kche309
kche309
The `test_ThatParameterisedXmlExamplesRuns` method from `ExampleXmlParsingTest` uses `user.dir` paths for inputs RSV2.json, RSV2.xml and output /tmp/RSV2.out.xml When I run `ant build_all_` or `ant junit_` for my package, it fails to find...
Allow as optional inputs for TreeLikelihood and GenericTreeLikelihood: * RootDistribution for specifying root frequencies or a root sequence (for usage with rootfreqs package https://github.com/rbouckaert/rootfreqs) * TipDistribution for specifying error models...
Viewer for large alignments should only display the first 100 or 1000 sites rather than the whole alignment.
https://github.com/LinguaPhylo/linguaPhylo/blob/master/lphy-base/src/main/java/lphy/base/evolution/alignment/ErrorAlignment.java For large alignments, if the fraction of error is small use a memory efficient version of ErrorAlignment (e.g., fraction estimated from a sample of 1000 sites). Memory efficient version...
https://en.wikipedia.org/wiki/Multinomial_distribution Allow sampling from a Multinomial distribution with `n` trials, `k` events, and `p = (p1, p2, ..., pk)` event probabilities.
On some versions of Intellij, opening the linguaPhylo project causes an error: ``` java.lang.IllegalStateException: Module entity with name: linguaPhylo should be available ``` This appears to be an Intellij bug....
Long numbers in LinguaPhylo studio graphical panel may be displayed incorrectly (truncated). This should instead be displayed in scientific notation with 3 or 4 significant figures.
LPhy Studio menu should allow exporting narrative as HTML file.
When more than one alternative is possible for a function/generator signature, the program should throw an Exception and fail early rather than failing at runtime. For example, when LPhy Studio...
The Categorical generators is listed under "Other generative distributions" in the documentation https://linguaphylo.github.io/linguaPhylo/index.html It should be listed under "Parametric distribution"