BufferFactors {AquaEnv}R Documentation



PUBLIC function: calculates buffer factors describing the sensitivity of pH and concentrations of acid-base species to a change in ocean chemistry


BufferFactors(ae = NULL, parameters = NA, species = c("SumCO2"),
                     k_w = NULL, k_co2 = NULL, k_hco3 = NULL, 
                     k_boh3 = NULL, k_hso4 = NULL,
                     k_hf = NULL, k1k2 = "lueker", 
                     khf = "dickson", khso4 = "dickson")



an object of class 'aquaenv'. An error is produced in case an object is provided that is not of class 'aquaenv',


a vector containing one or more of the following variables: "DIC" (mol/kg-soln), "TotNH3" (mol/kg-soln), "TotP" (mol/kg-soln), "TotNO3" (mol/kg-soln), "TotNO2" (mol/kg-soln), "TotS" (mol/kg-soln), "TotSi" (mol/kg-soln), "TB" (mol/kg-soln), "TotF" (mol/kg-soln), "TotSO4" (mol/kg-soln), "sal" (-), "temp" (deg C), "pres" (bar), "Alk" (mol/kg-soln). If a variable is not supplied and no object of class 'aquaenv' is provided, default values are assigned following Table 4 of Hagens and Middelburg (2016). If both ae and parameters are supplied, given parameters will overwrite the corresponding values of ae


a vector containing one or more of the following variables: "SumCO2", "SumNH4", "SumH3PO4", "SumHNO3", "SumHNO2", "SumH2S", "SumSiOH4", "SumBOH3", "SumHF", "SumH2SO4", "CO2", "HCO3", "CO3", "BOH3", "BOH4", "OH", "H3PO4", "H2PO4", "HPO4", "PO4", "SiOH4", "SiOOH3", "SiO2OH2", "H2S", "HS", "S2min", "NH4", "NH3", "H2SO4", "HSO4", "SO4", "HF", "F", "HNO3", "NO3", "HNO2", "NO2". Default is c("SumCO2"). This vector defines the species for which the sensitivities are calculated


a fixed K\_W can be specified


a fixed K\_CO2 can be specified


a fixed K\_HCO3 can be specified


a fixed K\_BOH3 can be specified


a fixed K\_HSO4 can be specified


a fixed K\_HF can be specified


either "lueker" (default, Lueker2000), "roy" (Roy1993a), or "millero" (Millero2006) for K\_CO2 and K\_HCO3


either "dickson" (default, Dickson1979a) or "perez" (Perez1987a) for K\_HF


either "dickson" (default, Dickson1990) or "khoo" (Khoo1977) for K\_HSO4


a list containing the objects "ae", "dTA.dH", "dtotX.dH", "dTA.dX", "dtotX.dX", "dTA.dpH", "dtotX.dpH", "dH.dTA", "dH.dtotX", "dX.dTA", "dX.dtotX", "dpH.dTA", "dpH.dtotX", "beta.H" and "RF".

The object 'ae' is of class 'aquaenv' and refers to the output of the aquaenv function that is always run as part of BufferFactors. Consult the vignette of AquaEnv for more information on this object. The other objects are vectors with the length and names of the input species. Exceptions here are dH.dtotX and dpH.dtotX, which also contain the numerically estimated sensitivities with respect to salinity, pressure and temperature, as well as two factors related to pH scale conversion (see the AquaEnv vignette for details on these latter conversion factors).

In case species are defined which corresponding total concentration equals zero, the corresponding output produces 'NaN'. This is with the exception of "dTA.dH" and "dTA.dpH", which are always calculated as they are linked to beta.H. Additionally, the Revelle factor is always calculated, as the function 'aquaenv' requires that the carbonate system be specified.


Mathilde Hagens (M.Hagens@uu.nl)


Hagens M. and J.J. Middelburg, 2016 Generalised expressions for the response of pH to changes in ocean chemistry. Geochimica et Cosmochimica Acta, in press.


## Not run: 
# Default run

# All carbonate system species
BufferFactors(species = c("CO2", "HCO3", "CO3"))

# Total concentrations of all species
BufferFactors(species = c("SumCO2", "SumNH4", "SumH3PO4", "SumHNO3",
                          "SumHNO2", "SumH2S", "SumSiOH4", "SumBOH3",
                          "SumHF", "SumH2SO4"))

# Different carbonate system equilibrium constants
BufferFactors(k1k2 = "roy")

# Object of class 'aquaenv' as input
ae_input <- aquaenv(S=35, t=25, SumCO2 = 0.0020, pH = 8.1,
                    skeleton = TRUE)
BufferFactors(ae = ae_input)

# Produces some NaNs as certain total concentrations are zero
BufferFactors(ae = ae_input, 
              species = c("SumCO2", "SumNH4", "SumH3PO4", "SumHNO3",
                          "SumHNO2", "SumH2S", "SumSiOH4", "SumBOH3",
                          "SumHF", "SumH2SO4"))

# Object of class 'aquaenv' as input, but different total alkalinity
parameters <- c(Alk = 0.0022)
BufferFactors(ae = ae_input, parameters = parameters)

## End(Not run)

[Package AquaEnv version 1.0-4 Index]