simulateEpidemic(Ninit = Inf, nu = 0, mu = 1/850, pe, sde, pg.init, GEValues, rateContact, rateInfect, rateDie, rateSample, rateMutate, rateTransTemplate = generateRateTransTemplate(numsAllelesAtSites), numsAllelesAtSites = NULL, eUniqForEachG = FALSE, selectWithinHost = FALSE, timeStep = 0.1, maxTime = 1200, maxNTips = 8000, expandTimeAfterMaxNTips = 1.5, reportInterval = 12, ...)
| Ninit | integer, initial population size |
|---|---|
| nu | numeric, birth rate (constant unit time influx in the population) |
| mu | numeric, natural death rate |
| pe | numeric vector of frequences for each environment type |
| sde | numeric, the standard deviation of the special environmental effects |
| pg.init | numeric initial frequencies from which the pathogen genotype of the first case is drawn |
| GEValues | numeric matrix with average value for individuals of specific immune system type infected by a specific pathogen. GEValues[i, j] is for individaul of immune type i and pathogen genotype j. |
| rateContact | numeric, the rate at which an infected individual has contact with a susceptible. |
| rateInfect | a function of two arguments, a numeric vector of trait values and a numeric rateContact parameter, returning a numeric vector of transmission rates corresponding z. |
| rateDie | a function of one argument, a numeric vector of trait values, returning a numeric vector of death rates corresponding to these values. |
| rateSample | numeric, the rate at which infected individuals get diagnozed and recover |
| rateMutate | a function of four arguments: the GEValues matrix (see above), a numeric vector es of special environmental effects, an integer vector envs of environment type indices and an integer vector genes of pathogen genotype indices, returning a numeric vector of the same size as the es with per-locus mutation rates. |
| rateTransTemplate | a square matrix of size n x (n-1) containing the factor by which the per locus mutation rate must be multiplied in order to obtain a transition rate between any two pathogen genotypes. See the function generateRateTransTemplate. rateTransTemplate[i,j] should be the factor for transition rate from state i to state j. By definition of transition rate matrices the transition from a state to itself is always the negative sum of the transition rates to the other states. This parameter needs not to be specified explicitly if the parameter numsAllelesAtSites is specified (see below). |
| numsAllelesAtSites | integer vector specifying the number of alleles at each site, the length of the vector defining the number of QTLs. |
| eUniqForEachG | logical indicating should the special environmental effect in an individual be drawn for each possible pathogen genotype or should there be a single special environmental effect for all genotypes. |
| selectWithinHost | logical indicating if there is selection for higher trait values within a host. When TRUE a mutation results in a transition from one genotype to another only if it results in a higher trait value for a host. |
| timeStep | numeric, the time resolution at which infection, mutation, sampling and death events are sampled. |
| maxTime | numeric, the maximum duration of a simulation before starting the graceful fade-away phase. |
| maxNTips | numeric, the maximum number of sampled individuals before starting the graceful fade-away phase. |
| expandTimeAfterMaxNTips | numeric greater or equal than 1 specifying how lone should the growth of the epidemic continue after reaching maxNTips or running the epidemic for maxTime/expandTimeAfterMaxNTips. |
| reportInterval | positive integer, time interval at which some statistics such as total infected and recovered counts and frequencies of genotypes in the population are stored. |
A list of objects