Estimate variance of measured Licor values — estimate_licor

Estimates variance and standard deviation of the net CO2 assimilation rate as measured by a Licor Li-6800 or similar portable photosynthesis system.

Usage

estimate_licor_variance(
    exdf_obj,
    sd_CO2_r,
    sd_CO2_s,
    sd_flow,
    sd_H2O_r,
    sd_H2O_s,
    a_column_name = 'A',
    co2_r_column_name = 'CO2_r',
    co2_s_column_name = 'CO2_s',
    corrfact_column_name = 'CorrFact',
    flow_column_name = 'Flow',
    h2o_r_column_name = 'H2O_r',
    h2o_s_column_name = 'H2O_s',
    s_column_name = 'S'
  )

Arguments

exdf_obj: An exdf object containing gas exchange data.
sd_CO2_r: The standard deviation of reference CO2 concentrations (CO2_r) in units of micromol mol^(-1).
sd_CO2_s: The standard deviation of sample CO2 concentrations (CO2_s) in units of micromol mol^(-1).
sd_flow: The standard deviation of flow rates (Flow) in units of micromol s^(-1).
sd_H2O_r: The standard deviation of reference H2O concentrations (H2O_r) in units of mmol mol^(-1).
sd_H2O_s: The standard deviation of reference H2O concentrations (H2O_r) in units of mmol mol^(-1).
a_column_name: The name of the column in exdf_obj that contains the net CO2 assimilation rate in micromol m^(-2) s^(-1).
co2_r_column_name: The name of the column in exdf_obj that contains the CO2 concentration in the reference line in micromol mol^(-1).
co2_s_column_name: The name of the column in exdf_obj that contains the CO2 concentration in the reference line in micromol mol^(-1).
corrfact_column_name: The name of the column in exdf_obj that contains the leak correction factor (dimensionless)
flow_column_name: The name of the column in exdf_obj that contains the flow rate of air entering the leaf chamber in micromol s^(-1).
h2o_r_column_name: The name of the column in exdf_obj that contains the H2O concentration in the reference line in mmol mol^(-1).
h2o_s_column_name: The name of the column in exdf_obj that contains the H2O concentration in the sample line in mmol mol^(-1).
s_column_name: The name of the column in exdf_obj that contains the leaf chamber area in cm^2.

Details

Uses the error propogation formula to calculate the influence of the variance in CO2_r, CO2_s, etc on the variance of A, as calculated by a Licor LI-6800.

Value

An exdf object based on exdf_obj that includes additional columns representing the standard deviation of A measurements (sd_A), and the individual terms comprising the total variance of A, such as var_CO2_r, var_CO2_s, etc.

Examples

# Read an example Licor file included in the PhotoGEA package
licor_file <- read_gasex_file(
  PhotoGEA_example_file_path('c3_aci_1.xlsx')
)

# Define a new column that uniquely identifies each curve
licor_file[, 'species_plot'] <-
  paste(licor_file[, 'species'], '-', licor_file[, 'plot'] )

# Organize the data
licor_file <- organize_response_curve_data(
    licor_file,
    'species_plot',
    c(9, 10, 16),
    'CO2_r_sp'
)

# Estimate variance in measured A values
licor_file <- estimate_licor_variance(
  licor_file,
  sd_CO2_r = 1,
  sd_CO2_s = 0.1,
  sd_flow = 0.2,
  sd_H2O_r = 0.5,
  sd_H2O_s = 0.1
)

# Plot each component of the total variance of A
lattice::xyplot(
    var_CO2_r + var_CO2_s + var_flow + var_H2O_r + var_H2O_s + var_A ~ Ci | species_plot,
    data = licor_file$main_data,
    type = 'b',
    pch = 16,
    auto = TRUE
)


# Plot the standard deviation of A
lattice::xyplot(
    sd_A ~ Ci,
    group = species_plot,
    data = licor_file$main_data,
    type = 'b',
    pch = 16,
    auto = TRUE
)