{ "_id": "6a180765acfb0bcc41dad0b0", "Package": "SurrogateRegression", "Title": "Surrogate Outcome Regression Analysis", "Date": "2026-02-26", "Version": "0.6.0.2", "Author": "Zachary McCaw [aut, cre]", "Maintainer": "Zachary McCaw ", "Authors@R": "person(given = \"Zachary\",\nfamily = \"McCaw\",\nrole = c(\"aut\", \"cre\"),\nemail = \"zmccaw@alumni.harvard.edu\",\ncomment = c(ORCID = \"0000-0002-2006-9828\"))", "Description": "Performs estimation and inference on a partially missing\ntarget outcome (e.g. gene expression in an inaccessible tissue)\nwhile borrowing information from a correlated surrogate outcome\n(e.g. gene expression in an accessible tissue). Rather than\nregarding the surrogate outcome as a proxy for the target\noutcome, this package jointly models the target and surrogate\noutcomes within a bivariate regression framework. Unobserved\nvalues of either outcome are treated as missing data. In\ncontrast to imputation-based inference, no assumptions are\nrequired regarding the relationship between the target and\nsurrogate outcomes. Estimation in the presence of bilateral\noutcome missingness is performed via an expectation conditional\nmaximization (ECME) algorithm. In the case of unilateral target\nmissingness, estimation is performed using an accelerated least\nsquares procedure. A flexible association test is provided for\nevaluating hypotheses about the target regression parameters.\nFor additional details, see: McCaw ZR, Gaynor SM, Sun R, Lin X:\n\"Leveraging a surrogate outcome to improve inference on a\npartially missing target outcome\" .", "License": "GPL-3", "Encoding": "UTF-8", "RoxygenNote": "7.3.3", "VignetteBuilder": "knitr", "Config/testthat/edition": "3", "Repository": "https://zrmacc.r-universe.dev", "Date/Publication": "2026-02-27 04:25:07 UTC", "RemoteUrl": "https://github.com/zrmacc/surrogateregression", "RemoteRef": "HEAD", "RemoteSha": "58396ade0166a0ac096b876a5438e3c7e8524234", "NeedsCompilation": "yes", "Packaged": { "Date": "2026-05-28 09:09:36 UTC", "User": "root" }, "MD5sum": "d4547b03569aabd1256822b409f97929", "_user": "zrmacc", "_type": "src", "_file": "SurrogateRegression_0.6.0.2.tar.gz", "_fileid": "4db6affc7bfdafdc43b24663b3e7572baee304340f3f6a9efaa97c1de7f8c5d6", "_filesize": 436376, "_sha256": "4db6affc7bfdafdc43b24663b3e7572baee304340f3f6a9efaa97c1de7f8c5d6", "_created": "2026-05-28T09:09:36.000Z", "_published": "2026-05-28T09:14:13.211Z", "_distro": "noble", "_jobs": [ { "job": 78259425635, "time": 129, "config": "linux-devel-arm64", "r": "4.7.0", "check": "OK", "artifact": "7262061123" }, { "job": 78259425651, "time": 155, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7262069766" }, { "job": 78259425639, "time": 133, "config": "linux-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7262062426" }, { "job": 78259425581, "time": 177, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7262076802" }, { "job": 78259425397, "time": 81, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7262045835" }, { "job": 78259425589, "time": 160, "config": "macos-oldrel-x86_64", "r": "4.5.3", "check": "OK", "artifact": "7262070563" }, { "job": 78259425508, "time": 135, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7262062817" }, { "job": 78259425490, "time": 224, "config": "macos-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7262092016" }, { "job": 78258974525, "time": 172, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7262018474" }, { "job": 78259425404, "time": 111, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7262055709" }, { "job": 78259425316, "time": 140, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "7262064777" }, { "job": 78259425277, "time": 122, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "7262059214" }, { "job": 78259425267, "time": 119, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "7262057131" } ], "_buildurl": "https://github.com/r-universe/zrmacc/actions/runs/26565478254", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/zrmacc/surrogateregression", "_commit": { "id": "58396ade0166a0ac096b876a5438e3c7e8524234", "author": "zrmacc ", "committer": "zrmacc ", "message": "Update 26-02-26\n", "time": 1772166307 }, "_maintainer": { "name": "Zachary McCaw", "email": "zmccaw@alumni.harvard.edu", "login": "zrmacc", "orcid": "0000-0002-2006-9828", "description": "", "uuid": 14017943 }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.4.0", "role": "Depends" }, { "package": "Rcpp", "role": "LinkingTo" }, { "package": "RcppArmadillo", "role": "LinkingTo" }, { "package": "methods", "role": "Imports" }, { "package": "Rcpp", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "testthat", "version": ">= 3.0.0", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "withr", "role": "Suggests" } ], "_owner": "zrmacc", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2026-09", "n": 4 } ], "_tags": [ { "name": "v0.6.0.2", "date": "2026-02-27" } ], "_topics": [ "statistical-inference", "openblas", "cpp" ], "_stars": 2, "_contributors": [ { "user": "zrmacc", "count": 4, "uuid": 14017943 } ], "_userbio": { "uuid": 14017943, "type": "user", "name": "Zachary R McCaw" }, "_downloads": { "count": 205, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/SurrogateRegression" }, "_devurl": "https://github.com/zrmacc/surrogateregression", "_searchresults": 15, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/readme.html", "extra/readme.md", "extra/SurrogateRegression.html", "manual.pdf" ], "_homeurl": "https://github.com/zrmacc/surrogateregression", "_realowner": "zrmacc", "_cranurl": true, "_releases": [ { "version": "0.5.0", "date": "2020-12-03" }, { "version": "0.6.0", "date": "2022-08-05" }, { "version": "0.6.0.1", "date": "2023-10-01" } ], "_exports": [ "FitBNR", "PartitionData", "rBNR", "TestBNR" ], "_help": [ { "page": "bnr-class", "title": "Bivariate Regression Model", "topics": [ "bnr-class" ] }, { "page": "CheckInit", "title": "Check Initiation", "topics": [ "CheckInit" ] }, { "page": "CheckTestSpec", "title": "Check Test Specification", "topics": [ "CheckTestSpec" ] }, { "page": "coef.bnr", "title": "Extract Coefficients from Bivariate Regression Model", "topics": [ "coef.bnr" ] }, { "page": "covInfo", "title": "Covariance Information Matrix", "topics": [ "CovInfo" ] }, { "page": "covTab", "title": "Tabulate Covariance Parameters", "topics": [ "CovTab" ] }, { "page": "covUpdate", "title": "Covariance Update", "topics": [ "CovUpdate" ] }, { "page": "FitBNEM", "title": "Fit Bivariate Normal Regression Model via Expectation Maximization.", "topics": [ "FitBNEM" ] }, { "page": "FitBNLS", "title": "Fit Bivariate Normal Regression Model via Least Squares", "topics": [ "FitBNLS" ] }, { "page": "FitBNR", "title": "Fit Bivariate Normal Regression Model", "topics": [ "FitBNR" ] }, { "page": "fitOLS", "title": "Ordinary Least Squares", "topics": [ "fitOLS" ] }, { "page": "FormatOutput", "title": "Format Output", "topics": [ "FormatOutput" ] }, { "page": "IterUpdate", "title": "Update Iteration", "topics": [ "IterUpdate" ] }, { "page": "linearPredictors", "title": "Linear predictors for bivariate regression", "topics": [ "linearPredictors" ] }, { "page": "matDet", "title": "Matrix Determinant", "topics": [ "matDet" ] }, { "page": "matInv", "title": "Matrix Inverse", "topics": [ "matInv" ] }, { "page": "matIP", "title": "Matrix Inner Product", "topics": [ "matIP" ] }, { "page": "matOP", "title": "Matrix Outer Product", "topics": [ "matOP" ] }, { "page": "matQF", "title": "Quadratic Form", "topics": [ "matQF" ] }, { "page": "MMP", "title": "Matrix Matrix Product", "topics": [ "MMP" ] }, { "page": "obsLogLik", "title": "Observed Data Log Likelihood", "topics": [ "ObsLogLik" ] }, { "page": "paramInit", "title": "Parameter Initialization", "topics": [ "ParamInit" ] }, { "page": "PartitionData", "title": "Partition Data by Outcome Missingness Pattern.", "topics": [ "PartitionData" ] }, { "page": "print.bnr", "title": "Print for Bivariate Regression Model", "topics": [ "print.bnr" ] }, { "page": "rBNR", "title": "Simulate Bivariate Normal Data with Missingness", "topics": [ "rBNR" ] }, { "page": "regInfo", "title": "Regression Information", "topics": [ "RegInfo" ] }, { "page": "regTab", "title": "Tabulate Regression Coefficients", "topics": [ "RegTab" ] }, { "page": "regUpdate", "title": "Regression Update", "topics": [ "RegUpdate" ] }, { "page": "residuals.bnr", "title": "Extract Residuals from Bivariate Regression Model", "topics": [ "residuals.bnr" ] }, { "page": "SchurC", "title": "Schur complement", "topics": [ "SchurC" ] }, { "page": "ScoreBNEM", "title": "Score Test via Expectation Maximization.", "topics": [ "ScoreBNEM" ] }, { "page": "bnr-method", "title": "Show for Bivariate Regression Model", "topics": [ "show,bnr-method" ] }, { "page": "TestBNR", "title": "Test Bivariate Normal Regression Model.", "topics": [ "TestBNR" ] }, { "page": "tr", "title": "Matrix Trace", "topics": [ "tr" ] }, { "page": "UpdateEM", "title": "EM Update", "topics": [ "UpdateEM" ] }, { "page": "vcov.bnr", "title": "Extract Covariance Matrix from Bivariate Normal Regression Model", "topics": [ "vcov.bnr" ] }, { "page": "WaldBNEM", "title": "Wald Test via Expectation Maximization.", "topics": [ "WaldBNEM" ] }, { "page": "WaldBNLS", "title": "Wald Test via Least Squares.", "topics": [ "WaldBNLS" ] } ], "_readme": "https://github.com/zrmacc/surrogateregression/raw/HEAD/README.md", "_rundeps": [ "Rcpp", "RcppArmadillo" ], "_sysdeps": [ { "shlib": "liblapack", "package": "libopenblas0-pthread", "source": "openblas", "version": "0.3.26+ds-1ubuntu0.1", "name": "openblas", "homepage": "https://www.openblas.net/", "description": "Optimized BLAS (linear algebra) library (shared lib, pthread)" }, { "shlib": "libblas", "package": "libopenblas0-pthread", "source": "openblas", "version": "0.3.26+ds-1ubuntu0.1", "name": "openblas", "homepage": "https://www.openblas.net/", "description": "Optimized BLAS (linear algebra) library (shared lib, pthread)" }, { "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": "SurrogateRegression.Rmd", "filename": "SurrogateRegression.html", "title": "Surrogate Outcome Regression Analysis", "author": "Zachary McCaw", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Data generation: rBNR", "Fitting the model: FitBNR", "Extracting results", "Hypothesis testing: TestBNR", "Partitioning by missingness: PartitionData" ], "created": "2026-02-27 03:19:31", "modified": "2026-02-27 03:19:31", "commits": 1 } ], "_score": 4.176091259055681, "_indexed": true, "_nocasepkg": "surrogateregression", "_universes": [ "zrmacc" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "0.6.0.2", "date": "2026-05-28T09:11:44.000Z", "distro": "noble", "arch": "aarch64", "commit": "58396ade0166a0ac096b876a5438e3c7e8524234", "fileid": "4a86b733e5dc7fdce18a63b29b936edf088a470f41eda2eb492f5711f69c1c99", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/zrmacc/actions/runs/26565478254" }, { "r": "4.7.0", "os": "linux", "version": "0.6.0.2", "date": "2026-05-28T09:12:08.000Z", "distro": "noble", "arch": "x86_64", "commit": "58396ade0166a0ac096b876a5438e3c7e8524234", "fileid": "5abb1380880c6781308a361dfaf4789f59ebb2b923767a8b3231ace7da6fa44b", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/zrmacc/actions/runs/26565478254" }, { "r": "4.6.0", "os": "linux", "version": "0.6.0.2", "date": "2026-05-28T09:11:48.000Z", "distro": "noble", "arch": "aarch64", "commit": "58396ade0166a0ac096b876a5438e3c7e8524234", "fileid": "61f4b3963cb73cc330f9ccd657c8a7c7a720bb88ce5c9fda8fea044cd791c1dc", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/zrmacc/actions/runs/26565478254" }, { "r": "4.6.0", "os": "linux", "version": "0.6.0.2", "date": "2026-05-28T09:12:30.000Z", "distro": "noble", "arch": "x86_64", "commit": "58396ade0166a0ac096b876a5438e3c7e8524234", "fileid": "060e05d7edbda41615f58fd17cb596fca338707acd2a90a90de59cd25fc6c4e0", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/zrmacc/actions/runs/26565478254" }, { "r": "4.5.3", "os": "mac", "version": "0.6.0.2", "date": "2026-05-28T09:11:09.000Z", "arch": "aarch64", "commit": "58396ade0166a0ac096b876a5438e3c7e8524234", "fileid": "a15a5785bd98a8546ec31abbe1e7d4149039bb0f14906e41258af361ebdcc066", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/zrmacc/actions/runs/26565478254" }, { "r": "4.5.3", "os": "mac", "version": "0.6.0.2", "date": "2026-05-28T09:12:00.000Z", "arch": "x86_64", "commit": "58396ade0166a0ac096b876a5438e3c7e8524234", "fileid": "fb2c7c0858e4ad1d7c73423e09bf8bf51af4604368cf0ddc9a8027a9fbb9f4d2", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/zrmacc/actions/runs/26565478254" }, { "r": "4.6.0", "os": "mac", "version": "0.6.0.2", "date": "2026-05-28T09:11:45.000Z", "arch": "aarch64", "commit": "58396ade0166a0ac096b876a5438e3c7e8524234", "fileid": "2c38ffad2ca9089be5759bc0d70adbfba0435792dc47a788873e93ee382a8693", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/zrmacc/actions/runs/26565478254" }, { "r": "4.6.0", "os": "mac", "version": "0.6.0.2", "date": "2026-05-28T09:12:40.000Z", "arch": "x86_64", "commit": "58396ade0166a0ac096b876a5438e3c7e8524234", "fileid": "6adea3f757db3158d72b1d5e826990dbdc19cc47dbb74e90e31ff3c62eb00c5a", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/zrmacc/actions/runs/26565478254" }, { "r": "4.6.0", "os": "wasm", "version": "0.6.0.2", "date": "2026-05-28T09:11:43.000Z", "arch": "emscripten", "commit": "58396ade0166a0ac096b876a5438e3c7e8524234", "fileid": "a0b81d2d36e0472fec7bdbb9a72034e4c01e253c93cf83625604da78b14b18d8", "status": "success", "buildurl": "https://github.com/r-universe/zrmacc/actions/runs/26565478254" }, { "r": "4.7.0", "os": "win", "version": "0.6.0.2", "date": "2026-05-28T09:11:05.000Z", "arch": "x86_64", "commit": "58396ade0166a0ac096b876a5438e3c7e8524234", "fileid": "cec73dd8080cf7c9dee0e9372f381a4e98eacaedc0ebc40b18e842e954ee58a1", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/zrmacc/actions/runs/26565478254" }, { "r": "4.5.3", "os": "win", "version": "0.6.0.2", "date": "2026-05-28T09:11:04.000Z", "arch": "x86_64", "commit": "58396ade0166a0ac096b876a5438e3c7e8524234", "fileid": "052c6cc9bcd0b844d6bf525851db1c448f636ab7ee4baaa881f691ddb6708317", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/zrmacc/actions/runs/26565478254" }, { "r": "4.6.0", "os": "win", "version": "0.6.0.2", "date": "2026-05-28T09:11:01.000Z", "arch": "x86_64", "commit": "58396ade0166a0ac096b876a5438e3c7e8524234", "fileid": "921231e5e138c254527c581dee85c8b25480f021132a0428fbadba28e84c97d5", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/zrmacc/actions/runs/26565478254" } ] }