extract_coded: Extract Quality Control Information from Coded Values
In lsigut/openeddy: Post-process eddy covariance data with ease

extract_coded

R Documentation

Extract Quality Control Information from Coded Values

Description

This function is called by extract_QC and is not intended to be used directly. Coded QC information for one or multiple variables stored in a character vector of certain properties is extracted and interpreted.

Usage

extract_coded(
  x,
  name_out_SA = "SA",
  name_out_GA = "GA",
  name_out_SAGA = "SAGA",
  name_out_ALL = "ALL",
  prefix = "[8]",
  split = "[/]",
  sf = FALSE
)

Arguments

`x`	An atomic type.
`name_out_SA, name_out_GA, name_out_SAGA, name_out_ALL`	A character string. Name of the output column with QC related to SA, GA, SAGA or ALL.
`prefix`	Character string containing a `regular expression` identifying the prefix of coded values.
`split`	Character string containing a `regular expression` identifying the separator of variable names in `units` attribute.
`sf`	A logical value. Coded variable represents hard flag (`sf = FALSE`; default) or soft flag (`sf = TRUE`). See Details.

Details

Each element of x is expected to have the same structure according to the format specified by units attribute of x. units format string (e.g. "8u/v/w/ts/h2o/co2") starts with a prefix ("8") that is followed by variable names ("u", "v", "w", "ts", "h2o", "co2") that are distinguished by a separator ("/"). Elements of x thus consist of either seven components (prefix and six flags for each variable) or one NA value. Flags of coded variables can have three values:

flag 0: measured variable passed the test.
flag 1: measured variable failed the test.
flag 9: flag could not be obtained for the given variable (NA).

The original flags are then interpreted within the QC scheme using QC flag range 0 - 2. Coded variable can represent either

hard flag (suffix "_hf" in EddyPro column name): flag 1 interpreted as flag 2.
soft flag (suffix "_sf" in EddyPro column name): flag 1 interpreted as flag 1.

x is interpreted in respect to instruments required to measure given fluxes. SA is required for measurements of all fluxes and solely provides data for computation of Tau and H fluxes. GA is used only for measurements of LE and NEE. A combination of SA and GA (SAGA) is used for measurements of LE and NEE. Filters where flags would be identical for both SA and GA have prefix ALL (QC flags in a single column applicable to all fluxes). To confirm the correct performance of SA, all variables "u", "v", "w", "ts" must have flag 0. In case of GA, all variables "co2", "h2o" must have flag 0. In case of SAGA, all variables "u", "v", "w", "ts", "h2o", "co2" must have flag 0.

Value

A data frame with relevant column names defined by name_out_SA, name_out_GA, name_out_SAGA and name_out_ALL. Each column has attributes "varnames" and "units" and length equal to that of x.

Abbreviations

QC: Quality Control
SA: Sonic Anemometer
GA: Gas Analyzer
Tau: Momentum flux [kg m-1 s-2]
H: Sensible heat flux [W m-2]
LE: Latent heat flux [W m-2]
NEE: Net ecosystem exchange [umol m-2 s-1]
u: Longitudinal wind speed component [m s-1]
v: Cross-wind wind speed component [m s-1]
w: Vertical wind speed component [m s-1]
ts: Sonic temperature [degC]
h2o: H2O concentration [mmol mol-1]
co2: CO2 concentration [umol mol-1]

Examples

set.seed(5)
xx <- replicate(10,
                paste0(c("8", sample(c(0:1, 9), 6, c(0.7, 0.2, 0.1),
                                    replace = TRUE)),
                      collapse = ""))
is.na(xx) <- c(2, 5)
units(xx) <- "8u/v/w/ts/h2o/co2"
cbind(xx, extract_coded(xx))

lsigut/openeddy documentation built on Aug. 5, 2023, 12:25 a.m.