{ "_id": "6a1d561b1d7bb097a0a46f51", "Package": "MicrobiomeStat", "Type": "Package", "Title": "Statistical Methods for Microbiome Compositional Data", "Version": "1.4", "Date": "2026-03-03", "Authors@R": "c(\nperson(\"Xianyang\", \"Zhang\", role = \"aut\", email = \"zhangxiany@stat.tamu.edu\"),\nperson(\"Jun\", \"Chen\", role = c(\"aut\", \"cre\"),\nemail = \"chen.jun2@mayo.edu\"),\nperson(\"Huijuan\", \"Zhou\", role = \"ctb\"),\nperson(\"Linsui\", \"Deng\", role = \"ctb\"))", "Author": "Xianyang Zhang [aut], Jun Chen [aut, cre], Huijuan Zhou [ctb],\nLinsui Deng [ctb]", "Maintainer": "Jun Chen ", "Description": "A suite of methods for powerful and robust microbiome data\nanalysis addressing zero-inflation, phylogenetic structure and\ncompositional effects. Includes the LinDA method for\ndifferential abundance analysis (Zhou et al.\n(2022)), the BMDD (Bimodal\nDirichlet Distribution) method for accurate modeling and\nimputation of zero-inflated microbiome sequencing data (Zhou et\nal. (2025)) and compositional\nsparse CCA methods for microbiome multi-omics data integration\n(Deng et al. (2024) ).", "NeedsCompilation": "yes", "SystemRequirements": "NLopt library (optional, for high-performance BMDD\nmode)", "License": "GPL-3", "Encoding": "UTF-8", "LazyData": "true", "RoxygenNote": "7.3.3", "Packaged": { "Date": "2026-06-01 09:46:57 UTC", "User": "root" }, "Repository": "https://cran.r-universe.dev", "Date/Publication": "2026-03-03 21:40:02 UTC", "RemoteUrl": "https://github.com/cran/MicrobiomeStat", "RemoteRef": "HEAD", "RemoteSha": "67a6cc7d7254a67dcbde91f7fba7819405345626", "MD5sum": "2f9cffc2b388ff8ba761bcc92513c418", "_user": "cran", "_type": "src", "_file": "MicrobiomeStat_1.4.tar.gz", "_fileid": "cde3138a8586c675b534c20658c3b22dd16354a43c49c6b1f00eca63680e9c07", "_filesize": 292668, "_sha256": "cde3138a8586c675b534c20658c3b22dd16354a43c49c6b1f00eca63680e9c07", "_created": "2026-06-01T09:46:57.000Z", "_published": "2026-06-01T09:51:23.644Z", "_distro": "noble", "_jobs": [ { "job": 78826788054, "time": 168, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7328366742" }, { "job": 78826788061, "time": 211, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7328381548" }, { "job": 78826008687, "time": 290, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7328306405" }, { "job": 78826788026, "time": 135, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7328354212" } ], "_buildurl": "https://github.com/r-universe/cran/actions/runs/26747288633", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/cran/MicrobiomeStat", "_commit": { "id": "67a6cc7d7254a67dcbde91f7fba7819405345626", "author": "Jun Chen ", "committer": "cran-robot ", "message": "version 1.4\n", "time": 1772574002 }, "_maintainer": { "name": "Jun Chen", "email": "chen.jun2@mayo.edu" }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.5.0", "role": "Depends" }, { "package": "Rcpp", "role": "LinkingTo" }, { "package": "RcppArmadillo", "role": "LinkingTo" }, { "package": "ggplot2", "role": "Imports" }, { "package": "matrixStats", "role": "Imports" }, { "package": "parallel", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "Matrix", "role": "Imports" }, { "package": "statmod", "role": "Imports" }, { "package": "MASS", "role": "Imports" }, { "package": "ggrepel", "role": "Imports" }, { "package": "lmerTest", "role": "Imports" }, { "package": "foreach", "role": "Imports" }, { "package": "modeest", "role": "Imports" }, { "package": "dplyr", "role": "Imports" }, { "package": "Rcpp", "role": "Imports" }, { "package": "mlr3", "role": "Imports" }, { "package": "mlr3mbo", "role": "Imports" }, { "package": "bbotk", "role": "Imports" }, { "package": "paradox", "role": "Imports" }, { "package": "DiceKriging", "role": "Suggests" }, { "package": "randomForest", "role": "Suggests" } ], "_owner": "cran", "_selfowned": false, "_usedby": 1, "_updates": [ { "week": "2026-02", "n": 1 }, { "week": "2026-10", "n": 1 } ], "_tags": [ { "name": "1.3", "date": "2026-01-09" }, { "name": "1.4", "date": "2026-03-03" } ], "_stars": 0, "_userbio": { "uuid": 6899542, "type": "organization", "name": "cran", "description": "Unofficial read-only mirror of all CRAN R packages" }, "_downloads": { "count": 1070, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/MicrobiomeStat" }, "_searchresults": 131, "_topics": [ "cpp" ], "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/MicrobiomeStat.html", "manual.pdf" ], "_realowner": "cran", "_cranurl": false, "_releases": [ { "version": "1.0", "date": "2021-11-19" }, { "version": "1.1", "date": "2022-01-24" }, { "version": "1.2", "date": "2024-04-02" }, { "version": "1.3", "date": "2026-01-09" }, { "version": "1.4", "date": "2026-03-03" } ], "_exports": [ "bmdd", "bmdd.nlopt", "cscca", "cscca.CV", "DGP_OC", "linda", "linda.plot", "linda.wald.test" ], "_datasets": [ { "name": "smokers", "title": "Microbiome data from the human upper respiratory tract (left and right throat)", "object": "smokers", "class": [ "list" ], "fields": [], "table": false, "tojson": true } ], "_help": [ { "page": "bmdd", "title": "Bimodal Dirichlet Distribution Estimation", "topics": [ "bmdd" ] }, { "page": "bmdd.nlopt", "title": "NLopt C++ Implementation of BMDD", "topics": [ "bmdd.nlopt" ] }, { "page": "cscca", "title": "Compositional Sparse Canonical Correlation Analysis", "topics": [ "cscca" ] }, { "page": "cscca.CV", "title": "Compositional Sparse Canonical Correlation Analysis (Cross Valication Version)", "topics": [ "cscca.CV" ] }, { "page": "DGP_OC", "title": "Data Generating Process (Omics Data versus Compositional data)", "topics": [ "DGP_OC" ] }, { "page": "linda", "title": "Linear (Lin) Model for Differential Abundance (DA) Analysis of High-dimensional Compositional Data", "topics": [ "linda" ] }, { "page": "linda.plot", "title": "Plot LinDA Results", "topics": [ "linda.plot" ] }, { "page": "linda.wald.test", "title": "Wald test for bias-corrected regression coefficients", "topics": [ "linda.wald.test" ] }, { "page": "smokers", "title": "Microbiome data from the human upper respiratory tract (left and right throat)", "topics": [ "smokers" ] } ], "_rundeps": [ "backports", "bbotk", "boot", "checkmate", "cli", "clue", "cluster", "codetools", "cpp11", "data.table", "digest", "dplyr", "evaluate", "farver", "fBasics", "foreach", "future", "future.apply", "generics", "ggplot2", "ggrepel", "globals", "glue", "gss", "gtable", "isoband", "iterators", "labeling", "lattice", "lgr", "lifecycle", "listenv", "lme4", "lmerTest", "magrittr", "MASS", "Matrix", "matrixStats", "minqa", "mirai", "mlbench", "mlr3", "mlr3mbo", "mlr3measures", "mlr3misc", "mlr3tuning", "modeest", "nanonext", "nlme", "nloptr", "numDeriv", "palmerpenguins", "paradox", "parallelly", "pillar", "pkgconfig", "PRROC", "R6", "rbibutils", "RColorBrewer", "Rcpp", "RcppArmadillo", "RcppEigen", "Rdpack", "reformulas", "rlang", "rmutil", "rpart", "S7", "scales", "spacefillr", "spatial", "stable", "stabledist", "statip", "statmod", "tibble", "tidyselect", "timeDate", "timeSeries", "utf8", "uuid", "vctrs", "viridisLite", "withr" ], "_sysdeps": [ { "shlib": "libstdc++", "package": "libstdc++6", "source": "gcc", "version": "14.2.0-4ubuntu2~24.04.1", "name": "c++", "homepage": "http://gcc.gnu.org/", "description": "GNU Standard C++ Library v3" } ], "_score": 2.9248063237246176, "_indexed": true, "_nocasepkg": "microbiomestat", "_universes": [ "cran" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.4", "date": "2026-05-02T08:50:15.000Z", "distro": "noble", "arch": "aarch64", "commit": "67a6cc7d7254a67dcbde91f7fba7819405345626", "fileid": "142d6cd0072ade2eb4007d11e2be1ac868cf577aff81313d06fb3761d93d6f52", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cran/actions/runs/25248171203" }, { "r": "4.6.0", "os": "linux", "version": "1.4", "date": "2026-05-02T08:50:22.000Z", "distro": "noble", "arch": "aarch64", "commit": "67a6cc7d7254a67dcbde91f7fba7819405345626", "fileid": "2d50cd502ce03a5f699142abade442b5319e88b52b680741a73c7a2ca02cc526", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cran/actions/runs/25248171203" }, { "r": "4.7.0", "os": "linux", "version": "1.4", "date": "2026-06-01T09:49:17.000Z", "distro": "noble", "arch": "x86_64", "commit": "67a6cc7d7254a67dcbde91f7fba7819405345626", "fileid": "a846af7bbb3fdd9a7e7965d802dfe2dcf9d69e5706f42c0f4508ae868081e718", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cran/actions/runs/26747288633" }, { "r": "4.6.0", "os": "linux", "version": "1.4", "date": "2026-06-01T09:49:41.000Z", "distro": "noble", "arch": "x86_64", "commit": "67a6cc7d7254a67dcbde91f7fba7819405345626", "fileid": "f3a84bc338a8fdd8de54f7059835c0d1ea5b5e485c40b0f3c3c4ef60f21b2a34", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cran/actions/runs/26747288633" }, { "r": "4.6.0", "os": "wasm", "version": "1.4", "date": "2026-06-01T09:49:39.000Z", "arch": "emscripten", "commit": "67a6cc7d7254a67dcbde91f7fba7819405345626", "fileid": "b4215dcf707d4d773bed0b1aab7bb839fba6a3be68363fde453f5d8418462655", "status": "success", "buildurl": "https://github.com/r-universe/cran/actions/runs/26747288633" } ] }