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]]
_______________________________________________
R-sig-phylo mailing list - [email protected]
https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
Searchable archive at http://www.mail-archive.com/[email protected]/
