calcMIC

the short name you have been using for the project.

projectName

specify whether the dataset to use is a dataframe with all data ("df") or an aggregated dataframe ("ag")

type

a numeric value the the critical level of the radius of inhibition (i.e., resistance) parameter to use for MIC. Currently only <code>RAD</code> = "80" (80% reduction in growth), <code>RAD</code> = "50" (50% reduction in growth), and <code>RAD</code> = "20" (20% reduction in growth) are supported [Default = "20"]

a numeric value indicating the height of the pdf file generated

height

a numeric value indicating the width of the pdf file generated

width

Indicates whether to add breakpoint lines to the standard curve plot (if the user has supplied data to generate a standard curve)

addBreakpoints

a logical value indicating whether to save a PDF file or open a new quartz window. Defaults to TRUE (saves a pdf file).

savePDF

a logical value indicating whether to pop up the figure after it has been created

popUp


Used to convert RAD into MIC. In all cases the linear relationship is log2(MIC) regressed onto RAD^2. This conversion can be based on a) existing built-in data from a number of species/drug combinations, b) a user-supplied slope and intercept of log2(MIC) regressed on RAD^2 for the species/drug combination of interest, c) a user supplied file containing MIC information from lines previously analyzed by diskImageR for RAD, or d) a user supplied file containing both RAD and MIC information. Note that user-supplied data should be MIC and RAD, not log2(MIC) and RAD^2 (the function will do this authomatically).


A pipeline to analyze photographs of disk diffusion plates. This removes the need to analyze the plates themselves, and thus analysis can be done separate from the assay. Furthermore, diskImageR removes potential researcher bias, by quantitative assessment of drug resistance as the zone diameter at multiple cutoff values of growth inhibition. This method also extends the disk diffusion assay by measuring drug tolerance (in addition to drug resistance) as the fraction of the subpopulation that is able to grow above the resistance point ("FoG"), and drug sensitivity as the rate of change from no growth to full growth ("slope").

calcMIC: Convert RAD to MIC based on built-in or provided parameters or datasets

Description

Usage

Arguments

Value