| aquaenv {AquaEnv} | R Documentation |
aquaenv
Description
PUBLIC function: the main function of the package AquaEnv: creates an object of class aquaenv
Usage
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 |
Value
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).
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)