{"id":32385892,"url":"https://github.com/lukasdsauer/baskoptr","last_synced_at":"2026-07-06T23:31:16.308Z","repository":{"id":291111069,"uuid":"595038886","full_name":"LukasDSauer/baskoptr","owner":"LukasDSauer","description":"Utility-based Optimization for Basket Trial Designs","archived":false,"fork":false,"pushed_at":"2025-09-19T09:10:27.000Z","size":304,"stargazers_count":0,"open_issues_count":0,"forks_count":0,"subscribers_count":1,"default_branch":"main","last_synced_at":"2025-09-19T11:30:12.540Z","etag":null,"topics":["basket-trials","clinical-trials","optimization","utility-functions"],"latest_commit_sha":null,"homepage":"","language":"R","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"other","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/LukasDSauer.png","metadata":{"files":{"readme":"README.Rmd","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null,"zenodo":null,"notice":null,"maintainers":null,"copyright":null,"agents":null,"dco":null,"cla":null}},"created_at":"2023-01-30T09:11:36.000Z","updated_at":"2025-09-19T09:10:31.000Z","dependencies_parsed_at":null,"dependency_job_id":"c5e96cf4-f443-4be2-b66d-fd00927fe40e","html_url":"https://github.com/LukasDSauer/baskoptr","commit_stats":null,"previous_names":["lukasdsauer/baskoptr"],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/LukasDSauer/baskoptr","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/LukasDSauer%2Fbaskoptr","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/LukasDSauer%2Fbaskoptr/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/LukasDSauer%2Fbaskoptr/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/LukasDSauer%2Fbaskoptr/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/LukasDSauer","download_url":"https://codeload.github.com/LukasDSauer/baskoptr/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/LukasDSauer%2Fbaskoptr/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":280897684,"owners_count":26409960,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","status":"online","status_checked_at":"2025-10-25T02:00:06.499Z","response_time":81,"last_error":null,"robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":true,"can_crawl_api":true,"host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["basket-trials","clinical-trials","optimization","utility-functions"],"created_at":"2025-10-25T02:53:09.367Z","updated_at":"2026-07-06T23:31:16.295Z","avatar_url":"https://github.com/LukasDSauer.png","language":"R","funding_links":[],"categories":[],"sub_categories":[],"readme":"---\noutput: github_document\n---\n\n\u003c!-- README.md is generated from README.Rmd. Please edit that file --\u003e\n\n```{r, include = FALSE}\nknitr::opts_chunk$set(\n  collapse = TRUE,\n  comment = \"#\u003e\",\n  fig.path = \"man/figures/README-\",\n  out.width = \"100%\"\n)\n```\n\n# baskoptr \u003cimg src=\"man/figures/logo.png\" align=\"right\" height=\"139\" /\u003e\n\n\u003c!-- badges: start --\u003e\n[![Codecov test coverage](https://codecov.io/gh/LukasDSauer/baskoptr/graph/badge.svg)](https://app.codecov.io/gh/LukasDSauer/baskoptr)\n[![R-CMD-check](https://github.com/LukasDSauer/baskoptr/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/LukasDSauer/baskoptr/actions/workflows/R-CMD-check.yaml)\n[![CRAN status](https://www.r-pkg.org/badges/version/baskoptr)](https://CRAN.R-project.org/package=baskoptr)\n\u003c!-- badges: end --\u003e\n\nThe goal of **baskoptr** is to supply a unified framework for optimizing\nbasket trial designs. To this end, the package supplies several utility\nfunctions and also a function for executing optimization algorithms on basket\ntrial designs.\n\n## Installation\n\nYou can install the development version of baskoptr from [GitHub](https://github.com/) with:\n\n``` r\n# install.packages(\"pak\")\npak::pak(\"LukasDSauer/baskoptr\")\n```\n\n## Example\n\nIn the following example, we optimize Fujikawa et al.'s basket trial design\nwith respect to the experiment-wise power utility function using the simulated\nannealing algorithm.\n\n```{r example}\nlibrary(baskoptr)\n# Optimizing a three-basket trial design using Fujikawa's beta-binomial\n# sharing approach\ndesign \u003c- baskwrap::setup_fujikawa_x(k = 3, shape1 = 1, shape2 = 1,\n                                     p0 = 0.2, backend = \"exact\")\ndetail_params \u003c- list(p1 = c(0.5, 0.2, 0.2),\n                      n = 20,\n                      weight_fun = baskwrap::weights_jsd,\n                      logbase = exp(1),\n                      verbose = FALSE)\nutility_params \u003c- list(penalty = 1, thresh = 0.1)\nopt_design_gen(design = design,\n               utility = u_ewp,\n               algorithm = optimizr::simann,\n               detail_params = detail_params,\n               utility_params = utility_params,\n               algorithm_params = list(par = c(lambda = 0.99,\n                                               epsilon = 2,\n                                               tau = 0.5),\n                                       lower = c(lambda = 0.001,\n                                                 epsilon = 1,\n                                                 tau = 0.001),\n                                       upper = c(lambda = 0.999,\n                                                 epsilon = 10,\n                                                 tau = 0.999),\n                                       control = list(maxit = 10,\n                                                      temp = 10,\n                                                      fnscale = -1,\n                                                      REPORT = -1)))\n```\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Flukasdsauer%2Fbaskoptr","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Flukasdsauer%2Fbaskoptr","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Flukasdsauer%2Fbaskoptr/lists"}