Dear Sir/Madam,
My name is Ni Ni Win and I am studying marine algae.
I am trying to create LTT plots using phytools in R but I am just a
beginner in using R and I even don't know how to start R for LTT plots too.
After studying about the LTT plots via the internet and reading the
books (Analysis of Phylogenetics and Evolution with R) and other related
links to LTT, I could understand a little but still have many problems.
Here I would like to explain what I have done so far and got stuck in one
step.
First, I loaded phytools in R Studio
> (Library("Phytools")
Loading required package: ape
Loading required package: maps
then I put a command to read a phylogenetic tree made by BEAST like this,
> tr <- read.tree("IshigeSyringo.trees", text = NULL, tree.names = NULL,
skip = 0, comment.char = "", keep.multi = FALSE, ... = )
Error in scan(file = file, what = "", sep = "\n", quiet = TRUE, skip =
skip, :
unused argument (alist(... = ))
Because of the above error, I changed the command like this.
> tr <- read.tree("IshigeSyringo.trees")
Error in if (all(phy$node.label == "")) phy$node.label <- NULL :
missing value where TRUE/FALSE needed
So, I don't know how to solve this problem. I even don't know what commands
I should put step by step to create LTT Plots using the existing tree file.
Could you please kindly teach me how to make LTT plots in R step by step?
I have attached the phylogenetic trees in this email and please kindly see
it.
I am looking forward to your reply soon.
Thank you.
Sincerely,
Ni Ni
IshigeSyringo.tre
<https://drive.google.com/file/d/17Zf1116ayMHt6QyZCc5S8VEaQ-is3_E5/view?usp=drive_web>
IshigeSyringo.trees
<https://drive.google.com/file/d/1qs5bls_EL9s4h8CL6g4Hnvcbve9rZVxP/view?usp=drive_web>
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