MGDrivE                 MGDrivE: Mosquito Gene Drive Explorer
MGDrivE-Cube            MGDrivE: Inheritance Cube
MGDrivE-Model           MGDrivE: Model's Mathematical Description
Network                 Network Class Definition
Patch                   Patch Class Definition
aggregateFemales        Aggregate Female Output by Genotype
aggregateOutput         Aggregate Output Over Landscape
basicBatchMigration     Make List of Batch Migration Parameters
basicRepeatedReleases   Make List of Modified Mosquito Releases
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
cubeRIDL                Inheritance Cube: RIDL (Release of Insects with
                        Dominant Lethality)
cubeReciprocalTranslocations
                        Inheritance Cube: Reciprocal Translocation
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
eraseDirectory          Erase all files in a directory
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_tNow_Network        Get tNow
get_tau_Network         Get Female Viability Mask (tau)
get_timeAq_Network      Get timeAq
get_xiF_Network         Get xiF
get_xiM_Network         Get xiM
ggColUtility            Utility to Imitate ggplot2 Colors
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
multRun_Network         Run Simulation
normalise               Normalise a Numeric Vector
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_PopDynamics_Patch
                        Daily Population Dynamics for a Patch
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_oviposit_deterministic_Patch
                        Deterministic Oviposition
oneDay_oviposit_stochastic_Patch
                        Stochastic Oviposition
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
parameterizeMGDrivE     parameterizeMGDrivE
plotMGDrivEMult         Plot
plotMGDrivESingle       Plot
quantileC               Quantiles Function
rDirichlet              Dirichlet Distribution
reset_Network           Reset Network
reset_Patch             Reset Patch to Initial Conditions
retrieveOutput          Retrieve Output
set_NetworkPointer_Patch
                        Set Network Pointer
set_initialPopulation_Patch
                        Set Initial Population
set_population_deterministic_Patch
                        Set Initial Population Deterministic
set_population_stochastic_Patch
                        Set Initial Population Stochastic
setupMGDrivE            Setup MGDrivE
splitOutput             Split Output by Patch
