{ "_id": "6a45aa1f6ff6f23575530605", "Package": "clerkR", "Title": "Publication-Ready Tables for Biomedical Research", "Version": "0.1.2", "Authors@R": "c(\nperson(\"Lucas\", \"França\",\nemail = \"lucas.franca@northumbria.ac.uk\",\nrole = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0003-0853-1319\")),\nperson(\"Mario\", \"Leocadio-Miguel\",\nemail = \"mario.miguel@northumbria.ac.uk\",\nrole = \"aut\",\ncomment = c(ORCID = \"0000-0002-7248-3529\"))\n)", "Description": "Transforms standard R data frames into publication-ready\ntables across a handful of common archetypes found in\nbiomedical and neuroscience manuscripts: descriptive/Table 1\nwith group comparisons, heritability and variance components,\ncorrelation and partial correlation, regression coefficients,\nand simple descriptive summaries. Provides a unified rendering\npipeline targeting 'gt' (Word/PDF), 'reactable' (HTML), and\nLaTeX outputs, with consistent theming, domain/section\ngrouping, footnote handling for transformed variables, and FDR\nannotation.", "License": "MIT + file LICENSE", "Encoding": "UTF-8", "Roxygen": "list(markdown = TRUE)", "Config/testthat/edition": "3", "VignetteBuilder": "knitr", "URL": "https://clerkr.circadia-lab.uk,\nhttps://github.com/circadia-bio/clerkR", "BugReports": "https://github.com/circadia-bio/clerkR/issues", "LazyData": "true", "Config/roxygen2/version": "8.0.0", "Config/pak/sysreqs": "cmake make libicu-dev libuv1-dev libxml2-dev\nlibssl-dev libnode-dev", "Repository": "https://circadia-bio.r-universe.dev", "Date/Publication": "2026-06-29 05:23:35 UTC", "RemoteUrl": "https://github.com/circadia-bio/clerkR", "RemoteRef": "main", "RemoteSha": "6fbd608d52b5ab7ac5b575a8ca5b4e5e4d45ba09", "NeedsCompilation": "no", "Packaged": { "Date": "2026-07-01 23:56:44 UTC", "User": "root" }, "Author": "Lucas França [aut, cre] (ORCID:\n),\nMario Leocadio-Miguel [aut] (ORCID:\n)", "Maintainer": "Lucas França ", "MD5sum": "c92d79eef3116484d9f2fc7188e66c2f", "_user": "circadia-bio", "_type": "src", "_file": "clerkR_0.1.2.tar.gz", "_fileid": "6f4037a830b55f1a19cea55336db31177255da9a45ad6f41538b3d00234032d5", "_filesize": 261912, "_sha256": "6f4037a830b55f1a19cea55336db31177255da9a45ad6f41538b3d00234032d5", "_created": "2026-07-01T23:56:44.000Z", "_published": "2026-07-02T00:00:31.669Z", "_distro": "resolute", "_jobs": [ { "job": 84662613443, "time": 141, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "8025556636" }, { "job": 84662613445, "time": 141, "config": "linux-release-x86_64", "r": "4.6.1", "check": "NOTE", "artifact": "8025556592" }, { "job": 84662613499, "time": 171, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "8025559823" }, { "job": 84662613468, "time": 163, "config": "macos-release-arm64", "r": "4.6.1", "check": "NOTE", "artifact": "8025553584" }, { "job": 84662183149, "time": 218, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "8025523825" }, { "job": 84662613432, "time": 146, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "8025557906" }, { "job": 84662613446, "time": 84, "config": "windows-devel", "r": "4.7.0", "check": "NOTE", "artifact": "8025544001" }, { "job": 84662613482, "time": 78, "config": "windows-oldrel", "r": "4.5.3", "check": "NOTE", "artifact": "8025543571" }, { "job": 84662613493, "time": 90, "config": "windows-release", "r": "4.6.1", "check": "NOTE", "artifact": "8025545749" } ], "_buildurl": "https://github.com/r-universe/circadia-bio/actions/runs/28555566608", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/circadia-bio/clerkR", "_commit": { "id": "6fbd608d52b5ab7ac5b575a8ca5b4e5e4d45ba09", "author": "Lucas França ", "committer": "GitHub ", "message": "Update README.md", "time": 1782710615 }, "_maintainer": { "name": "Lucas França", "email": "lucas.franca@northumbria.ac.uk", "login": "lucasfr", "description": "Immigrant, physicist, neuroscientist, open source and data science enthusiast.", "uuid": 502265, "orcid": "0000-0003-0853-1319" }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.1.0", "role": "Depends" }, { "package": "dplyr", "version": ">= 1.1.0", "role": "Imports" }, { "package": "tidyr", "role": "Imports" }, { "package": "rlang", "role": "Imports" }, { "package": "gt", "version": ">= 0.10.0", "role": "Imports" }, { "package": "reactable", "version": ">= 0.4.0", "role": "Imports" }, { "package": "htmltools", "role": "Imports" }, { "package": "knitr", "role": "Imports" }, { "package": "grDevices", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "testthat", "version": ">= 3.0.0", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" } ], "_owner": "circadia-bio", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2026-26", "n": 44 }, { "week": "2026-27", "n": 1 } ], "_tags": [], "_stars": 0, "_contributors": [ { "user": "lucasfr", "count": 45, "uuid": 502265 } ], "_userbio": { "uuid": 202348599, "type": "organization", "name": "Circadia Lab", "followers": 3 }, "_downloads": { "count": 0, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/clerkR" }, "_devurl": "https://github.com/circadia-bio/clerkr", "_pkgdown": "https://clerkr.circadia-lab.uk", "_searchresults": 0, "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/clerkR.html", "extra/contents.json", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "LICENSE", "manual.pdf" ], "_cranurl": false, "_exports": [ "clerk_colour", "clerk_diverging", "clerk_options", "clerk_palette", "clerk_render", "clerk_sequential", "clerk_theme", "render_gt", "render_latex", "render_reactable", "tbl_correlation", "tbl_descriptive", "tbl_heritability", "tbl_regression", "tbl_simple" ], "_datasets": [ { "name": "clerk_cor_example", "title": "Synthetic partial correlation results for clerkR examples", "object": "clerk_cor_example", "class": [ "data.frame" ], "fields": [ "variable", "outcome", "n", "r", "p" ], "rows": 16, "table": true, "tojson": true }, { "name": "clerk_example", "title": "Synthetic example dataset for clerkR", "object": "clerk_example", "class": [ "data.frame" ], "fields": [ "sex", "age", "hdl", "glucose", "bmi", "waist", "systolic_bp", "tmt_time", "verbal_fluency", "bdi", "panas_neg", "life_satisfaction" ], "rows": 300, "table": true, "tojson": true }, { "name": "clerk_h2_example", "title": "Synthetic heritability estimates for clerkR examples", "object": "clerk_h2_example", "class": [ "data.frame" ], "fields": [ "trait", "covariates", "h2", "ci_lo", "ci_hi", "pval", "sigma2_a", "sigma2_e" ], "rows": 12, "table": true, "tojson": true }, { "name": "clerk_reg_example", "title": "Synthetic regression results for clerkR examples", "object": "clerk_reg_example", "class": [ "data.frame" ], "fields": [ "term", "estimate", "std.error", "conf.low", "conf.high", "p.value" ], "rows": 7, "table": true, "tojson": true } ], "_help": [ { "page": "clerk_colour", "title": "Access a single clerkR colour by name", "topics": [ "clerk_colour" ] }, { "page": "clerk_cor_example", "title": "Synthetic partial correlation results for clerkR examples", "topics": [ "clerk_cor_example" ] }, { "page": "clerk_diverging", "title": "Build a clerkR diverging colour scale", "topics": [ "clerk_diverging" ] }, { "page": "clerk_example", "title": "Synthetic example dataset for clerkR", "topics": [ "clerk_example" ] }, { "page": "clerk_h2_example", "title": "Synthetic heritability estimates for clerkR examples", "topics": [ "clerk_h2_example" ] }, { "page": "clerk_options", "title": "clerkR session options", "topics": [ "clerk_options" ] }, { "page": "clerk_palette", "title": "clerkR colour palette", "topics": [ "clerk_palette" ] }, { "page": "clerk_reg_example", "title": "Synthetic regression results for clerkR examples", "topics": [ "clerk_reg_example" ] }, { "page": "clerk_render", "title": "Render a clerk_tbl to its target output format", "topics": [ "clerk_render" ] }, { "page": "clerk_sequential", "title": "Build a clerkR sequential colour scale", "topics": [ "clerk_sequential" ] }, { "page": "clerk_theme", "title": "Apply the clerkR gt theme to a gt table", "topics": [ "clerk_theme" ] }, { "page": "render_gt", "title": "Render a clerk_tbl as a gt table (Word / PDF)", "topics": [ "render_gt" ] }, { "page": "render_latex", "title": "Render a clerk_tbl as a LaTeX table", "topics": [ "render_latex" ] }, { "page": "render_reactable", "title": "Render a clerk_tbl as an interactive HTML table", "topics": [ "render_reactable" ] }, { "page": "tbl_correlation", "title": "Correlation / partial correlation table", "topics": [ "tbl_correlation" ] }, { "page": "tbl_descriptive", "title": "Descriptive summary table with group comparisons (Table 1)", "topics": [ "tbl_descriptive" ] }, { "page": "tbl_heritability", "title": "Heritability and variance components table", "topics": [ "tbl_heritability" ] }, { "page": "tbl_regression", "title": "Regression coefficients table", "topics": [ "tbl_regression" ] }, { "page": "tbl_simple", "title": "Simple descriptive summary table (no inferential tests)", "topics": [ "tbl_simple" ] } ], "_pkglogo": "https://github.com/circadia-bio/clerkR/raw/main/man/figures/logo.svg", "_readme": "https://github.com/circadia-bio/clerkR/raw/main/README.md", "_rundeps": [ "base64enc", "bigD", "bitops", "bslib", "cachem", "cli", "commonmark", "cpp11", "curl", "digest", "dplyr", "evaluate", "farver", "fastmap", "fontawesome", "fs", "generics", "glue", "gt", "highr", "htmltools", "htmlwidgets", "jquerylib", "jsonlite", "juicyjuice", "knitr", "labeling", "lifecycle", "litedown", "magrittr", "markdown", "memoise", "mime", "pillar", "pkgconfig", "purrr", "R6", "rappdirs", "RColorBrewer", "Rcpp", "reactable", "reactR", "rlang", "rmarkdown", "sass", "scales", "stringi", "stringr", "tibble", "tidyr", "tidyselect", "tinytex", "utf8", "V8", "vctrs", "viridisLite", "withr", "xfun", "xml2", "yaml" ], "_vignettes": [ { "source": "correlation.Rmd", "filename": "correlation.html", "title": "Correlation and partial correlation tables", "engine": "knitr::rmarkdown", "headings": [ "Overview", "Basic long-format table", "Including sample size", "Domain grouping", "FDR correction", "Wide (pivoted) format", "Custom column names", "HTML output" ], "created": "2026-06-26 15:08:38", "modified": "2026-06-26 15:08:38", "commits": 1 }, { "source": "descriptive-table1.Rmd", "filename": "descriptive-table1.html", "title": "Descriptive tables (Table 1)", "engine": "knitr::rmarkdown", "headings": [ "Overview", "Basic usage", "Group comparisons", "Domain grouping", "Log-transformed variables", "FDR correction", "Selecting variables", "HTML output", "Inspecting the underlying data" ], "created": "2026-06-26 15:08:38", "modified": "2026-06-26 15:08:38", "commits": 1 }, { "source": "formatting-options.Rmd", "filename": "formatting-options.html", "title": "Formatting options", "engine": "knitr::rmarkdown", "headings": [ "Overview", "P-value style", "Decimal places", "Significance stars", "FDR display", "Domain labels for unassigned variables", "Session-wide vs per-call options", "Full option reference" ], "created": "2026-06-27 01:31:26", "modified": "2026-06-27 01:42:16", "commits": 4 }, { "source": "getting-started.Rmd", "filename": "getting-started.html", "title": "Getting started with clerkR", "engine": "knitr::rmarkdown", "headings": [ "Overview", "Installation", "The example datasets", "A minimal Table 1", "Adding domain grouping", "Changing the output format", "The clerkR palette", "What next?" ], "created": "2026-06-26 15:08:38", "modified": "2026-06-26 15:08:38", "commits": 1 }, { "source": "heritability-ritable.Rmd", "filename": "heritability-ritable.html", "title": "Heritability tables with R-itable and clerkR", "engine": "knitr::rmarkdown", "headings": [ "Overview", "Setup", "1. Simulate a family cohort", "2. Build GRM and run batch estimation", "3. Render the full table", "Filtering to a single model", "HTML output" ], "created": "2026-06-26 14:38:38", "modified": "2026-06-26 23:00:00", "commits": 6 }, { "source": "regression.Rmd", "filename": "regression.html", "title": "Regression coefficient tables", "engine": "knitr::rmarkdown", "headings": [ "Overview", "Basic usage", "Domain grouping", "FDR correction", "Using broom::tidy() directly", "Logistic regression — exponentiated coefficients", "Custom column names", "HTML output" ], "created": "2026-06-26 15:08:38", "modified": "2026-06-26 15:08:38", "commits": 1 }, { "source": "simple-descriptive.Rmd", "filename": "simple-descriptive.html", "title": "Simple descriptive tables", "engine": "knitr::rmarkdown", "headings": [ "Overview", "Basic usage", "Selecting variables", "Domain grouping", "Log-transformed variables", "HTML output", "When to use tbl_simple() vs tbl_descriptive()" ], "created": "2026-06-26 15:08:38", "modified": "2026-06-26 15:08:38", "commits": 1 } ], "_score": 3.845098040014257, "_indexed": true, "_nocasepkg": "clerkr", "_universes": [ "circadia-bio", "lucasfr" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "0.1.2", "date": "2026-07-01T23:59:16.000Z", "distro": "resolute", "commit": "6fbd608d52b5ab7ac5b575a8ca5b4e5e4d45ba09", "fileid": "ad1c99c470f0ed66a684d6c5ad6b83c1c7bb806f7622fae59825d7dd7138218c", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/circadia-bio/actions/runs/28555566608" }, { "r": "4.6.1", "os": "linux", "version": "0.1.2", "date": "2026-07-01T23:59:17.000Z", "distro": "resolute", "commit": "6fbd608d52b5ab7ac5b575a8ca5b4e5e4d45ba09", "fileid": "15841d87ea3ace67775b97ae4e31d6ef9e05bfb6b6927e8d3afa5b8db66875fc", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/circadia-bio/actions/runs/28555566608" }, { "r": "4.5.3", "os": "mac", "version": "0.1.2", "date": "2026-07-01T23:59:31.000Z", "commit": "6fbd608d52b5ab7ac5b575a8ca5b4e5e4d45ba09", "fileid": "0b7d2131e9a32b87ac835ff28b2e5be7c1940ea8c36849d884a6aa0921df1b8b", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/circadia-bio/actions/runs/28555566608" }, { "r": "4.6.1", "os": "mac", "version": "0.1.2", "date": "2026-07-01T23:59:04.000Z", "commit": "6fbd608d52b5ab7ac5b575a8ca5b4e5e4d45ba09", "fileid": "3d63e9ce891ffe7bc8eed1cc430c647dbc7e830e256211ab43d0509c4ccb660a", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/circadia-bio/actions/runs/28555566608" }, { "r": "4.6.0", "os": "wasm", "version": "0.1.2", "date": "2026-07-01T23:59:39.000Z", "commit": "6fbd608d52b5ab7ac5b575a8ca5b4e5e4d45ba09", "fileid": "2587e63d5c1b738f2397e7d8279e7e8a58126e28098fd2f4e87f9bc7082ea478", "status": "success", "buildurl": "https://github.com/r-universe/circadia-bio/actions/runs/28555566608" }, { "r": "4.7.0", "os": "win", "version": "0.1.2", "date": "2026-07-01T23:58:16.000Z", "commit": "6fbd608d52b5ab7ac5b575a8ca5b4e5e4d45ba09", "fileid": "ca14577a1e02d6870470e0176d1846de6df4819436c1b0326bdae0645d79bd52", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/circadia-bio/actions/runs/28555566608" }, { "r": "4.5.3", "os": "win", "version": "0.1.2", "date": "2026-07-01T23:58:10.000Z", "commit": "6fbd608d52b5ab7ac5b575a8ca5b4e5e4d45ba09", "fileid": "878e4a6ca617cd161d724ecff934687bb68c31bfa666ee70fc3d679031b5f3ee", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/circadia-bio/actions/runs/28555566608" }, { "r": "4.6.1", "os": "win", "version": "0.1.2", "date": "2026-07-01T23:58:23.000Z", "commit": "6fbd608d52b5ab7ac5b575a8ca5b4e5e4d45ba09", "fileid": "c39cd896af84605a3241c0fc0342d2843783b7db83660645f8be2fc1e266be56", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/circadia-bio/actions/runs/28555566608" } ] }