Error to BactDating

[STChoudhury]

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:

res=bactdate(t,d)

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.

[xavierdidelot]

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 NAs 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.

[STChoudhury]

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.

[xavierdidelot]

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')