pair_gasex_and_tdl: Pair gas exchange and TDL data

In PhotoGEA: Photosynthetic Gas Exchange Analysis

Pair gas exchange and TDL data

Description

Identifies the closest TDL cycle corresponding to each entry in the gas exchange data and adds the TDL data to the gas exchange data.

Usage

  pair_gasex_and_tdl(
    gasex_exdf,
    tdl_exdf,
    max_allowed_time_difference = 1,
    gasex_timestamp_column_name = 'time',
    tdl_timestamp_column_name = 'TIMESTAMP'
  )

Arguments

gasex_exdf	An exdf object representing data from a photosynthetic gas exchange measurement system.
tdl_exdf	An exdf object representing calibrated data from a tunable diode laser absorption spectroscopy system. Typically this is the output from applying process_tdl_cycle_erml or process_tdl_cycle_polynomial to a set of uncalibrated TDL data.
max_allowed_time_difference	The maximum time difference (in minutes) to allow between gas exchange and TDL timestamp values.
gasex_timestamp_column_name	The name of the column in gasex_exdf that contains the timestamp values.
tdl_timestamp_column_name	The name of the column in tdl_exdf that contains the timestamp values.

Details

When making combined gas exchange and isotope discrimination measurements using a portable photosynthetic gas exchange system (such as a Licor LI-6800) coupled with a tunable diode laser (TDL) absorption spectroscopy system, the TDL's gas handling system cycles through several gas lines (or sites) by opening and closing valves. When analyzing such data, a key step is to combine TDL and gas exchange data that were measured at the same times.

The pair_gasex_and_tdl function performs this operation by locating the TDL cycle whose timestamp is closest to each Licor file entry. Then, the 12C, 13C, total CO2, and delta_13C values measured by the TDL from the Licor's sample and reference lines during that cycle are added to the gas exchange data as new columns.

Value

An exdf object based on gasex_exdf that includes TDL values measured at the same times as the original gas exchange logs. Several new columns are added: 'cycle_num', 'tdl_time_s', 'calibrated_12c_s', 'calibrated_13c_s', 'total_CO2_s', 'delta_C13_s', 'tdl_time_r', 'calibrated_12c_r', 'calibrated_13c_r', 'total_CO2_r', and 'delta_C13_r'. Variables with '_s' in the name refer to TDL measurements from the Licor sample line, and '_r' indicates the reference line. The category of each new column is pair_gasex_and_tdl to indicate that it was created using this function.

Examples

## In this example we load gas exchange and TDL data files, calibrate the TDL
## data, and pair the data tables together

# Read the TDL data file, making sure to interpret the time zone as US Central
# time
tdl_data <- read_gasex_file(
  PhotoGEA_example_file_path('tdl_for_gm.dat'),
  'TIMESTAMP',
  list(tz = 'America/Chicago')
)

# Identify cycles within the TDL data
tdl_data <- identify_tdl_cycles(
  tdl_data,
  valve_column_name = 'valve_number',
  cycle_start_valve = 20,
  expected_cycle_length_minutes = 2.7,
  expected_cycle_num_valves = 9,
  timestamp_colname = 'TIMESTAMP'
)

# Use reference tanks to calibrate the TDL data
processed_tdl <- consolidate(by(
  tdl_data,
  tdl_data[, 'cycle_num'],
  process_tdl_cycle_erml,
  noaa_valve = 2,
  calibration_0_valve = 20,
  calibration_1_valve = 21,
  calibration_2_valve = 23,
  calibration_3_valve = 26,
  noaa_cylinder_co2_concentration = 294.996,
  noaa_cylinder_isotope_ratio = -8.40,
  calibration_isotope_ratio = -11.505
))

# Read the gas exchange data, making sure to interpret the time stamp in the US
# Central time zone
licor_data <- read_gasex_file(
  PhotoGEA_example_file_path('licor_for_gm_site11.xlsx'),
  'time',
  list(tz = 'America/Chicago')
)
# Get TDL valve information from Licor file name; for this TDL system, the
# reference valve is 12 when the sample valve is 11
licor_data <- get_sample_valve_from_filename(licor_data, list('11' = 12))

# Pair the Licor and TDL data by locating the TDL cycle corresponding to each
# Licor measurement
licor_data <- pair_gasex_and_tdl(licor_data, processed_tdl$tdl_data)

# View some of the results
licor_data[, c('A', 'delta_C13_r', 'delta_C13_s', 'total_CO2_r', 'total_CO2_s')]

PhotoGEA documentation built on April 11, 2025, 5:48 p.m.