The hardware and bandwidth for this mirror is donated by dogado GmbH, the Webhosting and Full Service-Cloud Provider. Check out our Wordpress Tutorial.
If you wish to report a bug, or if you are interested in having us mirror your free-software or open-source project, please feel free to contact us at mirror[@]dogado.de.

Type: Package
Title: A Tool for Calculating Stoichiometric Equilibrium Constants (Ks) for Seawater
Version: 0.3.1
License: MIT + file LICENSE
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.
Encoding: UTF-8
Depends: R (≥ 4.0)
Imports: rjson (≥ 0.2.21), reticulate (≥ 1.26), rappdirs (≥ 0.3.3), checkmate (≥ 2.1.0), pbapply (≥ 1.7.0), data.table (≥ 1.14.6)
Suggests: testthat (≥ 3.0.0)
RoxygenNote: 7.2.3
Config/testthat/edition: 3
NeedsCompilation: no
Packaged: 2023-12-19 13:40:43 UTC; dm807cam
Author: Dennis Mayk ORCID iD [aut, cre]
Maintainer: Dennis Mayk <dm807@cantab.ac.uk>
Repository: CRAN
Date/Publication: 2023-12-19 14:10:02 UTC

kgen: 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.

Author(s)

Maintainer: Dennis Mayk dm807@cantab.ac.uk (ORCID)

List of all functions

Description

List of all functions

Usage

K_fns

Format

An object of class list of length 13.

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 = NULL,
  fluorine = NULL,
  method = "r_polynomial"
)

calc_all_Ks(
  temp_c = 25,
  sal = 35,
  p_bar = NULL,
  magnesium = 0.0528171,
  calcium = 0.0102821,
  sulphate = NULL,
  fluorine = NULL,
  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. If None, modern is assumed (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. If None, modern is assumed (0.0102821). Should be the average calcium concentration in seawater - a salinity correction is then applied to calculate the magnesium 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

Data.table of all Ks at given conditions

Functions

Author(s)

Dennis Mayk

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 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 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 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 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

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. If None, modern is assumed (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. If None, modern is assumed (0.0102821). Should be the average calcium concentration in seawater - a salinity correction is then applied to calculate the magnesium 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

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

Install MyAMI from pypi

Description

Function to install pymyami in a default location.

Usage

install_pymyami()

Check if OS is Linux

Description

Check if OS is Linux

Usage

is_linux()

Check if OS is OSX

Description

Check if OS is OSX

Usage

is_osx()

Check if OS is Windows

Description

Check if OS is Windows

Usage

is_windows()

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. If None, modern is assumed (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. If None, modern is assumed (0.0102821). Should be the average calcium concentration in seawater - a salinity correction is then applied to calculate the magnesium concentration in the sample.

Author(s)

Dennis Mayk

Check if miniconda exists

Description

Check if miniconda exists

Usage

mc_exists(path = miniconda_path())

Arguments

path

Path to miniconda

Check if miniconda is installed

Description

Check if miniconda is installed

Usage

miniconda_conda(path = miniconda_path())

Arguments

path

Path to miniconda

Get miniconda path

Description

Get miniconda path

Usage

miniconda_path()

Get miniconda default path

Description

Get miniconda default path

Usage

miniconda_path_default()

Check if pymyami is installed

Description

Check if pymyami is installed

Usage

pymyami_exists()

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
Health stats visible at Monitor.