makePop: Make a new population

Description Usage Arguments Value Examples

Description

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

Usage

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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

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p <- makePop()
p

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