eastman / spacodir Goto Github PK

Hello,

First thank you for your great package spacodiR.

I found a really small issue in your resamp.phy function:
I'm currently working with a tree I want to randomized that have named nodes. And if I want to launch the function resamp.phy on it I get the following error:

Error in if (node <= n) return(NULL) :
missing value where TRUE/FALSE needed

So a really simple fix is only to delete the node names with : tree$node.label <- NULL. But you'll agree for saying it's not really elegant ? So I wanted to correct myself the issue and suggest you a fix. I found the problem came from this line in resamp.phy function: tt = as.numeric(names(tt)[which(tt)]). It works well when you don't have node names because automatically this line tt = sapply(b, function(x) withinrange(x, 0, time.threshold)) will give numbers as node names. But if you do have node names the as.numeric function on a character vector will produce NA bringing the function to bug. As a conclusion I wasn't able to suggest you a fix because I don't really now if you can manage node labels with get.descendants.of.node function our if you can only accept numerical names for tree nodes.

Please find bellow an example of code triggering the bug:
library(spacodiR)
data(sp.example)
attach(sp.example)
phy$node.label <- c(letters)[1:length(branching.times(phy))] # Giving letter name to nodes
resamp.phy(phy)