That's really cool, Liam. Would it also be possible for one to do
multiple such error bars per node, for plotting ASRs for multiple

On Mon, Feb 27, 2017 at 12:13 PM, Liam J. Revell <> wrote:
> Hi Kevin.
> This is not automatic - but it is indeed fairly easy to do using phytools.
> To be honest, I thought this would look terrible - but it actually looks
> much better than I expected, at least for a relatively small tree. I have
> posted a demo to my blog here:
> All the best, Liam
> Liam J. Revell, Associate Professor of Biology
> University of Massachusetts Boston
> web:
> email:
> blog:
> On 2/27/2017 11:16 AM, Arbuckle, Kevin 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
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David W. Bapst, PhD
Adjunct Asst. Professor, Geology and Geol. Eng.
South Dakota School of Mines and Technology
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