# 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: 36500 # days to wait before logging output endDay: 43800 # number of days to simulate deltaT: 0.1 # number of days to move forward in a single timestep printStep: 7 # 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 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: ["A", "B", "C"] # deme names initialNs: [15000000, 15000000, 15000000] # inital deme population sizes # host parameters birthRate: 0.000055 # in births per individual per day, 1/50 years deathRate: 0.000055 # in deaths per individual per day, 1/50 years swapDemography: true # whether to keep overall population size constant # epidemiological parameters initialI: 10 # in individuals initialDeme: 1 # index of deme where infection starts, 1..n initialPrR: 0.8 # as proportion of population beta: 0.88 # in contacts per individual per day nu: 0.2 # in recoveries per individual per day betweenDemePro: 0.006 # 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., 0.15, 0.15] # amplitude of seasonality demeOffsets: [0., 0.5, 0.] # seasonal offset relative to the year # phenotype parameters phenotypeSpace: "geometric" # options include: geometric, geometric3d, geometric10d muPhenotype: 0.00005 # in mutations per individual per day smithConversion: 0.07 # multiplier to distance to give cross-immunity homologousImmunity: 0.95 # immunity raised to antigenically identical virus initialTraitA: -3. # 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 adultToAdultModifier: 0.26 adultToChildModifier: 0.21 childToChildModifier: 1.00 adultTravelModifier: 1.00 childTravelModifier: 0.19