parameters.yml

# 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