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FranzKrah / timetree

Interface to the TimeTree of Life website
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Issue running timetree.phylo #1

Open EwersAquaGenomics opened 8 years ago

EwersAquaGenomics commented 8 years ago

Dear Franz, I encountered the following issue when trying to use timetree.phylo on a cleaned version of the Open Tree of Life version of the Thecostracan phylogeny [clean_tree_for_timetree.tre.zip (https://github.com/FranzKrah/timetree/files/360306/clean_tree_for_timetree.tre.zip). The error displayed after evaluating all node.

install.packages("devtools")
devtools::install_github("Franzkrah/timetree")
library(timetree)

library(rncl)
syn.tree2 <- read.tree("clean_tree_for_timetree.tre")

# remove "_" identifiers
#syn.tree2$tip.label <- gsub("_", " ", syn.tree$tip.label)

# this step takes hours
tt <- timetree.phylo(syn.tree2, node.time=c("mean"))

Error in UseMethod("xmlNamespaceDefinitions") : no applicable method for 'xmlNamespaceDefinitions' applied to an object of class "NULL"

FranzKrah commented 8 years ago

Dear Christine,

the tree you are using is not suitable for the function timetree.phylo. timetree does not contain divergence times for non-linean species names like "Chthamalus_sp._HNC-2013”, variations...

Anyway, timetree is “build for" divergence times of larger clades like orders, families, maybe genera, however, not really for species divergences. I suggest you prune your tree to contain only valid species names and try again. Better would be to prune to tree containing only larger clades, like genera. As fas as I can see its about 280 genera; that would be a good starting point.

What you need the divergence times for?

Best, Franz

On 13 Jul 2016, at 00:15, Christine Ewers-Saucedo notifications@github.com wrote:

Dear Franz, I encountered the following issue when trying to use timetree.phylo on a cleaned version of the Open Tree of Life version of the Thecostracan phylogeny [clean_tree_for_timetree.tre.zip (https://github.com/FranzKrah/timetree/files/360306/clean_tree_for_timetree.tre.zip https://github.com/FranzKrah/timetree/files/360306/clean_tree_for_timetree.tre.zip). The error displayed after evaluating all node.

install.packages("devtools") devtools::install_github("Franzkrah/timetree") library(timetree)

library(rncl) syn.tree2 <- read.tree("clean_tree_for_timetree.tre")

remove "_" identifiers

syn.tree2$tip.label <- gsub("_", " ", syn.tree$tip.label)

this step takes hours

tt <- timetree.phylo(syn.tree2, node.time=c("mean")) Error in UseMethod("xmlNamespaceDefinitions") : no applicable method for 'xmlNamespaceDefinitions' applied to an object of class "NULL"

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