[R-sig-eco] mvabund: difference between 'glm1path' and 'manyglm'

[Joanne Potts]

<r-sig-ecology using r-project.org>Hi David and list,

Can someone please help me understand why, when changing the
'method=manyglm' argument to 'method=glm1path' under default settings
(negative binomial) the estimates of theta change in the 'trait.glm'
function?

I have provided example code below us the antTraits data set. And you
should see the plots for ft and ft3 are similar, yet ft2 is quite
different, so I think I am missing something (no doubt, probably very
obvious!).

Advice appreciated, thank you.

Jo



data(antTraits)

ft=traitglm(antTraits$abund,antTraits$env,antTraits$traits,method="manyglm")
ft$phi
ft$theta
qqnorm(residuals(ft)); abline(c(0,1),col="red")

ft2=traitglm(antTraits$abund,antTraits$env,antTraits$traits,method="glm1path")
mean(ft2$phis)
qqnorm(residuals(ft2)); abline(c(0,1),col="red")


ft3=traitglm(antTraits$abund,antTraits$env,antTraits$traits,method="glm1path",
negative.binomial(theta=1.641763))
1/mean(ft3$phis)
qqnorm(residuals(ft3)); abline(c(0,1),col="red")


-- 

Kind regards,

Joanne Potts


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