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 (d...@biomserv.univ-lyon1.fr )
Laboratoire BBE-CNRS-UMR-5558, Univ. C. Bernard - Lyon I
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
