[R] How can I get this function to work?

[Sarah Goslee]

On Thu, May 31, 2012 at 1:54 PM, Bert Gunter <gunter.berton at gene.com> wrote:
> Well, good luck finding someone to wade through your code --
> "small,reproducible" examples are requested for a reason -- but I will
> offer that I have no idea what you mean with your remark about
> anonymous functions, as the code you posted has none.

That's exactly as far as I got, and for just the same reasons.

I'll just add that if you're trying to make a function (the last
thing) that does the same thing as the sample code above it, then you
do rather need to include the same code in it. And if that's not what
you're trying to do, well, see Bert's request for small reproducible
example and clear explanation.

Sarah


> -- Bert
>
> On Thu, May 31, 2012 at 10:38 AM, Paul Miller <pjmiller_57 at yahoo.com> wrote:
>> Hello All,
>>
>> Can anyone tell help me understand why the function below doesn't work and how I can fix it? Below are some sample data, some code that works on individual rows of the data, and my attempt to translate that code into a function. My hope is to get the function working and then to apply it to the larger data frame using ddply() from the plyr package or possibly some other approach.
>>
>> As yet, I don't have much experience writing anonymous functions. I imagine I'm doing something that is obviously wrong, but I don't know what it is.
>>
>> Thanks,
>>
>> Paul
>>
>> #### Read in test data ####
>>
>> testData <-
>> structure(list(profile_key = structure(c(1L, 1L, 2L, 2L, 2L,
>> 3L, 3L, 4L, 4L, 5L, 5L, 5L, 6L, 6L, 7L, 7L), .Label = c("001-001 ",
>> "001-002 ", "001-003 ", "001-004 ", "001-005 ", "001-006 ", "001-007 "
>> ), class = "factor"), encounter_date = structure(c(9L, 10L, 11L,
>> 12L, 13L, 5L, 6L, 7L, 8L, 1L, 2L, 3L, 4L, 4L, 7L, 7L), .Label = c(" 2009-03-01 ",
>> " 2009-03-22 ", " 2009-04-01 ", " 2010-03-01 ", " 2010-10-15 ",
>> " 2010-11-15 ", " 2011-03-01 ", " 2011-03-14 ", " 2011-10-10 ",
>> " 2011-10-24 ", " 2012-09-15 ", " 2012-10-05 ", " 2012-10-17 "
>> ), class = "factor"), raw = c(" ordered kras testing on 10102010 results not yet available if patient has a mutation will start erbitux ",
>> " received kras results on 10202010 test results indicate tumor is wild type ua protein positve erpr positive her2neu positve ",
>> " will conduct kras mutation testing prior to initiation of therapy with erbitux ",
>> " still need to order kras mutation testing ", " ordered kras testing waiting for results ",
>> " kras test results pending note that patient was negative for lynch mutation ",
>> " kras results still pending note that patient was negative for lynch mutation ",
>> " kras mutated will not prescribe erbitux due to mutation ",
>> " kras mutated therefore did not prescribe erbitux ", " kras wild ",
>> " tumor is negative for mutation ", " tumor is wild type patient is eligible to receive eribtux ",
>> " 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 ",
>> " kras results are in patient has the mutation ", " ordered kras mutation testing on 02152011 results came back negative several lines of material patient kras mutation test is negative will start erbitux ",
>> " patient is kras negative started erbitux on 03012011 ")), .Names = c("profile_key",
>> "encounter_date", "raw"), row.names = c(NA, -16L), class = "data.frame")
>>
>> #### Convert text record to lowercase ####
>>
>> testData$raw <- tolower(testData$raw)
>>
>> #### Remove punctuation and any multiple spaces ####
>>
>> testData$raw <- gsub("[[:punct:]]", "", testData$raw)
>> testData$raw <- gsub(" +", " ", testData$raw)
>>
>> #### Select test row ####
>>
>> testRow <- testData[13,]
>> testRow
>>
>> #### Select terms +/- a specified number of words from "kras" ####
>>
>> Text <- unlist(strsplit(testRow$raw, " "))
>> Target <- grep("kras", Text)
>>
>> if (length(Target) == 0) {testRow$reduced <- ""} else{
>>
>> Length <- length(Text)
>> Keep <- rep(NA, Length)
>> Lower <- ifelse(Target - 6 > 0, Target - 6, 1)
>> Upper <- ifelse(Target + 6 < Length, Target + 6, Length)
>>
>> for(i in 1:length(Keep)){
>> for(j in 1:length(Lower)){
>>        Keep[i][i %in% seq(Lower[j], Upper[j])] <- i
>> }}
>>
>> testRow$reduced <- paste(Text[!is.na(Keep)], collapse=" ")
>>
>> }
>>
>> testRow
>>
>> length(Text)
>> length(Text[!is.na(Keep)])
>>
>> #### Function for selecting words within specified range of a target term ####
>>
>> nearTerms <- function(df, text, target, before, after, outvar){
>>
>>   Text <- with(df, strsplit(text, " "))
>>   Target <- grep(target, Text)
>>
>>   if (length(Target) == 0) {df$reduced <- ""} 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, outvar = paste(Text[!is.na(Keep)], collapse=" "))
>>
>>   }
>>
>> }
>>
>> nearTerms(testRow, raw, "kras", 6, 6)
>>
>> nearTerms(df = testRow, text = raw, target = "kras", before = 6, after = 6)
>>
>> ______________________________________________
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>> https://stat.ethz.ch/mailman/listinfo/r-help
>> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
>> and provide commented, minimal, self-contained, reproducible code.
>
>
>
> --

-- 
Sarah Goslee
http://www.functionaldiversity.org