Hello, I am currently trying to run make.simmap in Phytools ver 0.6-60 and
Geiger ver 2.0.6, I am running the function on a subsample of 500 trees from
the posterior distribution. I have included the full code, but there error I
get is found in the last line of code
simtrees<-list(500)
YY<-list(500)
for (i in 1:500){
simtrees[[i]]<-make.simmap(CrenuchidTreesLadderized[[i]], habitattrait,
model="ER", nsim=1000)
YY[[i]]<- describe.simmap(simtree[[i]], plot=F)
}
ERROR = Error in UseMethod("isSymmetric") :
no applicable method for 'isSymmetric' applied to an object of class
"c('double', 'numeric')"
Any help would be greatly appreciated, full code below:
require(phytools)
require(geiger)
habitat<-read.csv("C:/Users/XXX/Dropbox/Crenuchid R Files/Crenuchid R
Files/Crenuchid_2state_BvsP.csv", row.names=1)
habitat[habitat==0] <- "Pelagic"
habitat[habitat==1] <- "Benthic"
habitat_color <- habitat
habitat_color[habitat=="Benthic"] <- "#6EA0FF" ### blue
habitat_color[habitat=="Pelagic"] <- "#FFB322" ### Orange
############################# simmap multiple trees
################################################.
alltrees<-read.nexus("posteriorsamples.tre.trprobs") #reading trees from
posteior distribution
wib <- name.check(phy=alltrees[[1]], data=habitat)
wib ## will show what is in tree not data, data not tree
# ??name.check
# Now to drop tips
length(alltrees)
prunedpostsamp<-list(500)
for (i in 1:500){
prunedpostsamp[[i]]<-drop.tip(alltrees[[i]], wib$tree_not_data)
}
wib <- name.check(phy=prunedpostsamp[[1]], data=habitat)
prunedpostsamp[[1]]$tip.label
#Let's ladderize all trees in the distribution with lapply() and plot the
first tree again
CrenuchidTreesLadderized <- lapply(prunedpostsamp, ladderize)
plot(CrenuchidTreesLadderized[[1]], cex=0.4) #Plot the first ladderized tree
#However, does the order of tips in the plot match the order of tiplabels in
the tree object? #### NO help? is this the issue ???
#Please
compare######################################################################################
CrenuchidTreesLadderized[[1]]$tip.label
habitattrait<-habitat[CrenuchidTreesLadderized[[1]]$tip.label,]
names(habitattrait)<- CrenuchidTreesLadderized[[1]]$tip.label
length(habitattrait) ## 54
class(habitattrait) ## character
#Compare tree with data
compare <- treedata(CrenuchidTreesLadderized[[1]], habitattrait, sort=TRUE) #R
will inform you of any inconsistencies and how they were solved!
?treedata
####### SIMMAP for multiple trees this can take a while while while ########
simtrees<-list(500)
YY<-list(500)
for (i in 1:500){
simtrees[[i]]<-make.simmap(CrenuchidTreesLadderized[[i]], habitattrait,
model="ER", nsim=1000)
YY[[i]]<- describe.simmap(simtree[[i]], plot=F)
}
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