new_config: Create a simulation configuration

In thibautjombart/quicksim: Quick and simple outbreak simulator

Description

This function creates a list storing simulation settings - see details.

Usage

new_config(...)

Arguments

...	named simulation settings - see details

Details

Simulation settings include:

• x_min: lower bound of spatial coordinates (x-axis)

• x_max: upper bound of spatial coordinates (x-axis)

• y_min: lower bound of spatial coordinates (y-axis)

• y_max: upper bound of spatial coordinates (y-axis)

• sd_spatial: standard deviation for the spatial dispersal, only used for the default spatial kernel

• spatial_kernel: a function of 'x' (a vector of starting coordinates) implementing a kernel for spatial dispersion; defaults to a Normal distribution with standard deviation 1

• genome_length: number of nucleotides in the pathogen genome

• mutation_rate: per nucleotide and day

• separation_lineages: number of days to ancestral lineage for newly introduced pathogens

Author(s)

Thibaut Jombart [e-mail]

Examples

new_config()
new_config(genome_length = 100, x_max = 10)

thibautjombart/quicksim documentation built on May 5, 2019, 2:42 a.m.