Man pages for seedy
Simulation of Evolutionary and Epidemiological Dynamics

ancestorsVector of infection ancestors
deepseqDeep-sequenced bacterial samples
deepseqmatGenerate deep sequence observations
diversity.rangeRange of genetic diversity over time
estcoaltimeEstimate expected time to coalescence for sampled lineages in...
expsnpsDistribution of genetic distances
flatEquilibrium population growth model
gdGenetic distance matrix
humpSinusoidal population growth model
librtoDNAConvert simulation objects to DNA sequences or Nexus/Fasta...
meansnpsMean diversity within a single population
networkmatCreate adjacency matrix
outbreakOutbreak data
plotdistmatPlot genetic distance matrix
plotdiversityPlot genetic diversity over time
plotnetworkPlot weighted transmission network
plotobservedsnpsPlot expected frequency of polymorphic sites in a model deep...
plotoutbreakPlot outbreak
plotsnpfreqPlot frequency of polymorphic sites
seedy-packageSimulation of Evolutionary and Epidemiological Dynamics
sharedvariantsShared variants matrix
simfixoutbreakSimulate evolutionary dynamics on a given transmission tree
simulateoutbreakSimulate transmission and evolutionary dynamics
simulatepopulationSimulate a pathogen population
transmissionOutbreak data
transroutesAssessment of transmission routes using theoretical SNP...
withinhostWithin-host genomic data
seedy documentation built on May 29, 2017, 10:58 a.m.