{ "_id": "6a55e32eff0138dec5d6a324", "Package": "smashr", "Encoding": "UTF-8", "Type": "Package", "Maintainer": "Peter Carbonetto ", "Authors@R": "c(person(\"Zhengrong\",\"Xing\",role=\"aut\"),\nperson(\"Matthew\",\"Stephens\",role=\"aut\"),\nperson(\"Kaiqian\",\"Zhang\",role=\"ctb\"),\nperson(\"Daniel\",\"Nachun\",role=\"ctb\"),\nperson(\"Guy\",\"Nason\", role=\"cph\"),\nperson(\"Stuart\",\"Barber\",role=\"cph\"),\nperson(\"Tim\",\"Downie\",role=\"cph\"),\nperson(\"Piotr\",\"Frylewicz\",role=\"cph\"),\nperson(\"Arne\",\"Kovac\",role=\"cph\"),\nperson(\"Todd\",\"Ogden\",role=\"cph\"),\nperson(\"Bernard\",\"Silverman\",role=\"cph\"),\nperson(\"Peter\",\"Carbonetto\",role=c(\"aut\",\"cre\"),\nemail=\"pcarbo@uchicago.edu\"))", "Title": "Smoothing by Adaptive Shrinkage", "Version": "1.3-12", "Date": "2025-12-09", "Description": "Fast, wavelet-based Empirical Bayes shrinkage methods for\nsignal denoising, including smoothing Poisson-distributed data\nand Gaussian-distributed data with possibly heteroskedastic\nerror. The algorithms implement the methods described Z. Xing,\nP. Carbonetto & M. Stephens (2021)\n.", "License": "GPL (>= 3)", "Copyright": "file COPYRIGHTS", "NeedsCompilation": "yes", "LazyData": "true", "URL": "https://github.com/stephenslab/smashr", "BugReports": "https://github.com/stephenslab/smashr/issues", "VignetteBuilder": "knitr", "RoxygenNote": "7.3.1", "Repository": "https://stephenslab.r-universe.dev", "Date/Publication": "2025-12-09 16:43:52 UTC", "RemoteUrl": "https://github.com/stephenslab/smashr", "RemoteRef": "HEAD", "RemoteSha": "e06efa41a3a523833fc0ee743a34cb02da0f26a7", "Packaged": { "Date": "2026-07-14 07:13:18 UTC", "User": "root" }, "Author": "Zhengrong Xing [aut],\nMatthew Stephens [aut],\nKaiqian Zhang [ctb],\nDaniel Nachun [ctb],\nGuy Nason [cph],\nStuart Barber [cph],\nTim Downie [cph],\nPiotr Frylewicz [cph],\nArne Kovac [cph],\nTodd Ogden [cph],\nBernard Silverman [cph],\nPeter Carbonetto [aut, cre]", "_user": "stephenslab", "_type": "src", "_file": "smashr_1.3-12.tar.gz", "_fileid": "https://r2.ropensci.org/ae3ae1f9996d9d438cc27c865dc368c8bbfdb3463b22de5d6b1cb94f5b1f9191", "_filesize": 1352011, "_sha256": "ae3ae1f9996d9d438cc27c865dc368c8bbfdb3463b22de5d6b1cb94f5b1f9191", "_expires": "2026-10-22T07:20:11.000Z", "_created": "2026-07-14T07:13:18.000Z", "_published": "2026-07-14T07:20:13.833Z", "_jobs": [ { "job": 87023339510, "time": 156, "config": "linux-devel-arm64", "r": "4.7.0", "check": "OK", "artifact": "8303184623" }, { "job": 87023339520, "time": 172, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "8303188293" }, { "job": 87023339535, "time": 172, "config": "linux-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "8303189674" }, { "job": 87023339522, "time": 172, "config": "linux-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "8303188751" }, { "job": 87023339545, "time": 129, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "8303172481" }, { "job": 87023339608, "time": 354, "config": "macos-oldrel-x86_64", "r": "4.5.3", "check": "OK", "artifact": "8303252732" }, { "job": 87023339542, "time": 162, "config": "macos-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "8303185172" }, { "job": 87023339519, "time": 296, "config": "macos-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "8303231246" }, { "job": 87019161788, "time": 1483, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "8303127830" }, { "job": 87023339501, "time": 111, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "8303166821" }, { "job": 87023339496, "time": 143, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "8303178454" }, { "job": 87023339509, "time": 142, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "8303178962" }, { "job": 87023339561, "time": 148, "config": "windows-release", "r": "4.6.1", "check": "OK", "artifact": "8303180240" } ], "_host": "GitHub-Actions", "_buildurl": "https://github.com/r-universe/stephenslab/actions/runs/29312489538", "_status": "success", "_upstream": "https://github.com/stephenslab/smashr", "_commit": { "id": "e06efa41a3a523833fc0ee743a34cb02da0f26a7", "author": "Peter Carbonetto ", "committer": "Peter Carbonetto ", "message": "Added COPYRIGHTS.\n", "time": 1765298632 }, "_maintainer": { "name": "Peter Carbonetto", "email": "pcarbo@uchicago.edu", "login": "pcarbo", "description": "Research Assistant Prof, Human Genetics, U. Chicago; previously, Staff Scientist at Ancestry, postdoc & HFSP fellow at U. Chicago, & Ph.D. at UBC", "uuid": 1503904 }, "_distro": "resolute", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.1.1", "role": "Depends" }, { "package": "Rcpp", "role": "LinkingTo" }, { "package": "utils", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "data.table", "role": "Imports" }, { "package": "caTools", "role": "Imports" }, { "package": "wavethresh", "role": "Imports" }, { "package": "ashr", "role": "Imports" }, { "package": "Rcpp", "version": ">= 1.1.0", "role": "Imports" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "MASS", "role": "Suggests" }, { "package": "EbayesThresh", "role": "Suggests" }, { "package": "testthat", "role": "Suggests" } ], "_owner": "stephenslab", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-47", "n": 8 }, { "week": "2025-48", "n": 7 }, { "week": "2025-49", "n": 1 }, { "week": "2025-50", "n": 2 } ], "_tags": [ { "name": "v1.3-12", "date": "2025-12-09" } ], "_stars": 8, "_contributors": [ { "user": "pcarbo", "count": 96, "uuid": 1503904 }, { "user": "stephens999", "count": 16, "uuid": 1800389 }, { "user": "dongyuexie", "count": 5, "uuid": 26743940 }, { "user": "danielnachun", "count": 4, "uuid": 9205048 }, { "user": "kaiqianzhang", "count": 1, "uuid": 25370607 } ], "_userbio": { "uuid": 5939770, "type": "organization", "name": "Stephens lab", "followers": 118, "description": "Research in statistical and computational methods for genetics at the University of Chicago." }, "_downloads": { "count": 198, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/smashr" }, "_devurl": "https://github.com/stephenslab/smashr", "_searchresults": 156, "_topics": [ "cpp" ], "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/readme.html", "extra/readme.md", "extra/smashr.html", "manual.pdf" ], "_homeurl": "https://github.com/stephenslab/smashr", "_realowner": "stephenslab", "_cranurl": true, "_releases": [ { "version": "1.3-12", "date": "2025-12-15" } ], "_exports": [ "glm.approx", "reflect", "reverse.pwave", "sd_estimate_gasser_etal", "smash", "smash.gaus", "smash.poiss", "ti.thresh" ], "_datasets": [ { "name": "treas", "title": "Three-month treasury bill data.", "object": "treas", "class": [ "numeric" ], "fields": [], "table": false, "tojson": true } ], "_help": [ { "page": "glm.approx", "title": "Model fitting using weighted least squares or a GLM approach.", "topics": [ "glm.approx" ] }, { "page": "reflect", "title": "Reflect and extend a vector.", "topics": [ "reflect" ] }, { "page": "reverse.pwave", "title": "Reverse wavelet transform a set of probabilities in TItable format for Poisson data.", "topics": [ "reverse.pwave" ] }, { "page": "sd_estimate_gasser_etal", "title": "Estimate homoskedastic standard deviation from nonparamatric regression.", "topics": [ "sd_estimate_gasser_etal" ] }, { "page": "smash", "title": "Estimate the underlying mean or intensity function from Gaussian or Poisson data, respectively.", "topics": [ "smash" ] }, { "page": "smash.gaus", "title": "Estimate underlying mean function from noisy Gaussian data.", "topics": [ "smash.gaus" ] }, { "page": "smash.poiss", "title": "Estimate the underlying intensity for Poisson counts.", "topics": [ "smash.poiss" ] }, { "page": "smashr", "title": "smashr: Smoothing using Adaptive SHrinkage in R", "topics": [ "smashr-package", "smashr" ] }, { "page": "ti.thresh", "title": "TI thresholding with heteroskedastic errors.", "topics": [ "ti.thresh" ] }, { "page": "treas", "title": "Three-month treasury bill data.", "topics": [ "treas" ] } ], "_readme": "https://github.com/stephenslab/smashr/raw/HEAD/README.md", "_rundeps": [ "ashr", "bitops", "caTools", "data.table", "etrunct", "invgamma", "irlba", "lattice", "MASS", "Matrix", "mixsqp", "Rcpp", "RcppArmadillo", "SQUAREM", "truncnorm", "wavethresh" ], "_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": "smashr.Rmd", "filename": "smashr.html", "title": "ASH-based wavelet shrinkage for heteroskedastic models", "engine": "knitr::rmarkdown", "headings": [ "Set up environment", "Preparations", "Constant variance example", "Non-constant variance example", "Estimating the variance function", "Unevenly spaced data", "Unevenly spaced data with constant variance", "Unevenly spaced data with non-constant variance", "Poisson-distributed data example", "Constant variance", "Non-constant variance", "Simulation example from Fan & Yao (1998)", "Treasury Bill example from Fan & Yao (1998)", "Average replicate data", "Heavisine example from Delouille et al (2004)", "Motorcycle example from Delouille et al (2004)", "Session info" ], "created": "2018-05-08 03:31:13", "modified": "2024-07-08 22:23:07", "commits": 12 } ], "_score": 6.999304572338349, "_indexed": true, "_nocasepkg": "smashr", "_universes": [ "stephenslab", "pcarbo" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.3-12", "date": "2026-07-14T07:15:43.000Z", "distro": "resolute", "arch": "aarch64", "commit": "e06efa41a3a523833fc0ee743a34cb02da0f26a7", "fileid": "https://r2.ropensci.org/bb5786d5e7cf774f45cb88e4209a00d7ed4c19605c0f3e152a0a2bb47a2dc339", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/stephenslab/actions/runs/29312489538" }, { "r": "4.7.0", "os": "linux", "version": "1.3-12", "date": "2026-07-14T07:15:40.000Z", "distro": "resolute", "arch": "x86_64", "commit": "e06efa41a3a523833fc0ee743a34cb02da0f26a7", "fileid": "https://r2.ropensci.org/188bf4bfca564f33df3b8eef09d1a977a88b6fc590bf5af2f6e8cd2128804b43", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/stephenslab/actions/runs/29312489538" }, { "r": "4.6.1", "os": "linux", "version": "1.3-12", "date": "2026-07-14T07:15:57.000Z", "distro": "resolute", "arch": "aarch64", "commit": "e06efa41a3a523833fc0ee743a34cb02da0f26a7", "fileid": "https://r2.ropensci.org/74fb2d58390ca6e76e21198a7574d028c928873676decc612e0f49a7edf08601", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/stephenslab/actions/runs/29312489538" }, { "r": "4.6.1", "os": "linux", "version": "1.3-12", "date": "2026-07-14T07:15:41.000Z", "distro": "resolute", "arch": "x86_64", "commit": "e06efa41a3a523833fc0ee743a34cb02da0f26a7", "fileid": "https://r2.ropensci.org/4cfd31447234bf77247257999c5faba90722bcafe87ed63d7b94b31e2ad908fc", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/stephenslab/actions/runs/29312489538" }, { "r": "4.5.3", "os": "mac", "version": "1.3-12", "date": "2026-07-14T07:15:00.000Z", "arch": "aarch64", "commit": "e06efa41a3a523833fc0ee743a34cb02da0f26a7", "fileid": "https://r2.ropensci.org/d29149ce661b4c6b18d46b1937c6a8fd43b22584d7713d32dba3fef3bc09b7de", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/stephenslab/actions/runs/29312489538" }, { "r": "4.5.3", "os": "mac", "version": "1.3-12", "date": "2026-07-14T07:17:31.000Z", "arch": "x86_64", "commit": "e06efa41a3a523833fc0ee743a34cb02da0f26a7", "fileid": "https://r2.ropensci.org/6a2f31619313765d87cde9c42cd6873e6274e0a0bafd301b05add02bba88af6b", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/stephenslab/actions/runs/29312489538" }, { "r": "4.6.1", "os": "mac", "version": "1.3-12", "date": "2026-07-14T07:15:26.000Z", "arch": "aarch64", "commit": "e06efa41a3a523833fc0ee743a34cb02da0f26a7", "fileid": "https://r2.ropensci.org/56b88452adafd415d47074cb79313da7a7e98ca5262610b9956d60e466098e49", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/stephenslab/actions/runs/29312489538" }, { "r": "4.6.1", "os": "mac", "version": "1.3-12", "date": "2026-07-14T07:17:02.000Z", "arch": "x86_64", "commit": "e06efa41a3a523833fc0ee743a34cb02da0f26a7", "fileid": "https://r2.ropensci.org/40784bd3f0a3572bd0548a4d2050cf33a62e64102d465518d39887fea2811675", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/stephenslab/actions/runs/29312489538" }, { "r": "4.6.0", "os": "wasm", "version": "1.3-12", "date": "2026-07-14T07:15:30.000Z", "arch": "emscripten", "commit": "e06efa41a3a523833fc0ee743a34cb02da0f26a7", "fileid": "https://r2.ropensci.org/7c4fa61771dd958ed33f61b5156098eda5b243172a269df938b6c811a5e04e5f", "status": "success", "buildurl": "https://github.com/r-universe/stephenslab/actions/runs/29312489538" }, { "r": "4.7.0", "os": "win", "version": "1.3-12", "date": "2026-07-14T07:14:41.000Z", "arch": "x86_64", "commit": "e06efa41a3a523833fc0ee743a34cb02da0f26a7", "fileid": "https://r2.ropensci.org/c3f8095b3aca2d75691b43d065a09d9cc7a3b467b1b3fa662683e3d9a4ec9d55", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/stephenslab/actions/runs/29312489538" }, { "r": "4.5.3", "os": "win", "version": "1.3-12", "date": "2026-07-14T07:14:39.000Z", "arch": "x86_64", "commit": "e06efa41a3a523833fc0ee743a34cb02da0f26a7", "fileid": "https://r2.ropensci.org/bea21325d78840725c8c4e6afd146443546a0c0302d5c7c20fb2e8a5ec36df67", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/stephenslab/actions/runs/29312489538" }, { "r": "4.6.1", "os": "win", "version": "1.3-12", "date": "2026-07-14T07:14:42.000Z", "arch": "x86_64", "commit": "e06efa41a3a523833fc0ee743a34cb02da0f26a7", "fileid": "https://r2.ropensci.org/6d7028e3cd76885c3ef042d89a27c778867978fe50d3626d436628e88158840e", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/stephenslab/actions/runs/29312489538" } ] }