Re: [R] Looking for a sort of tapply() to data frames

From: Gabor Grothendieck <ggrothendieck_at_gmail.com>
Date: Sat 17 Dec 2005 - 03:51:37 EST

On 12/16/05, January Weiner <january@uni-muenster.de> wrote:
> Hi,
>
> On 12/15/05, Gabor Grothendieck <ggrothendieck@gmail.com> wrote:
> > You don't get them as a column but you get them as the
> > component labels.
> >
> > by(df, df$Day, function(x) colMeans(x[,-1]))
> >
> > If you convert it to a data frame you get them as the rownames:
> >
> > do.call("rbind", by(df, df$Day, function(x) colMeans(x[,-1])))
>
> Thanks! that helps a lot. But I still run into problems with this.
> Sorry for bothering you with newbie questions, if my problems are
> trivial, point me to a suitable guide (I did read the introductory
> materials on R).
>
> First: it works for colMeans, but it does not work for a function like this:
>
> do.call("rbind", by(df, df$Day, function(x) cor(df$val1, df$val2))

There are a number of problems:

  1. the function does not depend on x and therefore will return the same result for each day group.
  2. although ?by says it returns a list, it apparently simplifies the result, contrary to the documentation, in certain cases. Try this:

do.call("rbind", as.list(by(df, df$Day, function(x) cor(x$val1, x$val2))))

or this:

do.call("rbind", by(df, df$Day, function(x) list(cor = cor(x$val1, x$val2))))

3. In your sample data val1 is constant for Wed so you won't be able to get a correlation. That's the source of the warning that you get when running the line in #2.

>
> it says "Error in do.call(....) : second argument must be a list". I
> do not understand this, as the second argument is "b" of the class
> "by", as it was in the case of colMeans, so it did not change...?
>
> Second: in case of colMeans (where it works) it returns a matrix, and
> I have troubles getting it back to the data.frame, so I can access
> blah$Day. Instead, I have smth like that:

Try blah[,"Day"] which works with both matrices and data frames.

>
> > do.call("rbind",b)
> V2 V3 V4 V5 V7
> Tue 19 15 2 0 1.538462
> Wed 5 3 6 1 1.285714

Another possibility is to coerce it to a data frame:

as.data.frame(do.call("rbind", b))

or change your function to return a list.

>
> ...and I do not know how to acces, for example, values for "Tue",
> except with [1,] -- which is somewhat problematic. For example, I
> would like to display the 3 days for which V7 is highest. How can I
> do that?
>
> > I think you want class(df) which shows its a data frame.
>
> Ops. Sorry, I didn't guess it from the manual :-)
>
> > aggregate(df[,-1], df[,1,drop = FALSE], mean)
>
> But why is df[,1,drop=FALSE] a list? I don't get it...

Because df is a one column data frame and data frames are lists. Had we not specified drop, it would have automatically dropped it since it has only one dimension simplifying it to a non-list. We do not want that simplification here.

>
> > aggregate(df[,-1], list(Day = df$Day), mean)
>
> Yeah, I figured out that one.
>
> > Another alternative is to use summaryBy from the doBy package found
> > at http://genetics.agrsci.dk/~sorenh/misc/ :
> >
> > library(doBy)
> > summaryBy(cbind(var1, var2) ~ Day, data = df)
>
> I think I am not confident enough with the basic data types in R, I
> need to understand them before I go over to specialized packages :-)
> Again, thanks a lot,
> January
>
> --
> ------------ January Weiner 3 ---------------------+---------------
> Division of Bioinformatics, University of Muenster | Schloßplatz 4
> (+49)(251)8321634 | D48149 Münster
> http://www.uni-muenster.de/Biologie.Botanik/ebb/ | Germany
>
> ______________________________________________
> R-help@stat.math.ethz.ch mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
>



R-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html Received on Sat Dec 17 04:02:27 2005

This archive was generated by hypermail 2.1.8 : Fri 03 Mar 2006 - 03:41:39 EST