Tim Vaughan
Tim Vaughan
The current implementations of the `getIntensity()` and `getInverseIntensity()` methods for the exponential growth population model are numerically unstable for extremely small but non-zero growth rates. For instance, here is the...
The Nexus parser (beast.util.NexusParser) only handles a minimum subset of the Nexus format. I suggest we switch to the JEBL nexus parser which is much more complete (handles Taxa and...
The method `TraitSet::convertValueToDouble` is responsible for taking a string representation of a sampling time and converting this to a real number. For calendar dates, these are parsed using a date...
It is well-known amongst the development team that BEAUti can become "confused" - i.e. the BEAST model it holds in memory can become corrupted, or the model is in some...
Print out the full name of the plugin in an error message, since two plugins with the same name may exist (like Uniform and Uniform, distribution and operator)
Is there already a catch-all issue with which to associate commits that fix this kind of thing? BTW, I'm aware that fixing this kind of thing willy-nilly (sp??) can break...
Command-line BEAST processes are being killed on logout on my Debian machine, even when launched from the command line using nohup or from within a screen/tmux session. To replicate: 1....
Snippet from [a comment](https://github.com/CompEvol/beast2/issues/95#issuecomment-281466865) on issue #95 where this proposal was made: "It would be really helpful to have an actual official BEAST 2 manual. I can't believe I only...
LiTeX is a nice and useful plugin (thanks!), but I can't seem to navigate preview of the document being edited with the keyboard.
To reproduce, create a `TreeParser` instance with a labeled newick string and set IsLabelledTree="true". Following the [part of initAndValidate() responsible for sorting the labels alphabetically](https://github.com/CompEvol/beast2/blob/cb25234a1dab3c1fc5e511cb02322eefe09dfb2e/src/beast/base/evolution/tree/TreeParser.java#L187), the leaf nodes in `m_nodes[]`...