# Benchmark Suite for Indirect Methods for RI Estimation

## Documentation for package ‘RIbench’ version 1.0.2

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

RIbench-package | RIbench: Benchmark Suite for the Standardized Evaluation of Indirect Methods for Reference Interval Estimation
addGrid | Add a grid to an existing plot.
as.rgb | Convert color-names or RGB-code to possibly semi-transparent RGB-code.
BoxCox | One-parameter Box-Cox transformation.
computeDirect | Function to simulate the direct method
computePerfMeas | Function for computing performance measurements
computePerfMeasAll | Function for computing reference intervals for all markers
computeRIs | Function for computing reference intervals
computeRIsAll | Function for computing reference intervals for all markers
computeRuntimeAll | Function to compute runtime statistics for all analytes
computeSubResults | Helper function to compute the subscores for the distribution types and the mentioned categories
defineSubset | Function for defining a subset that is used for analyizing the computation time and can be used for other subanalyses.
evaluateAlgorithmResults | Convenience Function to generate all result plots and calculate the benchmark score
evaluateBiomarkerTestSets | Wrapper function to evaluate all test sets or a specified subset for a specified algorithm.
formatNumber | Rounding method with trailing zeros.
generateBiomarkerTestSets | Convenience function to generate simulated data and save each test set as a separate file
generateBoxPlotOneAnalyte | Wrapper function to generate one boxplot for a specified analyte
generateBoxplotsDistTypes | Wrapper function to generate all boxplots for the specified distribution types split by defined categories
generateBoxplotsMultipleCats | Wrapper function to generate all boxplots for the specified analytes split by defined categories
generateDataFiles | Generate simulated data with one start seed for each biomarker and save each test set as separate file
generateMD5 | Generate an MD5 hash sum for any R object.
generateScatterplotsAll | Wrapper function to generate scatterplots for the specified analytes
getBenchmarkResults | Computing benchmark table with the mean overall results.
getRI | Method to calculate reference intervals (percentiles) for objects of class 'RWDRI'
getRIsAllwithoutModel | Function for retrieving reference intervals if directly computed
getRuntime | Helper function to compute runtime statistics
getSubset | Function to group the data according to a specified feature.
getSubsetForDefinedCats | Function to group the data according to a specified feature.
invBoxCox | Inverse of the one-parameter Box-Cox transformation.
loadTestsetDefinition | Convenience function to load the table with the information about the pre-defined test sets
mergeAnalytes | Function to combine analytes for defined categories
mergeSummaryErrors | Helper function to combine all computed summary errors
plotBarplot | Plot method for generating a barplot out of the benchmark results
plotBoxplot | Plot method for generating a boxplot of the benchmark results
plotScatterplot | Plot method for generating a scatterplot
print.RWDRI | Standard print method for objects of class 'RWDRI'
progressInd | Function for setting up the progress indicator.
readResultFiles | Function for reading in the result files for one marker
readResultFilesAll | Function for reading all results files.
readResultsAndComputeErrors | Function to read the result files and compute performance measures to create customized plots afterwards
restrictSet | Function to get error subsets for defined category and restriction.
RIbench | RIbench: Benchmark Suite for the Standardized Evaluation of Indirect Methods for Reference Interval Estimation
runDirectMethod | Convenience function to simulate the direct method for the specified subset
runTC_usingRscript | Function for running test sets per algorithm per marker with calling Rscript for each test set
setupDirStructure | Convenience function to set up the directory structure used for storing data and results.
writeResFile | Helper function to write result file when time out occured or R session terminated