Hello Bert and Sarah,
Thank you for your replies. Helped me understand how people might perceive my
question and why they might not respond.
Spent some time learning about R's debugging tools this morning. Began to
realize why my function didn't work. My second argument was the name of a
variable. What I didn't realize is that R would immediately expect this to be a
previously defined object. I had thought that passing the name of the variable
to the body of the function would generate a correct line of code, and that
this was all that was required to get the function to work.
Below is a function that does work, at least when applied to a single row of
data. I had previously been reading about the Split-Apply-Combine strategy in
a paper about the plyr package. The paper advocates coming up with a function
that works for a subset of one's data and then using plyr to split up the data
and apply the function to each of the subsets. Was under the impression that
this last part would be easy. Seems not to be the case though.
So on to the next part.
Thanks again for your feedback.
Paul
#### Test row ####
testRow <-
structure(list(profile_key = structure(6L, .Label = c("001-001 ",
"001-002 ", "001-003 ", "001-004 ", "001-005 ", "001-006 ", "001-007 "
), class = "factor"), encounter_date = structure(4L, .Label = c(" 2009-03-01 ",
" 2009-03-22 ", " 2009-04-01 ", " 2010-03-01 ", " 2010-04-01 ",
" 2010-10-15 ", " 2010-11-15 ", " 2011-03-01 ", " 2011-03-14 ",
" 2011-04-01 ", " 2011-10-10 ", " 2011-10-24 ", " 2012-09-15 ",
" 2012-10-05 ", " 2012-10-17 "), class = "factor"), raw = " if patient kras
result is wild type they will start erbitux several lines of material ordered
kras mutation test 11112011 results are still not available "), .Names =
c("profile_key",
"encounter_date", "raw"), row.names = 13L, class = "data.frame")
testRow
#### Function for selecting words within specified range of a target term ####
nearTerms <- function(df, rawtext, target, before, after, reduced){
Text <- unlist(strsplit(df[,rawtext], " "))
Target <- grep(target, Text)
if (length(Target) == 0) {df <- transform(df, outtext = "")} else{
Length <- length(Text)
Keep <- rep(NA, Length)
Lower <- ifelse(Target - before > 0, Target - before, 1)
Upper <- ifelse(Target + after < Length, Target + after, Length)
for(i in 1:length(Keep)){
for(j in 1:length(Lower)){
Keep[i][i %in% seq(Lower[j], Upper[j])] <- i
}}
df <- transform(df, outtext = paste(Text[!is.na(Keep)], collapse=" "))
}
names(df)[names(df) == "outtext"] <- reduced
df <- df
}
testRow <- nearTerms(df = testRow, rawtext = "raw", target = "kras", before =
6, after = 6, reduced = "reduced")
testRow
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