parameterizeMGDrivE: parameterizeMGDrivE
In MGDrivE: Mosquito Gene Drive Explorer

Generate parameters for simulation on a Network. Parameters include: average generation time g, population growth rate R_{m}, aquatic mortality μ_{Aq}, and aquatic survival θ_{Aq}, which are shared between patches and calculated by calcAverageGenerationTime, calcPopulationGrowthRate, and calcLarvalStageMortalityRate.
Patch-specific parameters α 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
)

`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

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