S: salinity in practical salinity units (i.e. no unit)
t: temperature in degrees centigrade
p: gauge pressure (total pressure minus atmospheric pressure) in bars, standard is calculated either from the given P, or the given d, lat, and Pa
P: total pressure in bars, standard: Pa (at the surface)
Pa: atmospheric pressure in bars, standard: 1 atm (at sea-level)
d: depth below the surface in meters, standard: 0 (at the surface)
lat: latitude in degrees (-90 to +90) to calculate the gravitational constant g for calculating the water depth from the pressure and vice versa, standard: 0
SumCO2: total carbonate concentration in mol/kg-solution, if NULL is supplied it is calculated
SumNH4: total ammonium concentration in mol/kg-solution, optional
SumH2S: total sulfide concentration in mol/kg-solution, optional
SumH3PO4: total phosphate concentration in mol/kg-solution, optional
SumSiOH4: total silicate concentration in mol/kg-solution, optional
SumHNO3: total nitrate concentration in mol/kg-solution, optional
SumHNO2: total nitrite concentration in mol/kg-solution, optional
SumBOH3: total borate concentration in mol/kg-solution, calculated from S if not supplied
SumH2SO4: total sulfate concentration in mol/kg-solution, calculated from S if not supplied
SumHF: total fluoride concentration in mol/kg-solution, calculated from S if not supplied
TA: total alkalinity in mol/kg-solution, if supplied, pH will be calculated
pH: pH on the free proton concentration scale, if supplied, total alkalinity will be calculated
fCO2: fugacity of CO2 in the water in atm (i.e. the fugacity of CO2 in a small volume of air fully equilibrated with a sufficiently large sample of water), can be used with either [TA], pH, or [CO2] to define the system
CO2: concentration of CO2, can be used with either [TA], pH, or fCO2 to define the system
speciation: flag: TRUE = full speciation is calculated
dsa: flag: TRUE = all information necessary to build a pH model with the direct substitution approach (DSA, Hofmann2008) is calculated
ae: either an object of class aquaenv used for the cloning functionality or a dataframe used for the from.data.frame functionality. Note that for cloning the desired k1k2 and khf values need to be specified! (otherwise the default values are used for the cloned object)
from.data.frame: flag: TRUE = the object of class aquaenv is built from the data frame supplied in ae
SumH2SO4_Koffset: only used internally to calculate dTAdKdKdSumH2SO4
SumHF_Koffset: only used internally to calculate dTAdKdKdSumHF
revelle: flag: TRUE = the revelle factor is numerically calculated. We do however strongly encourage to use the analytical calculation from BufferFactors$RF
skeleton: flag: TRUE = a reduced amount of information is calculated yielding a smaller object of type aquaenv
k_w: a fixed K_W can be specified
k_co2: a fixed K_CO2 can be specified; used for TA fitting: give a K_CO2 and NOT calculate it from T and S: i.e. K_CO2 can be fitted in the routine as well
k_hco3: a fixed K_HCO3 can be specified
k_boh3: a fixed K_BOH3 can be specified
k_hso4: a fixed K_HSO4 can be specified
k_hf: a fixed K_HF can be specified
k1k2: either "lueker" (default, Lueker2000), "roy" (Roy1993a), or "millero" (Millero2006) for K_CO2 and K_HCO3.
khf: either "dickson" (default, Dickson1979a) or "perez" (Perez1987a) for K_HF
khso4: either "dickson" (default, Dickson1990) or "khoo" (Khoo1977) for K_HSO4
fCO2atm: atmospheric fugacity of CO2 in atm, default = 0.000400 atm
fO2atm: atmospheric fugacity of O2 in atm, default = 0.20946 atm