Calculate mesophyll conductance to CO2 diffusion
calculate_gm_ubierna.Rd
Calculates mesophyll conductance to CO2 diffusion (gmc
) from combined
gas exchange and isotope discrimination measurements as described in Ubierna
et al. (2018). 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_gm_ubierna(
exdf_obj,
e = -3,
f = 11,
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',
gamma_star_column_name = 'Gamma_star',
rl_column_name = 'RL',
total_pressure_column_name = 'total_pressure',
t_column_name = 't'
)
Arguments
- exdf_obj
An
exdf
object.- e
The isotopic fractionation during day respiration in
ppt
.- f
The isotopic fractionation during photorespiration 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
.- gamma_star_column_name
The name of the column in
exdf_obj
that contains the CO2 compensation point in the absence of day respiration inmicromol mol^(-1)
. Values ofGamma_star
are typically calculated usingcalculate_gamma_star
orcalculate_arrhenius
.- rl_column_name
The name of the column in
exdf_obj
that contains the rate of day respiration inmicromol m^(-2) s^(-1)
.- total_pressure_column_name
The name of the column in
exdf_obj
that contains the total pressure inbar
.- 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 comprehensive model for photosynthetic discrimination against 13C in C3 plants to calculate mesophyll conductance, as described in Ubierna et al. (2018). In particular, the following equations from that source are implemented in the code:
Isotopic fractionation due to day respiration (
e_prime
) is calculated using Equations 28 and 30.Isotopic discrimination due to photorespiration (
Delta_f
), due to day respiration (Delta_e
), and that would occur if Ci = Cc in the absence of any respiratory fractionation (Delta_i
) are calculated using Equations 34, 33, and 31, respectively.Mesophyll conductance to CO2 diffusion (
gmc
) is calculated using Equation 44. This equation is broken up into two factors calledDelta_difference
andequation_top
which are separately returned in the output fromcalculate_gm_ubierna
.
For an alternative method for calculating gmc
, see
calculate_gm_busch
.
References:
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 the following
additional columns, calculated as described above: e_prime
,
Delta_i
, Delta_e
, Delta_f
, Delta_difference
,
equation_top
, and gmc
. The category for each of these new
columns is calculate_gm_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 mesophyll conductance
# 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 = 'US/Central')
)
# 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 = 'US/Central')
)
# 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)
# Set Rubisco specificity (needed for calculate_gamma_star)
licor_data <- set_variable(
licor_data,
'specificity_at_tleaf',
'M / M',
value = 90
)
# Calculate Gamma_star (needed for calculate_gm_ubierna)
licor_data <- calculate_gamma_star(licor_data)
# Calculate isotope discrimination (needed for calculate_gm_ubierna)
licor_data <- calculate_isotope_discrimination(licor_data)
# Set respiration (needed for calculate_gm_ubierna)
licor_data <- set_variable(
licor_data,
'RL',
'micromol m^(-2) s^(-1)',
value = 1.2
)
# Calculate mesophyll conductance
licor_data <- calculate_gm_ubierna(licor_data)
# Calculate Cc using the new values of mesophyll conductance
licor_data <- apply_gm(licor_data)
# View some of the results
licor_data[, c('replicate', 'CO2_s', 'Delta_obs_tdl', 'gmc', 'Ci', 'Cc')]
#> replicate CO2_s Delta_obs_tdl gmc Ci Cc
#> 1 1 417.363 8.039825 0.1741069 286.7663 101.16460
#> 2 1 420.552 8.137268 0.1842769 276.9970 102.18154
#> 3 1 418.796 7.893969 0.1673113 291.8317 99.66079
#> 4 1 419.493 8.029239 0.1692570 291.1437 101.71697
#> 5 1 420.102 8.964915 0.1803390 293.7559 116.32286
#> 6 1 421.133 8.673921 0.1735334 295.9070 112.25005
#> 7 1 262.873 6.434975 0.1593770 182.7755 55.38615
#> 8 1 262.720 6.747186 0.1653412 181.1386 58.17641
#> 9 1 262.633 6.326945 0.1620221 179.6180 54.02724
#> 10 1 262.271 6.358834 0.1494173 191.7498 55.54918
#> 11 1 262.112 7.450206 0.1535156 199.2717 66.72640
#> 12 1 262.176 6.843263 0.1423399 204.1826 61.50326