Package: SMITIDstruct 0.0.5

Jean-Francois Rey

SMITIDstruct: Data Structure and Manipulations Tool for Host and Viral Population

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.

Authors:Jean-Francois Rey [aut, cre]

SMITIDstruct_0.0.5.tar.gz
SMITIDstruct_0.0.5.tar.gz(r-4.5-noble)SMITIDstruct_0.0.5.tar.gz(r-4.4-noble)
SMITIDstruct_0.0.5.tgz(r-4.4-emscripten)SMITIDstruct_0.0.5.tgz(r-4.3-emscripten)
SMITIDstruct.pdf |SMITIDstruct.html
SMITIDstruct/json (API)

# Install 'SMITIDstruct' in R:
install.packages('SMITIDstruct', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

1.00 score 1 scripts 120 downloads 35 exports 57 dependencies

Last updated 6 years agofrom:2cba935ea8. Checks:OK: 2. Indexed: yes.

TargetResultDate
Doc / VignettesOKDec 10 2024
R-4.5-linuxOKDec 10 2024

Exports:addHostaddViralObsconcatViralPopcreateAViralPopcreateHostcreateIndexdemo.SMITIDstruct.rundiversity.pDistancediversity.sfsgetCovgetDategetDiversity.pDistancegetDiversity.sfsgetInfosByHostAndTimegetStatesgetTimeLinegetTimestampgetTransmissionTreeis.juliendateis.StringDateis.timestampisInCodeloadCoordsloadCovsloadHostloadStatesloadTreeloadTreeDFloadViralObsloadViralPoploadViralPopSetmergeCodeplotDiversity.pDistanceplotDiversity.sfssimulateStates

Dependencies:askpassBiocGenericsBiostringsclassclassIntclicolorspacecrayoncurlDBIe1071fansifarvergenericsGenomeInfoDbGenomeInfoDbDataggplot2gluegtablehttrIRangesisobandjsonliteKernSmoothlabelinglatticelifecyclemagrittrMASSMatrixmgcvmimemunsellnlmeopensslpillarpkgconfigproxyR6RColorBrewerRcpprlangs2S4VectorsscalessfsystibbleUCSC.utilsunitsutf8vctrsviridisLitewithrwkXVectorzlibbioc

Readme and manuals

Help Manual

Help pageTopics
Data Structure and Manipulation Tool for Host and Viral PopulationSMITIDstruct-package SMITIDstruct _PACKAGE
addcodeaddcode
addHostaddHost
addIndexaddIndex
addViralObsaddViralObs
alleleCountalleleCount
concatViralPopconcatViralPop
createAViralPopcreateAViralPop
createHostcreateHost
createIndexcreateIndex
demo.SMITIDstruct.rundemo.SMITIDstruct.run
diversity.pDistancediversity.pDistance
diversity.sfsdiversity.sfs
getCovgetCov
getDategetDate
getDiversity.pDistancegetDiversity.pDistance
getDiversity.sfsgetDiversity.sfs
getInfosByHostAndTimegetInfosByHostAndTime
getStatesgetStates
getTimeLinegetTimeLine
getTimestampgetTimestamp
getTransmissionTreegetTransmissionTree
Class HostHost Host-class
is.juliendateis.juliendate
is.StringDateis.StringDate
is.timestampis.timestamp
isInCodeisInCode
loadCoordsloadCoords
loadCovsloadCovs
loadHostloadHost
loadStatesloadStates
loadTreeloadTree
loadTreeDFloadTreeDF
loadViralObsloadViralObs
loadViralPoploadViralPop
loadViralPopSetloadViralPopSet
mergeCodemergeCode
plotDiversity.pDistanceplotDiversity.pDistance
plotDiversity.sfsplotDiversity.sfs
setStatessetStates
simulateStatessimulateStates
Class ViralPopViralPop ViralPop-class