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/
