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Calculate gas properties that are typically not included in Licor files

calculate_gas_properties.Rd

Calculates gas properties that are typically not included in Licor files. This function can accomodate alternative column names for the variables taken from the Licor file in case they change at some point in the future. This function also checks the units of each required column and will produce an error if any units are incorrect.

Usage

calculate_gas_properties(
    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'
  )

Arguments

licor_exdf

An exdf object representing data from a Licor gas exchange measurement system.

a_column_name

The name of the column in licor_exdf that contains the net assimilation in micromol m^(-2) s^(-1).

ca_column_name

The name of the column in licor_exdf that contains the ambient CO2 concentration in the chamber in micromol mol^(-1).

total_pressure_column_name

The name of the column in licor_exdf that contains the total pressure in bar.

e_column_name

The name of the column in licor_exdf that contains the transpiration rate in mol m^(-2) s^(-1).

gbw_column_name

The name of the column in licor_exdf that contains the boundary layer conductance to water vapor in mol m^(-2) s^(-1).

gsw_column_name

The name of the column in licor_exdf that contains the stomatal conductance to water vapor in mol m^(-2) s^(-1).

h2o_s_column_name

The name of the column in licor_exdf that contains the sample cell H2O concentration in mmol mol^(-1).

tleaf_column_name

The name of the column in licor_exdf that contains the leaf temperature in degrees C.

Details

By default, a Licor file provides the following gas concentrations and conductances:

  • Water vapor conductance to diffusion through the stomata (gsw).

  • Water vapor conductance to diffusion through the boundary layer (gbw).

  • Water vapor conductance to diffusion from the leaf's intercellular spaces to the ambient air; in other words, the total conductance to water vapor (gtw).

  • Water vapor concentration in the sample cell (H2O_s).

  • CO2 conductance to diffusion from the leaf's intercellular spaces to the ambient air; in other words, the total conductance to CO2 (gtc).

  • CO2 concentration in the sample cell, corrected for any chamber leaks (Ca).

  • CO2 concentration in the leaf's intercellular spaces (Ci).

However, it is sometimes helpful to know the "missing" conductances and concentrations, for example, when calculating mesophyll conductances or Ball-Berry parameters. This function adds these missing values, along with a few related water vapor properties:

  • Water vapor concentration at the sample surface (H2O_surf).

  • Water vapor concentration in the leaf's intercellular spaces (H2O_i).

  • Saturation water vapor pressure at the leaf temperature (SVPleaf).

  • Relative humidity at the leaf surface (RHleaf).

  • CO2 conductance to diffusion through the stomata (gsc).

  • CO2 conductance to diffusion through the boundary layer (gbc).

  • CO2 concentration at the leaf surface (Cs).

Equations used for these calculations

The equations used to calculate these quantities can be found in the Licor Li-6800 manual (Appendix C), which relies heavily on Appendix 2 of the following paper: von Caemmerer, S. & Farquhar, G. D. "Some relationships between the biochemistry of photosynthesis and the gas exchange of leaves" Planta 153, 376–387 (1981) [doi:10.1007/BF00384257 ]

Equation C-79 in the Licor manual describes the total flow of water vapor from the leaf interior to the ambient air using gtw, H2O_i, H2O_s, and the transpiration rate E:

(1) gtw = E * (1000 - (H2O_i + H2O_s) / 2) / (H2O_i - H2O_s)

In steady-state conditions, the flux of H2O molecules across any portion of the gas flow is identical to E, so we can also apply this equation to the flow of water vapor from the leaf surface to the ambient air:

(2) gbw = E * (1000 - (H2O_surf + H2O_s) / 2) / (H2O_surf - H2O_s)

Equation (2) can be solved for H2O_surf:

(3) H2O_surf = (E * (1000 - H2O_s / 2) + gbw * H2O_s) / (gbw + E / 2)

Equation C-70 in the Licor manual describes how to calculate saturation water vapor pressure from air temperature. At the leaf surface, the air temperature should be the same as the leaf temperature (Tleaf; in degrees C), so we can determine SVPleaf using Equation C-70 as follows:

(4) SVPleaf = 0.6135 * e^((17.502 * Tleaf) / (240.97 + Tleaf))

For gas exchange measurements, we assume that water vapor is saturated in the leaf's intecellular spaces, so we can determine H2O_i from SVPleaf and the relationship between partial pressure and molar gas concentration:

(5) H2O_i = SVPleaf / Pcham = SVPleaf / (Pa + deltaPcham)

where Pcham is th total pressure in the sample chamber, Pa is the atmospheric pressure, and deltaPcham is the chamber overpressure. These are related by Pcham = Pa + deltaPcham.

The relative humidity at the leaf surface RHleaf can be determined from H2O_surf and SVPleaf using the definitions of relative humidity and partial pressure:

(6) RHleaf = Pwl / SVPleaf = H2O_surf * (Pa + deltaPcham) / SVPleaf

where Pwl, the partial pressure of H2O at the leaf surface, is given by H2O_surf * Pcham.

The CO2 conductances through the stomata and boundary layer can be determined from the corresponding H2O conductances using the ratios of molecular diffusivities for the two molecules, as explained in the vicinty of Equation C-106 in the Licor manual:

(7) gsc = gsw / 1.6

(8) gbc = gbw / 1.37

Equation C-105 in the Licor manual describes the flow of CO2 from the ambient air to the intercellular spaces:

(9) C_i = ((gtc - E / 2) * Ca - A) / (gtc + E / 2)

where we have replaced C_s (the CO2 concentration in the sample chamber) with Ca for clarity. In steady state conditions, the flows of H2O and CO2 are identical to E and A, respectively, so we can also apply this equation to the flow of CO2 from the ambient air to the leaf surface:

(10) Csurface = ((gbc - E / 2) * Ca - A) / (gbc + E / 2)

This function uses Equations (3)-(8) and (10) to calculate the desired values.

Value

An exdf object based on licor_exdf that includes the following additional columns, calculated as described above: H2O_surf, SVPleaf, H2O_i, RHleaf, gsc, gbc, and Csurface. The category for each of these new columns is calculate_gas_properties to indicate that they were created using this function.

Examples

# Read an example Licor file included in the PhotoGEA package, calculate the
# total pressure, and calculate additional gas properties.
licor_file <- read_gasex_file(
  PhotoGEA_example_file_path('ball_berry_1.xlsx')
)

licor_file <- calculate_total_pressure(licor_file)

licor_file <- calculate_gas_properties(licor_file)

licor_file$units$RHleaf      # View the units of the new `RHleaf` column
#> [1] "%"
licor_file$categories$RHleaf # View the category of the new `RHleaf` column
#> [1] "calculate_gas_properties"
licor_file[,'RHleaf']        # View the values of the new `RHleaf` column
#>  [1] 72.82992 73.97870 74.65520 73.30259 73.32851 73.76332 74.02142 83.24810
#>  [9] 82.76472 81.59332 82.83944 79.67378 79.80127 79.81986 81.01622 81.70109
#> [17] 81.91860 81.55661 81.12870 78.16409 77.93890 76.56099 78.22673 78.97098
#> [25] 78.41431 78.65405 79.31713 76.73647