Dear John.
You could try running .uncompressTipLabel on the "multiPhylo" object.
Let us know if that works.
All the best, Liam
Liam J. Revell, Associate Professor of Biology
University of Massachusetts Boston
& Profesor Asociado, Programa de Biología
Universidad del Rosario
web: http://faculty.umb.edu/liam.revell/
On 4/9/2018 9:46 AM, jschenk wrote:
Hi Folks,
I have been banging my head against what appears to be an easy coding problem
for a while now and haven’t been able to hack my way out of it. I am running a
function to identify a posterior set of node ages for a particular node. The
function I wrote works just fine, but when I use lapply to sample across a
posterior distribution, I get the “not of class ‘phylo’” error, even when I
input a single tree of class phylo. I have tried every typical solution (e.g.,
reassigning class), but haven’t identified a solution. Does anyone know a
workaround?
Please see the example code below.
Thanks,
John
library(ape)
#simulate a single tree with 20 tips
simtree <- rtree(20)
#Make sure the tree exists
plot(simtree)
#Function I wrote to find a node and then tell me the age of the node. I
realize that the simulated tree is not ultrametric in this example, in real
life it will be - ultrametric trees also result in the same error
AgeDensity <- function(phy, species1, species2){
NodeNumber <- mrca(phy)[species1, species2]
ages <- branching.times(phy)[as.character(NodeNumber)]
return(as.numeric(ages))
}
#check the class of the tree object, it will say that it is of class phylo
class(simtree)
#Run my function AgeDensity and it works just fine
AgeDensity(simtree, "t3", "t15")
#When I use the lapply function, I get an error that the object is not a of
class phylo, although I already verified that it is of class phylo.
lapply(simtree, AgeDensity, species1="t3", species2="t15")
#here is the same analysis conducted with multiple trees
multiTrees <- rmtree(20, 10)
class(multiTrees)
#I get the same error when I run my function across multiple trees
lapply(multiTrees, AgeDensity, species1="t3", species2="t15")
______________________________________________________________
John J. Schenk, Ph.D.
Assistant Professor of Plant Biology
Georgia Southern University Herbarium (GAS), Curator
Department of Biology
4324 Old Register Road
Georgia Southern University
Statesboro, GA 30460-8042
Office: 2260 Biology Building
Office phone: (912) 478-0848
Lab website: sites.google.com/a/georgiasouthern.edu/schenk
Herbarium website: sites.google.com/a/georgiasouthern.edu/gasherbarium
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