R/data.R

#' Example parameters
#'
#' A list of parameters to use for the simulation as an example.
#' @format A list with 4 elements:
#' \describe{
#' \item{\strong{hostpars}, the vector of host parameters:
#' \itemize{
#' \item{S0: Starting susceptible population size}
#' \item{I0: Initial infecteds}
#' \item{R0: Initial recovered}
#' \item{c: Contact rate per day (ie. each person makes on average 0.7 contacts per day)}
#' \item{mu: Birth and death rate per day}
#' \item{w: Immunity waning rate}
#' \item{g: Recovery rate}
#' \item{iniBind: Initial binding avidity of seed virus}
#' \item{meanBoost: Average (of poisson) antibody boosting upon recovery}
#' \item{iniDist: Initial antigenic distance of seed virus to "root"}
#' \item{saveFreq: How often the distribution of host immunity values are saved}
#' \item{maxTitre: Maximum attainable titre for hosts}
#' }}
#' \item{\strong{viruspars}, the vector of virus parameters:
#' \itemize{
#' \item{p: parameter to control degree by which changes in binding avidity affect probability of escape from immune response}
#' \item{r: parameter to control degree by which previous exposure reduce probability of immune escape}
#' \item{q: parameter to control the shape of the relationship between binding avidity and immune escape (shift on the x-axis)}
#' \item{a: controls rate of changes of relationship between probability of successful replication and change in binding avidity}
#' \item{b: parameter to control the shape of the relationship between probability of successful replication and changes in binding avidity}
#' \item{n: number of offspring per virus replication event}
#' \item{v: number of virions initially transmitted}
#' \item{probMut: Probability of a mutation in antigenic properties in a given infection}
#' \item{expDist: Average of the exponential distribution from which the size of antigenic mutatations is drawn}
#' \item{kc: Rate of binding avidity adaptation}
#' \item{VtoD: Proportion mediating how much antigenic change occurs given a unit of binding avidity change}
#' }}
#' \item{\strong{flags}, the vector of flags for saving output options:
#' \itemize{
#' \item{SIR_flag: Flag to save SIR dynamics}
#' \item{voutput_phylogenetic_flag: Flag to save virus information for phylogenetic tree analysis (ie. virus parent information)}
#' \item{voutput_pairwise_flag: Flag to save pairwise distance matrix}
#' \item{time_flag: Flag to record time taken for simulation}
#' \item{save_state: Flag to save the final state of the simulation}
#' \item{input_flag_generated: Flag to use specified file as input for simulation}
#' \item{input_flag_saved: Flag to use specified file as input for simulation}
#' \item{save_k: Flag to save the distribution of hosts in each K value at regular intervals}
#' }}
#' \item{\strong{deltaVMat}, the numeric matrix of binding avidity vs. host immunity gradients for working out within-host binding avidity adaptation}
#' }
#' @seealso \code{\link{calculate_deltaV_matrix}}, \code{\link{run_simulation}}
#' @docType data
#' @keywords datasets
#' @name exampleParameters
#' @usage attach(exampleParameters)
"exampleParameters"
jameshay218/driftSim documentation built on Jan. 24, 2020, 6:14 p.m.