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neonUtilities

Utilities for Working with NEON Data

NEON data packages can be accessed through the NEON Data Portal <https://data.neonscience.org/home> 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>.

Functions (46)

assignClasses

Assign correct column classes

byFileAOP

Serially download all AOP files for a given site, year, and product

byTileAOP

Download AOP tiles overlapping specified coordinates for a given site, year, and product

chem_bundles

Bundled chemistry data product information

cleanUp

Clean up folder after stacking

convByteSize

Convert a number of bytes into megabytes or gigabytes

dateConvert

Convert date stamps from character

eddyStampCheck

Convert date stamps from character and check for only one record in a day

findDatatables

Find data tables

findTablesByFormat

Find unique data tables in dataset

findTablesUnique

Find unique data tables in dataset

footRaster

Extract eddy covariance footprint data from HDF5 format

getAPI

Get the data from API

getAPIHeaders

Get only headers from API

getAvg

Get a list of the available averaging intervals for a data product

getDatatable

Get NEON data table

getFileUrls

Get and store the file names, S3 URLs, file size, and download status (default = 0) in a data frame

getPackage

Get NEON data package

getProductInfo

Get NEON data product information

getProductSensors

Get data product-sensor relationships

getReadmePublicationDate

Scrape the publication date from each ReadMe file

getRecentPublication

Returns the most recent files for those that do not need stacking

getTaxonTable

Get NEON taxon table

getTileUrls

Get and store the file names, S3 URLs, file size, and download status (default = 0) in a data frame

getTimeIndex

Get a list of the available time intervals for a data product

getTitle

Get NEON data product title

getVariables

Get correct data types

getVarsEddy

Extract list of eddy covariance tables from HDF5 files

getZipUrls

Get and store the file names, S3 URLs, file size, and download status (default = 0) in a data frame

listFilesInZip

Get a data frame with the names of all files within a zipped NEON data package

listZipfiles

Get all zip file names within a zipped NEON data package

loadByProduct

Get files from NEON API, stack tables, and load into the current environment

makePosColumns

Create position (horizontal and vertical) columns

quietMessages

Will suppress all output messages, while retaining the output dataframe

readTableNEON

Read a NEON data table with correct data types for each variable

shared_aquatic

Terrestrial-aquatic shared data information

shared_flights

Flight coverage information

stackByTable

Join data files in a zipped NEON data package by table type

stackDataFilesParallel

Join data files in a unzipped NEON data package by table type

stackEddy

Extract eddy covariance data from HDF5 format

stackFromStore

Select files from a stored set of NEON data, created by neonstore package methods or another method

table_types

Publication table information

transformFileToGeoCSV

Transform NEON CSV file to GeoCSV

unzipZipfileParallel

Unzip a zip file either at just the top level or recursively through the file

zipsByProduct

Get files from NEON API to feed the stackByTable() function

zipsByURI

Get files from NEON ECS Bucket using URLs in stacked data

neonUtilities

Utilities for Working with NEON Data

v2.0.1

AGPL-3

Authors

Claire Lunch [aut, cre, ctb], Christine Laney [aut, ctb], Nathan Mietkiewicz [aut, ctb], Eric Sokol [aut, ctb], Kaelin Cawley [aut, ctb], NEON (National Ecological Observatory Network) [aut]

Initial release

2021-03-04

neonUtilities

Functions (46)

neonUtilities

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