[R] sapply following using by with a list of factors
Gabor Grothendieck
ggrothendieck at gmail.com
Mon May 30 05:42:12 CEST 2005
On 5/29/05, McClatchie, Sam (PIRSA-SARDI)
<mcclatchie.sam at saugov.sa.gov.au> wrote:
> Background:
> OS: Linux Mandrake 10.1
> release: R 2.0.0
> editor: GNU Emacs 21.3.2
> front-end: ESS 5.2.3
> ---------------------------------
> Colleagues
>
> I am having some trouble extracting results from the function by, used to
> average variables in a data.frame first by one factor (depth) and then by a
> second factor (station). The real data.frame is quite large
> > dim(data.2001)
> [1] 32049 11
>
> Here is a snippet of code:
>
> ## bin density data for each station into 1 m depth bins, containing means
> data.2001.test$integer.Depth <- as.factor(round(data.2001.test$Depth,
> digits=0))
> attach(data.2001.test)
> binned.data.2001 <- by(data.2001.test[,5:11], list(depth=integer.Depth,
> station=Station), mean)
>
> and here is a snippet of the data.frame
>
> > dim(data.2001.test)
> [1] 150 11
> > dump("data.2001.test", file=stdout())
> data.2001.test <-
> structure(list(Cruise = structure(as.integer(c(1, 1, 1, 1, 1,
Try the following. To keep this short lets just take a subset
of rows called dd. Also, we drop the Station levels
that are not being used since this test only uses 2 levels
and there are 288 Station levels in total. The function that we apply using
by returns a vector consisting of the integer.Depth, Station
and the column means of columns 5 to 10. (Asking for just the
mean of those, as in your example, would take all the numbers
in all the columns passed to mean and give back a grand mean
rather than a mean per column.) Finally we rbind it all back together.
> # data.2001.test is your data frame including the integer.Depth column
> dd <- data.2001.test[50:60,]
> dd$Station <- dd$Station[drop = TRUE]
> dd.bin <- by(dd, list(dd$integer.Depth, dd$Station), function(x)
+ c(integer.Depth = x$integer.Depth[1], Station = x$Station[1],
+ colMeans(x[,5:10])))
> do.call("rbind", dd.bin)
integer.Depth Station Depth Temperature.oC Salinity Fluoresence.Volts
[1,] 20 1 23.90167 17.67420 35.47650 1.107433
[2,] 21 1 24.75350 17.33355 35.59050 1.060400
[3,] 1 2 5.19000 19.61510 35.54870 0.726500
[4,] 2 2 5.82950 19.61305 35.55025 0.719200
[5,] 3 2 6.81250 19.61300 35.58345 0.741150
[6,] 4 2 7.55000 19.61180 35.60460 0.754600
Density.kg.m3 Brunt.Vaisala.Freq.cycl.h
[1,] 25.82400 -5.095467
[2,] 25.99820 16.030975
[3,] 25.30560 -6.261240
[4,] 25.31015 4.051561
[5,] 25.33985 8.893225
[6,] 25.35960 -8.167610
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