calculate_temperature_response_polynomial: Calculate temperature-dependent values using polynomial...

In PhotoGEA: Photosynthetic Gas Exchange Analysis

Calculate temperature-dependent values using polynomial equations

Description

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

Usage

  calculate_temperature_response_polynomial(
    exdf_obj,
    polynomial_parameters,
    tleaf_column_name = 'TleafCnd'
  )

Arguments

exdf_obj	An exdf object representing data from a Licor gas exchange measurement system.
polynomial_parameters	A list of named lists. Each list element should describe the polynomial coefficients (coef) and units (units) for a variable that follows a polynomial 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

Polynomial equations are often used to calculate the temperature dependence of the rates of chemical reactions. For example, a second-order polynomial could be given as follows:

(1) rate = R_0 + R_1 * T + R_2 * T^2

where R_0, R_1, and R_2 are the zeroth, first, and second order coefficients and T is the temperature. Higher order polynomials can also be defined, where an order-N polynomial is given by

(2) rate = R_0 + R_1 * T + R_2 * T^2 + ... + R_N * T^N

In general, an order-N polynomial has N coefficients, although some of them may be zero.

In calculate_temperature_response_polynomial, the coefficients (coef) and units (units) for a variable must be specified as elements of a list, which itself is a named element of polynomial_parameters. The coefficients must be specified as a numeric vector, where the ith element represents the ith coefficient. For example, if a dimensionless variable called theta is calculated according to theta = 0.352 + 0.022 * T - 3.4e-4 * T^2, the polynomial_parameters argument could be supplied as follows: list(theta = list(coef = c(0.352, 0.022, -3.4e-4), units = 'dimensionless')).

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

Value

An exdf object based on exdf_obj that includes one new column for each element of polynomial_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_polynomial 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_polynomial(
  licor_file,
  list(theta = list(coef = c(0.352, 0.022, -3.4e-4), units = 'dimensionless'))
)

licor_file$units$theta      # View the units of the new `theta` column
licor_file$categories$theta # View the category of the new `theta` column
licor_file[,'theta']        # View the values of the new `theta` column

PhotoGEA documentation built on April 11, 2025, 5:48 p.m.