SciML / JumpProcesses.jl

Build and simulate jump equations like Gillespie simulations and jump diffusions with constant and state-dependent rates and mix with differential equations and scientific machine learning (SciML)
https://docs.sciml.ai/JumpProcesses/stable/
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Ficticious jump algorithm for time-dependent variable rate jumps. #252

Open pihop opened 2 years ago

pihop commented 2 years ago

Extends the VariableRateJump interface to allow for user-defined bounds on time-dependent jump rates and look-ahead horizons for which the bound is valid. Implements a fictitious jump rejection algorithm based on https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1004923.

Relevant issue: https://github.com/SciML/JumpProcesses.jl/issues/28

coveralls commented 2 years ago

Pull Request Test Coverage Report for Build 4127486574

Warning: This coverage report may be inaccurate.

This pull request's base commit is no longer the HEAD commit of its target branch. This means it includes changes from outside the original pull request, including, potentially, unrelated coverage changes.

Details


Changes Missing Coverage Covered Lines Changed/Added Lines %
src/jumps.jl 9 11 81.82%
<!-- Total: 66 68 97.06% -->
Files with Coverage Reduction New Missed Lines %
src/aggregators/aggregated_api.jl 4 77.27%
src/jumps.jl 10 84.39%
<!-- Total: 14 -->
Totals Coverage Status
Change from base Build 3856869287: 1.5%
Covered Lines: 2165
Relevant Lines: 2446

💛 - Coveralls
isaacsas commented 2 years ago

@pihop still taking a look over this -- I've been delayed by the US holiday and travel for it. One quick comment is it would be great if you could add a test that actually tests accuracy by comparing some statistic against simulations using the current approach.

isaacsas commented 2 years ago

@pihop looks like tests are passing now. Please let me know when you feel this is done and you have added an accuracy test that compares against the current solvers (to check you are getting the correct statistics on some simple example like A+B -> C). I'll then go through and give it a review. Thanks!!!

isaacsas commented 1 year ago

Looks like a real CI failure.