Re: [R] assistance with RDAtest beta version application

From: Guillaume Blanchet <gblanchet.list_at_gmail.com>
Date: Thu, 27 Mar 2008 14:17:55 -0600

Hi !!

Stanfield, Les (MNR) a écrit :
> Thank you so much for coming to my rescue!:
>
> OK I have been able to open it (but only in the R editor. I assumed that we had to generate our own files of XX.txt and YY.txt and bring them into R before the program could run.... Is this right?
>
>

Yon do not have to, but you can. I personally like to import the whole file I'm working (here "Table_11-3.txt") and go from there. If you feel more comfortable to do it another way there is no problem there !
> So I created two as tab delimited text files (Here they are). I am able to bring them into R and when I edit them, they look fine.
>
>

OK

> This is the code to this stage:
>
> rdaTest <- function(YY.mat, XX.mat, WW.mat=NULL,
> scale.Y=FALSE, testF=NULL, nperm=NULL, print.results=TRUE, print.cum=FALSE)
> {
> library(MASS)
>
> # Read the data tables. Transform them into matrices Y, X, and W
> YY.mat = -read.table("YY.txt")
> XX.mat = -read.table("XX.txt")
>
> Y.mat=as.matrix(YY.mat)
>
>> X.mat=as.matrix(XX.mat)
>>
> bb<-edit(y.mat)
> bb<-edit(x.mat)
>
>
> But when I try to then convert these two files to mat files, nothing happens? I'm assuming it has something to do with this step, but I can't figure it out. Note: I tried creating base yy.mat and xx.mat files, by just changing the file names, but that didn't work.....
>
> So is this the problem, When I look at the y.mat and x.mat they look no different than the original txt files
>
>
>

Here I get a bit confused

Here is what I propose:

### Load the whole file
tab11.3<-read.table("Table_11-3.txt",header=TRUE,row.names=1)

### Extract the species (Y) and the environmental variables (X) from tab11.3 Y<-tab11.3[,1:6]
X<-tab11.3[,7:10]

### Calculate the RDA
coco<-rdaTest(Y,X,testF=TRUE,nperm=999)
coco

### Draw the triplot
graph.rdaTest(coco,plot.type="F")

With these couple of lines you should get the same results as the ones presented in Legendre and Legendre (1998).

> Les Stanfield
>
>

Have a nice day !!

Guillaume Blanchet



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