michelleckelly/mimsy

Calculate MIMS dissolved gas concentrations without getting a headache

mimsy

"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 (mg, micromole) of N2, O2, and Ar based on gas solubility at temperature, pressure, and salinity. Supports both single and dual-temperature standard calibration MIMS setups with either one or two water baths, and uses a drift correction method to calculate gas concentration values. mimsy is designed to be simple and accessible for non-R users.

This package incorporates portions of the MIMS R functions written by Hilary Madinger and Bob Hall, available on Hilary Madinger's website.

Click on the Get started tab above to read through the 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

# Download package
install.packages("mimsy")

# 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 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

mimsy's Issues

Newer MIMS machines are set up to output a "99" column which just shows a reading of the internal pressure inside the machine when you're taking a sample. The script will run totally fine even if you don't have that column in your MIMS output.

Newer MIMS machines are set up to output a "99" column which just shows a reading of the internal pressure inside the machine when you're taking a sample. The script will run totally fine even if you don't have that column in your MIMS output.

I'll go ahead and remove the 99 column from the example on the Get Started page of the website, since it's definitely going to confuse people! Thanks so much for pointing that out!!

Originally posted by @michelleckelly in #5 (comment)

Add support for single-point temperature standard in `mimsy()`

Single-point temperature calibration is not currently supported. Most of the architecture to support single-temperature can be borrowed from the dual-temperature portion of the script, but will need ground-truthing against example Excel sheets. It may also be advantageous to write this as an internal function.

Add user-input checks to `mimsy()`

Check user input CSV file for correct column names, barometric pressure units, and consistent standard temperatures. Return useful warning message if errors detected.

2 point temperature calibration

Michelle, Thank you for clarifying the 99 column issue. I also have a question about the requirement for 2 temperatures for the standard calibration. Is that also with newer MIMS? Our temperature is the same throughout a run on our output. We are very excited about your program and hope it works for us!

Add support for background corrections in `mimsy()`

Background corrections are currently not supported in mimsy(). This feature will require:

1. Examining how background corrections are performed (reading MIMS protocol, reviewing example Excel datasheets)
2. Determining the best way to prompt the user for background correction values
3. Implementing the feature without causing a breaking change

question

Michelle, What is the column of data labeled 99? It is not present in the output from my MIMS

one-point temp results

When I run MIMSY using the one-temp standard, only group 1 results are shown in the output. It does appear that the calibration factors and drift correction factors for each group are presented. When using the two-temp standards all group results display fine. Is there something that I am missing in the code to get all group results to display?