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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 |