[R] ade4 and inertia of axis 2
John Poulsen
jpoulsen at zoo.ufl.edu
Sun May 10 17:00:44 CEST 2009
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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