# Mosquito Gene Drive Explorer

## Documentation for package ‘MGDrivE’ version 1.6.2

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

aggregateFemales | Aggregate Female Output by Genotype
aggregateOutput | Aggregate Output Over Landscape
basicBatchMigration | Make List of Batch Migration Parameters
calcCos | Calculate Geodesic Distance - Cosine Method
calcExpKernel | Calculate Exponential Stochastic Matrix
calcGammaKernel | Calculate Gamma Stochastic Matrix
calcHaversine | Calculate Geodesic Distance - Haversine Method
calcHurdleExpKernel | Calculate Zero-inflated Exponential Stochastic Matrix
calcLognormalKernel | Calculate Lognormal Stochastic Matrix
calcOmega | Solve for Omega (additional genotype-specific mortality)
calcQuantiles | Summary Statistics for Stochastic MGDrivE
calcVinEll | Calculate Geodesic Distance - Vincenty Ellipsoid Method
calcVinSph | Calculate Geodesic Distance - Vincenty Sphere Method
calcZeroInflation | Calculates the zero-inflation part of a hurdle exponential kernel.
cube2csv | Export a Cube to .csv
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
cubeConfinableHomingJOHN | Inheritance Cube: Confinable Homing Drive, John
cubeConfinableHomingX | Inheritance Cube: Confinable Homing, X-Linked
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
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
cubeOneLocusTA | Inheritance Cube: 1 Locus Maternal-Toxin/Zygotic-Antidote System
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
cubeTGD | Inheritance Cube: tGD
cubeTGDX | Inheritance Cube: tGDX
cubeTwoLocusTA | Inheritance Cube: 2 Locus Maternal-Toxin/Zygotic-Antidote System
cubeWolbachia | Inheritance Cube: Wolbachia
cubeXHomingDeposition | Inheritance Cube: CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) X-linked with 2 Resistance Allele and Maternal Deposition
cubeXShredderMF | Inheritance Cube: Autosomal X-Shredder
cubeXShredderY | Inheritance Cube: Y-Linked X-Shredder
eraseDirectory | Erase all files in a directory
generateReleaseVector | Make List of Modified Mosquito Releases
kernels | Kernels Parameters
MGDrivE | MGDrivE: Mosquito Gene Drive Explorer
MGDrivE-Cube | MGDrivE: Inheritance Cube
MGDrivE-Model | MGDrivE: Model's Mathematical Description
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
multRun_Network | Run Simulation
Network | Network Class Definition
oneRun_Network | Run Simulation
parameterizeMGDrivE | parameterizeMGDrivE
Patch | Patch Class Definition
plotMGDrivEMult | Plot
plotMGDrivESingle | Plot
reset_Network | Reset Network
retrieveOutput | Retrieve Output
setupMGDrivE | Setup MGDrivE
splitOutput | Split Output by Patch