parameterizeMGDrivE function

parameterizeMGDrivE

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.

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())