identify_c3_limiting_processes: Identify C3 Limiting Processes

In PhotoGEA: Photosynthetic Gas Exchange Analysis

Identify C3 Limiting Processes

Description

Identify limiting processes in a C3 curve, typically the result of a fit. It is rate for users to call this function directly because it is used internally by fit_c3_aci and fit_c3_variable_j.

Usage

  identify_c3_limiting_processes(
    data_table,
    a_column_name = 'A_fit',
    ac_column_name = 'Ac',
    aj_column_name = 'Aj',
    ap_column_name = 'Ap',
    tol = 1e-3
)

Arguments

data_table	A table-like R object such as a data frame or an exdf.
a_column_name	The name of the column in data_table that contains the modeled net CO2 assimilation rate in micromol m^(-2) s^(-1).
ac_column_name	The name of the column in data_table that contains the modeled Rubisco-limited net CO2 assimilation rate in micromol m^(-2) s^(-1).
aj_column_name	The name of the column in data_table that contains the modeled RuBP-regeneration-limited net CO2 assimilation rate in micromol m^(-2) s^(-1).
ap_column_name	The name of the column in data_table that contains the modeled TPU-limited net CO2 assimilation rate in micromol m^(-2) s^(-1).
tol	A relative tolerance factor used to identify when two rates are equal.

Details

For a C3 leaf, An is given by either Ac, Aj, or Ap. See the documentation for calculate_c3_assimilation for more information.

This function first identifies points where An = Ac, An = Aj, and An = Ap. The results are stored in columns called Ac_limiting, Aj_limiting, and Ap_limiting, where a value of TRUE indicates that the corresponding process is limiting.

Then, the overall limiting state is specified in the limiting_process column. For example, points where An equals Ac but not Aj or Ap are designated by limiting_process = 'Ac', and likewise for the other potential limiting processes. If more than one process is limiting for a point, limiting_process is set to 'co-limited'.

Value

An exdf object based on licor_exdf that includes new columns as described above: Ac_limiting, Aj_limiting, Ap_limiting, and limiting_process. The categories of these new columns are set to identify_c3_limiting_processes to indicate that they were created using this function.

Examples

# Identify limiting processes in an example curve
example_curve <- exdf(
  data.frame(
    A_fit = c(1.0, 2.0, 3.0, 4.0, 4.0),
    Ac    = c(1.0, 2.0, 5.0, 8.0, 9.0),
    Aj    = c(2.0, 2.5, 3.0, 4.0, 8.0),
    Ap    = c(NA,  NA,  4.0, 4.0, 4.0)
  ),
  units = data.frame(
    A_fit = 'micromol m^(-2) s^(-1)',
    Ac    = 'micromol m^(-2) s^(-1)',
    Aj    = 'micromol m^(-2) s^(-1)',
    Ap    = 'micromol m^(-2) s^(-1)',
    stringsAsFactors = FALSE
  )
)

identify_c3_limiting_processes(example_curve)

# This function also works for data frames
identify_c3_limiting_processes(example_curve$main_data)

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