Package: MGDrivE 1.6.2

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]

MGDrivE_1.6.2.tar.gz
MGDrivE_1.6.2.zip(r-4.7)MGDrivE_1.6.2.zip(r-4.6)MGDrivE_1.6.2.zip(r-4.5)
MGDrivE_1.6.2.tgz(r-4.6-x86_64)MGDrivE_1.6.2.tgz(r-4.6-arm64)MGDrivE_1.6.2.tgz(r-4.5-x86_64)MGDrivE_1.6.2.tgz(r-4.5-arm64)
MGDrivE_1.6.2.tar.gz(r-4.7-arm64)MGDrivE_1.6.2.tar.gz(r-4.7-x86_64)MGDrivE_1.6.2.tar.gz(r-4.6-arm64)MGDrivE_1.6.2.tar.gz(r-4.6-x86_64)
MGDrivE_1.6.2.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
MGDrivE/json (API)

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

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

Pkgdown/docs site:https://marshalllab.github.io

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

On CRAN:

Conda:

cpp

7.96 score 8 stars 122 scripts 581 downloads 7 mentions 56 exports 4 dependencies

Last updated from:f7ec820e8a. Checks:13 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-arm64OK218
linux-devel-x86_64OK265
source / vignettesOK408
linux-release-arm64OK226
linux-release-x86_64OK242
macos-release-arm64OK237
macos-release-x86_64OK356
macos-oldrel-arm64OK170
macos-oldrel-x86_64OK305
windows-develOK224
windows-releaseOK215
windows-oldrelOK188
wasm-releaseOK149

Exports:aggregateFemalesaggregateOutputbasicBatchMigrationcalcCoscalcExpKernelcalcGammaKernelcalcHaversinecalcHurdleExpKernelcalcLognormalKernelcalcOmegacalcQuantilescalcVinEllcalcVinSphcalcZeroInflationcube2csvcubeAlleleSailcubeASmidlercubeCLEAVRMFcubeCLEAVRXcubeClvRcubeClvR2cubeConfinableHomingcubeConfinableHomingJOHNcubeConfinableHomingXcubeECHACRcubeECHACRXcubeHoming1RAcubeHomingDrivecubeHomingDriveSMcubeImmunizingReversalMFcubeImmunizingReversalXcubeKillerRescuecubeMEDEAcubeMendeliancubeOneLocusTAcubeReciprocalTranslocationscubeRIDLcubeSplitDrivecubeSplitDriveXcubeSplitDriveYcubeTGDcubeTGDXcubeTwoLocusTAcubeWolbachiacubeXHomingDepositioncubeXShredderMFcubeXShredderYeraseDirectorygenerateReleaseVectorNetworkparameterizeMGDrivEplotMGDrivEMultplotMGDrivESingleretrieveOutputsetupMGDrivEsplitOutput

Dependencies:R6rbibutilsRcppRdpack

MGDrivE Examples
Landscape Setup | Single Population | Two Populations | n Populations | Realistic Location | Inheritance Simulations | Mendelian Inheritance Simulations, Single Population | Deterministic | Deterministic, With Fitness Cost | Stochastic | Mendelian Inheritance Simulations, Two Populations | Deterministic, No Migration | Deterministic, Small Migration | Stochastic, Small Migration | Stochastic, Small Migration and Fitness Cost | Reciprocal Translocation Gene Drive Simulations, One Population | Deterministic, Below Threshold | Deterministic, Above Threshold | Stochastic, "Above" Threshold
Rendered frommgdrive_examples.Rmdusingknitr::rmarkdown

Last update: 2025-08-27
Started: 2019-08-02

MGDrivE Mathematical Description
Introduction | Brief Description | Previous Work: | Notation and Conventions | Mathematical Framework | Inheritance Cube | Drive-specific Cubes | Population Dynamics | Larval Stages | Adult Stages | Gene Drive Releases and Effects | Migration | Stochasticity | Mosquito Biology | References
Rendered frommgdrive_math.Rmdusingknitr::rmarkdown

Last update: 2025-08-27
Started: 2019-08-02

MGDrivE Run Example
MGDrivE, One Run | Mendelian Inheritance, Stochastic, Multiple Populations | Full Code | Load Libraries | Setup Folder Directory | Simulation Parameters | Inheritance Pattern | Releases | Setup and Run | Post Processing | Plotting
Rendered frommgdrive_run.Rmdusingknitr::rmarkdown

Last update: 2025-08-27
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
Calculate Geodesic Distance - Cosine MethodcalcCos
Calculate Exponential Stochastic MatrixcalcExpKernel
Calculate Gamma Stochastic MatrixcalcGammaKernel
Calculate Geodesic Distance - Haversine MethodcalcHaversine
Calculate Zero-inflated Exponential Stochastic MatrixcalcHurdleExpKernel
Calculate Lognormal Stochastic MatrixcalcLognormalKernel
Solve for Omega (additional genotype-specific mortality)calcOmega
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: 3-Piece Allele SailcubeAlleleSail
Inheritance Cube: Split-Drive for Andrea SmidlercubeASmidler
Inheritance Cube: CLEAVR - Cleave and RescuecubeCLEAVRMF
Inheritance Cube: CLEAVR - Cleave and RescuecubeCLEAVRX
Inheritance Cube: ClvR (Cleave and Rescue)cubeClvR
Inheritance Cube: 2-Locus ClvR (Cleave and Rescue)cubeClvR2
Inheritance Cube: Confinable HomingcubeConfinableHoming
Inheritance Cube: Confinable Homing Drive, JohncubeConfinableHomingJOHN
Inheritance Cube: Confinable Homing, X-LinkedcubeConfinableHomingX
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: CRISPR-SM (Clustered Regularly Interspaced Short Palindromic Repeats) with Small-Molecule Induction and 1 Resistance Allele and Maternal DepositioncubeHomingDriveSM
Inheritance Cube: Immunizing Reversal/Basic ReversalcubeImmunizingReversalMF
Inheritance Cube: Immunizing ReversalcubeImmunizingReversalX
Inheritance Cube: Killer-Rescue SystemcubeKillerRescue
Inheritance Cube: MEDEA (Maternal Effect Dominant Embryonic Arrest)cubeMEDEA
Inheritance Cube: MendeliancubeMendelian
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: X-linked Split CRISPR Drive with 2 Resistance Alleles and male/female specific homingcubeSplitDriveX
Inheritance Cube: Y-linked Split CRISPR Drive with 2 Resistance AllelescubeSplitDriveY
Inheritance Cube: tGDcubeTGD
Inheritance Cube: tGDXcubeTGDX
Inheritance Cube: 2 Locus Maternal-Toxin/Zygotic-Antidote SystemcubeTwoLocusTA
Inheritance Cube: WolbachiacubeWolbachia
Inheritance Cube: CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) X-linked with 2 Resistance Allele and Maternal DepositioncubeXHomingDeposition
Inheritance Cube: Autosomal X-ShreddercubeXShredderMF
Inheritance Cube: Y-Linked X-ShreddercubeXShredderY
Erase all files in a directoryeraseDirectory
Make List of Modified Mosquito ReleasesgenerateReleaseVector
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
Run SimulationoneRun_Network
parameterizeMGDrivEparameterizeMGDrivE
Patch Class DefinitionPatch
PlotplotMGDrivEMult
PlotplotMGDrivESingle
Reset Networkreset_Network
Retrieve OutputretrieveOutput
Setup MGDrivEsetupMGDrivE
Split Output by PatchsplitOutput