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There is a potential "null" problem, if a beast object does not has id in the xml. This is caused by BEASTObject.toString() == null.
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In BEAST log, each row also has an extra "tab" in the end, which causes an empty column, if you load it to R.
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Given that the terms dictionary has the structure of a trie, it compresses better when there are shared prefixes. By putting the mac address before the timestamp in our auto-generated ids, the `_uid` …
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How to replicate: Open BEAUTI, and on the menu go to File / Template / AutoPartition. Nothing happens. If you try to load the example RBS.xml file, BEAUTI gives Error 1006, with Error detected about h…
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The `narrow()` method of the `Exchange` class contains an "alternative" implementation of the proposal that is wrapped in the else block following an `if (true)`. No-doubt this is optimized out, but …
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Research.demo.RMD as it is here doesn't work ( plot_posterior_nltts, line 230) and despite trying to reverse the edits I made while adding my PATH, we can't get it to work on my computer. Even while c…
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When running phylogeography:
"I get four trees all annotated slightly different when compared in a text editor. In SPREAD there are polygons for the B1TA1 tree, but not for the B1TA2 tree. Neither of…
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```
What steps will reproduce the problem?
1. Run the attached XML
What do you see instead?
Parsing XML file: pp.rag.beast2.xml
Read alignment, 'alignment':
Sequences = 9
Sites = 4753
Dataty…
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@JolienGay : if and only if you like, I can give some detailed feedback on the presentation. You probably already have a lot you want to change, let me know when you need my precise eye.
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Current parameter settings for simulating birth-death trees are basically arbitrary.
Either:
- justify these specific values;
- evaluate a range of values (increases replicates combinatorially)
- fit …