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.
amf_extract_badm(bif_data, select_group)A data frame consists of 5 columns: SITE_ID, GROUP_ID,
VARIABLE_GROUP, VARIABLE, DATAVALUE, imported from function
amf_read_bif.
A string (character), selected from VARIABLE_GROUP
in the bif_data
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
...
# 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)
#> [1] "GRP_ACKNOWLEDGEMENT" "GRP_CLIM_AVG"
#> [3] "GRP_COUNTRY" "GRP_DOI"
#> [5] "GRP_DOI_CONTRIBUTOR" "GRP_DOI_ORGANIZATION"
#> [7] "GRP_DOM_DIST_MGMT" "GRP_FLUX_MEASUREMENTS"
#> [9] "GRP_HEADER" "GRP_HEIGHTC"
#> [11] "GRP_IGBP" "GRP_LAND_OWNERSHIP"
#> [13] "GRP_LOCATION" "GRP_NETWORK"
#> [15] "GRP_REFERENCE_PAPER" "GRP_SHIPPING_ADDRESS"
#> [17] "GRP_SITE_CHAR" "GRP_SITE_DESC"
#> [19] "GRP_SITE_FUNDING" "GRP_STATE"
#> [21] "GRP_TEAM_MEMBER" "GRP_TOWER_POWER"
#> [23] "GRP_TOWER_TYPE" "GRP_URL"
#> [25] "GRP_URL_AMERIFLUX" "GRP_UTC_OFFSET"
#> [27] "GRP_AG_BIOMASS_OTHER" "GRP_LAI"
#> [29] "GRP_NEP" "GRP_RESEARCH_TOPIC"
#> [31] "GRP_SA" "GRP_SOIL_CHEM"
#> [33] "GRP_SOIL_CLASSIFICATION" "GRP_SPP_O"
# extract the selected VARIALBE_GROUP
amf_extract_badm(bif_data = bif, select_group = "GRP_FLUX_MEASUREMENTS")
#> GROUP_ID SITE_ID FLUX_MEASUREMENTS_METHOD FLUX_MEASUREMENTS_VARIABLE
#> 5 12767 US-CRT Eddy Covariance CO2
#> 6 12782 US-CRT Eddy Covariance H2O
#> 7 12786 US-CRT Eddy Covariance H
#> 8 12787 US-CRT Eddy Covariance CH4
#> 9 12791 US-Oho Eddy Covariance CO2
#> 10 12806 US-Oho Eddy Covariance H2O
#> 11 12812 US-Oho Eddy Covariance H
#> 1 12741 US-WPT Eddy Covariance CO2
#> 2 12756 US-WPT Eddy Covariance H2O
#> 3 12761 US-WPT Eddy Covariance H
#> 4 12762 US-WPT Eddy Covariance CH4
#> FLUX_MEASUREMENTS_DATE_START FLUX_MEASUREMENTS_DATE_END
#> 5 20110101 20131231
#> 6 20110101 20131231
#> 7 20110101 20131231
#> 8 20110511 20120520
#> 9 2004 2013
#> 10 2004 2013
#> 11 2004 2013
#> 1 20110101 20131231
#> 2 20110101 20131231
#> 3 20110101 20131231
#> 4 20110311 20131231
#> FLUX_MEASUREMENTS_OPERATIONS
#> 5 Continuous operation
#> 6 Continuous operation
#> 7 Continuous operation
#> 8 Continuous operation
#> 9 Continuous operation
#> 10 Continuous operation
#> 11 Continuous operation
#> 1 Continuous operation
#> 2 Continuous operation
#> 3 Continuous operation
#> 4 Continuous operation
amf_extract_badm(bif_data = bif, select_group = "GRP_IGBP")
#> GROUP_ID SITE_ID IGBP
#> 2 12768 US-CRT CRO
#> 3 12792 US-Oho DBF
#> 1 12742 US-WPT WET