{ "_id": "6a1082b5acfb0bcc41caef97", "Package": "CJAMP", "Type": "Package", "Title": "Copula-Based Joint Analysis of Multiple Phenotypes", "Version": "0.1.1", "Authors@R": "c( person(\"Stefan\", \"Konigorski\", email = \"stefan.konigorski@gmail.com\", role = c(\"aut\", \"cre\")), person(\"Yildiz E.\", \"Yilmaz\", email = \"yyilmaz@mun.ca\", role = c(\"ctb\", \"ths\")))", "Description": "We provide a computationally efficient and robust\nimplementation of the recently proposed C-JAMP (Copula-based\nJoint Analysis of Multiple Phenotypes) method (Konigorski et\nal., 2019, submitted). C-JAMP allows estimating and testing the\nassociation of one or multiple predictors on multiple outcomes\nin a joint model, and is implemented here with a focus on\nlarge-scale genome-wide association studies with two\nphenotypes. The use of copula functions allows modeling a wide\nrange of multivariate dependencies between the phenotypes, and\nprevious results are supporting that C-JAMP can increase the\npower of association studies to identify associated genetic\nvariants in comparison to existing methods (Konigorski, Yilmaz,\nPischon, 2016, ; Konigorski,\nYilmaz, Bull, 2014, ). In\naddition to the C-JAMP functions, functions are available to\ngenerate genetic and phenotypic data, to compute the minor\nallele frequency (MAF) of genetic markers, and to estimate the\nphenotypic variance explained by genetic markers.", "License": "GPL-2", "Encoding": "UTF-8", "VignetteBuilder": "knitr", "RoxygenNote": "6.1.1", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-06 05:27:11 UTC", "User": "root" }, "Author": "Stefan Konigorski [aut, cre], Yildiz E. Yilmaz [ctb, ths]", "Maintainer": "Stefan Konigorski ", "Config/pak/sysreqs": "cmake", "Repository": "https://skonigor.r-universe.dev", "Date/Publication": "2019-03-20 21:23:33 UTC", "RemoteUrl": "https://github.com/cran/CJAMP", "RemoteRef": "HEAD", "RemoteSha": "ad7c345200433035a8b4d747d5a1093d85478843", "MD5sum": "0e37744c8ae98bbf1a00076b615bcf44", "_user": "skonigor", "_type": "src", "_file": "CJAMP_0.1.1.tar.gz", "_fileid": "e60a1fbf3c83d17a75902c3e5fbe4e08ccd9bd729b0f97e3fe2533efbab8d81d", "_filesize": 1425694, "_sha256": "e60a1fbf3c83d17a75902c3e5fbe4e08ccd9bd729b0f97e3fe2533efbab8d81d", "_created": "2026-05-06T05:27:11.000Z", "_published": "2026-05-22T16:22:13.302Z", "_distro": "noble", "_jobs": [ { "job": 77419791381, "time": 138, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "WARNING", "artifact": "6823285083" }, { "job": 77419791219, "time": 115, "config": "linux-release-x86_64", "r": "4.6.0", "check": "WARNING", "artifact": "6823281886" }, { "job": 77419791374, "time": 212, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "WARNING", "artifact": "6823288005" }, { "job": 77419791346, "time": 152, "config": "macos-release-arm64", "r": "4.6.0", "check": "WARNING", "artifact": "6823281837" }, { "job": 77419790747, "time": 188, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "6823257358" }, { "job": 77419790669, "time": 101, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7165333641" }, { "job": 77419791228, "time": 78, "config": "windows-devel", "r": "4.7.0", "check": "WARNING", "artifact": "6823273310" }, { "job": 77419791765, "time": 85, "config": "windows-oldrel", "r": "4.5.3", "check": "WARNING", "artifact": "6823274757" }, { "job": 77419791457, "time": 77, "config": "windows-release", "r": "4.6.0", "check": "WARNING", "artifact": "6823273156" } ], "_buildurl": "https://github.com/r-universe/skonigor/actions/runs/25418050186", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/cran/CJAMP", "_commit": { "id": "ad7c345200433035a8b4d747d5a1093d85478843", "author": "Stefan Konigorski ", "committer": "cran-robot ", "message": "version 0.1.1\n", "time": 1553117013 }, "_maintainer": { "name": "Stefan Konigorski", "email": "stefan.konigorski@gmail.com", "login": "skonigor", "uuid": 19798044 }, "_registered": true, "_dependencies": [ { "package": "stats", "role": "Imports" }, { "package": "optimx", "role": "Imports" }, { "package": "MASS", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" } ], "_owner": "cran", "_selfowned": true, "_usedby": 0, "_updates": [], "_tags": [], "_stars": 0, "_contributors": [ { "user": "skonigor", "count": 2, "uuid": 19798044 } ], "_userbio": { "uuid": 19798044, "type": "user", "name": "Stefan Konigorski", "description": "Senior Researcher" }, "_downloads": { "count": 243, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/CJAMP" }, "_searchresults": 11, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/CJAMP.html", "extra/contents.json", "manual.pdf" ], "_realowner": "skonigor", "_cranurl": false, "_releases": [ { "version": "0.1.0", "date": "2018-04-24" }, { "version": "0.1.1", "date": "2019-03-20" } ], "_exports": [ "cjamp", "cjamp_loop", "compute_expl_var", "compute_MAF", "generate_clayton_copula", "generate_doubleton_data", "generate_genodata", "generate_phenodata_1", "generate_phenodata_1_simple", "generate_phenodata_2_bvn", "generate_phenodata_2_copula", "generate_singleton_data", "get_estimates_naive", "lrt_copula", "lrt_param", "minusloglik" ], "_help": [ { "page": "cjamp", "title": "C-JAMP: Copula-based joint analysis of multiple phenotypes.", "topics": [ "cjamp", "cjamp_loop" ] }, { "page": "compute_expl_var", "title": "Phenotypic variance explained by genetic variants.", "topics": [ "compute_expl_var" ] }, { "page": "compute_MAF", "title": "Compute minor allele frequency of genetic variants.", "topics": [ "compute_MAF" ] }, { "page": "generate_clayton_copula", "title": "Generate data from the Clayton copula.", "topics": [ "generate_clayton_copula" ] }, { "page": "generate_genodata", "title": "Functions to generate genetic data.", "topics": [ "generate_doubleton_data", "generate_genodata", "generate_singleton_data" ] }, { "page": "generate_phenodata", "title": "Functions to generate phenotype data.", "topics": [ "generate_phenodata", "generate_phenodata_1", "generate_phenodata_1_simple", "generate_phenodata_2_bvn", "generate_phenodata_2_copula" ] }, { "page": "get_estimates_naive", "title": "Naive estimates of the copula and marginal parameters.", "topics": [ "get_estimates_naive" ] }, { "page": "lrt", "title": "Compute likelihood ratio tests.", "topics": [ "lrt", "lrt_copula", "lrt_param" ] }, { "page": "minusloglik", "title": "Minus log-likelihood of copula models.", "topics": [ "minusloglik" ] }, { "page": "summary.cjamp", "title": "Summary function.", "topics": [ "summary.cjamp" ] } ], "_rundeps": [ "nloptr", "numDeriv", "optimx", "pracma" ], "_vignettes": [ { "source": "cjamp.Rmd", "filename": "cjamp.html", "title": "C-JAMP: Copula-based Joint Analysis of Multiple Phenotypes", "author": "Stefan Konigorski", "engine": "knitr::rmarkdown", "headings": [ "Overview", "Background on copula functions", "Data generation functions", "C-JAMP: Copula-based joint analysis of multiple phenotypes", "References" ], "created": "2018-04-24 09:00:42", "modified": "2019-03-20 21:23:33", "commits": 2 } ], "_score": 2.0413926851582254, "_indexed": true, "_nocasepkg": "cjamp", "_universes": [ "skonigor" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "0.1.1", "date": "2026-05-06T05:29:33.000Z", "distro": "noble", "commit": "ad7c345200433035a8b4d747d5a1093d85478843", "fileid": "a91ec48435238aebbd9099760ce511b209f98f0f949e38c08559422ee28c83e3", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/skonigor/actions/runs/25418050186" }, { "r": "4.6.0", "os": "linux", "version": "0.1.1", "date": "2026-05-06T05:29:16.000Z", "distro": "noble", "commit": "ad7c345200433035a8b4d747d5a1093d85478843", "fileid": "60b3a9e4612c86b19bbafe3097d42abcaf67e56c7380a75122670872ef8c6e9f", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/skonigor/actions/runs/25418050186" }, { "r": "4.5.3", "os": "mac", "version": "0.1.1", "date": "2026-05-06T05:29:50.000Z", "commit": "ad7c345200433035a8b4d747d5a1093d85478843", "fileid": "c199175e97162f3b8c9777de1ae4199b8fedb5deeb825ec23acc52efc926a40a", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/skonigor/actions/runs/25418050186" }, { "r": "4.6.0", "os": "mac", "version": "0.1.1", "date": "2026-05-06T05:29:19.000Z", "commit": "ad7c345200433035a8b4d747d5a1093d85478843", "fileid": "96be80ce8cf4735aae6196eb1eba09af2123715811cf4a6fb1c04cc8276d681e", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/skonigor/actions/runs/25418050186" }, { "r": "4.7.0", "os": "win", "version": "0.1.1", "date": "2026-05-06T05:28:27.000Z", "commit": "ad7c345200433035a8b4d747d5a1093d85478843", "fileid": "acec5307fb929d6077a2c994aefaaf1bf2853fe8c5bde9d3efd94446cb3af8f7", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/skonigor/actions/runs/25418050186" }, { "r": "4.5.3", "os": "win", "version": "0.1.1", "date": "2026-05-06T05:28:36.000Z", "commit": "ad7c345200433035a8b4d747d5a1093d85478843", "fileid": "b578e5a102195ef614514326331d9639d5e6588c5a68dd7a3c5e4d0db328a959", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/skonigor/actions/runs/25418050186" }, { "r": "4.6.0", "os": "win", "version": "0.1.1", "date": "2026-05-06T05:28:25.000Z", "commit": "ad7c345200433035a8b4d747d5a1093d85478843", "fileid": "260426ac04a025eed6c3c64e2aa951f1edb9bcae7d715a797f769d7fcae2ea7e", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/skonigor/actions/runs/25418050186" }, { "r": "4.6.0", "os": "wasm", "version": "0.1.1", "date": "2026-05-22T16:21:56.000Z", "commit": "ad7c345200433035a8b4d747d5a1093d85478843", "fileid": "2fbe4571490749c08c1b937f1a355b6e2429a4e4760defb3cb3c22b4865b0853", "status": "success", "buildurl": "https://github.com/r-universe/skonigor/actions/runs/25418050186" } ] }