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... |
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... |
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... |
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... |
withinhost | Within-host genomic data |
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