Function reference • MGDrivE

Inheritance Cubes A description of the available inheritance cubes for simulation, and some associated helper functions.
`cubeClvR()`	Inheritance Cube: ClvR (Cleave and Rescue)
`cubeClvR2()`	Inheritance Cube: 2-Locus ClvR (Cleave and Rescue)
`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
`cubeKillerRescue()`	Inheritance Cube: Killer-Rescue System
`cubeMEDEA()`	Inheritance Cube: MEDEA (Maternal Effect Dominant Embryonic Arrest)
`cubeMendelian()`	Inheritance Cube: Mendelian
`cubeModifiers()`	Generate and Modify Default Genotype-specific Parameters
`cubeOneLocusTA()`	Inheritance Cube: 1 Locus Maternal-Toxin/Zygotic-Antidote System
`cubeTwoLocusTA()`	Inheritance Cube: 2 Locus Maternal-Toxin/Zygotic-Antidote System
`cubeRIDL()`	Inheritance Cube: RIDL (Release of Insects with Dominant Lethality)
`cubeReciprocalTranslocations()`	Inheritance Cube: Reciprocal Translocation
`cubeWolbachia()`	Inheritance Cube: Wolbachia
`cube2csv()`	Export a Cube to .csv
`cubeSplitDrive()`	Inheritance Cube: Split CRISPR drive with 2 Resistance Alleles and male/female specific homing
`cubeTGD()`	Inheritance Cube: tGD
`cubeTGDX()`	Inheritance Cube: tGDX
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

Reference

Inheritance Cubes

Kernel & Geographic Distance

Population Dynamics Parameters

Data

Analysis of Output

Network Class

Contents