[R] summarizing replicates with multiple treatments

[Gabor Grothendieck]

Try this:

library(doBy)
summaryBy(. ~ day + treat, exampledata, FUN = c(mean, sd))


On Tue, Mar 4, 2008 at 5:24 PM, Levi Waldron <leviwaldron at gmail.com> wrote:
> I have a dataframe with several different treatment variables, and
> would like to calculate the mean and standard deviation of the
> replicates for each day and treatment variable.  It seems like it
> should be easy, but I've only managed to do it for one treatment at a
> time using subset and tapply.  Here is an example dataset:
>
> > `exampledata` <-
> structure(list(day = c(1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L,
> 2L, 2L, 3L, 3L, 3L, 3L, 3L, 3L), treat = structure(c(1L, 1L,
> 1L, 2L, 2L, 2L, 1L, 1L, 1L, 2L, 2L, 2L, 1L, 1L, 1L, 2L, 2L, 2L
> ), .Label = c("a", "b"), class = "factor"), replicate = c(1L,
> 2L, 3L, 1L, 2L, 3L, 1L, 2L, 3L, 1L, 2L, 3L, 1L, 2L, 3L, 1L, 2L,
> 3L), height = c(1.1, 1.2, 1.3, 1.4, 1.5, 1.6, 2.1, 2.2, 2.3,
> 2.4, 2.5, 2.6, 3.1, 3.2, 3.3, 3.4, 3.5, 3.6), weight = c(11.1,
> 11.2, 11.3, 11.4, 11.5, 11.6, 12.1, 12.2, 12.3, 12.4, 12.5, 12.6,
> 13.1, 13.2, 13.3, 13.4, 13.5, 13.6)), .Names = c("day", "treat",
> "replicate", "height", "weight"), class = "data.frame", row.names = c(NA,
> -18L))
>
> > exampledata
>   day treat replicate height weight
> 1    1     a         1    1.1   11.1
> 2    1     a         2    1.2   11.2
> 3    1     a         3    1.3   11.3
> 4    1     b         1    1.4   11.4
> 5    1     b         2    1.5   11.5
> 6    1     b         3    1.6   11.6
> 7    2     a         1    2.1   12.1
> 8    2     a         2    2.2   12.2
> 9    2     a         3    2.3   12.3
> 10   2     b         1    2.4   12.4
> 11   2     b         2    2.5   12.5
> 12   2     b         3    2.6   12.6
> 13   3     a         1    3.1   13.1
> 14   3     a         2    3.2   13.2
> 15   3     a         3    3.3   13.3
> 16   3     b         1    3.4   13.4
> 17   3     b         2    3.5   13.5
> 18   3     b         3    3.6   13.6
>
> I would like to combine the replicates and get a dataframe like:
>
> day     treat   height.mean     height.sd       weight.mean     weight.sd
> 1       a       1.2     0.1     11.2    0.1
> 1       b       1.5     0.1     11.5    0.1
> 2       a       2.2     0.1     12.2    0.1
> 2       b       2.5     0.1     12.5    0.1
> 3       a       3.2     0.1     13.2    0.1
> 3       b       3.5     0.1     13.5    0.1
>
> or two dataframes, one with means and the other with standard deviations.
>
> Thus far I have been doing it a piece at a time, like below (extra
> verbose since tapply doesn't accept the data= argument!), but would
> like to do it for all the measurement columns and all the treatments
> in one go.  Thanks!
>
> > tapply(exampledata[exampledata$treat=="a",]$height,exampledata[exampledata$treat=="a",]$day,mean)
>  1   2   3
> 1.2 2.2 3.2
> >
>
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