Calculate temperature-dependent parameter values — calculate_temperature

Calculate leaf-temperature-dependent values of various parameters using various temperature response functions.

Usage

calculate_temperature_response(
    exdf_obj,
    temperature_response_parameters,
    tleaf_column_name = 'TleafCnd'
  )

Arguments

exdf_obj: An exdf object representing data from a Licor gas exchange measurement system.
temperature_response_parameters: A list, where each element describes the temperature response of a parameter value. The name of each element must be the name of the parameter. Each element must be a list itself, whose named elements must include the type of temperature response function to use (type), thee units of the parameter (units), and the values of necessary temperature response parameters. See below for more details.
tleaf_column_name: The name of the column in exdf_obj that contains the leaf temperature in units of degrees C.

Details

Some key photosynthetic parameters are known to vary with temperature according to well-established temperature response functions such as the Arrhenius equation. The calculate_temperature_response function can be used to calculate such temperature-dependent parameter values at leaf temperature.

Depending on the type value supplied in each element of temperature_response_parameters, one of several possible functions will be used to calculate the temperature response:

When type is 'Arrhenius', the calculate_temperature_response_arrhenius function will be used.
When type is 'Gaussian', the calculate_temperature_response_gaussian function will be used.
When type is 'Johnson', the calculate_temperature_response_johnson function will be used.
When type is 'Polynomial', the calculate_temperature_response_polynomial function will be used.

Values of type are not case-sensitive.

It is rare to directly specify these parameters; instead, it is more typical to use one of the pre-set values such as those included in c3_temperature_param_sharkey.

Value

An exdf object based on exdf_obj that includes one new column for each element of temperature_response_parameters, where the temperature-dependent values of these new columns are determined using the temperature values specified by the tleaf_column_name column. The category of each of these new columns is calculate_temperature_response to indicate that they were created using this function.

Examples

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

# In this example we will calculate temperature-dependent values of two
# parameters:
#
# - The `Kc` parameter (in units of `micromol mol^(-1)`) will be calculated
#   using an Arrhenius function with scaling constant `c` = 38.05 and activation
#   energy `Ea` = 79.43 kJ / mol.
#
# - The `Jmax` parameter (in units of `micromol m^(-2) s^(-1)) will be
#   using a Gaussian function with optimal temperature `t_opt` = 43 degrees C
#   and width `sigma` = 16 degrees C.
#
# So the `temperature_response_parameters` list will contain two elements,
# defined as follows:

trp <- list(
  Kc = list(
    type = 'Arrhenius',
    c = 38.05,
    Ea = 79.43,
    units = 'micromol mol^(-1)'
  ),
  Jmax = list(
    type = 'Gaussian',
    optimum_rate = 4,
    t_opt = 43,
    sigma = 16,
    units = 'micromol m^(-2) s^(-1)'
  )
)

# Now we can calculate the values of Kc and Jmax at the measured leaf
# temperatures recorded in the log file
licor_file <- calculate_temperature_response(licor_file, trp)

licor_file$units$Kc      # View the units of the new `Kc` column
#> [1] "micromol mol^(-1)"
licor_file$categories$Kc # View the category of the new `Kc` column
#> [1] "calculate_temperature_response_arrhenius"
licor_file[,'Kc']        # View the values of the new `Kc` column
#>  [1]  767.4637  711.9313  675.4765  663.2831  663.2278  656.3085  639.7526
#>  [8]  897.6007  829.9775  830.9330  810.6390  830.9928  830.1736  833.0697
#> [15]  972.8348  917.6827  886.6074  882.3539  879.3607  837.0317  868.3010
#> [22] 1009.1405  938.3377  891.6276  871.3303  879.3247  836.6192  833.9686

licor_file$units$Jmax      # View the units of the new `Jmax` column
#> [1] "micromol m^(-2) s^(-1)"
licor_file$categories$Jmax # View the category of the new `Jmax` column
#> [1] "calculate_temperature_response_gaussian"
licor_file[,'Jmax']        # View the values of the new `Jmax` column
#>  [1] 2.284431 2.130094 2.023803 1.987372 1.987206 1.966336 1.915832 2.610843
#>  [9] 2.447311 2.449712 2.398141 2.449862 2.447804 2.455073 2.777885 2.656938
#> [17] 2.585136 2.575099 2.568006 2.464978 2.541577 2.853101 2.703194 2.596917
#> [25] 2.548850 2.567920 2.463949 2.457324