{ "_id": "6a10442dacfb0bcc41c9e344", "Package": "dentist", "Title": "Dents the Likelihood Surface to Estimate Parameter Uncertainty", "Version": "0.0.4", "Authors@R": "c(person(given = \"Brian\",\nfamily = \"O'Meara\",\nrole = c(\"aut\", \"cre\"),\nemail = \"omeara.brian@gmail.com\",\ncomment = c(ORCID = \"0000-0002-0337-5997\")),\nperson(given = \"James\",\nfamily = \"Boyko\",\nrole = c(\"aut\"),\ncomment = c(ORCID = \"0000-0003-0952-169X\"))\n)", "Description": "This will sample points around a specified distance from\nthe maximum likelihood estimates. This should be a better way\nto estimate uncertainty than using the Hessian of the\nlikelihood equation. It works by \"denting\" the likelihood\nsurface to make a ridge at the desired difference in log\nlikelihood and then \"walks\" around this dented surface,\nsampling points.", "License": "GPL (>= 3)", "URL": "https://bomeara.github.io/dentist/,\nhttps://github.com/bomeara/dentist", "BugReports": "https://github.com/bomeara/dentist/issues", "Config/testthat/edition": "3", "Encoding": "UTF-8", "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "7.3.2", "Repository": "https://phylotastic.r-universe.dev", "Date/Publication": "2024-10-29 18:09:53 UTC", "RemoteUrl": "https://github.com/bomeara/dentist", "RemoteRef": "HEAD", "RemoteSha": "44f0c3eee2873ad14563a68ab27603f7bdeeb1f1", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-11 06:38:43 UTC", "User": "root" }, "Author": "Brian O'Meara [aut, cre] (ORCID:\n),\nJames Boyko [aut] (ORCID: )", "Maintainer": "Brian O'Meara ", "MD5sum": "be3f9e3b6b7d339d8d37ec4be7ec8d0b", "_user": "phylotastic", "_type": "src", "_file": "dentist_0.0.4.tar.gz", "_fileid": "c5c321771e4121ee2b05c53dfc1551f4b419a10c8c69d225815ae60ce2a189e7", "_filesize": 450360, "_sha256": "c5c321771e4121ee2b05c53dfc1551f4b419a10c8c69d225815ae60ce2a189e7", "_created": "2026-05-11T06:38:43.000Z", "_published": "2026-05-22T11:55:25.395Z", "_distro": "noble", "_jobs": [ { "job": 77374454772, "time": 112, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "6911847698" }, { "job": 77374454747, "time": 109, "config": "linux-release-x86_64", "r": "4.6.0", "check": "NOTE", "artifact": "6911846885" }, { "job": 77374454670, "time": 95, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "6911843673" }, { "job": 77374454955, "time": 86, "config": "macos-release-arm64", "r": "4.6.0", "check": "NOTE", "artifact": "6911841699" }, { "job": 77374454517, "time": 136, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "6911821584" }, { "job": 77374454031, "time": 80, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7159867288" }, { "job": 77374454611, "time": 69, "config": "windows-devel", "r": "4.7.0", "check": "NOTE", "artifact": "6911837898" }, { "job": 77374454837, "time": 69, "config": "windows-oldrel", "r": "4.5.3", "check": "NOTE", "artifact": "6911837691" }, { "job": 77374454616, "time": 76, "config": "windows-release", "r": "4.6.0", "check": "NOTE", "artifact": "6911839201" } ], "_buildurl": "https://github.com/r-universe/phylotastic/actions/runs/25654362562", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bomeara/dentist", "_commit": { "id": "44f0c3eee2873ad14563a68ab27603f7bdeeb1f1", "author": "Brian O'Meara ", "committer": "Brian O'Meara ", "message": "option for color gradients\n", "time": 1730225393 }, "_maintainer": { "name": "Brian OMeara", "email": "omeara.brian@gmail.com", "login": "bomeara", "mastodon": "@omearabrian@mastodon.social", "bluesky": "@omearabrian.bsky.social", "orcid": "0000-0002-0337-5997", "uuid": 1612612 }, "_registered": true, "_dependencies": [ { "package": "graphics", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "testthat", "version": ">= 3.0.0", "role": "Suggests" } ], "_owner": "bomeara", "_selfowned": false, "_usedby": 0, "_updates": [], "_tags": [], "_stars": 3, "_contributors": [ { "user": "bomeara", "count": 41, "uuid": 1612612 }, { "user": "jboyko", "count": 6, "uuid": 44244507 } ], "_userbio": { "uuid": 1652822, "type": "organization", "name": "phylotastic" }, "_downloads": { "count": 0, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/dentist" }, "_devurl": "https://github.com/bomeara/dentist", "_pkgdown": "https://bomeara.github.io/dentist/", "_searchresults": 21, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/dentist.html", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_cranurl": false, "_exports": [ "dent_likelihood", "dent_walk" ], "_help": [ { "page": "dent_likelihood", "title": "Dents the likelihood surface", "topics": [ "dent_likelihood" ] }, { "page": "dent_propose", "title": "Propose new values This proposes new values using a normal distribution centered on the original parameter values, with desired standard deviation. If any proposed values are outside the bounds, it will propose again.", "topics": [ "dent_propose" ] }, { "page": "dent_walk", "title": "Sample points from along a ridge", "topics": [ "dent_walk" ] }, { "page": "plot.dentist", "title": "Plot the dented samples This will show the univariate plots of the parameter values versus the likelihood as well as bivariate plots of pairs of parameters to look for ridges.", "topics": [ "plot.dentist" ] }, { "page": "print.dentist", "title": "Print dentist print summary of output from dent_walk", "topics": [ "print.dentist" ] }, { "page": "quiet_fn", "title": "Quiet internal functions", "topics": [ "quiet_fn" ] }, { "page": "sphere_propose", "title": "Propose new values based on points near bounds This proposes new values based on wiggling a little bit away from the values near the bounds of the good region", "topics": [ "sphere_propose" ] }, { "page": "summary.dentist", "title": "Summarize dentist Display summary of output from dent_walk", "topics": [ "summary.dentist" ] } ], "_readme": "https://github.com/bomeara/dentist/raw/HEAD/README.md", "_rundeps": [], "_score": 2.4983105537896004, "_indexed": false, "_nocasepkg": "dentist", "_universes": [ "phylotastic" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "0.0.4", "date": "2026-05-11T06:40:44.000Z", "distro": "noble", "commit": "44f0c3eee2873ad14563a68ab27603f7bdeeb1f1", "fileid": "04cb4d9cf5fc6e191ce8de2105078234a23987b0c6f87fbcfaa6b02c2931b36b", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/phylotastic/actions/runs/25654362562" }, { "r": "4.6.0", "os": "linux", "version": "0.0.4", "date": "2026-05-11T06:40:38.000Z", "distro": "noble", "commit": "44f0c3eee2873ad14563a68ab27603f7bdeeb1f1", "fileid": "052f4cd4169e16c35ce871e72c7dca5069860c0b86ee7a01e64b0035f1d4948b", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/phylotastic/actions/runs/25654362562" }, { "r": "4.5.3", "os": "mac", "version": "0.0.4", "date": "2026-05-11T06:40:29.000Z", "commit": "44f0c3eee2873ad14563a68ab27603f7bdeeb1f1", "fileid": "009594bd9745e46087a04eeea440b2b1d35cb683ea6388da0fd8e828ba5f977c", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/phylotastic/actions/runs/25654362562" }, { "r": "4.6.0", "os": "mac", "version": "0.0.4", "date": "2026-05-11T06:40:18.000Z", "commit": "44f0c3eee2873ad14563a68ab27603f7bdeeb1f1", "fileid": "2ed75c4504a3afadcd72c502a1add33efa0f2b018cd12a4af8b086f1f4a4a0aa", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/phylotastic/actions/runs/25654362562" }, { "r": "4.7.0", "os": "win", "version": "0.0.4", "date": "2026-05-11T06:39:55.000Z", "commit": "44f0c3eee2873ad14563a68ab27603f7bdeeb1f1", "fileid": "d6ce7510ede2114d69ba4534db1d3d0a310f7c8298f7e3aa524082c0b36246d5", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/phylotastic/actions/runs/25654362562" }, { "r": "4.5.3", "os": "win", "version": "0.0.4", "date": "2026-05-11T06:39:53.000Z", "commit": "44f0c3eee2873ad14563a68ab27603f7bdeeb1f1", "fileid": "68c2f075f8bbbaae1ac4eac83cbf12d7ce481b8355be6dfb25ab9762271da978", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/phylotastic/actions/runs/25654362562" }, { "r": "4.6.0", "os": "win", "version": "0.0.4", "date": "2026-05-11T06:39:51.000Z", "commit": "44f0c3eee2873ad14563a68ab27603f7bdeeb1f1", "fileid": "c0a5b4582a77c688387ef8a0cf850cc8552b60edb1a4e13e647a1f32b1b5ea52", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/phylotastic/actions/runs/25654362562" }, { "r": "4.6.0", "os": "wasm", "version": "0.0.4", "date": "2026-05-22T11:55:06.000Z", "commit": "44f0c3eee2873ad14563a68ab27603f7bdeeb1f1", "fileid": "5a4e0f7cb554e8f0492f407c6e3ce9cfb8f7da8b3c9304e1f72ceb6fd463e442", "status": "success", "buildurl": "https://github.com/r-universe/phylotastic/actions/runs/25654362562" } ] }