Thank you Graham, Liam, and Emmanuel for your suggestions. Applying the
.uncompressTipLabel did the trick for my code. If anyone is interested in
using the code to identify the 95% HPD for a single node from a set of
chronograms, you can find the code here
(https://github.com/johnjschenk/Rcode/blob/master/NodeAgeDensity.R
<https://github.com/johnjschenk/Rcode/blob/master/NodeAgeDensity.R>) or below.
~John
library(ape)
library(coda)
#Function to estimate the age of a node given two members of a clade.
AgeDensity <- function(phy, species1, species2){
NodeNumber <- mrca(phy)[species1, species2]
ages <- branching.times(phy)[as.character(NodeNumber)]
return(as.numeric(ages))
}
#read in tree
tree <- read.nexus(file="")
#Apply function across the posterior distribution to obtain node ages. This
will take some time to run, depending on the number of trees. It took me about
20 minutes.
NodeAges <- unlist(lapply(.uncompressTipLabel(tree), AgeDensity, "species1",
"species2"))
#estimate the HPD interval for the node ages
HPD <- HPDinterval(as.mcmc(NodeAges), prob = 0.95)
#Density plot for 95% HPD
plot(density(as.numeric(NodeAges[which(NodeAges > HPD[1, 1] & NodeAges < HPD[1,
2])])), main="", las=1, xlab = "Million of years before present", lwd = 2)
______________________________________________________________
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
> On Apr 9, 2018, at 10:56 AM, Liam J. Revell <liam.rev...@umb.edu> wrote:
>
> 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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