[R] summarizing replicates with multiple treatments

From: Levi Waldron <leviwaldron_at_gmail.com>
Date: Tue, 04 Mar 2008 17:24:54 -0500


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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