calibrate_carbon_bymonth: calibrate_carbon_bymonth

In NEONiso: Tools to Calibrate and Work with NEON Atmospheric Isotope Data

calibrate_carbon_bymonth

Description

This function drives a workflow that reads in NEON carbon isotope data of atmospheric CO2, calibrates it to the VPDB scale, and (optionally) writes the calibrated data to a new HDF5 file. Two different approaches are possible: a) a calibration on 12CO2 and 13CO2 isotopologues separately, after Bowling et al. 2003 (Agr. For. Met.), or b) a direct calibration of d13C and CO2 values using linear regression. The vast majority of the time the results generated from either method are extremely similar to each other. Wen et al. 2013 compared several different carbon isotope calibration techniques and found this to be the superior method under most circumstances. We also found this to be the case for NEON data (Fiorella et al. 2021; JGR-Biogeosciences).

Usage

calibrate_carbon_bymonth(
  inname,
  outname,
  site,
  method = "Bowling_2003",
  calibration_half_width = 0.5,
  force_cal_to_beginning = TRUE,
  force_cal_to_end = TRUE,
  gap_fill_parameters = FALSE,
  filter_ambient = TRUE,
  r2_thres = 0.95,
  correct_refData = TRUE,
  write_to_file = TRUE
)

Arguments

inname	Name of the input file. (character)
outname	Name of the output file. (character)
site	Four letter NEON site code for site being processed. (character)
method	Are we using the Bowling et al. 2003 method ("Bowling_2003") or direct linear regression of d13C and CO2 mole fractions ("linreg")?
calibration_half_width	Determines the period (in days) from which reference data are selected (period is 2*calibration_half_width).
force_cal_to_beginning	Extend first calibration to the beginning of the file? (default true)
force_cal_to_end	Extend last calibration to the end of the file? (default true)
gap_fill_parameters	Should function attempt to 'gap-fill' across a bad calibration by carrying the last known good calibration forward? Implementation is fairly primitive currently, as it only carries the last known good calibration that's available forward rather than interpolating, etc. Default FALSE.
filter_ambient	Apply the median absolute deviation filter (Brock 86) to remove impulse spikes in output ambient data? (logical; default true)
r2_thres	Minimum r2 threshold of an "acceptable" calibration. Acts to remove calibration periods where a measurement error makes relationship nonlinear. Default = 0.95
correct_refData	NEON has indicated there are a few instances where reported d13C or CO2 reference values are wrong. If set to true, correct known incorrect values. This argument will (hopefully, eventually) go away after NEON has fixed the reference database. Users will be warned prior to removal of this argument.
write_to_file	Write calibrated ambient data to file? (Mostly used for testing)

Details

The 'linreg' method simply takes measured and reference d13C and CO2 values and generates a transfer function between them using lm(). For the gain-and-offset method, d13C and CO2 values are converted to 12CO2 and 13CO2 mole fractions. Gain and offset parameters are calculated for each isotopologue independently, and are analogous to regression slope and intercepts, but jointly correct for CO2 concentration dependence and place d13C values on the VPDB scale. The gain and offset parameters are defined by:

G = (X_{2,ref}-X_{1,ref})/(X_{2,meas}-X_{1,meas})

O = X_{2,ref}- G X_{2,meas}

Calibrated ambient isotopologues are then given as:

X_{cal} = X_{meas} G + O

Measurements of reference materials were considered "good" if the following conditions were met:

• Measured CO2 concentrations were within 10 ppm of known "reference" concentrations.

• Variance of the CO2 concentration in standard peak was < 5 ppm.

• Measured d13C value must be within 5 per mil of known "reference" d13C value.

The first two criteria are intended to filter out periods where there is a clear issue with the gas delivery system (i.e., nearly empty gas tank, problem with a valve in the manifold, etc.); the third criterion was adopted after visual inspection of data timeseries revealed that often the first standard measurement following an instrument issue had higher-than-expected error. This criterion clips clearly poor values. Selection of these criteria will become a function argument, and therefore customizable, in a future release.

Value

Returns nothing to the environment, but creates a new output HDF5 file containing calibrated carbon isotope values.

Author(s)

Rich Fiorella [e-mail]

Examples

## Not run: fin <- system.file('extdata',
'NEON.D15.ONAQ.DP4.00200.001.nsae.2019-05.basic.20201020T211037Z.packed.h5',
         package = 'NEONiso', mustWork = TRUE)
calibrate_carbon_bymonth(inname = fin, outname = 'out.h5',
         site = 'ONAQ', write_to_file = FALSE)
calibrate_carbon_bymonth(inname = fin, outname = 'out.h5',
         site = 'ONAQ', method = 'linreg', write_to_file = FALSE)
## End(Not run)

NEONiso documentation built on Sept. 20, 2023, 9:07 a.m.