diskImageR: A Pipeline to Analyze Resistance and Tolerance from Drug Disk Diffusion Assays
Version 1.0.0

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").

Browse man pages Browse package API and functions Browse package files

AuthorAleeza Gerstein [aut, cre], Inbal Hecht [ctb]
Date of publication2016-04-03 16:29:24
MaintainerAleeza Gerstein <gerst035@umn.edu>
LicenseGPL-3
Version1.0.0
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("diskImageR")

Man pages

addType: Add factor column
aggregateData: Averages photographs of the same type
calcMIC: Convert RAD to MIC based on built-in or provided parameters...
createDataframe: Dataframe creation
IJMacro: Run an imageJ analysis macro on the folder that contains the...
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

Functions

IJMacro Man page Source code
ML2param Source code
MLparam Source code
ReadIn_DirCreate Source code
addType Man page Source code
aggregateData Man page Source code
anova.fit.mle Source code
argnames Source code
argnames.constrained Source code
boxconstrain Source code
calcMIC Man page Source code
check.bounds Source code
coef.fit.mle Source code
constrain Source code
constrain.i Source code
constrain.i2 Source code
constrain.parse Source code
createDataframe Man page Source code
curve Source code
curve2 Source code
cv Source code
discplotNoRep Source code
do.constrain Source code
do.mle.search Source code
do.mle.search.optim Source code
do.mle.search.subplex Source code
drop.likelihood Source code
expand.parameters Source code
extractAIC.fit.mle Source code
find.mle Source code
find.mle.default Source code
findFoG Source code
findSlope Source code
get.likelihood Source code
getstats2Log Source code
getstatsLog Source code
guess.constrained.start Source code
invert Source code
is.constrained Source code
load.data Source code
logLik.fit.mle Source code
maxLik Man page Source code
oneParamPlot Man page Source code
plotParam Source code
plotRaw Man page Source code
protect Source code
readExistingDF Man page Source code
readIn Source code
readInExistingIJ Man page Source code
saveAveLine Source code
saveMLParam Man page Source code
se Source code
set.defaults Source code
singleFoG Source code
threeParamPlot Man page Source code
twoParamPlot Man page Source code

Files

inst
inst/walkthrough.R
inst/diskImageR_vignette.html
inst/IJ_diskImageR.ijm
inst/knownMIC-RAD.csv
NAMESPACE
R
R/saveMLParam.R
R/readExistingDF.R
R/mle.R
R/IJMacro.R
R/addType.R
R/aggregateData.R
R/createDataframe.R
R/readExistingIJ.R
R/maxLik.R
R/plotRaw.R
R/twoParamPlot.R
R/calcMIC.R
R/oneParamPlot.R
R/threeParamPlot.R
README.md
MD5
DESCRIPTION
man
man/plotRaw.Rd
man/addType.Rd
man/readExistingDF.Rd
man/threeParamPlot.Rd
man/twoParamPlot.Rd
man/maxLik.Rd
man/readInExistingIJ.Rd
man/createDataframe.Rd
man/saveMLParam.Rd
man/calcMIC.Rd
man/oneParamPlot.Rd
man/IJMacro.Rd
man/aggregateData.Rd
diskImageR documentation built on May 20, 2017, 12:41 a.m.