{ "_id": "6a47ad7de06c18f0a651a8be", "Package": "optedr", "Title": "Calculating Optimal and D-Augmented Designs for Single- and\nMulti-Factor Models", "Version": "3.0.1", "Authors@R": "c(person(given = \"Carlos\",\nfamily = \"de la Calle-Arroyo\",\nrole = c(\"aut\", \"cre\"),\nemail = \"carlos.calle.arroyo@gmail.com\",\ncomment = c(ORCID = \"0000-0002-5099-888X\")),\nperson(given = \"Jesús\",\nfamily = \"López-Fidalgo\",\nrole = c(\"aut\"),\ncomment = c(ORCID = \"0000-0001-7502-8188\")),\nperson(given = \"Licesio J.\",\nfamily = \"Rodríguez-Aragón\",\nrole = c(\"aut\"),\ncomment = c(ORCID = \"0000-0003-4970-3877\"))\n)", "Description": "Calculates D-, Ds-, A-, I- and L-optimal designs, weighted\ncombinations of these via a Compound criterion, and KL-optimal\ndesigns for model discrimination, for non-linear single- and\nmulti-factor models, via an implementation of the cocktail\nalgorithm (Yu, 2011, ).\nMulti-factor models use design variables x1, x2, … with a\nnamed-list design space; single-factor models remain backward\ncompatible. Compares designs via their efficiency, augments any\ndesign with a controlled efficiency loss, and provides\nefficient rounding functions to convert approximate designs to\nexact ones.", "License": "GPL-3", "Encoding": "UTF-8", "URL": "https://github.com/kezrael/optedr,\nhttps://github.com/Kezrael/optedr", "BugReports": "https://github.com/Kezrael/optedr/issues", "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "7.3.1", "VignetteBuilder": "knitr", "Config/testthat/edition": "3", "Config/pak/sysreqs": "cmake make libuv1-dev zlib1g-dev", "Repository": "https://kezrael.r-universe.dev", "Date/Publication": "2026-07-03 09:27:36 UTC", "RemoteUrl": "https://github.com/kezrael/optedr", "RemoteRef": "HEAD", "RemoteSha": "f80e2bcc8188317d63bdc7acb1ef3158a52b02ec", "NeedsCompilation": "no", "Packaged": { "Date": "2026-07-03 12:34:19 UTC", "User": "root" }, "Author": "Carlos de la Calle-Arroyo [aut, cre] (ORCID:\n),\nJesús López-Fidalgo [aut] (ORCID:\n),\nLicesio J. Rodríguez-Aragón [aut] (ORCID:\n)", "Maintainer": "Carlos de la Calle-Arroyo ", "_user": "kezrael", "_type": "src", "_file": "optedr_3.0.1.tar.gz", "_fileid": "https://r2.ropensci.org/0035d5bcbf956041936512561bc3942d243bd54fdc25f3c474713ebb69fc7e88", "_filesize": 2230190, "_sha256": "0035d5bcbf956041936512561bc3942d243bd54fdc25f3c474713ebb69fc7e88", "_expires": "2026-10-11T12:39:24.000Z", "_created": "2026-07-03T12:34:19.000Z", "_published": "2026-07-03T12:39:25.797Z", "_jobs": [ { "job": 85000888052, "time": 268, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "8066686970" }, { "job": 85000888045, "time": 226, "config": "linux-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "8066672622" }, { "job": 85000888051, "time": 166, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "8066651699" }, { "job": 85000888064, "time": 161, "config": "macos-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "8066650384" }, { "job": 85000230052, "time": 235, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "8066594839" }, { "job": 85000888043, "time": 177, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "8066656238" }, { "job": 85000888104, "time": 217, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "8066669784" }, { "job": 85000888129, "time": 215, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "8066669198" }, { "job": 85000888074, "time": 214, "config": "windows-release", "r": "4.6.1", "check": "OK", "artifact": "8066668331" } ], "_host": "GitHub-Actions", "_buildurl": "https://github.com/r-universe/kezrael/actions/runs/28660658538", "_status": "success", "_upstream": "https://github.com/kezrael/optedr", "_commit": { "id": "f80e2bcc8188317d63bdc7acb1ef3158a52b02ec", "author": "Kezrael ", "committer": "Kezrael ", "message": "Fix CRAN test failure under ATLAS BLAS (R-devel r90186)\n\nWith ATLAS, a non-identifiable model causes the gradient to return NA/NaN,\nso dcrit() produces NA instead of Inf. The old crit_val trimming expression\n(1L:(length(v) - sum(v == 0))) crashes on NA input. Replace with seq_len(index)\nand add an explicit is.finite() guard that throws an informative 'not identifiable'\nerror across all four criterion functions (D, Ds, I/A/L, Compound).\n\nAlso extends the guard from anyNA() to !all(is.finite()) to catch the Inf path\n(det(M) = 0 exactly) with the same clear message, rather than relying on the\nlater update_weights() check.\n\nBump version to 3.0.1.\n\nCo-Authored-By: Claude Sonnet 4.6 \n", "time": 1783070856 }, "_maintainer": { "name": "Carlos de la Calle-Arroyo", "email": "carlos.calle.arroyo@gmail.com", "orcid": "0000-0002-5099-888X" }, "_distro": "resolute", "_registered": true, "_dependencies": [ { "package": "ggplot2", "role": "Imports" }, { "package": "purrr", "role": "Imports" }, { "package": "rlang", "role": "Imports" }, { "package": "crayon", "role": "Imports" }, { "package": "cli", "role": "Imports" }, { "package": "shiny", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "testthat", "version": ">= 3.0.0", "role": "Suggests" }, { "package": "mockery", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "markdown", "role": "Suggests" }, { "package": "DT", "role": "Suggests" }, { "package": "shinydashboard", "role": "Suggests" }, { "package": "shinyalert", "role": "Suggests" }, { "package": "plotly", "role": "Suggests" }, { "package": "hrbrthemes", "role": "Suggests" }, { "package": "shinyjs", "role": "Suggests" }, { "package": "orthopolynom", "role": "Suggests" }, { "package": "magrittr", "role": "Suggests" }, { "package": "tidyverse", "role": "Suggests" }, { "package": "nleqslv", "role": "Suggests" } ], "_owner": "kezrael", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2026-21", "n": 25 }, { "week": "2026-22", "n": 2 }, { "week": "2026-26", "n": 2 }, { "week": "2026-27", "n": 1 } ], "_tags": [], "_stars": 5, "_contributors": [ { "user": "kezrael", "count": 98, "uuid": 7874989 } ], "_userbio": { "uuid": 7874989, "type": "user", "name": "Kezrael", "followers": 1 }, "_downloads": { "count": 359, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/optedr" }, "_devurl": "https://github.com/kezrael/optedr", "_searchresults": 26, "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/NEWS.html", "extra/NEWS.txt", "extra/optedr.html", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_homeurl": "https://github.com/kezrael/optedr", "_realowner": "kezrael", "_cranurl": true, "_releases": [ { "version": "1.0.0", "date": "2021-12-01" }, { "version": "1.0.1", "date": "2022-01-20" }, { "version": "2.0.0", "date": "2022-11-18" }, { "version": "2.2.0", "date": "2025-02-11" }, { "version": "3.0.0", "date": "2026-06-23" } ], "_exports": [ "augment_design", "combinatorial_round", "design_efficiency", "efficient_round", "get_augment_region", "make_glm_family", "make_kl_fun", "opt_des", "shiny_augment", "shiny_optimal" ], "_help": [ { "page": "add_design", "title": "Add two designs", "topics": [ "add_design" ] }, { "page": "add_points", "title": "Update design given crosspoints and alpha", "topics": [ "add_points" ] }, { "page": "augment_design", "title": "Augment Design", "topics": [ "augment_design" ] }, { "page": "check_inputs", "title": "Check Inputs", "topics": [ "check_inputs" ] }, { "page": "combinatorial_round", "title": "Combinatorial round", "topics": [ "combinatorial_round" ] }, { "page": "crit", "title": "Master function for the criterion function", "topics": [ "crit" ] }, { "page": "crosspoints", "title": "Calculate crosspoints", "topics": [ "crosspoints" ] }, { "page": "CWFMult", "title": "Cocktail Algorithm implementation for Compound Optimality", "concept": [ "cocktail algorithms" ], "topics": [ "CWFMult" ] }, { "page": "daugment_design", "title": "D-Augment Design", "concept": [ "augment designs" ], "topics": [ "daugment_design" ] }, { "page": "dcrit", "title": "Criterion function for D-Optimality", "topics": [ "dcrit" ] }, { "page": "delete_points", "title": "Remove low weight points", "topics": [ "delete_points" ] }, { "page": "design_efficiency", "title": "Efficiency between optimal design and a user given design", "topics": [ "design_efficiency" ] }, { "page": "detect_design_vars", "title": "Detect design variables from a model formula", "topics": [ "detect_design_vars" ] }, { "page": "dsaugment_design", "title": "Ds-Augment Design", "concept": [ "augment designs" ], "topics": [ "dsaugment_design" ] }, { "page": "dscrit", "title": "Criterion function for Ds-Optimality", "topics": [ "dscrit" ] }, { "page": "dsens", "title": "Sensitivity function for D-Optimality", "topics": [ "dsens" ] }, { "page": "dssens", "title": "Sensitivity function for Ds-Optimality", "topics": [ "dssens" ] }, { "page": "DsWFMult", "title": "Cocktail Algorithm implementation for Ds-Optimality", "concept": [ "cocktail algorithms" ], "topics": [ "DsWFMult" ] }, { "page": "DWFMult", "title": "Cocktail Algorithm implementation for D-Optimality", "concept": [ "cocktail algorithms" ], "topics": [ "DWFMult" ] }, { "page": "eff", "title": "Efficiency between two Information Matrices", "topics": [ "eff" ] }, { "page": "efficient_round", "title": "Efficient Round", "topics": [ "efficient_round" ] }, { "page": "findmax", "title": "Find Maximum", "topics": [ "findmax" ] }, { "page": "findmaxval", "title": "Find Maximum Value", "topics": [ "findmaxval" ] }, { "page": "findminval", "title": "Find Minimum Value", "topics": [ "findminval" ] }, { "page": "get_augment_region", "title": "Get Augment Regions", "topics": [ "get_augment_region" ] }, { "page": "get_daugment_region", "title": "Get D-augment region", "concept": [ "augment regions" ], "topics": [ "get_daugment_region" ] }, { "page": "get_dsaugment_region", "title": "Get Ds-augment region", "concept": [ "augment region" ], "topics": [ "get_dsaugment_region" ] }, { "page": "get_laugment_region", "title": "Get L-augment region", "concept": [ "augment region" ], "topics": [ "get_laugment_region" ] }, { "page": "getCross2", "title": "Give effective limits to candidate points region", "topics": [ "getCross2" ] }, { "page": "getPar", "title": "Parity of the crosspoints", "topics": [ "getPar" ] }, { "page": "getStart", "title": "Find where the candidate points region starts", "topics": [ "getStart" ] }, { "page": "gradient", "title": "Gradient function", "topics": [ "gradient" ] }, { "page": "gradient22", "title": "Gradient function for a subset of variables", "topics": [ "gradient22" ] }, { "page": "icrit", "title": "Criterion function for I-Optimality and L-Optimality", "topics": [ "icrit" ] }, { "page": "inf_mat", "title": "Information Matrix", "topics": [ "inf_mat" ] }, { "page": "integrate_reg_int", "title": "Integrate IM", "topics": [ "integrate_reg_int" ] }, { "page": "isens", "title": "Sensitivity function for I-Optimality", "topics": [ "isens" ] }, { "page": "IWFMult", "title": "Cocktail Algorithm implementation for L-, I- and A-Optimality", "concept": [ "cocktail algorithms" ], "topics": [ "IWFMult" ] }, { "page": "KLWFMult", "title": "Cocktail Algorithm for KL-Optimality", "concept": [ "cocktail algorithms" ], "topics": [ "KLWFMult" ] }, { "page": "laugment_design", "title": "L-Augment Design", "concept": [ "augment designs" ], "topics": [ "laugment_design" ] }, { "page": "make_glm_family", "title": "GLM family specification for KL-Optimality", "topics": [ "make_glm_family" ] }, { "page": "make_kl_fun", "title": "Build a KL-divergence point function for use with opt_des()", "topics": [ "make_kl_fun" ] }, { "page": "opt_des", "title": "Calculates the optimal design for a specified criterion", "topics": [ "opt_des" ] }, { "page": "plot_convergence", "title": "Plot Convergence of the algorithm", "topics": [ "plot_convergence" ] }, { "page": "plot_sens", "title": "Plot sensitivity function", "topics": [ "plot_sens" ] }, { "page": "plot.optdes", "title": "Plot function for optdes", "topics": [ "plot.optdes" ] }, { "page": "print.augment_region", "title": "Print method for augment_region objects", "topics": [ "print.augment_region" ] }, { "page": "print.optdes", "title": "Print function for optdes", "topics": [ "print.optdes" ] }, { "page": "sens", "title": "Master function to calculate the sensitivity function", "topics": [ "sens" ] }, { "page": "shiny_augment", "title": "Shiny D-augment", "topics": [ "shiny_augment" ] }, { "page": "shiny_optimal", "title": "Shiny Optimal", "topics": [ "shiny_optimal" ] }, { "page": "summary.optdes", "title": "Summary function for optdes", "topics": [ "summary.optdes" ] }, { "page": "tr", "title": "Trace", "topics": [ "tr" ] }, { "page": "update_design", "title": "Update Design with new point", "topics": [ "update_design" ] }, { "page": "update_design_total", "title": "Merge close points of a design", "topics": [ "update_design_total" ] }, { "page": "update_sequence", "title": "Deletes duplicates points", "topics": [ "update_sequence" ] }, { "page": "update_weights", "title": "Update weight D-Optimality", "topics": [ "update_weights" ] }, { "page": "update_weightsDS", "title": "Update weight Ds-Optimality", "topics": [ "update_weightsDS" ] }, { "page": "update_weightsI", "title": "Update weight I-Optimality", "topics": [ "update_weightsI" ] }, { "page": "weight_function", "title": "Weight function per distribution", "topics": [ "weight_function" ] }, { "page": "WFMult", "title": "Master function for the cocktail algorithm, that calls the appropriate one given the criterion.", "concept": [ "cocktail algorithms" ], "topics": [ "WFMult" ] } ], "_readme": "https://github.com/kezrael/optedr/raw/HEAD/README.md", "_rundeps": [ "base64enc", "bslib", "cachem", "cli", "commonmark", "cpp11", "crayon", "digest", "farver", "fastmap", "fontawesome", "fs", "ggplot2", "glue", "gtable", "htmltools", "httpuv", "isoband", "jquerylib", "jsonlite", "labeling", "later", "lifecycle", "magrittr", "memoise", "mime", "otel", "promises", "purrr", "R6", "rappdirs", "RColorBrewer", "Rcpp", "rlang", "S7", "sass", "scales", "shiny", "sourcetools", "vctrs", "viridisLite", "withr", "xtable" ], "_vignettes": [ { "source": "optedr-augment.Rmd", "filename": "optedr-augment.html", "title": "Augmenting designs with controlled efficiency loss", "engine": "knitr::rmarkdown", "headings": [ "Motivation", "Key parameters", "One-factor augmentation", "Step 1: compute the candidate region", "Step 2: choose a point and augment", "Comparing efficiency before and after", "Using the optimal design as reference (calc_optimal_design = TRUE)", "Two-factor augmentation", "Initial design and candidate region", "Three-factor augmentation", "Augmenting with Ds-Optimality", "Interactive mode" ], "created": "2026-06-22 12:21:33", "modified": "2026-06-22 12:21:33", "commits": 1 }, { "source": "optedr-intro.Rmd", "filename": "optedr-intro.html", "title": "Introduction to optedr: optimal designs for non-linear models", "engine": "knitr::rmarkdown", "headings": [ "The optimal design problem", "A first example: D-Optimality in one factor", "Other optimality criteria", "Ds-Optimality", "A-Optimality", "I-Optimality", "L-Optimality", "Multi-dimensional design spaces", "Two-factor model: bisubstrate Michaelis-Menten", "Three factors and beyond", "Compound criterion", "Design efficiency", "Rounding to exact designs", "efficient_round()", "combinatorial_round()" ], "created": "2026-06-22 12:21:33", "modified": "2026-06-22 12:21:33", "commits": 1 }, { "source": "optedr-kl.Rmd", "filename": "optedr-kl.html", "title": "KL-Optimality: designs for model discrimination", "engine": "knitr::rmarkdown", "headings": [ "Background", "API overview", "Example 1: Michaelis-Menten vs linear rival (Normal, 1D)", "Example 2: exponential decay, Poisson family", "Using make_kl_fun() for custom KL functions", "Supported pairs", "Example 3: Normal with different variances (1D)", "Example 4: two-factor MM vs linear rival (make_kl_fun, 2D)", "Example 5: discriminating error structures — the Hill model" ], "created": "2026-06-22 12:21:33", "modified": "2026-06-22 12:21:33", "commits": 1 } ], "_score": 5.892094602690481, "_indexed": true, "_nocasepkg": "optedr", "_universes": [ "kezrael" ], "_previous": "3.0.0", "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "3.0.1", "date": "2026-07-03T12:37:04.000Z", "distro": "resolute", "commit": "f80e2bcc8188317d63bdc7acb1ef3158a52b02ec", "fileid": "https://r2.ropensci.org/e51b283a8e93fe69332dbcc59e821bbb59b1fea58e3ff54560294a6eee22b1f7", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/kezrael/actions/runs/28660658538" }, { "r": "4.6.1", "os": "linux", "version": "3.0.1", "date": "2026-07-03T12:36:40.000Z", "distro": "resolute", "commit": "f80e2bcc8188317d63bdc7acb1ef3158a52b02ec", "fileid": "https://r2.ropensci.org/c4c4c0828f978dd1349587149a477a7b1d38c4ad0e173254b72385a9743a535b", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/kezrael/actions/runs/28660658538" }, { "r": "4.5.3", "os": "mac", "version": "3.0.1", "date": "2026-07-03T12:36:00.000Z", "commit": "f80e2bcc8188317d63bdc7acb1ef3158a52b02ec", "fileid": "https://r2.ropensci.org/e1634261c2d1b4267277813d7b53bc2fd69919d72fa37636145ac92a96f65247", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/kezrael/actions/runs/28660658538" }, { "r": "4.6.1", "os": "mac", "version": "3.0.1", "date": "2026-07-03T12:36:04.000Z", "commit": "f80e2bcc8188317d63bdc7acb1ef3158a52b02ec", "fileid": "https://r2.ropensci.org/1b7fa6b1d05398affdf85e52742ed7212a0e138b8009750fd0a8ac78755d23ed", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/kezrael/actions/runs/28660658538" }, { "r": "4.6.0", "os": "wasm", "version": "3.0.1", "date": "2026-07-03T12:37:33.000Z", "commit": "f80e2bcc8188317d63bdc7acb1ef3158a52b02ec", "fileid": "https://r2.ropensci.org/f2b50120f7b4cf297ba70177464887926f87885404cf1f728ca2f8f8cafc2e7e", "status": "success", "buildurl": "https://github.com/r-universe/kezrael/actions/runs/28660658538" }, { "r": "4.7.0", "os": "win", "version": "3.0.1", "date": "2026-07-03T12:35:43.000Z", "commit": "f80e2bcc8188317d63bdc7acb1ef3158a52b02ec", "fileid": "https://r2.ropensci.org/8ca9ac7058ba239c8560286b5a457b15d44d9ffdc57bf944dbd3eaa0a336eb01", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/kezrael/actions/runs/28660658538" }, { "r": "4.5.3", "os": "win", "version": "3.0.1", "date": "2026-07-03T12:35:47.000Z", "commit": "f80e2bcc8188317d63bdc7acb1ef3158a52b02ec", "fileid": "https://r2.ropensci.org/a1aec2ec6fca317c134f9db34bf02d7f9a5b49ed1b54d8ef70643c335ddcd393", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/kezrael/actions/runs/28660658538" }, { "r": "4.6.1", "os": "win", "version": "3.0.1", "date": "2026-07-03T12:35:30.000Z", "commit": "f80e2bcc8188317d63bdc7acb1ef3158a52b02ec", "fileid": "https://r2.ropensci.org/10906fd0756ba3c62bbb9e95fd90c0f87327c3ee433896b2c1e80e88a749a28a", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/kezrael/actions/runs/28660658538" } ] }