Not sure if a function for that already exists. You could plot posterior distributions at each node (or perhaps, nodes of interest) if that is workable graphically…Alternatively you could print the numerical 95% ci or HPD interval at each node, along with mean or median value (for a bayesian recon).
Jake Berv > On Feb 27, 2017, at 11:16 AM, Arbuckle, Kevin <k.arbuc...@liverpool.ac.uk> > wrote: > > Hi all, > > I was wondering about plotting the output of an ancestral state > 'reconstruction' of a continuous trait while incorporating at least some of > the uncertainty around the estimates. > > One approach I thought of was to map the ASR onto a tree in a standard way, > then at each node have essentially a mini-legend that is of a length > reflecting the width of the confidence interval of the estimate at that node, > and is coloured on the same colour-scale as the overall tree legend. For > instance, if the colour scheme for the tree goes from blue through yellow to > red as the value increases, then a node with a relatively precise and high > estimate will have a short bar only ranging through different shades of red, > whereas a highly uncertain low estimate will have a wider bar coloured from > (say) dark blue to orange/light red. I hope that description makes sense. > > I was wondering if anyone is aware of a function that already implements such > an approach, otherwise I'll try to put one together myself. I am aware of > phytool's fancyTree(type="phenogram95") as a way of incorporating uncertainty > into a plotted ASR for continuous traits. However, this often results in > difficulty in distinguishing different nodes where estimates are similar and > also does not lend itself easily to, for instance, plotting pie charts > representing discrete trait ASRs onto a tree mapped with a continuous trait. > Hence I can imagine a more general approach as above but don't want to > duplicate effort if a function already exists (and also if others feel this > is a useful idea it can be added to existing packages If I share it as above). > > Best wishes, > Kev > _______________________________________________ > 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/ _______________________________________________ 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/
