Package 'kgen'

Title: A Tool for Calculating Stoichiometric Equilibrium Constants (Ks) for Seawater
Description: A unified software package simultaneously implemented in 'Python', 'R', and 'Matlab' providing a uniform and internally-consistent way of calculating stoichiometric equilibrium constants in modern and palaeo seawater as a function of temperature, salinity, pressure and the concentration of magnesium, calcium, sulphate, and fluorine.
Authors: Dennis Mayk [aut, cre] (ORCID: <https://orcid.org/0000-0002-5017-1495>)
Maintainer: Dennis Mayk <[email protected]>
License: MIT + file LICENSE
Version: 1.1.1
Built: 2026-05-27 07:40:44 UTC
Source: https://github.com/cran/kgen

Help Index

Calculate fluorine

Description

Calculate fluorine

Usage

calc_fluorine(sal)

Arguments

sal

Salinity

Value

fluorine

References

From Dickson et al., 2007, Table 2, Note: Sal / 1.80655 = Chlorinity

Ionic strength after Dickson (1990a); see Dickson et al. (2007)

Description

Ionic strength after Dickson (1990a); see Dickson et al. (2007)

Usage

calc_ionic_strength(sal)

Arguments

sal

Salinity

Value

Ionic strength

Calculate a single equilibrium constant

Description

Calculate a single specified stoichiometric equilibrium constant at given temperature, salinity, pressure and the concentration of magnesium, calcium, sulphate, and fluorine.

Usage

calc_K(
  k,
  temp_c = 25,
  sal = 35,
  p_bar = NULL,
  magnesium = 0.0528171,
  calcium = 0.0102821,
  sulphate = NULL,
  fluorine = NULL,
  method = "r_polynomial"
)

calc_Ks(
  ks = NULL,
  temp_c = 25,
  sal = 35,
  p_bar = NULL,
  magnesium = 0.0528171,
  calcium = 0.0102821,
  sulphate = calc_sulphate(sal = sal),
  fluorine = calc_fluorine(sal = sal),
  method = "r_polynomial"
)

Arguments

k

K to be calculated
temp_c

Temperature (Celcius)
sal

Salinity
p_bar

Pressure (Bar) (optional)
magnesium

Magnesium concentration in mol/kgsw. Default is modern seawater (0.0528171). Should be the average magnesium concentration in seawater - a salinity correction is then applied to calculate the magnesium concentration in the sample.
calcium

Calcium concentration in mol/kgsw. Default is modern seawater (0.0102821). Should be the average calcium concentration in seawater - a salinity correction is then applied to calculate the calcium concentration in the sample.
sulphate

Sulphate concentration in mol/kgsw. Calculated from salinity if not given.
fluorine

Fluorine concentration in mol/kgsw. Calculated from salinity if not given.
method

string describing method which should be either 'myami', 'myami_polynomial', or 'r_polynomial' (Default: 'r_polynomial').
ks

character vectors of Ks to be calculated e.g., c("K0", "K1") (Default: NULL, calculate all Ks)

Value

A single K at given conditions

Data.table of multiple Ks at given conditions

Functions

  • calc_Ks(): Wrapper to calculate multiple stoichiometric equilibrium constants at given temperature, salinity, pressure and the concentration of magnesium, calcium, sulphate, and fluorine.

Author(s)

Dennis Mayk

Examples

# Calculate K1 at default conditions
calc_K("K1", temp_c = 25, sal = 35)

# Calculate K1 with pressure correction
calc_K("K1", temp_c = 25, sal = 35, p_bar = 100)
# Calculate all Ks at default conditions
calc_Ks(temp_c = 25, sal = 35)

# Calculate specific Ks
calc_Ks(ks = c("K1", "K2"), temp_c = 25, sal = 35)


# Parallel execution (requires future + future.apply packages)
if (requireNamespace("future", quietly = TRUE)) {
  future::plan(future::multisession,
    workers = future::availableCores() - 1
  )

  dt_list <- as.list(data.table::CJ(
    temp_c = seq_len(40),
    sal = 30:40,
    p_bar = 0:100,
    magnesium = seq(0, 0.06, by = 0.01),
    calcium = seq(0, 0.06, by = 0.01)
  ))

  res <- do.call(what = calc_Ks, args = dt_list)
  future::plan(future::sequential)
}

Calculate K0

Description

Calculate K0

Usage

calc_K0(coefficients, temp_c, sal)

Arguments

coefficients

Coefficients for K calculation
temp_c

Temperature (Celcius)
sal

Salinity

Value

K0

Calculate K1

Description

Calculate K1

Usage

calc_K1(coefficients, temp_c, sal)

Arguments

coefficients

Coefficients for K calculation
temp_c

Temperature (Celcius)
sal

Salinity

Value

K1

Calculate K2

Description

Calculate K2

Usage

calc_K2(coefficients, temp_c, sal)

Arguments

coefficients

Coefficients for K calculation
temp_c

Temperature (Celcius)
sal

Salinity

Value

K2

Calculate KB

Description

Calculate KB

Usage

calc_KB(coefficients, temp_c, sal)

Arguments

coefficients

Coefficients for K calculation
temp_c

Temperature (Celcius)
sal

Salinity

Value

KB

Calculate KF

Description

Calculate KF

Usage

calc_KF(coefficients, temp_c, sal)

Arguments

coefficients

Coefficients for K calculation
temp_c

Temperature (Celcius)
sal

Salinity

Value

KF

Calculate KP1

Description

Calculate KP1

Usage

calc_KP1(coefficients, temp_c, sal)

Arguments

coefficients

Coefficients for K calculation
temp_c

Temperature (Celcius)
sal

Salinity

Value

KP1

Calculate KP2

Description

Calculate KP2

Usage

calc_KP2(coefficients, temp_c, sal)

Arguments

coefficients

Coefficients for K calculation
temp_c

Temperature (Celcius)
sal

Salinity

Value

KP2

Calculate KP3

Description

Calculate KP3

Usage

calc_KP3(coefficients, temp_c, sal)

Arguments

coefficients

Coefficients for K calculation
temp_c

Temperature (Celcius)
sal

Salinity

Value

KP3

Calculate KS

Description

Calculate KS

Usage

calc_KS(coefficients, temp_c, sal)

Arguments

coefficients

Coefficients for K calculation
temp_c

Temperature (Celcius)
sal

Salinity

Value

KS

Calculate KSi

Description

Calculate KSi

Usage

calc_KSi(coefficients, temp_c, sal)

Arguments

coefficients

Coefficients for K calculation
temp_c

Temperature (Celcius)
sal

Salinity

Value

KSi

Calculate Ksp

Description

Calculate Ksp

Usage

calc_Ksp(coefficients, temp_c, sal)

Arguments

coefficients

Coefficients for K calculation
temp_c

Temperature (Celcius)
sal

Salinity

Value

Ksp

Calculate KW

Description

Calculate KW

Usage

calc_KW(coefficients, temp_c, sal)

Arguments

coefficients

Coefficients for K calculation
temp_c

Temperature (Celcius)
sal

Salinity

Value

KW

Calculate pressure correction factor for Ks

Description

Calculate pressure correction factor for Ks

Usage

calc_pc(coefficients, temp_c, p_bar)

Arguments

coefficients

Coefficients for K calculation
temp_c

Temperature (Celcius)
p_bar

Pressure (Bar)

Value

Pressure correction factor

References

From Millero et al. (2007, doi:10.1021/cr0503557), Eqns 38-40

Calculate pressure correction factor

Description

Calculate pressure correction factor for a specified equilibrium constant.

Usage

calc_pressure_correction(k, temp_c, p_bar)

Arguments

k

K to be calculated
temp_c

Temperature (Celcius)
p_bar

Pressure (Bar)

Value

pressure correction factor

Author(s)

Dennis Mayk

Examples

calc_pressure_correction("K1", temp_c = 25, p_bar = 100)

Kgen seawater composition correction function

Description

Kgen seawater composition correction function

Usage

calc_seawater_correction(
  k,
  sal,
  temp_c,
  magnesium = 0.0528171,
  calcium = 0.0102821,
  method = "r_polynomial"
)

Arguments

k

K to be calculated
sal

Salinity
temp_c

Temperature (Celcius)
magnesium

Magnesium concentration in mol/kgsw. Default is modern seawater (0.0528171). Should be the average magnesium concentration in seawater - a salinity correction is then applied to calculate the magnesium concentration in the sample.
calcium

Calcium concentration in mol/kgsw. Default is modern seawater (0.0102821). Should be the average calcium concentration in seawater - a salinity correction is then applied to calculate the calcium concentration in the sample.
method

string describing method which should be either 'myami', 'myami_polynomial', or 'r_polynomial' (Default: 'r_polynomial').

Value

list of seawater correction factors

Author(s)

Dennis Mayk

Examples

calc_seawater_correction("K1", sal = 35, temp_c = 25)

Calculate sulphate

Description

Calculate sulphate

Usage

calc_sulphate(sal)

Arguments

sal

Salinity

Value

sulphate

References

From Dickson et al., 2007, Table 2, Note: Sal / 1.80655 = Chlorinity

List of all functions

Description

List of all functions

Usage

K_fns

Format

An object of class list of length 13.

Kgen R polynomial function

Description

Kgen R polynomial function

Usage

kgen_poly(sal, temp_c, magnesium = 0.0528171, calcium = 0.0102821)

Arguments

sal

Salinity
temp_c

Temperature (Celcius)
magnesium

Magnesium concentration in mol/kgsw. Default is modern seawater (0.0528171). Should be the average magnesium concentration in seawater - a salinity correction is then applied to calculate the magnesium concentration in the sample.
calcium

Calcium concentration in mol/kgsw. Default is modern seawater (0.0102821). Should be the average calcium concentration in seawater - a salinity correction is then applied to calculate the calcium concentration in the sample.

Author(s)

Dennis Mayk