YosefLab / Cassiopeia

A Package for Cas9-Enabled Single Cell Lineage Tracing Tree Reconstruction
https://cassiopeia-lineage.readthedocs.io/en/latest/
MIT License
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Branch length estimation bayesian #134

Closed sprillo closed 3 years ago

sprillo commented 3 years ago

This PR implements Bayesian branch length estimation under a birth process prior w/subsampling.

The class that implements this is IIDExponentialBayesian. The main dynamic programming recurrence is cythonized for speed.

Test plan:

codecov[bot] commented 3 years ago

Codecov Report

Merging #134 (8e23e94) into master (81fbdc0) will increase coverage by 0.08%. The diff coverage is 89.85%.

Impacted file tree graph

@@            Coverage Diff             @@
##           master     #134      +/-   ##
==========================================
+ Coverage   86.76%   86.84%   +0.08%     
==========================================
  Files          67       68       +1     
  Lines        4579     4714     +135     
==========================================
+ Hits         3973     4094     +121     
- Misses        606      620      +14     
Impacted Files Coverage Δ
...tools/branch_length_estimator/IIDExponentialMLE.py 96.42% <ø> (ø)
.../branch_length_estimator/IIDExponentialBayesian.py 89.25% <89.25%> (ø)
cassiopeia/data/CassiopeiaTree.py 92.31% <93.33%> (-0.01%) :arrow_down:
cassiopeia/tools/__init__.py 100.00% <100.00%> (ø)
...ssiopeia/tools/branch_length_estimator/__init__.py 100.00% <100.00%> (ø)

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sprillo commented 3 years ago

@Lioscro seems like you have to approve this for me to merge