Stefan:
Use the droplevels function...
dat <- read.table(textConnection("
  treat yield
1  cont  98.7
2  cont  97.2
3  cont  96.1
4  cont  98.1
5    10 103.0
6    10 101.3
7    10 102.1
8    10 101.9
9    30 121.1
10    30 123.1
11    30 119.7
12    30 118.9
13    60 109.9
14    60 110.1
15    60 113.1
16    60 112.3"),header=T)
dat
 plot(dat$treat,dat$yield)
 dat.sub <- subset(dat,treat!="cont");dat.sub
 dat.sub <- droplevels(dat.sub)    # drop unwanted levels
plot(dat.sub$treat,dat.sub$yield)

Felipe D. Carrillo
Supervisory Fishery Biologist
Department of the Interior
US Fish & Wildlife Service
California, USA
http://www.fws.gov/redbluff/rbdd_jsmp.aspx


From: "Schreiber, Stefan" <Stefan.Schreiber@ales.ualberta.ca>
>To: r-help@r-project.org
>Sent: Tuesday, November 1, 2011 2:28 PM
>Subject: [R] factor level issue after subsetting
>
>Dear list,
>
>I cannot figure out why, after sub-setting my data, that particular item
>which I don't want to plot is still in the newly created subset (please
>see example below). R somehow remembers what was in the original data
>set. A work around is exporting and importing the new subset. Then it's
>all fine; but I don't like this idea and was wondering what am I missing
>here?
>
>Thanks!
>Stefan
>
>P.S. I am using R 2.13.2 for Mac.
>
>> dat<-read.csv("~/MyFiles/data.csv")
>> class(dat$treat)
>[1] "factor"
>> dat
>  treat yield
>1  cont  98.7
>2  cont  97.2
>3  cont  96.1
>4  cont  98.1
>5    10 103.0
>6    10 101.3
>7    10 102.1
>8    10 101.9
>9    30 121.1
>10    30 123.1
>11    30 119.7
>12    30 118.9
>13    60 109.9
>14    60 110.1
>15    60 113.1
>16    60 112.3
>> plot(dat$treat,dat$yield)
>> dat.sub<-dat[which(dat$treat!='cont')]
>> class(dat.sub$treat)
>[1] "factor"
>> dat.sub
>  treat yield
>5    10 103.0
>6    10 101.3
>7    10 102.1
>8    10 101.9
>9    30 121.1
>10    30 123.1
>11    30 119.7
>12    30 118.9
>13    60 109.9
>14    60 110.1
>15    60 113.1
>16    60 112.3
>> plot(dat.sub$treat,dat.sub$yield)
>
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>
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>and provide commented, minimal, self-contained, reproducible code.
>
>
>
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