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

Gabor Grothendieck ggrothendieck at gmail.com
Fri Dec 16 17:51:37 CET 2005

On 12/16/05, January Weiner <january at uni-muenster.de> wrote:
> Hi,
> On 12/15/05, Gabor Grothendieck <ggrothendieck at 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  |  Schloßplatz 4
> (+49)(251)8321634                                   |  D48149 Münster
> http://www.uni-muenster.de/Biologie.Botanik/ebb/    |  Germany
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