no core rate shift in BAMM run?

[Francis Nge]

Hi there,

Just confirming here for this example, I have this result after running this:

plot.bammdata(edata, lwd=1, legend=T)
axis(1, at=max(branching.times(tree))-0:80, labels=0:80)
css <- credibleShiftSet(edata, expectedNumberOfShifts=1, threshold=5, set.limit = 0.95)
css$number.distinct
summary(css)
plot.credibleshiftset(css)

output:

 summary(css)

 95 % credible set of rate shift configurations sampled with BAMM

Distinct shift configurations in credible set:  1

Frequency of 1 shift configurations with highest posterior probability:


   rank     probability cumulative  Core_shifts
         1          1          1          0

> plot.credibleshiftset(css)
Omitted 0 plots

~~~~~~~~~~~~~~~~~~~~~~~~~~

Does this mean that there is no core shift identified for this empirical tree and BAMM run? And in the figure (attached), there is an f value of 1.

Cheers

Francis 

[Dan Rabosky]

I would agree with your interpretation - no substantive evidence for among-lineage rate heterogeneity.

[Francis Nge]

Hi Dan, great thanks for the clarification. I noticed in the figure though the colours are different across the tree and it suggests perhaps that the backbone has higher rates of speciation/diversification? Or can we not really interpret this? As I saw in your webpage that you mentioned the colours mean different things dependent on what we specify it to be e.g. linear, linear-log, jenks etc.

Cheers

Francis