes, the early results can be
# salvaged by:
#   sp.bootind.crash <- matrix(scan("indexfile"), nrow = k, byrow = T)
# where k is the number of replicates completed before the crash.
# The remaining replicates can then be made up by restarting the
# oter.boot.func function.
#
# ** IMPORTANT NOTE **
# When restarting any Splus simulation after a crash, be sure to reset the
# random seed before resuming: otherwise the previous results (before the 
# crash) will just be repeated.  The easiest way to reset the seed is
# simply to generate some new random numbers: e.g. runif(100).
# So (e.g.) if the procedure crashed after replicate 50 out of 399, the
# full run and salvage operation would be something like:
#    cb.bootind.399.10 <- outer.boot.func(cb, 10, 399,"cb.results")
#        (this crashes and the object cb.bootind.399.10 is never formed)
#    cb.bootind.crash50 <- matrix(scan("cb.results"), nrow=50, byrow=T)
#    runif(100)
#    cb.bootind.last349 <- outer.boot.func(cb, 10, 349, "cb.results2")
#    cb.bootind.399.10 <- rbind(cb.bootind.crash50, cb.bootind.last349)
#      
# 
# START OF FUNCTION
# some housekeeping jobs first:
	if(!is.character(indexfile)) stop(
			"filenames have to be character strings")	#
# the dataset sp is assumed to have NO MISSING ENTRIES:
	if(length(sp$count[is.na(sp$count)]) > 0) stop(
			"no missing data allowed")	#
# start bootstrap loop:
	assign("sp", sp, frame = 1)
	assign("defree", defree, frame = 1)
	assign("indexfile", indexfile, frame = 1)
	replicate.func <- function(i)
	{
		print(i)
		rep.indices <- irreg.bootstrap.func(sp, defree = defree)
		write(rep.indices, file = indexfile, ncolumns = 4, append = T)
		rep.indices
	}
	index.matrix <- sapply(1:Nrep, replicate.func)
	matrix(unlist(index.matrix), byrow = T, nrow = Nrep)
}