[R] summing NAs in aggregate

[Spitzer, Matthew]

Hello,
I would like to please ask for assistance with aggregate sum.  I have a data set with consisting of two grouping variables (id, visit) and several other variables.  I would like to sum the variables for each id and visit, but am having problems with na.rm.  na.rm=TRUE seems to replace all NAs with zeros, or better stated results in a zero when summing a set of NAs.  I would like to remove NAs when some NAs are present in a group (1+NA + NA =1 or NA + 1 +1=2), but retain/keep the NA if the entire group consists of NAs (NA + NA + NA=NA).  

I have created an truncated example (my data set has many more rows):

example <-
structure(list(id = c(4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 
4L, 4L, 4L, 12L, 12L, 12L, 12L, 12L, 12L, 12L, 12L, 12L, 12L, 
12L, 12L, 12L, 43L, 43L, 43L, 43L, 43L, 43L, 43L, 43L, 43L, 43L, 
43L, 43L), visit = c(3L, 3L, 3L, 3L, 5L, 5L, 5L, 9L, 9L, 9L, 
9L, 12L, 12L, 3L, 3L, 3L, 5L, 5L, 5L, 5L, 5L, 9L, 9L, 12L, 12L, 
12L, 3L, 3L, 3L, 3L, 5L, 5L, 5L, 5L, 12L, 12L, 12L, 12L), var1 = c(1L, 
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 
1L, 1L, 1L, 1L, 1L), var2 = c(1L, NA, NA, NA, NA, 1L, NA, 0L, 
1L, 0L, NA, 0L, NA, NA, NA, 1L, 0L, NA, 0L, 1L, 1L, 1L, NA, 1L, 
0L, NA, NA, 1L, 1L, 0L, NA, 1L, NA, NA, 0L, 1L, 1L, 1L), var3 = c(NA, 
NA, NA, NA, 1L, 0L, 1L, NA, 1L, 1L, NA, 0L, 1L, NA, 0L, 1L, NA, 
1L, 0L, NA, 1L, 0L, 1L, NA, NA, NA, NA, 1L, 1L, 1L, 1L, 0L, 1L, 
NA, NA, NA, NA, 1L), var4 = c(0L, 1L, NA, NA, NA, 1L, 1L, 0L, 
NA, NA, 0L, 1L, 1L, NA, 1L, 1L, 0L, 1L, 1L, NA, 1L, NA, 0L, 0L, 
0L, NA, NA, NA, NA, NA, NA, 1L, 1L, NA, 0L, 0L, 0L, NA)), .Names = c("id", 
"visit", "var1", "var2", "var3", "var4"), class = "data.frame", row.names = c(NA, 
-38L))
example<-as.data.frame(example)

#generates 0s for groups with all NAs such as id 43, visit 3, var4 that I would like to be NA
agex1 <-aggregate.data.frame(example, by=list(example$id,example$visit),FUN=sum,na.rm=TRUE)

#discards sums with any NAs in it, including many data that I would like to analyze, too many NAs
agex2<-aggregate.data.frame(example, by=list(example$id,example$visit),FUN=sum)

na.action does not seem to work with data frames in this instance.  I have tried to create a function to fix this, but have had great difficulty.  I have thought about ddply but cannot figure out how to apply this.  Would anyone be able to please suggest an alternate means of summing by group to retain NAs when I would like but not when they are part of an entire set of NAs?  I would be very grateful for a suggestion for an alternate way to process these data.

Thanks, Matt

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