unused argument (splist = mylist)

[visamilar]

Hi Jinyi,

I tried to build the tree with S.Phylomaker, however it returns this error message:
Error in S.PhyloMaker(splist = mylist, tree = phylo, nodes = nodes) :
unused argument (splist = mylist)

My full commands are just like the examples:
mylist<-read.csv("cnphmLIST.csv",header=T)
phylo<-read.tree("phytophylo.tre")
nodes<-read.csv("nodes.csv",header=T)
result<-S.PhyloMaker(splist=mylist,tree=phylo,nodes=nodes)

Any ideal?
Thank you

[flakesw]

Hi visamilar,

There is a typo in the example code. The argument that S.PhyloMaker needs is spList = ..., with a capital L. You've probably resolved this issue already, but for others who haven't, it's easy to fix.

Sam

[jinyizju]

Thanks for answering this, Sam! My apologies, visamilar. I just notice this message.

[visamilar]

Hi Jinyi
I have new error popped up, it says

Error: $ operator is invalid for atomic vectors

any ideal?

[jinyizju]

Hello visamilar,

The Error you shown indicates that there is an atomic vector from which you were trying to indexing an object. Since $ does not apply to an atomic vector in R, the error popped up.

More information is needed to intrepret why the error happened.

Yi

[visamilar]

Hi Yi
This is all the script I use, it seems all same as your example.

library(ape)
library(maps)
library(phytools)
setwd("~/Desktop")

mylist<-read.csv("cnphmLIST.csv",header=T)
phylo<-read.tree("phytophylo.tre")
nodes<-read.csv("nodes.csv",header=T)
result<-S.PhyloMaker(spList=mylist,tree=phylo,nodes=nodes)
str(result)
plot(result)

Cheers
Di

[jinyizju]

Hello visamilar,

Maybe you could try your run again with the new version of S.PhyloMaker I just uploaded. If it still does not work, you could show me some rows of your species list if you want.

cheers,

Yi