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