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RIbench (version 1.0.2)

Benchmark Suite for Indirect Methods for RI Estimation

Description

The provided benchmark suite enables the automated evaluation and comparison of any existing and novel indirect method for reference interval ('RI') estimation in a systematic way. Indirect methods take routine measurements of diagnostic tests, containing pathological and non-pathological samples as input and use sophisticated statistical methods to derive a model describing the distribution of the non-pathological samples, which can then be used to derive reference intervals. The benchmark suite contains 5,760 simulated test sets with varying difficulty. To include any indirect method, a custom wrapper function needs to be provided. The package offers functions for generating the test sets, executing the indirect method and evaluating the results. See ?RIbench or vignette("RIbench_package") for a more comprehensive description of the features. A detailed description and application is described in Ammer T., Schuetzenmeister A., Prokosch H.-U., Zierk J., Rank C.M., Rauh M. "RIbench: A Proposed Benchmark for the Standardized Evaluation of Indirect Methods for Reference Interval Estimation". Clinical Chemistry (2022) .

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Version

Install

install.packages('RIbench')

Monthly Downloads

236

Version

1.0.2

License

GPL (>= 3)

Maintainer

Tatjana Ammer

Last Published

November 27th, 2022

Functions in RIbench (1.0.2)

computePerfMeasAll

Function for computing reference intervals for all markers
computeRIs

Function for computing reference intervals
generateBoxplotsMultipleCats

Wrapper function to generate all boxplots for the specified analytes split by defined categories
computeDirect

Function to simulate the direct method
generateDataFiles

Generate simulated data with one start seed for each biomarker and save each test set as separate file
getBenchmarkResults

Computing benchmark table with the mean overall results.
RIbench-package

RIbench: Benchmark Suite for the Standardized Evaluation of Indirect Methods for Reference Interval Estimation
as.rgb

Convert color-names or RGB-code to possibly semi-transparent RGB-code.
computePerfMeas

Function for computing performance measurements
formatNumber

Rounding method with trailing zeros.
generateMD5

Generate an MD5 hash sum for any R object.
generateScatterplotsAll

Wrapper function to generate scatterplots for the specified analytes
generateBoxPlotOneAnalyte

Wrapper function to generate one boxplot for a specified analyte
progressInd

Function for setting up the progress indicator.
computeRIsAll

Function for computing reference intervals for all markers
getRI

Method to calculate reference intervals (percentiles) for objects of class 'RWDRI'
mergeAnalytes

Function to combine analytes for defined categories
computeSubResults

Helper function to compute the subscores for the distribution types and the mentioned categories
computeRuntimeAll

Function to compute runtime statistics for all analytes
readResultFiles

Function for reading in the result files for one marker
defineSubset

Function for defining a subset that is used for analyizing the computation time and can be used for other subanalyses.
generateBiomarkerTestSets

Convenience function to generate simulated data and save each test set as a separate file
getSubset

Function to group the data according to a specified feature.
generateBoxplotsDistTypes

Wrapper function to generate all boxplots for the specified distribution types split by defined categories
getRIsAllwithoutModel

Function for retrieving reference intervals if directly computed
evaluateBiomarkerTestSets

Wrapper function to evaluate all test sets or a specified subset for a specified algorithm.
evaluateAlgorithmResults

Convenience Function to generate all result plots and calculate the benchmark score
invBoxCox

Inverse of the one-parameter Box-Cox transformation.
mergeSummaryErrors

Helper function to combine all computed summary errors
restrictSet

Function to get error subsets for defined category and restriction.
loadTestsetDefinition

Convenience function to load the table with the information about the pre-defined test sets
plotBarplot

Plot method for generating a barplot out of the benchmark results
getRuntime

Helper function to compute runtime statistics
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'
getSubsetForDefinedCats

Function to group the data according to a specified feature.
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.
readResultFilesAll

Function for reading all results files.
readResultsAndComputeErrors

Function to read the result files and compute performance measures to create customized plots afterwards
writeResFile

Helper function to write result file when time out occured or R session terminated
addGrid

Add a grid to an existing plot.
BoxCox

One-parameter Box-Cox transformation.