R help - Jan 2015 - Re-order levels of a categorical (factor) variable

Hi,
I have a fairly elementary problem that I am unable to figure out.  I have a
continuous variable, Y, repeatedly measured at multiple times, T.  The variable
T is however is coded as a factor variable having these levels:
c("Presurgery", "Day 30", "Day 60",  "Day
180", "Day 365").
When I plot the boxplot, e.g., boxplot(Y ~ T), it displays the boxes in this
order:  c("Day 180", "Day 30", "Day 365",
"Day 60",  "Presurgery").
Is there a way to control the order of the boxes such that they are plotted in a
particular order that I want, for example:  c("Presurgery", "Day
30", "Day 60",  "Day 180", "Day 365")?

More generally, is there a simple way to redefine the ordering of the
categorical variable such that this ordering will be used in whatever operation
is done?  I looked at relevel, reorder, etc., but they did not seem to be
applicable to my problem.

Thanks for any help.

Best,
Ravi


	[[alternative HTML version deleted]]

Are you sure the factors of T are in the order you think they are?  (Are you
sure you are using the expected version of T.)   Use print(levels(T)) to
make
sure.

I tried
   timeCats <- c("Presurgery", "Day 30", "Day
60",  "Day 180", "Day 365")
   d <- data.frame(T = factor(rep(timeCats, 11:15), levels=timeCats),
      Y=seq_len(sum(11:15)))
   boxplot(Y ~ T, data=d)
and the boxes and labels are in the order given in 'timeCats'.




Bill Dunlap
TIBCO Software
wdunlap tibco.com

On Wed, Jan 21, 2015 at 2:37 PM, Ravi Varadhan <ravi.varadhan at jhu.edu>
wrote:
> Hi,
> I have a fairly elementary problem that I am unable to figure out.  I have
> a continuous variable, Y, repeatedly measured at multiple times, T.  The
> variable T is however is coded as a factor variable having these levels:
> c("Presurgery", "Day 30", "Day 60", 
"Day 180", "Day 365").
> When I plot the boxplot, e.g., boxplot(Y ~ T), it displays the boxes in
> this order:  c("Day 180", "Day 30", "Day
365", "Day 60",  "Presurgery").
> Is there a way to control the order of the boxes such that they are
> plotted in a particular order that I want, for example: 
c("Presurgery",
> "Day 30", "Day 60",  "Day 180", "Day
365")?
>
> More generally, is there a simple way to redefine the ordering of the
> categorical variable such that this ordering will be used in whatever
> operation is done?  I looked at relevel, reorder, etc., but they did not
> seem to be applicable to my problem.
>
> Thanks for any help.
>
> Best,
> Ravi
>
>
>         [[alternative HTML version deleted]]
>
> ______________________________________________
> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
> 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.
>
	[[alternative HTML version deleted]]

Bill/Ravi:

I believe the problem is that the factor is automatically created when
a data frame is created by read.table(). By default, the levels are
lexicographically ordered. The following reproduces the problem and
gives a solution.
>library(lattice)
> z <- data.frame(y = 1:9, x = rep(c("pre",
"day2","day10")))
> xyplot(y~x,data=z) ## x axis order is day 10, day2, pre
> levels(z$x)
[1] "day10" "day2"  "pre"
> z$x <- factor(as.character(z$x),levels=c(levels(z$x)[3:1])) ##
explicitly defines level order
> xyplot(y~x,data=z) ##  desired plot
Cheers,
Bert


Bert Gunter
Genentech Nonclinical Biostatistics
(650) 467-7374

"Data is not information. Information is not knowledge. And knowledge
is certainly not wisdom."
Clifford Stoll




On Wed, Jan 21, 2015 at 4:36 PM, William Dunlap <wdunlap at tibco.com>
wrote:
> Are you sure the factors of T are in the order you think they are?  (Are
you
> sure you are using the expected version of T.)   Use print(levels(T)) to
> make
> sure.
>
> I tried
>    timeCats <- c("Presurgery", "Day 30", "Day
60",  "Day 180", "Day 365")
>    d <- data.frame(T = factor(rep(timeCats, 11:15), levels=timeCats),
>       Y=seq_len(sum(11:15)))
>    boxplot(Y ~ T, data=d)
> and the boxes and labels are in the order given in 'timeCats'.
>
>
>
>
> Bill Dunlap
> TIBCO Software
> wdunlap tibco.com
>
> On Wed, Jan 21, 2015 at 2:37 PM, Ravi Varadhan <ravi.varadhan at
jhu.edu>
> wrote:
>
>> Hi,
>> I have a fairly elementary problem that I am unable to figure out.  I
have
>> a continuous variable, Y, repeatedly measured at multiple times, T. 
The
>> variable T is however is coded as a factor variable having these
levels:
>> c("Presurgery", "Day 30", "Day 60", 
"Day 180", "Day 365").
>> When I plot the boxplot, e.g., boxplot(Y ~ T), it displays the boxes in
>> this order:  c("Day 180", "Day 30", "Day
365", "Day 60",  "Presurgery").
>> Is there a way to control the order of the boxes such that they are
>> plotted in a particular order that I want, for example: 
c("Presurgery",
>> "Day 30", "Day 60",  "Day 180", "Day
365")?
>>
>> More generally, is there a simple way to redefine the ordering of the
>> categorical variable such that this ordering will be used in whatever
>> operation is done?  I looked at relevel, reorder, etc., but they did
not
>> seem to be applicable to my problem.
>>
>> Thanks for any help.
>>
>> Best,
>> Ravi
>>
>>
>>         [[alternative HTML version deleted]]
>>
>> ______________________________________________
>> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
>> 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.
>>
>
>         [[alternative HTML version deleted]]
>
> ______________________________________________
> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
> 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.