R: Bjerrum plot

bjerrum {seacarb} | R Documentation

## Bjerrum plot

### Description

Plot the concentration of the various ionic forms of a molecule as a function of pH

### Usage

    bjerrum(K1=K1(), K2=NULL, K3=NULL, phmin=2, phmax=12, by=0.1, conc=1,
         type="l", col="black",  ylab="Concentration (mol/kg)", add=FALSE, ...)

### Arguments

`K1` | First dissociation constant
`K2` | Second dissociation constant, default is NULL
`K3` | Third dissociation constant, default is NULL
`phmin` | Minimum pH value, default is 2
`phmax` | Maximum pH value, default is 12
`by` | Increment on the pH axis, default is 0.1
`conc` | concentration of molecule, default is 1
`type` | Type of plot, default is line
`col` | Color of plot, default is black
`ylab` | Label of Y axis, default is (mol/kg)
`add` | false:start new, true: add to current, default is false
`...` | Graphical parameters (see `par`) and any further arguments of plot, typically `plot.default`, may also be supplied as arguments to this function. Hence, the high-level graphics control arguments described under `par` and the arguments to `title` may be supplied to this function.

### Details

Note that the concentration is plotted in mol/kg only if conc is given is mol/kg

### Author(s)

Karline Soetaert K.Soetaert@nioo.knaw.nl

### References

Zeebe, R. E. and Wolf-Gladrow D. A., 2001 CO2 in seawater: equilibrium, kinetics, isotopes. Amsterdam: Elsevier, 346 pp.

### See Also

`matplot`, `par`, `speciation`.

### Examples

    ## Plot the bjerrum plot for the carbonate system using the default values
    bjerrum(K1(),K2(),main="DIC speciation",lwd=2)
    abline(v=-log10(K1()),col="grey")
    mtext(side=3,at=-log10(K1()),"pK1")
    abline(v=-log10(K2()),col="grey")
    mtext(side=3,at=-log10(K2()),"pK2")
    legend("left",lty=1:3,lwd=2,legend=c(expression(CO[2]),expression(HCO[3]^"-"),
    	expression(CO[3]^"2-")))

    ## Plot the bjerrum plot for phosphate using the default values
    bjerrum(K1p(),K2p(),K3p(),main="phosphate speciation",lwd=2)
    legend("left",lty=1:4,lwd=2,legend=c(expression(H[3]~PO[4]),
    	expression(H[2]~PO[4]^"-"),
    expression(HPO[4]^"2-"),expression(PO[4]^"3-")))

    ## Plot the bjerrum plot for the carbonate system using the values other
    ##	than the default ones, showing the effect of temperature
    bjerrum(K1(T=25,S=35),K2(T=25,S=35),conc=1.3,main="effect of temperature" )
    bjerrum(K1(T=0,S=35),K2(T=0,S=35),conc=1.3,add=TRUE,col="red")
    legend("left",lty=1,col=c("black","red"),legend=c("T=25 oC","T=0 oC"))
    legend("right",lty=1:3,legend=c(expression(CO[2]),expression(HCO[3]^"-"),
    	expression(CO[3]^"2-")))

    ## Plot the bjerrum plot for the carbonate system using the values other
    ##	than the default ones, showing the effect of salinity
    bjerrum(K1(T=25,S=35),K2(T=25,S=35),conc=1.3,main="effect of salinity" )
    bjerrum(K1(T=25,S=5),K2(T=25,S=5),conc=1.3,add=TRUE,col="blue")
    legend("left",lty=1,col=c("black","blue"),legend=c("S=35","S=5"))
    legend("right",lty=1:3,legend=c(expression(CO[2]),expression(HCO[3]^"-"),
    	expression(CO[3]^"2-")))

    ## Plot the bjerrum plot for the carbonate system using the values other
    ##	than the default ones, showing the effect of pressure
    bjerrum(K1(P=0),K2(P=0),conc=1.3,main="effect of pressure" )
    bjerrum(K1(P=300),K2(P=300),conc=1.3,add=TRUE,col="green")
    legend("left",lty=1,col=c("black","green"),legend=c("P=0","P=300"),title="atm")
    legend("right",lty=1:3,legend=c(expression(CO[2]),expression(HCO[3]^"-"),
    	expression(CO[3]^"2-")))

[Package seacarb version 3.1.1 Index]