search

macroevolution / bamm

A program for multimodel inference on speciation and trait evolution
GNU General Public License v2.0
33 stars 10 forks source link

node labels cause problems in plotting #120

Closed cew35 closed 9 years ago

cew35 commented 10 years ago

node labels on the tree cause plot functions to crash

redcurry commented 10 years ago

Do you refer to BAMMtools plot functions? Could you be more specific about the node labels? Are they tip labels or internal labels? How do you know it is the node labels and not something else? Thank you.

cew35 commented 10 years ago

Hi Carlos,

Yes, BAMMtools plot functions — Dan found the issue and asked me to post something on github to remind him about it.

Katie

On Jun 12, 2014, at 4:34 PM, Carlos Anderson notifications@github.com wrote:

Do you refer to BAMMtools plot functions? Could you be more specific about the node labels? Are they tip labels or internal labels? How do you know it is the node labels and not something else? Thank you.

— Reply to this email directly or view it on GitHub.

blueraleigh commented 10 years ago

I have trouble reproducing this error, can you describe the circumstances under which it occurs?

cew35 commented 10 years ago

Hi,

I wrote to Carlos yesterday also, but the issue was one that Dan found during the workshop yesterday and asked me to post so he would remember. getEventData() runs without error if you give it a tree with node labels, but the event vectors are all filled with NAs. Then when you try to use plotting functions you get an error ("Error in seq.default(ephy$begin[i]/tH, ephy$end[i]/tH, tau) : 'from' cannot be NA, NaN or infinite”).

The fix is simple. Just replace node labels with “NULL” if a user tries to use a tree that already has node labels.

Cheers, Katie

On Jun 12, 2014, at 6:45 PM, blueraleigh notifications@github.com wrote:

I have trouble reproducing this error, can you describe the circumstances under which it occurs?

— Reply to this email directly or view it on GitHub.