Hi R community, 
I have a question concerning passing arguments between apply and lapply?  Or maybe, once my problem is explained, the question is really about how to best transform my nested for loops into list/matrix operations;  I am just beginning this transformation away from nested  for  loops, so I beg of you to have some lenience regarding my ignorance.

Part I:
I used a set of nested for loops for a computation, which works as fine as it is slow--very slow.  My needs are on the order of about 20000 iterations; in nested loop format this is millions of calculations.   To give you a sense of what I'm trying to do, it may help to first see the nested for loop (this code is run-able via copy-and-paste):

#START CODE SNIPPET

#LIST AND VECTOR
rm(list=ls())
l <- list(1:3,2:3,4:10,7:9)
v <- 1:3

#USED IN j loop to catch values
catch.mat <- matrix(NA,nrow=length(v),ncol=length(l))

#LOOPS
for (i in 1:length(v)){
  for (j in 1:length(l)) {
    catch.mat[i,j] <- sum(l[[j]]==i)
  }
}

#SIMPLY APPLY OVER catch.mat
catch.all <- apply(catch.mat,1,sum) 

catch.mat
catch.all

#END CODE SNIPPET

This does exactly what I want, < catch.all> provides the number of elements in < l > for which each element of < v > is a member, given the constraint that within each element in < l > the sub-elements are unique.


Part II:  
However, for my data set it takes about 3 days to run.  So, I stumbled onto list and matrix operations (apply family of functions) and have been working to coerce my code above into an apply-like format.  Here is my best example (of several failings of different sorts), after trying for several hours and reading much on the web and in some books: 


#THIS CODE SNIPPET IS PASTE-ABLE AFTER RUNNING FIRST SNIPPET ABOVE

#SIMPLE TEST TO SHOW THAT apply is passing elements from mat.1 to f.1
f.1 <- function(x){
  i <- x
  print(x)
  print(i)
}

mat.1 <- matrix(1:2318,nrow=1,ncol=2318)
apply(mat.1,1,f.1)

#THAT GAVE EXPECTED RESULTS

#THEN I ADD A NEW FUNCTION
f.2 <- function(x,l=l){
  i <- x
  rm(x)
  return(sum(lapply(l,function(x) sum(x==i))))
}

mat.1 <- matrix(1:2318,nrow=1,ncol=2318)
apply(mat.1,1,f.2)

#BUT GET ERROR
#> apply(mat.1,1,f.2)
#Error in lapply(l, function(x) sum(x == i)) : 
# promise already under evaluation: recursive default argument reference or earlier problems?

#BUT I KNOW THAT the lapply in f.2 works
sapply(l,function(x) sum(x==2))
sum(sapply(l,function(x) sum(x==2)))

#END CODE SNIPPET


I Am totally stuck, as I really don't understand the internals of R or S well enough to get a sense of what is the root of this problem in my code.

I would appreciate some guidance by example, not by reference.  I don't think further reading of existing texts, unless extremely basic, is going to help me.  

Thanks, 
Mark Orr

----------------------------------------------------
Mark G. Orr, Ph.D.
Epidemiology Merit Fellow
Assoc. Research Scientist
Columbia Univ.-Mailman Sch. Public Health
Department of Epidemiology
722 W. 168th St., RM 528
New York, NY

T:  212-305-3815
F:  212-342-5168

mo2259@columbia.edu

http://chbdlab.org/



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