# Tools to Calibrate and Work with NEON Atmospheric Isotope Data

## Documentation for package ‘NEONiso’ version 0.8.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

calculate_12CO2 | Calculate 12C-CO2 Mole Fractions
calculate_13CO2 | Calculate 13C-CO2 Mole Fractions
calibrate_ambient_carbon_gainoffset | Calibrate ambient carbon isotope data using gain-and-offset method
calibrate_ambient_carbon_linreg | Calibrate ambient carbon isotope data using linear regression
calibrate_ambient_water_linreg | calibrate_ambient_water_isotopes
calibrate_carbon | Calibrate NEON carbon isotope data using validation data sets.
calibrate_water | Calibrate NEON water isotope ratios using validation data sets.
carbon_regression_plots | Make plots of carbon calibration data for debugging
convert_NEONhdf5_to_POSIXct_time | Convert NEON HDF5 file time to POSIXct
convert_POSIXct_to_NEONhdf5_time | Convert a POSIXct object to the format used in NEON HDF5 files
correct_carbon_ref_cval | correct_carbon_ref_cval
correct_carbon_ref_output | Correct carbon ref output
delta_to_R | Converts delta value to heavy-to-light isotope ratio
estimate_calibration_error | Produce estimates of the calibration error.
extract_carbon_cal_data | Extract only the data corresponding to validation/calibration time periods.
extract_water_calibration_data | Extract only the data corresponding to validation/calibration time periods.
filter_median_brock86 | Apply a median absolute deviation filter
fit_carbon_regression | Estimate slope/intercept of carbon isotope calibration regression
fit_water_regression | Estimate slope/intercept of water isotope calibration regression
get_Rstd | Return heavy-to-light isotope ratio of primary standard.
ingest_data | Ingest and stack variables needed in calibration.
loocv | Leave-one-out cross validation
manage_local_EC_archive | Manage a local eddy covariance (EC) data archive.
restructure_carbon_variables | Restructure ingested variables for the carbon isotope system.
restructure_variables | Restructures data.frames imported by ingest_data to shorten variable names and Wrapper function around restructure_carbon_variables and restructure_water_variables.
restructure_water_variables | Restructure ingested variables for the water isotope system.
R_to_delta | Convert heavy-to-light isotope ratio to delta values.
select_daily_reference_data | Select validation data corresponding to a particular day
setup_output_file | Structure a new HDF5 file
swap_standard_isotoperatios | swap_standard_isotoperatios
terrestrial_core_sites | List terrestrial core sites
terrestrial_gradient_sites | List terrestrial gradient sites
validate_analyte | Standardize analyte names
validate_output_file | Validate output file.
water_isotope_sites | List sites with water vapor isotope ratios.
write_carbon_ambient_data | Write calibrated carbon ambient data to file
write_carbon_calibration_data | Write carbon calibrations to file
write_water_ambient_data | Write calibrated ambient water isotope ratio observations to file.
write_water_calibration_data | Write water calibration parameters to file