{ "_id": "6a3d6423a319ef9414479210", "Package": "CAFT", "Type": "Package", "Title": "Rank-Based Compositional Analysis using Log-Linear Models for\nMicrobiome Data with Zero Cells", "Version": "0.1.0", "Date": "2026-06-09", "Authors@R": "c(person(\"Glen A.\", \"Satten\", email=\"gsatten@emory.edu\", role=c(\"aut\", \"ctb\", \"cph\")),\nperson(\"Mo\", \"Li\", email=\"mo.li@louisiana.edu\", role=c(\"aut\", \"ctb\", \"cre\", \"cph\")),\nperson(\"Ni\", \"Zhao\", role=c(\"aut\", \"ctb\", \"cph\")))", "Description": "Provides rank-based compositional differential abundance\nanalysis for microbiome count data with zero cells using the\ncompositional accelerated failure time model of Satten, Li and\nZhao (2025) \"CAFT: A Compositional Log-Linear Model for\nMicrobiome Data with Zero Cells\"\n. Zero counts are treated as\ncensored observations below sample-specific detection limits,\navoiding the use of pseudocounts. The package implements\nestimation and hypothesis testing procedures for assessing\nassociations between microbial taxa and covariates while\naccounting for the compositional structure of sequencing count\ndata. It supports taxon-level differential abundance analysis,\nestimation of regression effects under censoring induced by\ndetection limits, and inference based on rank-based methods\nthat remain applicable in the presence of excess zeros.\nFunctions are provided for model fitting, significance testing,\nextraction of effect estimates, and summarization of results\nacross taxa. The package also provides optional bootstrap\ncalibration of taxon-level p-values for sensitivity analysis in\nsmall-taxon settings.", "License": "LGPL (>= 2)", "URL": "https://github.com/mli171/CAFT", "BugReports": "https://github.com/mli171/CAFT/issues", "Encoding": "UTF-8", "LazyData": "true", "LazyDataCompression": "bzip2", "VignetteBuilder": "knitr", "Config/testthat/edition": "3", "Config/roxygen2/version": "8.0.0", "NeedsCompilation": "no", "Packaged": { "Date": "2026-06-25 17:19:47 UTC", "User": "root" }, "Author": "Glen A. Satten [aut, ctb, cph], Mo Li [aut, ctb, cre, cph], Ni\nZhao [aut, ctb, cph]", "Maintainer": "Mo Li ", "Repository": "https://cran.r-universe.dev", "Date/Publication": "2026-06-25 11:20:14 UTC", "RemoteUrl": "https://github.com/cran/CAFT", "RemoteRef": "HEAD", "RemoteSha": "377bd6a984aea604304f7d79b475dd2bb099d902", "MD5sum": "f3f2525d726fcd6c836f12f592e2036e", "_user": "cran", "_type": "src", "_file": "CAFT_0.1.0.tar.gz", "_fileid": "1b65105100619e1cb407a51aa79cee9194b4bf8c79252a414874c9657a0da44f", "_filesize": 634876, "_sha256": "1b65105100619e1cb407a51aa79cee9194b4bf8c79252a414874c9657a0da44f", "_created": "2026-06-25T17:19:47.000Z", "_published": "2026-06-25T17:23:47.859Z", "_distro": "resolute", "_jobs": [ { "job": 83494963545, "time": 194, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7885783521" }, { "job": 83494963353, "time": 175, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7885776079" }, { "job": 83493909555, 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