Dear all,
I'm trying to perform a PGLS with arbitrary branch lengths (I used branch
lengths = 1). The tree is non-ultrametric. Here is a result with Pagel's
Lambda:
vf<-diag(vcv(tree))
fit<-gls(FCLrelative~LogBodymass,correlation=Pagel,data=DF,method="ML",weights=varFixed(-vf))
summary(fit)
Model: FCLrelative ~ LogBodymass
Data: DF
AIC BIC logLik
42.28777 49.77257 -17.14388
Correlation Structure: corPagel
Formula: ~1
Parameter estimate(s):
lambda
1.039835
Variance function:
Structure: fixed weights
Formula: ~vf
Coefficients:
Value Std.Error t-value
p-value
(Intercept) -0.17662926 0.26166738 -0.6750144
0.5030
LogBodymass 0.05865737 0.05766171 1.0172672 0.3143
Correlation:
(Intr)
LogBodymass -0.651
Standardized residuals:
Min Q1 Med Q3 Max
-2.36346640 -0.21848447 0.08326376 0.46156642 1.15440168
Residual standard error: 0.2388999
Degrees of freedom: 48 total; 46 residual
As you see my lambda is >1, what shouldn't happen. Is this normal when we
set all branch lengths to an arbitrary value?
Thank you very much in advance.
Best regards,
Sérgio.
--
Com os melhores cumprimentos,
Sérgio Ferreira Cardoso.
--------------------
Best regards,
Sérgio Ferreira Cardoso
MSc. Paleontology candidate
Departamento de Ciências da Terra - FCT /Universidade Nova de Lisboa
Geociências - Universidade de Évora
Lisboa, Portugal
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