[R] cca in ade4

[Gavin Simpson]

On Sat, 2010-07-17 at 13:31 +0800, elaine kuo wrote:
> Dear List,
> 
> I used spec and envi for cca in ade4. (both are data.frame)
> 
> However, there is a message telling that
> error in if (nf > rank) nf <- rank R
> missing value in  TRUE/FALSE
> 
> Please kindly help how to modify the code below.
> Thank you.

We can't possibly diagnose the problem as we don't have spec or envi.

If this is anything like the same data used in the vegan:::cca question
posted earlier, then you have samples with no species data recorded.
Drop those and fit the model again and see if you get any further.

HTH

G

> 
> Elaine
> 
> 
> code
> rm(list=ls())
> spec <-read.csv("c:/migration/M_R_20100718_winterM_spec_vegan.csv",header=T,
> row.names=1)
> dim(spec)
> spec[1,]
> 
> envi <-read.csv("c:/migration/M_R_20100718_winterM_envi_vegan.csv",header=T,
> row.names=1)
> dim(envi)
> envi[1,]
> 
> library(ade4)
> 
> w.cca  <-  cca(spec, envi, scan=TRUE)
> 
> 	[[alternative HTML version deleted]]
> 
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