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.zip(r-4.7)SMITIDstruct_0.0.5.zip(r-4.6)SMITIDstruct_0.0.5.zip(r-4.5)
SMITIDstruct_0.0.5.tgz(r-4.6-any)SMITIDstruct_0.0.5.tgz(r-4.5-any)
SMITIDstruct_0.0.5.tar.gz(r-4.7-any)SMITIDstruct_0.0.5.tar.gz(r-4.6-any)
SMITIDstruct_0.0.5.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
SMITIDstruct/json (API)

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

Bug tracker:https://github.com/cranhaven/cranhaven.r-universe.dev/issues

On CRAN:

Conda:

archivedpackagesr-universe

1.70 score 5 stars 1 scripts 180 downloads 35 exports 37 dependencies

Last updated from:661fd8bd8b (on package/SMITIDstruct). Checks:7 NOTE, 2 OK. Indexed: no.

TargetResultTimeFilesSyslog
linux-devel-x86_64NOTE196
source / vignettesOK224
linux-release-x86_64NOTE179
macos-release-arm64NOTE126
macos-oldrel-arm64NOTE162
windows-develNOTE140
windows-releaseNOTE133
windows-oldrelNOTE133
wasm-releaseOK128

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

Dependencies:BiocGenericsBiostringsclassclassIntclicpp11crayonDBIe1071farvergenericsggplot2gluegtableIRangesisobandKernSmoothlabelinglifecycleMASSproxyR6RColorBrewerRcpprlangs2S4VectorsS7scalesSeqinfosfunitsvctrsviridisLitewithrwkXVector

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