Package index • MGDrivE

Software Introduction

Articles which describe key mathematical points and features of the MGDrivE simulation.

MGDrivE: MGDrivE: Mosquito Gene Drive Explorer

MGDrivE-Model: MGDrivE: Model's Mathematical Description

MGDrivE-Cube: MGDrivE: Inheritance Cube

Inheritance Cubes

A description of the available inheritance cubes for simulation, and some associated helper functions.

cubeAlleleSail(): Inheritance Cube: 3-Piece Allele Sail

cubeASmidler(): Inheritance Cube: Split-Drive for Andrea Smidler

cubeCLEAVRMF(): Inheritance Cube: CLEAVR - Cleave and Rescue

cubeCLEAVRX(): Inheritance Cube: CLEAVR - Cleave and Rescue

cubeClvR(): Inheritance Cube: ClvR (Cleave and Rescue)

cubeClvR2(): Inheritance Cube: 2-Locus ClvR (Cleave and Rescue)

cubeConfinableHoming(): Inheritance Cube: Confinable Homing

cubeConfinableHomingX(): Inheritance Cube: Confinable Homing, X-Linked

cubeConfinableHomingJOHN(): Inheritance Cube: Confinable Homing Drive, John

cubeECHACR(): Inheritance Cube: ECHACR

cubeECHACRX(): Inheritance Cube: ECHACRX

cubeHoming1RA(): Inheritance Cube: Homing Drive with 1 Resistance Allele

cubeHomingDrive(): Inheritance Cube: CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) with 2 Resistance Alleles and maternal deposition

cubeHomingDriveSM(): Inheritance Cube: CRISPR-SM (Clustered Regularly Interspaced Short Palindromic Repeats) with Small-Molecule Induction and 1 Resistance Allele and Maternal Deposition

cubeXHomingDeposition(): Inheritance Cube: CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) X-linked with 2 Resistance Allele and Maternal Deposition

cubeImmunizingReversalMF(): Inheritance Cube: Immunizing Reversal/Basic Reversal

cubeImmunizingReversalX(): Inheritance Cube: Immunizing Reversal

cubeKillerRescue(): Inheritance Cube: Killer-Rescue System

cubeMEDEA(): Inheritance Cube: MEDEA (Maternal Effect Dominant Embryonic Arrest)

cubeMendelian(): Inheritance Cube: Mendelian

cubeReciprocalTranslocations(): Inheritance Cube: Reciprocal Translocation

cubeRIDL(): Inheritance Cube: RIDL (Release of Insects with Dominant Lethality)

cubeSplitDrive(): Inheritance Cube: Split CRISPR Drive with 2 Resistance Alleles and male/female specific homing

cubeSplitDriveX(): Inheritance Cube: X-linked Split CRISPR Drive with 2 Resistance Alleles and male/female specific homing

cubeSplitDriveY(): Inheritance Cube: Y-linked Split CRISPR Drive with 2 Resistance Alleles

cubeOneLocusTA(): Inheritance Cube: 1 Locus Maternal-Toxin/Zygotic-Antidote System

cubeTwoLocusTA(): Inheritance Cube: 2 Locus Maternal-Toxin/Zygotic-Antidote System

cubeTGD(): Inheritance Cube: tGD

cubeTGDX(): Inheritance Cube: tGDX

cubeWolbachia(): Inheritance Cube: Wolbachia

cubeXShredderMF(): Inheritance Cube: Autosomal X-Shredder

cubeXShredderY(): Inheritance Cube: Y-Linked X-Shredder

cube2csv(): Export a Cube to .csv

Kernel & Geographic Distance

Functions to generate movement matrices based on parameteric dispersal kernels and function to calculate distance matrices between latitude/longitude pairs of points.

calcCos(): Calculate Geodesic Distance - Cosine Method

calcHaversine(): Calculate Geodesic Distance - Haversine Method

calcVinSph(): Calculate Geodesic Distance - Vincenty Sphere Method

calcVinEll(): Calculate Geodesic Distance - Vincenty Ellipsoid Method

calcZeroInflation(): Calculates the zero-inflation part of a hurdle exponential kernel.

calcLognormalKernel(): Calculate Lognormal Stochastic Matrix

calcGammaKernel(): Calculate Gamma Stochastic Matrix

calcExpKernel(): Calculate Exponential Stochastic Matrix

calcHurdleExpKernel(): Calculate Zero-inflated Exponential Stochastic Matrix

Population Dynamics Parameters

A description of model parameters governing population dynamics, not including inheritance, which is described in its own section. This section also includes functions that generate mosquito release events and set up probabilities for batch migration, and the functions which select between deterministic or stochastic simulation.

calcOmega(): Solve for Omega (additional genotype-specific mortality)

parameterizeMGDrivE(): parameterizeMGDrivE

generateReleaseVector(): Make List of Modified Mosquito Releases

basicRepeatedReleases(): Make List of Modified Mosquito Releases

basicBatchMigration(): Make List of Batch Migration Parameters

setupMGDrivE(): Setup MGDrivE

Data

Data files included in MGDrivE, contains fitted parameters for parameteric mosquito dispersal kernels and movement matrices for illustrative simulations.

kernels: Kernels Parameters

moveMatAll2: Movement Matrix: All 2

moveMatCascade3: Movement Matrix: Cascade 3

moveMatDiag: Movement Matrix: Diagonal

moveMatDiagOneCity: Movement Matrix: Diagonal One City

moveMatDie: Movement Matrix: Die

moveMatIndependent3: Movement Matrix: Independent 3

moveMatMixedSpil: Movement Matrix: Mixed Spill

moveMatTaleOfTwoCities: Movement Matrix: Tale of Two Cities

moveMatTriDiagonal: Movement Matrix: Tri-diagonal

moveMatTriple: Movement Matrix: Triple

Analysis of Output

Functions that allow the output to be summarized and plotted.

eraseDirectory(): Erase all files in a directory

retrieveOutput(): Retrieve Output

splitOutput(): Split Output by Patch

aggregateFemales(): Aggregate Female Output by Genotype

aggregateOutput(): Aggregate Output Over Landscape

calcQuantiles(): Summary Statistics for Stochastic MGDrivE

plotMGDrivESingle(): Plot

plotMGDrivEMult(): Plot

Network Class

The Network object class which is the main object with which to interact with the MGDrivE simulation, and manages the metapopulation dynamics upon which the simulation runs.

Network: Network Class Definition

oneRun_Network(): Run Simulation

multRun_Network(): Run Simulation

reset_Network(): Reset Network

Patch Class

A Patch is a single well-mixed population that is the smallest unit of simulation for MGDrivE.

Patch: Patch Class Definition