how to get the group mean deviation data ? - R-help

ronggui

Mon, Jul 25, 2005 1:32 AM #

Yeah,I meant n=10000,but i just missed a zero.

If n=10000,t=3,it take about 3 seconds.
If n=2000,t=7,it takes about 10 seconds.
I want to write a function to fit a model,and the data maybe quite large (maybe n<=20000,t<=10).When n and t become larger and larger,the time will be much longer. It is of course reasonable.But I think there should be much pretty code to do this job,so I post here.

What I really want to konw is how to optimize the code for this purpose.Of course, I can still fit my model even I use this code.and I still like R much as it's free ,flexibile and powerfull.

I want to deal with the case with different number of replications for each cell too.

I would use this as a n x 3 x t array (a 
simple call to dim and aperem).  Then rowMeans will find the group means, 
and you can just subtract those to get the deviations from the means, 
making use of recycling.

E.g.

D <- d[,-1]
dim(D) <- c(t,n,3)
D <- aperm(D, c(2,3,1))
gmeans <- rowMeans(D, dims=2)
d[,-1] - rep(gmeans, each=3)

That takes under 10ms for n=1000


On Mon, 25 Jul 2005, ronggui wrote:

n=10;t=3
d<-cbind(id=rep(1:n,each=t),y=rnorm(n*t),x=rnorm(n*t),z=rnorm(n*t))
head(d)

    id          y           x          z
[1,]  1 -2.1725379  0.07629954 -0.3985258
[2,]  1 -1.2383038 -2.49667038  0.6966127
[3,]  1 -1.2642401 -0.50613307  0.4895856
[4,]  2  0.2171246  0.86711864 -0.6660036
[5,]  2  2.2765760 -0.48547142 -1.4496664
[6,]  2  0.5985345 -1.06427035  2.1761071

first,i want to get the group mean of each variable,which i can use

d<-data.frame(d)
aggregate(d,list(d$id),mean)[,-1]

  id           y          x           z
1   1 -1.55836060 -0.9755013  0.26255754
2   2  1.03074502 -0.2275410  0.02014565
3   3  0.20700121 -0.7159450  1.35890176
4   4  0.17839650  1.2575891  0.04135165
5   5 -0.20012508  0.4310221  0.55458899
6   6 -0.13084185 -0.2953392  0.28229068
7   7  0.20737288 -0.8863761 -0.50793880
8   8  0.07512612 -0.6591304 -0.21656533
9   9  0.94727796 -0.6108891  0.13529884
10 10 -0.04434875  0.1332086 -0.88229808

then i want the  group mean deviation data,like

head(sapply(d[,2:4],function(x) x-ave(x,d$id)))

             y          x          z
[1,] -0.6141773  1.0518008 -0.6610833
[2,]  0.3200568 -1.5211691  0.4340552
[3,]  0.2941205  0.4693682  0.2270281
[4,] -0.8136205  1.0946597 -0.6861493
[5,]  1.2458310 -0.2579304 -1.4698121
[6,] -0.4322105 -0.8367293  2.1559614

both above are what i want.though i can do it use the function  to do it.but if n id quite large,say n=1000 and t=3, it require too much time.so i want to know any more efficient way to do it?

myfun<-function(x,id)
{
x<-as.matrix(x)
id<-as.factor(id)
xm<- apply(x,2,function(y,z) tapply(y,z, mean), z=id)
xdm<- x[] <- x-xm[id,]
re<-list(xm=xm, xdm=xdm)
re
}

-- 
Brian D. Ripley,                  ripley at stats.ox.ac.uk
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel:  +44 1865 272861 (self)
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