Calculate MIMS Dissolved Gas Concentrations Without Getting a Headache

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) , Garcia and Gordon (1992) , Stull (1947) , and Hamme and Emerson (2004) for more information. Easily save the output to a nicely-formatted multi-tab 'Excel' workbook with mimsy.save(). Supports dual-temperature standard calibration for dual-bath MIMS setups.


Travis CI Build Status Lifecycle: maturing

"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.

Crunch data in 5 lines of code or less

# Load data into R
data <- read.csv(file = "data.csv", header = TRUE, stringsAsFactors = FALSE)
 
# Run the mimsy function
results <- mimsy(data, baromet.press = 977.2, units = "hPa")
 
# Save the results
mimsy.save(results, file = "results.xlsx") # To Excel file
save(results, file = "results.RData") # To RData file
 
# Done! :)

Installation instructions

# Pull package from github using devtools
library(devtools)
install_github("michelleckelly/mimsy", dependencies = "Depends")
 
# Load package into your R environment
library(mimsy)

Recommended citation

To see the recommended citation for this package, run citation("mimsy") in the R console:

citation("mimsy")

Disclaimer

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.

References

Garcia, H., and L. Gordon (1992), Oxygen solubility in seawater: Better fitting equations. Limnology and Oceanography, 37(6). https://doi.org/10.4319/lo.1992.37.6.1307

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

News

mimsy 0.4.2

Minor changes

  • Preparation for submission to CRAN
  • README.md updated with full workflow example
  • logo updated

mimsy 0.4.1

Major changes

  • mimsy() takes data input as a dataframe, no longer internally loads from file path

Minor changes

  • vignettes/mimsy.Rmd rewritten for clarity and screenshots added

mimsy 0.3.1

Major changes

  • mimsy() std.temps pulled from CollectionTemps column of Group 1 Standards, std.temps input argument now depreciated

Minor changes

  • 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

Bug fixes

  • update mimsy.save() to rely on non-depreciated forms of openxlsx functions

mimsy 0.2.1

Minor changes

  • vignettes/mimsy.Rmd now includes directions to save output as RData file

Bug fixes

  • vignettes/mimsy.Rmd and README.md install instructions updated to fix bug where depenencies weren't downloading properly.

mimsy 0.2.0

Major changes

  • Added vignettes/mimsy.Rmd quick start guide for package.
  • Added NEWS.md file to track changes to the package.

Reference manual

It appears you don't have a PDF plugin for this browser. You can click here to download the reference manual.

install.packages("mimsy")

0.4.2 by Michelle C. Kelly, 6 months ago


https://github.com/michelleckelly/mimsy, https://michelleckelly.github.io/mimsy/


Report a bug at https://github.com/michelleckelly/mimsy/issues


Browse source code at https://github.com/cran/mimsy


Authors: Michelle C. Kelly [aut, cre]


Documentation:   PDF Manual  


MIT + file LICENSE license


Imports dplyr, magrittr, lubridate, openxlsx, utils

Suggests knitr, rmarkdown


See at CRAN