Hi folks,
I'm trying to generate the thresholds and liabilities plot, including the
posterior support values, from Revell (2014) Evolution 68(3), Figure 6B. Does
anybody have a script for this? I see the liabilities output from ancThresh(),
but no thresholds.
Thanks!
~John
John S. S.
Hi John.
The posterior sample of the relative positions of the thresholds (if
there is more than one) are output in the matrix par, i.e.:
mcmc-ancThresh(...)
mcmc$par ## contains the posterior sample of the thresholds
To get a visualization of the posterior density you can, for instance,
Hi all:
I am using the phylock package to read and plot a BEAST tree in R. I want to
remove outgroups from my plot, therefore I used the extract.clade2() from the
phylock package. But, when I try to plot the new phylogeny with the extracted
clade, R quits unexpectedly. I have tried to plot that
Hi Mariana,
extract.clades2 hasn't been well tested. I wrote it for a specific dataset two
years ago and I don't know if someone else has used it successfully. You can
send me your tree off list and I'll see if I can fix it. Alternatively, you can
identify the nodes concerned (?nodelabels,