Walter

Allow replicates to be a vector: `LogNormal(meanlog=3.0, sdlog=1.0, replicates=[11,2,10,...]);`

Conditional coalescent on root age, it may take the `PopulationFunction` as input. `tree ~ AgedConditionalCoalescent( ... , ParametricDistribution);` 1. simulate 1000 trees from PopulationFunction; 2. weight each tree by Pr(tree,...

Too many places to use System.out.print..., when simulating big data, these lines of code increase the time. Replace to `LoggerUtils.log.fine` for debugging or tracing.

Why we need BasicFunction?

2

It seems every functions are inherited from DeterministicFunction. The direct child class of BasicFunction is only DeterministicFunction.

Add ProgressBar for : 1. Sample; 2. LLT plotting?

merge PopulationFunctionCoalescent to SerialCoalescent, by adding another constructor in SerialCoalescent.

Simplify the SPI framework in lphy

1

- Use the ServiceLoader to load different types, instead of one loader for every types. - In addition, move all declaration into `module-info.java`, so that eventually remove all classes inheriting...

Data clamp needs to check if both sequence types are same

1

Data clamp needs to check if both sequence types are same, such as both should be `SequenceType.NUCLEOTIDE` or ... : GraphicalModel ```java default boolean isClamped(String id) { return (id !=...

Create new lphy extension to use beast2 nexus parser

1

Create new lphy extension to use beast2 nexus parser. Maybe, other models, which can save many development in simulations for new Generators.

Implement language models

1

https://taming-the-beast.org/tutorials/LanguagePhylogenies/ Requie: 1. Nexus importer of binary data. 2. Binary Covarion model. 3. The site mode and birth-death may appear to be present at LPhy language level.