# This contains all the parameters used in the model.
# These values correspond to defaults.
# Leaving an entry out is fine, the value will remain at its default.
# simulation parameters
burnin: 0 # days to wait before logging output
endDay: 5000 # number of days to simulate
deltaT: 0.1 # number of days to move forward in a single timestep
printStep: 10 # print to out.timeseries every X days
tipSamplingRate: 0.0002 # store X samples per deme per day
tipSamplesPerDeme: 2000 # cap number of samples per deme
tipSamplingProportional: true # whether to sample proportional to prevalence
treeProportion: 0.1 # proportion of tips to use in tree reconstruction
diversitySamplingCount: 1000 # how many samples to draw to calculate diversity, netau and serial interval
netauWindow: 100 # window in days to calculate Ne*tau
repeatSim: true # repeat simulation until endDay is reached?
immunityReconstruction: false # whether to print immunity reconstruction to out.immunity
memoryProfiling: false # requires -javaagent:classmexer.jar to run
yearsFromMK: 1.0 # how many years to consider present when calculating MK
pcaSamples: false # whether to rotate and flip virus tree
reducedOutput: false # whether to output only out.summary and out.timeseries
detailedOutput: false # whether to output out.hosts and out.viruses files enabling checkpointing
restartFromCheckpoint: false # whether to load population from out.hosts
# metapopulation parameters
demeCount: 3 # number of demes
demeNames: ["north", "tropics", "south"] # deme names
initialNs: [1000000, 1000000, 1000000] # inital deme population sizes
# host parameters
birthRate: 0.000091 # in births per individual per day, 1/30 years = 0.000091
deathRate: 0.000091 # in deaths per individual per day, 1/30 years = 0.000091
swapDemography: true # whether to keep overall population size constant
# epidemiological parameters
initialI: 10 # in individuals
initialDeme: 2 # index of deme where infection starts, 1..n
initialPrR: 0.5 # as proportion of population
beta: 0.36 # in contacts per individual per day
nu: 0.2 # in recoveries per individual per day
betweenDemePro: 0.0005 # relative to within-deme beta
# transcendental parameters
transcendental: false # whether to include a general recovered class
immunityLoss: 0.01 # in R->S per individual per day
initialPrT: 0.1 # initial faction in general recovered class
# seasonal parameters
demeBaselines: [1., 1., 1.] # baseline of seasonality
demeAmplitudes: [0.1, 0., 0.1] # amplitude of seasonality
demeOffsets: [0., 0., 0.5] # seasonal offset relative to the year
# immune parameters
phenotypeSpace: "geometric" # options include: geometric, geometric3d, geometric10d
muPhenotype: 0.005 # in mutations per individual per day
waning: false # whether to allow waning of host immunity
waningRate: 0.01 # rate per day of a host removing a random phenotype from their immune history
smithConversion: 0.1 # multiplier to distance to give cross-immunity
homologousImmunity: 0.95 # immunity raised to antigenically identical virus
initialTraitA: -6. # value in dimension 1 for initial host immunity
meanStep: 0.3 # mean mutation size
sdStep: 0.3 # standard deviation of mutation size
mut2D: false # whether to mutate in a full 360 degree arc
fixedStep: false # whether to fix step size, i.e. ignore sdStep