Dear all,
Sorry if this subject scapes the list scopes, but it is my first time with
phylogenetic analysis and I never saw this error in others analysis.
Please, I am using phytools and picante packages. I have a large
phylogenetic tree constructed using Phytophylo (Qiang & Jin 2016) as
megaphyogeny from my species list. Also I have a species x sample
data.frame (community). Species names are the same in both species list and
community.
This is my script:
list<-read.csv("list.csv", header = T, sep = ";") #load species list
nodes<-read.csv("nodes.csv", header = T) #load nodes file (from Qiang & Jin
2016 appendix_S5)
phylo<-read.tree("Phytophylo.tre")#load megaphylogeny
result<-S.PhyloMaker(list, phylo, nodes, output.splist = T, scenarios =
"S3")#builds my phylogenetic tree (PHYTOOLS)
comm<-read.table("community_t.txt", header = T, sep = "\t", row.names = 1)#load
my community data.frame
phydist<-cophenetic(S3)#builds distance matrix
ses.mpd.result<-ses.mpd(comm, phydist, null.model = "taxa,labels", runs =
999, iterations = 1000)# calculate SES.MPD (PICANTE)
In this line appears "Error in dis[sppInSample, sppInSample] : subscript
out of bounds". I checked in forums and 1 explanation was "different name":
species names in community and phylogenetic are slightly different. I
checked again in my species list and community data-frame and species names
are the same! But I don't know how to check if species names in my
phylogenetic tree are the same as mine community data.frame neither export
my phylogenetic tree to check out of R.
I appreciate any suggestion or comment.
Best regards,
Jhonny Capichoni Massante
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