{ "_id": "6a1f37a7b401979e73428d62", "Package": "CLRtools", "Title": "Diagnostic Tools for Logistic and Conditional Logistic\nRegression", "Version": "0.1.1", "Authors@R": "c(\nperson(\"Brenda\", \"Contla Hernández\",\nemail = \"B.Hernandez@massey.ac.nz\",\nrole = c(\"aut\", \"cre\")),\nperson(\"Matthieu\", \"Vignes\",\nrole = \"ctb\",\ncomment = \"Provided statistical guidance, conceptual feedback, and supervision\"),\nperson(\"Chris\", \"Compton\",\nrole = \"ctb\",\ncomment = \"Provided statistical guidance, conceptual feedback, and supervision\")\n)", "Description": "Provides tools for fitting, assessing, and comparing\nlogistic and conditional logistic regression models. Includes\nresidual diagnostics and goodness of fit measures for model\ndevelopment and evaluation in matched case control studies.", "License": "GPL-3", "Encoding": "UTF-8", "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "7.3.3", "VignetteBuilder": "knitr", "LazyData": "true", "URL": "https://github.com/brendacontla/CLRtools", "BugReports": "https://github.com/brendacontla/CLRtools/issues", "Config/pak/sysreqs": "cmake make libicu-dev", "Repository": "https://brendacontla.r-universe.dev", "Date/Publication": "2026-03-15 23:36:30 UTC", "RemoteUrl": "https://github.com/brendacontla/clrtools", "RemoteRef": "HEAD", "RemoteSha": "095d2d61e48faa2fb8fea5283aa8cafd2fe41f77", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-15 05:50:46 UTC", "User": "root" }, "Author": "Brenda Contla Hernández [aut, cre],\nMatthieu Vignes [ctb] (Provided statistical guidance, conceptual\nfeedback, and supervision),\nChris Compton [ctb] (Provided statistical guidance, conceptual\nfeedback, and supervision)", "Maintainer": "Brenda Contla Hernández ", "MD5sum": "854e55785fbdcfdce4eafe1c124ea3c8", "_user": "brendacontla", "_type": "src", "_file": "CLRtools_0.1.1.tar.gz", "_fileid": "784445a0d6ee3b6485613842c745a9a0c6b491b745755930d5d6b997de85c679", "_filesize": 8101891, "_sha256": "784445a0d6ee3b6485613842c745a9a0c6b491b745755930d5d6b997de85c679", "_created": "2026-05-15T05:50:46.000Z", "_published": "2026-06-02T20:05:59.340Z", "_distro": "noble", "_jobs": [ { "job": 79161258320, "time": 284, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7011004441" }, { "job": 79161258504, "time": 264, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7011000142" }, { "job": 79161259346, "time": 213, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7011161980" }, { "job": 79161258360, "time": 238, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7011133761" }, { "job": 79161257441, "time": 458, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7010946816" }, { "job": 79161257507, "time": 179, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7368545562" }, { "job": 79161258630, "time": 194, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "7010986229" }, { "job": 79161259119, "time": 166, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "7010980690" }, { "job": 79161259092, "time": 209, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "7010988872" } ], "_buildurl": "https://github.com/r-universe/brendacontla/actions/runs/25902470640", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/brendacontla/clrtools", "_commit": { "id": "095d2d61e48faa2fb8fea5283aa8cafd2fe41f77", "author": "Brenda Contla Hernandez <57643005+brendacontla@users.noreply.github.com>", "committer": "GitHub ", "message": "Delete cran-comments.md", "time": 1773617790 }, "_maintainer": { "name": "Brenda Contla Hernández", "email": "b.hernandez@massey.ac.nz" }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.5", "role": "Depends" }, { "package": "bayesplot", "role": "Imports" }, { "package": "caret", "role": "Imports" }, { "package": "dplyr", "role": "Imports" }, { "package": "ggplot2", "role": "Imports" }, { "package": "ggpubr", "role": "Imports" }, { "package": "lmtest", "role": "Imports" }, { "package": "loo", "role": "Imports" }, { "package": "patchwork", "role": "Imports" }, { "package": "RColorBrewer", "role": "Imports" }, { "package": "rlang", "role": "Imports" }, { "package": "rstan", "role": "Imports" }, { "package": "survival", "role": "Imports" }, { "package": "tidyr", "role": "Imports" }, { "package": "dagitty", "role": "Suggests" }, { "package": "ggdag", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "rstanarm", "role": "Suggests" } ], "_owner": "brendacontla", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2026-05", "n": 4 }, { "week": "2026-06", "n": 1 }, { "week": "2026-11", "n": 2 } ], "_tags": [], "_stars": 0, "_contributors": [ { "user": "brendacontla", "count": 7, "uuid": 57643005 } ], "_userbio": { "uuid": 57643005, "type": "user", "name": "Brenda Contla Hernandez" }, "_downloads": { "count": 552, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/CLRtools" }, "_devurl": "https://github.com/brendacontla/clrtools", "_searchresults": 0, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/CLRtools.html", "extra/contents.json", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_homeurl": "https://github.com/brendacontla/clrtools", "_realowner": "brendacontla", "_cranurl": true, "_releases": [ { "version": "0.1.0", "date": "2026-01-29" }, { "version": "0.1.1", "date": "2026-03-16" } ], "_exports": [ "check_coef_change", "check_coef_significant", "check_interactions", "coeff.OR", "compare_bayesm", "compare_bayesm_by_predictor", "compare_models_loo", "confidence.interval", "cov.patterns", "cutpoints", "delta.coefficient", "diagnostic_bayes", "diagnosticplots_class", "discordant.pairs", "DRtest", "logit_prob_plot", "osius_rojek", "r_measures", "rcv_measures", "residuals_clog", "residuals_logistic", "stukels_test", "summarize_results", "univariable.clogmodels", "univariable.models" ], "_datasets": [ { "name": "glow11m", "title": "GLOW11M dataset", "object": "glow11m", "class": [ "data.frame" ], "fields": [ "pair", "sub_id", "site_id", "phy_id", "age", "height", "weight", "bmi", "priorfrac", "premeno", "momfrac", "armassist", "smoke", "raterisk", "fracscore", "fracture" ], "rows": 238, "table": true, "tojson": true }, { "name": "glow500", "title": "GLOW500 dataset", "object": "glow500", "class": [ "data.frame" ], "fields": [ "sub_id", "site_id", "phy_id", "priorfrac", "age", "weight", "height", "bmi", "premeno", "momfrac", "armassist", "smoke", "raterisk", "fracscore", "fracture" ], "rows": 500, "table": true, "tojson": true } ], "_help": [ { "page": "check_coef_change", "title": "Assess Coefficient Change After Variable Removal", "topics": [ "check_coef_change" ] }, { "page": "check_coef_significant", "title": "Check Significance of Excluded Variables", "topics": [ "check_coef_significant" ] }, { "page": "check_interactions", "title": "Check Pairwise Interactions in Logistic Regression", "topics": [ "check_interactions" ] }, { "page": "coeff.OR", "title": "Compute Odds Ratios for Logistic and Conditional Logistic Regression Models", "topics": [ "coeff.OR" ] }, { "page": "compare_bayesm", "title": "Posterior Predictive Check for Multiple Bayesian Models", "topics": [ "compare_bayesm" ] }, { "page": "compare_bayesm_by_predictor", "title": "Compare Bayesian Models by Predictor Using Posterior Predictive Simulations", "topics": [ "compare_bayesm_by_predictor" ] }, { "page": "compare_models_loo", "title": "Compare Bayesian Models Using PSIS-LOO", "topics": [ "compare_models_loo" ] }, { "page": "confidence.interval", "title": "Compute Wald-Based Confidence Intervals for Logit and Predicted Probability", "topics": [ "confidence.interval" ] }, { "page": "cov.patterns", "title": "Extract Unique Covariate Patterns from a Logistic Regression Model", "topics": [ "cov.patterns" ] }, { "page": "cutpoints", "title": "Table with Sensitivity and Specificity at Different Cutpoints", "topics": [ "cutpoints" ] }, { "page": "delta.coefficient", "title": "Delta-beta hat percentage: Change in Coefficients when Adding a Variable", "topics": [ "delta.coefficient" ] }, { "page": "diagnostic_bayes", "title": "Generate MCMC Diagnostic Plots for a Bayesian Model", "topics": [ "diagnostic_bayes" ] }, { "page": "diagnosticplots_class", "title": "Diagnostic Plots for Model Discrimination", "topics": [ "diagnosticplots_class" ] }, { "page": "discordant.pairs", "title": "Count Discordant Pairs in Matched Case-Control Data", "topics": [ "discordant.pairs" ] }, { "page": "DRtest", "title": "Deviance Residuals Test (HL Test)", "topics": [ "DRtest" ] }, { "page": "glow11m", "title": "GLOW11M dataset", "topics": [ "glow11m" ] }, { "page": "glow500", "title": "GLOW500 dataset", "topics": [ "glow500" ] }, { "page": "logit_prob_plot", "title": "Plot Predicted Probabilities from a Logistic Model", "topics": [ "logit_prob_plot" ] }, { "page": "osius_rojek", "title": "Osius and Rojek Goodness-of-Fit Test for Logistic Regression", "topics": [ "osius_rojek" ] }, { "page": "r_measures", "title": "Model Fit Evaluation: R^2-like Measures for Logistic Regression Models with J=n", "topics": [ "r_measures" ] }, { "page": "rcv_measures", "title": "Model Fit Evaluation: R^2-like Measures for Logistic Regression Models with J < n", "topics": [ "rcv_measures" ] }, { "page": "residuals_clog", "title": "Model Diagnostic for Conditional Logistic Regression", "topics": [ "residuals_clog" ] }, { "page": "residuals_logistic", "title": "Model Diagnostic for Logistic Regression Models", "topics": [ "residuals_logistic" ] }, { "page": "stukels_test", "title": "Stukel’s Test for Logistic Regression Model Fit", "topics": [ "stukels_test" ] }, { "page": "summarize_results", "title": "Summarize Bayesian Logistic Regression Model Results", "topics": [ "summarize_results" ] }, { "page": "univariable.clogmodels", "title": "Univariable Conditional Logistic Regression Models", "topics": [ "univariable.clogmodels" ] }, { "page": "univariable.models", "title": "Univariable Logistic Regression Summary Table", "topics": [ "univariable.models" ] } ], "_readme": "https://github.com/brendacontla/clrtools/raw/HEAD/README.md", "_rundeps": [ "abind", "backports", "bayesplot", "BH", "boot", "broom", "callr", "car", "carData", "caret", "checkmate", "class", "cli", "clock", "codetools", "colorspace", "corrplot", "cowplot", "cpp11", "data.table", "Deriv", "desc", "diagram", "digest", "distributional", "doBy", "dplyr", "e1071", "farver", "foreach", "forecast", "Formula", "fracdiff", "future", "future.apply", "generics", "ggplot2", "ggpubr", "ggrepel", "ggridges", "ggsci", "ggsignif", "globals", "glue", "gower", "gridExtra", "gtable", "hardhat", "inline", "ipred", "isoband", "iterators", "KernSmooth", "labeling", "lattice", "lava", "lifecycle", "listenv", "lme4", "lmtest", "loo", "lubridate", "magrittr", "MASS", "Matrix", "MatrixModels", "matrixStats", "mgcv", "microbenchmark", "minqa", "ModelMetrics", "modelr", "nlme", "nloptr", "nnet", "numDeriv", "parallelly", "patchwork", "pbkrtest", "pillar", "pkgbuild", "pkgconfig", "plyr", "polynom", "posterior", "pROC", "processx", "prodlim", "progressr", "proxy", "ps", "purrr", "quantreg", "QuickJSR", "R6", "rbibutils", "RColorBrewer", "Rcpp", "RcppArmadillo", "RcppEigen", "RcppParallel", "Rdpack", "recipes", "reformulas", "reshape2", "rlang", "rpart", "rstan", "rstatix", "S7", "scales", "shape", "SparseM", "sparsevctrs", "SQUAREM", "StanHeaders", "stringi", "stringr", "survival", "tensorA", "tibble", "tidyr", "tidyselect", "timechange", "timeDate", "tzdb", "urca", "utf8", "vctrs", "viridisLite", "withr", "zoo" ], "_vignettes": [ { "source": "Bayesian_Logistic_regression.Rmd", "filename": "Bayesian_Logistic_regression.html", "title": "Bayesian_Logistic_regression", "engine": "knitr::rmarkdown", "headings": [ "Causal Diagram", "Bayesian Analysis", "Weight", "Direct effect", "Checking priors", "Posterior distribution", "Total effect", "Conclusion" ], "created": "2026-01-30 04:26:20", "modified": "2026-03-13 04:02:12", "commits": 2 }, { "source": "Conditional_Logistic_Regression.Rmd", "filename": "Conditional_Logistic_Regression.html", "title": "Conditional_Logistic_Regression", "engine": "knitr::rmarkdown", "headings": [ "Step 1. Fit univariable models", "Step 2: Fit Initial multivariate Model and Refine Predictors", "Step 3: Assess Potential Confounding", "Step 4: Reassess Excluded Variables", "Step 5: Assess Linearity of Continuous Predictors with Respect to the Logit", "Step 6: Assess Interaction Terms", "Step 7: Perform Model Assessment" ], "created": "2026-01-30 04:26:20", "modified": "2026-01-30 04:26:20", "commits": 1 }, { "source": "Logistic_Regression.Rmd", "filename": "Logistic_Regression.html", "title": "Logistic_Regression", "engine": "knitr::rmarkdown", "headings": [ "Step 1. Fit univariable models", "Step 2: Fit Initial multivariable Model and Refine Predictors", "Step 3: Assess Potential Confounding", "Step 4: Reassess Excluded Variables", "Step 5: Assess Linearity of Continuous Predictors with Respect to the Logit", "Step 6: Assess Interaction Terms", "Step 7: Perform Model Assessment", "Measure of goodness of fit", "Classification tables", "$R^2$ measures", "Logistic regression diagnostics" ], "created": "2026-01-30 04:26:20", "modified": "2026-01-30 04:26:20", "commits": 1 } ], "_score": 4.653212513775344, "_indexed": true, "_nocasepkg": "clrtools", "_universes": [ "brendacontla" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "0.1.1", "date": "2026-05-15T05:54:33.000Z", "distro": "noble", "commit": "095d2d61e48faa2fb8fea5283aa8cafd2fe41f77", "fileid": "e38d5cd5129b901482c92fac1e8f73268b762c1633c46a291e22d078d98dc2ad", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/brendacontla/actions/runs/25902470640" }, { "r": "4.6.0", "os": "linux", "version": "0.1.1", "date": "2026-05-15T05:54:10.000Z", "distro": "noble", "commit": "095d2d61e48faa2fb8fea5283aa8cafd2fe41f77", "fileid": "058d1fe85adbfd35480cc5ed83515c4d11696e1ad2a99291ed2d997b678fb77b", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/brendacontla/actions/runs/25902470640" }, { "r": "4.5.3", "os": "mac", "version": "0.1.1", "date": "2026-05-15T06:08:11.000Z", "commit": "095d2d61e48faa2fb8fea5283aa8cafd2fe41f77", "fileid": "c79178fecb9ad4d74cd3e8c8af35629f76b11d6922a71e9fbcaa236a9b6dc232", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/brendacontla/actions/runs/25902470640" }, { "r": "4.6.0", "os": "mac", "version": "0.1.1", "date": "2026-05-15T06:05:33.000Z", "commit": "095d2d61e48faa2fb8fea5283aa8cafd2fe41f77", "fileid": "4270098ccb7db5ce28f01a46da2620f87962e039be28f9b62cac0b8bf7c29543", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/brendacontla/actions/runs/25902470640" }, { "r": "4.7.0", "os": "win", "version": "0.1.1", "date": "2026-05-15T05:52:54.000Z", "commit": "095d2d61e48faa2fb8fea5283aa8cafd2fe41f77", "fileid": "6225e122187f9c8cebde9e762460635ee228c60119dc5e94bf5776fb10c2fde8", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/brendacontla/actions/runs/25902470640" }, { "r": "4.5.3", "os": "win", "version": "0.1.1", "date": "2026-05-15T05:52:48.000Z", "commit": "095d2d61e48faa2fb8fea5283aa8cafd2fe41f77", "fileid": "b7f2470bc933af992dca36d262caeb3ff35588011fc4971a5df02c8f0a590dba", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/brendacontla/actions/runs/25902470640" }, { "r": "4.6.0", "os": "win", "version": "0.1.1", "date": "2026-05-15T05:53:13.000Z", "commit": "095d2d61e48faa2fb8fea5283aa8cafd2fe41f77", "fileid": "fd5e58d59e2c5a02825efb744acc9401d5408ab4f4b79dd9b87d1c34e62d09bf", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/brendacontla/actions/runs/25902470640" }, { "r": "4.6.0", "os": "wasm", "version": "0.1.1", "date": "2026-06-02T20:05:36.000Z", "commit": "095d2d61e48faa2fb8fea5283aa8cafd2fe41f77", "fileid": "53892a5985c6169ad9e4f41b2f534f7241f78be97b3910e14a3f1a18c51e96fe", "status": "success", "buildurl": "https://github.com/r-universe/brendacontla/actions/runs/25902470640" } ] }