extending the epochal discrete CTMC model

[jsigao]

This PR is modified from a previous PR following @msuchard's suggestion. One of the commits (commit 859f33f) contained in this pull request has been fully revised to remove the unnecessary code duplication caused by the (trivial version of) getBranchRateModelMapping function copied across all the branchratemodel classes (now the trivial version of this function is implemented in the AbstractBranchRateModel class so this function has been removed from all the branchRate classes extending the abstract class). (The other two commits in this PR remain unchanged.)

I have done an additional experiment to validate the implementation extension contained in this pull request. Please see this synopsis.pdf document for a brief summary of the experiment. (The supplementary files that I used to perform this experiment is available in this Qmu_bothvary_test.zip folder).

Please let me know if there is anything unclear or missing in the experiment. I have also changed the target branch of this pull request to hmc-clock as advised. Thanks again for reviewing this PR.

For the sake of completeness, the PR message from the previous PR is included below.

This pull request contains three commits that extend the epochal discrete CTMC (substitution/dispersal) model. Specifically, this extension allows the transition-probability (P) matrix to be computed correctly along a branch that overlaps with multiple Q-matrix epochs (Bielejec et al., 2014) and multiple average-substitution/dispersal-rate epochs (Membrebe et al., 2019), and the stochastic-mapping function (the endpoint-conditioned uniformization algorithm; Hobolth and Stone, 2009) to work under the epochal model (either epochal matrices or epochal rates or both). A more detailed description about the extension can be found in S1 (S1.1 for the P-matrix computation and S1.2 for the stochastic-mapping function) of Gao et al., 2021.

The first commit (94e91fe) added a getBranchRateModelMapping function to each BranchRateModel class (where the only non-trivial implementation is in the RateEpochBranchRateModel class), imitating the getBranchModelMapping function of the BranchModel classes.

In the second commit (e86792c), this added mapping function is invoked in the SubstitutionModelDelegate class very similarly as the getBranchModelMapping function, allowing the average rate of each Q-matrix epoch that overlaps with a given branch to be computed correctly (instead of assuming that it is the average rate of the entire branch).

The third commit (9e81125) extends the endpoint-conditioned uniformization algorithm to work under the epochal model by (1) dividing a branch into pieces (where each piece only overlaps with one Q-matrix epoch and one average-rate epoch), (2) drawing the state at the end of each piece according to the probability conditioned on the start state of the piece and the end state of the branch, and (3) simulating history over each piece using the time-homogeneous algorithm.

Please let me know if I failed to follow the preferred coding style in this extension or if some of the functionalities introduced here would be preferred to be implemented in an alternative way. Thank you in advance for reviewing this PR.