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Calculate temperature-dependent values using Johnson-Eyring-Williams equations

calculate_temperature_response_johnson.Rd

Calculate leaf-temperature-dependent values of various parameters using Johnson-Eyring-Williams equations. It is rare for users to call this function directly; instead, it is used internally by calculate_temperature_response.

Usage

calculate_temperature_response_johnson(
    exdf_obj,
    johnson_parameters,
    tleaf_column_name = 'TleafCnd'
  )

Arguments

exdf_obj

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

johnson_parameters

A list of named lists. Each list element should describe the scaling factor (c), enthalpy of activation in kJ / mol (Ha), enthalpy of deactivation in kJ / mol (Hd), entropy in kJ / K / mol (S), and units (units) for a variable that follows a Johnson-Eyring-Williams temperature dependence. The name of each list element should be the corresponding name of the variable.

tleaf_column_name

The name of the column in exdf_obj that contains the leaf temperature in units of degrees C.

Details

The Johnson-Eyring-Williams equation is often used to calculate the temperature dependence of the rate of a chemical reaction. It can be stated as follows:

rate = exp(c - Ha / (R * T)) / (1 + exp(S / R - Hd / (R * T)))

where c is the scaling factor that sets the overall magnitude of the rate, Ha is the enthalpy of activation, Hd is the enthalpy of deactivation, S is the entropy, R is the ideal gas constant, and T is the temperature in Kelvin.

This equation exhibits a peak; in other words, there is a particular temperature (the optimal temperature) where the rate is maximized. Thus, it is often used in place of an Arrhenius equation (see calculate_temperature_response_arrhenius) for photosynthetic parameters that exhibit a decrease at high temperatures.

This equation was originally published in Johnson, Eyring, & Williams (1942) and has been used to model the temperature dependence of key photosynthetic parameters, as in Harley et al. (1992), Bernacchi et al. (2003), Sharkey et al. (2007), and others.

In calculate_temperature_response_johnson, the scaling factor (c), enthalpy of activation (Ha), enthalpy of deactivation (Hd), entopy (S), and units (units) for a variable must be specified as elements of a list, which itself is a named element of johnson_parameters. For example, if a variable called Tp has c = 21.46, Ha = 53.1, Hd = 201.8, S = 0.65, and units of micromol mol^(-1), the johnson_parameters argument could be specified as follows: list(Tp = list(c = 21.46, Ha = 53.1, Hd = 201.8, S = 0.65, units = 'micromol mol^(-1)')).

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.

References:

  • Johnson, F. H., Eyring, H. & Williams, R. W. "The nature of enzyme inhibitions in bacterial luminescence: Sulfanilamide, urethane, temperature and pressure." Journal of Cellular and Comparative Physiology 20, 247–268 (1942) [doi:10.1002/jcp.1030200302 ].

  • Harley, P. C., Thomas, R. B., Reynolds, J. F. & Strain, B. R. "Modelling photosynthesis of cotton grown in elevated CO2." Plant, Cell & Environment 15, 271–282 (1992) [doi:10.1111/j.1365-3040.1992.tb00974.x ].

  • Bernacchi, C. J., Pimentel, C. & Long, S. P. "In vivo temperature response functions of parameters required to model RuBP-limited photosynthesis." Plant, Cell & Environment 26, 1419–1430 (2003) [doi:10.1046/j.0016-8025.2003.01050.x ].

  • Sharkey, T. D., Bernacchi, C. J., Farquhar, G. D. & Singsaas, E. L. "Fitting photosynthetic carbon dioxide response curves for C3 leaves." Plant, Cell & Environment 30, 1035–1040 (2007) [doi:10.1111/j.1365-3040.2007.01710.x ].

Value

An exdf object based on exdf_obj that includes one new column for each element of johnson_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_johnson 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')
)

licor_file <- calculate_temperature_response_johnson(
  licor_file,
  list(Tp_norm = c3_temperature_param_sharkey$Tp_norm)
)

licor_file$units$Tp_norm      # View the units of the new `Tp_norm` column
#> [1] "normalized to Tp at 25 degrees C"
licor_file$categories$Tp_norm # View the category of the new `Tp_norm` column
#> [1] "calculate_temperature_response_johnson"
licor_file[,'Tp_norm']        # View the values of the new `Tp_norm` column
#>  [1] 1.326839 1.299281 1.276934 1.268687 1.268649 1.263793 1.251659 1.362874
#>  [9] 1.348922 1.349189 1.343067 1.349206 1.348977 1.349779 1.367378 1.365159
#> [17] 1.361272 1.360585 1.360078 1.350845 1.358042 1.365798 1.366671 1.362035
#> [25] 1.358625 1.360072 1.350736 1.350024