{ "_id": "6a1d62e91d7bb097a0a4b282", "Package": "lab2clean", "Title": "Automation and Standardization of Cleaning Clinical Laboratory\nData", "Version": "2.0.0", "Authors@R": "c(person(\"Ahmed\", \"Zayed\", , \"ahmed.zayed@kuleuven.be\", role = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0001-7797-1655\")),\nperson(\"Ilias\", \"Sarikakis\", , \"sarikakisilias@gmail.com\", role = c(\"aut\", \"ctb\")),\nperson(\"Arne\", \"Janssens\", , \"arne.janssens@kuleuven.be\", role = c(\"aut\", \"ctb\")),\nperson(\"Pavlos\", \"Mamouris\", , \"pavlos.mamouris@kuleuven.be\", role = c(\"ctb\")))", "Description": "Navigating the shift of clinical laboratory data from\nprimary everyday clinical use to secondary research purposes\npresents a significant challenge. Given the substantial time\nand expertise required for lab data pre-processing and cleaning\nand the lack of all-in-one tools tailored for this need, we\ndeveloped our algorithm 'lab2clean' as an open-source\nR-package. 'lab2clean' package is set to automate and\nstandardize the intricate process of cleaning clinical\nlaboratory results. With a keen focus on improving the data\nquality of laboratory result values and units, our goal is to\nequip researchers with a straightforward, plug-and-play tool,\nmaking it smoother for them to unlock the true potential of\nclinical laboratory data in clinical research and clinical\nmachine learning (ML) model development. Functions to clean &\nvalidate result values (Version 1.0) are described in detail in\n'Zayed et al. (2024)' .\nFunctions to standardize & harmonize result units (added in\nVersion 2.0) are described in detail in 'Zayed et al. (2025)'\n.", "License": "GPL (>= 3)", "Encoding": "UTF-8", "VignetteBuilder": "knitr", "RoxygenNote": "7.3.2", "LazyData": "true", "NeedsCompilation": "no", "Packaged": { "Date": "2026-06-01 10:43:10 UTC", "User": "root" }, "Author": "Ahmed Zayed [aut, cre] (ORCID:\n), Ilias Sarikakis [aut,\nctb], Arne Janssens [aut, ctb], Pavlos Mamouris [ctb]", "Maintainer": "Ahmed Zayed ", "Repository": "https://cran.r-universe.dev", "Date/Publication": "2025-10-04 14:00:02 UTC", "RemoteUrl": "https://github.com/cran/lab2clean", "RemoteRef": "HEAD", "RemoteSha": "6a33662aa69803be01fe7e6c8c4cb554e7823112", "MD5sum": "867d4da272399f2195a7d8f35295c9fd", "_user": "cran", "_type": "src", "_file": "lab2clean_2.0.0.tar.gz", "_fileid": "54b69dcf84f43a2d3af0da6db4a346c665d8f28bfcbb1bf118ec958f708502ec", "_filesize": 840033, "_sha256": "54b69dcf84f43a2d3af0da6db4a346c665d8f28bfcbb1bf118ec958f708502ec", "_created": "2026-06-01T10:43:10.000Z", "_published": "2026-06-01T10:46:01.004Z", "_distro": "noble", "_jobs": [ { "job": 78835460250, "time": 132, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7329449466" }, { "job": 78835460208, "time": 129, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7329448195" }, { "job": 78834973851, "time": 190, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7329406434" }, { "job": 78835460238, "time": 110, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7329442367" } ], "_buildurl": "https://github.com/r-universe/cran/actions/runs/26749901524", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/cran/lab2clean", "_commit": { "id": "6a33662aa69803be01fe7e6c8c4cb554e7823112", "author": "Ahmed Zayed ", "committer": "cran-robot ", "message": "version 2.0.0\n", "time": 1759586402 }, "_maintainer": { "name": "Ahmed Zayed", "email": "ahmed.zayed@kuleuven.be", "orcid": "0000-0001-7797-1655" }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.5", "role": "Depends" }, { "package": "data.table", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "fansi", "role": "Suggests" }, { "package": "kableExtra", "role": "Suggests" }, { "package": "printr", "role": "Suggests" } ], "_owner": "cran", "_selfowned": false, "_usedby": 0, "_updates": [ { "week": "2025-40", "n": 1 } ], "_tags": [ { "name": "2.0.0", "date": "2025-10-04" } ], "_stars": 2, "_userbio": { "uuid": 6899542, "type": "organization", "name": "cran", "description": "Unofficial read-only mirror of all CRAN R packages" }, "_downloads": { "count": 126, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/lab2clean" }, "_searchresults": 2, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/lab2clean.html", "manual.pdf" ], "_realowner": "cran", "_cranurl": false, "_releases": [ { "version": "1.0.0", "date": "2024-09-09" }, { "version": "2.0.0", "date": "2025-10-04" } ], "_exports": [ "clean_lab_result", "harmonize_lab_unit", "standardize_lab_unit", "validate_lab_result" ], "_datasets": [ { "name": "annotable_strings", "title": "Annotable Strings for Unit Standardization", "object": "annotable_strings", "class": [ "data.frame" ], "fields": [ "annotation" ], "rows": 2678, "table": true, "tojson": true }, { "name": "common_words", "title": "Data for the common words", "object": "common_words", "class": [ "data.frame" ], "fields": [ "Language", "Positive", "Negative", "Not_detected", "High", "Low", "Normal", "Sample", "Specimen" ], "rows": 19, "table": true, "tojson": true }, { "name": "Function_1_dummy", "title": "Dummy Data for demonstrating function 1", "object": "Function_1_dummy", "class": [ "data.frame" ], "fields": [ "raw_result", "frequency" ], "rows": 87, "table": true, "tojson": true }, { "name": "Function_2_dummy", "title": "Dummy Data for demonstrating function 2", "object": "Function_2_dummy", "class": [ "data.frame" ], "fields": [ "patient_id", "lab_datetime1", "loinc_code", "result_value", "result_unit" ], "rows": 86863, "table": true, "tojson": true }, { "name": "Function_3_dummy", "title": "Dummy Data for demonstrating function 3", "object": "Function_3_dummy", "class": [ "data.frame" ], "fields": [ "unit_raw", "n_records", "note" ], "rows": 32, "table": true, "tojson": true }, { "name": "Function_4_dummy", "title": "Dummy Data for demonstrating function 4", "object": "Function_4_dummy", "class": [ "tbl_df", "tbl", "data.frame" ], "fields": [ "loinc_code", "result_value", "result_unit" ], "rows": 48, "table": true, "tojson": true }, { "name": "logic_rules", "title": "Data for the logic rules", "object": "logic_rules", "class": [ "data.table", "data.frame" ], "fields": [ "rule_id", "rule_index", "rule_part", "rule_part_type" ], "rows": 18, "table": true, "tojson": true }, { "name": "loinc_reference_unit_v1", "title": "Data for the Reference Harmonized Units for LOINC Groups", "object": "loinc_reference_unit_v1", "class": [ "data.frame" ], "fields": [ "loinc_code", "unit_system", "reference_unit", "OMOP_concept_id", "mass_molar_unit", "molecular_weight", "mass_molar_loinc", "property_group_id" ], "rows": 33197, "table": true, "tojson": true }, { "name": "parsed_units_df", "title": "Data for the parsed UCUM units", "object": "parsed_units_df", "class": [ "data.frame" ], "fields": [ "csCode_", "ciCode_", "magnitude_", "dim_", "cnv_", "cnvPfx_", "isArbitrary_", "moleExp_", "source", "starts_with_si", "flag" ], "rows": 1540, "table": true, "tojson": true }, { "name": "reportable_interval", "title": "Data for the reportable interval", "object": "reportable_interval", "class": [ "data.table", "data.frame" ], "fields": [ "interval_loinc_code", "UCUM_unit", "low_reportable_limit", "high_reportable_limit" ], "rows": 493, "table": true, "tojson": true }, { "name": "RWD_units_to_UCUM_V2", "title": "Data for the RWD units mapped to standard UCUM-valid units", "object": "RWD_units_to_UCUM_V2", "class": [ "data.frame" ], "fields": [ "clean_unit_lower", "ucum_code", "source_match" ], "rows": 5131, "table": true, "tojson": true } ], "_help": [ { "page": "annotable_strings", "title": "Annotable Strings for Unit Standardization", "topics": [ "annotable_strings" ] }, { "page": "clean_lab_result", "title": "Clean and Standardize Laboratory Result Values", "topics": [ "clean_lab_result" ] }, { "page": "common_words", "title": "Data for the common words", "topics": [ "common_words" ] }, { "page": "Function_1_dummy", "title": "Dummy Data for demonstrating function 1", "topics": [ "Function_1_dummy" ] }, { "page": "Function_2_dummy", "title": "Dummy Data for demonstrating function 2", "topics": [ "Function_2_dummy" ] }, { "page": "Function_3_dummy", "title": "Dummy Data for demonstrating function 3", "topics": [ "Function_3_dummy" ] }, { "page": "Function_4_dummy", "title": "Dummy Data for demonstrating function 4", "topics": [ "Function_4_dummy" ] }, { "page": "harmonize_lab_unit", "title": "Harmonizing Laboratory Units of Measurement through Unit Conversion", "topics": [ "harmonize_lab_unit" ] }, { "page": "logic_rules", "title": "Data for the logic rules", "topics": [ "logic_rules" ] }, { "page": "loinc_reference_unit_v1", "title": "Data for the Reference Harmonized Units for LOINC Groups", "topics": [ "loinc_reference_unit_v1" ] }, { "page": "parsed_units_df", "title": "Data for the parsed UCUM units", "topics": [ "parsed_units_df" ] }, { "page": "reportable_interval", "title": "Data for the reportable interval", "topics": [ "reportable_interval" ] }, { "page": "RWD_units_to_UCUM_V2", "title": "Data for the RWD units mapped to standard UCUM-valid units", "topics": [ "RWD_units_to_UCUM_V2" ] }, { "page": "standardize_lab_unit", "title": "Clean and Standardize Formats of Laboratory Units of Measurement", "topics": [ "standardize_lab_unit" ] }, { "page": "validate_lab_result", "title": "Validate Quantitative Laboratory Result Values", "topics": [ "validate_lab_result" ] } ], "_rundeps": [ "data.table" ], "_vignettes": [ { "source": "lab2clean.Rmd", "filename": "lab2clean.html", "title": "Automatically Cleaning Laboratory Results in R using the 'lab2clean' package", "author": "Ahmed Zayed, Ilias Sarikakis, Arne Janssens, Pavlos Mamouris", "engine": "knitr::rmarkdown", "headings": [ "1. Introduction", "2. Setup", "Installing and loading the lab2clean package", "3. Function 1: Clean and Standardize results", "4. Function 2: Validate results", "4. Function 3: Clean and Standardize units of measurement:", "5. Function 4: Harmonize results to reference units", "6. Customization" ], "created": "2024-09-10 02:56:14", "modified": "2025-10-04 14:00:02", "commits": 2 } ], "_score": 2.3010299956639813, "_indexed": true, "_nocasepkg": "lab2clean", "_universes": [ "cran" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "2.0.0", "date": "2026-06-01T10:45:20.000Z", "distro": "noble", "commit": "6a33662aa69803be01fe7e6c8c4cb554e7823112", "fileid": "041d993c88366c9391fd79508b9288a950375daafb006e404b30de6adffbdb46", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cran/actions/runs/26749901524" }, { "r": "4.6.0", "os": "linux", "version": "2.0.0", "date": "2026-06-01T10:45:16.000Z", "distro": "noble", "commit": "6a33662aa69803be01fe7e6c8c4cb554e7823112", "fileid": "47d36d72dfe01a8e36f9ab603eb5f72c77ed470cf4fa04743c848e7c5d5f8cc6", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cran/actions/runs/26749901524" }, { "r": "4.6.0", "os": "wasm", "version": "2.0.0", "date": "2026-06-01T10:45:18.000Z", "commit": "6a33662aa69803be01fe7e6c8c4cb554e7823112", "fileid": "2757fb29c92669041eb20f1b8ace0d8339b9750bff37d20bcd61a2b2f9cef8f0", "status": "success", "buildurl": "https://github.com/r-universe/cran/actions/runs/26749901524" } ] }