Package: neonUtilities 2.4.3.9000

Claire Lunch

neonUtilities: Utilities for Working with NEON Data

NEON data packages can be accessed through the NEON Data Portal <https://www.neonscience.org> or through the NEON Data API (see <https://data.neonscience.org/data-api> for documentation). Data delivered from the Data Portal are provided as monthly zip files packaged within a parent zip file, while individual files can be accessed from the API. This package provides tools that aid in discovering, downloading, and reformatting data prior to use in analyses. This includes downloading data via the API, merging data tables by type, and converting formats. For more information, see the readme file at <https://github.com/NEONScience/NEON-utilities>.

Authors:Claire Lunch [aut, cre, ctb], Christine Laney [aut, ctb], Nathan Mietkiewicz [aut, ctb], Eric Sokol [aut, ctb], Kaelin Cawley [aut, ctb], NEON [aut]

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neonUtilities.pdf |neonUtilities.html✨
neonUtilities/json (API)
NEWS

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

Peer review:

Bug tracker:https://github.com/neonscience/neon-utilities/issues

Datasets:

On CRAN:

23 exports 57 stars 4.38 score 35 dependencies 13 dependents 3 mentions 880 scripts 1.8k downloads

Last updated 5 months agofrom:a2d4dc231a. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKSep 12 2024
R-4.5-winOKSep 12 2024
R-4.5-linuxOKSep 12 2024
R-4.4-winOKSep 12 2024
R-4.4-macOKSep 12 2024
R-4.3-winOKSep 12 2024
R-4.3-macOKSep 12 2024

Exports:byFileAOPbyTileAOPconvByteSizefootRastergetAvggetCitationgetDatatablegetIssueLoggetNeonDOIgetPackagegetProductInfogetProductSensorsgetTaxonTablegetTimeIndexgetVarsEddyloadByProductreadTableNEONstackByTablestackEddystackFromStoretransformFileToGeoCSVzipsByProductzipsByURI

Dependencies:askpassclicpp11curldata.tabledigestdownloaderdplyrfansigenericsgluehttrjsonlitelifecyclemagrittrmimeopensslpbapplypillarpkgconfigpurrrR.methodsS3R.ooR.utilsR6rlangstringistringrsystibbletidyrtidyselectutf8vctrswithr

Readme and manuals

Help Manual

Help pageTopics
Serially download all AOP files for a given site, year, and productbyFileAOP
Download AOP tiles overlapping specified coordinates for a given site, year, and productbyTileAOP
Bundled chemistry data product informationchem_bundles
Convert a number of bytes into megabytes or gigabytesconvByteSize
Extract eddy covariance footprint data from HDF5 formatfootRaster
Get the data from APIgetAPI
Get only headers from APIgetAPIHeaders
Get a list of the available averaging intervals for a data productgetAvg
Get a Bibtex citation for NEON data with a DOI, or generate a provisional Bibtex citationgetCitation
Get NEON data tablegetDatatable
Get the full issue log set for the SAE bundlegetEddyLog
Get and store the file names, S3 URLs, file size, and download status (default = 0) in a data framegetFileUrls
Get the issue log for a specific data productgetIssueLog
Get either a list of NEON DOIs, or the DOI for a specific data product and releasegetNeonDOI
Get NEON data packagegetPackage
Get NEON data product informationgetProductInfo
Get data product-sensor relationshipsgetProductSensors
Scrape the publication date from each ReadMe filegetReadmePublicationDate
Returns the most recent files for those that do not need stackinggetRecentPublication
Get NEON taxon tablegetTaxonTable
Get and store the file names, S3 URLs, file size, and download status (default = 0) in a data framegetTileUrls
Get a list of the available time intervals for a data productgetTimeIndex
Extract list of eddy covariance tables from HDF5 filesgetVarsEddy
Get and store the file names, S3 URLs, file size, and download status (default = 0) in a data framegetZipUrls
Get a data frame with the names of all files within a zipped NEON data packagelistFilesInZip
Get all zip file names within a zipped NEON data packagelistZipfiles
Get files from NEON API, stack tables, and load into the current environmentloadByProduct
Bundled vegetation and sediment data product informationother_bundles
Will suppress all output messages, while retaining the output dataframequietMessages
Read a NEON data table with correct data types for each variablereadTableNEON
Terrestrial-aquatic shared data informationshared_aquatic
Flight coverage informationshared_flights
Join data files in a zipped NEON data package by table typestackByTable
Join data files in a unzipped NEON data package by table typestackDataFilesParallel
Extract eddy covariance data from HDF5 formatstackEddy
Select files from a stored set of NEON data, created by neonstore package methods or another methodstackFromStore
Publication table informationtable_types
Transform NEON CSV file to GeoCSVtransformFileToGeoCSV
Unzip a zip file either at just the top level or recursively through the fileunzipZipfileParallel
Get files from NEON API to feed the stackByTable() functionzipsByProduct
Get files from NEON ECS Bucket using URLs in stacked datazipsByURI