That’s right Jacob. Tracer will do the same thing if, and unfortunately only if, you predefine taxon sets in BEAUti. The problems with predefining clades in BEAUti are that (1) it is kind of a pain, (2) you often don’t know what the clades will be until after you conduct the analysis (as in my case where I am interested in shifts in diversification rates, which I won’t know until after I build the chronogram and conduct downstream analyses), and (3) Tracer doesn’t allow for any options on figure configuration.
~John ______________________________________________________________ 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 10, 2018, at 7:34 AM, Jacob Berv <jakeberv.r.sig.ph...@gmail.com> > wrote: > > This is cool — so this looks like it will work on a set of posterior trees > even if they don’t all share the same topology? > Jake > >> On Apr 10, 2018, at 3:37 AM, jschenk <jsch...@georgiasouthern.edu >> <mailto:jsch...@georgiasouthern.edu>> wrote: >> >> 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><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 >> <http://sites.google.com/a/georgiasouthern.edu/schenk> >> Herbarium website: sites.google.com/a/georgiasouthern.edu/gasherbarium >> <http://sites.google.com/a/georgiasouthern.edu/gasherbarium> >> >> >> >> >> >> >> >>> On Apr 9, 2018, at 10:56 AM, Liam J. Revell <liam.rev...@umb.edu >>> <mailto: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/ >>> <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 >>>> <http://sites.google.com/a/georgiasouthern.edu/schenk> >>>> Herbarium website: sites.google.com/a/georgiasouthern.edu/gasherbarium >>>> <http://sites.google.com/a/georgiasouthern.edu/gasherbarium> >>>> [[alternative HTML version deleted]] >>>> _______________________________________________ >>>> R-sig-phylo mailing list - R-sig-phylo@r-project.org >>>> <mailto:R-sig-phylo@r-project.org> >>>> https://stat.ethz.ch/mailman/listinfo/r-sig-phylo >>>> <https://stat.ethz.ch/mailman/listinfo/r-sig-phylo> >>>> Searchable archive at >>>> http://www.mail-archive.com/r-sig-phylo@r-project.org/ >> >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> R-sig-phylo mailing list - R-sig-phylo@r-project.org >> <mailto:R-sig-phylo@r-project.org> >> https://stat.ethz.ch/mailman/listinfo/r-sig-phylo >> <https://stat.ethz.ch/mailman/listinfo/r-sig-phylo> >> Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/ >> <http://www.mail-archive.com/r-sig-phylo@r-project.org/> [[alternative HTML version deleted]] _______________________________________________ R-sig-phylo mailing list - R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/
