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https://github.com/chuhousen/amerifluxr
An R programmatic interface for AmeriFlux data and metadata
https://github.com/chuhousen/amerifluxr
ameriflux api carbon-flux data time-series
Last synced: 22 days ago
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An R programmatic interface for AmeriFlux data and metadata
- Host: GitHub
- URL: https://github.com/chuhousen/amerifluxr
- Owner: chuhousen
- License: other
- Created: 2021-02-03T22:48:11.000Z (almost 4 years ago)
- Default Branch: master
- Last Pushed: 2024-10-02T16:06:50.000Z (3 months ago)
- Last Synced: 2024-10-24T23:21:36.663Z (2 months ago)
- Topics: ameriflux, api, carbon-flux, data, time-series
- Language: R
- Homepage: https://chuhousen.github.io/amerifluxr/
- Size: 40.9 MB
- Stars: 21
- Watchers: 3
- Forks: 6
- Open Issues: 1
-
Metadata Files:
- Readme: README.md
- Changelog: NEWS.md
- License: LICENSE
- Code of conduct: CODE_OF_CONDUCT.md
Awesome Lists containing this project
- open-sustainable-technology - ameriflux - A network of PI-managed sites measuring ecosystem CO2, water, and energy fluxes in North, Central and South America. (Emissions / Emission Observation and Modeling)
README
# amerifluxr 
[](https://github.com/chuhousen/amerifluxr/actions/workflows/R-CMD-check.yaml)
[](https://app.codecov.io/gh/chuhousen/amerifluxr)
[](https://cran.r-project.org/package=amerifluxr)
An R programmatic interface for querying, downloading, and handling [AmeriFlux](https://ameriflux.lbl.gov/) data and metadata.
## Installation
### Stable release
To install the current stable release use a CRAN repository:
``` r
install.packages("amerifluxr")
library("amerifluxr")
```
### Development release
To install the development releases of the package run the following
commands:
``` r
if(!require(devtools)){install.packages("devtools")}
devtools::install_github("chuhousen/amerifluxr")
library("amerifluxr")
```
Vignettes are not rendered by default, if you want to include additional
documentation please use:
``` r
if(!require(devtools)){install.packages("devtools")}
devtools::install_github("chuhousen/amerifluxr", build_vignettes = TRUE)
library("amerifluxr")
```
## Use
### Obtain an AmeriFlux site list
This function obtains the latest AmeriFlux site list and
sites' general info through the AmeriFlux web service.
``` r
site <- amf_site_info()
```
### Download all-site metadata
Access to AmeriFlux data requires creating an AmeriFlux account first.
Register an account through the
[link](https://ameriflux-data.lbl.gov/Pages/RequestAccount.aspx).
The following downloads a single file containing all AmeriFlux sites'
metadata (i.e., BADM data product) for sites under the CC-BY-4.0 data
use policy. The downloaded file is a Excel file saved to tempdir()
(e.g., AMF\_\{SITES\}\_BIF\_\{POLICY\}\_\{VERSION\}\.xlsx, SITES
= AA-Net (all registered sites) or AA-Flx (all sites with flux/met
data available); POLICY = CCBY4 (shared under AmeriFlux CC-BY-4.0
data use policy) or LEGACY (shared under AmeriFlux Legacy data use
policy)).
For details about BADM data files, see AmeriFlux
[web page](https://ameriflux.lbl.gov/data/aboutdata/badm-data-product/).
``` r
floc1 <- amf_download_bif(user_id = "my_user",
user_email = "[email protected]",
data_policy = "CCBY4.0",
agree_policy = TRUE,
intended_use = "synthesis",
intended_use_text = "obtain AmeriFlux sites' geolocation, IGBP, and climate classification",
out_dir = tempdir(),
verbose = TRUE,
site_w_data = TRUE)
```
| Parameter | Description |
| ------------------ | ------------------------------------------------------------------------------------------------------------------------------- |
| user_id | AmeriFlux account username |
| user_email | AmeriFlux account user email |
| data_policy | "CCBY4.0" or "LEGACY". AmeriFlux data are shared under two tiers of licenses as chosen by site's PI. |
| agree_policy | Acknowledge you read and agree to the AmeriFlux Data use policy |
| intended_use | The intended use category. It needs to be "synthesis", "model", "remote_sensing","other_research", "education", or "other" |
| intended_use_text | Brief description of intended use.This will be recorded in the data download log and emailed to site's PI. |
| out_dir | Output directory for downloaded data, default to tempdir() |
| verbose | Show feedback on download progress |
| site_w_data | Logical, download all registered sites (FALSE) or only sites with available BASE data (TRUE) |
The amf_download_bif() returns the full file path to the downloaded file,
which can be used to read the file into R.
``` r
bif <- amf_read_bif(file = floc1)
```
### Download single-site flux/met data
The following downloads AmeriFlux flux/met data (aka BASE data product)
from a single site. For details about BASE data files, see AmeriFlux
[BASE data](https://ameriflux.lbl.gov/data/data-processing-pipelines/base-publish/)
page.
The downloaded file is a zipped file saved in tempdir()
(e.g., AMF\_\{SITE_ID\}\_BASE-BADM\_\{VERSION\}\.zip), which contains a BASE data
file (e.g., AMF\_\{SITE_ID\}\_BASE\_\{RESOLUTION\}\_\{VERSION\}\.csv,
RESOLUTION = HH (half-hourly) or HR (hourly)) and a BADM data file (e.g.,
AMF\_\{SITE_ID\}\_BIF\_\{VERSION\}\.xlsx). The BADM data file is a site subset of
the all-site BADM downloaded through amf_download_bif().
``` r
floc2 <- amf_download_base(user_id = "my_user",
user_email = "[email protected]",
site_id = "US-CRT",
data_product = "BASE-BADM",
data_policy = "CCBY4.0",
agree_policy = TRUE,
intended_use = "remote_sensing",
intended_use_text = "validate the model of GPP estimation",
verbose = TRUE,
out_dir = tempdir())
```
| Parameter | Description |
| ------------------ | ------------------------------------------------------------------------------------------------------------------------------- |
| user_id | AmeriFlux account username |
| user_email | AmeriFlux account user email |
| site_id | A scalar or vector of character specifying the AmeriFlux Site ID (CC-Sss) |
| data_product | AmeriFlux data product. Currently, only "BASE-BADM" is currently supported and used as default. |
| data_policy | "CCBY4.0" or "LEGACY". AmeriFlux data are shared under two tiers of licenses as chosen by site's PI. |
| agree_policy | Acknowledge you read and agree to the AmeriFlux Data use policy |
| intended_use | The intended use category. It needs to be "synthesis", "model", "remote_sensing","other_research", "education", or "other" |
| intended_use_text | Brief description of intended use.This will be recorded in the data download log and emailed to site's PI. |
| out_dir | Output directory for downloaded data, default to tempdir() |
| verbose | Show feedback on download progress |
The amf_download_base() returns the full file path to the downloaded file,
which can be used to read the file into R.
``` r
base <- amf_read_base(file = floc2,
unzip = TRUE,
parse_timestamp = TRUE)
```
| Parameter | Description |
| ------------------ | ------------------------------------------------------------------------------------------------------------------------------- |
| file | file path |
| unzip | logical, whether to unzip. Set TRUE if reading from a zipped file |
| parse_timestamp | logical, whether to parse the timestamp |
### Download multiple-site flux/met data
The following downloads AmeriFlux flux/met data from multiple sites.
The downloaded files are organized by sites, with one zipped file for
each site, similar to single-site download.
``` r
amf_download_base(user_id = "my_user",
user_email = "[email protected]",
site_id = c("US-CRT", "US-WPT", "US-Oho"),
data_product = "BASE-BADM",
data_policy = "CCBY4.0",
agree_policy = TRUE,
intended_use = "model",
intended_use_text = "Data-driven modeling, for training models and cross-validation",
verbose = TRUE,
out_dir = tempdir())
```
### Additional functionalities
* [Site Selection Vignette](https://chuhousen.github.io/amerifluxr/articles/site_selection.html)
demonstrates examples to query a list of target sites based on
sites' general information and availability of metadata and data.
* [Data Import Vignette](https://chuhousen.github.io/amerifluxr/articles/data_import.html)
demonstrates examples to import data and metadata downloaded from
AmeriFlux, and parse and clean data for further use.
## Citation
Chu, Housen, and Hufkens, Koen. "amerifluxr v1.0.0." Computer software. May 10, 2021. https://github.com/chuhousen/amerifluxr. https://doi.org/10.11578/dc.20210730.2.
## Acknowledgement
We thank the AmeriFlux site teams for sharing their data and
metadata with the network. Funding for these flux sites is
acknowledged in the site data DOI on
[AmeriFlux website](https://ameriflux.lbl.gov/).
This package was supported in part by funding provided to the
AmeriFlux Management Project by the U.S. Department of Energy’s
Office of Science under Contract No. DE-AC0205CH11231.
We also thank Adam Young, Minkyu Moon, Erica Orcutt, Manuel Helbig
for testing the package and providing valuable feedback.