Simulation of Evolutionary and Epidemiological Dynamics


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Documentation for package ‘seedy’ version 1.3

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seedy-package Simulation of Evolutionary and Epidemiological Dynamics
ancestors Vector of infection ancestors
deepseq Deep-sequenced bacterial samples
deepseqmat Generate deep sequence observations
diversity.range Range of genetic diversity over time
estcoaltime Estimate expected time to coalescence for sampled lineages in bottlenecked population
expsnps Distribution of genetic distances
flat Equilibrium population growth model
gd Genetic distance matrix
hump Sinusoidal population growth model
librtoDNA Convert simulation objects to DNA sequences or Nexus/Fasta files.
meansnps Mean diversity within a single population
networkmat Create adjacency matrix
outbreak Outbreak data
plotdistmat Plot genetic distance matrix
plotdiversity Plot genetic diversity over time
plotnetwork Plot weighted transmission network
plotobservedsnps Plot expected frequency of polymorphic sites in a model deep sequencing project
plotoutbreak Plot outbreak
plotsnpfreq Plot frequency of polymorphic sites
seedy Simulation of Evolutionary and Epidemiological Dynamics
sharedvariants Shared variants matrix
simfixoutbreak Simulate evolutionary dynamics on a given transmission tree
simulateoutbreak Simulate transmission and evolutionary dynamics
simulatepopulation Simulate a pathogen population
transmission Outbreak data
transroutes Assessment of transmission routes using theoretical SNP distribution
withinhost Within-host genomic data