Hi Emmanuel,
Thanks for your answer. So that means I can still use that Lambda estimated
value, I suppose. In the case of Lambda>1, it then means that species are
more similar than expected, right?
Best regards,
Sérgio.
2015-07-17 15:57 GMT+01:00 Emmanuel Paradis <emmanuel.para...@ird.fr>:
> Hi Sérgio,
>
> In phytools, lambda is constrained to be positive, not in ape. A negative
> value of lambda is the consequence of closely related species being more
> dissimilar than expected under phylogenetic dependence (lambda = 1) or
> under independence (lambda = 0). This can be interpreted biologically as
> close species diverging into distinct niches and/or phenotypes.
>
> Best,
>
> Emmanuel
>
>
> Le 16/07/2015 20:34, Sergio Ferreira Cardoso a écrit :
>
>> Hello all,
>>
>> I'm trying to estimate a lambda for my phylogeny but something strange
>> happened. I used 3 different packages to confirm the estimated lambda
>> value. My tree is ultrametric (with branchlengths in million years), it
>> has
>> 59 tips and 58 internal nodes. Here is what I did:
>>
>> df<-data.frame(y,x)
>>> df$Species<-rownames(df)
>>> tree<-read.nexus("TTOL_tree.nex")
>>> vf<-diag(vcv(tree))
>>> phyl.resid(tree,x,y,method="lambda")
>>>
>>
>> ## phytools lambda = 0.741795
>>
>> fit<-gls(y~x, correlation = corPagel(value=1,phy=tree,fixed=FALSE), data
>>>
>> = df, method="ML",weights=varFixed(~vf))
>>
>> ## ape & nlme lambda = -0.6863758
>>
>> fit<-pgls(y~x,comparative.data(tree,df,"Species"), lambda="ML")
>>>
>>
>> ## caper lambda = 0.742
>>
>>
>> Does anyone know why ape's gls estimates a value as different as that?
>> Lambda varies between 0 and 1. Is there any other way to estimate Lambda
>> (just to make another check). This is not the first time Lambda
>> estimations
>> of my trees deliver values as strange as this one...
>>
>> Cheers,
>> 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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