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seedy (version 1.3)

Simulation of Evolutionary and Epidemiological Dynamics

Description

Suite of functions for the simulation, visualisation and analysis of bacterial evolution within- and between-host.

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Version

Install

install.packages('seedy')

Monthly Downloads

25

Version

1.3

License

GPL-3

Maintainer

Colin Worby

Last Published

November 6th, 2015

Functions in seedy (1.3)

seedy-package

Simulation of Evolutionary and Epidemiological Dynamics
expsnps

Distribution of genetic distances
librtoDNA

Convert simulation objects to DNA sequences or Nexus/Fasta files.
estcoaltime

Estimate expected time to coalescence for sampled lineages in bottlenecked population
deepseq

Deep-sequenced bacterial samples
diversity.range

Range of genetic diversity over time
flat

Equilibrium population growth model
plotnetwork

Plot weighted transmission network
plotsnpfreq

Plot frequency of polymorphic sites
withinhost

Within-host genomic data
gd

Genetic distance matrix
ancestors

Vector of infection ancestors
plotdistmat

Plot genetic distance matrix
sharedvariants

Shared variants matrix
simulatepopulation

Simulate a pathogen population
outbreak

Outbreak data
transroutes

Assessment of transmission routes using theoretical SNP distribution
deepseqmat

Generate deep sequence observations
plotobservedsnps

Plot expected frequency of polymorphic sites in a model deep sequencing project
networkmat

Create adjacency matrix
plotoutbreak

Plot outbreak
plotdiversity

Plot genetic diversity over time
hump

Sinusoidal population growth model
simulateoutbreak

Simulate transmission and evolutionary dynamics
meansnps

Mean diversity within a single population
transmission

Outbreak data
simfixoutbreak

Simulate evolutionary dynamics on a given transmission tree