{ "_id": "6a103e4dacfb0bcc41c9c897", "Package": "secuTrialR", "Type": "Package", "Title": "Handling of Data from the Clinical Data Management System\n'secuTrial'", "Version": "1.3.3", "Authors@R": "c(person(given = \"Alan G.\",\nfamily = \"Haynes\",\nrole = c(\"cre\", \"aut\", \"cph\"),\nemail = \"alan.haynes@unibe.ch\"),\nperson(given = \"Patrick R.\",\nfamily = \"Wright\",\nrole = c(\"aut\", \"cph\"),\nemail = \"patrick.wright@usb.ch\"),\nperson(given = \"Milica\",\nfamily = \"Markovic\",\nrole = c(\"aut\", \"cph\"),\nemail = \"milica.markovic@usb.ch\"),\nperson(given = \"Gilles\",\nfamily = \"Dutilh\",\nrole = c(\"ctb\")),\nperson(given = \"Armando\",\nfamily = \"Lenz\",\nrole = c(\"ctb\")),\nperson(given = \"Pascal\",\nfamily = \"Benkert\",\nrole = c(\"com\"),\nemail = \"pascal.benkert@usb.ch\"),\nperson(given = \"Silvia\",\nfamily = \"Grieder\",\nrole = c(\"ctb\")),\nperson(given = \"Pia\",\nfamily = \"Neuschwander\",\nrole = c(\"ctb\")),\nperson(given = \"Constantin\",\nfamily = \"Sluka\",\nrole = c(\"ctb\"))\n)", "Maintainer": "Alan G. Haynes ", "Description": "Seamless and standardized interaction with data exported\nfrom the clinical data management system (CDMS)\n'secuTrial'. The primary data export\nthe package works with is a standard non-rectangular export.", "License": "MIT + file LICENSE", "Encoding": "UTF-8", "RoxygenNote": "7.3.1", "VignetteBuilder": "knitr", "URL": "https://github.com/SwissClinicalTrialOrganisation/secuTrialR", "BugReports": "https://github.com/SwissClinicalTrialOrganisation/secuTrialR/issues", "Config/pak/sysreqs": "make libicu-dev libx11-dev zlib1g-dev", "Repository": "https://dcr-unibe-ch.r-universe.dev", "Date/Publication": "2024-05-30 09:07:02 UTC", "RemoteUrl": "https://github.com/SwissClinicalTrialOrganisation/secuTrialR", "RemoteRef": "HEAD", "RemoteSha": "9583775b467a5bba35bb1b57328b3e1292150816", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-11 09:20:35 UTC", "User": "root" }, "Author": "Alan G. Haynes [cre, aut, cph],\nPatrick R. Wright [aut, cph],\nMilica Markovic [aut, cph],\nGilles Dutilh [ctb],\nArmando Lenz [ctb],\nPascal Benkert [com],\nSilvia Grieder [ctb],\nPia Neuschwander [ctb],\nConstantin Sluka [ctb]", "MD5sum": "c23914ad3a61d073d915326d01fbdc60", "_user": "dcr-unibe-ch", "_type": "src", "_file": "secuTrialR_1.3.3.tar.gz", "_fileid": "eea8f24d54cd584a25a91c8ec325529bdf5922c95e96a35ad1245c83b065e3f3", "_filesize": 1984271, "_sha256": "eea8f24d54cd584a25a91c8ec325529bdf5922c95e96a35ad1245c83b065e3f3", "_created": "2026-05-11T09:20:35.000Z", "_published": "2026-05-22T11:30:21.576Z", "_distro": "noble", "_jobs": [ { "job": 77370759038, "time": 142, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "6914786901" }, { "job": 77370759345, "time": 171, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "6914796610" }, { "job": 77370759298, "time": 87, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "6914766870" }, { "job": 77370759012, "time": 134, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "6914783806" }, { "job": 77370758602, "time": 200, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "6914734308" }, { "job": 77370758759, "time": 125, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7159433879" }, { "job": 77370758969, "time": 116, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "6914777748" }, { "job": 77370759491, "time": 101, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "6914773086" }, { "job": 77370759173, "time": 102, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "6914772745" } ], "_buildurl": "https://github.com/r-universe/dcr-unibe-ch/actions/runs/25661378271", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/SwissClinicalTrialOrganisation/secuTrialR", "_commit": { "id": "9583775b467a5bba35bb1b57328b3e1292150816", "author": "Alan Haynes ", "committer": "GitHub ", "message": "Merge pull request #267 from aghaynes/master\n\nclear more notes", "time": 1717060022 }, "_maintainer": { "name": "Alan G. Haynes", "email": "alan.haynes@unibe.ch", "login": "aghaynes", "twitter": "@aghaynes", "uuid": 6594028 }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.5", "role": "Depends" }, { "package": "haven", "version": ">= 2.2.0", "role": "Imports" }, { "package": "readr", "role": "Imports" }, { "package": "readxl", "role": "Imports" }, { "package": "stringr", "role": "Imports" }, { "package": "tibble", "role": "Imports" }, { "package": "magrittr", "role": "Imports" }, { "package": "purrr", "role": "Imports" }, { "package": "tidyr", "role": "Imports" }, { "package": "dplyr", "role": "Imports" }, { "package": "rlang", "role": "Imports" }, { "package": "lubridate", "role": "Imports" }, { "package": "knitr", "role": "Suggests" }, { "package": "lintr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "testthat", "role": "Suggests" }, { "package": "tufte", "role": "Suggests" }, { "package": "tcltk", "role": "Suggests" }, { "package": "igraph", "role": "Suggests" } ], "_owner": "swissclinicaltrialorganisation", "_selfowned": false, "_usedby": 0, "_updates": [], "_tags": [], "_stars": 10, "_contributors": [ { "user": "aghaynes", "count": 466, "uuid": 6594028 }, { "user": "markomi", "count": 93, "uuid": 9819134 }, { "user": "drespresso", "count": 16, "uuid": 45166575 }, { "user": "gillesdutilh", "count": 8, "uuid": 45421065 }, { "user": "sgrieder", "count": 6, "uuid": 44674512 }, { "user": "a-lenz", "count": 3, "uuid": 45206982 }, { "user": "danielskatz", "count": 1, "uuid": 2913845 } ], "_userbio": { "uuid": 264417472, "type": "organization", "name": "Department of Clinical Research (DCR)", "description": "As the University of Bern's Department of Clinical Research, we offer clinical researchers full support from study design to study conduct." }, "_downloads": { "count": 658, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/secuTrialR" }, "_devurl": "https://github.com/swissclinicaltrialorganisation/secutrialr", "_searchresults": 16, "_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/readme.html", "extra/readme.md", "extra/secuTrialR.html", "manual.pdf" ], "_homeurl": "https://github.com/swissclinicaltrialorganisation/secutrialr", "_realowner": "swissclinicaltrialorganisation", "_cranurl": true, "_releases": [ { "version": "1.0.3", "date": "2020-04-24" }, { "version": "1.0.6", "date": "2020-10-26" }, { "version": "1.0.8", "date": "2020-12-07" }, { "version": "1.0.9", "date": "2021-03-11" }, { "version": "1.1.1", "date": "2023-03-06" }, { "version": "1.3.3", "date": "2024-05-30" } ], "_exports": [ "annual_recruitment", "build_secuTrial_url", "dates_secuTrial", "dictionary_secuTrial", "diff_secuTrial", "export_date", "export_datetime", "factorize_secuTrial", "form_status_counts", "form_status_summary", "get_participants", "label", "label_secuTrial", "label<-", "labels_secuTrial", "links_secuTrial", "plot_recruitment", "read_secuTrial", "read_secuTrial_raw", "read_validation_overview", "return_hidden_items", "return_random_participants", "return_scores", "subset_secuTrial", "units", "units<-", "visit_structure", "write_secuTrial" ], "_help": [ { "page": "annual_recruitment", "title": "Returns a data.frame showing the annual recruitment per center", "topics": [ "annual_recruitment" ] }, { "page": "as.data.frame.secuTrialdata", "title": "as.data.frame method for secuTrialdata objects Make the data from the exports more easily accessible by placing them in another environment (e.g. place them in the global environment ('.GlobalEnv') and you can reference them without referring to the 'secuTrialdata' object anymore. Ie. they become regular 'data.frame's).", "topics": [ "as.data.frame.secuTrialdata" ] }, { "page": "assess_form_variable_completeness", "title": "Asses completeness of data for each variable in a secuTrial export", "topics": [ "assess_form_variable_completeness" ] }, { "page": "build_secuTrial_url", "title": "Compose a secuTrial URL", "topics": [ "build_secuTrial_url" ] }, { "page": "check_export_options", "title": "Returns deviations from suggested export options", "topics": [ "check_export_options" ] }, { "page": "dates_secuTrial", "title": "Methods to handle date(times)s in secuTrial exports", "topics": [ "dates_secuTrial", "dates_secuTrial.secuTrialdata" ] }, { "page": "dictionary_secuTrial", "title": "Data dictionary for secuTrialdata objects", "topics": [ "dictionary_secuTrial" ] }, { "page": "diff_secuTrial", "title": "Returns differences in the setup of two 'secuTrialdata' objects", "topics": [ "diff_secuTrial" ] }, { "page": "export_date", "title": "Return the date and time that an export was performed", "topics": [ "export_date", "export_datetime" ] }, { "page": "factorize", "title": "Add factors to 'secuTrialdata' objects", "topics": [ "factorize", "factorize_secuTrial", "factorize_secuTrial.secuTrialdata" ] }, { "page": "form_status_counts", "title": "A function to assess the status of forms", "topics": [ "form_status_counts" ] }, { "page": "form_status_summary", "title": "A function to show summary statistics for form statuses", "topics": [ "form_status_summary" ] }, { "page": "get_participants", "title": "Retrieves participants present in 'secuTrialdata'", "topics": [ "get_participants" ] }, { "page": "labels_secuTrial", "title": "Get variable labels for secuTrialdata objects", "topics": [ "label", "label<-", "labels_secuTrial", "label_secuTrial", "units", "units<-" ] }, { "page": "links_secuTrial", "title": "Show links between forms", "topics": [ "links_secuTrial" ] }, { "page": "plot_recruitment", "title": "Plots the recruitment over time for 'secuTrialdata' objects", "topics": [ "plot_recruitment" ] }, { "page": "read_secuTrial", "title": "Read secuTrial export", "topics": [ "read_secuTrial" ] }, { "page": "read_validation_overview", "title": "This function loads a multi-page secuTrial 'Validation Overview' report into an R tibble.", "topics": [ "read_validation_overview" ] }, { "page": "return_hidden_items", "title": "Returns hidden items (variables) from 'secuTrialdata' objects", "topics": [ "return_hidden_items" ] }, { "page": "return_random_participants", "title": "Returns the random participants from a secuTrial export", "topics": [ "return_random_participants" ] }, { "page": "return_scores", "title": "Returns the score (calculated) items from 'secuTrialdata' objects", "topics": [ "return_scores" ] }, { "page": "secuTrialdata", "title": "This function loads a secuTrial export", "topics": [ "print.secuTrialdata", "read_secuTrial_raw", "secuTrialdata" ] }, { "page": "subset_secuTrial", "title": "Subsets a 'secuTrialdata' object", "topics": [ "subset_secuTrial" ] }, { "page": "visit_structure", "title": "Get the visit structure of 'secuTrialdata' objects", "topics": [ "plot.secuTrialvisit", "visit_structure" ] }, { "page": "write_secuTrial", "title": "Write secuTrial exports to other formats", "topics": [ "write_secuTrial", "write_secuTrial.data.frame", "write_secuTrial.secuTrialdata" ] } ], "_readme": "https://github.com/SwissClinicalTrialOrganisation/secuTrialR/raw/HEAD/README.md", "_rundeps": [ "bit", "bit64", "cellranger", "cli", "clipr", "cpp11", "crayon", "dplyr", "forcats", "generics", "glue", "haven", "hms", "lifecycle", "lubridate", "magrittr", "pillar", "pkgconfig", "prettyunits", "progress", "purrr", "R6", "readr", "readxl", "rematch", "rlang", "stringi", "stringr", "tibble", "tidyr", "tidyselect", "timechange", "tzdb", "utf8", "vctrs", "vroom", "withr" ], "_vignettes": [ { "source": "secuTrialR-package-vignette.Rmd", "filename": "secuTrialR-package-vignette.pdf", "title": "secuTrialR - a walkthrough", "author": "Patrick R. 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Haynes", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Install", "The CTU05 dataset", "secuTrial export options", "Reading a secuTrial data export into R", "The secuTrialdata object", "The data tables in the secuTrialdata object", "Accessing the tables and values", "Data transformations", "Export options", "Generic functions for secuTrialdata objects", "Show the study participants", "Recruitment over time", "Visit plan visualization", "Completeness of forms", "Form linkage", "Sampling random participants", "Retrieve score variables", "Retrieve hidden variables", "Finding changes/differences in project setup implementations", "Conversion to SPSS, STATA, SAS", "Subsetting secuTrialdata", "Building URLs to your secuTrial server", "The as.data.frame function", "Frequent warning messages", "Dates", "Factors", "Labels", "Merging forms in the secuTrialdata object", "A note on mnp* variables" ], "created": "2019-03-25 17:03:10", "modified": "2020-08-27 10:49:52", "commits": 19 } ], "_score": 5.681241237375588, "_indexed": false, "_nocasepkg": "secutrialr", "_universes": [ "dcr-unibe-ch" ], "_indexurl": "https://swissclinicaltrialorganisation.r-universe.dev/secuTrialR", "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.3.3", "date": "2026-05-11T09:22:39.000Z", "distro": "noble", "commit": "9583775b467a5bba35bb1b57328b3e1292150816", "fileid": "0ebf0902e875fd7cbaaf6e27e1c8086cfb3e257a9892f345b723a62cb04a8b30", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/dcr-unibe-ch/actions/runs/25661378271" }, { "r": "4.6.0", "os": "linux", "version": "1.3.3", "date": "2026-05-11T09:23:10.000Z", "distro": "noble", "commit": "9583775b467a5bba35bb1b57328b3e1292150816", "fileid": "f86fabc4e5a7eff989a17a6c5c2970ecea80b3a3f1fd67e07a05f61438733b19", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/dcr-unibe-ch/actions/runs/25661378271" }, { "r": "4.5.3", "os": "mac", "version": "1.3.3", "date": "2026-05-11T09:21:57.000Z", "commit": "9583775b467a5bba35bb1b57328b3e1292150816", "fileid": "2a6f1513de0159dbaa18e4fbfa96544cc332243a6463882fa7f493a048d7227e", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/dcr-unibe-ch/actions/runs/25661378271" }, { "r": "4.6.0", "os": "mac", "version": "1.3.3", "date": "2026-05-11T09:22:34.000Z", "commit": "9583775b467a5bba35bb1b57328b3e1292150816", "fileid": "c8c95aaeab83a1aaab89f2ebe1a93ef128e51cce19807dbb949d27e52ce5bf7e", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/dcr-unibe-ch/actions/runs/25661378271" }, { "r": "4.7.0", "os": "win", "version": "1.3.3", "date": "2026-05-11T09:22:02.000Z", "commit": "9583775b467a5bba35bb1b57328b3e1292150816", "fileid": "3f1a463945a6796116bcbae098d147da0c9166fefdee660000c515b10b878eaf", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/dcr-unibe-ch/actions/runs/25661378271" }, { "r": "4.5.3", "os": "win", "version": "1.3.3", "date": "2026-05-11T09:21:51.000Z", "commit": "9583775b467a5bba35bb1b57328b3e1292150816", "fileid": "75dd5a0a147f64d713ceecce93b8927708faa68cb394a78842288eceea10f1e2", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/dcr-unibe-ch/actions/runs/25661378271" }, { "r": "4.6.0", "os": "win", "version": "1.3.3", "date": "2026-05-11T09:21:48.000Z", "commit": "9583775b467a5bba35bb1b57328b3e1292150816", "fileid": "6c9adc8de8afd51bb9ea26a08eb3031421ef1344ae286459b77dea75f1ec519a", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/dcr-unibe-ch/actions/runs/25661378271" }, { "r": "4.6.0", "os": "wasm", "version": "1.3.3", "date": "2026-05-22T11:30:04.000Z", "commit": "9583775b467a5bba35bb1b57328b3e1292150816", "fileid": "2b63087faa511f2c270af3bc6df9819f87f748f4ff4b4dccb17be4a02ca7eeb1", "status": "success", "buildurl": "https://github.com/r-universe/dcr-unibe-ch/actions/runs/25661378271" } ] }