Josef Uyeda issues

Results 10 issues of


                                            Josef Uyeda

name_column requires won't take column name

instead needs column number, should be either.

make.refFn error for bounded distributions on continuous parameters

Offending line: `test.dists

makeBayouModel should check if the predictor has NAs and impute=FALSE

Currently doesn't give an informative error message.

Closing unused connections

If a bayou run is interrupted, these warnings show up. I need to make a way so that runs that are interrupted still produce a fit object that can be...

summary.bayouMCMC has errors summarizing location

Values >1.

Numerical errors when the data have a very small variance

bayou.lik can return a infinite likelihood when the distribution of trait values is very small.

Shouldn't have to specify starting parameters when the model has fixed parameters

When the prior has been specified to have "fixed" parameters, instead of simulating variable parameters from the prior, bayou.mcmc requires that the starting parameters be specified, otherwise it will auto...

plotSimmap.mcmc/phenogram.density when no shifts are large

throws the 1:o too long a vector error. Just need to add an if statement...

Error is thrown with zero length branches

If zero length branches are used then the following error gets thrown when executing a slide move on the zero length branch: Error in if (m.i - 1 == 1)...

Trees produced from Treetimer (OpenTree) can only be downloaded/visualized/saved as json

Here is an example output tree. Any ideas why this tree isn't being converted to other formats? [Link to file on arbor1](http://54.83.6.133:9080/girder#item/577fc68d4c46530515578d85)