| Type: | Package |
| Title: | Interface to 'AmeriFlux' Data Services |
| Version: | 1.0.0 |
| Description: | Programmatic interface to the 'AmeriFlux' database (https://ameriflux.lbl.gov/). Provide query, download, and data summary tools. |
| License: | BSD_3_clause + file LICENSE |
| Encoding: | UTF-8 |
| LazyData: | true |
| URL: | https://github.com/chuhousen/amerifluxr |
| BugReports: | https://github.com/chuhousen/amerifluxr/issues |
| Depends: | R (≥ 3.6) |
| Imports: | heatmaply, httr, jsonlite, memoise, RCurl, readxl, tools |
| RoxygenNote: | 7.1.2 |
| Suggests: | covr, data.table, knitr, pander, qpdf, remotes, rmarkdown, testthat, mockr |
| VignetteBuilder: | knitr |
| NeedsCompilation: | no |
| Packaged: | 2022-02-08 00:21:08 UTC; HChu |
| Author: | Housen Chu  [aut,
cre],
Koen Hufkens
[ctb] |
| Maintainer: | Housen Chu <hchu@lbl.gov> |
| Repository: | CRAN |
| Date/Publication: | 2022-02-08 16:30:08 UTC |
BASE data example
Description
Continuous flux/met data (i.e., AmeriFlux BASE data product) for the US-CRT site, as an example for demonstration. Also see AmeriFlux webpage https://ameriflux.lbl.gov/data/aboutdata/data-variables/#base for variable definitions and details.
Usage
amf_base
Format
A data frame with 336 rows and 36 variables
Details
TIMESTAMP_START - ISO timestamp start of averaging period (YYYYMMDDHHMM)
TIMESTAMP_END - ISO timestamp end of averaging period (YYYYMMDDHHMM)
CO2 - Carbon Dioxide (CO2) mole fraction in wet air (µmolCO2 mol-1)
H2O - Water (H2O) vapor in mole fraction of wet air (mmolH2O mol-1)
FC - Carbon Dioxide (CO2) turbulent flux (µmolCO2 m-2 s-1)
NEE_PI - Net Ecosystem Exchange (µmolCO2 m-2 s-1)
CH4 - Methane (CH4) mole fraction in wet air (nmolCH4 mol-1)
FCH4 - Methane (CH4) turbulent flux (nmolCH4 m-2 s-1)
H - Sensible heat turbulent flux (W m-2)
LE - Latent heat turbulent flux (W m-2)
G_1_1_1 - Soil heat flux at horizontal location #1 (W m-2)
G_2_1_1 - Soil heat flux at horizontal location #2 (W m-2)
WD - Wind direction (Decimal degrees)
WS - Wind speed (m s-1)
USTAR - Friction velocity (m s-1)
ZL - data value
MO_LENGTH - Monin-Obukhov Stability parameter (nondimensional)
W_SIGMA - Standard deviation of vertical velocity fluctuations (m s-1)
V_SIGMA - Standard deviation of lateral velocity fluctuations (m s-1)
U_SIGMA - Standard deviation of along-wind velocity fluctuations (m s-1)
T_SONIC - Sonic temperature (deg C)
T_SONIC_SIGMA - Standard deviation of sonic temperature (deg C)
PA - Atmospheric pressure (kPa)
RH - Relative humidity (%)
TA - Air temperature (deg C)
TS_1_1_1 - Soil temperature at horizontal location #1 (deg C)
TS_2_1_1 - Soil temperature at horizontal location #2 (deg C)
WTD - Water table depth (m)
SWC - Soil water content (%)
NETRAD - Net radiation (W m-2)
PPFD_IN - Photosynthetic photon flux density, incoming (µmolPhoton m-2 s-1)
SW_IN - Shortwave radiation, incoming (W m-2)
SW_OUT - Shortwave radiation, outgoing (W m-2)
LW_IN - Longwave radiation, incoming (W m-2)
LW_OUT - Longwave radiation, outgoing (W m-2)
P - Rainfall (mm)
Source
BADM data example
Description
The BADM file provides a description, general background, geo-location, relevant publications and references for the site. The BADM files also list what is measured at the site (this list may include chamber, gradient or other eddy covariance measurements that are a super-set of the data available in AmeriFlux). Also see AmeriFlux web page https://ameriflux.lbl.gov/data/aboutdata/badm-data-product/ for details.
Usage
amf_bif
Format
A data frame with 443 rows and 5 variables
Details
SITE_ID - 6 digit AmeriFlux site ID (CC-Sss)
GROUP_ID - A unique identifier for data entries belonging to the same instance of a reported variable group
VARIABLE_GROUP - Define a set of variables that are reported together
VARIABLE - Variable names
DATAVALUE - Data value
Source
Check valid AmeriFlux site ID
Description
Check if the character is a valid AmeriFlux site ID (CC-Sss)
Usage
amf_check_site_id(x)
Arguments
x |
A vector or scalar of characters |
Value
logical vector or scalar
Examples
## Not run:
# Check if valid site ID
check_id <- amf_check_site_id(c("US-CRT", "US-crt", "USCRT"))
## End(Not run)
Returns a list of data coverage
Description
AmeriFlux data coverage statistics
Usage
amf_data_coverage(data_product = "BASE-BADM", data_policy = "CCBY4.0")
Arguments
data_product |
A scalar of character specifying the data product Currently, only "BASE-BADM" is supported. |
data_policy |
A scalar of character specifying the data policy Currently, "CCBY4.0" and "LEGACY" are supported. The default is "CCBY4.0". |
Value
AmeriFlux data coverage
SITE_ID - Six character site identifier (CC-Sss)
URL - Site page link (url)
publish_years - List of data available years (YYYY)
Examples
## Not run:
# download the variable availability
data_year <- amf_data_coverage()
# download variable availability for LEGACY policy
data_year <- amf_data_coverage(data_policy = "LEGACY")
## End(Not run)
Download AmeriFlux BASE data product
Description
This function downloads AmeriFlux BASE and BADM data files. Note: Access to AmeriFlux data requires creating an AmeriFlux account first. Register an account through the link https://ameriflux-data.lbl.gov/Pages/RequestAccount.aspx.
For details about BASE and BADM data files, see AmeriFlux web pages https://ameriflux.lbl.gov/data/data-processing-pipelines/base-publish/ and https://ameriflux.lbl.gov/data/aboutdata/badm-data-product/.
Usage
amf_download_base(
user_id,
user_email,
site_id,
data_product = "BASE-BADM",
data_policy,
agree_policy,
intended_use,
intended_use_text,
out_dir = tempdir(),
verbose = TRUE
)
Arguments
user_id |
AmeriFlux account username (character) |
user_email |
AmeriFlux account user email (character) |
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 supported and used as default. (character) |
data_policy |
"CCBY4.0" or "LEGACY" (character). AmeriFlux data are shared under two tiers of licenses as chosen by site's PI. See https://ameriflux.lbl.gov/data/data-policy/#data-use for data use guidelines under each license. Note: Data use policy selected affects which sites’ data are available for download. |
agree_policy |
Acknowledge you read and agree to the AmeriFlux Data use policy (TRUE/FALSE) |
intended_use |
The intended use category. Currently, it needs to be one of the followings:
|
intended_use_text |
Enter a brief description of intended use. This will be recorded in the download log and emailed to site's PI (character). |
out_dir |
Output directory for downloaded data, default tempdir() |
verbose |
Show feedback on download progress (TRUE/FALSE) |
Value
A vector of download file names on the local drive
Examples
## Not run:
## Download a single site, under CCBY4.0 policy
amf_download_base(user_id = "test",
user_email = "test _at_ mail.com",
site_id = "US-CRT",
data_product = "BASE-BADM",
data_policy = "CCBY4.0",
agree_policy = TRUE,
intended_use = "other",
intended_use_text = "testing download",
out_dir = tempdir())
## Download several sites, under LEGACY data policy
# When finished, return a list of downloaded files
# in your local drive.
file.ls <- amf_download_base(user_id = "test",
user_email = "test _at_ mail.com",
site_id = c("US-CRT", "US-WPT", "US-Oho"),
data_product = "BASE-BADM",
data_policy = "LEGACY",
agree_policy = TRUE,
intended_use = "other",
intended_use_text = "testing download",
out_dir = tempdir())
## End(Not run)
Download AmeriFlux BADM data product
Description
This function downloads all AmeriFlux sites' BADM data files in a single file. Note: Access to AmeriFlux data requires creating an AmeriFlux account first. Register an account through the link https://ameriflux-data.lbl.gov/Pages/RequestAccount.aspx.
For details about BADM data files, see AmeriFlux web page https://ameriflux.lbl.gov/data/aboutdata/badm-data-product/.
Usage
amf_download_bif(
user_id,
user_email,
data_policy,
agree_policy,
intended_use,
intended_use_text,
out_dir = tempdir(),
verbose = TRUE,
site_w_data = FALSE
)
Arguments
user_id |
AmeriFlux account username (character) |
user_email |
AmeriFlux account user email (character) |
data_policy |
"CCBY4.0" or "LEGACY". AmeriFlux data are shared under two tiers of licenses as chosen by site's PI. See https://ameriflux.lbl.gov/data/data-policy/#data-use for data use guidelines under each license. Note: Data use policy selected affects which sites’ data are available for download. |
agree_policy |
Acknowledge you read and agree to the AmeriFlux Data use policy (TRUE/FALSE) |
intended_use |
The intended use category. Currently, it needs to be one of the followings:
|
intended_use_text |
Enter a brief description of intended use. This will be recorded in the data download log and emailed to site's PI (character). |
out_dir |
Output directory for downloaded data, default tempdir() |
verbose |
Show feedback on download progress (TRUE/FALSE) |
site_w_data |
Logical, download all registered sites (FALSE) or only sites with available BASE data (TRUE) |
Value
A vector of download file names on the local drive
See Also
Examples
## Not run:
## Download all sites with BASE data, under CCBY4.0 policy
amf_download_bif(user_id = "test",
user_email = "test@mail.com",
data_policy = "CCBY4.0",
agree_policy = TRUE,
intended_use = "other",
intended_use_text = "testing download",
out_dir = tempdir(),
site_w_data = TRUE)
## Download all registered sites, under LEGACY policy
amf_download_bif(user_id = "test",
user_email = "test@mail.com",
data_policy = "LEGACY",
agree_policy = TRUE,
intended_use = "other",
intended_use_text = "testing download",
out_dir = tempdir(),
site_w_data = FALSE)
## End(Not run)
Extract BADM data of a specific BADM group
Description
This function extracts BADM data of a specific BADM group
from the imported BADM (BIF) file. Use function amf_read_bif
to import BADM (BIF) file.
Usage
amf_extract_badm(bif_data, select_group)
Arguments
bif_data |
A data frame consists of 5 columns: SITE_ID, GROUP_ID,
VARIABLE_GROUP, VARIABLE, DATAVALUE, imported from function
|
select_group |
A string (character), selected from VARIABLE_GROUP
in the |
Value
A data frame of re-structured BADM data with the following columns:
GROUP_ID - A unique identifier for data belonging to the same instance of a reported variable group
SITE_ID - Six character site identifier (CC-Sss)
VALUE - Values for all available VARIABLES in the selected group
...
See Also
Examples
# read the BADM BIF file, using an example data file
bif <- amf_read_bif(file = system.file("extdata",
"AMF_AA-Flx_BIF_CCBY4_20201218.xlsx",
package = "amerifluxr"))
# get a list of valid VARIALBE_GROUP
unique(bif$VARIABLE_GROUP)
# extract the selected VARIALBE_GROUP
amf_extract_badm(bif_data = bif, select_group = "GRP_FLUX_MEASUREMENTS")
amf_extract_badm(bif_data = bif, select_group = "GRP_IGBP")
Filter AmeriFlux BASE data based on plausible range
Description
The function filters BASE data based on the expected plausible ranges specified for each variable. See AmeriFlux web site https://ameriflux.lbl.gov/data/data-processing-pipelines/data-qaqc/ for description of the plausible ranges.
Usage
amf_filter_base(
data_in,
limit_ls = NULL,
basename_decode = NULL,
loose_filter = 0.05
)
Arguments
data_in |
A data frame containing BASE data, e.g.,
import from |
limit_ls |
A data frame with at least three columns:
If not specified, use |
basename_decode |
A data frame with at least two columns:
If not specified, use |
loose_filter |
A number in ratio (0-1) used to adjust the physical range for filtering. Set it to 0 if not used. The default is 0.05. |
Value
A data frame similar to data_in filtered out off-range points
Examples
## Not run:
# read the BASE from a csv file
base <- amf_read_base(file = system.file("extdata",
"AMF_US-CRT_BASE_HH_2-5.csv",
package = "amerifluxr"),
unzip = FALSE,
parse_timestamp = FALSE)
# filter data, using default physical range +/- 5% buffer
base_f <- amf_filter_base(data_in = base)
# filter data, using default physical range without buffer
base_f <- amf_filter_base(data_in = base, loose_filter = 0)
## End(Not run)
Get BASE data variable availability
Description
This function obtains the BASE data availability for all or selected AmeriFlux sites. See AmeriFlux page https://ameriflux.lbl.gov/data/aboutdata/data-variables/ for details about the variable naming.
Usage
amf_list_data(site_set = NULL, var_set = NULL)
Arguments
site_set |
A scalar or vector of character specifying the target AmeriFlux Site ID (CC-Sss). If not specified, it returns all sites. |
var_set |
A scalar or vector of character specifying the target variables as in basename. See AmeriFlux pagehttps://ameriflux.lbl.gov/data/aboutdata/data-variables/#base for a list of variable names. If not specified, it returns all variables. |
Value
A data frame of variable-specific data availability (per year) for selected AmeriFlux sites.
Site_ID - Six character site identifier (CC-Sss)
VARIABLE - Variable name of the data included in the BASE file
BASENAME - Variable base name of the data included in the BASE file.
GAP_FILLED - Whether a variable is a gap-filled variable (TRUE/FALSE)
Y1990 - Percentage of data availability in the year 1990 (0-1).
Y1991 - Percentage of data availability in the year 1991 (0-1).
Y1992 - Percentage of data availability in the year 1992 (0-1).
...
Examples
## Not run:
# obtain the data variable availability for all sites
data_aval <- amf_list_data()
# obtain the data variable availability for selected sites
data_aval <- amf_list_data(site_set = c("US-CRT","US-WPT"))
# obtain the data variable availability for selected variables
data_aval <- amf_list_data(var_set = c("FCH4", "WTD"))
## End(Not run)
Get metadata availability
Description
This function obtains the metadata (i.e., BADM) availability for all or selected AmeriFlux sites. See AmeriFlux page https://ameriflux.lbl.gov/data/badm/ for details about the BADM.
Usage
amf_list_metadata(site_set = NULL, group_only = TRUE)
Arguments
site_set |
A scalar or vector of character specifying the target AmeriFlux Site ID (CC-Sss). If not specified, it returns all sites. |
group_only |
Logical (TRUE/FALSE). Should it return availability for BADM variable groups or variables? BADM Groups contain Variables that describe related metadata or an observation with related metadata. |
Value
A data frame of data variable availability (per year) for selected AmeriFlux sites. The first column contains the SITE ID. The remaining columns contains the number of entries for a variable or a variable group, with column names specifying the BADM variable or group names.
Site_ID - Six character site identifier (CC-Sss)
...
Examples
## Not run:
# obtain the metadata availability for all sites, at variable group levels
metadata_aval <- amf_list_metadata()
# obtain the metadata availability for selected sites, at variable levels
metadata_aval <- amf_list_metadata(site_set = c("US-CRT","US-WPT"),
group_only = FALSE)
## End(Not run)
Parse BASE data variable name and qualifier
Description
This function parse variable names and qualifiers of AmeriFlux BASE data product. See AmeriFlux web page https://ameriflux.lbl.gov/data/aboutdata/data-variables/ about the details of variable naming and qualifiers.
Usage
amf_parse_basename(var_name, FP_ls = NULL, gapfill_postfix = "_PI_F")
Arguments
var_name |
A vector of variable names (character) to be parsed |
FP_ls |
A vector of standard variable names. If not specified,
use |
gapfill_postfix |
A scalar of expected suffix (character) appended to a variable that is gap-filled. The default is "_PI_F". |
Value
A data frame containing the parsed results for all variables in
var_name:
variable_name - original variable name
basename - associated basename, w/o qualifier
qualifier_gf - qualifier associated with gap-filling
qualifier_pi - qualifier associated with PI version, excluding gap-filling
qualifier_pos - qualifier associated with position
qualifier_ag - qualifier associated with layer-aggregation, e.g., _N, _SD
layer_index - layer index provided, if any
H_index - H index provided, if any
V_index - V index provided, if any
R_index - R index provided, if any
is_correct_basename - is the parsed basename recognized in FP-Standard
is_pi_provide - is this a PI provided variable e.g., _PI
is_gapfill - is this a gap-filled variable, _PF_F or _F
is_fetch - is this a fetch quantile variable, e.g., FETCH_70...
is_layer_aggregated - is this a layer-integrated variable, i.e., _#
is_layer_SD - is this a standard deviation of layer-integrated variable, i.e., spatial variability
is_layer_number - is this a number of samples of layer-integrated variable, i.e., spatial variability
is_replicate_aggregated - is this a replicate-averaged variable, e.g., _1_1_A
is_replicate_SD - is this a standard deviation of replicate-averaged variable, e.g., _1_1_A_SD
is_replicate_number - is this a number of samples of replicate-averaged variable, e.g., _1_1_A_N
is_quadruplet - is this a quadruplet, e.g., _1_1_1
See Also
Examples
## Not run:
# read the BASE from a csv file
base <- amf_read_base(file = system.file("extdata",
"AMF_US-CRT_BASE_HH_2-5.csv",
package = "amerifluxr"),
unzip = FALSE,
parse_timestamp = FALSE)
# parse variable names/qualifiers
basename_decode <- amf_parse_basename(var_name = colnames(base))
## End(Not run)
Plot data summary
Description
This function visualizes the BASE data summary for
selected AmeriFlux sites and variables. This is a wrapper around
amf_summarize_data. However, it is strongly advised to
subset either sites or variables for faster processing and better
visualization.
Usage
amf_plot_datasummary(
data_sum = NULL,
site_set = NULL,
var_set = NULL,
nonfilled_only = TRUE,
show_cluster = FALSE,
scale = FALSE
)
Arguments
data_sum |
A data frame with following columns:
If not specified, use |
site_set |
A scalar or vector of character specifying the target AmeriFlux Site ID (CC-Sss). If not specified, it returns all sites. |
var_set |
A scalar or vector of character specifying the target variables as in basename. See AmeriFlux pagehttps://ameriflux.lbl.gov/data/aboutdata/data-variables/#base for a list of variable names. If not specified, it returns all variables. |
nonfilled_only |
Logical, whether only showing non-filled variables, or both non- and gap-filled variables. The default is TRUE. |
show_cluster |
Logical, whether showing clustering (dendrogram) of site-variables. The default is FALSE. |
scale |
Logical, whether the values should be centered and scaled among site-variables. The default is FALSE. |
Value
An object of class 'plotly' from heatmaply
See Also
Examples
## Not run:
# plot data summary for selected variables at two sites
amf_plot_datasummary(site_set = c("US-CRT", "US-WPT"),
var_set = c("H", "LE", "NETRAD"))
# plot data summary for FCH4 at all sites, and show
# clustering among sites
amf_plot_datasummary(var_set = "FCH4",
show_cluster = TRUE)
# plot data summary for TA at all grassland sites,
# and show clustering among sites
sites <- amf_site_info()
sites <- subset(sites, IGBP == "CRO")
amf_plot_datasummary(site_set = sites$SITE_ID,
var_set = "TA",
show_cluster = TRUE)
# normalize TA among sites
amf_plot_datasummary(site_set = sites$SITE_ID,
var_set = "TA",
show_cluster = TRUE,
scale = TRUE)
## End(Not run)
Plot data availability
Description
This function visualizes the BASE data availability for
selected AmeriFlux sites, variables, and years. This is a wrapper around
amf_list_data. However, it is strongly advised to subset
the sites, variables, and/or years for faster processing and better
visualization.
Usage
amf_plot_datayear(
data_aval = NULL,
site_set = NULL,
var_set = NULL,
nonfilled_only = TRUE,
year_set = NULL
)
Arguments
data_aval |
A data frame with at least five columns:
If not specified, use |
site_set |
A scalar or vector of character specifying the target AmeriFlux Site ID (CC-Sss). If not specified, it returns all sites. |
var_set |
A scalar or vector of character specifying the target variables as in basename. See AmeriFlux pagehttps://ameriflux.lbl.gov/data/aboutdata/data-variables/#base for a list of variable names. If not specified, it returns all variables. |
nonfilled_only |
Logical, whether only showing non-filled variables, or both non- and gap-filled variables. The default is TRUE. |
year_set |
A scalar or vector of integers. If not specified, it plots only years with any available data in selected sites and variables |
Value
An object of class 'plotly' from heatmaply
See Also
Examples
## Not run:
# plot data availability for all variables at a single site
# in all years
amf_plot_datayear(site_set = "US-CRT",
nonfilled_only = FALSE)
# plot data availability for non-filled FCH4 and WTD at all
# sites in all years
amf_plot_datayear(var_set = c("FCH4", "WTD"),
nonfilled_only = TRUE)
# plot data availability for non-filled FCH4 at all sites
# in 2018-2020
amf_plot_datayear(var_set = "FCH4",
year_set = c(2018:2020),
nonfilled_only = TRUE)
## End(Not run)
Read AmeriFlux BASE data product
Description
This function read in the BASE data file downloaded
from AmeriFlux. See AmeriFlux web page
https://ameriflux.lbl.gov/data/data-processing-pipelines/base-publish/
for details about BASE data product. Use amf_variables
to get a list of standard variable names and units.
Usage
amf_read_base(file, unzip = TRUE, parse_timestamp = FALSE)
Arguments
file |
A BASE data file, either in a zipped file or a comma-separate value (csv) file |
unzip |
Logical, whether to unzip. The default is TRUE. Set FALSE if reading from a previously unzipped csv file. |
parse_timestamp |
Logical, whether to parse the time stamp. Set TRUE to parse and add timekeeping columns. |
Value
A data frame containing data. See AmeriFlux website
https://ameriflux.lbl.gov/data/aboutdata/data-variables/
for details about file format, variable definition, units, and convention.
If parse_timestamp = TRUE, the following six time-keeping columns are
added in the returned data frame:
YEAR - Year (YYYY)
MONTH - Month (MM)
DAY - Day of the month (DD)
DOY - Day of the year (DDD)
HOUR - Hour of the day (HH), based on the middle time of the interval
MINUTE - Minute of the hour (mm), based on the middle time of the interval
TIMESTAMP - An object of class "POSIXlt" in the UTC time zone, based on the middle time of the interval
See Also
amf_parse_basename, amf_filter_base
Examples
# read the BASE from a zip file, using the example data file
base <- amf_read_base(file = system.file("extdata",
"AMF_US-CRT_BASE-BADM_2-5.zip",
package = "amerifluxr"),
unzip = TRUE,
parse_timestamp = TRUE)
# read the BASE from a csv file
base <- amf_read_base(file = system.file("extdata",
"AMF_US-CRT_BASE_HH_2-5.csv",
package = "amerifluxr"),
unzip = FALSE,
parse_timestamp = FALSE)
Read AmeriFlux BADM data product
Description
This function read in the BADM data file formatted in BADM Interchange Format (BIF).
Usage
amf_read_bif(file)
Arguments
file |
A BADM data file |
Value
A data frame containing the following 5 columns. See AmeriFlux website https://ameriflux.lbl.gov/data/aboutdata/badm-data-product/ for details.
SITE_ID - Six character site identifier (CC-Sss)
GROUP_ID - A unique identifier for data belonging to the same instance of a reported variable group
VARIABLE_GROUP - A set of variables that are reported together
VARIABLE - The variable name
DATAVALUE - The reported value of a variable
Examples
# read the BADM BIF file, using an example data file
bif <- amf_read_bif(file = system.file("extdata",
"AMF_AA-Flx_BIF_CCBY4_20201218.xlsx",
package = "amerifluxr"))
Get AmeriFlux site general info
Description
This function obtains the latest AmeriFlux site list and sites' general info through the AmeriFlux web service.
Usage
amf_site_info()
Details
This combines the information of various other functions.
Value
A data frame containing the following columns. See AmeriFlux BADM standard https://ameriflux.lbl.gov/data/badm/ for detailed explanation.
SITE_ID - Six character site identifier (CC-Sss)
SITE_NAME - Site name (free text)
COUNTRY - Country (free text)
STATE - State (free text)
IGBP - Vegetation type based on the IGBP definition (character)
URL_AMERIFLUX - Site web site URL, maintained by AmeriFlux (URL)
TOWER_BEGAN - The starting year of flux measurement (YYYY)
TOWER_END - The ending year of flux measurement (YYYY), NA if still active or unspecified
LOCATION_LAT - Latitude of the site (decimal deg ref WGS84)
LOCATION_LONG - Longitude of the site (decimal deg ref WGS84)
LOCATION_ELEV - Elevation of the site above sea level (m)
CLIMATE_KOEPPEN - Koppen climate classification (character)
MAT - Long-term mean annual average air temperature (degree C)
MAP - Long-term mean annual average precipitation (mm)
DATA_POLICY - LEGACY / CCBY4.0 (character)
DATA_START - The starting year with published AmeriFlux BASE data (YYYY)
DATA_END - The ending year with published AmeriFlux BASE data (YYYY)
Examples
## Not run:
# obtain the basic general info for all sites
site <- amf_site_info()
## End(Not run)
## End(Not run)
Lists AmeriFlux sites
Description
Lists available site (names) and basic meta-data
Usage
amf_sites()
Value
A data frame containing the following columns. See AmeriFlux BADM standard https://ameriflux.lbl.gov/data/badm/ for detailed explanation.
SITE_ID - Six character site identifier (CC-Sss)
SITE_NAME - Site name (free text)
COUNTRY - Country (free text)
STATE - State (free text)
IGBP - Vegetation type based on the IGBP definition (character)
URL_AMERIFLUX - Site web site URL, maintained by AmeriFlux (URL)
TOWER_BEGAN - The starting year of flux measurement (YYYY)
TOWER_END - The ending year of flux measurement (YYYY), NA if still active or unspecified
LOCATION_LAT - Latitude of the site (decimal deg ref WGS84)
LOCATION_LONG - Longitude of the site (decimal deg ref WGS84)
LOCATION_ELEV - Elevation of the site above sea level (m)
CLIMATE_KOEPPEN - Koppen climate classification (character)
MAT - Long-term mean annual average air temperature (degree C)
MAP - Long-term mean annual average precipitation (mm)
DATA_POLICY - LEGACY / CCBY4.0 (character)
Examples
## Not run:
# download a list of sites and basic info
sites <- amf_sites()
## End(Not run)
Get BASE data summary
Description
This function obtains the BASE data summary for all or selected AmeriFlux sites. See AmeriFlux page https://ameriflux.lbl.gov/data/aboutdata/data-variables/ for details about the variable naming.
Usage
amf_summarize_data(site_set = NULL, var_set = NULL)
Arguments
site_set |
A scalar or vector of character specifying the target AmeriFlux Site ID (CC-Sss). If not specified, it returns all sites. |
var_set |
A scalar or vector of character specifying the target variables as in basename. See AmeriFlux pagehttps://ameriflux.lbl.gov/data/aboutdata/data-variables/#base for a list of variable names. If not specified, it returns all variables. |
Value
A data frame of site-specific variable summary statistics (selected percentiles) for selected AmeriFlux sites.
Site_ID - Six character site identifier (CC-Sss)
VARIABLE - Variable name of the data included in the BASE file
BASENAME - Variable base name of the data included in the BASE file.
GAP_FILLED - Whether a variable is a gap-filled variable (TRUE/FALSE)
DATA_RECORD - Number of supposed data record (counts)
DATA_MISSING - Number of missing data record (counts)
Q01 - 1th percentile of the data
Q05 - 5th percentile of the data
...
Q95 - 95th percentile of the data
Q99 - 99th percentile of the data
Examples
## Not run:
# obtain the data variable availability for all sites & variables
data_sum <- amf_summarize_data()
# obtain the data variable availability for selected sites, all variables
data_sum <- amf_summarize_data(site_set = c("US-CRT","US-WPT"))
# obtain the data variable availability for selected sites & variables
data_sum <- amf_summarize_data(site_set = c("US-CRT","US-WPT"),
var_set = c("FC", "LE", "H"))
## End(Not run)
Get variable information
Description
This function obtains the measurement height metadata for the AmeriFlux BASE data product. See AmeriFlux page https://ameriflux.lbl.gov/data/measurement-height/ for details.
Usage
amf_var_info(out_dir = tempdir(), verbose = TRUE)
Arguments
out_dir |
The output directory (default = tempdir()) |
verbose |
Logical, whether to show download progress (TRUE/FALSE) |
Value
A data frame of measurement height data for all AmeriFlux sites #'
Site_ID - Six character site identifier (CC-Sss)
Variable - Variable name of the data included in the BASE file
Start_Date - Date when the information first applies
Height - Distance above the ground surface in meters
Instrument_Model - Instrument model used to collect the data variable
Instrument_Model2 - A second instrument model used to collect the data variable
Comment - Additional information provided by the site team
BASE_Version - The most recent BASE data product version number for which the information applies
Examples
## Not run:
# download the measurement height data for all sites
var_info <- amf_var_info()
## End(Not run)
Get FP (Flux-Processing) Standard Variable List
Description
This function obtains the latest AmeriFlux FP (Flux-Processing) standard variable list. FP standard defines the variable names and units used for continuously sampled data within the AmeriFlux. Also see AmeriFlux Data Variables page https://ameriflux.lbl.gov/data/aboutdata/data-variables/ for details.
Usage
amf_variables()
Value
A data frame containing the following columns:
Name - Standard variable name
Description - Description of the variable
Units - Standard variable unit
Min - Expected minimal value
Max - Expected maximal value
Examples
## Not run:
# download the list of standard variable names and units
FP_ls <- amf_variables()
## End(Not run)