# A Pipeline to Analyze Resistance and Tolerance from Drug Disk Diffusion Assays

## Documentation for package ‘diskImageR’ version 1.0.0

- DESCRIPTION file.

## Help Pages

addType | Add factor column
aggregateData | Averages photographs of the same type
calcMIC | Convert RAD to MIC based on built-in or provided parameters or datasets
createDataframe | Dataframe creation
IJMacro | Run an imageJ analysis macro on the folder that contains the photograph to be analyzed
maxLik | Maximum Likelihood Inference
oneParamPlot | Used to plot a single parameter
plotRaw | Used to plot the results of the imageJ analysis
readExistingDF | Read in an existing dataframe using the tcltk interface
readInExistingIJ | Used to read in existing imageJ analyses
saveMLParam | Save maximum likelihood output
threeParamPlot | Used to plot the RAD, slope and FoG parameter results
twoParamPlot | Used to plot the RAD and FoG results