Package: BOLDconnectR 1.0.0
BOLDconnectR: Retrieve, Transform and Analyze the Barcode of Life Data Systems Data
Facilitates retrieval, transformation and analysis of the data from the Barcode of Life Data Systems (BOLD) database <https://boldsystems.org/>. This package allows both public and private user data to be easily downloaded into the R environment using a variety of inputs such as: IDs (processid, sampleid), BINs, dataset codes, project codes, taxonomy, geography etc. It provides frictionless data conversion into formats compatible with other R-packages and third-party tools, as well as functions for sequence alignment & clustering, biodiversity analysis and spatial mapping.
Authors:
BOLDconnectR_1.0.0.tar.gz
BOLDconnectR_1.0.0.zip(r-4.7)BOLDconnectR_1.0.0.zip(r-4.6)BOLDconnectR_1.0.0.zip(r-4.5)
BOLDconnectR_1.0.0.tgz(r-4.6-any)BOLDconnectR_1.0.0.tgz(r-4.5-any)
BOLDconnectR_1.0.0.tar.gz(r-4.7-any)BOLDconnectR_1.0.0.tar.gz(r-4.6-any)
BOLDconnectR_1.0.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
BOLDconnectR/json (API)
| # Install 'BOLDconnectR' in R: |
| install.packages('BOLDconnectR', repos = c('https://sameerpadhye.r-universe.dev', 'https://cloud.r-project.org')) |
- test.data - Canadian spider data by Blagoev et al.
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated from:42d7ca921c. Checks:9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-x86_64 | OK | 305 | ||
| source / vignettes | OK | 247 | ||
| linux-release-x86_64 | OK | 321 | ||
| macos-release-arm64 | OK | 369 | ||
| macos-oldrel-arm64 | OK | 265 | ||
| windows-devel | OK | 254 | ||
| windows-release | OK | 235 | ||
| windows-oldrel | OK | 243 | ||
| wasm-release | OK | 179 |
Exports:bold.analyze.alignbold.analyze.diversitybold.analyze.mapbold.analyze.treebold.apikeybold.data.summarizebold.exportbold.fetchbold.fields.infobold.full.searchbold.public.search
Dependencies:abindapeaskpassbase64encBATbitbit64bootcaretclassclassIntcliclockclusterclusterGenerationcodacodetoolscombinatcpp11crayoncurldata.tableDBIDEoptimdiagramdigestdoParalleldplyre1071evaluateexpmfarverfastclusterfastmapfastmatchFNNforeachfuturefuture.applygenericsgeometryggplot2globalsgluegowergtablehardhathighrhitandrunhmshtmltoolshttrhypervolumeigraphipredisobanditeratorsjsonlitekernlabKernSmoothknitrkslabelinglatticelavalifecyclelinproglistenvlpSolvelubridatemagicmagrittrmapsMASSMatrixmclustmgcvmimemnormtModelMetricsmulticoolmvtnormnlmenls2nnetnumDerivopenssloptimParallelpalmerpenguinsparallellypbapplypdistpermutephangornphytoolspillarpkgconfigPlotToolsplyrpracmaprettyunitspROCprodlimprogressprogressrprotoproxypurrrquadprogR6rasterrbibutilsrcddRColorBrewerRcppRcppArmadilloRcppProgressRdpackrecipesreprreshape2rlangrnaturalearthrparts2S7scalesscatterplot3dsfshapeskimrspsparsevctrsSQUAREMstringistringrsurvivalsysterratibbletidyrtidyselecttimechangetimeDateTreeToolstzdbunitsutf8vctrsveganviridisLitewithrwkxfunyaml
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Transform and align the sequence data retrieved from BOLD | bold.analyze.align |
| Create a biodiversity profile of the retrieved data | bold.analyze.diversity |
| Visualize BIN occurrence data on maps | bold.analyze.map |
| Analyze and visualize the multiple sequence alignment | bold.analyze.tree |
| Set the BOLD private data API key | bold.apikey |
| Generate specific summaries from the downloaded BCDM data | bold.data.summarize |
| Export files generated by BOLDconnectR | bold.export |
| Retrieve data from the BOLD database | bold.fetch |
| Retrieve metadata of the BOLD data fields | bold.fields.info |
| Search user based (private) and publicly available data on the BOLD database | bold.full.search |
| Search publicly available data on the BOLD database | bold.public.search |
| Canadian spider data by Blagoev et al.(2015) | test.data |
