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'seacarbx' Manual

Description

seacarbx is a seacarb extension written in R, which enables to use seacarb (Gattuso et al., 2019) for deep-time carbonate system calculations or for culturing studies carried out in seawater with modified [Mg2+] and [Ca2+]. For this, the functions carb, K0, K1, K2, Ks, Kw, Kb, Kspa, and Kspc were modfied to account for the effect of seawater [Mg2+] and [Ca2+] on the dissociation constants of carbonic and boric acid. Their names are based on the original names, and suffixed with a ‘x’. In addition to the modified functions, seacarbx contains MyAMI that are tabulated parameters defining the temperature and salinity dependencies of the conditional equilibrium constants for [Mg2+] and [Ca2+] in the range 1–60 mM (from Hain et al., 2015, and revised by Hain et al., 2018), as well as a function for bilinear interpolation.

Prerequisites

seacarbx requires a base R installation (recommended with an installation of RStudio) and an installation of the package seacarb. You may install it with:

install.packages("seacarb")

Then load the required library:

library(seacarb)

Usage

First, load the rda file, which contains the functions and the tabulated MYAMI data:

load("~/path-to-your-directory/seacarbx.rda")

The syntax is basically the same as for the original functions, except the additional input parameters [Mg2+] and [Ca2+] (in mol/L), which are, as an example, called like this:

carbx(flag=1, var1=8.1, var2=12e-6, S=35, T=25, ca=10.2821e-03, mg=52.8171e-03,...)

NOTE that the argument k1k2 is not accessible for the functions carbx, K1x and K2x, but the empirical equilibrium constants from Lueker et al. (2000) are used in the MyAMI model (Hain et al., 2015).

Every time that the input variables [Ca2+] and/or [Mg2+] are changed in the seacarbx functions, the bilinear interpolation function lookup_fn is called automatically, which computes accurate parameters from the MyAMI lookup table. lookup_fn can also be used as a separate lookup function to calculate the MyAMI parameters for a given set of [Mg2+] and [Ca2+], which can optionally be saved as a text file ("MyAMI_param_output.txt") to your working directory by using the print argument:

lookup_fn(ca=10.2821e-03, mg=52.8171e-03, print=TRUE)

As a side note, if the output file should be saved to another folder, the working directory must be changed by:

setwd("~/path-to-your-directory")

To retrieve the current working directory, call:

getwd()

Functions

  • carbx() is the equivalent to the function carb(), and returns parameters of the seawater carbonate system, based on a given pair of known carbonate system variables.

  • K0x() is the equivalent to the function K0(), and returns Henry’s constant mol/(kg/atm).

  • K1x() is the equivalent to the function K1(), and returns the first dissociation constant of carbonic acid (mol/kg).

  • K2x() is the equivalent to the function K2(), and returns the second dissociation constant of carbonic acid (mol/kg).

  • Ksx() is the equivalent to the function Ks(), and returns the stability constant of hydrogen sulfate (mol/kg).

  • Kwx() is the equivalent to the function Kw(), and returns the ion product of water (mol2/kg2).

  • Kbx() is the equivalent to the function Kb(), and returns the dissociation constant of boric acid (mol/kg).

  • Kspax() is the equivalent to the function Kspa(), and returns the solubility product of aragonite (mol/kg).

  • Kspcx() is the equivalent to the function Kspc(), and returns the solubility product of calcite (mol/kg).

For more details, we refer here to the manual of the original seacarb package.

  • lookup_fn() takes the arguments ca and mg and interpolates the MyAMI parameters between tabulated data from the lookup table myami.