[R] How can this code be improved?

[Richard R. Liu]

I am running the following code on a MacBook Pro 17" Unibody early  
2009 with 8GB RAM, OS X 10.5.8, R 2.10.0 Patch from Nov. 2, 2009, in  
64-bit mode.

freq.stopwords <- numeric(0)
freq.nonstopwords <- numeric(0)
token.tables <- list(0)
i.ss <- c(0)
cat("Beginning at ", date(), ".\n")
for (i.d in 1:length(tokens)) {
	tt <- list(0)
	for (i.s in 1:length(tokens[[i.d]])) {
		t <- tolower(tokens[[i.d]][[i.s]])
		t <- sub("^[[:punct:]]*", "", t)
		t <- sub("[[:punct:]]*$", "", t)
		t <- as.data.frame(table(t))
		i.m <- match(t$t, stopwords)
		i.m.is.na <- is.na(i.m)
		i.ss <- i.ss + 1
		freq.stopwords[i.ss] <- sum(t$Freq * !i.m.is.na)
		freq.nonstopwords[i.ss] <- sum(t$Freq * i.m.is.na)
		tt[[i.s]] <- data.frame(token = t$t, freq = t$Freq, matches.stopword  
= i.m)
	}
	token.tables[[i.d]] <- tt
	if (i.d %% 5 == 0) cat(i.d, "reports completed at ", date(), ".\n")
}
cat("Terminating at ", date(), ".\n")

The object in the innermost loop are:
* tokens:  a list of lists.  In the expression tokens[[i.d]][[i.s]],  
the first index runs over 1697 reports, the second over the sentences  
in the report, each of which consists of a vector of tokens, i.e., the  
character strings between the white spaces in the sentence.  One of  
the largest reports takes up 58MB on the harddisk.  Thus, the number  
of sentences can be quite large, and some of the sentences are quite  
long (measure in tokens as well as in characters).
* stopwords:  is a vector of 571 words that occur very often in  
written English.

The code operates on sentences, converting each token in the sentence  
to lowercase, removing punctuation at the beginning and end of the  
token, tabulating the frequency of the unique tokens, and generating  
an array that indicates which tokens correspond to stopwords.  It also  
sums the frequencies of the stopwords and that of the non-stopwords.   
The result is a list of list of dataframes.

I began running on Thursday Nov. 12, 2009 at 01:56:36.  As of 7:52:00  
510 reports had been processed.  The Activity Monitor indicates no  
memory bottleneck.  R is using 4.31 GB of real memory, 7.23 GB of  
virtual memory, and 1.67 GB of real memory are free.

I admit that I am an R newbie.  From my understanding of the "apply"  
functions (e.g., lapply), I see no way to use them to simplify the  
loops.  I would appreciate any suggestions about making the code more  
"R-like" and, above all, much faster.

Regards,
Richard