makePop: Make a new population

In timcdlucas/MetapopEpi: Functions to run multipathogen, metapopulation epidemiological simulations

Description

Make a new population at time 0. The resultant population object will then contain all the information needed to update the population.

Usage

makePop(model = "SIS", nColonies = 5, colonyDistr = "equal",
  space = 100, maxDistance = 200, kernel = "unweighted", events = 10000,
  colonySpatialDistr = "uniform", nPathogens = 3, meanColonySize = 10000,
  birth = 0.001, death = 0.001, dispersal = 0.001, transmission = 0.01,
  recovery = 0.005, crossImmunity = 0.1, sample = 1000, infectDeath = 0)

Arguments

model	Define the model type with a string e.g. 'SI', 'SIS'.
nColonies	How many colonies/subpopulations do you want.
colonyDistr	The model for colony size distirbution. Currently one of 'equal', 'exponential', 'poisson'.
space	How large should the space be. A positive number giving the length along a side.
maxDistance	The maximum distance within which two colonies can be connected in the network.
kernel	How should the network be weighted with respect to distance between colonies. 'inverse', 'linear', 'unweighted'
events	Integer defining the number of events to run before stopping the simulation. A single event is an infection, death, birth, migration etc.
colonySpatialDistr	How are the colonies distributed in space. 'uniform', 'circle'
nPathogens	Integer defining the number of pathogen species or strains.
meanColonySize	Colony size.
birth	Positive numeric. Birth rate per individual per unit time.
death	Positive numeric. Death rate per individual per unit time.
dispersal	Positive numeric. Dispersal rate per individual per unit time.
transmission	Positive numeric. Transmission rate per unit time.
recovery	Positive numeric. Recovery rate per individual per unit time. Disease duration is therefore 1/recovery
crossImmunity	Numeric between 0 and 1 that governs cross immunity. 0 is full cross immunity, 1 is no cross immunity.
sample	The sample rate of population states to store. Default is to store every 1000 events.
infectDeath	Additional death rate due to infection. Death rate will be death + infectDeath * n. infections.

Value

A large list that contains the model parameters (numeric in 'parameters' and strings in 'models'. The actual time course of the population is in 'I', nColonies x nPathogens x events array. The spatial locations of colonies are in 'locations' and 'adjacency' is the weighted (if applicable) adjacency matric for the population network. 'waiting' is the interevent times. diseaseClasses, diseaseList and whichClasses are mostly references for the relationships between multidisease states.

Examples

p <- makePop()
p

timcdlucas/MetapopEpi documentation built on May 31, 2019, 1:47 p.m.