bake function

Leaf parameter temperature responses

'bake' leaf parameters using temperature response functions UTF-8

bake(leaf_par, enviro_par, bake_par, constants, assert_units = TRUE)

temp_resp1(par25, E_a, R, T_leaf, T_ref, unitless)

temp_resp2(par25, D_s, E_a, E_d, R, T_leaf, T_ref, unitless)

Arguments

• leaf_par: A list of leaf parameters inheriting class leaf_par. This can be generated using the make_leafpar function.
• enviro_par: A list of environmental parameters inheriting class enviro_par. This can be generated using the make_enviropar function.
• bake_par: A list of temperature response parameters inheriting class bake_par. This can be generated using the make_bakepar function.
• constants: A list of physical constants inheriting class constants. This can be generated using the make_constants function.
• assert_units: Logical. Should parameter units be checked? The function is faster when FALSE, but input must be in correct units or else results will be incorrect without any warning.
• par25: Parameter value at 25 °C of class units.
• E_a: Empirical temperature response value in J/mol of class units.
• R: Ideal gas constant in J / (mol K) of class units. See make_constants().
• T_leaf: Leaf temperature in K of class units. Will be converted to °C.
• T_ref: Reference temperature in K of class units.
• unitless: Logical. Should units be set? The function is faster when FALSE, but input must be in correct units or else results will be incorrect without any warning.
• D_s: Empirical temperature response value in J / (mol K) of class units.
• E_d: Empirical temperature response value in J/mol of class units.

Returns

Constructor function for baked class. This will also inherit class leaf_par() and list(). This function ensures that temperature is "baked in" to leaf parameter calculations T_leaf using temperature response functions detailed below.

Details

Several leaf parameters (leaf_par()) are temperature sensitive. Temperature-sensitive parameters are input at a reference temperature of 25 °C. These parameters are provided as par_name25 and then "baked" using the appropriate temperature response function and parameters in bake_par(). The "baked" parameter will have the name without "25" appended (par_name). E.g. V_cmax25 becomes V_cmax.

Temperature response functions following Buckley and Diaz-Espejo (2015)

Temperature response function 1 (temp_response1):

$T_ref$ is the reference temperature in K

$T_leaf$ is the leaf temperature in °C

Temperature response function 2 (temp_response2) is the above equation multiplied by:

Function 1 increases exponentially with temperature; Function 2 peaks a particular temperature.

Examples

bake_par = make_bakepar()
constants = make_constants(use_tealeaves = FALSE)
enviro_par = make_enviropar(use_tealeaves = FALSE)
leaf_par = make_leafpar(
  replace = list(T_leaf = set_units(293.15, K)),
  use_tealeaves = FALSE
)
baked_leafpar = bake(leaf_par, enviro_par, bake_par, constants)

baked_leafpar$V_cmax25
baked_leafpar$V_cmax

References

Buckley TN, Diaz-Espejo A. 2015. Partitioning changes in photosynthetic rate into contributions from different variables. Plant, Cell and Environment 38: 1200-1211.