calibrate_water — calibrate

This function uses NEON validation data to apply drift corrections to measured ambient water isotope ratios. In brief, ambient water isotope ratios are calibrated by generating regressions using reference water measurements bracketing an ambient period. Three reference waters are measured once per day, with several injections per reference water. Due to memory effects, only the last three are used currently to generate calibration equations. Regressions between measured d18O and d2H values and NEON-provisioned known reference values are generated, and used to calibrate the period of ambient measurements between them if the r2 of the regression is greater than a threshold value (by default, this is 0.95). Most of this function deals with selecting the appropriate calibration data and determining calibration quality. This function also contains a wrapper for calibrate_ambient_water_linreg, which calibrates the ambient water data using the calibration parameters generated in this function. This function also copies over data in the qfqm and ucrt hdf5 data groups.

Usage

calibrate_water(
  inname,
  outname,
  site,
  calibration_half_width = 14,
  filter_data = TRUE,
  force_cal_to_beginning = FALSE,
  force_cal_to_end = FALSE,
  r2_thres = 0.95,
  slope_tolerance = 9999,
  correct_ref_data = TRUE,
  write_to_file = TRUE
)

Arguments

inname: Input file(s) that are to be calibrated. If a single file is given, output will be a single file per site per month. If a list of files corresponding to a timeseries at a given site is provided, will calibrate the whole time series.
outname: Name of the output file. (character)
site: Four-letter NEON code for site being processed.
calibration_half_width: Determines the range of standard measurements to use in determining the calibration regression dataset. Creates a moving window that is 2*calibration_half_width days wide. Default is set to 14 for a 28 day moving window.
filter_data: Apply median absolute deviation filter from Brock 86 to remove impulse spikes?
force_cal_to_beginning: Extend first calibration to the beginning of the file?
force_cal_to_end: Extend last calibration to the end of the file?
r2_thres: Minimum r2 threshold of an "acceptable" calibration. Acts to remove calibration periods where a measurement error makes relationship nonlinear. Default = 0.95
slope_tolerance: How different from 1 should we allow 'passing' regression slopes to be? Experimental parameter, off by default (e.g., default slope parameter = 9999)
correct_ref_data: There are a few instances where the reference d18O and d2H values may have been switched, causing very anomalous d-excess values. If TRUE, implement a switch that corrects this issue.
write_to_file: Write calibrated ambient data to file? (Mostly used for testing)

Value

nothing to the workspace, but creates a new output file of calibrated water isotope data.

Details

IMPORTANT NOTE Currently this function does not apply a correction for humidity dependence of Picarro isotopic measurements. This is because the data to implement these corrections is not yet publicly available. Caution is suggested when analyzing data at low humidities, below ~5000 ppm, with likely higher biases at lower humidity values.

Additionally, please note that this function is meant to work on all files for a given site at the same time. A more flexible version that can handle all files or monthly files will be added to a future release.

Author

Rich Fiorella rfiorella@lanl.gov