On Fri, 2007-04-27 at 12:58 +0100, Simon Pickett wrote:> Hi all,
>
> I have been using princomp() recently, its very useful indeed, but I have
> a question about how to specify the rows of data you want it to choose.
>
> I have a set of variables relating to bird characteristics and I have been
> using princomp to produce PC scores from these.
>
> However since I have multiple duplicate entries per individual (each bird
> had a varying number of chicks), I only want princomp to treat each
> individual bird as the sample and not include all the duplicates. Then I
> want to replicate the pc scores for all the duplicated rows for that
> individual.
>
> Any idea how to do this?
## example data using the vegan package
require(vegan)
data(varespec)
## duplicate some rows
vare2 <- varespec
vare2 <- rbind(vare2, varespec[sample(nrow(varespec), 50, replace TRUE), ])
## build the model using prcomp - it is better - on the original data
## without duplicates
mod <- prcomp(varespec, centre = TRUE, scale. = TRUE)
## predict for full matrix inc duplicated rows
pred <- predict(mod, vare2)
Takes 0.005 seconds on my machine. So get a subset of your data without
the duplicates, then use the predict method for prcomp.
See ?predict.prcomp.
Is that what you wanted?
G
>
> Up to now I have been using princomp to only select the entries which are
> not duplicated which is easy, but the difficult bit is the programming to
> duplicate the pc scores across the entries for each individual.
>
> (I developed something that worked but it takes about 5 minutes to run!)
>
> Thanks for all your help,
>
> very much appreciated,
>
> Simon.
>
>
>
>
> Simon Pickett
> PhD student
> Centre For Ecology and Conservation
> Tremough Campus
> University of Exeter in Cornwall
> TR109EZ
> Tel 01326371852
>
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> and provide commented, minimal, self-contained, reproducible code.
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Gavin Simpson [t] +44 (0)20 7679 0522
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