Make sure that species names match tree tip labels

[clementviolet]

Hi!

I recently ran into a problem. In a dataset some species have a subgenus between parenthesis. I wasn't able to create a heatmap of the parameter estimates of species' environmental responses including a phylogeny tree.

I digged into the code and found that the issue is due to ape::write.tree.

HMSC/R/plotBeta.R

Line 94 in 7b9b185

tree <- ape::read.tree(text=ape::write.tree(tree))

The ape::write.tree() doc specify that:

The tip labels (and the node labels if present) are checked before being printed: the leading and trailing spaces, and the leading left and trailing right parentheses are deleted; the other spaces are replaced by underscores; the commas, colons, semicolons, and the other parentheses are replaced with dashes.

Now, when commas, colons, semicolons or parentheses are present in the species name they are temporarily replaced by - to match the name of the tree tips.

[jarioksa]

It seems that HMSC also means "Honda Malaysia Suppliers Club".