{ "_id": "6a229e5fcd65a98ecbd58064", "Type": "Package", "Package": "RIbench", "Version": "1.0.2", "Date": "2022-11-25", "Title": "Benchmark Suite for Indirect Methods for RI Estimation", "Author": "Tatjana Ammer [aut, cre], Christopher Rank [aut], Andre\nSchuetzenmeister [aut]", "Maintainer": "Tatjana Ammer ", "Authors@R": "c(\nperson(given =\"Tatjana\", family =\"Ammer\", email =\"tatjana.ammer@roche.com\", role =c(\"aut\", \"cre\")),\nperson(given =\"Christopher\", family = \"Rank\", email =\"christopher.rank@roche.com\", role =\"aut\"),\nperson(given =\"Andre\", family =\"Schuetzenmeister\", email =\"andre.schuetzenmeister@roche.com\", role =\"aut\"))", "Description": "The provided benchmark suite enables the automated\nevaluation and comparison of any existing and novel indirect\nmethod for reference interval ('RI') estimation in a systematic\nway. Indirect methods take routine measurements of diagnostic\ntests, containing pathological and non-pathological samples as\ninput and use sophisticated statistical methods to derive a\nmodel describing the distribution of the non-pathological\nsamples, which can then be used to derive reference intervals.\nThe benchmark suite contains 5,760 simulated test sets with\nvarying difficulty. To include any indirect method, a custom\nwrapper function needs to be provided. The package offers\nfunctions for generating the test sets, executing the indirect\nmethod and evaluating the results. See ?RIbench or\nvignette(\"RIbench_package\") for a more comprehensive\ndescription of the features. A detailed description and\napplication is described in Ammer T., Schuetzenmeister A.,\nProkosch H.-U., Zierk J., Rank C.M., Rauh M. \"RIbench: A\nProposed Benchmark for the Standardized Evaluation of Indirect\nMethods for Reference Interval Estimation\". Clinical Chemistry\n(2022) .", "License": "GPL (>= 3)", "VignetteBuilder": "knitr, rmarkdown", "NeedsCompilation": "no", "Packaged": { "Date": "2026-06-05 09:56:53 UTC", "User": "root" }, "Repository": "https://cran.r-universe.dev", "Date/Publication": "2022-11-27 16:40:02 UTC", "RemoteUrl": "https://github.com/cran/RIbench", "RemoteRef": "HEAD", "RemoteSha": "ae837ae59f88ef2dbc0c6ff71d3ab945cee50598", "MD5sum": "d8b720a397eac5d2362efd36c694a5e9", "_user": "cran", "_type": "src", "_file": "RIbench_1.0.2.tar.gz", "_fileid": "3ca61d9a07d619c84c6671aade7ed42b6fabfc52a41ebf4c43aa8570775f861c", "_filesize": 1154629, "_sha256": "3ca61d9a07d619c84c6671aade7ed42b6fabfc52a41ebf4c43aa8570775f861c", "_created": "2026-06-05T09:56:53.000Z", "_published": "2026-06-05T10:01:03.170Z", "_distro": "noble", "_jobs": [ { "job": 79705332191, "time": 120, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7433889877" }, { "job": 79705332178, "time": 162, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7433902264" }, { "job": 79704929433, "time": 163, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7433852146" }, { "job": 79705332215, "time": 101, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7433884378" } ], "_buildurl": "https://github.com/r-universe/cran/actions/runs/27008158725", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/cran/RIbench", "_commit": { "id": "ae837ae59f88ef2dbc0c6ff71d3ab945cee50598", "author": "Tatjana Ammer ", "committer": "cran-robot ", "message": "version 1.0.2\n", "time": 1669567202 }, "_maintainer": { "name": "Tatjana Ammer", "email": "tatjana.ammer@roche.com" }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.3.0", "role": "Depends" }, { "package": "stats", "role": "Imports" }, { "package": "optparse", "role": "Imports" }, { "package": "digest", "role": "Imports" }, { "package": "data.table", "role": "Imports" }, { "package": "graphics", "role": "Imports" }, { "package": "grDevices", "role": "Imports" }, { "package": "RColorBrewer", "role": "Imports" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" } ], "_owner": "cran", "_selfowned": false, "_usedby": 0, "_updates": [], "_tags": [], "_stars": 1, "_userbio": { "uuid": 6899542, "type": "organization", "name": "cran", "description": "Unofficial read-only mirror of all CRAN R packages" }, "_downloads": { "count": 157, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/RIbench" }, "_searchresults": 3, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/NEWS.html", "extra/NEWS.txt", "extra/RIbench.html", "manual.pdf" ], "_realowner": "cran", "_cranurl": false, "_releases": [ { "version": "1.0.0", "date": "2022-08-29" }, { "version": "1.0.1", "date": "2022-09-17" }, { "version": "1.0.2", "date": "2022-11-27" } ], "_exports": [ "computePerfMeasAll", "computeRIsAll", "evaluateAlgorithmResults", "evaluateBiomarkerTestSets", "generateBiomarkerTestSets", "generateBoxPlotOneAnalyte", "generateBoxplotsDistTypes", "generateBoxplotsMultipleCats", "generateScatterplotsAll", "getBenchmarkResults", "getRI", "getSubset", "getSubsetForDefinedCats", "loadTestsetDefinition", "mergeAnalytes", "plotBarplot", "plotBoxplot", "plotScatterplot", "print.RWDRI", "readResultFilesAll", "readResultsAndComputeErrors", "runDirectMethod" ], "_help": [ { "page": "RIbench-Package", "title": "RIbench: Benchmark Suite for the Standardized Evaluation of Indirect Methods for Reference Interval Estimation", "topics": [ "RIbench-package", "RIbench" ] }, { "page": "addGrid", "title": "Add a grid to an existing plot.", "topics": [ "addGrid" ] }, { "page": "as.rgb", "title": "Convert color-names or RGB-code to possibly semi-transparent RGB-code.", "topics": [ "as.rgb" ] }, { "page": "BoxCox", "title": "One-parameter Box-Cox transformation.", "topics": [ "BoxCox" ] }, { "page": "computeDirect", "title": "Function to simulate the direct method", "topics": [ "computeDirect" ] }, { "page": "computePerfMeas", "title": "Function for computing performance measurements", "topics": [ "computePerfMeas" ] }, { "page": "computePerfMeasAll", "title": "Function for computing reference intervals for all markers", "topics": [ "computePerfMeasAll" ] }, { "page": "computeRIs", "title": "Function for computing reference intervals", "topics": [ "computeRIs" ] }, { "page": "computeRIsAll", "title": "Function for computing reference intervals for all markers", "topics": [ "computeRIsAll" ] }, { "page": "computeRuntimeAll", "title": "Function to compute runtime statistics for all analytes", "topics": [ "computeRuntimeAll" ] }, { "page": "computeSubResults", "title": "Helper function to compute the subscores for the distribution types and the mentioned categories", "topics": [ "computeSubResults" ] }, { "page": "defineSubset", "title": "Function for defining a subset that is used for analyizing the computation time and can be used for other subanalyses.", "topics": [ "defineSubset" ] }, { "page": "evaluateAlgorithmResults", "title": "Convenience Function to generate all result plots and calculate the benchmark score", "topics": [ "evaluateAlgorithmResults" ] }, { "page": "evaluateBiomarkerTestSets", "title": "Wrapper function to evaluate all test sets or a specified subset for a specified algorithm.", "topics": [ "evaluateBiomarkerTestSets" ] }, { "page": "formatNumber", "title": "Rounding method with trailing zeros.", "topics": [ "formatNumber" ] }, { "page": "generateBiomarkerTestSets", "title": "Convenience function to generate simulated data and save each test set as a separate file", "topics": [ "generateBiomarkerTestSets" ] }, { "page": "generateBoxPlotOneAnalyte", "title": "Wrapper function to generate one boxplot for a specified analyte", "topics": [ "generateBoxPlotOneAnalyte" ] }, { "page": "generateBoxplotsDistTypes", "title": "Wrapper function to generate all boxplots for the specified distribution types split by defined categories", "topics": [ "generateBoxplotsDistTypes" ] }, { "page": "generateBoxplotsMultipleCats", "title": "Wrapper function to generate all boxplots for the specified analytes split by defined categories", "topics": [ "generateBoxplotsMultipleCats" ] }, { "page": "generateDataFiles", "title": "Generate simulated data with one start seed for each biomarker and save each test set as separate file", "topics": [ "generateDataFiles" ] }, { "page": "generateMD5", "title": "Generate an MD5 hash sum for any R object.", "topics": [ "generateMD5" ] }, { "page": "generateScatterplotsAll", "title": "Wrapper function to generate scatterplots for the specified analytes", "topics": [ "generateScatterplotsAll" ] }, { "page": "getBenchmarkResults", "title": "Computing benchmark table with the mean overall results.", "topics": [ "getBenchmarkResults" ] }, { "page": "getRI", "title": "Method to calculate reference intervals (percentiles) for objects of class 'RWDRI'", "topics": [ "getRI" ] }, { "page": "getRIsAllwithoutModel", "title": "Function for retrieving reference intervals if directly computed", "topics": [ "getRIsAllwithoutModel" ] }, { "page": "getRuntime", "title": "Helper function to compute runtime statistics", "topics": [ "getRuntime" ] }, { "page": "getSubset", "title": "Function to group the data according to a specified feature.", "topics": [ "getSubset" ] }, { "page": "getSubsetForDefinedCats", "title": "Function to group the data according to a specified feature.", "topics": [ "getSubsetForDefinedCats" ] }, { "page": "invBoxCox", "title": "Inverse of the one-parameter Box-Cox transformation.", "topics": [ "invBoxCox" ] }, { "page": "loadTestsetDefinition", "title": "Convenience function to load the table with the information about the pre-defined test sets", "topics": [ "loadTestsetDefinition" ] }, { "page": "mergeAnalytes", "title": "Function to combine analytes for defined categories", "topics": [ "mergeAnalytes" ] }, { "page": "mergeSummaryErrors", "title": "Helper function to combine all computed summary errors", "topics": [ "mergeSummaryErrors" ] }, { "page": "plotBarplot", "title": "Plot method for generating a barplot out of the benchmark results", "topics": [ "plotBarplot" ] }, { "page": "plotBoxplot", "title": "Plot method for generating a boxplot of the benchmark results", "topics": [ "plotBoxplot" ] }, { "page": "plotScatterplot", "title": "Plot method for generating a scatterplot", "topics": [ "plotScatterplot" ] }, { "page": "print.RWDRI", "title": "Standard print method for objects of class 'RWDRI'", "topics": [ "print.RWDRI" ] }, { "page": "progressInd", "title": "Function for setting up the progress indicator.", "topics": [ "progressInd" ] }, { "page": "readResultFiles", "title": "Function for reading in the result files for one marker", "topics": [ "readResultFiles" ] }, { "page": "readResultFilesAll", "title": "Function for reading all results files.", "topics": [ "readResultFilesAll" ] }, { "page": "readResultsAndComputeErrors", "title": "Function to read the result files and compute performance measures to create customized plots afterwards", "topics": [ "readResultsAndComputeErrors" ] }, { "page": "restrictSet", "title": "Function to get error subsets for defined category and restriction.", "topics": [ "restrictSet" ] }, { "page": "runDirectMethod", "title": "Convenience function to simulate the direct method for the specified subset", "topics": [ "runDirectMethod" ] }, { "page": "runTC_usingRscript", "title": "Function for running test sets per algorithm per marker with calling Rscript for each test set", "topics": [ "runTC_usingRscript" ] }, { "page": "setupDirStructure", "title": "Convenience function to set up the directory structure used for storing data and results.", "topics": [ "setupDirStructure" ] }, { "page": "writeResFile", "title": "Helper function to write result file when time out occured or R session terminated", "topics": [ "writeResFile" ] } ], "_rundeps": [ "data.table", "digest", "optparse", "RColorBrewer" ], "_vignettes": [ { "source": "RIbench_package.Rmd", "filename": "RIbench_package.html", "title": "RIbench: Benchmark Suite for the Standardized Evaluation of Indirect Methods for Reference Interval Estimation", "author": "Tatjana Ammer & Christopher M Rank", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Process Overview", "Generate Biomarker Test Sets", "Evaluate Biomarker Test Sets", "Inclusion of New Indirect Method", "Indirect Method that Estimates the Parameters of a (Shifted) Box-Cox Transformed Normal Distribution", "Indirect Method that Estimates Reference Intervals Directly", "Evaluate Biomarker Test Sets using Indirect Method", "Custom Options", "Definition of Subsets", "Configuration of Additional Parameters", "Evaluate Algorithm Results", "Default Evaluation", "Example: Application of RIbench with refineR", "References" ], "created": "2022-08-29 08:20:14", "modified": "2022-09-17 18:56:27", "commits": 2 } ], "_score": 2, "_indexed": true, "_nocasepkg": "ribench", "_universes": [ "cran" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.0.2", "date": "2026-06-05T09:58:54.000Z", "distro": "noble", "commit": "ae837ae59f88ef2dbc0c6ff71d3ab945cee50598", "fileid": "378eaa352cda52dd0e712436080678a372ff0c9d953ad724a678727678aba76e", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cran/actions/runs/27008158725" }, { "r": "4.6.0", "os": "linux", "version": "1.0.2", "date": "2026-06-05T09:59:35.000Z", "distro": "noble", "commit": "ae837ae59f88ef2dbc0c6ff71d3ab945cee50598", "fileid": "7a622f31a34dedca5b278657feb5fc90120773afbe77e7a9d4f425f1141114e8", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cran/actions/runs/27008158725" }, { "r": "4.6.0", "os": "wasm", "version": "1.0.2", "date": "2026-06-05T09:58:53.000Z", "commit": "ae837ae59f88ef2dbc0c6ff71d3ab945cee50598", "fileid": "59408d98ac40a9729f63fcdfb0cc97900248cef2bc268b9372751c4cd58389ac", "status": "success", "buildurl": "https://github.com/r-universe/cran/actions/runs/27008158725" } ] }