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-4.5-noble)RIbench_1.0.2.tar.gz(r-4.4-noble)
RIbench_1.0.2.tgz(r-4.4-emscripten)RIbench_1.0.2.tgz(r-4.3-emscripten)
RIbench.pdf |RIbench.html✨
RIbench/json (API)
NEWS

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

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 302 downloads 22 exports 5 dependencies

Last updated 2 years agofrom:ae837ae59f. Checks:2 OK. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKJan 29 2025
R-4.5-linuxOKJan 29 2025

Exports:computePerfMeasAllcomputeRIsAllevaluateAlgorithmResultsevaluateBiomarkerTestSetsgenerateBiomarkerTestSetsgenerateBoxPlotOneAnalytegenerateBoxplotsDistTypesgenerateBoxplotsMultipleCatsgenerateScatterplotsAllgetBenchmarkResultsgetRIgetSubsetgetSubsetForDefinedCatsloadTestsetDefinitionmergeAnalytesplotBarplotplotBoxplotplotScatterplotprint.RWDRIreadResultFilesAllreadResultsAndComputeErrorsrunDirectMethod

Dependencies:data.tabledigestgetoptoptparseRColorBrewer

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

Tatjana Ammer & Christopher M Rank

Rendered fromRIbench_package.Rmdusingknitr::rmarkdownon Jan 29 2025.

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

Readme and manuals

Help Manual

Help pageTopics
RIbench: Benchmark Suite for the Standardized Evaluation of Indirect Methods for Reference Interval EstimationRIbench-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 methodcomputeDirect
Function for computing performance measurementscomputePerfMeas
Function for computing reference intervals for all markerscomputePerfMeasAll
Function for computing reference intervalscomputeRIs
Function for computing reference intervals for all markerscomputeRIsAll
Function to compute runtime statistics for all analytescomputeRuntimeAll
Helper function to compute the subscores for the distribution types and the mentioned categoriescomputeSubResults
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 scoreevaluateAlgorithmResults
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 filegenerateBiomarkerTestSets
Wrapper function to generate one boxplot for a specified analytegenerateBoxPlotOneAnalyte
Wrapper function to generate all boxplots for the specified distribution types split by defined categoriesgenerateBoxplotsDistTypes
Wrapper function to generate all boxplots for the specified analytes split by defined categoriesgenerateBoxplotsMultipleCats
Generate simulated data with one start seed for each biomarker and save each test set as separate filegenerateDataFiles
Generate an MD5 hash sum for any R object.generateMD5
Wrapper function to generate scatterplots for the specified analytesgenerateScatterplotsAll
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 computedgetRIsAllwithoutModel
Helper function to compute runtime statisticsgetRuntime
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 setsloadTestsetDefinition
Function to combine analytes for defined categoriesmergeAnalytes
Helper function to combine all computed summary errorsmergeSummaryErrors
Plot method for generating a barplot out of the benchmark resultsplotBarplot
Plot method for generating a boxplot of the benchmark resultsplotBoxplot
Plot method for generating a scatterplotplotScatterplot
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 markerreadResultFiles
Function for reading all results files.readResultFilesAll
Function to read the result files and compute performance measures to create customized plots afterwardsreadResultsAndComputeErrors
Function to get error subsets for defined category and restriction.restrictSet
Convenience function to simulate the direct method for the specified subsetrunDirectMethod
Function for running test sets per algorithm per marker with calling Rscript for each test setrunTC_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 terminatedwriteResFile