[R-sig-eco] PCA as a predictive model

[Jari Oksanen]

Marc,

Basic R stats functions like prcomp have a predict method that can be used to "predict" (calculate) scores with 'newdata'. This is standard, and has been in R for ever. Most textbooks of multivariate analysis should handle this issue. 

In community ecological context, see functions predict.cca and predict.rda in vegan. These take argument 'newdata' which can be new community data -- depending on what you want to predict (argument 'type'). Function calibrate.cca documented in the same help page can be used to predict values of constraining variables in constrained ordination (CCA, RDA) from community composition, also with 'newdata' communities.

Cheers, Jari Oksanen

________________________________________
From: r-sig-ecology-bounces at r-project.org [r-sig-ecology-bounces at r-project.org] on behalf of Marc Taylor [marchtaylor at gmail.com]
Sent: 23 May 2012 10:19
To: r-sig-ecology at r-project.org
Subject: [R-sig-eco] PCA as a predictive model

Hello R-sig-ecology group,

I was wondering if anyone is aware of an example where PCA is used as a
predictive model? A community analysis example might be to predict the PC
values of a sample given its community composition. I had thrown this
question up on a statistics forum (
http://stats.stackexchange.com/questions/28916/can-empirical-orthogonal-function-eof-analysis-be-used-as-a-predictive-model)
but have gotten hardly any response. I imagined that there are some folks
here that would have some insight into this problem.

Many thanks,
Marc

        [[alternative HTML version deleted]]

_______________________________________________
R-sig-ecology mailing list
R-sig-ecology at r-project.org
https://stat.ethz.ch/mailman/listinfo/r-sig-ecology