Calculate leakiness
calculate_leakiness_ubierna.Rd
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 inppt
. Values ofa_bar
are typically calculated usingcalculate_ternary_correction
.- a_column_name
The name of the column in
exdf_obj
that contains the net CO2 assimilation rate inmicromol m^(-2) s^(-1)
.- ci_column_name
The name of the column in
exdf_obj
that contains the intercellular CO2 concentration inmicromol 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) inmicromol mol^(-1)
.- csurface_column_name
The name of the column in
exdf_obj
that contains the CO2 concentration at the leaf surface inmicromol mol^(-1)
. Values ofCsurface
are typically calculated usingcalculate_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) inppt
.- delta_obs_tdl_column_name
The name of the column in
exdf_obj
that contains the observed isotope discrimination values inppt
.- rl_column_name
The name of the column in
exdf_obj
that contains the rate of day respiration inmicromol m^(-2) s^(-1)
.- t_column_name
The name of the column in
exdf_obj
that contains the ternary correction factor (dimensionless
). Values oft
are typically calculated usingcalculate_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 ].