Package: RIbench 1.0.2

Tatjana Ammer

RIbench: Benchmark Suite for Indirect Methods for RI Estimation

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) <doi:10.1093/clinchem/hvac142>.

Authors:Tatjana Ammer [aut, cre], Christopher Rank [aut], Andre Schuetzenmeister [aut]

RIbench_1.0.2.tar.gz
RIbench_1.0.2.tar.gz(r-4.7-any)RIbench_1.0.2.tar.gz(r-4.6-any)
RIbench_1.0.2.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
RIbench/json (API)

# Install 'RIbench' in R:

install.packages('RIbench', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org'))

On CRAN:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

2.00 score 1 stars 4 scripts 319 downloads 22 exports 4 dependencies

Last updated from:ae837ae59f. Checks:4 OK. Indexed: yes.

Target	Result	Time
linux-devel-x86_64	OK	116
source / vignettes	OK	224
linux-release-x86_64	OK	125
wasm-release	OK	103

Exports:computePerfMeasAll computeRIsAll evaluateAlgorithmResults evaluateBiomarkerTestSets generateBiomarkerTestSets generateBoxPlotOneAnalyte generateBoxplotsDistTypes generateBoxplotsMultipleCats generateScatterplotsAll getBenchmarkResults getRI getSubset getSubsetForDefinedCats loadTestsetDefinition mergeAnalytes plotBarplot plotBoxplot plotScatterplot print.RWDRI readResultFilesAll readResultsAndComputeErrors runDirectMethod

Dependencies:data.table digest optparse RColorBrewer

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

Rendered fromRIbench_package.Rmdusingknitr::rmarkdown

Last update: 2022-09-17
Started: 2022-08-29

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

Package: RIbench 1.0.2

RIbench: Benchmark Suite for Indirect Methods for RI Estimation

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