I want to be able to manipulate objects in class 'phylo' - ie. round/ turn my bootstrap values from decimals (.998) into percentages (99%)

Question

I am using RStudio, programs ape and phytools. I've generated a tree with 500 bootstrap replicates stored in an object of class phylo.

Where cw is the name of my tree, I've tried the following:

round(cw, digits = 2)

and I get the following error message:

Error in round(cw, digits = 2) : non-numeric argument to mathematical function

I feel like it's probably a very simple manipulation but I'm not sure how to get there.

Answer 1

Hard to tell without a reproducible example but I guess that your bootstrap scores are probably stored in the $node.label subset of your tree.

You can try the following:

## Are the bootstraps in the $node.label object?
if(!is.null(cw$node.label)) {
    ## Are they as character or numeric?
    class(cw$node.label)
}

If they are numeric values:

cw$node.label <- round(cw$node.label, digits = 2)

If they are characters, you can probably coerce them (that can produce some NAs)

cw$node.label <- round(as.numeric(cw$node.label), digits = 2)