carb {seacarb}R Documentation

Parameters of the seawater carbonate system

Description

Returns parameters of the seawater carbonate system.

Usage

carb(flag, var1, var2, S=35, T=25, P=0, Pt=0, Sit=0, k1k2="l", kf="pf", pHscale="T")

Arguments

flag select the couple of variables available. The flags which can be used are:
flag = 1 pH and CO2 given
flag = 2 CO2 and HCO3 given
flag = 3 CO2 and CO3 given
flag = 4 CO2 and ALK given
flag = 5 CO2 and DIC given
flag = 6 pH and HCO3 given
flag = 7 pH and CO3 given
flag = 8 pH and ALK given
flag = 9 pH and DIC given
flag = 10 HCO3 and CO3 given
flag = 11 HCO3 and ALK given
flag = 12 HCO3 and DIC given
flag = 13 CO3 and ALK given
flag = 14 CO3 and DIC given
flag = 15 ALK and DIC given
flag = 21 pCO2 and pH given
flag = 22 pCO2 and HCO3 given
flag = 23 pCO2 and CO3 given
flag = 24 pCO2 and ALK given
flag = 25 pCO2 and DIC given
var1 enter value of the first variable in mol/kg, except for pH and for pCO2 in μatm
var2 enter value of the second variable in mol/kg, except for pH
S Salinity
T Temperature in degrees Celsius
P Hydrostatic pressure in bar (surface = 0)
Pt Concentration of total phosphate in mol/kg
Sit Concentration of total silicate in mol/kg
k1k2 "l" for using K1 and K2 from Lueker et al. and "r" for using K1 and K2 from Roy et al. , default is "l"
kf "pf" for using Kf from Perez and Fraga (1987) and "dg" for using Kf from Dickson and Goyet (1979), default is "pf"
pHscale choice of pH scale: "T" for the total scale, "F" for the free scale and "SWS" for using the seawater scale, default is "T" (total scale)

Details

Note that the arguments can be given as a unique number or as vectors. If the lengths of the vectors are different, the longer vector is retained and only the first value of the other vectors is used. It can therefore be critical to use vectors of the same length. For instance, to compute parameters from one couple of variable for a range of temperatures, a vector with temperatures required can be given in enter and other arguments can be completed be one variable this variable will be used for each temperatures.

Value

The function returns a data frame containing the following columns:

S Salinity
T Temperature in degrees Celsius
P Pressure in bar
pH pH
CO2 CO2 concentration (mol/kg)
pCO2 pCO2, CO2 partial pressure (μatm)
fCO2 fCO2, CO2 fugacity (μatm)
HCO3 HCO3 concentration (mol/kg)
CO3 CO3 concentration (mol/kg)
DIC DIC concentration (mol/kg)
ALK ALK, total alkalinity (mol/kg)
OmegaAragonite Omega aragonite, aragonite saturation state
OmegaCalcite Omega calcite, calcite saturation state

Author(s)

Héloïse Lavigne, Aurélien Proye and Jean-Pierre Gattuso gattuso@obs-vlfr.fr

References

Dickson A. G., Sabine C. L. and Christian J. R., 2007 Guide to best practices for ocean CO2 measurements. PICES Special Publication 3, 1-191.

Lueker, T. J. Dickson, A. G. and Keeling, C. D. 2000 Ocean pCO2 calculated from dissolved inorganic carbon, alkalinity, and equations for K1 and K2: validation based on laboratory measurements of CO2 in gas and seawater at equilibrium. Marine Chemistry 70 105-119.

Roy, R. N. Roy, L. N. Vogel, K. M. Porter-Moore, C. Pearson, T. Good C. E., Millero F. J. and Campbell D. M., 1993. The dissociation constants of carbonic acid in seawater at salinities 5 to 45 and temperatures 0 to 45°C. Marine Chemistry 44, 249-267.

Perez, F. F. and Fraga, F. 1987 Association constant of fluoride and hydrogen ions in seawater. Marine Chemistry 21, 161-168.

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

Examples


## With a couple of variables
carb(flag=8, var1=8.2, var2=0.00234, S=35, T=25, P=0, Pt=0, Sit=0, pHscale="T", kf="pf", k1k2="l")

## Using vectors as arguments
flag <- c(8, 2, 8)
var1 <- c(8.2, 7.477544e-06, 8.2)
var2 <- c(0.002343955, 0.001649802, 2400e-6)
S <- c(35, 35, 30)
T <- c(25, 25, 30)
P <- c(0, 0, 0)
Pt <- c(0, 0, 0)
Sit <- c(0, 0, 0)
kf <- c("pf", "pf", "pf")
k1k2 <- c("l", "l", "l")
pHscale <- c("T", "T", "T")
carb(flag=flag, var1=var1, var2=var2, S=S, T=T, P=P, Pt=Pt, Sit=Sit, kf=kf, k1k2=k1k2, pHscale=pHscale)

## Test with all flags 
flag <- c(1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 21, 22, 23, 24, 25)
var1 <- c(8.200000, 7.477544e-06, 7.477544e-06, 7.477544e-06, 7.477544e-06, 8.2, 
8.2, 8.2, 8.2, 0.001685024, 0.001685024, 0.001685024,  0.0002888382, 0.0002888382, 
0.002391252, 264.2008, 264.2008, 264.2008, 264.2008, 264.2008)
var2 <- c(7.477544e-06, 0.001685024, 0.0002888382, 0.002391252, 0.001981340, 
0.001685024, 0.0002888382, 0.002391252, 0.001981340, 0.0002888382, 0.002391252, 
0.001981340,  0.002391252, 0.001981340, 0.001981340, 8.2, 0.001685024, 0.0002888382, 
0.002391252, 0.001981340)
carb(flag=flag, var1=var1, var2=var2)

## Test using a data frame 
data(seacarb_test)
tab <- seacarb_test

## method 1 using the column numbers
carb(flag=tab[[1]], var1=tab[[2]], var2=tab[[3]], S=tab[[4]], T=tab[[5]], P=tab[[6]], 
Sit=tab[[7]], Pt=tab[[8]])

## method 2 using the column names
carb(flag=tab$flag, var1=tab$var1, var2=tab$var2, S=tab$S, T=tab$T, P=tab$P, Sit=tab$Sit, 
Pt=tab$Pt)


[Package seacarb version 2.1.2 Index]