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

Documentation for package ‘diskImageR’ version 1.0.0

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