seedy: Simulation of Evolutionary and Epidemiological Dynamics

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Suite of functions for the simulation, visualisation and analysis of bacterial evolution within- and between-host.

Author
Colin Worby
Date of publication
2015-11-06 23:58:19
Maintainer
Colin Worby <cworby@hsph.harvard.edu>
License
GPL-3
Version
1.3

View on CRAN

Man pages

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

Files in this package

seedy
seedy/NAMESPACE
seedy/data
seedy/data/outbreak.rda
seedy/data/transmission.rda
seedy/data/withinhost.rda
seedy/data/deepseq.rda
seedy/R
seedy/R/diversity.range.R
seedy/R/plotoutbreak.R
seedy/R/expsnps.R
seedy/R/simulateoutbreak.R
seedy/R/plotdistmat.R
seedy/R/transroutes.r
seedy/R/networkmat.R
seedy/R/librtoDNA.R
seedy/R/plotobservedsnps.R
seedy/R/gd.R
seedy/R/sharedvariants.r
seedy/R/flat.r
seedy/R/estcoaltime.R
seedy/R/plotdiversity.R
seedy/R/deepseqmat.r
seedy/R/plotsnpfreq.r
seedy/R/simfixoutbreak.r
seedy/R/simulatepopulation.R
seedy/R/plotnetwork.R
seedy/R/ancestors.R
seedy/R/meansnps.R
seedy/R/hump.r
seedy/MD5
seedy/DESCRIPTION
seedy/man
seedy/man/deepseqmat.Rd
seedy/man/diversity.range.Rd
seedy/man/simulateoutbreak.Rd
seedy/man/plotdiversity.Rd
seedy/man/plotoutbreak.Rd
seedy/man/transroutes.Rd
seedy/man/meansnps.Rd
seedy/man/plotdistmat.Rd
seedy/man/withinhost.Rd
seedy/man/librtoDNA.Rd
seedy/man/estcoaltime.Rd
seedy/man/flat.Rd
seedy/man/plotobservedsnps.Rd
seedy/man/networkmat.Rd
seedy/man/gd.Rd
seedy/man/sharedvariants.Rd
seedy/man/ancestors.Rd
seedy/man/transmission.Rd
seedy/man/plotsnpfreq.Rd
seedy/man/simulatepopulation.Rd
seedy/man/hump.Rd
seedy/man/outbreak.Rd
seedy/man/plotnetwork.Rd
seedy/man/seedy-package.Rd
seedy/man/deepseq.Rd
seedy/man/simfixoutbreak.Rd
seedy/man/expsnps.Rd