| Title: | Integrated Development Toolbox for Aquatic Chemical Model Generation |
|---|---|
| Description: | Toolbox for the experimental aquatic chemist, focused on acidification and CO2 air-water exchange. It contains all elements to model the pH, the related CO2 air-water exchange, and aquatic acid-base chemistry for an arbitrary marine, estuarine or freshwater system. It contains a suite of tools for sensitivity analysis, visualisation, modelling of chemical batches, and can be used to build dynamic models of aquatic systems. As from version 1.0-4, it also contains functions to calculate the buffer factors. |
| Authors: | Andreas F. Hofmann, Karline Soetaert, Filip J.R. Meysman, Mathilde Hagens |
| Maintainer: | Karline Soetaert <[email protected]> |
| License: | GPL (>= 2) |
| Version: | 1.0-4 |
| Built: | 2024-11-18 06:10:29 UTC |
| Source: | https://github.com/cran/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)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)
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 |
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
Andreas F. Hofmann. Maintained by Karline Soetaert ([email protected]).
## 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)## 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)
AquaEnv is an integrated development toolbox for aquatic chemical model generation focused on (ocean) acidification and CO2 air-water exchange.
It contains all elements necessary to model the pH, the related CO2 air-water exchange, as well as aquatic acid-base chemistry in general for an arbitrary marine, estuarine or freshwater system. Also chemical batches can be modelled.
Next to the routines necessary to calculate desired information, AquaEnv also contains a suite of tools to visualize this information. Furthermore, AquaEnv can not only be used to build dynamic models of aquatic systems, but it can also serve as a simple desktop tool for the experimental aquatic chemist to generate and visualize all possible derived information from a set of measurements with one single easy to use R function.
Additionally, the sensitivity of the system to variations in the input variables can be visualized.
| Package: | AquaEnv |
| Type: | Package |
| Version: | 1.1 |
| Date: | 2016-05-18 |
| License: | GNU Public License 2 or above |
Karline Soetaert (Maintainer), Andreas F. Hofmann, Mathilde Hagens
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.
Hofmann A. F., K. Soetaert, J.J. Middelburg, F. J. R. Meysman, 2010 AquaEnv: An Aquatic Acid-Base Modelling Environment in R. Aquatic Geochemistry 16: 507-546.
## Not run: ## show examples (see respective help pages for details) example(aquaenv) ## open the directory with source code of demos browseURL(paste(system.file(package="AquaEnv"), "/demo", sep="")) ## run demos demo(basicfeatures ) ## show package vignette with tutorial about how to use aquaenv vignette("AquaEnv") edit(vignette("AquaEnv")) browseURL(paste(system.file(package="AquaEnv"), "/doc", sep="")) ## show index file of package vignettes and documentation files browseURL(paste(system.file(package="AquaEnv"), "/doc/index.html", sep="")) ## show documentation about private functions in the packet browseURL(paste(system.file(package="AquaEnv"), "/doc/AquaEnv-PrivateFunctions.pdf", sep="")) ## show documentation about physical-chemical constants and formulae used in the packet browseURL(paste(system.file(package="AquaEnv"), "/doc/AquaEnv-ConstantsAndFormulae.pdf", sep="")) ## End(Not run)## Not run: ## show examples (see respective help pages for details) example(aquaenv) ## open the directory with source code of demos browseURL(paste(system.file(package="AquaEnv"), "/demo", sep="")) ## run demos demo(basicfeatures ) ## show package vignette with tutorial about how to use aquaenv vignette("AquaEnv") edit(vignette("AquaEnv")) browseURL(paste(system.file(package="AquaEnv"), "/doc", sep="")) ## show index file of package vignettes and documentation files browseURL(paste(system.file(package="AquaEnv"), "/doc/index.html", sep="")) ## show documentation about private functions in the packet browseURL(paste(system.file(package="AquaEnv"), "/doc/AquaEnv-PrivateFunctions.pdf", sep="")) ## show documentation about physical-chemical constants and formulae used in the packet browseURL(paste(system.file(package="AquaEnv"), "/doc/AquaEnv-ConstantsAndFormulae.pdf", sep="")) ## End(Not run)
PUBLIC function: converts an object of class aquaenv to a standard R data frame
## S3 method for class 'aquaenv' as.data.frame(x, ...)## S3 method for class 'aquaenv' as.data.frame(x, ...)
x |
object of type aquaenv |
... |
further arguments are passed on |
data frame containing all elements of aquaenv
Andreas F. Hofmann. Maintained by Karline Soetaert ([email protected]).
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")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")
ae |
an object of class 'aquaenv'. An error is produced in case an object is provided that is not of class 'aquaenv', |
parameters |
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 |
species |
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 |
k_w |
a fixed K\_W can be specified |
k_co2 |
a fixed K\_CO2 can be specified |
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 |
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 ([email protected])
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 BufferFactors() # 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)## Not run: # Default run BufferFactors() # 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)
PRIVATE function: adds an element to an object of class aquaenv
## S3 method for class 'aquaenv' c(aquaenv, x, ...)## S3 method for class 'aquaenv' c(aquaenv, x, ...)
aquaenv |
object of class aquaenv |
x |
a vector of the form c(value, name) representing the element to be inserted into the object of class aquaenv |
... |
further arguments will be passed |
object of class aquaenv with the added element
Andreas F. Hofmann. Maintained by Karline Soetaert ([email protected]).
PUBLIC data frame: a collection of concentrations of key chemical species in seawater, relative with respect to chlorinity (DOE1994))
Andreas F. Hofmann. Maintained by Karline Soetaert ([email protected]).
PUBLIC function: converts either a single value (the pH scale of a pH value, the pH scale of a dissociation constant (K*), the unit of a concentration value), or all elements of a special unit or pH scale in an object of class aquaenv
x |
object to be converted: either a single value (pH value, K* value, or concentration value) or an object of class aquaenv |
vartype |
only valid if x is a single value: the type of x, either "pHscale", "KHscale", or "conc" |
what |
only valid if x is a single value: only valid if x is a single value: the type of conversion to be done, for pH scales one of "free2tot", "free2sws", "free2nbs", ... (any combination of "free", "tot", "sws", and "nbs"); for concentrations one of "molar2molal", "molar2molin", ... (any combination of "molar" (mol/l), "molal" (mol/kg-H2O), and "molin" (mol/kg-solution)) |
S |
only valid if x is a single value: salinity (in practical salinity units: no unit) |
t |
only valid if x is a single value: temperature in degrees centigrade |
p |
only valid if x is a single value: gauge pressure (total pressure minus atmospheric pressure) in bars |
SumH2SO4 |
only valid if x is a single value: total sulfate concentration in mol/kg-solution; if not supplied this is calculated from S |
SumHF |
only valid if x is a single value: total fluoride concentration in mol/kg-solution; if not supplied this is calculated from S |
khf |
only valid if x is a single value: either "dickson" (default, Dickson1979a) or "perez" (Perez1987a) for K\_HF |
khso4 |
only valid if x is a single value: either "dickson" (default, Dickson1990) or "khoo" (Khoo1977) for K\_HSO4 |
from |
only valid if x is an object of class aquaenv: the unit which needs to be converted (as a string; must be a perfect match) |
to |
only valid if x is an object of class aquaenv: the unit to which the conversion should go |
factor |
only valid if x is an object of class aquaenv: the conversion factor to be applied: can either be a number (e.g. 1000 to convert from mol to mmol), or any of the conversion factors given in an object of class aquaenv |
convattr |
only valid if x is an object of class aquaenv: which attribute should be converted? can either be "unit" or "pH scale" |
Possible usages are
convert(x, vartype, what, S, t, p, SumH2SO4, SumHF, khf) convert(x, from, to, factor, convattr)
converted single value or object of class aquaenv with converted elements
Andreas F. Hofmann. Maintained by Karline Soetaert ([email protected]).
## Not run: ### 1 ##### t <- 15 S <- 10 pH_NBS <- 8.142777 SumCO2molar <- 0.002016803 pH_free <- convert(pH_NBS, "pHscale", "nbs2free", S=S, t=t) SumCO2molin <- convert(SumCO2molar, "conc", "molar2molin", S=S, t=t) ae <- aquaenv(S, t, SumCO2=SumCO2molin, pH=pH_free) ae$pH ae$SumCO2 ### 2 ##### ae <- aquaenv(30,10) ae$SumBOH3 ae <- convert(ae, "mol/kg-soln", "umol/kg-H2O", 1e6/ae$molal2molin, "unit") ae$SumBOH3 ## End(Not run)## Not run: ### 1 ##### t <- 15 S <- 10 pH_NBS <- 8.142777 SumCO2molar <- 0.002016803 pH_free <- convert(pH_NBS, "pHscale", "nbs2free", S=S, t=t) SumCO2molin <- convert(SumCO2molar, "conc", "molar2molin", S=S, t=t) ae <- aquaenv(S, t, SumCO2=SumCO2molin, pH=pH_free) ae$pH ae$SumCO2 ### 2 ##### ae <- aquaenv(30,10) ae$SumBOH3 ae <- convert(ae, "mol/kg-soln", "umol/kg-H2O", 1e6/ae$molal2molin, "unit") ae$SumBOH3 ## End(Not run)
PUBLIC data frame: a collection of coefficients for the pressure correction of dissociation constants and solubility products (Millero1995 WITH CORRECTIONS BY Lewis1998 (CO2Sys)!)
Andreas F. Hofmann. Maintained by Karline Soetaert ([email protected]).
PUBLIC function: calculates the gauge pressure (total pressure minus atmospheric pressure) from the depth (in m) and the latitude (in degrees: -90 to 90) and the atmospheric pressure (in bar)
gauge_p(d, lat=0, Pa=1.01325)gauge_p(d, lat=0, Pa=1.01325)
d |
water depth in meters |
lat |
latitude in degrees: -90 to 90, standard: 0 |
Pa |
atmospheric pressure in bar, standard: 1 atm (at sea level) |
gauge pressure (total pressure minus atmospheric pressure) p in bars
Andreas F. Hofmann. Maintained by Karline Soetaert ([email protected]).
Fofonoff1983
gauge_p(100) plot(gauge_p(1:100))gauge_p(100) plot(gauge_p(1:100))
PUBLIC function: calculates the dissociation constant of B(OH)3
K_BOH3(S, t, p=0, SumH2SO4=NULL, SumHF=NULL, khf="dickson", khso4="dickson")K_BOH3(S, t, p=0, SumH2SO4=NULL, SumHF=NULL, khf="dickson", khso4="dickson")
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 |
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) |
khf |
S, t relation for K\_HF needed for scale conversion: either "dickson" (default, Dickson1979a) or "perez" (Perez1987a) |
khso4 |
S, t relation for K\_HSO4 needed for scale conversion: either "dickson" (default, Dickson1990) or "khoo" (Khoo1977) |
the dissociation constant of B(OH)3 in mol/kg-solution on the free proton pH scale
Andreas F. Hofmann. Maintained by Karline Soetaert ([email protected]).
Dickson1990, DOE1994, Millero1995 (molality version given), Zeebe2001
K_BOH3(35, 15) K_BOH3(35, 15, 10) K_BOH3(S=35, t=15, p=10, SumH2SO4=0.03) plot(K_BOH3(35, 1:25), xlab="temperature / degC")K_BOH3(35, 15) K_BOH3(35, 15, 10) K_BOH3(S=35, t=15, p=10, SumH2SO4=0.03) plot(K_BOH3(35, 1:25), xlab="temperature / degC")
PUBLIC function: calculates the dissociation constant of CO2
K_CO2(S, t, p=0, SumH2SO4=NULL, SumHF=NULL, k1k2="lueker", khf="dickson", khso4="dickson")K_CO2(S, t, p=0, SumH2SO4=NULL, SumHF=NULL, k1k2="lueker", khf="dickson", khso4="dickson")
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 |
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) |
k1k2 |
"lueker", "roy", or "millero": specifies the S, t, dependency to be used. Default is "lueker". (see section below for references) |
khf |
S, t relation for K\_HF needed for scale conversion: either "dickson" (default, Dickson1979a) or "perez" (Perez1987a) |
khso4 |
S, t relation for K\_HSO4 needed for scale conversion: either "dickson" (default, Dickson1990) or "khoo" (Khoo1977) |
the dissociation constant of CO2 in mol/kg-solution on the free proton pH scale
Andreas F. Hofmann. Maintained by Karline Soetaert ([email protected]).
k1k2 = "roy": Roy1993b, DOE1994, Millero1995, Zeebe2001; k1k2 = "lueker": Lueker2000; k1k2 = "millero": Millero2006
K_CO2(35, 15) K_CO2(35, 15, 10) K_CO2(S=35, t=15, p=10, SumH2SO4=0.03) plot(K_CO2(35, 1:25), xlab="temperature / degC")K_CO2(35, 15) K_CO2(35, 15, 10) K_CO2(S=35, t=15, p=10, SumH2SO4=0.03) plot(K_CO2(35, 1:25), xlab="temperature / degC")
PUBLIC function: calculates the dissociation constant of H2PO4
K_H2PO4(S, t, p=0, SumH2SO4=NULL, SumHF=NULL, khf="dickson", khso4="dickson")K_H2PO4(S, t, p=0, SumH2SO4=NULL, SumHF=NULL, khf="dickson", khso4="dickson")
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 |
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) |
khf |
S, t relation for K\_HF needed for scale conversion: either "dickson" (default, Dickson1979a) or "perez" (Perez1987a) |
khso4 |
S, t relation for K\_HSO4 needed for scale conversion: either "dickson" (default, Dickson1990) or "khoo" (Khoo1977) |
the dissociation constant of H2PO4 in mol/kg-solution on the free proton pH scale
Andreas F. Hofmann. Maintained by Karline Soetaert ([email protected]).
Millero1995 (original, SWS pH version), DOE1994 (in a later revision cites Millero1995)
K_H2PO4(35, 15) K_H2PO4(35, 15, 10) K_H2PO4(S=35, t=15, p=10, SumH2SO4=0.03) plot(K_H2PO4(35, 1:25), xlab="temperature / degC")K_H2PO4(35, 15) K_H2PO4(35, 15, 10) K_H2PO4(S=35, t=15, p=10, SumH2SO4=0.03) plot(K_H2PO4(35, 1:25), xlab="temperature / degC")
PUBLIC function: calculates the dissociation constant of H2S
K_H2S(S, t, p=0, SumH2SO4=NULL, SumHF=NULL, khf="dickson", khso4="dickson")K_H2S(S, t, p=0, SumH2SO4=NULL, SumHF=NULL, khf="dickson", khso4="dickson")
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 |
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) |
khf |
S, t relation for K\_HF needed for scale conversion: either "dickson" (default, Dickson1979a) or "perez" (Perez1987a) |
khso4 |
S, t relation for K\_HSO4 needed for scale conversion: either "dickson" (default, Dickson1990) or "khoo" (Khoo1977) |
the dissociation constant of H2S in mol/kg-solution on the free proton pH scale
Andreas F. Hofmann. Maintained by Karline Soetaert ([email protected]).
Millero1988, Millero1995
K_H2S(35, 15) K_H2S(35, 15, 10) K_H2S(S=35, t=15, p=10, SumH2SO4=0.03) plot(K_H2S(35, 1:25), xlab="temperature / degC")K_H2S(35, 15) K_H2S(35, 15, 10) K_H2S(S=35, t=15, p=10, SumH2SO4=0.03) plot(K_H2S(35, 1:25), xlab="temperature / degC")
PUBLIC function: calculates the dissociation constant of H3PO4
K_H3PO4(S, t, p=0, SumH2SO4=NULL, SumHF=NULL, khf="dickson", khso4="dickson")K_H3PO4(S, t, p=0, SumH2SO4=NULL, SumHF=NULL, khf="dickson", khso4="dickson")
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 |
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) |
khf |
S, t relation for K\_HF needed for scale conversion: either "dickson" (default, Dickson1979a) or "perez" (Perez1987a) |
khso4 |
S, t relation for K\_HSO4 needed for scale conversion: either "dickson" (default, Dickson1990) or "khoo" (Khoo1977) |
the dissociation constant of H3PO4 in mol/kg-solution on the free proton pH scale
Andreas F. Hofmann. Maintained by Karline Soetaert ([email protected]).
Millero1995 (original, SWS pH version), DOE1994 (in a later revision cites Millero1995)
K_H3PO4(35, 15) K_H3PO4(35, 15, 10) K_H3PO4(S=35, t=15, p=10, SumH2SO4=0.03) plot(K_H3PO4(35, 1:25), xlab="temperature / degC")K_H3PO4(35, 15) K_H3PO4(35, 15, 10) K_H3PO4(S=35, t=15, p=10, SumH2SO4=0.03) plot(K_H3PO4(35, 1:25), xlab="temperature / degC")
PUBLIC function: calculates the dissociation constant of HCO3
K_HCO3(S, t, p=0, SumH2SO4=NULL, SumHF=NULL, k1k2="lueker", khf="dickson", khso4="dickson")K_HCO3(S, t, p=0, SumH2SO4=NULL, SumHF=NULL, k1k2="lueker", khf="dickson", khso4="dickson")
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 |
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) |
k1k2 |
"lueker", "roy", or "millero": specifies the S, t, dependency to be used. Default is "lueker". (see section below for references) |
khf |
S, t relation for K\_HF needed for scale conversion: either "dickson" (default, Dickson1979a) or "perez" (Perez1987a) |
khso4 |
S, t relation for K\_HSO4 needed for scale conversion: either "dickson" (default, Dickson1990) or "khoo" (Khoo1977) |
the dissociation constant of HCO3 in mol/kg-solution on the free proton pH scale
Andreas F. Hofmann. Maintained by Karline Soetaert ([email protected]).
k1k2 = "roy": Roy1993b, DOE1994, Millero1995, Zeebe2001; k1k2 = "lueker": Lueker2000; k1k2 = "millero": Millero2006
K_HCO3(35, 15) K_HCO3(35, 15, 10) K_HCO3(S=35, t=15, p=10, SumH2SO4=0.03) plot(K_HCO3(35, 1:25), xlab="temperature / degC")K_HCO3(35, 15) K_HCO3(35, 15, 10) K_HCO3(S=35, t=15, p=10, SumH2SO4=0.03) plot(K_HCO3(35, 1:25), xlab="temperature / degC")
PUBLIC function: calculates the dissociation constant of HF
K_HF(S, t, p=0, SumH2SO4=NULL, SumHF=NULL, khf="dickson", khso4="dickson")K_HF(S, t, p=0, SumH2SO4=NULL, SumHF=NULL, khf="dickson", khso4="dickson")
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 |
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) |
khf |
"dickson" or "perez": specifies the S, t, dependency to be used. Default is "dickson". (see section below for references) |
khso4 |
S, t relation for K\_HSO4 needed for scale conversion: either "dickson" (default, Dickson1990) or "khoo" (Khoo1977) |
the dissociation constant of HF in mol/kg-solution on the free proton pH scale
Andreas F. Hofmann. Maintained by Karline Soetaert ([email protected]).
khf = "dickson": Dickson1979a, Dickson1987, Roy1993b, DOE1994, Millero1995, Zeebe2001; khf = "perez": Perez1987
K_HF(35, 15) K_HF(35, 15, 10) plot(K_HF(35, 1:25), xlab="temperature / degC")K_HF(35, 15) K_HF(35, 15, 10) plot(K_HF(35, 1:25), xlab="temperature / degC")
PUBLIC function: calculates the dissociation constant of HPO4
K_HPO4(S, t, p=0, SumH2SO4=NULL, SumHF=NULL, khf="dickson", khso4="dickson")K_HPO4(S, t, p=0, SumH2SO4=NULL, SumHF=NULL, khf="dickson", khso4="dickson")
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 |
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) |
khf |
S, t relation for K\_HF needed for scale conversion: either "dickson" (default, Dickson1979a) or "perez" (Perez1987a) |
khso4 |
S, t relation for K\_HSO4 needed for scale conversion: either "dickson" (default, Dickson1990) or "khoo" (Khoo1977) |
the dissociation constant of HPO4 in mol/kg-solution on the free proton pH scale
Andreas F. Hofmann. Maintained by Karline Soetaert ([email protected]).
Millero1995 (original, SWS pH version), DOE1994 (in a later revision cites Millero1995)
K_HPO4(35, 15) K_HPO4(35, 15, 10) K_HPO4(S=35, t=15, p=10, SumH2SO4=0.03) plot(K_HPO4(35, 1:25), xlab="temperature / degC")K_HPO4(35, 15) K_HPO4(35, 15, 10) K_HPO4(S=35, t=15, p=10, SumH2SO4=0.03) plot(K_HPO4(35, 1:25), xlab="temperature / degC")
PUBLIC function: calculates the dissociation constant of HSO4
K_HSO4(S, t, p=0, khso4="dickson")K_HSO4(S, t, p=0, khso4="dickson")
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 |
khso4 |
"dickson" or "khoo": specifies the S, t, dependency to be used. Default is "dickson". (see section below for references) |
the dissociation constant of HSO4 in mol/kg-solution on the free proton pH scale
Andreas F. Hofmann. Maintained by Karline Soetaert ([email protected]).
"dickson": Dickson1990, DOE1994, Zeebe2001; "khoo": Khoo1977, Roy1993, Millero1995
K_HSO4(35, 15) K_HSO4(35, 15, 10) plot(K_HSO4(35, 1:25), xlab="temperature / degC")K_HSO4(35, 15) K_HSO4(35, 15, 10) plot(K_HSO4(35, 1:25), xlab="temperature / degC")
PUBLIC function: calculates the dissociation constant of NH4
K_NH4(S, t, p=0, SumH2SO4=NULL, SumHF=NULL, khf="dickson", khso4="dickson")K_NH4(S, t, p=0, SumH2SO4=NULL, SumHF=NULL, khf="dickson", khso4="dickson")
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 |
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) |
khf |
S, t relation for K\_HF needed for scale conversion: either "dickson" (default, Dickson1979a) or "perez" (Perez1987a) |
khso4 |
S, t relation for K\_HSO4 needed for scale conversion: either "dickson" (default, Dickson1990) or "khoo" (Khoo1977) |
the dissociation constant of NH4 in mol/kg-solution on the free proton pH scale
Andreas F. Hofmann. Maintained by Karline Soetaert ([email protected]).
Millero1995a, Millero1995, corrected by Lewis1998
K_NH4(35, 15) K_NH4(35, 15, 10) K_NH4(S=35, t=15, p=10, SumH2SO4=0.03) plot(K_NH4(35, 1:25), xlab="temperature / degC")K_NH4(35, 15) K_NH4(35, 15, 10) K_NH4(S=35, t=15, p=10, SumH2SO4=0.03) plot(K_NH4(35, 1:25), xlab="temperature / degC")
PUBLIC function: calculates the dissociation constant of SiOH4
K_SiOH4(S, t, p=0, SumH2SO4=NULL, SumHF=NULL, khf="dickson", khso4="dickson")K_SiOH4(S, t, p=0, SumH2SO4=NULL, SumHF=NULL, khf="dickson", khso4="dickson")
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 |
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) |
khf |
S, t relation for K\_HF needed for scale conversion: either "dickson" (default, Dickson1979a) or "perez" (Perez1987a) |
khso4 |
S, t relation for K\_HSO4 needed for scale conversion: either "dickson" (default, Dickson1990) or "khoo" (Khoo1977) |
the dissociation constant of SiOH4 in mol/kg-solution on the free proton pH scale
Andreas F. Hofmann. Maintained by Karline Soetaert ([email protected]).
Millero1988, DOE1994, Millero1995
K_SiOH4(35, 15) K_SiOH4(35, 15, 10) K_SiOH4(S=35, t=15, p=10, SumH2SO4=0.03) plot(K_SiOH4(35, 1:25), xlab="temperature / degC")K_SiOH4(35, 15) K_SiOH4(35, 15, 10) K_SiOH4(S=35, t=15, p=10, SumH2SO4=0.03) plot(K_SiOH4(35, 1:25), xlab="temperature / degC")
PUBLIC function: calculates the dissociation constant of SiOOH3
K_SiOOH3(S, t, p=0, SumH2SO4=NULL, SumHF=NULL, khf="dickson", khso4="dickson")K_SiOOH3(S, t, p=0, SumH2SO4=NULL, SumHF=NULL, khf="dickson", khso4="dickson")
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 |
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) |
khf |
S, t relation for K\_HF needed for scale conversion: either "dickson" (default, Dickson1979a) or "perez" (Perez1987a) |
khso4 |
S, t relation for K\_HSO4 needed for scale conversion: either "dickson" (default, Dickson1990) or "khoo" (Khoo1977) |
the dissociation constant of SiOOH3 in mol/kg-solution on the free proton pH scale
Andreas F. Hofmann. Maintained by Karline Soetaert ([email protected]).
Wischmeyer2003 (incl. corrections)
K_SiOOH3(35, 15) K_SiOOH3(35, 15, 10) K_SiOOH3(S=35, t=15, p=10, SumH2SO4=0.03) plot(K_SiOOH3(35, 1:25), xlab="temperature / degC")K_SiOOH3(35, 15) K_SiOOH3(35, 15, 10) K_SiOOH3(S=35, t=15, p=10, SumH2SO4=0.03) plot(K_SiOOH3(35, 1:25), xlab="temperature / degC")
PUBLIC function: calculates the ion product of H2O
K_W(S, t, p=0, SumH2SO4=NULL, SumHF=NULL, khf="dickson", khso4="dickson")K_W(S, t, p=0, SumH2SO4=NULL, SumHF=NULL, khf="dickson", khso4="dickson")
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 |
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) |
khf |
S, t relation for K\_HF needed for scale conversion: either "dickson" (default, Dickson1979a) or "perez" (Perez1987a) |
khso4 |
S, t relation for K\_HSO4 needed for scale conversion: either "dickson" (default, Dickson1990) or "khoo" (Khoo1977) |
the ion product of H2O in (mol/kg-solution)2 on the free proton pH scale
Andreas F. Hofmann. Maintained by Karline Soetaert ([email protected]).
Millero1995 (SWS pH version), DOE1994 (cites Millero1995), Zeebe2001
K_W(35, 15) K_W(35, 15, 10) K_W(S=35, t=15, p=10, SumH2SO4=0.03) plot(K_W(35, 1:25), xlab="temperature / degC")K_W(35, 15) K_W(35, 15, 10) K_W(S=35, t=15, p=10, SumH2SO4=0.03) plot(K_W(35, 1:25), xlab="temperature / degC")
PUBLIC function: calculates the Henry's constant (solubility) for CO2
K0_CO2(S, t)K0_CO2(S, t)
S |
salinity in practical salinity units (i.e. no unit) |
t |
temperature in degrees centigrade |
the Henry's constant for CO2 in mol/(kg-solution*atm)
Andreas F. Hofmann. Maintained by Karline Soetaert ([email protected]).
Weiss1974, DOE1994, Millero1995, Zeebe2001
K0_CO2(35, 15) plot(K0_CO2(35, 1:25), xlab="temperature / degC")K0_CO2(35, 15) plot(K0_CO2(35, 1:25), xlab="temperature / degC")
PUBLIC function: calculates the Henry's constant (solubility) for O2
K0_O2(S, t)K0_O2(S, t)
S |
salinity in practical salinity units (i.e. no unit) |
t |
temperature in degrees centigrade |
the Henry's constant for CO2 in mol/(kg-solution*atm)
Andreas F. Hofmann. Maintained by Karline Soetaert ([email protected]).
derived from a formulation for [O2]sat given in Weiss1970
K0_O2(35, 15) plot(K0_O2(35, 1:25), xlab="temperature / degC")K0_O2(35, 15) plot(K0_O2(35, 1:25), xlab="temperature / degC")
PUBLIC function: calculates the solubility product for aragonite
Ksp_aragonite(S, t, p=0)Ksp_aragonite(S, t, p=0)
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 |
the solubility product for aragonite in (mol/kg-solution)2
Andreas F. Hofmann. Maintained by Karline Soetaert ([email protected]).
Mucci1983, Boudreau1996
Ksp_aragonite(35, 15) Ksp_aragonite(35, 15, 10) plot(Ksp_aragonite(35, 1:25), xlab="temperature / degC")Ksp_aragonite(35, 15) Ksp_aragonite(35, 15, 10) plot(Ksp_aragonite(35, 1:25), xlab="temperature / degC")
PUBLIC function: calculates the solubility product for aragonite
Ksp_calcite(S, t, p=0)Ksp_calcite(S, t, p=0)
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 |
the solubility product for calcite in (mol/kg-solution)2
Andreas F. Hofmann. Maintained by Karline Soetaert ([email protected]).
Mucci1983, Boudreau1996
Ksp_calcite(35, 15) Ksp_calcite(35, 15, 10) plot(Ksp_aragonite(35, 1:25), xlab="temperature / degC")Ksp_calcite(35, 15) Ksp_calcite(35, 15, 10) plot(Ksp_aragonite(35, 1:25), xlab="temperature / degC")
PRIVATE function: returns the (maximal) length of the elements in an object of class aquaenv (i.e. > 1 if one of the input variables was a vector)
## S3 method for class 'aquaenv' length(x, ...)## S3 method for class 'aquaenv' length(x, ...)
x |
object of class aquaenv |
... |
further arguments will be passed |
the maximal length of the elements in the object of class aquaenv
Andreas F. Hofmann. Maintained by Karline Soetaert ([email protected]).
PUBLIC data frame: a collection of mean molecular masses of key chemical species in seawater in g/mol (DOE1994))
Andreas F. Hofmann. Maintained by Karline Soetaert ([email protected]).
PRIVATE function: merges the elements of two objects of class aquaenv: element names are taken from the first argument, the elements of which are also first in the merged object
## S3 method for class 'aquaenv' merge(x, y, ...)## S3 method for class 'aquaenv' merge(x, y, ...)
x |
object of class aquaenv: this is where the element names are taken from |
y |
object of class aquaenv: must contain at leas all the element (names) as aquaenv1, extra elements are ignored |
... |
further arguments will be passed |
object of class aquaenv with merged elements
Andreas F. Hofmann. Maintained by Karline Soetaert ([email protected]).
PUBLIC list: a collection of physical and chemical constants
A list containing:
R |
(bar*cm3)/(mol*K) the gas constant (corrected after Lewis1998, in Millero1995: R = 83.131); digits extended after Dickson2007) |
F |
C/mol the Faraday constant (charge per mol of electrons) (N\_A*e-): Dickson2007 |
uMolToMol |
conversion factor from umol to mol |
absZero |
absolute zero in degrees centigrade |
e |
relative dielectric constanf of seawater (Zeebe2001) |
K_HNO2 |
dissociation constant of HNO2: mol/l, NBS pH scale, hybrid constant (Riordan2005) |
K_HNO3 |
dissociation constant of HNO3: assumed on mol/kg-soln and free pH scale, stoichiometric constant (Soetaert pers. comm.) |
K_H2SO4 |
dissociation constant of H2SO4: assumed on mol/kg-soln and free pH scale, stoichiometric constant (Atkins1996) |
K_HS |
dissociation constant of HHS: assumed on mol/kg-soln and free pH scale, stoichiometric constant (Atkins1996) |
Andreas F. Hofmann. Maintained by Karline Soetaert ([email protected]).
PUBLIC function: high level plot function for objects of class aquaenv
x |
object of class aquaenv |
xval |
only valid if bjerrum=FALSE: a vector of the (maximal) length of the elements of aquaenv against which they are to be plotted |
what |
a list of names of the elements of aquaenv that are to be plotted, if not supplied and bjerrum=FALSE and cumulative=FALSE: all elements are plotted, if not supplied and bjerrum=TRUE then what is set to be c("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"), needs to be supplied for cumulative=TRUE |
bjerrum |
flag: TRUE = a bjerrum plot is done (by calling bjerrumplot) |
cumulative |
flag: TRUE = a cumulative plot is done (by calling cumulativeplot) |
newdevice |
flag: if TRUE, new plot device is opened |
setpar |
flag: if TRUE parameters are set with the function par |
xlab |
x axis label |
log |
only valif if bjerrum=TRUE: should the plot be on a logarithmic y axis? |
total |
only valid if cumulative=TRUE: should the sum of all elements specified in what be plotted as well? |
device |
the device to plot on; default: "x11" (can also be "eps" or "pdf") |
filename |
filename to be used if "eps" or "pdf" is selected for device |
size |
the size of the plot device; default: 12 (width) by 10 (height) inches |
ylim |
standard plot parameter; if not supplied it will be calculated by range() of the elements to plot |
lwd |
standard plot parameter; width of the lines in the plot |
mgp |
standard plot parameter; default: axis title on line 1.8, axis labels on line 0.5, axis on line 0 |
mar |
standard plot parameter; default: margin of 3 lines bottom and left and 0.5 lines top and right |
oma |
standard plot parameter; default: no outer margin |
palette |
only valid if bjerrum=TRUE or cumulative=TRUE: a vector of colors to use in the plot (either numbers or names given in colors()) |
legendposition |
only valid if bjerrum=TRUE or cumulative=TRUE: position of the legend |
legendinset |
only valid if bjerrum=TRUE or cumulative=TRUE: standard legend parameter inset |
legendlwd |
only valid if bjerrum=TRUE or cumulative=TRUE: standard legend parameter lwd: line width of lines in legend |
bg |
only valid if bjerrum=TRUE or cumulative=TRUE: standard legend parameter: default background color: white |
y.intersp |
standard legend parameter; if cumulative=TRUE then default: 1.2 lines space between the lines in the legend |
... |
further arguments are passed on to the plot function |
Top level generic usage is
plot.aquaenv(x, xval, what=NULL, bjerrum=FALSE,
cumulative=FALSE, newdevice=TRUE, setpar=TRUE,
device="x11", ...)
Generic usages for standard plotting are
plot.aquaenv(x, xval, ...)
plot.aquaenv(x, xval, what, mfrow=c(1,1), size=c(7,7), ...)
Generic usage for creating a bjerrum plot is
plot.aquaenv(x, what, log=FALSE, palette=NULL,
device="x11", filename="aquaenv",
size=c(12,10), ylim=NULL, lwd=2, xlab="free scale pH",
mgp=c(1.8, 0.5, 0), mar=c(3,3,0.5,0.5), oma=c(0,0,0,0),
legendposition="bottomleft", legendinset=0.05,
legendlwd=4, bg="white", newdevice=TRUE, setpar=TRUE,
device="x11",...)
Generic usage for creating a cumulative plot is
plot.aquaenv(x, xval, what, total=TRUE, palette=NULL,
device="x11", filename="aquaenv", size=c(12,10), ylim=NULL,
lwd=2, mgp=c(1.8, 0.5, 0), mar=c(3,3,0.5,0.5), oma=c(0,0,0,0),
legendposition="bottomleft", legendinset=0.05, legendlwd=4,
bg="white", y.intersp=1.2, newdevice=TRUE, setpar=TRUE,
device="x11",...)
Andreas F. Hofmann. Maintained by Karline Soetaert ([email protected]).
## Not run: ### 0 ##### A <- aquaenv(35, 15, SumCO2=0.003, TA=seq(0.001,0.004, 0.0001)) plot(A, xval=A$TA, xlab="[TA]/(mol/kg-soln)") plot(A, what=c("CO2", "HCO3", "CO3"), bjerrum=TRUE, log=TRUE) plot(A, xval=A$TA, xlab="[TA]/(mol/kg-soln)", what=c("CO2", "HCO3", "CO3"), cumulative=TRUE, ylab="mol/kg-soln", ylim=c(0,0.0031)) ### 1 ##### SumCO2 <- 0.0020 pH <- 8 S <- 30 t <- 1:15 p <- 10 ae <- aquaenv(S, t, p, SumCO2=SumCO2, pH=pH, revelle=TRUE, dsa=TRUE) plot(ae, xval=t, xlab="T/(deg C)", newdevice=FALSE) ### 2 ##### S <- 35 t <- 15 SumCO2 <- 0.003500 SumNH4 <- 0.000020 mass_sample <- 0.01 # the mass of the sample solution in kg mass_titrant <- 0.02 # the total mass of the added titrant solution in # kg conc_titrant <- 0.01 # the concentration of the titrant solution in # mol/kg-soln S_titrant <- 0.5 # the salinity of the titrant solution (the # salinity of a solution with a ionic strength of # 0.01 according to: I = (19.924 S) / (1000 - 1.005S) steps <- 50 # the amount of steps the mass of titrant is added # in type <- "HCl" pHstart <- 11.3 ae <- titration(aquaenv(S=S, t=t, SumCO2=SumCO2, SumNH4=SumNH4, pH=pHstart), mass_sample, mass_titrant, conc_titrant, S_titrant, steps, type) # plotting everything plot(ae, xval=ae$delta_mass_titrant, xlab="HCl solution added [kg]", mfrow=c(10,10)) # plotting selectively size <- c(12,8) #inches mfrow <- c(4,4) what <- c("TA", "pH", "CO2", "HCO3", "CO3", "BOH3", "BOH4", "OH", "NH4", "NH3", "H2SO4", "HSO4", "SO4", "HF", "F", "pCO2") plot(ae, xval=ae$delta_mass_titrant, xlab="HCl solution added [kg]", what=what, size=size, mfrow=mfrow) plot(ae, xval=ae$pH, xlab="free scale pH", what=what, size=size, mfrow=mfrow) # different x values plot(ae, xval=ae$delta_conc_titrant, xlab="[HCl] offset added [mol/kg-soln]", what=what, size=size, mfrow=mfrow) plot(ae, xval=ae$delta_moles_titrant, xlab="HCl added [mol]", what=what, size=size, mfrow=mfrow, newdevice=FALSE) # bjerrum plots plot(ae, bjerrum=TRUE) what <- c("CO2", "HCO3", "CO3") plot(ae, what=what, bjerrum=TRUE) plot(ae, what=what, bjerrum=TRUE, lwd=4, palette=c("cyan", "magenta", "yellow"), bg="gray", legendinset=0.1, legendposition="topleft") what <- c("CO2", "HCO3", "CO3", "BOH3", "BOH4", "OH", "NH4", "NH3", "H2SO4", "HSO4", "SO4", "HF", "F") plot(ae, what=what, bjerrum=TRUE, log=TRUE, newdevice=FALSE) plot(ae, what=what, bjerrum=TRUE, log=TRUE, ylim=c(-6,-1), legendinset=0, lwd=3, palette=c(1,3,4,5,6,colors()[seq(100,250,6)])) ### 3 ##### parameters <- list( t = 15 , # degrees C S = 35 , # psu SumCO2_t0 = 0.002 , # mol/kg-soln (comparable to Wang2005) TA_t0 = 0.0022 , # mol/kg-soln (comparable to Millero1998) kc = 0.5 , # 1/d proportionality factor # for air-water exchange kp = 0.000001 , # mol/(kg-soln*d) max rate of calcium # carbonate precipitation n = 2.0 , # - exponent for kinetic # rate law of precipitation modeltime = 20 , # d duration of the model outputsteps = 100 # number of outputsteps ) boxmodel <- function(timestep, currentstate, parameters) { with ( as.list(c(currentstate,parameters)), { ae <- aquaenv(S=S, t=t, SumCO2=SumCO2, pH=-log10(H), SumSiOH4=0, SumBOH3=0, SumH2SO4=0, SumHF=0, dsa=TRUE) Rc <- kc * ((ae$CO2_sat) - (ae$CO2)) Rp <- kp * (1-ae$omega_calcite)^n dSumCO2 <- Rc - Rp dHRc <- ( -(ae$dTAdSumCO2*Rc ))/ae$dTAdH dHRp <- (-2*Rp -(ae$dTAdSumCO2*(-Rp)))/ae$dTAdH dH <- dHRc + dHRp ratesofchanges <- c(dSumCO2, dH) processrates <- c(Rc=Rc, Rp=Rp) outputvars <- c(dHRc=dHRc, dHRp=dHRp) return(list(ratesofchanges, list(processrates, outputvars, ae))) } ) } with (as.list(parameters), { aetmp <- aquaenv(S=S, t=t, SumCO2=SumCO2_t0, TA=TA_t0, SumSiOH4=0, SumBOH3=0, SumH2SO4=0, SumHF=0) H_t0 <- 10^(-aetmp$pH) initialstate <<- c(SumCO2=SumCO2_t0, H=H_t0) times <<- seq(0,modeltime,(modeltime/outputsteps)) output <<- as.data.frame(vode(initialstate,times, boxmodel,parameters, hmax=1)) }) what <- c("SumCO2", "TA", "Rc", "Rp", "omega_calcite", "pH", "dHRc", "dHRp") plot(aquaenv(ae=output, from.data.frame=TRUE), xval=output$time, xlab="time/d", mfrow=c(3,3), size=c(15,10), what=what) what <- c("dHRc", "dHRp") plot(aquaenv(ae=output, from.data.frame=TRUE), xval=output$time, xlab="time/d", what=what, ylab="mol-H/(kg-soln*d)", legendposition="topright", cumulative=TRUE) ## End(Not run)## Not run: ### 0 ##### A <- aquaenv(35, 15, SumCO2=0.003, TA=seq(0.001,0.004, 0.0001)) plot(A, xval=A$TA, xlab="[TA]/(mol/kg-soln)") plot(A, what=c("CO2", "HCO3", "CO3"), bjerrum=TRUE, log=TRUE) plot(A, xval=A$TA, xlab="[TA]/(mol/kg-soln)", what=c("CO2", "HCO3", "CO3"), cumulative=TRUE, ylab="mol/kg-soln", ylim=c(0,0.0031)) ### 1 ##### SumCO2 <- 0.0020 pH <- 8 S <- 30 t <- 1:15 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) ### 2 ##### S <- 35 t <- 15 SumCO2 <- 0.003500 SumNH4 <- 0.000020 mass_sample <- 0.01 # the mass of the sample solution in kg mass_titrant <- 0.02 # the total mass of the added titrant solution in # kg conc_titrant <- 0.01 # the concentration of the titrant solution in # mol/kg-soln S_titrant <- 0.5 # the salinity of the titrant solution (the # salinity of a solution with a ionic strength of # 0.01 according to: I = (19.924 S) / (1000 - 1.005S) steps <- 50 # the amount of steps the mass of titrant is added # in type <- "HCl" pHstart <- 11.3 ae <- titration(aquaenv(S=S, t=t, SumCO2=SumCO2, SumNH4=SumNH4, pH=pHstart), mass_sample, mass_titrant, conc_titrant, S_titrant, steps, type) # plotting everything plot(ae, xval=ae$delta_mass_titrant, xlab="HCl solution added [kg]", mfrow=c(10,10)) # plotting selectively size <- c(12,8) #inches mfrow <- c(4,4) what <- c("TA", "pH", "CO2", "HCO3", "CO3", "BOH3", "BOH4", "OH", "NH4", "NH3", "H2SO4", "HSO4", "SO4", "HF", "F", "pCO2") plot(ae, xval=ae$delta_mass_titrant, xlab="HCl solution added [kg]", what=what, size=size, mfrow=mfrow) plot(ae, xval=ae$pH, xlab="free scale pH", what=what, size=size, mfrow=mfrow) # different x values plot(ae, xval=ae$delta_conc_titrant, xlab="[HCl] offset added [mol/kg-soln]", what=what, size=size, mfrow=mfrow) plot(ae, xval=ae$delta_moles_titrant, xlab="HCl added [mol]", what=what, size=size, mfrow=mfrow, newdevice=FALSE) # bjerrum plots plot(ae, bjerrum=TRUE) what <- c("CO2", "HCO3", "CO3") plot(ae, what=what, bjerrum=TRUE) plot(ae, what=what, bjerrum=TRUE, lwd=4, palette=c("cyan", "magenta", "yellow"), bg="gray", legendinset=0.1, legendposition="topleft") what <- c("CO2", "HCO3", "CO3", "BOH3", "BOH4", "OH", "NH4", "NH3", "H2SO4", "HSO4", "SO4", "HF", "F") plot(ae, what=what, bjerrum=TRUE, log=TRUE, newdevice=FALSE) plot(ae, what=what, bjerrum=TRUE, log=TRUE, ylim=c(-6,-1), legendinset=0, lwd=3, palette=c(1,3,4,5,6,colors()[seq(100,250,6)])) ### 3 ##### parameters <- list( t = 15 , # degrees C S = 35 , # psu SumCO2_t0 = 0.002 , # mol/kg-soln (comparable to Wang2005) TA_t0 = 0.0022 , # mol/kg-soln (comparable to Millero1998) kc = 0.5 , # 1/d proportionality factor # for air-water exchange kp = 0.000001 , # mol/(kg-soln*d) max rate of calcium # carbonate precipitation n = 2.0 , # - exponent for kinetic # rate law of precipitation modeltime = 20 , # d duration of the model outputsteps = 100 # number of outputsteps ) boxmodel <- function(timestep, currentstate, parameters) { with ( as.list(c(currentstate,parameters)), { ae <- aquaenv(S=S, t=t, SumCO2=SumCO2, pH=-log10(H), SumSiOH4=0, SumBOH3=0, SumH2SO4=0, SumHF=0, dsa=TRUE) Rc <- kc * ((ae$CO2_sat) - (ae$CO2)) Rp <- kp * (1-ae$omega_calcite)^n dSumCO2 <- Rc - Rp dHRc <- ( -(ae$dTAdSumCO2*Rc ))/ae$dTAdH dHRp <- (-2*Rp -(ae$dTAdSumCO2*(-Rp)))/ae$dTAdH dH <- dHRc + dHRp ratesofchanges <- c(dSumCO2, dH) processrates <- c(Rc=Rc, Rp=Rp) outputvars <- c(dHRc=dHRc, dHRp=dHRp) return(list(ratesofchanges, list(processrates, outputvars, ae))) } ) } with (as.list(parameters), { aetmp <- aquaenv(S=S, t=t, SumCO2=SumCO2_t0, TA=TA_t0, SumSiOH4=0, SumBOH3=0, SumH2SO4=0, SumHF=0) H_t0 <- 10^(-aetmp$pH) initialstate <<- c(SumCO2=SumCO2_t0, H=H_t0) times <<- seq(0,modeltime,(modeltime/outputsteps)) output <<- as.data.frame(vode(initialstate,times, boxmodel,parameters, hmax=1)) }) what <- c("SumCO2", "TA", "Rc", "Rp", "omega_calcite", "pH", "dHRc", "dHRp") plot(aquaenv(ae=output, from.data.frame=TRUE), xval=output$time, xlab="time/d", mfrow=c(3,3), size=c(15,10), what=what) what <- c("dHRc", "dHRp") plot(aquaenv(ae=output, from.data.frame=TRUE), xval=output$time, xlab="time/d", what=what, ylab="mol-H/(kg-soln*d)", legendposition="topright", cumulative=TRUE) ## End(Not run)
PUBLIC dataset: theoretical titration curve for TA
determination as given in table 1 of Dickson1981
Meta-data:
| x-value | mass of titrant added (in g) |
| y-value | pH measured on the free proton scale |
| t | 25 | degC |
| S | 35 | |
| mass\_sample | 200 | g |
| conc\_titrant | 0.3000 | mol/kg-soln |
| TA | 0.00245 | mol/kg-soln |
| SumCO2 | 0.00220 | mol/kg-soln |
| SumBOH3 | 0.00042 | mol/kg-soln |
| SumH2SO4 | 0.02824 | mol/kg-soln |
| SumHF | 0.00007 | mol/kg-soln |
| K\_W | 4.32e-14 | (mol/kg-soln)*(mol/kg-soln) |
| K\_CO2 | 1.00e-6 | mol/kg-soln |
| K\_HCO3 | 8.20e-10 | mol/kg-soln |
| K\_BOH3 | 1.78e-9 | mol/kg-soln |
| K\_HSO4 | 1/1.23e1 | mol/kg-soln |
| K\_HF | 1/4.08e2 | mol/kg-soln |
Andreas F. Hofmann. Maintained by Karline Soetaert ([email protected]).
PUBLIC dataset: titration curve for TA determination as
given on p. 11 of SOP3b in Dickson2007
Metadata:
| x-value | mass of titrant added (in cubic centimeters) |
| y-value | E in V |
| t | 24.25 | degC |
| S | 33.923 | |
| mass\_sample | 140.32 | g |
| conc\_titrant | 0.10046 | mol/kg-soln |
| density titrant | 1.02393 | g/cm3 |
| calculated TA | 2260.06 | umol/kg-soln |
| calculated E0 | 0.394401 | V |
Andreas F. Hofmann. Maintained by Karline Soetaert ([email protected]).
PUBLIC function: calculates [TA] and [SumCO2] (and optionally K\_C02 and E0) from a titration curve using an optimization procedure (nls.lm from R package minpack.lm)
TAfit(ae, titcurve, conc_titrant, mass_sample, S_titrant=NULL, TASumCO2guess=0.0025, E0guess=0.4, type="HCl", Evals=FALSE, electrode_polarity="pos", K_CO2fit=FALSE, equalspaced=TRUE, seawater_titrant=FALSE, pHscale="free", debug=FALSE, k_w=NULL, k_co2=NULL, k_hco3=NULL, k_boh3=NULL, k_hso4=NULL, k_hf=NULL, nlscontrol=nls.lm.control(), verbose=FALSE, k1k2="roy", khf="dickson", datxbegin=0, SumCO2Zero=FALSE)TAfit(ae, titcurve, conc_titrant, mass_sample, S_titrant=NULL, TASumCO2guess=0.0025, E0guess=0.4, type="HCl", Evals=FALSE, electrode_polarity="pos", K_CO2fit=FALSE, equalspaced=TRUE, seawater_titrant=FALSE, pHscale="free", debug=FALSE, k_w=NULL, k_co2=NULL, k_hco3=NULL, k_boh3=NULL, k_hso4=NULL, k_hf=NULL, nlscontrol=nls.lm.control(), verbose=FALSE, k1k2="roy", khf="dickson", datxbegin=0, SumCO2Zero=FALSE)
ae |
an object of type aquaenv: minimal definition, contains all information about the system: T, S, d, total concentrations of nutrients etc (Note that it is possible to give values for SumBOH4, SumHSO4, and SumHF in the sample other than the ones calculated from salinity) |
titcurve |
a table containing the titration curve: basically a series of tuples of added titrant solution mass and pH values (pH on free proton scale) or E values in V |
conc_titrant |
concentration of the titrant solution in mol/kg-soln |
mass_sample |
the mass of the sample solution in kg |
S_titrant |
the salinity of the titrant solution, if not supplied it is assumed that the titrant solution has the same salinity as the sample solution |
TASumCO2guess |
a first guess for [TA] and [SumCO2] to be used as initial values for the optimization procedure |
E0guess |
first guess for E0 in V |
type |
the type of titrant: either "HCl" or "NaOH" |
Evals |
are the supplied datapoints pH or E (V) values? |
electrode_polarity |
either "pos" or "neg": how is the polarity of the Electrode: E = E0 -(RT/F)ln(H+) ("pos") or -E = E0 -(RT/F)ln(H+) ("neg")? |
K_CO2fit |
should K\_CO2 be fitted as well? |
equalspaced |
are the mass values of titcurve equally spaced? |
seawater_titrant |
is the titrant based on natural seawater? (does it contain SumBOH4, SumHSO4, and SumHF in the same proportions as seawater, i.e., correlated to S?); Note that you can only assume a seawater based titrant (i.e. SumBOH4, SumHSO4, and SumHF ~ S) or a water based titrant (i.e. SumBOH4, SumHSO4, and SumHF = 0). It is not possible to give values for SumBOH4, SumHSO4, and SumHF of the titrant. |
pHscale |
either "free", "total", "sws" or "nbs": if the titration curve contains pH data: on which scale is it measured? |
debug |
debug mode: the last simulated titration tit, the converted pH profile calc, and the nls.lm output out are made global variables for investigation and plotting |
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 |
nlscontrol |
nls.lm.control() can be specified |
verbose |
verbose mode: show the traject of the fitting in a plot |
k1k2 |
either "roy" (default, Roy1993a) or "lueker" (Lueker2000) for K\_CO2 and K\_HCO3. |
khf |
either "dickson" (default, Dickson1979a) or "perez" (Perez1987a) for K\_HF |
datxbegin |
at what x value (amount of titrant added) does the supplied curve start? (i.e. is the complete curve supplied or just a part?) |
SumCO2Zero |
should SumCO2==0? |
a list of up to five values ([TA] in mol/kg-solution, [SumCO2] in mol/kg-solution, E0 in V, K1 in mol/kg-solution and on free scale, sum of the squared residuals)
Andreas F. Hofmann. Maintained by Karline Soetaert ([email protected]).
## Not run: #################################### # Calculating TA from titration data #################################### #### 1.) proof of concept ########## #################################### #################################### # generate "data": S <- 35 t <- 15 SumCO2 <- 0.002000 TA <- 0.002200 initial_ae <- aquaenv(S=S, t=t, SumCO2=SumCO2, TA=TA) mass_sample <- 0.01 # the mass of the sample solution in kg mass_titrant <- 0.003 # the total mass of the added titrant solution # in kg conc_titrant <- 0.01 # the concentration of the titrant solution in # mol/kg-soln S_titrant <- 0.5 # the salinity of the titrant solution (the # salinity of a solution with a ionic strength # of 0.01 according to: # I = (19.924 S) / (1000 - 1.005 S) steps <- 20 # the amount of steps the mass of titrant is # added in type <- "HCl" ae <- titration(initial_ae, mass_sample, mass_titrant, conc_titrant, S_titrant, steps, type) plot(ae, ae$delta_mass_titrant, what="pH", newdevice=FALSE) # the input data for the TA fitting routine: a table with the added # mass of the titrant and the resulting free scale pH titcurve <- cbind(ae$delta_mass_titrant, ae$pH) # for the TA fitting procedure all total quantities except SumCO2 # (SumNH4, SumH2S, SumH3PO4, SumSiOH4, SumHNO3, SumHNO2, SumBOH3, # SumH2SO4, SumHF) need to be known. However, the latter three # can be calculated from salinity as it is done in this example. fit1 <- TAfit(initial_ae, titcurve, conc_titrant, mass_sample, S_titrant) fit1 # E (V) values as input variables: generate E values using # E0=0.4 V and the nernst equation tottitcurve <- convert(titcurve[,2], "pHscale", "free2sws", S=S, t=t) # (Nernst equation relates E to TOTAL [H+] (DOE1994, p.7, # ch.4, sop.3), BUT, if fluoride is present, its SWS, so # we use SWS! Etitcurve <- cbind(titcurve[,1], (0.4 - ((PhysChemConst$R/10) *initial_ae$T/PhysChemConst$F) *log(10^-tottitcurve))) # Nernst equation fit2 <- TAfit(initial_ae, Etitcurve, conc_titrant, mass_sample, S_titrant, Evals=TRUE, verbose=TRUE) fit2 # k_co2 fitting: one K_CO2 (k_co2) for the whole titration curve # is fitted, i.e. there is NO correction for K_CO2 changes due to # changing S due to mixing with the titrant fit3 <- TAfit(initial_ae, titcurve, conc_titrant, mass_sample, S_titrant, K_CO2fit=TRUE) fit3 # assume the titrant has the same salinity as the sample # (and is made up of natural seawater, i.e. containing SumBOH4, # SumH2SO4 and SumHF as functions of S), then the "right" K_CO2 # should be fitted i.e we do NOT give the argument S_titrant # and set the flag seawater_titrant to TRUE ae <- titration(initial_ae, mass_sample, mass_titrant, conc_titrant, steps=steps, type=type, seawater_titrant=TRUE) titcurve <- cbind(ae$delta_mass_titrant, ae$pH) fit4 <- TAfit(initial_ae, titcurve, conc_titrant, mass_sample, K_CO2fit=TRUE, seawater_titrant=TRUE) fit4 # fitting of TA, SumCO2, K_CO2 and E0 Etitcurve <- cbind(titcurve[,1], (0.4 - ((PhysChemConst$R/10) *initial_ae$T/PhysChemConst$F) *log(10^-titcurve[,2]))) fit5 <- TAfit(initial_ae, Etitcurve, conc_titrant, mass_sample, K_CO2fit=TRUE, seawater_titrant=TRUE, Evals=TRUE) fit5 # fitting of non equally spaced data: neqsptitcurve <- rbind(titcurve[1:9,], titcurve[11:20,]) fit6 <- TAfit(initial_ae, neqsptitcurve, conc_titrant, mass_sample, seawater_titrant=TRUE, equalspaced=FALSE) fit6 #add some "noise" on the generated data noisetitcurve <- titcurve * rnorm(length(titcurve), mean=1, sd=0.01) #one percent error possible plot(ae, ae$delta_mass_titrant, what="pH", type="l", col="red", xlim=c(0,0.003), ylim=c(3,8.1), newdevice=FALSE) par(new=TRUE) plot(noisetitcurve[,1],noisetitcurve[,2], type="l", xlim=c(0,0.003), ylim=c(3,8.1)) fit7 <- TAfit(initial_ae, noisetitcurve, conc_titrant, mass_sample, seawater_titrant=TRUE) fit7 # 2.) test with generated data from Dickson1981 # ################################################# ################################################# conc_titrant = 0.3 # mol/kg-soln mass_sample = 0.2 # kg S_titrant = 14.835 # is aequivalent to the ionic strength # of 0.3 mol/kg-soln SumBOH3 = 0.00042 # mol/kg-soln SumH2SO4 = 0.02824 # mol/kg-soln SumHF = 0.00007 # mol/kg-soln # convert mass of titrant from g to kg sam <- cbind(sample_dickson1981[,1]/1000, sample_dickson1981[,2]) dicksonfit <- TAfit(aquaenv(t=25, S=35, SumBOH3=SumBOH3, SumH2SO4=SumH2SO4, SumHF=SumHF), sam, conc_titrant, mass_sample, S_titrant=S_titrant, debug=TRUE) dicksonfit #TA Dickson1981: 0.00245 #SumCO2 Dickson1981: 0.00220 # => not exactly the same! why? # a.) does salinity correction (S_titrant) matter or not? ########################################################## # without salinity correction dicksontitration1 <- titration(aquaenv(t=25, S=35, SumCO2=0.00220, SumBOH3=SumBOH3, SumH2SO4=SumH2SO4, SumHF=SumHF, TA=0.00245), mass_sample=mass_sample, mass_titrant=0.0025, conc_titrant=conc_titrant, steps=50, type="HCl") # with salinity correction dicksontitration2 <- titration(aquaenv(t=25, S=35, SumCO2=0.00220, SumBOH3=SumBOH3, SumH2SO4=SumH2SO4, SumHF=SumHF, TA=0.00245), mass_sample=mass_sample, mass_titrant=0.0025, conc_titrant=conc_titrant, S_titrant=S_titrant, steps=50, type="HCl") plot(dicksontitration1, xval=dicksontitration1$delta_mass_titrant, what="pH", xlim=c(0,0.0025), ylim=c(3,8.2), newdevice=FALSE, col="red") par(new=TRUE) plot(dicksontitration2, xval=dicksontitration2$delta_mass_titrant, what="pH", xlim=c(0,0.0025), ylim=c(3,8.2), newdevice=FALSE, col="blue") par(new=TRUE) plot(sam[,1], sam[,2], type="l", xlim=c(0,0.0025), ylim=c(3,8.2)) # => salinity correction makes NO difference, because the relation # between total sample and added titrant is very large: # salinity only drops from 35 to 34.75105 #BUT: there is an offset between the "Dickson" curve and our curve: plot(dicksontitration2$pH - sam[,2]) # b.) does it get better if we fit K_CO2 as well? ################################################# dicksonfit2 <- TAfit(aquaenv(t=25, S=35, SumBOH3=SumBOH3, SumH2SO4=SumH2SO4, SumHF=SumHF), sam, conc_titrant, mass_sample, S_titrant=S_titrant, debug=TRUE, K_CO2fit=TRUE) dicksonfit2 #TA Dickson1981: 0.00245 #SumCO2 Dickson1981: 0.00220 # => yes it does, but it is not perfect yet! # c.) differing K values ######################### # Dickson uses fixed K values that are slightly different than ours dicksontitration3 <- titration(aquaenv(t=25, S=35, SumCO2=0.00220, SumBOH3=SumBOH3, SumH2SO4=SumH2SO4, SumHF=SumHF, TA=0.00245, k_w=4.32e-14, k_co2=1e-6, k_hco3=8.20e-10, k_boh3=1.78e-9, k_hso4=(1/1.23e1), k_hf=(1/4.08e2)), mass_sample=mass_sample, mass_titrant=0.0025, conc_titrant=conc_titrant, steps=50, type="HCl", S_titrant=S_titrant, k_w=4.32e-14, k_co2=1e-6, k_hco3=8.20e-10, k_boh3=1.78e-9, k_hso4=(1/1.23e1), k_hf=(1/4.08e2)) plot(dicksontitration3, xval=dicksontitration3$delta_mass_titrant, what="pH", xlim=c(0,0.0025), ylim=c(3,8.2), newdevice=FALSE, col="blue") par(new=TRUE) plot(sam[,1], sam[,2], type="l", xlim=c(0,0.0025), ylim=c(3,8.2)) plot(dicksontitration3$pH - sam[,2]) # => no offset between the pH curves # => exactly the same curves! dicksonfit3 <- TAfit(aquaenv(t=25, S=35, SumBOH3=SumBOH3, SumH2SO4=SumH2SO4, SumHF=SumHF, k_w=4.32e-14, k_co2=1e-6, k_hco3=8.20e-10, k_boh3=1.78e-9, k_hso4=(1/1.23e1), k_hf=(1/4.08e2)), sam, conc_titrant, mass_sample, S_titrant=S_titrant, debug=TRUE, k_w=4.32e-14, k_co2=1e-6, k_hco3=8.20e-10, k_boh3=1.78e-9, k_hso4=(1/1.23e1), k_hf=(1/4.08e2)) dicksonfit3 # PERFECT fit! plot(sam[,1], sam[,2], xlim=c(0,0.0025), ylim=c(3,8.2), type="l") par(new=TRUE) plot(tit$delta_mass_titrant, calc, xlim=c(0,0.0025), ylim=c(3,8.2), type="l", col="red") ## End(Not run)## Not run: #################################### # Calculating TA from titration data #################################### #### 1.) proof of concept ########## #################################### #################################### # generate "data": S <- 35 t <- 15 SumCO2 <- 0.002000 TA <- 0.002200 initial_ae <- aquaenv(S=S, t=t, SumCO2=SumCO2, TA=TA) mass_sample <- 0.01 # the mass of the sample solution in kg mass_titrant <- 0.003 # the total mass of the added titrant solution # in kg conc_titrant <- 0.01 # the concentration of the titrant solution in # mol/kg-soln S_titrant <- 0.5 # the salinity of the titrant solution (the # salinity of a solution with a ionic strength # of 0.01 according to: # I = (19.924 S) / (1000 - 1.005 S) steps <- 20 # the amount of steps the mass of titrant is # added in type <- "HCl" ae <- titration(initial_ae, mass_sample, mass_titrant, conc_titrant, S_titrant, steps, type) plot(ae, ae$delta_mass_titrant, what="pH", newdevice=FALSE) # the input data for the TA fitting routine: a table with the added # mass of the titrant and the resulting free scale pH titcurve <- cbind(ae$delta_mass_titrant, ae$pH) # for the TA fitting procedure all total quantities except SumCO2 # (SumNH4, SumH2S, SumH3PO4, SumSiOH4, SumHNO3, SumHNO2, SumBOH3, # SumH2SO4, SumHF) need to be known. However, the latter three # can be calculated from salinity as it is done in this example. fit1 <- TAfit(initial_ae, titcurve, conc_titrant, mass_sample, S_titrant) fit1 # E (V) values as input variables: generate E values using # E0=0.4 V and the nernst equation tottitcurve <- convert(titcurve[,2], "pHscale", "free2sws", S=S, t=t) # (Nernst equation relates E to TOTAL [H+] (DOE1994, p.7, # ch.4, sop.3), BUT, if fluoride is present, its SWS, so # we use SWS! Etitcurve <- cbind(titcurve[,1], (0.4 - ((PhysChemConst$R/10) *initial_ae$T/PhysChemConst$F) *log(10^-tottitcurve))) # Nernst equation fit2 <- TAfit(initial_ae, Etitcurve, conc_titrant, mass_sample, S_titrant, Evals=TRUE, verbose=TRUE) fit2 # k_co2 fitting: one K_CO2 (k_co2) for the whole titration curve # is fitted, i.e. there is NO correction for K_CO2 changes due to # changing S due to mixing with the titrant fit3 <- TAfit(initial_ae, titcurve, conc_titrant, mass_sample, S_titrant, K_CO2fit=TRUE) fit3 # assume the titrant has the same salinity as the sample # (and is made up of natural seawater, i.e. containing SumBOH4, # SumH2SO4 and SumHF as functions of S), then the "right" K_CO2 # should be fitted i.e we do NOT give the argument S_titrant # and set the flag seawater_titrant to TRUE ae <- titration(initial_ae, mass_sample, mass_titrant, conc_titrant, steps=steps, type=type, seawater_titrant=TRUE) titcurve <- cbind(ae$delta_mass_titrant, ae$pH) fit4 <- TAfit(initial_ae, titcurve, conc_titrant, mass_sample, K_CO2fit=TRUE, seawater_titrant=TRUE) fit4 # fitting of TA, SumCO2, K_CO2 and E0 Etitcurve <- cbind(titcurve[,1], (0.4 - ((PhysChemConst$R/10) *initial_ae$T/PhysChemConst$F) *log(10^-titcurve[,2]))) fit5 <- TAfit(initial_ae, Etitcurve, conc_titrant, mass_sample, K_CO2fit=TRUE, seawater_titrant=TRUE, Evals=TRUE) fit5 # fitting of non equally spaced data: neqsptitcurve <- rbind(titcurve[1:9,], titcurve[11:20,]) fit6 <- TAfit(initial_ae, neqsptitcurve, conc_titrant, mass_sample, seawater_titrant=TRUE, equalspaced=FALSE) fit6 #add some "noise" on the generated data noisetitcurve <- titcurve * rnorm(length(titcurve), mean=1, sd=0.01) #one percent error possible plot(ae, ae$delta_mass_titrant, what="pH", type="l", col="red", xlim=c(0,0.003), ylim=c(3,8.1), newdevice=FALSE) par(new=TRUE) plot(noisetitcurve[,1],noisetitcurve[,2], type="l", xlim=c(0,0.003), ylim=c(3,8.1)) fit7 <- TAfit(initial_ae, noisetitcurve, conc_titrant, mass_sample, seawater_titrant=TRUE) fit7 # 2.) test with generated data from Dickson1981 # ################################################# ################################################# conc_titrant = 0.3 # mol/kg-soln mass_sample = 0.2 # kg S_titrant = 14.835 # is aequivalent to the ionic strength # of 0.3 mol/kg-soln SumBOH3 = 0.00042 # mol/kg-soln SumH2SO4 = 0.02824 # mol/kg-soln SumHF = 0.00007 # mol/kg-soln # convert mass of titrant from g to kg sam <- cbind(sample_dickson1981[,1]/1000, sample_dickson1981[,2]) dicksonfit <- TAfit(aquaenv(t=25, S=35, SumBOH3=SumBOH3, SumH2SO4=SumH2SO4, SumHF=SumHF), sam, conc_titrant, mass_sample, S_titrant=S_titrant, debug=TRUE) dicksonfit #TA Dickson1981: 0.00245 #SumCO2 Dickson1981: 0.00220 # => not exactly the same! why? # a.) does salinity correction (S_titrant) matter or not? ########################################################## # without salinity correction dicksontitration1 <- titration(aquaenv(t=25, S=35, SumCO2=0.00220, SumBOH3=SumBOH3, SumH2SO4=SumH2SO4, SumHF=SumHF, TA=0.00245), mass_sample=mass_sample, mass_titrant=0.0025, conc_titrant=conc_titrant, steps=50, type="HCl") # with salinity correction dicksontitration2 <- titration(aquaenv(t=25, S=35, SumCO2=0.00220, SumBOH3=SumBOH3, SumH2SO4=SumH2SO4, SumHF=SumHF, TA=0.00245), mass_sample=mass_sample, mass_titrant=0.0025, conc_titrant=conc_titrant, S_titrant=S_titrant, steps=50, type="HCl") plot(dicksontitration1, xval=dicksontitration1$delta_mass_titrant, what="pH", xlim=c(0,0.0025), ylim=c(3,8.2), newdevice=FALSE, col="red") par(new=TRUE) plot(dicksontitration2, xval=dicksontitration2$delta_mass_titrant, what="pH", xlim=c(0,0.0025), ylim=c(3,8.2), newdevice=FALSE, col="blue") par(new=TRUE) plot(sam[,1], sam[,2], type="l", xlim=c(0,0.0025), ylim=c(3,8.2)) # => salinity correction makes NO difference, because the relation # between total sample and added titrant is very large: # salinity only drops from 35 to 34.75105 #BUT: there is an offset between the "Dickson" curve and our curve: plot(dicksontitration2$pH - sam[,2]) # b.) does it get better if we fit K_CO2 as well? ################################################# dicksonfit2 <- TAfit(aquaenv(t=25, S=35, SumBOH3=SumBOH3, SumH2SO4=SumH2SO4, SumHF=SumHF), sam, conc_titrant, mass_sample, S_titrant=S_titrant, debug=TRUE, K_CO2fit=TRUE) dicksonfit2 #TA Dickson1981: 0.00245 #SumCO2 Dickson1981: 0.00220 # => yes it does, but it is not perfect yet! # c.) differing K values ######################### # Dickson uses fixed K values that are slightly different than ours dicksontitration3 <- titration(aquaenv(t=25, S=35, SumCO2=0.00220, SumBOH3=SumBOH3, SumH2SO4=SumH2SO4, SumHF=SumHF, TA=0.00245, k_w=4.32e-14, k_co2=1e-6, k_hco3=8.20e-10, k_boh3=1.78e-9, k_hso4=(1/1.23e1), k_hf=(1/4.08e2)), mass_sample=mass_sample, mass_titrant=0.0025, conc_titrant=conc_titrant, steps=50, type="HCl", S_titrant=S_titrant, k_w=4.32e-14, k_co2=1e-6, k_hco3=8.20e-10, k_boh3=1.78e-9, k_hso4=(1/1.23e1), k_hf=(1/4.08e2)) plot(dicksontitration3, xval=dicksontitration3$delta_mass_titrant, what="pH", xlim=c(0,0.0025), ylim=c(3,8.2), newdevice=FALSE, col="blue") par(new=TRUE) plot(sam[,1], sam[,2], type="l", xlim=c(0,0.0025), ylim=c(3,8.2)) plot(dicksontitration3$pH - sam[,2]) # => no offset between the pH curves # => exactly the same curves! dicksonfit3 <- TAfit(aquaenv(t=25, S=35, SumBOH3=SumBOH3, SumH2SO4=SumH2SO4, SumHF=SumHF, k_w=4.32e-14, k_co2=1e-6, k_hco3=8.20e-10, k_boh3=1.78e-9, k_hso4=(1/1.23e1), k_hf=(1/4.08e2)), sam, conc_titrant, mass_sample, S_titrant=S_titrant, debug=TRUE, k_w=4.32e-14, k_co2=1e-6, k_hco3=8.20e-10, k_boh3=1.78e-9, k_hso4=(1/1.23e1), k_hf=(1/4.08e2)) dicksonfit3 # PERFECT fit! plot(sam[,1], sam[,2], xlim=c(0,0.0025), ylim=c(3,8.2), type="l") par(new=TRUE) plot(tit$delta_mass_titrant, calc, xlim=c(0,0.0025), ylim=c(3,8.2), type="l", col="red") ## End(Not run)
PUBLIC list: a collection programming-technical constants
A list with elements:
Haccur |
accuracy for iterative (Follows2006) pH calculations (max. deviation in [H+]) |
Hstart |
start [H+] for an iterative pH calculation |
maxiter |
maximum number of iterations for iterative (Follows2006) pH calculation method as well as for the application of the standard R function uniroot |
unirootinterval |
the interval (in terms of [H+]) for pH calculation using the standard R function uniroot |
uniroottol |
the interval (in terms of [H+]) for pH calculation using the standard R function uniroot |
epsilon_fraction |
fraction of disturbance for the numerical calculation of derivatives of TA with respect to changes in the dissociation constants |
revelle_fraction |
fraction of disturbance for the numerical calculation of the revelle factor |
CO2 |
fugacity of CO2 in atm |
Andreas F. Hofmann. Maintained by Karline Soetaert ([email protected]).
PUBLIC function: creates an object of class aquaenv which contains a titration simulation
titration(aquaenv, mass_sample, mass_titrant, conc_titrant, S_titrant=NULL, steps, type="HCl", seawater_titrant=FALSE, k_w=NULL, k_co2=NULL, k_hco3=NULL, k_boh3=NULL, k_hso4=NULL, k_hf=NULL, k1k2="lueker", khf="dickson")titration(aquaenv, mass_sample, mass_titrant, conc_titrant, S_titrant=NULL, steps, type="HCl", seawater_titrant=FALSE, k_w=NULL, k_co2=NULL, k_hco3=NULL, k_boh3=NULL, k_hso4=NULL, k_hf=NULL, k1k2="lueker", khf="dickson")
aquaenv |
an object of type aquaenv: minimal definition, contains all information about the system: T, S, d, total concentrations of nutrients etc (Note that it is possible to give values for SumBOH4, SumHSO4, and SumHF in the sample other than the ones calculated from salinity) |
mass_sample |
the mass of the sample solution in kg |
mass_titrant |
the total mass of the added titrant solution in kg |
conc_titrant |
the concentration of the titrant solution in mol/kg-soln |
S_titrant |
the salinity of the titrant solution, if not supplied it is assumed that the titrant solution has the same salinity as the sample solution |
steps |
the amount of steps the mass of titrant is added in |
type |
the type of titrant: either "HCl" or "NaOH", default: "HCl" |
seawater_titrant |
is the titrant based on natural seawater? (does it contain SumBOH4, SumHSO4, and SumHF in the same proportions as seawater, i.e., correlated to S?); Note that you can only assume a seawater based titrant (i.e. SumBOH4, SumHSO4, and SumHF ~ S) or a water based titrant (i.e. SumBOH4, SumHSO4, and SumHF = 0). It is not possible to give values for SumBOH4, SumHSO4, and SumHF of the titrant. |
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) or "roy" (Roy1993a) for K\_CO2 and K\_HCO3. |
khf |
either "dickson" (default, Dickson1979a) or "perez" (Perez1987a) for K\_HF |
object of class aquaenv which contains a titration simulation
Andreas F. Hofmann. Maintained by Karline Soetaert ([email protected]).
## Not run: #################### # Titration with HCl #################### S <- 35 t <- 15 SumCO2 <- 0.003500 SumNH4 <- 0.000020 mass_sample <- 0.01 # the mass of the sample solution in kg mass_titrant <- 0.02 # the total mass of the added titrant solution in # kg conc_titrant <- 0.01 # the concentration of the titrant solution in # mol/kg-soln S_titrant <- 0.5 # the salinity of the titrant solution (the # salinity of a solution with a ionic strength of # 0.01 according to: I = (19.924 S) / (1000 - 1.005S) steps <- 50 # the amount of steps the mass of titrant is added # in type <- "HCl" pHstart <- 11.3 ae <- titration(aquaenv(S=S, t=t, SumCO2=SumCO2, SumNH4=SumNH4, pH=pHstart), mass_sample, mass_titrant, conc_titrant, S_titrant, steps, type) # plotting everything plot(ae, xval=ae$delta_mass_titrant, xlab="HCl solution added [kg]", mfrow=c(10,10)) # plotting selectively size <- c(12,8) #inches mfrow <- c(4,4) what <- c("TA", "pH", "CO2", "HCO3", "CO3", "BOH3", "BOH4", "OH", "NH4", "NH3", "H2SO4", "HSO4", "SO4", "HF", "F", "pCO2") plot(ae, xval=ae$delta_mass_titrant, xlab="HCl solution added [kg]", what=what, size=size, mfrow=mfrow) plot(ae, xval=ae$pH, xlab="free scale pH", what=what, size=size, mfrow=mfrow) # different x values plot(ae, xval=ae$delta_conc_titrant, xlab="[HCl] offset added [mol/kg-soln]", what=what, size=size, mfrow=mfrow) plot(ae, xval=ae$delta_moles_titrant, xlab="HCl added [mol]", what=what, size=size, mfrow=mfrow) # bjerrum plots par(mfrow=c(1,1)) plot(ae, bjerrum=TRUE) what <- c("CO2", "HCO3", "CO3") plot(ae, what=what, bjerrum=TRUE) plot(ae, what=what, bjerrum=TRUE, lwd=4, palette=c("cyan", "magenta", "yellow"), bg="gray", legendinset=0.1, legendposition="topleft") what <- c("CO2", "HCO3", "CO3", "BOH3", "BOH4", "OH", "NH4", "NH3", "H2SO4", "HSO4", "SO4", "HF", "F") plot(ae, what=what, bjerrum=TRUE, log=TRUE) plot(ae, what=what, bjerrum=TRUE, log=TRUE, ylim=c(-6,-1), legendinset=0, lwd=3, palette=c(1,3,4,5,6,colors()[seq(100,250,6)])) ## End(Not run)## Not run: #################### # Titration with HCl #################### S <- 35 t <- 15 SumCO2 <- 0.003500 SumNH4 <- 0.000020 mass_sample <- 0.01 # the mass of the sample solution in kg mass_titrant <- 0.02 # the total mass of the added titrant solution in # kg conc_titrant <- 0.01 # the concentration of the titrant solution in # mol/kg-soln S_titrant <- 0.5 # the salinity of the titrant solution (the # salinity of a solution with a ionic strength of # 0.01 according to: I = (19.924 S) / (1000 - 1.005S) steps <- 50 # the amount of steps the mass of titrant is added # in type <- "HCl" pHstart <- 11.3 ae <- titration(aquaenv(S=S, t=t, SumCO2=SumCO2, SumNH4=SumNH4, pH=pHstart), mass_sample, mass_titrant, conc_titrant, S_titrant, steps, type) # plotting everything plot(ae, xval=ae$delta_mass_titrant, xlab="HCl solution added [kg]", mfrow=c(10,10)) # plotting selectively size <- c(12,8) #inches mfrow <- c(4,4) what <- c("TA", "pH", "CO2", "HCO3", "CO3", "BOH3", "BOH4", "OH", "NH4", "NH3", "H2SO4", "HSO4", "SO4", "HF", "F", "pCO2") plot(ae, xval=ae$delta_mass_titrant, xlab="HCl solution added [kg]", what=what, size=size, mfrow=mfrow) plot(ae, xval=ae$pH, xlab="free scale pH", what=what, size=size, mfrow=mfrow) # different x values plot(ae, xval=ae$delta_conc_titrant, xlab="[HCl] offset added [mol/kg-soln]", what=what, size=size, mfrow=mfrow) plot(ae, xval=ae$delta_moles_titrant, xlab="HCl added [mol]", what=what, size=size, mfrow=mfrow) # bjerrum plots par(mfrow=c(1,1)) plot(ae, bjerrum=TRUE) what <- c("CO2", "HCO3", "CO3") plot(ae, what=what, bjerrum=TRUE) plot(ae, what=what, bjerrum=TRUE, lwd=4, palette=c("cyan", "magenta", "yellow"), bg="gray", legendinset=0.1, legendposition="topleft") what <- c("CO2", "HCO3", "CO3", "BOH3", "BOH4", "OH", "NH4", "NH3", "H2SO4", "HSO4", "SO4", "HF", "F") plot(ae, what=what, bjerrum=TRUE, log=TRUE) plot(ae, what=what, bjerrum=TRUE, log=TRUE, ylim=c(-6,-1), legendinset=0, lwd=3, palette=c(1,3,4,5,6,colors()[seq(100,250,6)])) ## End(Not run)
PUBLIC function: calculates the depth (in m) from the gauge pressure p (or the total pressure P) and the latitude (in degrees: -90 to 90) and the atmospheric pressure Pa (in bar)
watdepth(P=Pa, p=pmax(0, P-Pa), lat=0, Pa=1.013253)watdepth(P=Pa, p=pmax(0, P-Pa), lat=0, Pa=1.013253)
P |
total pressure in bar, standard: 1 atm (at the sea surface) |
p |
gauge pressure in bar (total pressure minus atmospheric pressure), standard: 0 (at the water surface) |
lat |
latitude in degrees: -90 to 90, standard: 0 |
Pa |
atmospheric pressure in bar, standard: 1 atm (at sea level) |
water depth d in meters
Andreas F. Hofmann. Maintained by Karline Soetaert ([email protected]).
Fofonoff1983
watdepth(100) plot(watdepth(1:100))watdepth(100) plot(watdepth(1:100))