{ "_id": "6ae37fc88d250e7ad09f0b04", "Package": "LOCOM2", "Type": "Package", "Title": "A Logistic Regression Model for Testing Microbial Differential\nAbundance", "Version": "1.1", "Date": "2026-10-29", "Authors@R": "person(given = \"Yi-Juan\",\nfamily = \"Hu\",\nrole = c(\"aut\", \"cre\"),\nemail = \"yijuanhu@bicmr.pku.edu.cn\")", "Maintainer": "Yi-Juan Hu ", "Description": "Testing differential abundance at individual taxa and in a\nwhole microbial community. The tests are based on the log-ratio\nof relative abundances. The tests accommodate continuous,\ndiscrete (binary, categorical), and multivariate traits, and\nallow adjustment of confounders. For more details see He (2026)\n. This package also includes\nthe 'com2seq' function that combines two sequencing datasets\n(e.g., from 16S marker-gene and shotgun sequencing) for\nintegrative analysis of differential abundance. For more\ndetails see .", "License": "GPL (>= 2)", "RoxygenNote": "7.3.2", "URL": "https://github.com/yijuanhu/LOCOM2", "BugReports": "https://github.com/yijuanhu/LOCOM2/issues", "Encoding": "UTF-8", "LazyData": "true", "NeedsCompilation": "yes", "Packaged": { "Date": "2026-10-29 17:12:40 UTC", "User": "root" }, "Author": "Yi-Juan Hu [aut, cre]", "Repository": "https://cran.r-universe.dev", "Date/Publication": "2026-10-29 16:16:04 UTC", "RemoteUrl": "https://github.com/cran/LOCOM2", "RemoteRef": "HEAD", "RemoteSha": "74554e3fdc666a2bb65b8ae557a8c113f9f0fd49", "_user": "cran", "_type": "src", "_file": "LOCOM2_1.1.tar.gz", "_fileid": "https://r2.ropensci.org/a363ae70c5435906b6d83ddd4b10aa3970896260a4ce79ad87d698ffeae60602", "_filesize": 220315, "_sha256": "a363ae70c5435906b6d83ddd4b10aa3970896260a4ce79ad87d698ffeae60602", "_expires": "2027-02-06T17:17:58.000Z", "_created": "2026-10-29T17:12:40.000Z", "_published": "2026-10-29T17:18:00.683Z", "_upstream": "https://github.com/cran/LOCOM2", "_status": "success", "_maintainer": { "name": "Yi-Juan Hu", "email": "yijuanhu@bicmr.pku.edu.cn" }, "_jobs": [ { "job": 123607643637, "time": 134, "config": "linux-devel-arm64", "r": "4.7.0", "check": "OK", "artifact": "12917457927" }, { "job": 123607643663, "time": 175, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "12917862110" }, { "job": 123607643560, "time": 130, "config": "linux-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "12918180764" }, { "job": 123607643615, "time": 131, "config": "linux-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "12917981286" }, { "job": 123605253776, "time": 248, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "12915774980" }, { "job": 123607643501, "time": 142, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "12917681841" }, { "job": 123607643596, "time": 234, "config": "windows-devel-arm64", "r": "4.7.0", "check": "OK", "artifact": "12916294417" }, { "job": 123607643743, "time": 173, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "12918135665" }, { "job": 123607643595, "time": 256, "config": "windows-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "12917422607" }, { "job": 123607643575, "time": 118, "config": "windows-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "12917816848" } ], "_buildurl": "https://github.com/r-universe/cran/actions/runs/40918486909", "_commit": { "id": "74554e3fdc666a2bb65b8ae557a8c113f9f0fd49", "author": "Yi-Juan Hu ", "committer": "cran-robot ", "message": "version 1.1\n", "time": 1793290564 }, "_distro": "resolute", "_host": "GitHub-Actions", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.5.0", "role": "Depends" }, { "package": "Rcpp", "role": "LinkingTo" }, { "package": "RcppArmadillo", "role": "LinkingTo" }, { "package": "Rcpp", "version": ">= 1.0.11", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "permute", "role": "Imports" }, { "package": "parallel", "role": "Imports" }, { "package": "BiocParallel", "role": "Imports" }, { "package": "matrixStats", "role": "Imports" }, { "package": "abind", "role": "Imports" }, { "package": "car", "role": "Imports" }, { "package": "testthat", "role": "Suggests" }, { "package": "survival", "role": "Suggests" } ], "_owner": "cran", "_selfowned": false, "_usedby": 0, "_updates": [ { "week": "2026-19", "n": 1 }, { "week": "2026-44", "n": 1 } ], "_tags": [ { "name": "1.0", "date": "2026-05-04" }, { "name": "1.1", "date": "2026-10-29" } ], "_stars": 0, "_userbio": { "uuid": 6899542, "type": "organization", "name": "cran", "followers": 634, "description": "Unofficial read-only mirror of all CRAN R packages" }, "_downloads": { "count": 425, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/LOCOM2" }, "_devurl": "https://github.com/yijuanhu/locom2", "_searchresults": 1, "_topics": [ "openblas", "cpp", "openmp" ], "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/LOCOM2.html", "extra/manual.pdf", "extra/readme.html", "extra/readme.md" ], "_homeurl": "https://github.com/yijuanhu/locom2", "_realowner": "yijuanhu", "_cranurl": false, "_releases": [ { "version": "1.0", "date": "2026-05-04" } ], "_exports": [ "com2seq", "locom2" ], "_datasets": [ { "name": "meta.1", "title": "Metadata for samples in otu.table.1", "object": "meta.1", "class": [ "data.frame" ], "fields": [ "Y", "C" ], "rows": 80, "table": true, "tojson": true }, { "name": "meta.2", "title": "Metadata for samples in otu.table.2", "object": "meta.2", "class": [ "data.frame" ], "fields": [ "Y", "C" ], "rows": 60, "table": true, "tojson": true }, { "name": "otu.table.1", "title": "Simulated OTU count table", "object": "otu.table.1", "class": [ "matrix", "array" ], "fields": [], "rows": 80, "table": true, "tojson": true }, { "name": "otu.table.2", "title": "Simulated OTU count table", "object": "otu.table.2", "class": [ "matrix", "array" ], "fields": [], "rows": 60, "table": true, "tojson": true }, { "name": "throat.meta.filter", "title": "Metadata of the throat microbiome samples", "object": "throat.meta.filter", "class": [ "data.frame" ], "fields": [ "BarcodeSequence", "LinkerPrimerSequence", "SmokingStatus", "PatientID", "SampleIndex", "AirwaySite", "SideOfBody", "SampleType", "RespiratoryDiseaseStatus_severity_timeframe", "AntibioticUsePast3Months_TimeFromAntibioticUsage", "Age", "Sex", "PackYears", "TimeFromLastCig", "TimeFromLastMeal", "Description" ], "rows": 57, "table": true, "tojson": true }, { "name": "throat.otu.table.filter", "title": "OTU count table from 16S sequencing of the throat microbiome samples", "object": "throat.otu.table.filter", "class": [ "data.frame" ], "fields": [], "rows": 57, "table": true, "tojson": true }, { "name": "throat.otu.taxonomy", "title": "Taxonomy names for OTUs from 16S sequencing of the throat microbiome samples", "object": "throat.otu.taxonomy", "class": [ "character" ], "fields": [], "table": false, "tojson": true } ], "_help": [ { "page": "com2seq", "title": "com2seq: combining two sequencing datasets (e.g., from 16S marker-gene and shotgun metagenomic sequencing) for integrative analysis of differential abundance at both the genus and community levels", "topics": [ "com2seq" ] }, { "page": "locom2", "title": "A logistic regression model for testing differential abundance in compositional microbiome data (LOCOM2)", "topics": [ "locom2" ] }, { "page": "meta.1", "title": "Metadata for samples in otu.table.1", "topics": [ "meta.1" ] }, { "page": "meta.2", "title": "Metadata for samples in otu.table.2", "topics": [ "meta.2" ] }, { "page": "otu.table.1", "title": "Simulated OTU count table", "topics": [ "otu.table.1" ] }, { "page": "otu.table.2", "title": "Simulated OTU count table", "topics": [ "otu.table.2" ] }, { "page": "throat.meta.filter", "title": "Metadata of the throat microbiome samples", "topics": [ "throat.meta.filter" ] }, { "page": "throat.otu.table.filter", "title": "OTU count table from 16S sequencing of the throat microbiome samples", "topics": [ "throat.otu.table.filter" ] }, { "page": "throat.otu.taxonomy", "title": "Taxonomy names for OTUs from 16S sequencing of the throat microbiome samples", "topics": [ "throat.otu.taxonomy" ] } ], "_readme": "https://github.com/cran/LOCOM2/raw/HEAD/README.md", "_rundeps": [ "abind", "backports", "BH", "BiocParallel", "boot", "broom", "car", "carData", "cli", "codetools", "colorspace", "cowplot", "cpp11", "Deriv", "doBy", "dplyr", "farver", "forecast", "formatR", "Formula", "fracdiff", "futile.logger", "futile.options", "generics", "ggplot2", "glue", "gtable", "isoband", "labeling", "lambda.r", "lattice", "lifecycle", "lme4", "lmtest", "magrittr", "MASS", "Matrix", "MatrixModels", "matrixStats", "mgcv", "minqa", "modelr", "nlme", "nloptr", "nnet", "numDeriv", "pbkrtest", "permute", "pillar", "pkgconfig", "purrr", "quantreg", "R6", "rbibutils", "RColorBrewer", "Rcpp", "RcppArmadillo", "RcppEigen", "Rdpack", "reformulas", "rlang", "S7", "scales", "snow", "SparseM", "stringi", "stringr", "survival", "tibble", "tidyr", "tidyselect", "timeDate", "urca", "utf8", "vctrs", "viridisLite", "withr", "zoo" ], "_sysdeps": [ { "shlib": "liblapack", "package": "libopenblas0-pthread", "source": "openblas", "version": "0.3.32+ds-5", "name": "openblas", "homepage": "https://www.openblas.net/", "description": "Optimized BLAS (linear algebra) library (shared lib, pthread)" }, { "shlib": "libblas", "package": "libopenblas0-pthread", "source": "openblas", "version": "0.3.32+ds-5", "name": "openblas", "homepage": "https://www.openblas.net/", "description": "Optimized BLAS (linear algebra) library (shared lib, pthread)" }, { "shlib": "libstdc++", "package": "libstdc++6", "source": "gcc", "version": "16-20260322-1ubuntu1", "name": "c++", "homepage": "http://gcc.gnu.org/", "description": "GNU Standard C++ Library v3" }, { "shlib": "libgomp", "package": "libgomp1", "source": "gcc", "version": "16-20260322-1ubuntu1", "name": "openmp", "homepage": "http://gcc.gnu.org/", "description": "GCC OpenMP (GOMP) support library" } ], "_score": 2, "_indexed": false, "_nocasepkg": "locom2", "_universes": [ "cran" ], "_indexurl": "https://yijuanhu.r-universe.dev/LOCOM2", "_previous": "1.0", "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.1", "date": "2026-10-29T17:15:03.000Z", "distro": "resolute", "arch": "aarch64", "commit": "74554e3fdc666a2bb65b8ae557a8c113f9f0fd49", "fileid": "https://r2.ropensci.org/8a68c9cb073efb5aeefa3fa3e33bd43fd6f9300b36ded1fc3084488dfe527486", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cran/actions/runs/40918486909" }, { "r": "4.7.0", "os": "linux", "version": "1.1", "date": "2026-10-29T17:15:33.000Z", "distro": "resolute", "arch": "x86_64", "commit": "74554e3fdc666a2bb65b8ae557a8c113f9f0fd49", "fileid": "https://r2.ropensci.org/8f853f751ee5ddad0991829d85e8155ff3aaa838b60fc4018bc3be5fdb3acf3c", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cran/actions/runs/40918486909" }, { "r": "4.6.1", "os": "linux", "version": "1.1", "date": "2026-10-29T17:14:59.000Z", "distro": "resolute", "arch": "aarch64", "commit": "74554e3fdc666a2bb65b8ae557a8c113f9f0fd49", "fileid": "https://r2.ropensci.org/178de96eef4096c50a0d3ea700398a7c90e13a5a916b4c927f365fc505e7e652", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cran/actions/runs/40918486909" }, { "r": "4.6.1", "os": "linux", "version": "1.1", "date": "2026-10-29T17:15:05.000Z", "distro": "resolute", "arch": "x86_64", "commit": "74554e3fdc666a2bb65b8ae557a8c113f9f0fd49", "fileid": "https://r2.ropensci.org/3a186a918f177d40029e35c05f1dcbcc91174f693b319224e32e2580dabd8203", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cran/actions/runs/40918486909" }, { "r": "4.6.0", "os": "wasm", "version": "1.1", "date": "2026-10-29T17:15:31.000Z", "arch": "emscripten", "commit": "74554e3fdc666a2bb65b8ae557a8c113f9f0fd49", "fileid": "https://r2.ropensci.org/53545093747fe0403b0a36671392e14b09fef6a19e286943520def7d1502a96a", "status": "success", "buildurl": "https://github.com/r-universe/cran/actions/runs/40918486909" }, { "r": "4.7.0", "os": "win", "version": "1.1", "date": "2026-10-29T17:16:19.000Z", "arch": "aarch64", "commit": "74554e3fdc666a2bb65b8ae557a8c113f9f0fd49", "fileid": "https://r2.ropensci.org/865176078c7b17dbfe91ff997272c8986ce780321449cde9e7f8a733dee18d2d", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cran/actions/runs/40918486909" }, { "r": "4.7.0", "os": "win", "version": "1.1", "date": "2026-10-29T17:14:32.000Z", "arch": "x86_64", "commit": "74554e3fdc666a2bb65b8ae557a8c113f9f0fd49", "fileid": "https://r2.ropensci.org/0cef20ec333277bf0b383441101a30198661269a0ec23ec720543e0ab6e454ed", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cran/actions/runs/40918486909" }, { "r": "4.6.1", "os": "win", "version": "1.1", "date": "2026-10-29T17:16:43.000Z", "arch": "aarch64", "commit": "74554e3fdc666a2bb65b8ae557a8c113f9f0fd49", "fileid": "https://r2.ropensci.org/95ad2f5b31429bbafd9fbf18a336055fb898c5e6e02ce9ff42254a52ed4045d2", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cran/actions/runs/40918486909" }, { "r": "4.6.1", "os": "win", "version": "1.1", "date": "2026-10-29T17:14:27.000Z", "arch": "x86_64", "commit": "74554e3fdc666a2bb65b8ae557a8c113f9f0fd49", "fileid": "https://r2.ropensci.org/ab4cb5013a87762760d9f3498942b3cd18bf0568133bebea72e3b5a3b3571c76", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cran/actions/runs/40918486909" } ] }