A function to analyze data from a MouseOx Mouse and Rat Pulse Oximeter.

To load the alpha version of mouseoxR, paste the following line into your R terminal. You only need to do this if the mouseoxR function isn't already loaded in your environment.

devtools::source_url("https://raw.githubusercontent.com/jsodicoff/mouseoxR/main/mouseox.R")

There is one function in the file, also named mouseoxR. It takes 2 required parameters and two optional ones.

• Required
  • file - the output file from your MouseOx device, or some type of Excel file.
  • time.points - a named list of time points to use in analysis.
• Optional
  • out.loc - the directory to save the analyzed data to, in csv format.
  • start.time - the time recorded in your output file that your time points are measured from.

Here's an example call:

output = mouseoxR(file = "/Downloads/mouseox_out.txt",
                  out.loc = "Desktop/data/",
                  start.time = 567,
                  time.points = list(
                    pre_stim = 0,
                    stim_1 = 500,
                    stim_2 = 1000,
                    post_stim = 1250,
                    complete = 2000
                   )

The output object contains a nested list of generated results. Here's the structure.

• output
  • data
  • time_plot
  • bar_plot
  • individual_plots
    • time
      • o2
      • heart
      • breath
      • pulse
    • bar
      • o2
      • heart
      • breath
      • pulse

data returns a data frame of average recorded values by time point. All other terminal elements include plots.

To access the elements, use list indexing! output[["data"]] returns the data frame. output[["time_plot"]] returns a combined plot of heart rate and blood pressure over time. output[["individual_plots"]][["bar"]][["o2"]] returns a bar plot of arterial oxygen saturation by time point. But!, output[["individual_plots"]][["bar"]] returns a list, which is not that helpful for viewing or saving.

Once you have opened a plot in the Plots panel, save it by hitting Export.

Merry measurement!