Calculate intrinsic water use efficiency — calculate

Calculates the intrinsic water use efficiency (iWUE). This function can accomodate alternative column names for the variables taken from the data file in case they change at some point in the future. This function also checks the units of each required column and will produce an error if any units are incorrect.

Usage

calculate_wue(
    exdf_obj,
    calculate_c3 = FALSE,
    a_column_name = 'A',
    ca_column_name = 'Ca',
    cc_column_name = 'Cc',
    ci_column_name = 'Ci',
    e_column_name = 'E',
    gmc_column_name = 'gmc',
    gsw_column_name = 'gsw',
    h2o_a_column_name = 'H2O_s',
    h2o_i_column_name = 'H2O_i',
    total_pressure_column_name = 'total_pressure'
  )

Arguments

exdf_obj: An exdf object.
calculate_c3: A logical variable indicating whether to calculate additional variables that can be useful for C3 plants (g_ratio and drawdown_ct). Note that these quantities require values of mesophyll conductance and Cc, so it is not always possible to calculate them.
a_column_name: The name of the column in exdf_obj that contains the net CO2 assimilation rate in micromol m^(-2) s^(-1).
ca_column_name: The name of the column in exdf_obj that contains the ambient CO2 concentration in micromol mol^(-1).
cc_column_name: The name of the column in exdf_obj that contains the chloroplastic CO2 concentration in micromol mol^(-1). Typically these are calculated using apply_gm.
ci_column_name: The name of the column in exdf_obj that contains the intercellular CO2 concentration in micromol mol^(-1).
e_column_name: The name of the column in licor_exdf that contains the transpiration rate in mol m^(-2) s^(-1).
gmc_column_name: The name of the column in licor_exdf that contains the mesophyll conductance to CO2 in mol m^(-2) s^(-1) bar^(-1).
gsw_column_name: The name of the column in licor_exdf that contains the stomatal conductance to water vapor in mol m^(-2) s^(-1).
h2o_a_column_name: The name of the column in exdf_obj that contains the water vapor concentration in the air surrounding the leaf (i.e., the ambient water vapor concentration) in mmol mol^(-1).
h2o_i_column_name: The name of the column in exdf_obj that contains the water vapor concentration in the leaf's intercellular air spaces in mmol mol^(-1). Typically this value is calculated using calculate_gas_properties.
total_pressure_column_name: The name of the column in exdf_obj that contains the total pressure in bar. Typically this value is calculated using calculate_total_pressure.

Details

Leaf-level water use efficiency (lWUE) is defined as the ratio of net CO2 assimilation (An) to transpiration (E):

lWUE = An / E.

This quantity can also be expressed in terms of water and CO2 concentrations:

lWUE = 0.6 * Ca * (1 - Ci / Ca) / (H2Oi - H2Oa).

Here, Ca and Ci are the atmospheric and intercellular CO2 concentrations, and H2Oa and H2Oi are the atmospheric and intercellular water vapor concentrations. If differences in lWUE are measured between different groups of plants, it can be helpful to separately investigate Ci / Ca and H2Oi - H2Oa to see which factor is driving the differences.

The intrinsic water use efficiency iWUE is a measure of leaf-level water use efficiency, and it is defined to be the ratio An and the stomatal conductance to H2O diffusion (gsw):

iWUE = An / gsw.

For C3 plants, iWUE can be reexpressed as

iWUE = (gmc / gsw) / (1 + (gmc / gsw)) * (Ca - Cc),

where gmc is the mesophyll conductance to CO2 diffusion and Cc is the chloroplast CO2 concentration. If differences in iWUE are measured between different groups of plants, it can be helpful to separately investigate gmc / gsw and Ca - Cc to see which factor is driving the differences.

Note: both measures of water use efficiency depend directly or indirectly on stomatal conductance. Stomata are notoriously slow to reach steady-state, but water use efficiency is only reliable at steady-state. For this reason, it is recommended to only analyze water use efficiency for gas exchange measurements where stomatal conductance has stabilized. For an A-Ci or A-Q curve, only the first measured point has typically reached steady-state stomatal conductance. On the other hand, for a Ball-Berry curve, all measured points should have reached steady-state stomatal conductance.

For more details about these quantities, see Leakey et al. "Water Use Efficiency as a Constraint and Target for Improving the Resilience and Productivity of C3 and C4 Crops." Annual Review of Plant Biology 70 (1): 781–808 (2019) [doi:10.1146/annurev-arplant-042817-040305 ].

In this function, the following variables are calculated:

lWUE, given by iWUE = An / E
Cia_ratio, given by Cia_ratio = Ci / Ca
drawdown_sw, given by drawdown_sw = H2Oi - H2Oa (this is the drawdown of water vapor across the stomata)
iWUE, given by iWUE = An / gsw
g_ratio, given by g_ratio = gmc / gsw
drawdown_ct, given by drawdown_ct = Ca - Cc (this is the total drawdown of CO2 from the ambient air to the chloroplast)

Note: g_ratio and drawdown_ct are only calculated if calculate_c3 is TRUE.

Value

An exdf object based on exdf_obj that includes the quantities listed above, along with their units. The category of each of these new columns is calculate_wue to indicate that it was created using this function.

Examples

# Read an example Licor file included in the PhotoGEA package and calculate the
# water use efficiency.
licor_file <- read_gasex_file(
  PhotoGEA_example_file_path('ball_berry_1.xlsx')
)

licor_file <- calculate_total_pressure(licor_file)

licor_file <- calculate_gas_properties(licor_file)

licor_file <- set_variable(
  licor_file,
  'gmc',
  'mol m^(-2) s^(-1) bar^(-1)',
  value = 0.5
)

licor_file <- apply_gm(licor_file)

licor_file <- calculate_wue(licor_file, calculate_c3 = TRUE)

licor_file$units$iWUE      # View the units of the new `iWUE` column
#> [1] "micromol CO2 / mol H2O"
licor_file$categories$iWUE # View the category of the new `iWUE` column
#> [1] "calculate_wue"
licor_file[, 'iWUE']       # View the values of the new `iWUE` column
#>  [1]  91.19402  75.52585  90.68321 106.78757  78.24615  66.21068  33.68671
#>  [8]  52.19154  54.09650  58.52669  39.81239  57.99448  49.35733  33.84908
#> [15]  68.74848  53.75126  51.55032  56.41271  40.15597  92.38880  45.67573
#> [22] 102.10911  97.68654  89.89394  72.98826  54.17163  58.44461  94.55687