{ "_id": "6a495a43f6c47c441949e131", "Package": "SimReg", "Type": "Package", "Title": "Similarity Regression", "Version": "3.4", "Date": "2024-02-20", "Encoding": "UTF-8", "Author": "Daniel Greene", "Maintainer": "Daniel Greene ", "Description": "Similarity regression, evaluating the probability of\nassociation between sets of ontological terms and binary\nresponse vector. A no-association model is compared with one in\nwhich the log odds of a true response is linked to the semantic\nsimilarity between terms and a latent characteristic\nontological profile - 'Phenotype Similarity Regression for\nIdentifying the Genetic Determinants of Rare Diseases', Greene\net al 2016 .", "License": "GPL (>= 2)", "VignetteBuilder": "knitr", "RoxygenNote": "7.3.1", "NeedsCompilation": "yes", "Packaged": { "Date": "2026-07-04 19:04:44 UTC", "User": "root" }, "Config/pak/sysreqs": "zlib1g-dev", "Repository": "https://daniel-jg.r-universe.dev", "Date/Publication": "2024-02-22 02:29:30 UTC", "RemoteUrl": "https://github.com/cran/SimReg", "RemoteRef": "HEAD", "RemoteSha": "d53275aea9f925d2fae1801411859b7cdf9e777f", "_user": "daniel-jg", "_type": "src", "_file": "SimReg_3.4.tar.gz", "_fileid": "https://r2.ropensci.org/876132dbd4ad49ad0a23c86f0023adaf8e29252ad355088303ad5a47f701a338", "_filesize": 224783, "_sha256": "876132dbd4ad49ad0a23c86f0023adaf8e29252ad355088303ad5a47f701a338", "_expires": "2026-10-12T19:08:50.000Z", "_created": "2026-07-04T19:04:44.000Z", "_published": "2026-07-04T19:08:51.793Z", "_jobs": [ { "job": 85158988675, "time": 180, "config": "linux-devel-arm64", "r": "4.7.0", "check": "OK", "artifact": "8084594501" }, { "job": 85158988683, "time": 146, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "8084590434" }, { "job": 85158988687, "time": 173, "config": "linux-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "8084593701" }, { "job": 85158988690, "time": 190, "config": "linux-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "8084595323" }, { "job": 85158988727, "time": 102, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "8084585344" }, { "job": 85158988741, "time": 165, "config": "macos-oldrel-x86_64", "r": "4.5.3", "check": "OK", "artifact": "8084592591" }, { "job": 85158988733, "time": 83, "config": "macos-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "8084583011" }, { "job": 85158988736, "time": 201, "config": "macos-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "8084596811" }, { "job": 85158668488, "time": 268, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "8084571227" }, { "job": 85158988672, "time": 159, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "8084591857" }, { "job": 85158988691, "time": 104, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "8084585527" }, { "job": 85158988693, "time": 109, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "8084586091" }, { "job": 85158988732, "time": 118, "config": "windows-release", "r": "4.6.1", "check": "OK", "artifact": "8084587169" } ], "_host": "GitHub-Actions", "_buildurl": "https://github.com/r-universe/daniel-jg/actions/runs/28716465649", "_status": "success", "_upstream": "https://github.com/cran/SimReg", "_commit": { "id": "d53275aea9f925d2fae1801411859b7cdf9e777f", "author": "Daniel Greene ", "committer": "cran-robot ", "message": "version 3.4\n", "time": 1708568970 }, "_maintainer": { "name": "Daniel Greene", "email": "dg333@cam.ac.uk", "login": "daniel-jg", "description": "", "uuid": 25660818 }, "_distro": "resolute", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.0.0", "role": "Depends" }, { "package": "Rcpp", "role": "LinkingTo" }, { "package": "Rcpp", "version": ">= 0.11.1", "role": "Imports" }, { "package": "ontologyIndex", "version": ">= 2.0", "role": "Imports" }, { "package": "ontologySimilarity", "version": ">= 2.0", "role": "Imports" }, { "package": "ontologyPlot", "role": "Imports" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" } ], "_owner": "cran", "_selfowned": true, "_usedby": 0, "_updates": [], "_tags": [], "_stars": 0, "_contributors": [ { "user": "daniel-jg", "count": 8, "uuid": 25660818 } ], "_userbio": { "uuid": 25660818, "type": "user", "name": "Daniel", "followers": 4 }, "_downloads": { "count": 303, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/SimReg" }, "_mentions": 3, "_searchresults": 9, "_topics": [ "cpp" ], "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/SimReg.html", "manual.pdf" ], "_realowner": "daniel-jg", "_cranurl": false, "_releases": [ { "version": "1.1", "date": "2015-08-27" }, { "version": "1.2", "date": "2015-09-15" }, { "version": "1.3", "date": "2016-01-13" }, { "version": "1.4", "date": "2016-03-06" }, { "version": "2.1", "date": "2016-08-16" }, { "version": "3.0", "date": "2016-10-15" }, { "version": "3.3", "date": "2021-02-15" }, { "version": "3.4", "date": "2024-02-21" } ], "_exports": [ "get_term_marginals", "get_terms", "log_BF", "plot_term_marginals", "posterior_prediction", "prob_association", "sim_reg", "sum_log_probs", "term_marginals" ], "_help": [ { "page": "SimReg-package", "title": "Similarity Regression Functions", "topics": [ "SimReg-package", "SimReg" ] }, { "page": "get_term_marginals", "title": "Calculate marginal probability of terms inclusion in 'phi' from 'sim_reg_out' object", "topics": [ "get_term_marginals" ] }, { "page": "get_terms", "title": "Get full set of terms to use in inference procedure based on similarity function arguments", "topics": [ "get_terms" ] }, { "page": "log_BF", "title": "Calculate log Bayes factor for similarity the model, 'gamma=1' and baseline model, 'gamma=0'.", "topics": [ "log_BF", "log_BF.default", "log_BF.sim_reg_output" ] }, { "page": "plot_term_marginals", "title": "Create ontological plot of marginal probabilities of terms", "topics": [ "plot_term_marginals" ] }, { "page": "plot.sim_reg_summary", "title": "Plot summary of 'sim_reg_output' object", "topics": [ "plot.sim_reg_output", "plot.sim_reg_summary" ] }, { "page": "posterior_prediction", "title": "Predicted probability of 'y' given 'x' conditional on association and given data.", "topics": [ "posterior_prediction" ] }, { "page": "print.sim_reg_output", "title": "Print 'sim_reg_output' object", "topics": [ "print.sim_reg_output" ] }, { "page": "print.sim_reg_summary", "title": "Print 'sim_reg_summary' object", "topics": [ "print.sim_reg_summary" ] }, { "page": "prob_association", "title": "Calculate probability of association between 'y' and 'x'", "topics": [ "prob_association" ] }, { "page": "sim_reg", "title": "Similarity regression", "topics": [ "sim_reg" ] }, { "page": "sum_log_probs", "title": "Calculate sum of log probabilities on log scale without over/under-flow", "topics": [ "sum_log_probs" ] }, { "page": "summary.sim_reg_output", "title": "Get summary of 'sim_reg_output' object", "topics": [ "summary.sim_reg_output" ] }, { "page": "term_marginals", "title": "Calculate marginal probability of terms inclusion in 'phi'", "topics": [ "term_marginals" ] } ], "_rundeps": [ "BiocGenerics", "generics", "graph", "ontologyIndex", "ontologyPlot", "ontologySimilarity", "paintmap", "Rcpp", "Rgraphviz" ], "_sysdeps": [ { "shlib": "libstdc++", "package": "libstdc++6", "source": "gcc", "version": "16-20260322-1ubuntu1", "name": "c++", "homepage": "http://gcc.gnu.org/", "description": "GNU Standard C++ Library v3" } ], "_vignettes": [ { "source": "SimReg-Priors.Rmd", "filename": "SimReg-Priors.html", "title": "Prior phenotypic information", "author": "Daniel Greene", "engine": "knitr::rmarkdown", "headings": [ "References" ], "created": "2016-03-06 23:17:22", "modified": "2024-02-22 02:29:30", "commits": 5 }, { "source": "SimReg-Introduction.Rmd", "filename": "SimReg-Introduction.html", "title": "Similarity Regression - Introduction", "author": "Daniel Greene", "engine": "knitr::rmarkdown", "headings": [ "References" ], "created": "2016-08-16 19:47:22", "modified": "2024-02-22 02:29:30", "commits": 4 } ], "_score": 2.778151250383644, "_indexed": true, "_nocasepkg": "simreg", "_universes": [ "daniel-jg" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "3.4", "date": "2026-07-04T19:07:53.000Z", "distro": "resolute", "arch": "aarch64", "commit": "d53275aea9f925d2fae1801411859b7cdf9e777f", "fileid": "https://r2.ropensci.org/f194435932976ec23c59fb40942a5809bb1cc180a7118502be39a1a03e090f59", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/daniel-jg/actions/runs/28716465649" }, { "r": "4.7.0", "os": "linux", "version": "3.4", "date": "2026-07-04T19:07:08.000Z", "distro": "resolute", "arch": "x86_64", "commit": "d53275aea9f925d2fae1801411859b7cdf9e777f", "fileid": "https://r2.ropensci.org/aa6a2fc8c659d1d523483a6b4eb5ccd7d8f5296f5e639e75170c98cf6b4e544a", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/daniel-jg/actions/runs/28716465649" }, { "r": "4.6.1", "os": "linux", "version": "3.4", "date": "2026-07-04T19:07:44.000Z", "distro": "resolute", "arch": "aarch64", "commit": "d53275aea9f925d2fae1801411859b7cdf9e777f", "fileid": "https://r2.ropensci.org/240a100c1c07d8b2766a7add5d38293067cc9e3ebd36cc283c8ed8088bc67546", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/daniel-jg/actions/runs/28716465649" }, { "r": "4.6.1", "os": "linux", "version": "3.4", "date": "2026-07-04T19:07:52.000Z", "distro": "resolute", "arch": "x86_64", "commit": "d53275aea9f925d2fae1801411859b7cdf9e777f", "fileid": "https://r2.ropensci.org/47a8b139d15ea7a1711e9071563c1ed26b69b5f99402a162cdcf606b7d03210f", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/daniel-jg/actions/runs/28716465649" }, { "r": "4.5.3", "os": "mac", "version": "3.4", "date": "2026-07-04T19:06:31.000Z", "arch": "aarch64", "commit": "d53275aea9f925d2fae1801411859b7cdf9e777f", "fileid": "https://r2.ropensci.org/1dff7b50f3e2f527b1fc39e71998a4297a35cc489637c127c0aa021731367a59", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/daniel-jg/actions/runs/28716465649" }, { "r": "4.5.3", "os": "mac", "version": "3.4", "date": "2026-07-04T19:07:17.000Z", "arch": "x86_64", "commit": "d53275aea9f925d2fae1801411859b7cdf9e777f", "fileid": "https://r2.ropensci.org/bcfde392509e0c71aa8bc45611c1c61336dce71d404497d4ccb5412bccdcaa54", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/daniel-jg/actions/runs/28716465649" }, { "r": "4.6.1", "os": "mac", "version": "3.4", "date": "2026-07-04T19:06:11.000Z", "arch": "aarch64", "commit": "d53275aea9f925d2fae1801411859b7cdf9e777f", "fileid": "https://r2.ropensci.org/e016abdce30022e5bddaf03f9d5460154015ccedf29c2367495c57f1104b7395", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/daniel-jg/actions/runs/28716465649" }, { "r": "4.6.1", "os": "mac", "version": "3.4", "date": "2026-07-04T19:07:41.000Z", "arch": "x86_64", "commit": "d53275aea9f925d2fae1801411859b7cdf9e777f", "fileid": "https://r2.ropensci.org/d0b0e972fd6f6eb16fd14548ff6783ee058af0d9096f7a08f6f3e450ecadc27b", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/daniel-jg/actions/runs/28716465649" }, { "r": "4.6.0", "os": "wasm", "version": "3.4", "date": "2026-07-04T19:07:40.000Z", "arch": "emscripten", "commit": "d53275aea9f925d2fae1801411859b7cdf9e777f", "fileid": "https://r2.ropensci.org/fe21319a61e846f514c84b1de5e4544ad0a319d174f9530ccee641105558093d", "status": "success", "buildurl": "https://github.com/r-universe/daniel-jg/actions/runs/28716465649" }, { "r": "4.7.0", "os": "win", "version": "3.4", "date": "2026-07-04T19:06:02.000Z", "arch": "x86_64", "commit": "d53275aea9f925d2fae1801411859b7cdf9e777f", "fileid": "https://r2.ropensci.org/eca8bf60576a08c960b0dc0d6748a6d6196e65cce1514c6bb18f8e85d78df1e0", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/daniel-jg/actions/runs/28716465649" }, { "r": "4.5.3", "os": "win", "version": "3.4", "date": "2026-07-04T19:06:03.000Z", "arch": "x86_64", "commit": "d53275aea9f925d2fae1801411859b7cdf9e777f", "fileid": "https://r2.ropensci.org/31a1f7fd1be7c2d5a4d1d59e04e7e0ddda40d703c3cf2253d8b13aeeec4c2bae", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/daniel-jg/actions/runs/28716465649" }, { "r": "4.6.1", "os": "win", "version": "3.4", "date": "2026-07-04T19:06:14.000Z", "arch": "x86_64", "commit": "d53275aea9f925d2fae1801411859b7cdf9e777f", "fileid": "https://r2.ropensci.org/82cbdb807e30abe36f0ce832abaaac127d74c7ca74393e4ed87a819ca17d40ff", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/daniel-jg/actions/runs/28716465649" } ] }