{
  "_id": "6a311e533efcd9bda435c642",
  "Package": "power.nb",
  "Title": "Power and Sample Size Calculation for Differential Abundance\nMicrobiome Studies",
  "Version": "0.1.0",
  "Authors@R": "c(person(\"Michael\", \"Agronah\",\nemail =  \"michaelagronah@gmail.com\", role = c(\"aut\",\"cre\"),\ncomment = c(ORCID = \"0009-0007-2655-4094\")),\nperson(\"Ben\",\"Bolker\", role=\"aut\",\nemail =  \"bolker@mcmaster.ca\",\ncomment=c(ORCID=\"0000-0002-2127-0443\"))\n)",
  "Description": "Provides functions for estimating statistical power and\nrequired sample sizes in differential abundance microbiome\nstudies using negative binomial models. The methods are based\non Agronah and Bolker (2025)\n<doi:10.1371/journal.pone.0318820>. The package includes tools\nfor simulation-based power analysis and sample size estimation\nusing generalized additive models (GAMs), and visualization\nutilities for exploring the relationship between power, effect\nsize, abundance, and sample size.",
  "License": "MIT + file LICENSE",
  "URL": "https://michaelagronah.com/power.nb/",
  "BugReports": "https://github.com/magronah/power.nb/issues",
  "Encoding": "UTF-8",
  "VignetteBuilder": "knitr",
  "Roxygen": "list(markdown = TRUE)",
  "biocViews": "",
  "RoxygenNote": "7.3.3",
  "Config/pak/sysreqs": "libabsl-dev libcairo2-dev cmake libfontconfig1-dev\nlibfreetype6-dev libfribidi-dev libgdal-dev gdal-bin\nlibgeos-dev make libharfbuzz-dev libicu-dev libjpeg-dev\nlibpng-dev libtiff-dev libuv1-dev libwebp-dev libssl-dev\nlibproj-dev libsqlite3-dev libudunits2-dev zlib1g-dev",
  "Repository": "https://magronah.r-universe.dev",
  "Date/Publication": "2026-06-12 00:48:53 UTC",
  "RemoteUrl": "https://github.com/magronah/power.nb",
  "RemoteRef": "HEAD",
  "RemoteSha": "26d33e296987930e8752c1cfda18a20bf17358df",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-06-16 09:52:19 UTC",
    "User": "root"
  },
  "Author": "Michael Agronah [aut, cre] (ORCID:\n<https://orcid.org/0009-0007-2655-4094>),\nBen Bolker [aut] (ORCID: <https://orcid.org/0000-0002-2127-0443>)",
  "Maintainer": "Michael Agronah <michaelagronah@gmail.com>",
  "MD5sum": "14ba1ff5019f0b0afdcdda72f6b98050",
  "_user": "magronah",
  "_type": "src",
  "_file": "power.nb_0.1.0.tar.gz",
  "_fileid": "fa3b191d01a9a675d9f1745af9c0a8dbcc77e4345011ab7af2e876239d6af075",
  "_filesize": 7285478,
  "_sha256": "fa3b191d01a9a675d9f1745af9c0a8dbcc77e4345011ab7af2e876239d6af075",
  "_created": "2026-06-16T09:52:19.000Z",
  "_published": "2026-06-16T09:58:43.121Z",
  "_distro": "noble",
  "_jobs": [
    {
      "job": 81629281866,
      "time": 311,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7663384775"
    },
    {
      "job": 81629281851,
      "time": 287,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7663372475"
    },
    {
      "job": 81629281847,
      "time": 274,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7663355199"
    },
    {
      "job": 81629281854,
      "time": 220,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7663332407"
    },
    {
      "job": 81627874799,
      "time": 447,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7663251929"
    },
    {
      "job": 81629281832,
      "time": 186,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7663332683"
    },
    {
      "job": 81629281959,
      "time": 252,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7663365970"
    },
    {
      "job": 81629281911,
      "time": 238,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7663352606"
    },
    {
      "job": 81629281899,
      "time": 209,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7663340440"
    }
  ],
  "_buildurl": "https://github.com/r-universe/magronah/actions/runs/27608862013",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/magronah/power.nb",
  "_commit": {
    "id": "26d33e296987930e8752c1cfda18a20bf17358df",
    "author": "pkgdown-bot <pkgdown-bot@users.noreply.github.com>",
    "committer": "pkgdown-bot <pkgdown-bot@users.noreply.github.com>",
    "message": "Site rebuild\n",
    "time": 1781225333
  },
  "_maintainer": {
    "name": "Michael Agronah",
    "email": "michaelagronah@gmail.com"
  },
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 4.1.0",
      "role": "Depends"
    },
    {
      "package": "DESeq2",
      "role": "Imports"
    },
    {
      "package": "fitdistrplus",
      "role": "Imports"
    },
    {
      "package": "rlang",
      "role": "Imports"
    },
    {
      "package": "minpack.lm",
      "role": "Imports"
    },
    {
      "package": "foreach",
      "role": "Imports"
    },
    {
      "package": "tibble",
      "role": "Imports"
    },
    {
      "package": "purrr",
      "role": "Imports"
    },
    {
      "package": "mixtools",
      "role": "Imports"
    },
    {
      "package": "scam",
      "role": "Imports"
    },
    {
      "package": "ggplot2",
      "role": "Imports"
    },
    {
      "package": "ggrastr",
      "role": "Imports"
    },
    {
      "package": "metR",
      "role": "Imports"
    },
    {
      "package": "DEoptim",
      "role": "Imports"
    },
    {
      "package": "latex2exp",
      "role": "Imports"
    },
    {
      "package": "parallel",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "doParallel",
      "role": "Imports"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "kableExtra",
      "role": "Suggests"
    },
    {
      "package": "tidyverse",
      "role": "Suggests"
    },
    {
      "package": "patchwork",
      "role": "Suggests"
    },
    {
      "package": "dplyr",
      "role": "Suggests"
    },
    {
      "package": "rlist",
      "role": "Suggests"
    }
  ],
  "_owner": "magronah",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-26",
      "n": 28
    },
    {
      "week": "2025-27",
      "n": 6
    },
    {
      "week": "2025-29",
      "n": 2
    },
    {
      "week": "2025-36",
      "n": 1
    },
    {
      "week": "2025-37",
      "n": 4
    },
    {
      "week": "2025-39",
      "n": 2
    },
    {
      "week": "2025-40",
      "n": 6
    },
    {
      "week": "2025-41",
      "n": 3
    },
    {
      "week": "2025-42",
      "n": 3
    },
    {
      "week": "2025-43",
      "n": 2
    },
    {
      "week": "2025-45",
      "n": 11
    },
    {
      "week": "2025-46",
      "n": 17
    },
    {
      "week": "2026-05",
      "n": 10
    },
    {
      "week": "2026-06",
      "n": 3
    },
    {
      "week": "2026-07",
      "n": 4
    },
    {
      "week": "2026-09",
      "n": 3
    },
    {
      "week": "2026-10",
      "n": 3
    },
    {
      "week": "2026-11",
      "n": 7
    },
    {
      "week": "2026-12",
      "n": 2
    },
    {
      "week": "2026-15",
      "n": 1
    },
    {
      "week": "2026-24",
      "n": 3
    }
  ],
  "_tags": [],
  "_stars": 0,
  "_contributors": [
    {
      "user": "bbolker",
      "count": 63,
      "uuid": 78918
    },
    {
      "user": "beautifulmarriagegarden",
      "count": 25,
      "uuid": 224727497
    },
    {
      "user": "magronah",
      "count": 17,
      "uuid": 70163204
    }
  ],
  "_userbio": {
    "uuid": 70163204,
    "type": "user",
    "name": "magronah",
    "followers": 1
  },
  "_downloads": {
    "count": 0,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/power.nb"
  },
  "_devurl": "https://github.com/magronah/power.nb",
  "_pkgdown": "https://michaelagronah.com/power.nb/",
  "_searchresults": 1,
  "_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/power.nb.html",
    "extra/readme.html",
    "extra/readme.md",
    "LICENSE",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/magronah/power.nb",
  "_realowner": "magronah",
  "_cranurl": true,
  "_releases": [
    {
      "version": "0.1.0",
      "date": "2026-06-15"
    }
  ],
  "_exports": [
    "contour_plot_fun",
    "countdata_sim_fun",
    "deseq_fun_est",
    "deseqfun",
    "dispersion_fit",
    "dispersion_fun",
    "dnormmix",
    "dnormmix0",
    "filter_low_count",
    "gam_fit",
    "gen_parnames",
    "genmixpars",
    "logfoldchange_fit",
    "logfoldchange_sim_fun",
    "logmean_fit",
    "logmean_sim_fun",
    "myrnormmix",
    "optimal.comp",
    "polyfun",
    "power_fun_ss",
    "read_data",
    "rnormmix0",
    "sample_size_ss_interp",
    "ss_solver",
    "uniroot_ss"
  ],
  "_help": [
    {
      "page": "contour_plot_fun",
      "title": "Contour plot for showing predicted power",
      "topics": [
        "contour_plot_fun"
      ]
    },
    {
      "page": "countdata_sim_fun",
      "title": "Simulate Count Data for Microbiome Studies",
      "topics": [
        "countdata_sim_fun"
      ]
    },
    {
      "page": "deseq_fun_est",
      "title": "Fold change and p-value estimations for simulations",
      "topics": [
        "deseq_fun_est"
      ]
    },
    {
      "page": "deseqfun",
      "title": "Estimate log fold changes using 'DESeq2'.",
      "topics": [
        "deseqfun"
      ]
    },
    {
      "page": "dispersion_fit",
      "title": "Fit the non-linear function to dispersion estimates",
      "topics": [
        "dispersion_fit"
      ]
    },
    {
      "page": "dispersion_fun",
      "title": "Calculate Dispersion for Microbiome Data",
      "topics": [
        "dispersion_fun"
      ]
    },
    {
      "page": "dnormmix",
      "title": "Density of a Normal Mixture Model",
      "topics": [
        "dnormmix"
      ]
    },
    {
      "page": "dnormmix0",
      "title": "Density function for the mixture of Gaussian distributions",
      "topics": [
        "dnormmix0"
      ]
    },
    {
      "page": "filter_low_count",
      "title": "Filter to remove low abundant taxa",
      "topics": [
        "filter_low_count"
      ]
    },
    {
      "page": "gam_fit",
      "title": "Title",
      "topics": [
        "gam_fit"
      ]
    },
    {
      "page": "gen_parnames",
      "title": "Generate Parameter Names for Mixture Model",
      "topics": [
        "gen_parnames"
      ]
    },
    {
      "page": "genmixpars",
      "title": "generate normal mixture parameters (prob vector, mean vector, sd vector for a specified set of 'x' values (logmean)",
      "topics": [
        "genmixpars"
      ]
    },
    {
      "page": "logfoldchange_fit",
      "title": "Fit a mixture of Gaussian distributions to log fold change",
      "topics": [
        "logfoldchange_fit"
      ]
    },
    {
      "page": "logfoldchange_sim_fun",
      "title": "Simulate Log Fold Change Values",
      "topics": [
        "logfoldchange_sim_fun"
      ]
    },
    {
      "page": "logmean_fit",
      "title": "Fit a mixture of Gaussian Distributions to log mean count of taxa.",
      "topics": [
        "logmean_fit"
      ]
    },
    {
      "page": "logmean_sim_fun",
      "title": "Simulate Log Means for OTUs",
      "topics": [
        "logmean_sim_fun"
      ]
    },
    {
      "page": "myrnormmix",
      "title": "Simulating from a mixture of Gaussian",
      "topics": [
        "myrnormmix"
      ]
    },
    {
      "page": "nllfun",
      "title": "Objective function",
      "topics": [
        "nllfun"
      ]
    },
    {
      "page": "optimal.comp",
      "title": "Computes the optimal number of gaussian components for log mean count",
      "topics": [
        "optimal.comp"
      ]
    },
    {
      "page": "polyfun",
      "title": "General-purpose log-likelihood function, vectorized sum(pars*x^i)",
      "topics": [
        "polyfun"
      ]
    },
    {
      "page": "power_fun_ss",
      "title": "Fit a smooth power model for sample size estimation",
      "topics": [
        "power_fun_ss"
      ]
    },
    {
      "page": "read_data",
      "title": "Extract specified data from a list of datasets",
      "topics": [
        "read_data"
      ]
    },
    {
      "page": "rnormmix0",
      "title": "general-purpose normal-mixture deviate generator: takes _matrices_ of probabilities, means, sds",
      "topics": [
        "rnormmix0"
      ]
    },
    {
      "page": "sample_size_ss_interp",
      "title": "Estimate sample size required to achieve a target statistical power",
      "topics": [
        "sample_size_ss_interp"
      ]
    },
    {
      "page": "ss_solver",
      "title": "Solve for the sample size required to achieve a target statistical power",
      "topics": [
        "ss_solver"
      ]
    },
    {
      "page": "uniroot_ss",
      "title": "Sample Size estimation function using uniroot",
      "topics": [
        "uniroot_ss"
      ]
    }
  ],
  "_readme": "https://github.com/magronah/power.nb/raw/HEAD/README.md",
  "_rundeps": [
    "abind",
    "askpass",
    "backports",
    "base64enc",
    "beeswarm",
    "BH",
    "Biobase",
    "BiocGenerics",
    "BiocParallel",
    "bslib",
    "cachem",
    "Cairo",
    "checkmate",
    "class",
    "classInt",
    "cli",
    "codetools",
    "cpp11",
    "crosstalk",
    "curl",
    "data.table",
    "DBI",
    "DelayedArray",
    "DEoptim",
    "DESeq2",
    "digest",
    "doParallel",
    "dplyr",
    "e1071",
    "evaluate",
    "farver",
    "fastmap",
    "fitdistrplus",
    "fontawesome",
    "foreach",
    "formatR",
    "Formula",
    "formula.tools",
    "fs",
    "futile.logger",
    "futile.options",
    "generics",
    "GenomicRanges",
    "ggbeeswarm",
    "ggplot2",
    "ggrastr",
    "glue",
    "gtable",
    "highr",
    "htmltools",
    "htmlwidgets",
    "httr",
    "IRanges",
    "isoband",
    "iterators",
    "jquerylib",
    "jsonlite",
    "kernlab",
    "KernSmooth",
    "knitr",
    "labeling",
    "lambda.r",
    "later",
    "latex2exp",
    "lattice",
    "lazyeval",
    "lifecycle",
    "locfit",
    "lubridate",
    "magrittr",
    "MASS",
    "Matrix",
    "MatrixGenerics",
    "matrixStats",
    "memoise",
    "metR",
    "mgcv",
    "mime",
    "minpack.lm",
    "mixtools",
    "nlme",
    "openssl",
    "operator.tools",
    "otel",
    "pillar",
    "pkgconfig",
    "plotly",
    "plyr",
    "png",
    "promises",
    "proxy",
    "purrr",
    "R6",
    "ragg",
    "rappdirs",
    "RColorBrewer",
    "Rcpp",
    "RcppArmadillo",
    "rlang",
    "rmarkdown",
    "s2",
    "S4Arrays",
    "S4Vectors",
    "S7",
    "sass",
    "scales",
    "scam",
    "segmented",
    "Seqinfo",
    "sf",
    "snow",
    "SparseArray",
    "stringi",
    "stringr",
    "SummarizedExperiment",
    "survival",
    "sys",
    "systemfonts",
    "textshaping",
    "tibble",
    "tidyr",
    "tidyselect",
    "timechange",
    "tinytex",
    "units",
    "utf8",
    "vctrs",
    "vipor",
    "viridisLite",
    "withr",
    "wk",
    "xfun",
    "XVector",
    "yaml"
  ],
  "_vignettes": [
    {
      "source": "stub.rmd",
      "filename": "stub.html",
      "title": "Power and Sample Size Estimation for Microbiome Analysis",
      "author": "Michael Agronah and Benjamin Bolker",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Package Description and Functionalities",
        "Installation",
        "Simulating microbiome data",
        "Two ways to obtain parameters for data simulation using MixGaussSim",
        "Dataset",
        "Pre-filtering low abundant taxa",
        "Fold change and Dispersion Estimation",
        "Modeling the distribution of log mean counts",
        "Modelling the distribution of log fold change estimates",
        "Modelling the dispersion estimates",
        "Simulate count microbiome data",
        "Simulate log mean count and log fold change",
        "Simulate counts from the negative binomial distribution",
        "Comparing the distributions between simulated count d of mean count and fold change from simulation with actual data",
        "Estimating Statistical Power for Individual Taxa",
        "Estimate p-values associated with simulated fold changes",
        "Fitting the Generalized Additive Model (GAM)",
        "Contour plot showing power for various combinations of mean abundance and fold change",
        "Sample size calculation",
        "Simulate count data for various sample sizes",
        "Estimate p-values associated to fold changes for each taxa for simulated data per sample size",
        "Fit Generalized Additive Model (GAM) for power estimation",
        "Estimate sample size for a given statistical power, fold change and mean abundance",
        "Appendix",
        "Data description and parameter estimates from actual microbiome datasets",
        "Acknowledgments",
        "References"
      ],
      "created": "2025-06-26 18:09:27",
      "modified": "2026-06-08 17:27:33",
      "commits": 43
    }
  ],
  "_score": 5.3222192947339195,
  "_indexed": true,
  "_nocasepkg": "power.nb",
  "_universes": [
    "magronah"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "0.1.0",
      "date": "2026-06-16T09:56:02.000Z",
      "distro": "noble",
      "commit": "26d33e296987930e8752c1cfda18a20bf17358df",
      "fileid": "ababe3c61b9110b655df02702f76c5ae5713cb30acd14695e35ec7e0b7008dff",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/magronah/actions/runs/27608862013"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "0.1.0",
      "date": "2026-06-16T09:55:43.000Z",
      "distro": "noble",
      "commit": "26d33e296987930e8752c1cfda18a20bf17358df",
      "fileid": "5df6849204ffbb0a8791ffaf54dce3ec80c4521831c24b593feb2792cff24326",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/magronah/actions/runs/27608862013"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "0.1.0",
      "date": "2026-06-16T09:55:29.000Z",
      "commit": "26d33e296987930e8752c1cfda18a20bf17358df",
      "fileid": "09484dcf883a572496671674626f0ec4a42179c8b7a6628bf8acf5a728760fed",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/magronah/actions/runs/27608862013"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "0.1.0",
      "date": "2026-06-16T09:54:48.000Z",
      "commit": "26d33e296987930e8752c1cfda18a20bf17358df",
      "fileid": "91fe4826c967444d3b90748c3b41edc0b0ab2bba9ff40f5f97b39e471573a9ab",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/magronah/actions/runs/27608862013"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "0.1.0",
      "date": "2026-06-16T09:56:07.000Z",
      "commit": "26d33e296987930e8752c1cfda18a20bf17358df",
      "fileid": "c2e4d4162863db41528c90e0709809a7cbcae077a8f3b9ac9957d3e5610f7b60",
      "status": "success",
      "buildurl": "https://github.com/r-universe/magronah/actions/runs/27608862013"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "0.1.0",
      "date": "2026-06-16T09:55:10.000Z",
      "commit": "26d33e296987930e8752c1cfda18a20bf17358df",
      "fileid": "9fe0662a1ad626c7b81134a696bc7b37ef234f962b5ed1da922c2a900e6e9ba6",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/magronah/actions/runs/27608862013"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "0.1.0",
      "date": "2026-06-16T09:54:37.000Z",
      "commit": "26d33e296987930e8752c1cfda18a20bf17358df",
      "fileid": "f2c0afb6718fb1c5a62ca7ede481ce05a00ffca9129575352f658787bf8702ac",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/magronah/actions/runs/27608862013"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "0.1.0",
      "date": "2026-06-16T09:54:30.000Z",
      "commit": "26d33e296987930e8752c1cfda18a20bf17358df",
      "fileid": "dd24071e01e8bde46f03673de16a0b257576762f825d9340fcd971c7e7be8c9f",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/magronah/actions/runs/27608862013"
    }
  ]
}