R help - Aug 2009 - inserting into data frame gives "invalid factor level, NAs generated"

I am calculating some values that I am inserting into a data frame. From
what I have read, creating the dataframe ahead of time is more efficient,
since rbind (so far the only solution I have found to appending to a data
frame) is not very fast.

What I am doing is the following:

# create data frame

goframe = data.frame(goA = character(10), goB = character(10), value
numeric(10))
goframe[1,] = c("AA", "BB", 0.4)

Result is:
> goframe[1,] = c("AA", "BB", 0.4)
Warning messages:
1: In `[<-.factor`(`*tmp*`, iseq, value = "AA") :
  invalid factor level, NAs generated
2: In `[<-.factor`(`*tmp*`, iseq, value = "BB") :
  invalid factor level, NAs generated
>
Is there another/better/more recomended way of doing this? If not, how do
I do this without getting all the warnings?

Thanks!

Best,

Karin Lagesen

Your running into the pretty common factor vs character problem in R.
By default data.frame turns character vectors into factor (sort of
like ENUM in mysql) vectors. Since you only have 1 factor (empty
string '') in your starting dataframe, when you go to insert new data
R sees a new value and complains. You'd probably be pretty safe using
character columns instead of factors for now (by adding
stringsAsFactors=FALSE to data.frame()) e.g.:

goframe<-data.frame(goA = character(10), goB = character(10), value
=numeric(10),stringsAsFactors=FALSE)

Scott

Scott Sherrill-Mix
Department of Microbiology
University of Pennsylvania
402B Johnson Pavilion
3610 Hamilton Walk
Philadelphia, PA  19104-6076



On Wed, Aug 12, 2009 at 11:49 AM, <karinlag at ifi.uio.no>
wrote:
> I am calculating some values that I am inserting into a data frame. From
> what I have read, creating the dataframe ahead of time is more efficient,
> since rbind (so far the only solution I have found to appending to a data
> frame) is not very fast.
>
> What I am doing is the following:
>
> # create data frame
>
> goframe = data.frame(goA = character(10), goB = character(10), value >
numeric(10))
> goframe[1,] = c("AA", "BB", 0.4)
>
> Result is:
>
>> goframe[1,] = c("AA", "BB", 0.4)
> Warning messages:
> 1: In `[<-.factor`(`*tmp*`, iseq, value = "AA") :
> ?invalid factor level, NAs generated
> 2: In `[<-.factor`(`*tmp*`, iseq, value = "BB") :
> ?invalid factor level, NAs generated
>>
>
> Is there another/better/more recomended way of doing this? If not, how do
> I do this without getting all the warnings?
>
> Thanks!
>
> Best,
>
> Karin Lagesen
>
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