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())