MGDrivE (version 1.6.0)

parameterizeMGDrivE: 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

# NOT RUN {
# using default parameters for 2 patches
#  using different population sizes for patches
simPars <- parameterizeMGDrivE(nPatch = 2, simTime = 365,
                               AdPopEQ = c(100,200), inheritanceCube = cubeMendelian())

# }