{
  "_id": "6a16ca54acfb0bcc41d89749",
  "Package": "Rcurvep",
  "Type": "Package",
  "Title": "Concentration-Response Data Analysis using Curvep",
  "Version": "1.3.2",
  "Authors@R": "c(\nperson(\"Jui-Hua\", \"Hsieh\", email = \"juihua.hsieh@gmail.com\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0003-1620-1571\")),\nperson(\"Alexander\", \"Sedykh\", role = c(\"aut\")),\nperson(\"Fred\", \"Parham\", role = c(\"ctb\")),\nperson(\"Yuhong\", \"Wang\", role = c(\"ctb\")),\nperson(\"Tongan\", \"Zhao\", role = c(\"aut\")),\nperson(\"Ruili\", \"Huang\", role = c(\"ctb\"))\n)",
  "Description": "An R interface for processing concentration-response\ndatasets using Curvep, a response noise filtering algorithm.\nThe algorithm was described in the publications (Sedykh A et\nal. (2011) <doi:10.1289/ehp.1002476> and Sedykh A (2016)\n<doi:10.1007/978-1-4939-6346-1_14>). Other parametric fitting\napproaches (e.g., Hill equation) are also adopted for ease of\ncomparison. 3-parameter Hill equation from 'tcpl' package\n(Filer D et al., <doi:10.1093/bioinformatics/btw680>) and\n4-parameter Hill equation from Curve Class2 approach (Wang Y et\nal., <doi:10.2174/1875397301004010057>) are available. Also,\nmethods for calculating the confidence interval around the\nactivity metrics are also provided. The methods are based on\nthe bootstrap approach to simulate the datasets (Hsieh J-H et\nal. <doi:10.1093/toxsci/kfy258>). The simulated datasets can be\nused to derive the baseline noise threshold in an assay\nendpoint. This threshold is critical in the toxicological\nstudies to derive the point-of-departure (POD).",
  "Language": "en-US",
  "BugReports": "https://github.com/moggces/Rcurvep/issues",
  "License": "MIT + file LICENSE",
  "URL": "https://github.com/moggces/Rcurvep,\nhttps://moggces.github.io/Rcurvep/",
  "Encoding": "UTF-8",
  "LazyData": "true",
  "RdMacros": "Rdpack",
  "VignetteBuilder": "knitr",
  "SystemRequirements": "Java",
  "RoxygenNote": "7.2.3",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-05-27 10:36:50 UTC",
    "User": "root"
  },
  "Author": "Jui-Hua Hsieh [aut, cre] (ORCID:\n<https://orcid.org/0000-0003-1620-1571>), Alexander Sedykh\n[aut], Fred Parham [ctb], Yuhong Wang [ctb], Tongan Zhao [aut],\nRuili Huang [ctb]",
  "Maintainer": "Jui-Hua Hsieh <juihua.hsieh@gmail.com>",
  "Config/pak/sysreqs": "default-jdk",
  "Repository": "https://cran.r-universe.dev",
  "Date/Publication": "2025-05-31 21:10:02 UTC",
  "RemoteUrl": "https://github.com/cran/Rcurvep",
  "RemoteRef": "HEAD",
  "RemoteSha": "c352e34378432c8627682107512f785892a4d471",
  "MD5sum": "c20f5e38797e204a6d6e4aeff5466c20",
  "_user": "cran",
  "_type": "src",
  "_file": "Rcurvep_1.3.2.tar.gz",
  "_fileid": "886caeb2827cf610b5d5501144fcf2b82e2a7967dedd5d4de62421136cb875bc",
  "_filesize": 6069283,
  "_sha256": "886caeb2827cf610b5d5501144fcf2b82e2a7967dedd5d4de62421136cb875bc",
  "_created": "2026-05-27T10:36:50.000Z",
  "_published": "2026-05-27T10:41:24.846Z",
  "_distro": "noble",
  "_jobs": [
    {
      "job": 78058764459,
      "time": 226,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7238275334"
    },
    {
      "job": 78058764439,
      "time": 232,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7238277235"
    },
    {
      "job": 78058150489,
      "time": 240,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7238204361"
    },
    {
      "job": 78058764420,
      "time": 142,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7238249178"
    }
  ],
  "_buildurl": "https://github.com/r-universe/cran/actions/runs/26505901534",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/cran/Rcurvep",
  "_commit": {
    "id": "c352e34378432c8627682107512f785892a4d471",
    "author": "Jui-Hua Hsieh <juihua.hsieh@gmail.com>",
    "committer": "cran-robot <csardi.gabor+cran@gmail.com>",
    "message": "version 1.3.2\n",
    "time": 1748725802
  },
  "_maintainer": {
    "name": "Jui-Hua Hsieh",
    "email": "juihua.hsieh@gmail.com",
    "login": "moggces",
    "description": "",
    "uuid": 5603946,
    "orcid": "0000-0003-1620-1571"
  },
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 3.5",
      "role": "Depends"
    },
    {
      "package": "dplyr",
      "version": ">= 1.0.0",
      "role": "Imports"
    },
    {
      "package": "tibble",
      "role": "Imports"
    },
    {
      "package": "magrittr",
      "role": "Imports"
    },
    {
      "package": "tidyselect",
      "role": "Imports"
    },
    {
      "package": "boot",
      "role": "Imports"
    },
    {
      "package": "tidyr",
      "role": "Imports"
    },
    {
      "package": "purrr",
      "role": "Imports"
    },
    {
      "package": "rlang",
      "role": "Imports"
    },
    {
      "package": "stringr",
      "role": "Imports"
    },
    {
      "package": "ggplot2",
      "role": "Imports"
    },
    {
      "package": "Rdpack",
      "role": "Imports"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "rJava",
      "role": "Imports"
    },
    {
      "package": "furrr",
      "role": "Imports"
    },
    {
      "package": "testthat",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "tcpl",
      "role": "Suggests"
    },
    {
      "package": "future",
      "role": "Suggests"
    }
  ],
  "_owner": "cran",
  "_selfowned": false,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-22",
      "n": 1
    }
  ],
  "_tags": [
    {
      "name": "1.3.2",
      "date": "2025-05-31"
    }
  ],
  "_stars": 0,
  "_contributors": [
    {
      "user": "moggces",
      "count": 4,
      "uuid": 5603946
    }
  ],
  "_userbio": {
    "uuid": 6899542,
    "type": "organization",
    "name": "cran",
    "description": "Unofficial read-only mirror of all CRAN R packages"
  },
  "_downloads": {
    "count": 570,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/Rcurvep"
  },
  "_mentions": 1,
  "_devurl": "https://github.com/moggces/rcurvep",
  "_pkgdown": "https://moggces.github.io/Rcurvep/",
  "_searchresults": 17,
  "_topics": [
    "openjdk"
  ],
  "_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/Rcurvep.html",
    "extra/readme.html",
    "extra/readme.md",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/moggces/rcurvep",
  "_realowner": "moggces",
  "_cranurl": false,
  "_releases": [
    {
      "version": "1.2.0",
      "date": "2021-01-07"
    },
    {
      "version": "1.2.1",
      "date": "2022-08-25"
    },
    {
      "version": "1.3.1",
      "date": "2024-01-09"
    },
    {
      "version": "1.3.2",
      "date": "2025-05-31"
    }
  ],
  "_exports": [
    "cal_knee_point",
    "combi_run_rcurvep",
    "create_dataset",
    "curvep",
    "curvep_defaults",
    "estimate_dataset_bmr",
    "fit_cc2_modl",
    "fit_modls",
    "get_hill_fit_config",
    "merge_rcurvep_objs",
    "run_fit",
    "run_rcurvep",
    "summarize_fit_output",
    "summarize_rcurvep_output"
  ],
  "_datasets": [
    {
      "name": "zfishbeh",
      "title": "Subsets of concentration response datasets from zebrafish neurotoxicity assays",
      "object": "zfishbeh",
      "class": [
        "tbl_df",
        "tbl",
        "data.frame"
      ],
      "fields": [
        "endpoint",
        "chemical",
        "conc",
        "resp"
      ],
      "rows": 2123,
      "table": true,
      "tojson": true
    },
    {
      "name": "zfishdev",
      "title": "Subsets of concentration response datasets from zebrafish developmental toxicity assays",
      "object": "zfishdev",
      "class": [
        "tbl_df",
        "tbl",
        "data.frame"
      ],
      "fields": [
        "endpoint",
        "chemical",
        "conc",
        "n_in",
        "N"
      ],
      "rows": 96,
      "table": true,
      "tojson": true
    },
    {
      "name": "zfishdev_act",
      "title": "Activity output based on simulated datasets using zfishdev_all dataset",
      "object": "zfishdev_act",
      "class": [
        "rcurvep",
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "zfishdev_all",
      "title": "Full sets of concentration response datasets from zebrafish developmental toxicity assays",
      "object": "zfishdev_all",
      "class": [
        "tbl_df",
        "tbl",
        "data.frame"
      ],
      "fields": [
        "endpoint",
        "chemical",
        "conc",
        "n_in",
        "N"
      ],
      "rows": 512,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "cal_knee_point",
      "title": "Calculate the knee point on the exponential-like curve",
      "topics": [
        "cal_knee_point"
      ]
    },
    {
      "page": "combi_run_rcurvep",
      "title": "Run Curvep on datasets of concentration-response data with a combination of Curvep parameters",
      "topics": [
        "combi_run_rcurvep"
      ]
    },
    {
      "page": "create_dataset",
      "title": "Create concentration-response datasets that can be applied in the 'run_rcurvep()'",
      "topics": [
        "create_dataset"
      ]
    },
    {
      "page": "curvep",
      "title": "The Curvep function to process one set of concentration-response data",
      "topics": [
        "curvep"
      ]
    },
    {
      "page": "curvep_defaults",
      "title": "Default parameters of Curvep",
      "topics": [
        "curvep_defaults"
      ]
    },
    {
      "page": "estimate_dataset_bmr",
      "title": "Estimate benchmark response (BMR) for each dataset",
      "topics": [
        "estimate_dataset_bmr"
      ]
    },
    {
      "page": "fit_cc2_modl",
      "title": "Fit concentration-response data using Curve Class2 approach",
      "topics": [
        "fit_cc2_modl"
      ]
    },
    {
      "page": "fit_modls",
      "title": "Fit one set of concentration-response data using types of models",
      "topics": [
        "fit_modls"
      ]
    },
    {
      "page": "get_hill_fit_config",
      "title": "Get the default configurations for the Hill fit",
      "topics": [
        "get_hill_fit_config"
      ]
    },
    {
      "page": "merge_rcurvep_objs",
      "title": "Merge results from multiple rcurvep objects",
      "topics": [
        "merge_rcurvep_objs"
      ]
    },
    {
      "page": "plot.rcurvep_bmr",
      "title": "Plot BMR diagnostic curves",
      "topics": [
        "plot.rcurvep_bmr"
      ]
    },
    {
      "page": "run_fit",
      "title": "Run parametric fits using types of models on concentration-response datasets",
      "topics": [
        "run_fit"
      ]
    },
    {
      "page": "run_rcurvep",
      "title": "Run Curvep on datasets of concentration-response data",
      "topics": [
        "run_rcurvep"
      ]
    },
    {
      "page": "summarize_fit_output",
      "title": "Summarize the results from the parametric fitting using types of models",
      "topics": [
        "summarize_fit_output"
      ]
    },
    {
      "page": "summarize_rcurvep_output",
      "title": "Clean and summarize the output of rcurvep object",
      "topics": [
        "summarize_rcurvep_output"
      ]
    },
    {
      "page": "zfishbeh",
      "title": "Subsets of concentration response datasets from zebrafish neurotoxicity assays",
      "topics": [
        "zfishbeh"
      ]
    },
    {
      "page": "zfishdev",
      "title": "Subsets of concentration response datasets from zebrafish developmental toxicity assays",
      "topics": [
        "zfishdev"
      ]
    },
    {
      "page": "zfishdev_act",
      "title": "Activity output based on simulated datasets using zfishdev_all dataset",
      "topics": [
        "zfishdev_act"
      ]
    },
    {
      "page": "zfishdev_all",
      "title": "Full sets of concentration response datasets from zebrafish developmental toxicity assays",
      "topics": [
        "zfishdev_all"
      ]
    }
  ],
  "_readme": "https://github.com/cran/Rcurvep/raw/HEAD/README.md",
  "_rundeps": [
    "boot",
    "cli",
    "codetools",
    "cpp11",
    "digest",
    "dplyr",
    "farver",
    "furrr",
    "future",
    "generics",
    "ggplot2",
    "globals",
    "glue",
    "gtable",
    "isoband",
    "labeling",
    "lifecycle",
    "listenv",
    "magrittr",
    "parallelly",
    "pillar",
    "pkgconfig",
    "purrr",
    "R6",
    "rbibutils",
    "RColorBrewer",
    "Rdpack",
    "rJava",
    "rlang",
    "S7",
    "scales",
    "stringi",
    "stringr",
    "tibble",
    "tidyr",
    "tidyselect",
    "utf8",
    "vctrs",
    "viridisLite",
    "withr"
  ],
  "_sysdeps": [
    {
      "shlib": "libjvm",
      "package": "openjdk-21-jre-headless",
      "headers": "openjdk-21-jre-headless",
      "source": "openjdk",
      "version": "21.0.10+7-1~24.04",
      "name": "openjdk",
      "homepage": "https://openjdk.java.net/",
      "description": "OpenJDK Java runtime, using Hotspot JIT (headless)"
    }
  ],
  "_vignettes": [
    {
      "source": "future_rcurvep.Rmd",
      "filename": "future_rcurvep.html",
      "title": "Parallel Computing Examples Using Rcurvep",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Set up the packages",
        "datasets from Rcurvep package",
        "When no preferred BMR and would like to do a exhaustive search",
        "Calculate 10 times and compare the results",
        "When preferred BMRs are available for endpoints",
        "Get the BMRs for each endpoint",
        "Join the BMRs to the concentration-response data",
        "Set up the expressions",
        "Fitting based on simulated curves using run_fit",
        "Fitting based on simulated curves using run_fit and pmap",
        "Fitting based on original data",
        "Use modls = hill parameter",
        "Calculate 5 times and compare the results",
        "Use modls = cc2 parameter"
      ],
      "created": "2024-01-10 02:40:00",
      "modified": "2025-05-31 21:10:02",
      "commits": 2
    },
    {
      "source": "practical_rcurvep.Rmd",
      "filename": "practical_rcurvep.html",
      "title": "Practical applications using Rcurvep package",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Install the package",
        "Load the library",
        "Load the sample dataset",
        "Rcurvep method",
        "Run Rcurvep on datasets using combi_run_rcurvep()",
        "Run Rcurvep when there is a preferred BMR",
        "Summarize activity data from Rcurvep",
        "Add confidence interval for activity data from Rcurvep",
        "Run Rcurvep when an optimal/preferred BMR is unknown",
        "Estimate the BMR",
        "Display the diagnostic curves for BMR estimation",
        "Run parametric fitting on datasets",
        "Summarize parametric fitting results using a preferred BMR",
        "Inspect concordance between two parametric fits",
        "Add confidence interval for activity data from parametric fitting (currently is only available to 3-parameter Hill equation from tcpl)"
      ],
      "created": "2021-01-07 18:10:02",
      "modified": "2024-01-10 02:40:00",
      "commits": 2
    }
  ],
  "_score": 3.230448921378274,
  "_indexed": false,
  "_nocasepkg": "rcurvep",
  "_universes": [
    "cran"
  ],
  "_indexurl": "https://moggces.r-universe.dev/Rcurvep",
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.3.2",
      "date": "2026-05-27T10:39:35.000Z",
      "distro": "noble",
      "commit": "c352e34378432c8627682107512f785892a4d471",
      "fileid": "8426b3e893f76957cecf2d7c577ca9a61e6f7a0f8472551a2e96f1ebadc190af",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/cran/actions/runs/26505901534"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.3.2",
      "date": "2026-05-27T10:39:41.000Z",
      "distro": "noble",
      "commit": "c352e34378432c8627682107512f785892a4d471",
      "fileid": "5671d90d354e648356c5725cee0edcdd8445db6d4038a85426d0e680b6e071b4",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/cran/actions/runs/26505901534"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.3.2",
      "date": "2026-05-27T10:39:35.000Z",
      "commit": "c352e34378432c8627682107512f785892a4d471",
      "fileid": "bd1a34356527e36872d79466f9e1ae5b92ce1878d73a690d8a5707b37bca23c6",
      "status": "success",
      "buildurl": "https://github.com/r-universe/cran/actions/runs/26505901534"
    }
  ]
}