Open EvoLandEco opened 1 year ago
It seems that paleoPhylo generated a mal-formatted tree, but I think it is worthy to check if it could be a rare case that causes error
It seems that paleoPhylo generated a mal-formatted tree, but I think it is worthy to check if it could be a rare case that causes error
I'm not sure how to replicate this error, or what now caused the documented issue - I also can't really replicate the tree plotted here, what package did you use to read the weird newick string?
Hi @thijsjanzen, did you try the code in paleoPhylo.txt? This is the code the authors provided to convert their data (table stored in xlsx) into a phylo object.
Right, I'm not sure what happens during your newick conversion-reread, so I can't check that.
However, I do notice that treestats::crown_age provides a weird result when applied to the full tree (9.9, instead of 65). Dunno yet was is going on, interesting!
DATA Original data of the tree brv_178_sm_appendixs5.xls, from A phylogeny of Cenozoic macroperforate planktonic foraminifera from fossil data
A tree export to txt (github does not support uploading a .phy) I converted from sheet aMb (fully bifurcating morphospecies phylogeny) using their paleoPhylo code tree_morpho_aMb.txt
This is the code to convert the sheet data to phylo tree, the functions required are in paleoPhylo.txt
This is the complete tree:
EXAMPLE
Created on 2023-08-15 with reprex v2.0.2
MORE Also interesting that before I exported the tree to newick format and read it back again, applying
crown_age()
to the just-converted tree gave a different resultBy furthur inspecting the results, I found that the two trees
tree_morpho
(the one exported to newick and read back) andtree_morpho_bak
(originally converted by paleoPhylo) also differed in the following stats:But if extinct linneages were dropped, the two trees only differed in four stats: