MGSurvE
Project description
MGSurvE: Mosquito Gene SurveillancE
MGSurvE is a project oriented towards the optimization of traps' placement in complex heterogeneous landscapes in an effort to minimize the time to detection of genetic variants of interest.
Under Construction :construction: Please check back in a couple of weeks!
Please have a look at the documentation for more info and our pypi package for installation and versions.
Authors and Funders
- Lead and Dev: Héctor M. Sánchez C.
- Active Devs: Elijah Bartolome
- PIs: David L. Smith, John M. Marshall
Progress and Features
- Setup pkg skeleton
Setup pypi pkgSetup CISetup autodoc
- Landscape generation and variables update
Basic landscape and matrices initAuto-calculate distance matrixAuto-calculate migration matrixLandscape onbjects constructorsAuto distance and migration updates on changeUpdate traps migrations in place (avoids memory shifts)Update traps migrations with new array if traps number changes
- Plots
- Landscape
Auto-assign markers with point-typeAuto-assign colors with trap-typeAuto-assign edge to trap if non-movableAuto-plot trap radii- Spherical coordinates projection
- Directed networks
Migration matricesBlock Migration matricesRemove frames and axes
- Landscape
- Genetic Algorithm
Init chromosome- Fitness function
Canonical formGet steady absorbing statesPut the cost function togetherMarkov's fundamental matrix with no re-ordering- Test different fitness functions
Code new mutation functionsCode new crossover functionsImplement full optimization loop
- Code efficiency
Process traps movement in place
- Tests
Points and traps numbers are updated correctlyCheck matrices for Markov validity- Test landscape with external migrations
- Changing number of traps doesn't affect migration part
Selective mutation
- Wishlist
Non-movable trapsAdd to object propertiesAdd to mutationAdd to crossover
Different trap types- Male/Female kernel
- Point-processes generation
- Parallelize fitness function evaluation
Project details
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