{ "_id": "6ae448898d250e7ad09f11d1", "Package": "CCI", "Type": "Package", "Title": "Computational Test for Conditional Independence", "Version": "0.4.0", "Date": "2026-09-28", "Authors@R": "c(person(given = \"Christian\",\nfamily = \"Thorjussen\",\nrole = c(\"aut\", \"cre\"),\nemail = \"christianbern@gmail.com\",\ncomment = c(ORCID = \"0009-0005-5006-6491\")),\nperson(given = \"Kristian Hovde\",\nfamily = \"Liland\",\nrole = c(\"aut\"),\nemail = \"kristian.liland@nmbu.no\",\ncomment = c(ORCID = \"0000-0001-6468-9423\")))", "Maintainer": "Christian Thorjussen ", "Description": "Tool for performing computational testing for conditional\nindependence between variables in a dataset. 'CCI' implements\npermutation in combination with Monte Carlo Cross-Validation in\ngenerating null distributions and test statistics. For more\ndetails see Computational Test for Conditional Independence\n(2024) .", "License": "GPL (>= 2)", "URL": "https://github.com/khliland/CCI", "BugReports": "https://github.com/khliland/CCI/issues", "Encoding": "UTF-8", "LazyData": "true", "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "7.3.3", "VignetteBuilder": "knitr", "Config/testthat/edition": "3", "Config/pak/sysreqs": "libglpk-dev make libicu-dev libxml2-dev", "Repository": "https://khliland.r-universe.dev", "Date/Publication": "2026-09-29 14:34:47 UTC", "RemoteUrl": "https://github.com/khliland/cci", "RemoteRef": "HEAD", "RemoteSha": "2c71af0ecbcc9432c1b9358e8d7d84dd2e7e0487", "NeedsCompilation": "no", "Packaged": { "Date": "2026-10-29 12:49:16 UTC", "User": "root" }, "Author": "Christian Thorjussen [aut, cre] (ORCID:\n),\nKristian Hovde Liland [aut] (ORCID:\n)", "_user": "khliland", "_type": "src", "_file": "CCI_0.4.0.tar.gz", "_fileid": "https://r2.ropensci.org/0351d2b24e14b375acf9f62dd9daf0e0953a628ebc63cb8276fdc3a11108ec71", "_filesize": 1661527, "_sha256": "0351d2b24e14b375acf9f62dd9daf0e0953a628ebc63cb8276fdc3a11108ec71", "_expires": "2027-02-06T13:47:34.000Z", "_created": "2026-10-29T12:49:16.000Z", "_published": "2026-10-30T07:34:33.162Z", "_upstream": "https://github.com/khliland/cci", "_status": "success", "_maintainer": { "name": "Christian Thorjussen", "email": "christianbern@gmail.com", "login": "christianbht", "description": "Economist and data analyst researcher at Telemarksforskning Research Institute.", "uuid": 64216271, "orcid": "0009-0005-5006-6491" }, "_jobs": [ { "job": 123946270009, "time": 326, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "12899135578" }, { "job": 123946307212, "time": 232, "config": "linux-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "12899020823" }, { "job": 123946267597, "time": 152, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "12960494970" }, { "job": 123946298208, "time": 154, "config": "macos-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "12901788407" }, { "job": 123946268881, "time": 799, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "12897534108" }, { "job": 123946307247, "time": 140, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "12898576624" }, { "job": 123946310482, "time": 157, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "12898950697" }, { "job": 123946316867, "time": 167, "config": "windows-oldrel-x86_64", "r": "4.5.3", "check": "OK", "artifact": "12897839748" }, { "job": 123946269379, "time": 136, "config": "windows-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "12898033112" } ], "_buildurl": "https://github.com/r-universe/khliland/actions/runs/40874614052", "_commit": { "id": "2c71af0ecbcc9432c1b9358e8d7d84dd2e7e0487", "author": "Christian Thorjussen ", "committer": "Christian Thorjussen ", "message": "CCI 0.4.0: experimental CCI.crt() and reduce_Z_pca()\n\n- Add CCI.crt() (experimental): conditional randomization version of CCI.test.\n X is drawn from a QRF estimate of P(X | Z) instead of permuted, cross-fitted\n within each Monte Carlo sample; stratified permutation when all Z are\n categorical; residual_sampling = TRUE draws X* = m(z) + out-of-fold residual\n- Add null_method and residual_sampling to test.gen(); sampler draw_x_given_z()\n- Add reduce_Z_pca(): replaces numeric Z by principal components before testing\n- Help page notes when CCI.crt may help over CCI.test\n- Simulation script tests/testthat/check_crt.R, results in development/crt_results\n- Bump version to 0.4.0; update NEWS, AGENTS.md, DECISIONS.md, TODO.md\n\nCo-Authored-By: Claude Opus 5.5 \n", "time": 1790692487 }, "_distro": "resolute", "_host": "GitHub-Actions", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.5", "role": "Depends" }, { "package": "ggplot2", "role": "Imports" }, { "package": "dplyr", "role": "Imports" }, { "package": "caret", "role": "Imports" }, { "package": "xgboost", "role": "Imports" }, { "package": "ranger", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "data.table", "role": "Imports" }, { "package": "e1071", "role": "Imports" }, { "package": "rlang", "role": "Imports" }, { "package": "progress", "role": "Imports" }, { "package": "kknn", "role": "Imports" }, { "package": "testthat", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "dagitty", "role": "Suggests" } ], "_owner": "khliland", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-45", "n": 4 }, { "week": "2025-46", "n": 2 }, { "week": "2026-02", "n": 7 }, { "week": "2026-03", "n": 6 }, { "week": "2026-04", "n": 8 }, { "week": "2026-05", "n": 1 }, { "week": "2026-20", "n": 1 }, { "week": "2026-39", "n": 5 }, { "week": "2026-40", "n": 1 } ], "_tags": [], "_stars": 2, "_contributors": [ { "user": "christianbht", "count": 332, "uuid": 64216271 }, { "user": "khliland", "count": 5, "uuid": 9257806 } ], "_userbio": { "uuid": 9257806, "type": "user", "name": "Kristian Hovde Liland", "followers": 46 }, "_downloads": { "count": 463, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/CCI" }, "_devurl": "https://github.com/khliland/cci", "_searchresults": 12, "_rbuild": "4.6.1", "_assets": [ "extra/CCI.html", "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/manual.pdf", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md" ], "_homeurl": "https://github.com/khliland/cci", "_realowner": "khliland", "_cranurl": true, "_releases": [ { "version": "0.2.1", "date": "2025-08-19" }, { "version": "0.3.1", "date": "2025-08-28" }, { "version": "0.3.4", "date": "2025-09-11" }, { "version": "0.3.6", "date": "2026-01-21" }, { "version": "0.3.6.1", "date": "2026-03-03" }, { "version": "0.3.7", "date": "2026-09-23" } ], "_exports": [ "add_interaction_terms", "add_poly_terms", "build_formula", "CCI.crt", "CCI.direction", "CCI.pretuner", "CCI.test", "check_formula", "clean_formula", "get_pvalues", "get_tuned_params", "is_categorical_Z_any", "make_strata_from_categorical_Z", "perm.test", "permute_within_strata", "QQplot", "reduce_Z_pca", "test.gen", "unclean_formula", "wrapper_knn", "wrapper_ranger", "wrapper_svm", "wrapper_xgboost" ], "_datasets": [ { "name": "ExponentialNoise", "title": "Example dataset: ExponentialNoise", "object": "ExponentialNoise", "class": [ "data.frame" ], "fields": [ "Z1", "Z2", "X", "Y" ], "rows": 1000, "table": true, "tojson": true }, { "name": "HardCase", "title": "Example dataset: HardCase", "object": "HardCase", "class": [ "data.frame" ], "fields": [ "X", "Y", "Z1", "Z2" ], "rows": 500, "table": true, "tojson": true }, { "name": "NonLinearCategorization", "title": "Example dataset: NonLinearCategorization", "object": "NonLinearCategorization", "class": [ "data.frame" ], "fields": [ "Z", "X", "Y" ], "rows": 600, "table": true, "tojson": true }, { "name": "NonLinNormal", "title": "Example dataset: NonLinNormal", "object": "NonLinNormal", "class": [ "data.frame" ], "fields": [ "Z1", "Z2", "X", "Y" ], "rows": 500, "table": true, "tojson": true }, { "name": "NonLinNormalZs_d0", "title": "Example dataset: NonLinNormalZs_d0", "object": "NonLinNormalZs_d0", "class": [ "data.frame" ], "fields": [ "Z1", "Z2", "Z3", "Z4", "Z5", "Z6", "Z7", "Z8", "Z9", "Z10", "Z11", "Z12", "Z13", "Z14", "Z15", "X", "Y" ], "rows": 1000, "table": true, "tojson": true }, { "name": "NonLinNormalZs_d05", "title": "Example dataset: NonLinNormalZs_d05", "object": "NonLinNormalZs_d05", "class": [ "data.frame" ], "fields": [ "Z1", "Z2", "Z3", "Z4", "Z5", "Z6", "Z7", "Z8", "Z9", "Z10", "Z11", "Z12", "Z13", "Z14", "Z15", "X", "Y" ], "rows": 1000, "table": true, "tojson": true }, { "name": "NormalData", "title": "Example dataset: NormalData", "object": "NormalData", "class": [ "data.frame" ], "fields": [ "Z1", "Z2", "X", "Y" ], "rows": 400, "table": true, "tojson": true }, { "name": "PoissonNoise", "title": "Example dataset: PoissonNoise", "object": "PoissonNoise", "class": [ "data.frame" ], "fields": [ "Z1", "Z2", "X", "Y" ], "rows": 1000, "table": true, "tojson": true }, { "name": "PolyData", "title": "Example dataset: PolyData", "object": "PolyData", "class": [ "data.frame" ], "fields": [ "Z1", "Z2", "X", "Y" ], "rows": 600, "table": true, "tojson": true }, { "name": "UniformNoise_large", "title": "Example dataset: UniformNoise_large", "object": "UniformNoise_large", "class": [ "data.frame" ], "fields": [ "Z1", "Z2", "X", "Y" ], "rows": 20000, "table": true, "tojson": true } ], "_help": [ { "page": "add_interaction_terms", "title": "Creates interaction terms for specified variables in a data frame Interaction terms are named as '_int_' (e.g., 'Z1_int_Z2' for the product of 'Z1' and 'Z2').", "topics": [ "add_interaction_terms" ] }, { "page": "add_poly_terms", "title": "Creates polynomial terms for specified variables in a data frame Polynomial terms are named as '_d_' (e.g., 'Z1_d_2' for the square of 'Z1').", "topics": [ "add_poly_terms" ] }, { "page": "build_formula", "title": "Build an expanded formula with poly and interaction terms", "topics": [ "build_formula" ] }, { "page": "CCI.crt", "title": "Conditional randomization version of the CCI test (CRT-CCI, experimental)", "topics": [ "CCI.crt" ] }, { "page": "CCI.direction", "title": "Choose Direction for testing for the CCI test", "topics": [ "CCI.direction" ] }, { "page": "CCI.pretuner", "title": "CCI tuner function for CCI test", "topics": [ "CCI.pretuner", "tuner" ] }, { "page": "CCI.test", "title": "Computational test for conditional independence based on ML and Monte Carlo Cross Validation", "topics": [ "CCI", "CCI.test" ] }, { "page": "check_formula", "title": "Check the formula statement", "topics": [ "check_formula" ] }, { "page": "clean_formula", "title": "Clean and Reformat Formula String", "topics": [ "clean_formula" ] }, { "page": "ExponentialNoise", "title": "Example dataset: ExponentialNoise", "topics": [ "ExponentialNoise" ] }, { "page": "get_pvalues", "title": "P-value Calculation Based on Null Distribution and Test Statistic", "topics": [ "get_pvalues" ] }, { "page": "get_tuned_params", "title": "Get the best parameters after tuning with CCI.tuner", "topics": [ "get_tuned_params" ] }, { "page": "HardCase", "title": "Example dataset: HardCase", "topics": [ "HardCase" ] }, { "page": "is_categorical_Z_any", "title": "Check whether Z contains at least one categorical variable", "topics": [ "is_categorical_Z_any" ] }, { "page": "make_strata_from_categorical_Z", "title": "Create strata from the categorical subset of Z", "topics": [ "make_strata_from_categorical_Z" ] }, { "page": "NonLinearCategorization", "title": "Example dataset: NonLinearCategorization", "topics": [ "NonLinearCategorization" ] }, { "page": "NonLinNormal", "title": "Example dataset: NonLinNormal", "topics": [ "NonLinNormal" ] }, { "page": "NonLinNormalZs_d0", "title": "Example dataset: NonLinNormalZs_d0", "topics": [ "NonLinNormalZs_d0" ] }, { "page": "NonLinNormalZs_d05", "title": "Example dataset: NonLinNormalZs_d05", "topics": [ "NonLinNormalZs_d05" ] }, { "page": "NormalData", "title": "Example dataset: NormalData", "topics": [ "NormalData" ] }, { "page": "perm.test", "title": "Permutation Test for Conditional Independence", "topics": [ "perm.test" ] }, { "page": "permute_within_strata", "title": "Stratified permutation of x within strata", "topics": [ "permute_within_strata" ] }, { "page": "plot.CCI", "title": "Plot for CCI testing", "topics": [ "plot.CCI" ] }, { "page": "PoissonNoise", "title": "Example dataset: PoissonNoise", "topics": [ "PoissonNoise" ] }, { "page": "PolyData", "title": "Example dataset: PolyData", "topics": [ "PolyData" ] }, { "page": "reports", "title": "Print and summary methods for the CCI class", "topics": [ "print.CCI", "print.summary.CCI", "reports", "summary.CCI" ] }, { "page": "QQplot", "title": "QQ-plot for multiple testing in CCI", "topics": [ "QQplot" ] }, { "page": "reduce_Z_pca", "title": "Reduce the conditioning variables Z with principal component analysis", "topics": [ "reduce_Z_pca" ] }, { "page": "test.gen", "title": "Generate the Test Statistic or Null Distribution Using Permutation", "topics": [ "test.gen" ] }, { "page": "unclean_formula", "title": "Convert CI-style formula Y ~ X | Z into regression-style Y ~ X + Z", "topics": [ "unclean_formula" ] }, { "page": "UniformNoise_large", "title": "Example dataset: UniformNoise_large", "topics": [ "UniformNoise_large" ] }, { "page": "wrapper_knn", "title": "k-Nearest Neighbors (KNN) wrapper for CCI (kknn-based)", "topics": [ "wrapper_knn" ] }, { "page": "wrapper_ranger", "title": "Random Forest wrapper for CCI", "topics": [ "wrapper_ranger" ] }, { "page": "wrapper_svm", "title": "SVM wrapper for CCI", "topics": [ "wrapper_svm" ] }, { "page": "wrapper_xgboost", "title": "Extreme Gradient Boosting wrapper for CCI", "topics": [ "wrapper_xgboost" ] } ], "_readme": "https://github.com/khliland/cci/raw/HEAD/README.md", "_rundeps": [ "caret", "class", "cli", "clock", "codetools", "cpp11", "crayon", "data.table", "diagram", "digest", "dplyr", "e1071", "farver", "foreach", "future", "future.apply", "generics", "ggplot2", "globals", "glue", "gower", "gtable", "hardhat", "hms", "igraph", "ipred", "isoband", "iterators", "jsonlite", "KernSmooth", "kknn", "labeling", "lattice", "lava", "lifecycle", "listenv", "lubridate", "magrittr", "MASS", "Matrix", "ModelMetrics", "nlme", "nnet", "numDeriv", "parallelly", "pillar", "pkgconfig", "plyr", "prettyunits", "pROC", "prodlim", "progress", "progressr", "proxy", "purrr", "R6", "ranger", "RColorBrewer", "Rcpp", "RcppEigen", "recipes", "reshape2", "rlang", "rpart", "S7", "scales", "shape", "sparsevctrs", "SQUAREM", "stringi", "stringr", "survival", "tibble", "tidyr", "tidyselect", "timechange", "timeDate", "tzdb", "utf8", "vctrs", "viridisLite", "withr", "xgboost" ], "_vignettes": [ { "source": "applied-examples.Rmd", "filename": "applied-examples.html", "title": "Applied examples: causal models and time series", "engine": "knitr::rmarkdown", "headings": [ "Testing a causal model (DAG)", "Time series", "References" ], "created": "2026-09-23 11:30:25", "modified": "2026-09-23 11:30:25", "commits": 1 }, { "source": "custom-models-and-metrics.Rmd", "filename": "custom-models-and-metrics.html", "title": "Custom models and performance metrics", "engine": "knitr::rmarkdown", "headings": [ "Custom performance metrics with metricfunc", "Regression: $R^2$", "Classification: balanced accuracy and Brier score", "Custom learners with mlfunc", "A linear model", "Logistic regression with extra arguments", "Any model from caret", "Tips" ], "created": "2026-09-23 11:30:25", "modified": "2026-09-23 11:30:25", "commits": 1 }, { "source": "diagnostics-and-tuning.Rmd", "filename": "diagnostics-and-tuning.html", "title": "Diagnostics, tuning and test direction", "engine": "knitr::rmarkdown", "headings": [ "Look at the null distribution", "Number of Monte Carlo samples and parametric p-values", "QQ-plot of p-values", "Very high p-values", "Failed model fits", "Tuning the learner", "Choosing the direction of the test", "A checklist", "References" ], "created": "2026-09-23 11:30:25", "modified": "2026-09-23 11:30:25", "commits": 1 }, { "source": "Testing-CI-with-CCI.Rmd", "filename": "Testing-CI-with-CCI.html", "title": "Getting started with CCI", "engine": "knitr::rmarkdown", "headings": [ "The idea behind the test", "A first test", "The formula", "Choosing the learner", "Different types of data", "Large data sets", "References" ], "created": "2026-01-16 13:58:49", "modified": "2026-09-23 11:30:25", "commits": 2 } ], "_score": 5.635483746814913, "_indexed": true, "_nocasepkg": "cci", "_universes": [ "khliland", "christianbht" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "0.4.0", "date": "2026-10-29T12:54:18.000Z", "distro": "resolute", "commit": "2c71af0ecbcc9432c1b9358e8d7d84dd2e7e0487", "fileid": "https://r2.ropensci.org/8e62fcaec2985211b7dcd0ec49ebfb280f78c9f4c887250d8dc14a528b3436f8", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/khliland/actions/runs/40874614052" }, { "r": "4.6.1", "os": "linux", "version": "0.4.0", "date": "2026-10-29T12:52:29.000Z", "distro": "resolute", "commit": "2c71af0ecbcc9432c1b9358e8d7d84dd2e7e0487", "fileid": "https://r2.ropensci.org/690364508e86f6ab0aab95759f9984789f58a85d0542f02d642b713d6d1a2bcc", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/khliland/actions/runs/40874614052" }, { "r": "4.5.3", "os": "mac", "version": "0.4.0", "date": "2026-10-30T07:33:08.000Z", "commit": "2c71af0ecbcc9432c1b9358e8d7d84dd2e7e0487", "fileid": "https://r2.ropensci.org/9fa18489ec8bb588d2bb7b516717430b6aeae9bb8daa49b861cd60678228bccf", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/khliland/actions/runs/40874614052" }, { "r": "4.6.1", "os": "mac", "version": "0.4.0", "date": "2026-10-29T13:46:16.000Z", "commit": "2c71af0ecbcc9432c1b9358e8d7d84dd2e7e0487", "fileid": "https://r2.ropensci.org/91e6c74d5c1dfd8d0da8d6ec7f255091f4a0f05948e2ae7db316b2b163c6510b", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/khliland/actions/runs/40874614052" }, { "r": "4.6.0", "os": "wasm", "version": "0.4.0", "date": "2026-10-29T12:52:12.000Z", "commit": "2c71af0ecbcc9432c1b9358e8d7d84dd2e7e0487", "fileid": "https://r2.ropensci.org/040375bfa50f844c68a9cdf7d1e46713293c6434e0d073745c236ef3787847a8", "status": "success", "buildurl": "https://github.com/r-universe/khliland/actions/runs/40874614052" }, { "r": "4.7.0", "os": "win", "version": "0.4.0", "date": "2026-10-29T12:50:54.000Z", "commit": "2c71af0ecbcc9432c1b9358e8d7d84dd2e7e0487", "fileid": "https://r2.ropensci.org/46930f277c6dfac99da3e61327a720234a4d3703e0d0d32044cfb67f806e347c", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/khliland/actions/runs/40874614052" }, { "r": "4.5.3", "os": "win", "version": "0.4.0", "date": "2026-10-29T12:51:04.000Z", "commit": "2c71af0ecbcc9432c1b9358e8d7d84dd2e7e0487", "fileid": "https://r2.ropensci.org/2d0d515312b84313868612adeef23c3327352e3516223f4a0f8413f44e137d6f", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/khliland/actions/runs/40874614052" }, { "r": "4.6.1", "os": "win", "version": "0.4.0", "date": "2026-10-29T12:50:57.000Z", "commit": "2c71af0ecbcc9432c1b9358e8d7d84dd2e7e0487", "fileid": "https://r2.ropensci.org/46b963e5b54d88147c07b5b7ebd374cf18aaaf19d182b6d4d63ef7b8bb8107c2", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/khliland/actions/runs/40874614052" } ] }