Calculate dissolved gas concentrations from raw MIMS
(Membrane Inlet Mass Spectrometer, Bay Instruments) signal data.
Use mimsy() on a formatted CSV file to return dissolved gas
concentrations (mg and microMole) and ratios of N2, O2, Ar based on
gas solubility at temperature, pressure, and salinity. See references
Benson and Krause (1984)
"Calculate MIMS dissolved gas concentrations without getting a headache."
mimsy is a data analysis package that transforms raw MIMS (Membrane Inlet Mass Spectrometer) signal data into dissolved gas concentration readings using standard solubility equations.
mimsy is designed to be simple and accessible for non-R users.
Click on the Get started tab above to read through the detailed how-to guide.
# Load data into Rdata <- read.csv(file = "data.csv", header = TRUE, stringsAsFactors = FALSE)# Run the mimsy functionresults <- mimsy(data, baromet.press = 977.2, units = "hPa")# Save the resultsmimsy.save(results, file = "results.xlsx") # To Excel filesave(results, file = "results.RData") # To RData file# Done! :)
# Pull package from github using devtoolslibrary(devtools)install_github("michelleckelly/mimsy", dependencies = "Depends")# Load package into your R environmentlibrary(mimsy)
To see the recommended citation for this package, run
citation("mimsy") in the R console:
mimsy holds no official endorsement from the Bay Instruments company. This software is preliminary and subject to revision. By the use of this software, the user assumes their own responsibility for ensuring the accuracy of the program.
Garcia, H., and L. Gordon (1992), Oxygen solubility in seawater: Better fitting equations. Limnology and Oceanography, 37(6). https://doi.org/10.4319/lo.19184.108.40.2067
Benson, B. B. & Krause, D. (1984). The concentration and isotopic fractionation of oxygen dissolved in freshwater and seawater in equilibrium with the atmosphere. Limnology and Oceanography, 29(3), 620-632. https://doi.org/10.4319/lo.1984.29.3.0620
Stull, D. R. (1947). Vapor Pressure of Pure Substances. Organic and Inorganic Compounds. Industrial & Engineering Chemistry, 39(4), 517-540. https://doi.org/10.1021/ie50448a022
Hamme, R. C. & Emerson, S. R. (2004). The solubility of neon, nitrogen and argon in distilled water and seawater. Deep-Sea Research I, 51(11), 1517-1528. https://doi.org/10.1016/j.dsr.2004.06.009
README.mdupdated with full workflow example
datainput as a dataframe, no longer internally loads from file path
vignettes/mimsy.Rmdrewritten for clarity and screenshots added
mimsy()std.temps pulled from CollectionTemps column of Group 1 Standards, std.temps input argument now depreciated
mimsy()now indicates the standard temperatures used in an output message to the user
mimsy()now checks that the length of std.temps vector is appropriate
mimsy.save()to rely on non-depreciated forms of
vignettes/mimsy.Rmdnow includes directions to save output as RData file
README.mdinstall instructions updated to fix bug where depenencies weren't downloading properly.
vignettes/mimsy.Rmdquick start guide for package.
NEWS.mdfile to track changes to the package.