Benchmark Suite for Indirect Methods for RI Estimation

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Documentation for package ‘RIbench’ version 1.0.2

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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