{ "_id": "6a1adaf01d7bb097a09e8d3a", "Package": "designit", "Title": "Blocking and Randomization for Experimental Design", "Version": "0.5.0.9000", "Authors@R": "c(\nperson(given = c(first = \"Iakov\", middle = \"I.\"),\nfamily = \"Davydov\",\nrole = c(\"aut\", \"cre\", \"cph\"),\nemail = \"iakov.davydov@roche.com\",\ncomment = c(ORCID = \"0000-0003-3510-3926\")),\nperson(given = \"Juliane\",\nfamily = \"Siebourg-Polster\",\nrole = c(\"aut\", \"cph\"),\nemail = \"juliane.siebourg-polster@roche.com\",\ncomment = c(ORCID = \"0000-0002-1759-3223\")),\nperson(given = \"Guido\",\nfamily = \"Steiner\",\nrole = c(\"aut\", \"cph\"),\nemail = \"guido.steiner@roche.com\",\ncomment = c(ORCID = \"\")),\nperson(given = \"Konrad\",\nfamily = \"Rudolph\",\nrole = \"ctb\",\nemail = \"konrad.rudolph@roche.com\",\ncomment = c(ORCID = \"0000-0002-9866-7051\")),\nperson(given = \"Jitao David\",\nfamily = \"Zhang\",\nrole = c(\"aut\", \"cph\"),\nemail = \"jitao_david.zhang@roche.com\",\ncomment = c(ORCID=\"0000-0002-3085-0909\")),\nperson(given = \"Balazs\",\nfamily = \"Banfai\",\nrole = c(\"aut\", \"cph\"),\nemail = \"balazs.banfai@roche.com\",\ncomment = c(ORCID = \"0000-0003-0422-7977\")),\nperson(given = \"F. Hoffman-La Roche\", role = c(\"cph\", \"fnd\")))", "Description": "Intelligently assign samples to batches in order to reduce\nbatch effects. Batch effects can have a significant impact on\ndata analysis, especially when the assignment of samples to\nbatches coincides with the contrast groups being studied. By\ndefining a batch container and a scoring function that reflects\nthe contrasts, this package allows users to assign samples in a\nway that minimizes the potential impact of batch effects on the\ncomparison of interest. Among other functionality, we provide\nan implementation for OSAT score by Yan et al. (2012,\n).", "License": "MIT + file LICENSE", "URL": "https://bedapub.github.io/designit/,\nhttps://github.com/BEDApub/designit/", "BugReports": "https://github.com/BEDApub/designit/issues", "Encoding": "UTF-8", "LazyData": "true", "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "7.3.1", "VignetteBuilder": "knitr", "biocViews": "", "Config/pak/sysreqs": "libicu-dev", "Repository": "https://bedapub.r-universe.dev", "Date/Publication": "2026-03-27 15:38:22 UTC", "RemoteUrl": "https://github.com/bedapub/designit", "RemoteRef": "HEAD", "RemoteSha": "47079e63f925c352146298a97d708b54d2369391", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-30 09:13:26 UTC", "User": "root" }, "Author": "Iakov I. Davydov [aut, cre, cph] (ORCID:\n),\nJuliane Siebourg-Polster [aut, cph] (ORCID:\n),\nGuido Steiner [aut, cph],\nKonrad Rudolph [ctb] (ORCID: ),\nJitao David Zhang [aut, cph] (ORCID:\n),\nBalazs Banfai [aut, cph] (ORCID:\n),\nF. Hoffman-La Roche [cph, fnd]", "Maintainer": "Iakov I. Davydov ", "MD5sum": "bf7bbc81748e951a6281145fe10bc89a", "_user": "bedapub", "_type": "src", "_file": "designit_0.5.0.9000.tar.gz", "_fileid": "77e8b4fd8d16e7f5a5f69796d912d5b45d84e473c59b73256354fe4d3fbc9099", "_filesize": 6210131, "_sha256": "77e8b4fd8d16e7f5a5f69796d912d5b45d84e473c59b73256354fe4d3fbc9099", "_created": "2026-05-30T09:13:26.000Z", "_published": "2026-05-30T12:41:20.834Z", "_distro": "noble", "_jobs": [ { "job": 78638924413, "time": 195, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7307139302" }, { "job": 78638924410, "time": 199, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7307139572" }, { "job": 78638924399, "time": 97, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7308243786" }, { "job": 78638924396, "time": 106, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7308244691" }, { "job": 78638580421, "time": 411, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7307094777" }, { "job": 78638924395, "time": 166, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7307136421" }, { "job": 78638924402, "time": 112, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "7307131744" }, { "job": 78638924408, "time": 116, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "7307132101" }, { "job": 78638924415, "time": 126, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "7307133264" } ], "_buildurl": "https://github.com/r-universe/bedapub/actions/runs/26435998476", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bedapub/designit", "_commit": { "id": "47079e63f925c352146298a97d708b54d2369391", "author": "julianesiebourg <51031392+julianesiebourg@users.noreply.github.com>", "committer": "GitHub ", "message": "Merge pull request #49 from bedapub/hotfix_plate_wrapper\n\nhotfix plate wrapper", "time": 1774625902 }, "_maintainer": { "name": "Iakov I. 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"readout" ], "rows": 54, "table": true, "tojson": true } ], "_help": [ { "page": "accept_leftmost_improvement", "title": "Alternative acceptance function for multi-dimensional scores in which order (left to right, e.g. first to last) denotes relevance.", "topics": [ "accept_leftmost_improvement" ] }, { "page": "assign_from_table", "title": "Distributes samples based on a sample sheet.", "topics": [ "assign_from_table" ] }, { "page": "assign_in_order", "title": "Distributes samples in order.", "topics": [ "assign_in_order" ] }, { "page": "assign_random", "title": "Assignment function which distributes samples randomly.", "topics": [ "assign_random" ] }, { "page": "batch_container_from_table", "title": "Creates a BatchContainer from a table (data.frame/tibble::tibble) containing sample and location information.", "topics": [ "batch_container_from_table" ] }, { "page": "BatchContainer", "title": "R6 Class representing a batch container.", "topics": [ "BatchContainer" ] }, { "page": "BatchContainerDimension", "title": "R6 Class representing a batch container dimension.", "topics": [ "BatchContainerDimension" ] }, { "page": "compile_possible_subgroup_allocation", "title": "Compile list of all possible ways to assign levels of the allocation variable to a given set of subgroups", "topics": [ "compile_possible_subgroup_allocation" ] }, { "page": "complete_random_shuffling", "title": "Reshuffle sample indices completely randomly", "topics": [ "complete_random_shuffling" ] }, { "page": "drop_order", "title": "Drop highest order interactions", "topics": [ "drop_order" ] }, { "page": "first_score_only", "title": "Aggregation of scores: take first (primary) score only", "topics": [ "first_score_only" ] }, { "page": "form_homogeneous_subgroups", "title": "Form groups and subgroups of 'homogeneous' samples as defined by certain variables and size constraints", "topics": [ "form_homogeneous_subgroups" ] }, { "page": "generate_terms", "title": "Generate 'terms.object' (formula with attributes)", "topics": [ "generate_terms" ] }, { "page": "get_order", "title": "Get highest order interaction", "topics": [ "get_order" ] }, { "page": "invivo_study_samples", "title": "A sample list from an in vivo experiment with multiple treatments and 2 strains", "topics": [ "invivo_study_samples" ] }, { "page": "invivo_study_treatments", "title": "A treatment list together with additional constraints on the strain and sex of animals", "topics": [ "invivo_study_treatments" ] }, { "page": "L1_norm", "title": "Aggregation of scores: L1 norm", "topics": [ "L1_norm" ] }, { "page": "L2s_norm", "title": "Aggregation of scores: L2 norm squared", "topics": [ "L2s_norm" ] }, { "page": "locations_table_from_dimensions", "title": "Create locations table from dimensions and exclude table", "topics": [ "locations_table_from_dimensions" ] }, { "page": "longitudinal_subject_samples", "title": "Subject sample list with group and time plus controls", "topics": [ 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samples within certain subgroups of the container locations", "topics": [ "mk_subgroup_shuffling_function" ] }, { "page": "mk_swapping_function", "title": "Create function to propose swaps of samples on each call, either with a constant number of swaps or following a user defined protocol", "topics": [ "mk_swapping_function" ] }, { "page": "multi_trt_day_samples", "title": "Unbalanced treatment and time sample list", "topics": [ "multi_trt_day_samples" ] }, { "page": "optimize_design", "title": "Generic optimizer that can be customized by user provided functions for generating shuffles and progressing towards the minimal score", "topics": [ "optimize_design" ] }, { "page": "optimize_multi_plate_design", "title": "Convenience wrapper to optimize a typical multi-plate design", "topics": [ "optimize_multi_plate_design" ] }, { "page": "osat_score", "title": "Compute OSAT score for sample assignment.", "topics": [ "osat_score" ] }, { "page": "osat_score_generator", "title": "Convenience 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"headings": [ "Introduction", "Batch effects matter", "Go fully random?", "designit", "Sample Batching", "Setup", "Optimization", "Plate layouts", "Continuous confounding", "2-step optimization", "Across plate optimization using osat score as before", "Within plate optimization using distance based sample scoring function", "2-step optimization multi_plate_layout()", "Glimpse on more complex application", "Conclusion" ], "created": "2023-02-06 15:30:18", "modified": "2024-03-13 14:13:52", "commits": 6 }, { "source": "invivo_study_design.Rmd", "filename": "invivo_study_design.html", "title": "In-vivo study design", "engine": "knitr::rmarkdown", "headings": [ "Purpose of vignette", "Dataset and design task", "The animal (sample) sheet", "Treatment list", "Design constraints and data preparation", "Design steps", "Assign treatments to animal list", "Populate cages", "Arrange cages in rack(s)" ], "created": "2022-10-13 09:28:54", "modified": "2024-03-13 14:13:52", "commits": 5 }, { 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simulated annealing (SA) for optimization", "Full blown example" ], "created": "2022-10-13 09:28:54", "modified": "2024-03-13 14:13:52", "commits": 7 }, { "source": "osat.Rmd", "filename": "osat.html", "title": "OSAT and scoring functions", "engine": "knitr::rmarkdown", "headings": [ "Running OSAT optimization", "Visualize for plates", "Compare scores with various implementations", "Run using BatchContainer", "Using designit OSAT score implementation", "Manually work with data.table", "Shuffle optimization with burn-in", "Score demonstration" ], "created": "2022-10-13 09:28:54", "modified": "2024-10-16 12:15:04", "commits": 15 }, { "source": "plate_layouts.Rmd", "filename": "plate_layouts.html", "title": "Plate layouts", "engine": "knitr::rmarkdown", "headings": [], "created": "2022-10-13 09:28:54", "modified": "2024-03-13 14:16:38", "commits": 8 }, { "source": "shuffling_with_constraints.Rmd", "filename": "shuffling_with_constraints.html", "title": "Shuffling with constraints", 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