Suite of functions for the simulation, visualisation and analysis of bacterial evolution within- and between-host.
|Date of publication||2015-11-06 23:58:19|
|Maintainer||Colin Worby <firstname.lastname@example.org>|
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