Calculate the Ball-Berry index

Calculates the Ball-Berry index. This function can accomodate alternative column names for the variables taken from the Licor 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_ball_berry_index(
    licor_exdf,
    a_column_name = 'A',
    rhleaf_column_name = 'RHleaf',
    csurface_column_name = 'Csurface'
  )

Arguments

licor_exdf

An exdf object representing data from a Licor gas exchange measurement system.

a_column_name

The name of the column in licor_exdf that contains the net assimilation in micromol m^(-2) s^(-1).

rhleaf_column_name

The name of the column in licor_exdf that contains the relative humidity at the leaf surface in %.

csurface_column_name

The name of the column in licor_exdf that contains the CO2 concentration at the leaf surface in micromol mol^(-1).

Details

The Ball-Berry index is defined as A * h_s / c_s, where A is the net assimilation rate, h_s is the relative humidity at the leaf surface, and c_s is the CO2 concentration at the leaf surface. This variable is a key part of the Ball-Berry model, which assumes that stomatal conductance is linearly related to the Ball-Berry index. For more information, please see the original publication describing the model: Ball, J. T., Woodrow, I. E. and Berry, J. A. "A Model Predicting Stomatal Conductance and its Contribution to the Control of Photosynthesis under Different Environmental Conditions." in "Progress in Photosynthesis Research: Volume 4" (1986) [doi:10.1007/978-94-017-0519-6_48 ].

Typically, the relative humidity and CO2 concentration at the leaf surface are not included in Licor output files. Instead, the output files only include the relative humidity and CO2 concentration in the sample chamber, and conditions at the leaf surface may be slightly different. These required inputs can be calculated using the calculate_gas_properties function.

Value

An exdf object based on licor_exdf that includes the Ball-Berry index as a new column called bb_index. The category of this new column is calculate_ball_berry_index to indicate that it was created using this function.

Examples

# Read an example Licor file included in the PhotoGEA package, calculate the
# total pressure, calculate additional gas properties, and finally calculate the
# Ball-Berry index.
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 <- calculate_ball_berry_index(licor_file)

licor_file$units$bb_index      # View the units of the new `bb_index` column
#> [1] "mol m^(-2) s^(-1)"
licor_file$categories$bb_index # View the category of the new `bb_index` column
#> [1] "calculate_ball_berry_index"
licor_file[,'bb_index']        # View the values of the new `bb_index` column
#>  [1] 0.06487443 0.04217299 0.04717440 0.04230129 0.02995968 0.02208180
#>  [7] 0.01020448 0.09725402 0.07554299 0.06709379 0.04710046 0.04354188
#> [13] 0.03356910 0.02099952 0.09939125 0.06184597 0.05190328 0.05356902
#> [19] 0.03397142 0.02811785 0.01762407 0.05661131 0.04955238 0.04342732
#> [25] 0.03150718 0.02329131 0.02336237 0.01465243