PhotoGEA (version 1.4.0)

calculate_ternary_correction: Calculate ternary correction factor

Description

Calculates the ternary correction factor t that is used in many carbon isotope discrimination calculations.

Usage

calculate_ternary_correction(
    exdf_obj,
    ci_column_name = 'Ci',
    co2_s_column_name = 'CO2_s',
    csurface_column_name = 'Csurface',
    e_column_name = 'E',
    gtc_column_name = 'gtc'
  )

Value

An exdf object based on exdf_obj that includes values of

t, a_bar, and alpha_ac calculated as described above. The category of each new column is calculate_ternary_correction to indicate that it was created using this function.

Arguments

exdf_obj

An exdf object containing photosynthetic gas exchange data.

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 sample line (incoming air) CO2 concentration 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). This is typically calculated using calculate_gas_properties.

e_column_name

The name of the column in exdf_obj that contains the leaf transpiration rate in mol m^(-2) s^(-1).

gtc_column_name

The name of the column in exdf_obj that contains the total conductance to CO2 diffusion across the boundary layer and stomata in series in mol m^(-2) s^(-1).

Details

During photosynthetic gas exchange, there are separate fluxes of CO2 and H2O flowing in and out of the leaf. These gases interact with each other and with air, forming a ternary mixture. These interactions must be taken into account when modeling carbon isotope discrimination. Typically this is done via t, a ternary correction factor first introduced by Farquhar and Cernusak (2012). Here we calculate t as described in Equations 9 and 10 from Ubierna et al. (2018):

t = alpha_ac * E / (2 * g_ac)

and

a_bar = (a_b * (C_a - C_s) + a_s * (C_s - C_i)) / (C_a - C_i),

where E is the transpiration rate, g_ac is the total conductance to CO2 diffusion across the boundary layer and stomata in series, a_bar is the weighted fractionation across the boundary layer and stomata in series, a_b is the fractionation during diffusion through the boundary layer, a_s is the fractionation during diffusion through the stomata, C_a is the ambient CO2 concentration (in wet air), C_s is the CO2 concentration (in wet air) at the leaf surface, and C_i is the CO2 concentration (in wet air) in the intercellular spaces.

alpha_ac is the overall fractionation during diffusion through air; alpha_ac and a_bar are related according to an un-numbered equation in Ubierna et al. (2018) that appears just after Equation 9:

alpha_ac = 1 + a_bar

References:

Farquhar, G. D. and Cernusak, L. A. "Ternary effects on the gas exchange of isotopologues of carbon dioxide." Plant, Cell & Environment 35, 1221–1231 (2012) [tools:::Rd_expr_doi("10.1111/j.1365-3040.2012.02484.x")].

Ubierna, N., Holloway-Phillips, M.-M. and Farquhar, G. D. "Using Stable Carbon Isotopes to Study C3 and C4 Photosynthesis: Models and Calculations." in Photosynthesis: Methods and Protocols (ed. Covshoff, S.) 155–196 (Springer, 2018) [tools:::Rd_expr_doi("10.1007/978-1-4939-7786-4_10")].

Examples

## In this example we load a gas exchange data file and then calculate the
## ternary correction factor

# Read the gas exchange data
licor_data <- read_gasex_file(
  PhotoGEA_example_file_path('licor_for_gm_site11.xlsx'),
  'time'
)

# 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)

# View some of the results
licor_data[, c('replicate', 'A', 'E', 'Csurface', 't', 'a_bar', 'alpha_ac')]