Remco Bouckaert
Remco Bouckaert
Though the public release is still a bit off since we need to decide what will be included, this is a catch all issue for dealing with anything to do...
Keeping package loading working for both java 8 and java 9+ turns out to be quite hard work, and the current solution (start a Launcher that kicks of a second...
The Yule prior produces a warning about a missing MRCA prior on the root, even when the prior is present because `validateInputs()` is called before `initAndValidate()` is called, so the...
95% HPDs are constructed as follows: given N samples, x_1…x_N sorted by value, put a moving window of size n=(N-1)*95/100 over the sorted sequence and report the x_i and x_{i+n}...
`packagemanager -add ORC` gives a `javax.net.ssl.SSLHandshakeException`. The package manager in BEAUti BEAUti still lists all packages, but when you try to install a message saying: "Install failed because: java.security.cert.CertificateException: No...
Post processing programs that rely on multiple log files -- like Tracer for skyline analysis, or UglyTrees for visualising multi species coalescent trees -- rely on the log frequencies of...
The posterior of the testEBSP.xml fails for [TreePriorTest](https://github.com/CompEvol/beast2/blob/master/src/test/beast/beast2vs1/TreePriorTest.java). At some point it must have passed. When did this change and why? This might be a symptom of a bug introduced...
To reproduce: * Choose snapper template in BEAUti, and add `hemi129.nex` alignment. * In the priors panel, add MRCAPrior, there now is a choice of 4 taxa. * Go to...
The trie in the `State` is a data structure that stores paths through the calculation graph based on which set of `StateNode`s are changed by operators. Some models have operators...
The `LikelihoodCore` is created in `initAndValidate()` in this fragment: ``` if (stateCount == 4) { return new BeerLikelihoodCore4(); } else { return new BeerLikelihoodCore(stateCount); } ``` Putting this in a...