parameterizeMGDrivE: parameterizeMGDrivE

In MGDrivE: Mosquito Gene Drive Explorer

parameterizeMGDrivE

Description

Generate parameters for simulation on a Network. Parameters include: average generation time g, population growth rate R_{m}, aquatic mortality \mu_{Aq}, and aquatic survival \theta_{Aq}, which are shared between patches and calculated by calcAverageGenerationTime, calcPopulationGrowthRate, and calcLarvalStageMortalityRate.
Patch-specific parameters \alpha and L_{eq} are calculated for each patch by calcDensityDependentDeathRate and calcLarvalPopEquilibrium.

Usage

parameterizeMGDrivE(
  runID = 1L,
  nPatch,
  simTime,
  sampTime = 1L,
  tEgg = 1L,
  tLarva = 14L,
  tPupa = 1L,
  beta = 32,
  muAd = 0.123,
  popGrowth = 1.096,
  AdPopEQ,
  LarPopRatio,
  AdPopRatio_F,
  AdPopRatio_M,
  inheritanceCube
)

Arguments

runID	Begin counting runs with this set of parameters from this value
nPatch	Number of Patch
simTime	Maximum time to run simulation
sampTime	Times to sample, used as tNow %% sampTime, default is every day
tEgg	Length of egg stage
tLarva	Length of larval instar stage
tPupa	Length of pupal stage
beta	Female egg batch size of wild-type
muAd	Wild-type daily adult mortality (1/muAd is average wild-type lifespan)
popGrowth	Daily population growth rate (used to calculate equilibrium)
AdPopEQ	Single number or vector of adult population size at equilibrium (single number implies all patches have the same population)
LarPopRatio	May be empty; if not, a vector gives the wildtype gene frequencies among larval stages at the beginning of simulation or a matrix provides different initial frequencies for each patch (every row is a different patch, must have nrow = nPatch)
AdPopRatio_F	May be empty; if not, a vector gives the wildtype gene frequencies among adult females at the beginning of simulation or a matrix provides different initial frequencies for each patch (every row is a different patch, must have nrow = nPatch)
AdPopRatio_M	May be empty; if not, a vector gives the wildtype gene frequencies among adult males at the beginning of simulation or a matrix provides different initial frequencies for each patch (every row is a different patch, must have nrow = nPatch)
inheritanceCube	Inheritance cube to check/set population ratios at the beginning of the simulation

Examples

# using default parameters for 2 patches
#  using different population sizes for patches
simPars <- parameterizeMGDrivE(nPatch = 2, simTime = 365,
                               AdPopEQ = c(100,200), inheritanceCube = cubeMendelian())

MGDrivE documentation built on Sept. 9, 2025, 5:42 p.m.