Walter
It seems there is a bug to resume the XML containing monophyletic clade. The XML to replicate the problem is attached. Run the XML first and then run `beast -resume...
Select multiple logs (having same parameters) and traces, go to the joint marginal panel. There are 2 * 3 traces selected. So the overlapping circles look like a bug. Also...
If value range is very small decimal numbers but the relative difference is huge, such as [1E-308, 1E-79], the `int binCount = (int) ((axis.getMaxAxis() - axis.getMinAxis()) / binSize) + 2;`...
It looks the histogram of the discrete value having few issues: 1. The value "3" is inside HPD interval, but the plot shows its bar is yellow. 2. Alexei thinks...
replace `MAX_LAG = 2000` to the proportion of sample size (chain length). Alexei hates the magic number. 😊 ```java final int samples = values.length; int maxLag = Math.min(samples - 1,...
Add distance function: It computes a matrix of pairwise distances from a given alignment using an evolutionary model. If there is a gap or an ambiguous state, it is treated...
The tests in parent Maven build are default to run in the children projects. Set a flag to skip them for given modules. https://stackoverflow.com/questions/9279852/ignore-a-module-during-maven-test-build-for-multi-module-maven-project
Setup Maven repository in Github, which can solve the beast2 jars issue, and also can host the snapshot versions. https://gist.github.com/fernandezpablo85/03cf8b0cd2e7d8527063 https://maven.apache.org/repository-management.html
Implement "replicates" for functions. So `array = copy(1.0, replicates=10)` will create a double array with 10 1.0.
Need validation to all GenerativeDistribution and Function implemented correctly. They require either `setParams` or setter, otherwise the re-sampling will be broken. Same to `getParams`. So it will be nice to...