User: phylofun

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phylofun50
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Posts by phylofun

<prev • 19 results • page 1 of 2 • next >
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Drop tip from multiPhylo object in R
... I have 100s of phylogenetic trees in a multiPhylo object. There is one tip I need to drop from all of these trees. How can I do this in R? ...
phylogeny R written 10 weeks ago by phylofun50 • updated 9 weeks ago by Brice Sarver3.2k
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changing species names in phylogeny in R
... I have a column of species in the order in which they appear in my phylogeny (output from $tip.labels). I want to swap out this list of species with a new species list such that is in the same order as my original species list and replaces all the species in $tip.labels from an R phylo object. ...
R phylogenetics written 3 months ago by phylofun50 • updated 12 weeks ago by Brice Sarver3.2k
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Comment: C: root to node distance
... Do you know what function does the tree traversal method in ape? I can't find what I'm looking for in the manual ...
written 4 months ago by phylofun50
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Comment: C: root to node distance
... Thanks! Question, would this do the job? https://www.rdocumentation.org/packages/ape/versions/5.3/topics/branching.times ...
written 4 months ago by phylofun50
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Comment: C: root to node distance
... Any ideas on what R code I could use then? ...
written 5 months ago by phylofun50
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Comment: C: root to node distance
... I used a relaxed molecular clock, my tree is ultrametric ...
written 5 months ago by phylofun50
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Comment: C: root to node distance
... I’m curious how to do both. Thanks! ...
written 5 months ago by phylofun50
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root to node distance
... I want to calculate the relative time from the tree root to the species' creation node for all species in my phylogeny. Is this possible in R? ...
phylogeny written 5 months ago by phylofun50
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node height test in R
... How can I perform the node height test (described in Freckleton and Harvey, 2006) in R? ...
R phylogenetics written 5 months ago by phylofun50 • updated 5 months ago by Jean-Karim Heriche21k
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prunning posterior distribution of trees in R
... I have a posterior distribution of trees from a Bayesian analysis in `nexus` format. Is there a function in R to prune these trees to match my trait dataset? Something like the `treedata` function in the R package *geiger* seems to do what I want, but it does not handle multiple trees. ...
phylogeny R written 5 months ago by phylofun50 • updated 5 months ago by Klaus S100

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