Bug in congeneric.merge

[jonesor]

The congeneric.merge function includes partial matches, but I think it should only allow exact matches.

For example, in the following example, I would like to add the species "Aster_B" to the existing "Aster_alpinus". However, the grep command matches both "Aster" and "Asterostigma".

tree <- read.tree(text="((Aster_alpinus:1,Asterostigma_lividum:1):1, Aster_lanceolata:2):1;")
plot(tree)
tree <- pez::congeneric.merge(tree=tree, species=c("Aster_B"))
plot(tree)

The fix is simple - replace line 34 of build.phy with the following:
matches <- unique(grep(paste0("^",genus,split), tree$tip.label, value=TRUE))

I can submit a pull request if you prefer.

[willpearse]

Thank you for this. I'm just about to head out for the day, but when I get in tomorrow morning I'll check through this and then make the change. I need to get a new version up on CRAN, and this is a good opportunity for it. Thank you for bringing this to my attention, and I hope it hasn't caused you too much trouble.

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On Wed, 25 Jul 2018 at 16:45 Owen Jones ***@***.***> wrote: The congeneric.merge function includes partial matches, but I think it should only allow exact matches. For example, in the following example, I would like to add the species "Aster_B" to the existing "Aster_alpinus". However, the grep command matches both "Aster" and "Asterostigma". tree <- read.tree(text="((Aster_alpinus:1,Asterostigma_lividum:1):1, Aster_lanceolata:2):1;") plot(tree) tree <- pez::congeneric.merge(tree=tree, species=c("Aster_B")) plot(tree) The fix is simple - replace line 34 of build.phy with the following: matches <- unique(grep(paste0("^",genus,split), tree$tip.label, value=TRUE)) I can submit a pull request if you prefer. — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#69>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ABLcUuQ_L2CM_He6U8WoYFDpLjHjYn2jks5uKPUjgaJpZM4Vg6e-> .

[willpearse]

Thanks again for flagging this. I think that pez might be doing what I intend it to do, but that might not be what you want it to do, if that makes sense? If you run this:

tree <- read.tree(text="((Aster_alpinus-subspecies:1,Asterostigma_lividum-species:1):1, Aster_lanceolata-species:2):1;")
plot(tree)
tree <- pez::congeneric.merge(tree=tree, "Aster_alpinus-subspeciesb", "-")
plot(tree)

...I think you will get what you want. The function is splitting on the _, and is finding the clade that contains all of the Aster species - Asterostgima is getting caught up in this and, as I want the function to do, it's turning the entire thing into a polytomy to be "conservative". The reason for this is we don't know where to put the species within the clade that contains all the Aster species: it could be the sister to either of the two species, or even Asterostigma lividium. Does that make sense? I've been wrong many times before, so I'm happy to be so again! :D

If you give the function some more information, and let it know that you want to add something as a subspecies of Aster alpinus, then it is able to handle that when you give it a new split character. That's what I do above.

Does this help at all?