Closed STChoudhury closed 11 months ago
Since you have sampling dates for most and missing a few, your best option is probably to have d
being a named vector including some NA
s for the missing values. Check that d
is indeed a vector, if you type class(d)
you should get numeric
. Also check that the names in names(d)
are the same as in t$tip.label
. For example you could do setdiff(t$tip.label,names(d))
to see if there are any leaves of the tree not in the vector of dates d
.
Hello, Thank you so much. I finally have a time calibrated tree. I have two more questions, in my tree, the tips are all labelled. How can I remove them from the plot? And can I save the plot as a newick file so that I can open it in iTOL?
Thank you.
Great!
If you used res=bactdate(...)
then you can use plot(res)
to plot the tree with labels or plot(res,show.tip.label=F)
to plot the tree without the labels.
You can export the tree in Newick format using write.tree(res$tree,'filename.nwk')
Hello I am trying to make a time calibrated tree using 206 samples. I have the sampling date for most and missing for some. I am trying to follow this webpage, https://xavierdidelot.github.io/BactDating/articles/yourData.html
But I am getting an error when i try:
The error I am getting is: Error in if (var(date, na.rm = T) == 0 && is.na(rate)) { : missing value where TRUE/FALSE needed
I am very new to bactdating. It would be greatly appreciated if you could help me move forward.
Thank you.