R/calculate_gas_properties.R

In PhotoGEA: Photosynthetic Gas Exchange Analysis

calculate_gas_properties <- function(
    licor_exdf,
    a_column_name = 'A',
    ca_column_name = 'Ca',
    total_pressure_column_name = 'total_pressure',
    e_column_name = 'E',
    gbw_column_name = 'gbw',
    gsw_column_name = 'gsw',
    h2o_s_column_name = 'H2O_s',
    tleaf_column_name = 'TleafCnd'
)
{
    if (!is.exdf(licor_exdf)) {
        stop('calculate_gas_properties requires an exdf object')
    }

    # Make sure the required variables are defined and have the correct units
    required_variables <- list()
    required_variables[[a_column_name]] <- 'micromol m^(-2) s^(-1)'
    required_variables[[ca_column_name]] <- 'micromol mol^(-1)'
    required_variables[[total_pressure_column_name]] <- 'bar'
    required_variables[[e_column_name]] <- 'mol m^(-2) s^(-1)'
    required_variables[[gbw_column_name]] <- 'mol m^(-2) s^(-1)'
    required_variables[[gsw_column_name]] <- 'mol m^(-2) s^(-1)'
    required_variables[[h2o_s_column_name]] <- 'mmol mol^(-1)'
    required_variables[[tleaf_column_name]] <- 'degrees C'

    check_required_variables(licor_exdf, required_variables)

    # Extract some columns to make the calculations cleaner
    A <- licor_exdf[,a_column_name]                                 # micromol m^(-2) s^(-1)
    Ca <- licor_exdf[,ca_column_name]                               # micromol mol^(-1)
    total_pressure <- licor_exdf[,total_pressure_column_name] * 100 # kPa
    E <- licor_exdf[,e_column_name]                                 # mol m^(-2) s^(-1)
    gbw <- licor_exdf[,gbw_column_name]                             # mol m^(-2) s^(-1)
    gsw <- licor_exdf[,gsw_column_name]                             # mol m^(-2) s^(-1)
    H2O_s <- licor_exdf[,h2o_s_column_name]                         # mmol mol^(-1)
    Tleaf <- licor_exdf[,tleaf_column_name]                         # degrees C

    # Calculate new columns
    licor_exdf[,'H2O_surf'] <- (E * (1000 - H2O_s / 2) + gbw * H2O_s) /
                               (gbw + E / 2)

    licor_exdf[,'SVPleaf'] <- 0.6135 * exp((17.502 * Tleaf) / (240.97 + Tleaf))

    licor_exdf[,'H2O_i'] <- 1000 * licor_exdf[,'SVPleaf'] / total_pressure

    licor_exdf[,'RHleaf'] <- 0.1 * licor_exdf[,'H2O_surf'] * total_pressure /
                             licor_exdf[,'SVPleaf']

    licor_exdf[,'gsc'] <- gsw / 1.6

    licor_exdf[,'gbc'] <- gbw / 1.37

    licor_exdf[,'Csurface'] <- ((licor_exdf[,'gbc'] - E / 2) * Ca - A) /
                               (licor_exdf[,'gbc'] + E / 2)

    # Document the columns that were added
    licor_exdf <- document_variables(
        licor_exdf,
        c('calculate_gas_properties', 'H2O_surf', 'mmol mol^(-1)'),
        c('calculate_gas_properties', 'SVPleaf',  'kPa'),
        c('calculate_gas_properties', 'H2O_i',    'mmol mol^(-1)'),
        c('calculate_gas_properties', 'RHleaf',   '%'),
        c('calculate_gas_properties', 'gsc',      'mol m^(-2) s^(-1)'),
        c('calculate_gas_properties', 'gbc',      'mol m^(-2) s^(-1)'),
        c('calculate_gas_properties', 'Csurface', 'micromol mol^(-1)')
    )
}