exampleParameters: Example parameters

In jameshay218/driftSim: Short-sighted evolution of influenza cellular receptor binding avidity shapes influenza epidemic dynamics

Description

A list of parameters to use for the simulation as an example.

Usage

attach(exampleParameters)

Format

A list with 4 elements:

hostpars, the vector of host parameters:

• S0: Starting susceptible population size

• I0: Initial infecteds

• R0: Initial recovered

• c: Contact rate per day (ie. each person makes on average 0.7 contacts per day)

• mu: Birth and death rate per day

• w: Immunity waning rate

• g: Recovery rate

• iniBind: Initial binding avidity of seed virus

• meanBoost: Average (of poisson) antibody boosting upon recovery

• iniDist: Initial antigenic distance of seed virus to "root"

• saveFreq: How often the distribution of host immunity values are saved

• maxTitre: Maximum attainable titre for hosts

viruspars, the vector of virus parameters:

• p: parameter to control degree by which changes in binding avidity affect probability of escape from immune response

• r: parameter to control degree by which previous exposure reduce probability of immune escape

• q: parameter to control the shape of the relationship between binding avidity and immune escape (shift on the x-axis)

• a: controls rate of changes of relationship between probability of successful replication and change in binding avidity

• b: parameter to control the shape of the relationship between probability of successful replication and changes in binding avidity

• n: number of offspring per virus replication event

• v: number of virions initially transmitted

• probMut: Probability of a mutation in antigenic properties in a given infection

• expDist: Average of the exponential distribution from which the size of antigenic mutatations is drawn

• kc: Rate of binding avidity adaptation

• VtoD: Proportion mediating how much antigenic change occurs given a unit of binding avidity change

flags, the vector of flags for saving output options:

• SIR_flag: Flag to save SIR dynamics

• voutput_phylogenetic_flag: Flag to save virus information for phylogenetic tree analysis (ie. virus parent information)

• voutput_pairwise_flag: Flag to save pairwise distance matrix

• time_flag: Flag to record time taken for simulation

• save_state: Flag to save the final state of the simulation

• input_flag_generated: Flag to use specified file as input for simulation

• input_flag_saved: Flag to use specified file as input for simulation

• save_k: Flag to save the distribution of hosts in each K value at regular intervals

deltaVMat, the numeric matrix of binding avidity vs. host immunity gradients for working out within-host binding avidity adaptation

See Also

calculate_deltaV_matrix, run_simulation

jameshay218/driftSim documentation built on Jan. 24, 2020, 6:14 p.m.