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:
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')) |
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated 5 years agofrom:2cba935ea8. Checks:OK: 2. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Sep 11 2024 |
| R-4.5-linux | OK | Sep 11 2024 |
Exports:addHostaddViralObsconcatViralPopcreateAViralPopcreateHostcreateIndexdemo.SMITIDstruct.rundiversity.pDistancediversity.sfsgetCovgetDategetDiversity.pDistancegetDiversity.sfsgetInfosByHostAndTimegetStatesgetTimeLinegetTimestampgetTransmissionTreeis.juliendateis.StringDateis.timestampisInCodeloadCoordsloadCovsloadHostloadStatesloadTreeloadTreeDFloadViralObsloadViralPoploadViralPopSetmergeCodeplotDiversity.pDistanceplotDiversity.sfssimulateStates
Dependencies:askpassBiocGenericsBiostringsclassclassIntclicolorspacecrayoncurlDBIe1071fansifarverGenomeInfoDbGenomeInfoDbDataggplot2gluegtablehttrIRangesisobandjsonliteKernSmoothlabelinglatticelifecyclemagrittrMASSMatrixmgcvmimemunsellnlmeopensslpillarpkgconfigproxyR6RColorBrewerRcpprlangs2S4VectorsscalessfsystibbleUCSC.utilsunitsutf8vctrsviridisLitewithrwkXVectorzlibbioc
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Data Structure and Manipulation Tool for Host and Viral Population | SMITIDstruct-package SMITIDstruct _PACKAGE |
| addcode | addcode |
| addHost | addHost |
| addIndex | addIndex |
| addViralObs | addViralObs |
| alleleCount | alleleCount |
| concatViralPop | concatViralPop |
| createAViralPop | createAViralPop |
| createHost | createHost |
| createIndex | createIndex |
| demo.SMITIDstruct.run | demo.SMITIDstruct.run |
| diversity.pDistance | diversity.pDistance |
| diversity.sfs | diversity.sfs |
| getCov | getCov |
| getDate | getDate |
| getDiversity.pDistance | getDiversity.pDistance |
| getDiversity.sfs | getDiversity.sfs |
| getInfosByHostAndTime | getInfosByHostAndTime |
| getStates | getStates |
| getTimeLine | getTimeLine |
| getTimestamp | getTimestamp |
| getTransmissionTree | getTransmissionTree |
| Class Host | Host Host-class |
| is.juliendate | is.juliendate |
| is.StringDate | is.StringDate |
| is.timestamp | is.timestamp |
| isInCode | isInCode |
| loadCoords | loadCoords |
| loadCovs | loadCovs |
| loadHost | loadHost |
| loadStates | loadStates |
| loadTree | loadTree |
| loadTreeDF | loadTreeDF |
| loadViralObs | loadViralObs |
| loadViralPop | loadViralPop |
| loadViralPopSet | loadViralPopSet |
| mergeCode | mergeCode |
| plotDiversity.pDistance | plotDiversity.pDistance |
| plotDiversity.sfs | plotDiversity.sfs |
| setStates | setStates |
| simulateStates | simulateStates |
| Class ViralPop | ViralPop ViralPop-class |