Package: MGDrivE 1.6.0

Héctor Manuel Sánchez Castellanos

MGDrivE: Mosquito Gene Drive Explorer

Provides a model designed to be a reliable testbed where various gene drive interventions for mosquito-borne diseases control. It is being developed to accommodate the use of various mosquito-specific gene drive systems within a population dynamics framework that allows migration of individuals between patches in landscape. Previous work developing the population dynamics can be found in Deredec et al. (2001) <doi:10.1073/pnas.1110717108> and Hancock & Godfray (2007) <doi:10.1186/1475-2875-6-98>, and extensions to accommodate CRISPR homing dynamics in Marshall et al. (2017) <doi:10.1038/s41598-017-02744-7>.

Authors:Héctor Manuel Sánchez Castellanos [aut, cre], Jared Bennett [aut], Sean Wu [aut], John M. Marshall [aut]

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MGDrivE.pdf |MGDrivE.html✨
MGDrivE/json (API)
NEWS

# Install 'MGDrivE' in R:
install.packages('MGDrivE', repos = c('https://marshalllab.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/marshalllab/mgdrive/issues

Uses libs:
  • c++– GNU Standard C++ Library v3
Datasets:

On CRAN:

41 exports 3 stars 2.31 score 4 dependencies 7 mentions 61 scripts 192 downloads

Last updated 4 years agofrom:bcd714a107. Checks:OK: 4 NOTE: 5. Indexed: yes.

TargetResultDate
Doc / VignettesOKSep 08 2024
R-4.5-win-x86_64NOTESep 08 2024
R-4.5-linux-x86_64NOTESep 08 2024
R-4.4-win-x86_64NOTESep 08 2024
R-4.4-mac-x86_64NOTESep 08 2024
R-4.4-mac-aarch64NOTESep 08 2024
R-4.3-win-x86_64OKSep 08 2024
R-4.3-mac-x86_64OKSep 08 2024
R-4.3-mac-aarch64OKSep 08 2024

Exports:aggregateFemalesaggregateOutputbasicBatchMigrationcalcCoscalcExpKernelcalcGammaKernelcalcHaversinecalcHurdleExpKernelcalcLognormalKernelcalcOmegacalcQuantilescalcVinEllcalcVinSphcalcZeroInflationcube2csvcubeClvRcubeClvR2cubeECHACRcubeECHACRXcubeHoming1RAcubeHomingDrivecubeKillerRescuecubeMEDEAcubeMendeliancubeOneLocusTAcubeReciprocalTranslocationscubeRIDLcubeSplitDrivecubeTGDcubeTGDXcubeTwoLocusTAcubeWolbachiaeraseDirectorygenerateReleaseVectorNetworkparameterizeMGDrivEplotMGDrivEMultplotMGDrivESingleretrieveOutputsetupMGDrivEsplitOutput

Dependencies:R6rbibutilsRcppRdpack

MGDrivE Examples

Rendered frommgdrive_examples.Rmdusingknitr::rmarkdownon Sep 08 2024.

Last update: 2020-10-05
Started: 2019-08-02

MGDrivE Mathematical Description

Rendered frommgdrive_math.Rmdusingknitr::rmarkdownon Sep 08 2024.

Last update: 2020-10-05
Started: 2019-08-02

MGDrivE Run Example

Rendered frommgdrive_run.Rmdusingknitr::rmarkdownon Sep 08 2024.

Last update: 2020-01-22
Started: 2019-08-02

Readme and manuals

Help Manual

Help pageTopics
Aggregate Female Output by GenotypeaggregateFemales
Aggregate Output Over LandscapeaggregateOutput
Make List of Batch Migration ParametersbasicBatchMigration
Make List of Modified Mosquito ReleasesbasicRepeatedReleases
Calculate Aquatic Stage Survival ProbabilitycalcAquaticStageSurvivalProbability
Calculate Average Generation TimecalcAverageGenerationTime
Calculate Geodesic Distance - Cosine MethodcalcCos
Calculate Density-dependent Larval MortalitycalcDensityDependentDeathRate
Calculate Exponential Stochastic MatrixcalcExpKernel
Calculate Gamma Stochastic MatrixcalcGammaKernel
Calculate Geodesic Distance - Haversine MethodcalcHaversine
Calculate Zero-inflated Exponential Stochastic MatrixcalcHurdleExpKernel
Calculate Distribution of Larval PopulationcalcLarvalDist
Calculate Equilibrium Larval PopulationcalcLarvalPopEquilibrium
Calculate Larval Stage Mortality RatecalcLarvalStageMortalityRate
Calculate Lognormal Stochastic MatrixcalcLognormalKernel
Solve for Omega (additional genotype-specific mortality)calcOmega
Calculate Generational Population Growth RatecalcPopulationGrowthRate
Summary Statistics for Stochastic MGDrivEcalcQuantiles
Calculate Geodesic Distance - Vincenty Ellipsoid MethodcalcVinEll
Calculate Geodesic Distance - Vincenty Sphere MethodcalcVinSph
Calculates the zero-inflation part of a hurdle exponential kernel.calcZeroInflation
Export a Cube to .csvcube2csv
Inheritance Cube: ClvR (Cleave and Rescue)cubeClvR
Inheritance Cube: 2-Locus ClvR (Cleave and Rescue)cubeClvR2
Inheritance Cube: ECHACRcubeECHACR
Inheritance Cube: ECHACRXcubeECHACRX
Inheritance Cube: Homing Drive with 1 Resistance AllelecubeHoming1RA
Inheritance Cube: CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) with 2 Resistance Alleles and maternal depositioncubeHomingDrive
Inheritance Cube: Killer-Rescue SystemcubeKillerRescue
Inheritance Cube: MEDEA (Maternal Effect Dominant Embryonic Arrest)cubeMEDEA
Inheritance Cube: MendeliancubeMendelian
Generate and Modify Default Genotype-specific ParameterscubeModifiers
Inheritance Cube: 1 Locus Maternal-Toxin/Zygotic-Antidote SystemcubeOneLocusTA
Inheritance Cube: Reciprocal TranslocationcubeReciprocalTranslocations
Inheritance Cube: RIDL (Release of Insects with Dominant Lethality)cubeRIDL
Inheritance Cube: Split CRISPR drive with 2 Resistance Alleles and male/female specific homingcubeSplitDrive
Inheritance Cube: tGDcubeTGD
Inheritance Cube: tGDXcubeTGDX
Inheritance Cube: 2 Locus Maternal-Toxin/Zygotic-Antidote SystemcubeTwoLocusTA
Inheritance Cube: WolbachiacubeWolbachia
Erase all files in a directoryeraseDirectory
Make List of Modified Mosquito ReleasesgenerateReleaseVector
Get alphaget_alpha_Network
Get betaget_beta_Network
Get conADFget_conF_Network
Get conADMget_conM_Network
Get Element(s) of Drive Cube by Indexget_drivecubeindex_Network
Get etaget_eta_Network
Get female Populationget_femalePop_Patch
Get genotypesIDget_genotypesID_Network
Get genotypesNget_genotypesN_Network
Get male Populationget_malePop_Patch
Get muAdget_muAd_Network
Get muAqget_muAq_Network
Get nPatchget_nPatch_Network
Get omegaget_omega_Network
Get Patch Release Scheduleget_patchReleases_Network
Get phiget_phi_Network
Get sget_s_Network
Get Female Viability Mask (tau)get_tau_Network
Get timeAqget_timeAq_Network
Get tNowget_tNow_Network
Get xiFget_xiF_Network
Get xiMget_xiM_Network
Utility to Imitate ggplot2 ColorsggColUtility
Kernels Parameterskernels
MGDrivE: Mosquito Gene Drive ExplorerMGDrivE
MGDrivE: Inheritance CubeMGDrivE-Cube
MGDrivE: Model's Mathematical DescriptionMGDrivE-Model
Movement Matrix: All 2moveMatAll2
Movement Matrix: Cascade 3moveMatCascade3
Movement Matrix: DiagonalmoveMatDiag
Movement Matrix: Diagonal One CitymoveMatDiagOneCity
Movement Matrix: DiemoveMatDie
Movement Matrix: Independent 3moveMatIndependent3
Movement Matrix: Mixed SpillmoveMatMixedSpil
Movement Matrix: Tale of Two CitiesmoveMatTaleOfTwoCities
Movement Matrix: Tri-diagonalmoveMatTriDiagonal
Movement Matrix: TriplemoveMatTriple
Run SimulationmultRun_Network
Network Class DefinitionNetwork
Normalise a Numeric Vectornormalise
Deterministic Adult SurvivaloneDay_adultDeath_deterministic_Patch
Stochastic Adult SurvivaloneDay_adultDeath_stochastic_Patch
Deterministic Egg Death and PupationoneDay_eggDM_deterministic_Patch
Stochastic Egg Death and PupationoneDay_eggDM_stochastic_Patch
Release Eggs in a PatchoneDay_eggReleases_Patch
Initialize Output from Focal PatchoneDay_initOutput_Patch
Deterministic Larva Death and PupationoneDay_larvaDM_deterministic_Patch
Stochastic Larva Death and PupationoneDay_larvaDM_stochastic_Patch
Deterministic MatingoneDay_mating_deterministic_Patch
Stochastic MatingoneDay_mating_stochastic_Patch
Deterministic Inter-Patch MigrationoneDay_Migration_Deterministic_Network
Stochastic Inter-Patch MigrationoneDay_Migration_Stochastic_Network
Inbound MigrationoneDay_migrationIn_Patch
Run a Single Day on a NetworkoneDay_Network
Deterministic OvipositiononeDay_oviposit_deterministic_Patch
Stochastic OvipositiononeDay_oviposit_stochastic_Patch
Daily Population Dynamics for a PatchoneDay_PopDynamics_Patch
Deterministic Pupa Death and PupationoneDay_pupaDM_deterministic_Patch
Stochastic Pupa Death and PupationoneDay_pupaDM_stochastic_Patch
Deterministic PupationoneDay_pupation_deterministic_Patch
Stochastic PupationoneDay_pupation_stochastic_Patch
Release Male/Female/Mated-Female Mosquitoes in a PatchoneDay_releases_Patch
Write Output from Focal PatchoneDay_writeOutput_Patch
Run SimulationoneRun_Network
parameterizeMGDrivEparameterizeMGDrivE
Patch Class DefinitionPatch
PlotplotMGDrivEMult
PlotplotMGDrivESingle
Quantiles FunctionquantileC
Dirichlet DistributionrDirichlet
Reset Networkreset_Network
Reset Patch to Initial Conditionsreset_Patch
Retrieve OutputretrieveOutput
Set Initial Populationset_initialPopulation_Patch
Set Network Pointerset_NetworkPointer_Patch
Set Initial Population Deterministicset_population_deterministic_Patch
Set Initial Population Stochasticset_population_stochastic_Patch
Setup MGDrivEsetupMGDrivE
Split Output by PatchsplitOutput