GilChrist19 / mPlex

Gene drive multiplex model using an ABM.

Agent-based Modeling of Mosquitoes

This repository contains two models that were developed at the Marshall Lab, University of California, Berkeley.

• mPlex - an agent-based model for multiplexing (one locus, multiple gRNA or multiple loci, single gRNAs at each) gene drives and daisy-drives.
  • mPlexR: Pure R-based implementation of mPlex
    This was the original test bed and is now out-of-date
  • mPlexCpp: Current, C++11/14-based package
• CKMR - an agent-based adaptation of mPlex to study close-kin mark-recapture methods in mosquitoes. This adaptation removes much of the genetics and allows for more appropriate population sampling and geneology tracing.

Repository

• CKMR - C++ package for close-kin mark-recapture studies
• Main - Project directories and scripts
• mPlexCpp - C++ package for multiplex studies
• mPlexR - R package for multiplex studies (old, consider this deprecated)
• ComparisonScript - Comparison of mPlex vs MGDrivE to check population dynamics and simple one-locus homing constructs.

Authors

Jared Bennett (lead), Sean Wu, Héctor Manuel Sánchez Castellanos, and John M. Marshall

To-do

1. Write out pseudocode of offspringDistribution function.
   • goal is to de-couple the tightly coupled reference and offspringDistribution elements; we want a generic offspringDistribution so the only variant type is reference.
2. Check move semantics between stl containers working properly for Mosquito for low overhead migration functions.
3. Should steal the output/input classes from MGDrivECpp for better performance.

Notes and References

1. Short and sweet OMP guide
2. RcppArmadillo reference
3. Rcpp reference