Data Structure and Manipulations Tool for Host and Viral Population
addcode
addHost
addIndex
addViralObs
alleleCount
concatViralPop
createAViralPop
createHost
createIndex
demo.SMITIDstruct.run
diversity.pDistance
diversity.sfs
getCov
getDate
getDiversity.pDistance
getDiversity.sfs
getInfosByHostAndTime
getStates
getTimeLine
getTimestamp
getTransmissionTree
Class Host
is.juliendate
is.StringDate
is.timestamp
isInCode
loadCoords
loadCovs
loadHost
loadStates
loadTree
loadTreeDF
loadViralObs
loadViralPop
loadViralPopSet
mergeCode
plotDiversity.pDistance
plotDiversity.sfs
setStates
simulateStates
Data Structure and Manipulation Tool for Host and Viral Population
Class ViralPop
Statistical Methods for Inferring Transmissions of Infectious Diseases from deep sequencing data (SMITID). It allow sequence-space-time host and viral population data storage, indexation and querying.
Useful links