{
  "_id": "6a102860acfb0bcc41c909ff",
  "Type": "Package",
  "Package": "microdiluteR",
  "Title": "Analysis of Broth Microdilution Assays",
  "Version": "1.0.1",
  "Date": "2024-04-16",
  "Authors@R": "person(\"Silvia\", \"Eckert\", email = \"seckert-dev@posteo.de\", role = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0002-8896-1046\"))",
  "Description": "A framework for analyzing broth microdilution assays in\nvarious 96-well plate designs, visualizing results and\nproviding descriptive and (simple) inferential statistics (i.e.\nsummary statistics and sign test). The functions are designed\nto add metadata to 8 x 12 tables of absorption values, creating\na tidy data frame. Users can choose between clean-up procedures\nvia function parameters (which covers most cases) or user\nprompts (in cases with complex experimental designs). Users can\nalso choose between two validation methods, i.e. exclusion of\nabsorbance values above a certain threshold or manual exclusion\nof samples. A function for visual inspection of samples with\ntheir absorption values over time for certain group\ncombinations helps with the decision. In addition, the package\nincludes functions to subtract the background absorption\n(usually at time T0) and to calculate the growth performance\ncompared to a baseline. Samples can be visually inspected with\ntheir absorption values displayed across time points for\nspecific group combinations. Core functions of this package\n(i.e. background subtraction, sample validation and statistics)\nwere inspired by the manual calculations that were applied in\nTewes and Muller (2020) <doi:10.1038/s41598-020-67600-7>.",
  "URL": "https://silvia-eckert.github.io/microdiluteR/",
  "BugReports": "https://github.com/silvia-eckert/microdiluteR/issues",
  "License": "GPL (>=3)",
  "Encoding": "UTF-8",
  "LazyData": "true",
  "RoxygenNote": "7.3.1",
  "Config/pak/sysreqs": "cmake make libicu-dev",
  "Repository": "https://silvia-eckert.r-universe.dev",
  "Date/Publication": "2024-05-25 10:55:12 UTC",
  "RemoteUrl": "https://github.com/silvia-eckert/microdiluter",
  "RemoteRef": "HEAD",
  "RemoteSha": "106a132b083c0400f395e54f68877c6eaa32d1d2",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-05-13 08:06:07 UTC",
    "User": "root"
  },
  "Author": "Silvia Eckert [aut, cre] (ORCID:\n<https://orcid.org/0000-0002-8896-1046>)",
  "Maintainer": "Silvia Eckert <seckert-dev@posteo.de>",
  "MD5sum": "b8f6820b94e147b61c291b9eb6d9cede",
  "_user": "silvia-eckert",
  "_type": "src",
  "_file": "microdiluteR_1.0.1.tar.gz",
  "_fileid": "43fce6f65d5bf60870b9e44e14f5d6e8cb1f54ae1f27c8d98196d5b831aa2d70",
  "_filesize": 293153,
  "_sha256": "43fce6f65d5bf60870b9e44e14f5d6e8cb1f54ae1f27c8d98196d5b831aa2d70",
  "_created": "2026-05-13T08:06:07.000Z",
  "_published": "2026-05-22T09:56:48.748Z",
  "_distro": "noble",
  "_jobs": [
    {
      "job": 77356978464,
      "time": 184,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "6964807460"
    },
    {
      "job": 77356978620,
      "time": 150,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "6964795514"
    },
    {
      "job": 77356978803,
      "time": 167,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "6964793566"
    },
    {
      "job": 77356978669,
      "time": 212,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "6964793064"
    },
    {
      "job": 77356978003,
      "time": 196,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "6964746557"
    },
    {
      "job": 77356977891,
      "time": 131,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7157778898"
    },
    {
      "job": 77356978801,
      "time": 106,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "6964780985"
    },
    {
      "job": 77356978698,
      "time": 98,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "6964778659"
    },
    {
      "job": 77356979231,
      "time": 96,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "6964777888"
    }
  ],
  "_buildurl": "https://github.com/r-universe/silvia-eckert/actions/runs/25786397691",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/silvia-eckert/microdiluter",
  "_commit": {
    "id": "106a132b083c0400f395e54f68877c6eaa32d1d2",
    "author": "silvia-eckert <silvia.eckert@posteo.de>",
    "committer": "silvia-eckert <silvia.eckert@posteo.de>",
    "message": "Update README.Rmd\n",
    "time": 1716634512
  },
  "_maintainer": {
    "name": "Silvia Eckert",
    "email": "seckert-dev@posteo.de",
    "orcid": "0000-0002-8896-1046"
  },
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 4.3",
      "role": "Depends"
    },
    {
      "package": "dplyr",
      "version": ">= 1.1.4",
      "role": "Imports"
    },
    {
      "package": "ggh4x",
      "version": ">= 0.2.8",
      "role": "Imports"
    },
    {
      "package": "ggplot2",
      "version": ">= 3.5.0",
      "role": "Imports"
    },
    {
      "package": "ggthemes",
      "version": ">= 5.0.1",
      "role": "Imports"
    },
    {
      "package": "magrittr",
      "version": ">= 2.0.3",
      "role": "Imports"
    },
    {
      "package": "purrr",
      "version": ">= 1.0.2",
      "role": "Imports"
    },
    {
      "package": "rlang",
      "version": ">= 1.1.3",
      "role": "Imports"
    },
    {
      "package": "rstatix",
      "version": ">= 0.7.2",
      "role": "Imports"
    },
    {
      "package": "stringr",
      "version": ">= 1.5.1",
      "role": "Imports"
    },
    {
      "package": "tibble",
      "version": ">= 3.2.1",
      "role": "Imports"
    },
    {
      "package": "tools",
      "version": ">= 4.3.3",
      "role": "Imports"
    },
    {
      "package": "vctrs",
      "version": ">= 0.6.5",
      "role": "Imports"
    },
    {
      "package": "knitr",
      "version": ">= 1.4.6",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "version": ">= 2.26",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "version": ">= 3.0.0",
      "role": "Suggests"
    }
  ],
  "_owner": "silvia-eckert",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [],
  "_tags": [],
  "_stars": 0,
  "_contributors": [
    {
      "user": "silvia-eckert",
      "count": 101,
      "uuid": 66693620
    }
  ],
  "_userbio": {
    "uuid": 66693620,
    "type": "user",
    "name": "Silvia Eckert",
    "description": "Tax Assistant Trainee | PhD in Biology | Bridging Data Science with Finance"
  },
  "_downloads": {
    "count": 592,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/microdiluteR"
  },
  "_devurl": "https://github.com/silvia-eckert/microdiluter",
  "_pkgdown": "https://silvia-eckert.github.io/microdiluteR/",
  "_searchresults": 6,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/microdiluteR.html",
    "extra/readme.html",
    "extra/readme.md",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/silvia-eckert/microdiluter",
  "_realowner": "silvia-eckert",
  "_cranurl": true,
  "_releases": [
    {
      "version": "1.0.1",
      "date": "2024-05-13"
    }
  ],
  "_exports": [
    "add_concentration",
    "add_treatment",
    "apply_sign_test",
    "apply_validation_method",
    "ask_concentration_list",
    "ask_experiment_list",
    "ask_group_list",
    "ask_treatment_list",
    "calculate_growth_performance",
    "calculate_percentage_change",
    "check_monotonicity",
    "check_well_positions",
    "generate_concentration_list",
    "generate_experiment_list",
    "generate_group_list",
    "generate_treatment_list",
    "match_concentration",
    "match_treatment",
    "plot_growth_performance",
    "read_plate",
    "read_plates",
    "subtract_T0",
    "summarize_growth_performance",
    "tidy_plates",
    "tidy_plates_via_params",
    "tidy_plates_via_prompts",
    "tidy_single_plate",
    "update_validity",
    "validate_cells"
  ],
  "_datasets": [
    {
      "name": "bma",
      "title": "Absorption values from six broth microdilution assays conducted on 96-well plates",
      "object": "bma",
      "class": [
        "list"
      ],
      "fields": [],
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "add_concentration",
      "title": "Add concentration metadata",
      "topics": [
        "add_concentration",
        "ask_concentration_list",
        "generate_concentration_list",
        "match_concentration"
      ]
    },
    {
      "page": "add_treatment",
      "title": "Add treatment metadata",
      "topics": [
        "add_treatment",
        "ask_treatment_list",
        "generate_treatment_list",
        "match_treatment"
      ]
    },
    {
      "page": "apply_sign_test",
      "title": "Apply sign test",
      "topics": [
        "apply_sign_test"
      ]
    },
    {
      "page": "bma",
      "title": "Absorption values from six broth microdilution assays conducted on 96-well plates",
      "topics": [
        "bma"
      ]
    },
    {
      "page": "calculate_growth_performance",
      "title": "Calculate and visualize growth performance",
      "topics": [
        "calculate_growth_performance",
        "calculate_percentage_change",
        "plot_growth_performance",
        "summarise_growth_performance",
        "summarize_growth_performance"
      ]
    },
    {
      "page": "check_well_positions",
      "title": "Check monotonicity of well positions across groups",
      "topics": [
        "check_monotonicity",
        "check_well_positions"
      ]
    },
    {
      "page": "generate_experiment_list",
      "title": "Generate list of experiment names from user parameters",
      "topics": [
        "ask_experiment_list",
        "generate_experiment_list"
      ]
    },
    {
      "page": "generate_group_list",
      "title": "Generate list of group IDs from user parameters",
      "topics": [
        "ask_group_list",
        "generate_group_list"
      ]
    },
    {
      "page": "read_plates",
      "title": "Read multiple text files from photometer measurement",
      "topics": [
        "read_plate",
        "read_plates"
      ]
    },
    {
      "page": "subtract_T0",
      "title": "Subtract timepoint T0 and remove from data",
      "topics": [
        "subtract_T0"
      ]
    },
    {
      "page": "tidy_plates",
      "title": "Add metadata to values from photometer measurements",
      "topics": [
        "tidy_plates"
      ]
    },
    {
      "page": "tidy_plates_via_params",
      "title": "Tidy multiple 96-well plates via parameters",
      "topics": [
        "tidy_plates_via_params"
      ]
    },
    {
      "page": "tidy_plates_via_prompts",
      "title": "Read raw photometry data and add meta data based on user input",
      "topics": [
        "tidy_plates_via_prompts"
      ]
    },
    {
      "page": "tidy_single_plate",
      "title": "Tidy single 96-well plate via parameters",
      "topics": [
        "tidy_single_plate"
      ]
    },
    {
      "page": "validate_cells",
      "title": "Check validity of each cell in data frame.",
      "topics": [
        "apply_validation_method",
        "ask_invalid_samples",
        "ask_threshold",
        "ask_validity_method",
        "update_validity",
        "validate_cells"
      ]
    }
  ],
  "_pkglogo": "https://github.com/silvia-eckert/microdiluter/raw/HEAD/man/figures/logo.png",
  "_readme": "https://github.com/silvia-eckert/microdiluter/raw/HEAD/README.md",
  "_rundeps": [
    "abind",
    "backports",
    "boot",
    "broom",
    "car",
    "carData",
    "cli",
    "colorspace",
    "corrplot",
    "cowplot",
    "cpp11",
    "Deriv",
    "doBy",
    "dplyr",
    "farver",
    "forecast",
    "Formula",
    "fracdiff",
    "generics",
    "ggh4x",
    "ggplot2",
    "ggthemes",
    "glue",
    "gtable",
    "isoband",
    "labeling",
    "lattice",
    "lifecycle",
    "lme4",
    "lmtest",
    "magrittr",
    "MASS",
    "Matrix",
    "MatrixModels",
    "mgcv",
    "microbenchmark",
    "minqa",
    "modelr",
    "nlme",
    "nloptr",
    "nnet",
    "numDeriv",
    "pbkrtest",
    "pillar",
    "pkgconfig",
    "purrr",
    "quantreg",
    "R6",
    "rbibutils",
    "RColorBrewer",
    "Rcpp",
    "RcppArmadillo",
    "RcppEigen",
    "Rdpack",
    "reformulas",
    "rlang",
    "rstatix",
    "S7",
    "scales",
    "SparseM",
    "stringi",
    "stringr",
    "survival",
    "tibble",
    "tidyr",
    "tidyselect",
    "timeDate",
    "urca",
    "utf8",
    "vctrs",
    "viridisLite",
    "withr",
    "zoo"
  ],
  "_score": 2.6989700043360187,
  "_indexed": true,
  "_nocasepkg": "microdiluter",
  "_universes": [
    "silvia-eckert"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.0.1",
      "date": "2026-05-13T08:09:00.000Z",
      "distro": "noble",
      "commit": "106a132b083c0400f395e54f68877c6eaa32d1d2",
      "fileid": "3fd37fb76e2d357e01611a9039aab554a906f1c94dfe8061eaa17991b8706ca7",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/silvia-eckert/actions/runs/25786397691"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.0.1",
      "date": "2026-05-13T08:08:24.000Z",
      "distro": "noble",
      "commit": "106a132b083c0400f395e54f68877c6eaa32d1d2",
      "fileid": "a589123c057e84981d6119a382672f3f6742a32bac7afd36dc8dcace9f348e83",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/silvia-eckert/actions/runs/25786397691"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.0.1",
      "date": "2026-05-13T08:08:26.000Z",
      "commit": "106a132b083c0400f395e54f68877c6eaa32d1d2",
      "fileid": "0dd34a45e0e68cf976862707c06ed1f92983019cca4a13d88a57ba389fc629fa",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/silvia-eckert/actions/runs/25786397691"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.0.1",
      "date": "2026-05-13T08:08:16.000Z",
      "commit": "106a132b083c0400f395e54f68877c6eaa32d1d2",
      "fileid": "9a312576730f441f2cfd1d7a76152bbdbab481441484081fdf64d00e3d76e91f",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/silvia-eckert/actions/runs/25786397691"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.0.1",
      "date": "2026-05-13T08:07:31.000Z",
      "commit": "106a132b083c0400f395e54f68877c6eaa32d1d2",
      "fileid": "bf460d39798cadee92f435187981236d79c4d89eef03fd84236c571ed40389e8",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/silvia-eckert/actions/runs/25786397691"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.0.1",
      "date": "2026-05-13T08:07:25.000Z",
      "commit": "106a132b083c0400f395e54f68877c6eaa32d1d2",
      "fileid": "50b7f6f9e56ac9a4883030d07fefa4aaec424b7d4484af12bd5dd9722ae81ad4",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/silvia-eckert/actions/runs/25786397691"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "1.0.1",
      "date": "2026-05-13T08:07:22.000Z",
      "commit": "106a132b083c0400f395e54f68877c6eaa32d1d2",
      "fileid": "7f4f35ca6e1c6c31356cdf153b56fc8c688e07edf3d81e8a025ea557b783d27b",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/silvia-eckert/actions/runs/25786397691"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.0.1",
      "date": "2026-05-22T09:56:31.000Z",
      "commit": "106a132b083c0400f395e54f68877c6eaa32d1d2",
      "fileid": "d0b94cd772adb10f564d6053d5f6321c26219bd88334e03917e126eb94c7d5e9",
      "status": "success",
      "buildurl": "https://github.com/r-universe/silvia-eckert/actions/runs/25786397691"
    }
  ]
}