Package: seacarb 3.4.1

James Orr

seacarb: Seawater Carbonate Chemistry

Calculates parameters of the seawater carbonate system and assists in design of ocean acidification perturbation experiments.

Authors:James Orr [aut, cre, cph], Jean-Pierre Gattuso [aut], Jean-Marie Epitalon [aut], Heloise Lavigne [aut], Bernard Gentili [ctb], Mathilde Hagens [ctb], Andreas Hofmann [ctb], Jens-Daniel Mueller [ctb], Aurélien Proye [ctb], James Rae [ctb], Karline Soetaert [ctb]

seacarb_3.4.1.tar.gz
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seacarb_3.4.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
seacarb/json (API)

# Install 'seacarb' in R:
install.packages('seacarb', repos = c('https://jpgattuso.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/jpgattuso/seacarb-git/issues

Datasets:
  • alkalinity - Example data file for function at
  • kfg - Variable for internal use
  • seacarb_test_P0 - Test data file (at P=0) to test the use of the carb function
  • seacarb_test_P300 - Test data file (at P=300) to test the use of the carb function
  • seaFET - Test seaFET data file

On CRAN:

Conda:

8.68 score 8 stars 4 packages 371 scripts 1.3k downloads 25 mentions 75 exports 4 dependencies

Last updated from:7603cf7fe1. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-develOK137
source / vignettesOK153
linux-releaseOK132
macos-releaseOK204
macos-oldrelOK145
windows-develOK103
windows-releaseOK90
windows-oldrelOK104
wasm-releaseOK81

Exports:ampbjerrumborbuffderivbufferbuffergenbuffesmbuffsunbuffzwgcarbcarbbcarbfulld2pderivnumeos2teos_chemeos2teos_geoerrorsf2pCO2fCO2insifHK0K1K1pK2K2pK2siK3pKbkconvKfKhsKnKsKsiKspaKspcKwoaOmp2dp2fCO2p2xCO2pCapCO2insiPcoeffsPcorrectpgaspHpHconvpHinsipHnbs2swspHslopepHspecpHsws2nbspmixppHpsipTArhosa2sp_chemsa2sp_geosf_calcsf_calibsirsir_bsir_fullsp2sa_chemsp2sa_geospeciationteos2eos_chemteos2eos_geothetatrisvapressx2pCO2

Dependencies:gswoceRcppSolveSAPHE

Readme and manuals

Help Manual

Help pageTopics
Example data file for function atalkalinity
pH value of the AMP bufferamp
Bjerrum plotbjerrum
Total boron concentration (mol/kg)bor
Analytic partial derivatives of the Bolin sensitivity Bebuffderiv
Buffer parameters of the seawater carbonate systembuffer
Buffer factors of the seawater carbonate system as defined by Hagens and Middelburg (2016)buffergen
Buffer capacities of the seawater carbonate system from Egleston et al. (2010), corrected and enhancedbuffesm
Bolin sensitivity and Revelle factor via the condensed common-template equation of Sundquist et al. (1979)buffsun
Bolin sensitivity and Revelle factor of the seawater carbonate system from Zeebe and Wolf-Gladrow (2001), corrected and enhancedbuffzwg
Parameters of the seawater carbonate systemcarb
Parameters of the seawater carbonate system with boron additioncarbb
Parameters of the seawater carbonate system - extension of carbcarbfull
Converts depth in meters to pressure in dbard2p
Numerical derivatives of seawater carbonate system variablesderivnum
Convert temperature and salinity from EOS-80 to TEOS-10eos2teos_chem
Convert temperature and salinity from EOS-80 to TEOS-10eos2teos_geo
Uncertainty propagation for computed marine carbonate system variableserrors
Converts the CO2 fugacity to CO2 partial pressuref2pCO2
fCO2 at in situ temperaturefCO2insi
Total activity coefficient for H+fH
Henry's constant mol/(kg/atm)K0
First dissociation constant of carbonic acid (mol/kg)K1
First dissociation constant of phosphoric acid (mol/kg)K1p
Second dissociation constant of carbonic acid (mol/kg)K2
Second dissociation constant of phosphoric acid (mol/kg)K2p
Second dissociation constant of Si(OH)4K2si
Third dissociation constant of phosphoric acid (mol/kg)K3p
Dissociation constant of boric acid (mol/kg)Kb
Conversion factors to change the pH scale of dissociation constantskconv
Equilibrium constant of hydrogen fluoride (mol/kg)Kf
variable for internal usekfg
Dissociation constant of hydrogen sulfide (mol/kg)Khs
Dissociation constant of ammonium (mol/kg)Kn
Stability constant of hydrogen sulfate (mol/kg)Ks
Dissociation constant of Si(OH)4Ksi
Solubility product of aragonite (mol/kg)Kspa
Solubility product of calcite (mol/kg)Kspc
Ion product of water (mol2/kg2)Kw
Perturbation of the seawater carbonate systemoa
Carbonate saturation state for magnesian calcitesOm
Converts pressure in dbar to depth in metersp2d
Converts pCO2 (partial pressure in CO2) into fCO2 (fugacity of CO2)p2fCO2
Converts partial pressure of CO2 to mole fraction of CO2p2xCO2
pCapCa
pCO2 at in situ temperaturepCO2insi
Coefficients used for pressure-correcting the equilibrium constantsPcoeffs
Pressure correction of equilibrium constantsPcorrect
pgaspgas
Potentiometric pHpH
Conversion of pHpHconv
pH at in situ temperature and pressurepHinsi
Converts pH from NBS to SWS scalepHnbs2sws
Slope of the calibration curve of a pH electrodepHslope
Calculates pHT from results of spectrophotometric measurementspHspec
Converts pH from SWS to NBS scalepHsws2nbs
pmixpmix
ppHppH
Molar ratio of CO2 released vs CaCO3 precipitatedpsi
pTApTA
Density of seawater (kg/m3)rho
From absolute to practical salinitysa2sp_chem
From absolute to practical salinitysa2sp_geo
Test data file (at P=0) to test the use of the carb functionseacarb_test_P0
Test data file (at P=300) to test the use of the carb functionseacarb_test_P300
Test seaFET data fileseaFET
Calculation of calibrated pH for seaFET sensorsf_calc
Calibration coefficients for seaFET sensorsf_calib
Parameters of the seawater carbonate system including the substrate-inhibitor-ratio (SIR)sir
Parameters of the seawater carbonate system with boron addition, including the substrate-inhibitor-ratio (SIR)sir_b
Parameters of the seawater carbonate system including the substrate-inhibitor-ratio (SIR) - extension of carbsir_full
From Practical to absolute salinitysp2sa_chem
From practical to absolute salinitysp2sa_geo
ionic forms as a function of pHspeciation
Convert temperature and salinity from TEOS-10 to EOS-80teos2eos_chem
Convert temperature and salinity from TEOS-10 to EOS-80teos2eos_geo
Potential temperature of seawatertheta
pH of TRIS buffertris
Computes vapor pressure of seawatervapress
Converts mole fraction to partial pressure of CO2x2pCO2