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-package           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
