Files in thibautjombart/OutbreakTools
Basic Tools for the Analysis of Disease Outbreaks
.Rbuildignore
.gitignore
.travis.yml
ChangeLog
DESCRIPTION
NAMESPACE
R/OutbreakTools.R
R/annotatedTreeReader.R
R/auxClasses.R
R/dna2uniqSequences.R
R/generics.R
R/get.incidence.R
R/importFromJSON.R
R/make.attributes.R
R/make.phylo.R
R/obkContacts.R
R/obkData.R
R/obkData_Accessors.R
R/obkData_basics.R
R/obkSequences.R
R/phylo2ggphy.R
R/plot.R
R/plotGeo.R
R/plotIndividualTimeline.R
R/plotggMST.R
R/plotggphy.R
R/simuEpi.R
R/subset.R
R/uniqSequences.R
R/utils.R
R/zzz.R
README.md
TITLE
data/FluH1N1pdm2009.RData
data/HorseFlu.RData
data/HorseFluRaw.RData
data/ToyOutbreak.RData
data/ToyOutbreakRaw.RData
inst/files/BEAST-expl.nex
man/FluH1N1pdm2009.Rd
man/HorseFlu.Rd
man/HorseFluRaw.Rd
man/OutbreakTools.package.Rd
man/ToyOutbreak.Rd
man/ToyOutbreakRaw.Rd
man/annotatedTreeReader.Rd
man/auxClasses.Rd
man/dna2uniqSequences.Rd
man/get.data.Rd
man/get.dates.Rd
man/get.incidence.Rd
man/get.individuals.Rd
man/importFromJSON.Rd
man/make.attributes.Rd
man/make.phylo.Rd
man/obkContacts.Rd
man/obkData.Rd
man/obkDataPlot.Rd
man/obkSequences.Rd
man/phylo2ggphy.Rd
man/phylofromtranstree.Rd
man/plotEpi.Rd
man/plotGeo.Rd
man/plotIndividualTimeline.Rd
man/plotggMST.Rd
man/plotggphy.Rd
man/simuEpi.Rd
man/subset.Rd
man/uniqSequences.Rd
misc/BEAST-expl.nex
misc/FakeInfluenza.RData
misc/FakeInfluenza.Rd
misc/FakeSarsHK2003.RData
misc/FakeSarsHK2003.Rd
misc/FluH1N1pdmExample.R
misc/H3_WD_n1000_GTRGI_E_skyline.trees_subst_MCC.txt
misc/H3_WD_n1000_GTRGI_E_skyline.trees_time_MCC.txt
misc/HorseFluOutbreak.RData
misc/ISOdate_format.R
misc/SarsSingapore2003.RData
misc/SarsSingapore2003.Rd
misc/annotated_example.R
misc/bestroot.R
misc/classes.old.R
misc/createRData.R
misc/demo.push2d3.R
misc/epibase.Rnw
misc/get.incidence.Rd
misc/ggplot2_example.R
misc/obkClinicalEvent.R
misc/obkClinicalEvent.Rd
misc/plot_ggphy_test.R
misc/plotggphyExample.R
misc/rabies.RData
misc/rabies.Rd
misc/roxygen.R
misc/sciencegallery.RData
misc/sciencegallery.Rd
misc/shedding_example.R
misc/simSIRmodel.R
misc/simSIRmodelKenah2008.R
misc/supgma.R
vignettes/OutbreakTools.Rnw
