Mosquito Gene Drive Explorer

Documentation for package ‘MGDrivE’ version 1.6.0

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-- 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