{ "_id": "6a1d5a241d7bb097a0a48062", "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": "2026-06-01 10:00:10 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", "MD5sum": "95e8a8a5ca3f4f6d78d22af59b701a86", "_user": "daniel-jg", "_type": "src", "_file": "SimReg_3.4.tar.gz", "_fileid": "3be4675fbea41ddca6b5cc447a91fad7e01ab611b41b0a666f5e8c643398965f", "_filesize": 222731, "_sha256": "3be4675fbea41ddca6b5cc447a91fad7e01ab611b41b0a666f5e8c643398965f", "_created": "2026-06-01T10:00:10.000Z", "_published": "2026-06-01T10:08:36.592Z", "_distro": "noble", "_jobs": [ { "job": 78828919427, "time": 157, "config": "linux-devel-arm64", "r": "4.7.0", "check": "OK", "artifact": "7328737486" }, { "job": 78828919419, "time": 161, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7328638423" }, { "job": 78828919393, "time": 168, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7328640949" }, { "job": 78828919505, "time": 102, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7328618718" }, { "job": 78828919408, "time": 165, "config": "macos-oldrel-x86_64", "r": "4.5.3", "check": "OK", "artifact": "7328639873" }, { "job": 78828919417, "time": 108, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7328620495" }, { "job": 78828919389, "time": 315, "config": "macos-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7328690048" }, { "job": 78828372809, "time": 194, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7328581644" }, { "job": 78828919381, "time": 134, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7328629187" }, { "job": 78828919376, "time": 129, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "7328627906" }, { "job": 78828919420, "time": 183, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "7328646318" }, { "job": 78828919388, "time": 140, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "7328631631" } ], "_buildurl": "https://github.com/r-universe/daniel-jg/actions/runs/26747978595", "_status": "success", "_host": "GitHub-Actions", "_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 }, "_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" }, "_downloads": { "count": 162, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/SimReg" }, "_mentions": 3, "_searchresults": 7, "_topics": [ "cpp" ], "_rbuild": "4.6.0", "_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": "14.2.0-4ubuntu2~24.04.1", "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": "4.6.0", "os": "linux", "version": "3.4", "date": "2026-05-02T08:29:31.000Z", "distro": "noble", "arch": "aarch64", "commit": "d53275aea9f925d2fae1801411859b7cdf9e777f", "fileid": "5dccb93b48278d26b7a37cbbcedd6ea8077923704b264fd7526c6b7b1b3f0486", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/daniel-jg/actions/runs/25247794418" }, { "r": "4.7.0", "os": "linux", "version": "3.4", "date": "2026-06-01T10:07:49.000Z", "distro": "noble", "arch": "aarch64", "commit": "d53275aea9f925d2fae1801411859b7cdf9e777f", "fileid": "f28dfe47a7592aa6bbb5b23a18b1a5edba90276d84ad656ce0e9263fb93f1979", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/daniel-jg/actions/runs/26747978595" }, { "r": "4.7.0", "os": "linux", "version": "3.4", "date": "2026-06-01T10:02:53.000Z", "distro": "noble", "arch": "x86_64", "commit": "d53275aea9f925d2fae1801411859b7cdf9e777f", "fileid": "7ded9109993cdd20ffa8f061f44c5023e5f4895cf66978087769eae2e9cef934", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/daniel-jg/actions/runs/26747978595" }, { "r": "4.6.0", "os": "linux", "version": "3.4", "date": "2026-06-01T10:02:55.000Z", "distro": "noble", "arch": "x86_64", "commit": "d53275aea9f925d2fae1801411859b7cdf9e777f", "fileid": "a916bdb38ca48fab74426ea25863a858b02fc5076c7fc48388df432a0f29bf62", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/daniel-jg/actions/runs/26747978595" }, { "r": "4.5.3", "os": "mac", "version": "3.4", "date": "2026-06-01T10:01:55.000Z", "arch": "aarch64", "commit": "d53275aea9f925d2fae1801411859b7cdf9e777f", "fileid": "6ec88887e2af0429043795d3895b2e7a9d10a3261ffeea941e99992aa8985bdd", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/daniel-jg/actions/runs/26747978595" }, { "r": "4.5.3", "os": "mac", "version": "3.4", "date": "2026-06-01T10:02:41.000Z", "arch": "x86_64", "commit": "d53275aea9f925d2fae1801411859b7cdf9e777f", "fileid": "c847b7a58862999660b154a1adb7d1ab5517d23d87164d4cbe667b126adbe71e", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/daniel-jg/actions/runs/26747978595" }, { "r": "4.6.0", "os": "mac", "version": "3.4", "date": "2026-06-01T10:01:52.000Z", "arch": "aarch64", "commit": "d53275aea9f925d2fae1801411859b7cdf9e777f", "fileid": "6e4a460ec77027cae427c00d1164969e67e5713721887d51bda7b1afcdc76cc4", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/daniel-jg/actions/runs/26747978595" }, { "r": "4.6.0", "os": "mac", "version": "3.4", "date": "2026-06-01T10:04:41.000Z", "arch": "x86_64", "commit": "d53275aea9f925d2fae1801411859b7cdf9e777f", "fileid": "20d296f7daa36f4d77a8de2309690e840b56d69b2a34e10ab46bb1ad854ad8f9", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/daniel-jg/actions/runs/26747978595" }, { "r": "4.6.0", "os": "wasm", "version": "3.4", "date": "2026-06-01T10:02:42.000Z", "arch": "emscripten", "commit": "d53275aea9f925d2fae1801411859b7cdf9e777f", "fileid": "75bf7138be78c10069009ced0ae04ab77374b4f852d2fa19f914e8721bfb54f4", "status": "success", "buildurl": "https://github.com/r-universe/daniel-jg/actions/runs/26747978595" }, { "r": "4.7.0", "os": "win", "version": "3.4", "date": "2026-06-01T10:01:39.000Z", "arch": "x86_64", "commit": "d53275aea9f925d2fae1801411859b7cdf9e777f", "fileid": "76bafdd4b48a1c4ac80efa7896b73c96a2e0f99d2c868359bbcefde3686e8653", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/daniel-jg/actions/runs/26747978595" }, { "r": "4.5.3", "os": "win", "version": "3.4", "date": "2026-06-01T10:02:13.000Z", "arch": "x86_64", "commit": "d53275aea9f925d2fae1801411859b7cdf9e777f", "fileid": "ccd900560c09ea2ee6f1ff76bfb3d8c8c17a47ac6c7af680d023729a737903c0", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/daniel-jg/actions/runs/26747978595" }, { "r": "4.6.0", "os": "win", "version": "3.4", "date": "2026-06-01T10:01:46.000Z", "arch": "x86_64", "commit": "d53275aea9f925d2fae1801411859b7cdf9e777f", "fileid": "1b79fe9888f5be123d25641a0a3201c8c15d02b1a03d498488a05088c8bd06c3", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/daniel-jg/actions/runs/26747978595" } ] }