{ "_id": "6a1e8be41d7bb097a0a69431", "Package": "ppseq", "Title": "Design Clinical Trials using Sequential Predictive Probability\nMonitoring", "Version": "0.2.5", "Authors@R": "c(person(given = \"Emily C.\",\nfamily = \"Zabor\",\nrole = c(\"aut\", \"cre\"),\nemail = \"zabore2@ccf.org\",\ncomment = c(ORCID = \"0000-0002-1402-4498\")),\nperson(given = \"Brian P.\",\nfamily = \"Hobbs\",\nrole = \"aut\"),\nperson(given = \"Michael J.\",\nfamily = \"Kane\",\nrole = \"aut\",\nemail = \"michael.kane@yale.edu\",\ncomment = c(ORCID = \"0000-0003-1899-6662\"))\n)", "Description": "Functions are available to calibrate designs over a range\nof posterior and predictive thresholds, to plot the various\ndesign options, and to obtain the operating characteristics of\noptimal accuracy and optimal efficiency designs.", "License": "MIT + file LICENSE", "URL": "https://github.com/zabore/ppseq, https://www.emilyzabor.com/ppseq/", "BugReports": "https://github.com/zabore/ppseq/issues", "Encoding": "UTF-8", "LazyData": "true", "Roxygen": "list(markdown = TRUE)", "VignetteBuilder": "knitr", "Config/testthat/edition": "3", "Language": "en-US", "RoxygenNote": "7.3.2", "Config/pak/sysreqs": "cmake make libicu-dev libuv1-dev libssl-dev", "Repository": "https://zabore.r-universe.dev", "Date/Publication": "2024-09-04 17:27:02 UTC", "RemoteUrl": "https://github.com/zabore/ppseq", "RemoteRef": "HEAD", "RemoteSha": "75eac30702c032418568bd84649cabde1bb9c955", "NeedsCompilation": "no", "Packaged": { "Date": "2026-06-02 07:47:50 UTC", "User": "root" }, "Author": "Emily C. Zabor [aut, cre] (ORCID:\n),\nBrian P. Hobbs [aut],\nMichael J. Kane [aut] (ORCID: )", "Maintainer": "Emily C. Zabor ", "MD5sum": "ff9dba04ee5fd6c6d37af54c49a8ccc6", "_user": "zabore", "_type": "src", "_file": "ppseq_0.2.5.tar.gz", "_fileid": "de1137316eac01f89580f8b3cb38e8294b02e54e42f11a07b53c3cf2f88c36b5", "_filesize": 636279, "_sha256": "de1137316eac01f89580f8b3cb38e8294b02e54e42f11a07b53c3cf2f88c36b5", "_created": "2026-06-02T07:47:50.000Z", "_published": "2026-06-02T07:53:08.804Z", "_distro": "noble", "_jobs": [ { "job": 79023734584, "time": 225, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7351955384" }, { "job": 79023734647, "time": 224, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7351955142" }, { "job": 79023734572, "time": 228, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7351948568" }, { "job": 79023734576, "time": 280, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7351964689" }, { "job": 79023015097, "time": 279, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7351878290" }, { "job": 79023734564, "time": 126, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7351920042" }, { "job": 79023734577, "time": 232, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "7351957892" }, { "job": 79023734582, "time": 258, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "7351966483" }, { "job": 79023734578, "time": 268, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "7351970088" } ], "_buildurl": "https://github.com/r-universe/zabore/actions/runs/26805834007", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/zabore/ppseq", "_commit": { "id": "75eac30702c032418568bd84649cabde1bb9c955", "author": "Emily C. Zabor ", "committer": "Emily C. Zabor ", "message": "Update CRAN-SUBMISSION\n", "time": 1725470822 }, "_maintainer": { "name": "Emily C. Zabor", "email": "zabore2@ccf.org", "login": "zabore", "description": "", "uuid": 24287346, "orcid": "0000-0002-1402-4498" }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.5.0", "role": "Depends" }, { "package": "dplyr", "role": "Imports" }, { "package": "furrr", "role": "Imports" }, { "package": "ggplot2", "role": "Imports" }, { "package": "plotly", "role": "Imports" }, { "package": "purrr", "role": "Imports" }, { "package": "tibble", "role": "Imports" }, { "package": "patchwork", "role": "Imports" }, { "package": "tidyr", "role": "Imports" }, { "package": "covr", "role": "Suggests" }, { "package": "gt", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "testthat", "version": ">= 3.0.0", "role": "Suggests" }, { "package": "vdiffr", "role": "Suggests" } ], "_owner": "zabore", "_selfowned": true, "_usedby": 0, "_updates": [], "_tags": [], "_stars": 5, "_contributors": [ { "user": "zabore", "count": 144, "uuid": 24287346 }, { "user": "kaneplusplus", "count": 17, "uuid": 175135 }, { "user": "basil-iii", "count": 1, "uuid": 60457248 }, { "user": "bphobbs", "count": 1, "uuid": 42594081 } ], "_userbio": { "uuid": 24287346, "type": "user", "name": "Emily C. Zabor" }, "_downloads": { "count": 180, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/ppseq" }, "_devurl": "https://github.com/zabore/ppseq", "_pkgdown": "https://www.emilyzabor.com/ppseq/", "_searchresults": 32, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/NEWS.html", "extra/NEWS.txt", "extra/ppseq.html", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_homeurl": "https://github.com/zabore/ppseq", "_realowner": "zabore", "_cranurl": true, "_releases": [ { "version": "0.1.1", "date": "2021-09-09" }, { "version": "0.2.0", "date": "2022-08-08" }, { "version": "0.2.2", "date": "2023-04-17" }, { "version": "0.2.3", "date": "2024-01-23" }, { "version": "0.2.4", "date": "2024-04-04" }, { "version": "0.2.5", "date": "2024-09-04" } ], "_exports": [ "calc_decision_rules", "calc_next", "calc_posterior", "calc_predictive", "calibrate_posterior_threshold", "calibrate_thresholds", "optimize_design", "sim_single_trial" ], "_datasets": [ { "name": "one_sample_cal_tbl", "title": "Output from a one-sample call to 'calibrate_thresholds'", "object": "one_sample_cal_tbl", "class": [ "calibrate_thresholds", "list" ], "fields": [], "table": false, "tojson": false }, { "name": "one_sample_decision_tbl", "title": "Output from a one-sample call to 'calc_decision_rules'", "object": "one_sample_decision_tbl", "class": [ "calc_decision_rules", "tbl_df", "tbl", "data.frame" ], "fields": [ "n", "r", "ppp" ], "rows": 19, "table": true, "tojson": true }, { "name": "two_sample_cal_tbl", "title": "Output from a two-sample call to 'calibrate_thresholds'", "object": "two_sample_cal_tbl", "class": [ "calibrate_thresholds", "list" ], "fields": [], "table": false, "tojson": false }, { "name": "two_sample_decision_tbl", "title": "Output from a two-sample call to 'calc_decision_rules'", "object": "two_sample_decision_tbl", "class": [ "calc_decision_rules", "tbl_df", "tbl", "data.frame" ], "fields": [ "n0", "n1", "r0", "r1", "ppp" ], "rows": 155, "table": true, "tojson": true } ], "_help": [ { "page": "calc_decision_rules", "title": "Calculate a decision rule table for interim monitoring of a pre-specified design", "topics": [ "calc_decision_rules" ] }, { "page": "calc_next", "title": "Calculate response probability for the next patient", "topics": [ "calc_next" ] }, { "page": "calc_posterior", "title": "Calculate a single posterior probability", "topics": [ "calc_posterior" ] }, { "page": "calc_predictive", "title": "Calculate a single posterior predictive probability", "topics": [ "calc_predictive" ] }, { "page": "calibrate_posterior_threshold", "title": "Calibrate the posterior probability threshold", "topics": [ "calibrate_posterior_threshold" ] }, { "page": "calibrate_thresholds", "title": "Calibrate according to posterior probability threshold and predictive probability threshold with interim futility monitoring", "topics": [ "calibrate_thresholds" ] }, { "page": "eval_thresh", "title": "Evaluate a single dataset for a single pp_threshold and ppp_threshold combination", "topics": [ "eval_thresh" ] }, { "page": "one_sample_cal_tbl", "title": "Output from a one-sample call to 'calibrate_thresholds'", "topics": [ "one_sample_cal_tbl" ] }, { "page": "one_sample_decision_tbl", "title": "Output from a one-sample call to 'calc_decision_rules'", "topics": [ "one_sample_decision_tbl" ] }, { "page": "optimize_design.calibrate_thresholds", "title": "Custom optimization method for 'calibrate_thresholds' objects", "topics": [ "optimize_design.calibrate_thresholds" ] }, { "page": "plot.calc_decision_rules", "title": "Plot method for 'calc_decision_rules' objects", "topics": [ "plot.calc_decision_rules" ] }, { "page": "plot.calibrate_thresholds", "title": "Plot method for 'calibrate_thresholds' objects", "topics": [ "plot.calibrate_thresholds" ] }, { "page": "print.calibrate_thresholds", "title": "Print method for 'calibrate_thresholds' objects", "topics": [ "print.calibrate_thresholds" ] }, { "page": "sim_dat1", "title": "Simulate a single dataset based on the response probability(ies), the total sample size(s), and the interim look schedule(s)", "topics": [ "sim_dat1" ] }, { "page": "sim_single_trial", "title": "Simulate a single trial with posterior probability monitoring", "topics": [ "sim_single_trial" ] }, { "page": "two_sample_cal_tbl", "title": "Output from a two-sample call to 'calibrate_thresholds'", "topics": [ "two_sample_cal_tbl" ] }, { "page": "two_sample_decision_tbl", "title": "Output from a two-sample call to 'calc_decision_rules'", "topics": [ "two_sample_decision_tbl" ] } ], "_readme": "https://github.com/zabore/ppseq/raw/HEAD/README.md", "_rundeps": [ "askpass", "base64enc", "bslib", "cachem", "cli", "codetools", "cpp11", "crosstalk", "curl", "data.table", "digest", "dplyr", "evaluate", "farver", "fastmap", "fontawesome", "fs", "furrr", "future", "generics", "ggplot2", "globals", "glue", "gtable", "highr", "htmltools", "htmlwidgets", "httr", "isoband", "jquerylib", "jsonlite", "knitr", "labeling", "later", "lazyeval", "lifecycle", "listenv", "magrittr", "memoise", "mime", "openssl", "otel", "parallelly", "patchwork", "pillar", "pkgconfig", "plotly", "promises", "purrr", "R6", "rappdirs", "RColorBrewer", "Rcpp", "rlang", "rmarkdown", "S7", "sass", "scales", "stringi", "stringr", "sys", "tibble", "tidyr", "tidyselect", "tinytex", "utf8", "vctrs", "viridisLite", "withr", "xfun", "yaml" ], "_vignettes": [ { "source": "one_sample_expansion.Rmd", "filename": "one_sample_expansion.html", "title": "One-sample expansion cohort", "author": "Emily C. Zabor", "engine": "knitr::rmarkdown", "headings": [ "Setup", "Introduction", "Case study background", "Re-design of case study", "Using calibrate_thresholds() to obtain design options", "Results", "print()", "optimize_design()", "calc_decision_rules()", "plot()", "References" ], "created": "2021-03-02 18:44:42", "modified": "2022-10-03 16:40:22", "commits": 35 }, { "source": "two_sample_randomized.Rmd", "filename": "two_sample_randomized.html", "title": "Two-sample randomized trial", "author": "Emily C. Zabor", "engine": "knitr::rmarkdown", "headings": [ "Setup", "Introduction", "Case study background", "Re-design of case study", "Using calibrate_thresholds() to obtain design options", "Results", "print()", "optimize_design()", "calc_decision_rules()", "plot()", "References" ], "created": "2021-04-13 19:10:58", "modified": "2022-10-03 16:40:22", "commits": 6 } ], "_score": 5.681241237375588, "_indexed": true, "_nocasepkg": "ppseq", "_universes": [ "zabore" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "0.2.5", "date": "2026-06-02T07:50:14.000Z", "distro": "noble", "commit": "75eac30702c032418568bd84649cabde1bb9c955", "fileid": "88a7b696305cd41da118019538173e25267cbf8732fb4032efa9ad951ac3b7bf", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/zabore/actions/runs/26805834007" }, { "r": "4.6.0", "os": "linux", "version": "0.2.5", "date": "2026-06-02T07:50:12.000Z", "distro": "noble", "commit": "75eac30702c032418568bd84649cabde1bb9c955", "fileid": "a75d0fa27581f0b037874011ab13ee478b322a2160d5552f025b41a69c5a3d35", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/zabore/actions/runs/26805834007" }, { "r": "4.5.3", "os": "mac", "version": "0.2.5", "date": "2026-06-02T07:50:11.000Z", "commit": "75eac30702c032418568bd84649cabde1bb9c955", "fileid": "6cadf9855872ff1dbec71fce86c66cb22935e808d2aa4f057253f24910ae598d", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/zabore/actions/runs/26805834007" }, { "r": "4.6.0", "os": "mac", "version": "0.2.5", "date": "2026-06-02T07:50:51.000Z", "commit": "75eac30702c032418568bd84649cabde1bb9c955", "fileid": "30a0c9489c7bcfeb73bc6d72c1f7a8e7e4368f961d5f9d90eba1f9dad74a190a", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/zabore/actions/runs/26805834007" }, { "r": "4.6.0", "os": "wasm", "version": "0.2.5", "date": "2026-06-02T07:50:14.000Z", "commit": "75eac30702c032418568bd84649cabde1bb9c955", "fileid": "6ebdf34a1cbbc1515d455a337bb94b983f9dd8b0db122ebb77944d68ea712b46", "status": "success", "buildurl": "https://github.com/r-universe/zabore/actions/runs/26805834007" }, { "r": "4.7.0", "os": "win", "version": "0.2.5", "date": "2026-06-02T07:49:04.000Z", "commit": "75eac30702c032418568bd84649cabde1bb9c955", "fileid": "70eeef53443ac10225e283c134260297c95954a2546cef5d0ecb1b79da3b71f3", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/zabore/actions/runs/26805834007" }, { "r": "4.5.3", "os": "win", "version": "0.2.5", "date": "2026-06-02T07:49:11.000Z", "commit": "75eac30702c032418568bd84649cabde1bb9c955", "fileid": "7d089656a589f836637ac7b1343b4c90135a74620abb5009ca864aa428cdf996", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/zabore/actions/runs/26805834007" }, { "r": "4.6.0", "os": "win", "version": "0.2.5", "date": "2026-06-02T07:49:32.000Z", "commit": "75eac30702c032418568bd84649cabde1bb9c955", "fileid": "55d93b727f614d0c685e7c8b9323564ced5d64ad9f422b5425aa3af118548b3e", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/zabore/actions/runs/26805834007" } ] }