aquaenv function

aquaenv

aquaenv

PUBLIC function: the main function of the package AquaEnv: creates an object of class aquaenv

aquaenv(S, t, p=pmax((P-Pa), gauge_p(d, lat, Pa)),
        P=Pa, Pa=1.01325, d=0, lat=0,
        SumCO2=0, SumNH4=0, SumH2S=0, SumH3PO4=0,
        SumSiOH4=0, SumHNO3=0, SumHNO2=0, SumBOH3=NULL,
        SumH2SO4=NULL, SumHF=NULL, TA=NULL, pH=NULL, fCO2=NULL, CO2=NULL,
        speciation=TRUE, dsa=FALSE, ae=NULL, from.data.frame=FALSE,
        SumH2SO4_Koffset=0, SumHF_Koffset=0, revelle=FALSE, skeleton=FALSE,
        k_w=NULL, k_co2=NULL, k_hco3=NULL, k_boh3=NULL, k_hso4=NULL,
        k_hf=NULL, k1k2="lueker", khf="dickson", khso4="dickson", 
        fCO2atm=0.000400, fO2atm=0.20946)

Arguments

  • 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

Examples

## Not run:

############################
# Minimal aquaenv definition
############################
ae <- aquaenv(S=30, t=15)
ae$K_CO2

ae$Ksp_calcite
ae$Ksp_aragonite

ae <- aquaenv(S=30, t=15, p=10)
ae <- aquaenv(S=30, t=15, P=11)
ae <- aquaenv(S=30, t=15, d=100)
ae <- aquaenv(S=30, t=15, d=100, Pa=0.5)
ae$K_CO2

ae$Ksp_calcite
ae$Ksp_aragonite

ae

########################################################
# Defining the complete aquaenv system in different ways
########################################################
S      <- 30
t      <- 15
p      <- gauge_p(d=10)  # ~ p <- 0.1*10*1.01325
SumCO2 <- 0.0020
pH     <- 8
TA     <- 0.002140798
fCO2   <- 0.0005326744
CO2    <- 2.051946e-05

ae <- aquaenv(S, t, p, SumCO2=SumCO2, pH=pH)
ae$TA

ae <- aquaenv(S, t, p, SumCO2=SumCO2, TA=TA)
ae$pH

ae <- aquaenv(S, t, p, SumCO2=SumCO2, CO2=CO2)
ae$pH

ae <- aquaenv(S, t, p, SumCO2=SumCO2, fCO2=fCO2)
ae$pH

ae <- aquaenv(S, t, p, SumCO2=SumCO2, CO2=CO2, fCO2=fCO2)
ae <- aquaenv(S, t, p, SumCO2=SumCO2, pH=pH, TA=TA)
ae <- aquaenv(S, t, p, SumCO2=SumCO2, pH=pH, CO2=CO2)
ae <- aquaenv(S, t, p, SumCO2=SumCO2, pH=pH, fCO2=fCO2)
ae <- aquaenv(S, t, p, SumCO2=SumCO2, TA=TA, CO2=CO2)
ae <- aquaenv(S, t, p, SumCO2=SumCO2, TA=TA, fCO2=fCO2)

################################################################
# Cloning the aquaenv system: 1 to 1 and with different pH or TA
################################################################
S      <- 30
t      <- 15
SumCO2 <- 0.0020
TA     <- 0.00214

ae <- aquaenv(S, t, SumCO2=SumCO2, TA=TA)

aeclone1 <- aquaenv(ae=ae)

pH <- 9

aeclone2 <- aquaenv(ae=ae, pH=pH)

TA <- 0.002

aeclone3 <- aquaenv(ae=ae, TA=TA)

ae$pH
aeclone1$pH
aeclone2$TA
aeclone3$pH


#########################################################################
# Vectors as input variables (only ONE input variable may be a vector)
# (with full output: including the Revelle factor and the DSA properties)
#########################################################################
SumCO2 <- 0.0020
pH     <- 8

S      <- 30
t      <- 1:15
p      <- gauge_p(10)
ae <- aquaenv(S, t, p, SumCO2=SumCO2, pH=pH, revelle=TRUE, dsa=TRUE)
plot(ae, xval=t, xlab="T/(deg C)", newdevice=FALSE)

S  <- 1:30
t  <- 15
ae <- aquaenv(S, t, p, SumCO2=SumCO2, pH=pH, revelle=TRUE, dsa=TRUE)
plot(ae, xval=S, xlab="S", newdevice=FALSE)

S  <- 30
p  <- gauge_p(seq(1,1000, 100))
ae <- aquaenv(S, t, p, SumCO2=SumCO2, pH=pH, revelle=TRUE, dsa=TRUE)
plot(ae, xval=p, xlab="gauge pressure/bar", newdevice=FALSE)


TA <- 0.0023

S  <- 30
t  <- 1:15
d  <- gauge_p(10)
ae <- aquaenv(S, t, p, SumCO2=SumCO2, TA=TA, revelle=TRUE, dsa=TRUE)
plot(ae, xval=t, xlab="T/(deg C)", newdevice=FALSE)

S  <- 1:30
t  <- 15
ae <- aquaenv(S, t, p, SumCO2=SumCO2, TA=TA, revelle=TRUE, dsa=TRUE)
plot(ae, xval=S, xlab="S", newdevice=FALSE)

S  <- 30
p  <- gauge_p(seq(1,1000, 100))
ae <- aquaenv(S, t, p, SumCO2=SumCO2, TA=TA, revelle=TRUE, dsa=TRUE)
plot(ae, xval=p, xlab="gauge pressure/bar", newdevice=FALSE)


##################################################################
# Calculating SumCO2 by giving a constant  pH&CO2, pH&fCO2, pH&TA,
# TA&CO2, or TA&fCO2
##################################################################
fCO2   <- 0.0006952296
CO2    <- 2.678137e-05
pH     <- 7.888573
TA     <- 0.0021

S  <- 30
t  <- 15
p  <- gauge_p(10)

ae <- aquaenv(S, t, p, SumCO2=NULL, pH=pH, CO2=CO2, dsa=TRUE, revelle=TRUE)
ae$SumCO2
ae$revelle
ae$dTAdH

ae <- aquaenv(S, t, p, SumCO2=NULL, pH=pH, fCO2=fCO2)
ae$SumCO2

ae <- aquaenv(S, t, p, SumCO2=NULL, pH=pH, TA=TA)
ae$SumCO2

ae <- aquaenv(S, t, p, SumCO2=NULL, TA=TA, CO2=CO2)
ae$SumCO2

ae <- aquaenv(S, t, p, SumCO2=NULL, TA=TA, fCO2=fCO2)
ae$SumCO2

t  <- 1:15
ae <- aquaenv(S, t, p, SumCO2=NULL, pH=pH, CO2=CO2)
plot(ae, xval=t, xlab="T/(deg C)", mfrow=c(9,10), newdevice=FALSE)

ae <- aquaenv(S, t, p, SumCO2=NULL, pH=pH, CO2=CO2, revelle=TRUE, dsa=TRUE)
plot(ae, xval=t, xlab="T/(deg C)", newdevice=FALSE)

S  <- 1:30
t  <- 15
ae <- aquaenv(S, t, p, SumCO2=NULL, pH=pH, fCO2=fCO2, revelle=TRUE, dsa=TRUE)
plot(ae, xval=S, xlab="S", newdevice=FALSE)

S  <- 30
p  <- gauge_p(seq(1,1000, 100))
ae <- aquaenv(S, t, p, SumCO2=NULL, pH=pH, TA=TA, revelle=TRUE, dsa=TRUE)
plot(ae, xval=p, xlab="gauge pressure/bar", newdevice=FALSE)
## End(Not run)

Returns

a list containing: "S" "t" "p" "T" "Cl" "I" "P" "Pa" "d" "density" "SumCO2" "SumNH4" "SumH2S" "SumHNO3" "SumHNO2" "SumH3PO4" "SumSiOH4" "SumBOH3" "SumH2SO4" "SumHF" "Br" "ClConc" "Na" "Mg" "Ca" "K" "Sr" "molal2molin" "free2tot" "free2sws" "tot2free" "tot2sws" "sws2free" "sws2tot" "K0_CO2" "K0_O2" "fCO2atm" "fO2atm" "CO2_sat" "O2_sat" "K_W" "K_HSO4" "K_HF" "K_CO2" "K_HCO3" "K_BOH3" "K_NH4" "K_H2S" "K_H3PO4" "K_H2PO4" "K_HPO4" "K_SiOH4" "K_SiOOH3" "K_HNO2" "K_HNO3" "K_H2SO4" "K_HS" "Ksp_calcite" "Ksp_aragonite" "TA" "pH" "fCO2" "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" "omega_calcite" "omega_aragonite" "revelle" "c1" "c2" "c3" "dTAdSumCO2" "b1" "b2" "dTAdSumBOH3" "so1" "so2" "so3" "dTAdSumH2SO4" "f1" "f2" "dTAdSumHF" "dTAdH" "dTAdKdKdS" "dTAdKdKdT" "dTAdKdKdd" "dTAdKdKdSumH2SO4" "dTAdKdKdSumHF" or a subset of this set. Please consult the vignette of AquaEnv for more details

Author(s)

Andreas F. Hofmann. Maintained by Karline Soetaert (Karline.Soetaert@nioz.nl).

AquaEnv packageRead PDF manual
  • Maintainer: Karline Soetaert
  • License: GPL (>= 2)
  • Last published: 2016-09-06

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