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NEONScience / NEON-utilities

Utilities and scripts for working with NEON data. Currently: an R package with functions to join (stack) the month-by-site files in downloaded NEON data, to convert data to geoCSV format, and to download data from the API.
GNU Affero General Public License v3.0
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Adding the ability to read a list of h5 files into stackEddy #102

Closed rqthomas closed 3 years ago

rqthomas commented 4 years ago

The PR provides the option for filepath to be a list of h5 files in the stackEddy function. This is intended to allow the stackEddy function interface with the neonstore package. The neon_index function returns a list of downloaded files that match specified criteria. For example:

neonstore::neon_download(product = "DP4.00200.001", site = "BART",start_date = "2020-05-01")

meta <- neonstore::neon_index(product = "DP4.00200.001", table = NA, site = "BART", start_date = NA, end_date = NA, type = NA, ext = "h5", hash = NULL, dir = neonstore::neon_dir()) returns a list of h5 files (meta$path). The updates in this PR allow meta$path to be directly passed to stackEddy

d <- stackEddy(filepath = meta$path,level="dp04")

Also, I allowed the filepath variable that is calculated internally to be a list of paths rather than requiring it to be a single path. This allows the h5 files to potentially be spread across different directories (only if a list of h5 files is provided).

cklunch commented 3 years ago

This is now implemented in a slightly different way in the latest updates to stackEddy(), merged to master just now. Headed to CRAN in the next few days.