bayou2OUwie error

[coyotree]

Hello,

I have successfully run bayou and now would like to export that information into an acceptable OUwie format. I am using the bayou2OUwie function. I have pars directed to the saved bayou run so that it can locate sb, loc and t2. I have the tree I used for the bayou run, and the tip data are in a named vector sorted in the same order at the tree labels.

I receive the following error:

> bayou2OUwie(chain.fit, fit.tree, fit.sorted2)
Error in table(pars$sb) : all arguments must have the same length

I have checked and all lists have 150001 items.

> length(chain.fit$sb)
[1] 150001
> length(chain.fit$loc)
[1] 150001
> length(chain.fit$t2)
[1] 150001

The number of tips in the tree match the number of rows for the tip data.

I cannot figure out why I am getting this error.

I am using bayou v2.1.1, R version 3.5.2.

Any advice appreciated. Thanks for this package!

Cody Coyotee

[uyedaj]

Hi Cody,
bayou2OUwie requires that you only provide it a single set of parameters rather than the full posterior. For example, you could use the function pull.pars to pull out a particular generation of the MCMC and return a bayou parameter list. Alternatively, you could use the function shiftSummaries to return a bayou parameter list for all shifts above a certain posterior probability (pp.cutoff). For example:

pp <- pull.pars(150001, chain.fit) # Get the last generation of the MCMC parameters
 bayou2OUwie(pp, fit.tree, fit.sorted2)

#OR

pp <- shiftSummaries(chain.fit, mcmc=your.mcmc.object, pp.cutoff=0.3)$pars
bayou2OUwie(pp, fit.tree, fit.sorted2)

[coyotree]

Thank so much for the clarification!