R help - Feb 2009 - subset problem (reducing from six to two levels)

Hi all,
I have got a seemingly simple problem (I am an R starter) with subsetting my
data set, but cannot figure out the solution: I want to subset a data set
from six to two levels, so that all analyses are done only with these two
remaining levels.
I tried

TOTAL<-read.delim('total.csv',header=T)
SUBSET.OF.TOTAL<-subset(TOTAL, FactorX %in%
c("Level1","Level2"))
attach(SUBSET.OF.TOTAL)

but R does not eliminate the remaining levels of FactorX, just assigns 'not
available' to the data. Like this, the other levels still show up in plots
etc., but without data entries. Anybody got a solution how to subset the
data so that I eliminate the other levels completely?

Thanks a lot for the help,

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On Thu, Feb 05, 2009 at 01:01:59PM -0800, Ine wrote:
> 
> Hi all,
> I have got a seemingly simple problem (I am an R starter) with subsetting
my
> data set, but cannot figure out the solution: I want to subset a data set
> from six to two levels, so that all analyses are done only with these two
> remaining levels.
> I tried
> 
> TOTAL<-read.delim('total.csv',header=T)
> SUBSET.OF.TOTAL<-subset(TOTAL, FactorX %in%
c("Level1","Level2"))
> attach(SUBSET.OF.TOTAL)
> 
> but R does not eliminate the remaining levels of FactorX,
One solution is to have the factors re-built after subsetting:

foo = factor(c('a','a','b','c','c'))

# unused levels persistent:
> foo[foo=='a']
[1] a a
Levels: a b c

# but:
> factor(foo[foo=='a'])
[1] a a
Levels: a

cu
	Philipp


-- 
Dr. Philipp Pagel
Lehrstuhl f?r Genomorientierte Bioinformatik
Technische Universit?t M?nchen
Wissenschaftszentrum Weihenstephan
85350 Freising, Germany
http://mips.gsf.de/staff/pagel

Hi,

does this help?

http://www.nabble.com/factor-question-to18638814.html#a18638814

HTH,
Stephan


Ine schrieb:
> Hi all,
> I have got a seemingly simple problem (I am an R starter) with subsetting
my
> data set, but cannot figure out the solution: I want to subset a data set
> from six to two levels, so that all analyses are done only with these two
> remaining levels.
> I tried
> 
> TOTAL<-read.delim('total.csv',header=T)
> SUBSET.OF.TOTAL<-subset(TOTAL, FactorX %in%
c("Level1","Level2"))
> attach(SUBSET.OF.TOTAL)
> 
> but R does not eliminate the remaining levels of FactorX, just assigns
'not
> available' to the data. Like this, the other levels still show up in
plots
> etc., but without data entries. Anybody got a solution how to subset the
> data so that I eliminate the other levels completely?
> 
> Thanks a lot for the help,
>

Ine wrote:
> Hi all,
> I have got a seemingly simple problem (I am an R starter) with subsetting
my
> data set, but cannot figure out the solution: I want to subset a data set
> from six to two levels, so that all analyses are done only with these two
> remaining levels.
> I tried
> 
> TOTAL<-read.delim('total.csv',header=T)
> SUBSET.OF.TOTAL<-subset(TOTAL, FactorX %in%
c("Level1","Level2"))
> attach(SUBSET.OF.TOTAL)
> 
> but R does not eliminate the remaining levels of FactorX, just assigns
'not
> available' to the data. Like this, the other levels still show up in
plots
> etc., but without data entries. Anybody got a solution how to subset the
> data so that I eliminate the other levels completely?
> 
> Thanks a lot for the help,
> 
R does not "assign 'not available'" (look at the subsetted
data).

However, factors do not lose levels just because they are not present in 
a subset of data. There are good reasons for that, but let's not go 
there this time (look in the list archives if you care). To get rid of 
unwanted levels, use

FactorXX <- factor(FactorX, levels=c("Level1","Level2"))

or just factor(FactorX) if you know that both levels are present (or 
don't care).


-- 
    O__  ---- Peter Dalgaard             ?ster Farimagsgade 5, Entr.B
   c/ /'_ --- Dept. of Biostatistics     PO Box 2099, 1014 Cph. K
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