[R] ade4 and inertia of axis 2

[Stéphane Dray]

Dear John,

In RLQ (similarly to other methods in ade4), inertia are given by 
eigenvalues. Thus, the percentage of inertia are obtained simply by:

rlq1$eig/sum(rlq1$eig)*100

For more details on outputs or RLQ, you can have a look at 
http://listes.univ-lyon1.fr/wws/arc/adelist/2009-03/msg00001.html

Lastly, if you have questions about ade4, please subscribe and send an 
email to adelist (http://listes.univ-lyon1.fr/wws/info/adelist)

Cheers.


John Poulsen wrote:
>
> Hello,
>
> Could someone please tell me how to find the estimate of inertia for 
> the second axis of an RLQ analysis using ade4? Using the example from 
> the ade4 package, I *suspect* that the inertia for the 2nd axis of the 
> R table would be 4.139332 (see below results summary from rlq1).  
> However, the row is labeled "12" not "2" which suggests this is not 
> correct.  In addition, this would mean that axis 2 of the RLQ would 
> explain more than 100% of the inertia of the separate ordination for 
> dudimil ((100*4.139)/dudimil$eig[2]=176%) which I believe is not 
> supposed to occur.
>
> Could anyone set me straight by either letting me know how to get the 
> inertia for axis 2 or that my thinking is perhaps wrong?
>
> Thanks,
> John
>
> data(aviurba)
>  coa1 <- dudi.coa(aviurba$fau, scannf = FALSE, nf = 2)
>  dudimil <- dudi.hillsmith(aviurba$mil, scannf = FALSE, nf = 2, row.w 
> = coa1$lw)
>  duditrait <- dudi.hillsmith(aviurba$traits, scannf = FALSE, nf = 2, 
> row.w = coa1$cw)
>  rlq1 <- rlq(dudimil, coa1, duditrait, scannf = FALSE, nf = 2)
>  plot(rlq1)
>  summary(rlq1)
>  randtest.rlq(rlq1)
>
>>    summary(rlq1)
>
> Eigenvalues decomposition:
>       eig     covar      sdR      sdQ      corr
> 1 0.4782826 0.6915798 1.558312 1.158357 0.3831293
> 2 0.1418508 0.3766308 1.308050 1.219367 0.2361331
>
> Inertia & coinertia R:
>   inertia      max     ratio
> 1  2.428337 2.996911 0.8102800
> 12 4.139332 5.345110 0.7744148
>
> Inertia & coinertia Q:
>   inertia      max     ratio
> 1  1.341791 2.603139 0.5154512
> 12 2.828648 4.202981 0.6730098
>
> Correlation L:
>      corr       max     ratio
> 1 0.3831293 0.6435487 0.5953384
> 2 0.2361331 0.5220054 0.4523576
>
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>
>

-- 
Stéphane DRAY (dray at biomserv.univ-lyon1.fr )
Laboratoire BBE-CNRS-UMR-5558, Univ. C. Bernard - Lyon I
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