Calculate ternary correction factor
calculate_ternary_correction.Rd
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'
)
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 inmicromol mol^(-1)
.- co2_s_column_name
The name of the column in
exdf_obj
that contains the sample line (incoming air) CO2 concentration 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)
. This is typically calculated usingcalculate_gas_properties
.- e_column_name
The name of the column in
exdf_obj
that contains the leaf transpiration rate inmol 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 inmol 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) [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) [doi:10.1007/978-1-4939-7786-4_10 ].
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.
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')]
#> replicate A E Csurface t a_bar alpha_ac
#> 1 1 32.01867 0.003450230 393.8416 0.006807155 4.129839 1.004130
#> 2 1 31.91890 0.003043435 397.1493 0.006651168 4.155466 1.004155
#> 3 1 31.85562 0.003456022 395.3211 0.006658893 4.122659 1.004123
#> 4 1 31.76382 0.003453230 396.1048 0.006745036 4.126666 1.004127
#> 5 1 31.69923 0.003469264 396.7615 0.006681366 4.122898 1.004123
#> 6 1 31.57078 0.003475612 397.9187 0.006658639 4.121931 1.004122
#> 7 1 20.11287 0.003470594 248.0834 0.006682212 4.123033 1.004123
#> 8 1 20.13905 0.003448952 247.9251 0.006757688 4.127973 1.004128
#> 9 1 20.15698 0.003445242 247.8209 0.006864369 4.132360 1.004132
#> 10 1 20.16227 0.003577178 247.4354 0.006038269 4.084444 1.004084
#> 11 1 20.16253 0.003679090 247.2586 0.005523946 4.045448 1.004045
#> 12 1 20.12078 0.003814051 247.3068 0.005285017 4.015407 1.004015