Hi Chris,
It is not clear from your message where the error occurred. Can you please send
a reproducible example? I don't think the last model fit (output named 'OLS')
gives an error since gls() with no correlation structure is equivalent to using
lm().
Also if you use fixed=1 this is the same thing than fixed=TRUE, not value=1
(supposing this is what you want to do) altough this is likely to not make a
difference here.
Best,
Emmanuel
----- Le 16 Déc 20, à 0:42, chris pestana pestanach...@gmail.com a écrit :
> Hi when I execute the code below I get the following message:
>
> Error in corFactor.corStruct(object) :
> NA/NaN/Inf in foreign function call (arg 1)In addition: Warning
> message:In Initialize.corPhyl(X[[i]], ...) : No covariate specified,
> species will be taken as ordered in the data frame. To avoid this
> message, specify a covariate containing the species names with the
> 'form' argument.
>
>
> If I used fixed=1, it resolves the problem, but wouldn't this impact my
> model selection structure as lambda is not permitted to vary?
>
>
> hominin_char<-read.csv("dropped-tips.csv", header=T, row.names=1)
> hominin_char
> tree1<-drop.tip(tree1, tip = c("African_H_erectus_DAN5_P1", "K_platyops"))
> #########################################
>
> ############
>
> plot(tree1)
> ########### This is a method for selecting a scalable model for
> encephalization
> BM<-gls(log(Brain_mass)~log(Body_mass),
> data=hominin_char,correlation=corBrownian(1,phy=tree1),
> method="ML")
>
> OU<-gls(log(Brain_mass)~log(Body_mass), data=hominin_char,
> correlation=corMartins(1, phy=tree1), method="ML")
>
> Lambda<-gls(log(Brain_mass)~log(Body_mass),
> data=hominin_char, correlation=corPagel(1, phy=tree1),
> method="ML")
>
> EB<-gls(log(Brain_mass)~log(Body_mass), data=hominin_char,
> correlation=corBlomberg(1, phy=tree1, fixed=TRUE),
> method="ML")
>
> OLS<-gls(log(Brain_mass)~log(Body_mass), data=hominin_char, method="ML")
>
> summary(Lambda)
> Cand.models = list()
> Cand.models[[1]] = BM
> Cand.models[[2]] = OU
> Cand.models[[3]] = Lambda
> Cand.models[[4]] = EB
> Cand.models[[5]] = OLS
>
> Modnames = paste(c("BM","OU", "Lambda", "EB", "OLS"), sep = " ")
> aictab(cand.set = Cand.models, modnames = Modnames, sort = T)
>
> [[alternative HTML version deleted]]
>
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