# Mosquito Gene Drive Explorer

## Documentation for package ‘MGDrivE’ version 1.6.0

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

## Help Pages

A B C E G K M N O P Q R S

## -- A --

aggregateFemales | Aggregate Female Output by Genotype
aggregateOutput | Aggregate Output Over Landscape

## -- B --

basicBatchMigration | Make List of Batch Migration Parameters
basicRepeatedReleases | Make List of Modified Mosquito Releases

## -- C --

calcAquaticStageSurvivalProbability | Calculate Aquatic Stage Survival Probability
calcAverageGenerationTime | Calculate Average Generation Time
calcCos | Calculate Geodesic Distance - Cosine Method
calcDensityDependentDeathRate | Calculate Density-dependent Larval Mortality
calcExpKernel | Calculate Exponential Stochastic Matrix
calcGammaKernel | Calculate Gamma Stochastic Matrix
calcHaversine | Calculate Geodesic Distance - Haversine Method
calcHurdleExpKernel | Calculate Zero-inflated Exponential Stochastic Matrix
calcLarvalDist | Calculate Distribution of Larval Population
calcLarvalPopEquilibrium | Calculate Equilibrium Larval Population
calcLarvalStageMortalityRate | Calculate Larval Stage Mortality Rate
calcLognormalKernel | Calculate Lognormal Stochastic Matrix
calcOmega | Solve for Omega (additional genotype-specific mortality)
calcPopulationGrowthRate | Calculate Generational Population Growth Rate
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
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
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
cubeTGD | Inheritance Cube: tGD
cubeTGDX | Inheritance Cube: tGDX
cubeTwoLocusTA | Inheritance Cube: 2 Locus Maternal-Toxin/Zygotic-Antidote System
cubeWolbachia | Inheritance Cube: Wolbachia

## -- E --

eraseDirectory | Erase all files in a directory

## -- G --

generateReleaseVector | Make List of Modified Mosquito Releases
get_alpha_Network | Get alpha
get_beta_Network | Get beta
get_conF_Network | Get conADF
get_conM_Network | Get conADM
get_drivecubeindex_Network | Get Element(s) of Drive Cube by Index
get_eta_Network | Get eta
get_femalePop_Patch | Get female Population
get_genotypesID_Network | Get genotypesID
get_genotypesN_Network | Get genotypesN
get_malePop_Patch | Get male Population
get_muAd_Network | Get muAd
get_muAq_Network | Get muAq
get_nPatch_Network | Get nPatch
get_omega_Network | Get omega
get_patchReleases_Network | Get Patch Release Schedule
get_phi_Network | Get phi
get_s_Network | Get s
get_tau_Network | Get Female Viability Mask (tau)
get_timeAq_Network | Get timeAq
get_tNow_Network | Get tNow
get_xiF_Network | Get xiF
get_xiM_Network | Get xiM
ggColUtility | Utility to Imitate ggplot2 Colors

## -- K --

kernels | Kernels Parameters

## -- M --

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

## -- N --

Network | Network Class Definition
normalise | Normalise a Numeric Vector

## -- O --

oneDay_adultDeath_deterministic_Patch | Deterministic Adult Survival
oneDay_adultDeath_stochastic_Patch | Stochastic Adult Survival
oneDay_eggDM_deterministic_Patch | Deterministic Egg Death and Pupation
oneDay_eggDM_stochastic_Patch | Stochastic Egg Death and Pupation
oneDay_eggReleases_Patch | Release Eggs in a Patch
oneDay_initOutput_Patch | Initialize Output from Focal Patch
oneDay_larvaDM_deterministic_Patch | Deterministic Larva Death and Pupation
oneDay_larvaDM_stochastic_Patch | Stochastic Larva Death and Pupation
oneDay_mating_deterministic_Patch | Deterministic Mating
oneDay_mating_stochastic_Patch | Stochastic Mating
oneDay_migrationIn_Patch | Inbound Migration
oneDay_Migration_Deterministic_Network | Deterministic Inter-Patch Migration
oneDay_Migration_Stochastic_Network | Stochastic Inter-Patch Migration
oneDay_Network | Run a Single Day on a Network
oneDay_oviposit_deterministic_Patch | Deterministic Oviposition
oneDay_oviposit_stochastic_Patch | Stochastic Oviposition
oneDay_PopDynamics_Patch | Daily Population Dynamics for a Patch
oneDay_pupaDM_deterministic_Patch | Deterministic Pupa Death and Pupation
oneDay_pupaDM_stochastic_Patch | Stochastic Pupa Death and Pupation
oneDay_pupation_deterministic_Patch | Deterministic Pupation
oneDay_pupation_stochastic_Patch | Stochastic Pupation
oneDay_releases_Patch | Release Male/Female/Mated-Female Mosquitoes in a Patch
oneDay_writeOutput_Patch | Write Output from Focal Patch
oneRun_Network | Run Simulation

## -- P --

parameterizeMGDrivE | parameterizeMGDrivE
Patch | Patch Class Definition
plotMGDrivEMult | Plot
plotMGDrivESingle | Plot

## -- Q --

quantileC | Quantiles Function

## -- R --

rDirichlet | Dirichlet Distribution
reset_Network | Reset Network
reset_Patch | Reset Patch to Initial Conditions
retrieveOutput | Retrieve Output

## -- S --

setupMGDrivE | Setup MGDrivE
set_initialPopulation_Patch | Set Initial Population
set_NetworkPointer_Patch | Set Network Pointer
set_population_deterministic_Patch | Set Initial Population Deterministic
set_population_stochastic_Patch | Set Initial Population Stochastic
splitOutput | Split Output by Patch