Calculate leakiness — calculate_leakiness

Calculates leakiness (phi) from combined gas exchange and isotope discrimination measurements as described in Ubierna et al. (2013). This function can accomodate alternative colum names for the variables taken from exdf_obj; it also checks the units of each required column and will produce an error if any units are incorrect.

Usage

calculate_leakiness_ubierna(
    exdf_obj,
    e = -3,
    a_bar_column_name = 'a_bar',
    a_column_name = 'A',
    ci_column_name = 'Ci',
    co2_s_column_name = 'CO2_s',
    csurface_column_name = 'Csurface',
    delta_c13_r_column_name = 'delta_C13_r',
    delta_obs_tdl_column_name = 'Delta_obs_tdl',
    rl_column_name = 'RL',
    t_column_name = 't'
  )

Arguments

exdf_obj: An exdf object.
e: The isotopic fractionation during day respiration in ppt.
a_bar_column_name: The name of the column in exdf_obj that contains the weighted isotopic fractionation across the boundary layer and stomata in ppt. Values of a_bar are typically calculated using calculate_ternary_correction.
a_column_name: The name of the column in exdf_obj that contains the net CO2 assimilation rate in micromol m^(-2) s^(-1).
ci_column_name: The name of the column in exdf_obj that contains the intercellular CO2 concentration in micromol mol^(-1).
co2_s_column_name: The name of the column in exdf_obj that contains the CO2 concentration in the sample line (outgoing air) in micromol mol^(-1).
csurface_column_name: The name of the column in exdf_obj that contains the CO2 concentration at the leaf surface in micromol mol^(-1). Values of Csurface are typically calculated using calculate_gas_properties.
delta_c13_r_column_name: The name of the column in exdf_obj that contains the CO2 isotope ratio in the reference line (incoming air) in ppt.
delta_obs_tdl_column_name: The name of the column in exdf_obj that contains the observed isotope discrimination values in ppt.
rl_column_name: The name of the column in exdf_obj that contains the rate of day respiration in micromol m^(-2) s^(-1).
t_column_name: The name of the column in exdf_obj that contains the ternary correction factor (dimensionless). Values of t are typically calculated using calculate_ternary_correction

Details

This function uses the model for photosynthetic discrimination against 13C in C4 plants to determine leakiness values, as described in Ubierna et al. (2013). In particular, the following equations from that source are implemented in the code:

Isotopic fractionation due to day respiration (e_prime) is calculated using Equation 21.
Leakiness including respiratory and photorespiratory fractionations under high light (phi_i) is calculated using Equation 16.
Leakiness including respiratory and photorespiratory fractionations and Cs under high light (phi_is) is calculated using Equation 15.
Leakiness ignoring respiratory and photorespiratory fractionations and Cs (phi_sim) is calculated using Equation 17.

References:

Ubierna, N., Sun, W., Kramer, D. M. and Cousins, A. B. "The efficiency of C4 photosynthesis under low light conditions in Zea mays, Miscanthus x giganteus and Flaveria bidentis." Plant, Cell & Environment 36, 365–381 (2013) [doi:10.1111/j.1365-3040.2012.02579.x ].

Value

An exdf object based on exdf_obj that includes the following additional columns, calculated as described above: e_prime, phi_i, phi_is, and phi_sim. The category for each of these new columns is calculate_leakiness_ubierna to indicate that they were created using this function.

Examples

## In this example we load gas exchange and TDL data files, calibrate the TDL
## data, pair the data tables together, and then calculate leakiness. The
## results from this example are not meaningful because these measurements
## were not collected from C4 plants.

# 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))

# Get oxygen info from the Licor file preamble (needed for calculate_gamma_star)
licor_data <- get_oxygen_from_preamble(licor_data)

# 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)

# Calculate total pressure (needed for calculate_gas_properties)
licor_data <- calculate_total_pressure(licor_data)

# Calculate Csurface (needed for calculate_ternary_correction)
licor_data <- calculate_gas_properties(licor_data)

# Calculate ternary correction
licor_data <- calculate_ternary_correction(licor_data)

# Calculate isotope discrimination (needed for calculate_leakiness_ubierna)
licor_data <- calculate_isotope_discrimination(licor_data)

# Set respiration (needed for calculate_leakiness_ubierna)
licor_data <- set_variable(
  licor_data,
  'RL',
  'micromol m^(-2) s^(-1)',
  value = 1.2
)

# Calculate leakiness
licor_data <- calculate_leakiness_ubierna(licor_data)

# View some of the results
licor_data[, c('replicate', 'CO2_s', 'Delta_obs_tdl', 'phi_i', 'phi_sim')]
#>    replicate   CO2_s Delta_obs_tdl     phi_i   phi_sim
#> 1          1 417.363      8.039825 0.5647984 0.5652561
#> 2          1 420.552      8.137268 0.5787469 0.5791113
#> 3          1 418.796      7.893969 0.5548495 0.5550261
#> 4          1 419.493      8.029239 0.5625286 0.5627514
#> 5          1 420.102      8.964915 0.6097656 0.6098926
#> 6          1 421.133      8.673921 0.5935674 0.5936957
#> 7          1 262.873      6.434975 0.4796541 0.4793111
#> 8          1 262.720      6.747186 0.4966989 0.4966153
#> 9          1 262.633      6.326945 0.4760775 0.4752982
#> 10         1 262.271      6.358834 0.4709619 0.4705850
#> 11         1 262.112      7.450206 0.5193723 0.5192365
#> 12         1 262.176      6.843263 0.4874634 0.4875021