{ "_id": "6abcba2999f7aa8c6aa4b05d", "Package": "FLORAL", "Type": "Package", "Title": "Fit Log-Ratio Lasso Regression for Compositional Data", "Version": "0.7.0", "Date": "2026-02-07", "Authors@R": "c(\nperson(\"Teng\", \"Fei\", , \"feit1@mskcc.org\", role = c(\"aut\", \"cre\", \"cph\"),\ncomment = c(ORCID = \"0000-0001-7888-1715\")),\nperson(\"Tyler\", \"Funnell\", role=c(\"aut\"),\ncomment = c(ORCID = \"0000-0003-1612-5644\")),\nperson(\"Nicholas\", \"Waters\", role=c(\"aut\"),\ncomment = c(ORCID = \"0000-0002-9035-2143\")),\nperson(\"Sandeep\", \"Raj\", role=c(\"aut\"),\ncomment = c(ORCID = \"0000-0003-4629-0528\"))\n)", "Description": "Log-ratio Lasso regression for continuous, binary, and\nsurvival outcomes with (longitudinal) compositional features.\nSee Fei and others (2024) .", "License": "GPL (>= 3)", "URL": "https://vdblab.github.io/FLORAL/", "BugReports": "https://github.com/vdblab/FLORAL/issues", "SystemRequirements": "C++17", "biocViews": "", "RoxygenNote": "7.3.2", "Encoding": "UTF-8", "Language": "en-US", "Config/testthat/edition": "3", "VignetteBuilder": "knitr", "Config/pak/sysreqs": "libglpk-dev libicu-dev libxml2-dev zlib1g-dev", "Repository": "https://vdblab.r-universe.dev", "Date/Publication": "2026-09-29 17:44:50 UTC", "RemoteUrl": "https://github.com/vdblab/floral", "RemoteRef": "HEAD", "RemoteSha": "dd9b47d56ffd92cd5cebaf3b74780ba68638f97c", "NeedsCompilation": "yes", "Packaged": { "Date": "2026-09-30 07:10:20 UTC", "User": "root" }, "Author": "Teng Fei [aut, cre, cph] (ORCID:\n),\nTyler Funnell [aut] (ORCID: ),\nNicholas Waters [aut] (ORCID: ),\nSandeep Raj [aut] (ORCID: )", "Maintainer": "Teng Fei ", "_user": "vdblab", "_type": "src", "_file": "FLORAL_0.7.0.tar.gz", "_fileid": "https://r2.ropensci.org/02bf18f336351b21da03d6697b963b97f1fb063188b499341e462a4532f47c46", "_filesize": 3230045, "_sha256": "02bf18f336351b21da03d6697b963b97f1fb063188b499341e462a4532f47c46", "_expires": "2027-01-08T07:28:39.000Z", "_created": "2026-09-30T07:10:20.000Z", "_published": "2026-09-30T07:28:41.808Z", "_jobs": [ { "job": 109780177823, "time": 284, "config": "linux-devel-arm64", "r": "4.7.0", "check": "OK", "artifact": "11081829360" }, { "job": 109780177793, "time": 324, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "11081479950" }, { "job": 109780177700, "time": 242, "config": "linux-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "11081404810" }, { "job": 109780177817, "time": 295, "config": "linux-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "11082362580" }, { "job": 109780177821, "time": 329, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "11082621825" }, { "job": 109780177701, "time": 553, "config": "macos-oldrel-x86_64", "r": "4.5.3", "check": "OK", "artifact": "11083016247" }, { "job": 109780177733, "time": 319, "config": "macos-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "11082214068" }, { "job": 109780177780, "time": 431, "config": "macos-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "11083036127" }, { "job": 109777623913, "time": 530, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "11081828755" }, { "job": 109780177649, "time": 192, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "11082292614" }, { "job": 109780177829, "time": 490, "config": "windows-devel-arm64", "r": "4.7.0", "check": "OK", "artifact": "11082955557" }, { "job": 109780177757, "time": 261, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "11082093562" }, { "job": 109780177910, "time": 244, "config": "windows-oldrel-x86_64", "r": "4.5.3", "check": "OK", "artifact": "11082606025" }, { "job": 109780177708, "time": 496, "config": "windows-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "11082328241" }, { "job": 109780177762, "time": 258, "config": "windows-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "11082730333" } ], "_host": "GitHub-Actions", "_buildurl": "https://github.com/r-universe/vdblab/actions/runs/36612646917", "_status": "success", "_upstream": "https://github.com/vdblab/floral", "_commit": { "id": "dd9b47d56ffd92cd5cebaf3b74780ba68638f97c", "author": "Teng Fei ", "committer": "GitHub ", "message": "Update pgee.cpp - fix small bug in SCAD penalty", "time": 1790703890 }, "_maintainer": { "name": "Teng Fei", "email": "feit1@mskcc.org", "login": "tengfei-emory", "description": "Biostatistician at MSKCC. Latent class analysis; microbiome data; competing risks; longitudinal data; batch effect adjustment", "uuid": 28678334, "orcid": "0000-0001-7888-1715" }, "_distro": "resolute", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.5.0", "role": "Depends" }, { "package": "Rcpp", "role": "LinkingTo" }, { "package": "RcppArmadillo", "role": "LinkingTo" }, { "package": "RcppProgress", "role": "LinkingTo" }, { "package": "Rcpp", "version": ">= 1.0.9", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "survival", "role": "Imports" }, { "package": "ggplot2", "role": "Imports" }, { "package": "reshape", "role": "Imports" }, { "package": "dplyr", "role": "Imports" }, { "package": "glmnet", "role": "Imports" }, { "package": "caret", "role": "Imports" }, { "package": "grDevices", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "mvtnorm", "role": "Imports" }, { "package": "doParallel", "role": "Imports" }, { "package": "doRNG", "role": "Imports" }, { "package": "foreach", "role": "Imports" }, { "package": "msm", "role": "Imports" }, { "package": "phyloseq", "role": "Imports" }, { "package": "covr", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "spelling", "role": "Suggests" }, { "package": "testthat", "version": ">= 3.0.0", "role": "Suggests" }, { "package": "patchwork", "role": "Suggests" }, { "package": "tidyverse", "role": "Suggests" } ], "_owner": "vdblab", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-47", "n": 1 }, { "week": "2026-06", "n": 3 }, { "week": "2026-40", "n": 1 } ], "_tags": [], "_stars": 16, "_contributors": [ { "user": "tengfei-emory", "count": 50, "uuid": 28678334 }, { "user": "nickp60", "count": 6, "uuid": 14367274 }, { "user": "davisvaughan", "count": 1, "uuid": 19150088 }, { "user": "funnell", "count": 1, "uuid": 381464 } ], "_userbio": { "uuid": 82675713, "type": "organization", "name": "Marcel van den Brink Lab", "followers": 8 }, "_downloads": { "count": 358, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/FLORAL" }, "_devurl": "https://github.com/vdblab/floral", "_pkgdown": "https://vdblab.github.io/FLORAL/", "_searchresults": 16, "_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/FLORAL.html", "extra/manual.pdf", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md" ], "_homeurl": "https://github.com/vdblab/floral", "_realowner": "vdblab", "_cranurl": true, "_releases": [ { "version": "0.1.0", "date": "2023-05-11" }, { "version": "0.2.0", "date": "2023-07-06" }, { "version": "0.3.0", "date": "2024-08-20" }, { "version": "0.4.0", "date": "2025-02-17" }, { "version": "0.5.0", "date": "2025-07-13" }, { "version": "0.6.0", "date": "2025-11-22" }, { "version": "0.7.0", "date": "2026-02-08" } ], "_exports": [ "a.FLORAL", "FLORAL", "mcv.FLORAL", "phy_to_floral_data", "simu" ], "_help": [ { "page": "a.FLORAL", "title": "Comparing prediction performances under different choices of weights for lasso/ridge penalty", "topics": [ "a.FLORAL" ] }, { "page": "FLORAL", "title": "Fit Log-ratio lasso regression for compositional covariates", "topics": [ "FLORAL" ] }, { "page": "mcv.FLORAL", "title": "Summarizing selected compositional features over multiple cross validations", "topics": [ "mcv.FLORAL" ] }, { "page": "phy_to_floral_data", "title": "Create data input list from phyloseq object", "topics": [ "phy_to_floral_data" ] }, { "page": "simu", "title": "Simulate data following log-ratio model", "topics": [ "simu" ] } ], "_pkglogo": "https://github.com/vdblab/floral/raw/HEAD/man/figures/logo.png", "_readme": "https://github.com/vdblab/floral/raw/HEAD/README.md", "_rundeps": [ "ade4", "ape", "Biobase", "BiocGenerics", "biomformat", "Biostrings", "caret", "class", "cli", "clock", "cluster", "codetools", "cpp11", "crayon", "data.table", "diagram", "digest", "doParallel", "doRNG", "dplyr", "e1071", "expm", "farver", "foreach", "future", "future.apply", "generics", "ggplot2", "glmnet", "globals", "glue", "gower", "gtable", "hardhat", "igraph", "ipred", "IRanges", "isoband", "iterators", "jsonlite", "KernSmooth", "labeling", "lattice", "lava", "lifecycle", "listenv", "lubridate", "magrittr", "MASS", "Matrix", "mgcv", "ModelMetrics", "msm", "multtest", "mvtnorm", "nlme", "nnet", "numDeriv", "parallelly", "permute", "phyloseq", "pillar", "pixmap", "pkgconfig", "plyr", "pROC", "prodlim", "progressr", "proxy", "purrr", "R6", "RColorBrewer", "Rcpp", "RcppArmadillo", "RcppEigen", "RcppProgress", "recipes", "reshape", "reshape2", "rlang", "rngtools", "rpart", "S4Vectors", "S7", "scales", "Seqinfo", "shape", "sp", "sparsevctrs", "SQUAREM", "stringi", "stringr", "survival", "tibble", "tidyr", "tidyselect", "timechange", "timeDate", "tzdb", "utf8", "vctrs", "vegan", "viridisLite", "withr", "XVector" ], "_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" } ], "_vignettes": [ { "source": "Using-FLORAL-for-Microbiome-Analysis.Rmd", "filename": "Using-FLORAL-for-Microbiome-Analysis.html", "title": "Using FLORAL for Microbiome Analysis", "engine": "knitr::rmarkdown", "headings": [ "Data", "Running FLORAL", "Interpreting the Model", "The Two-step Procedure", "Generating taxa selection probabilities", "Elastic net" ], "created": "2023-04-27 18:30:32", "modified": "2025-02-17 02:15:51", "commits": 5 }, { "source": "Using-FLORAL-for-survival-models-with-longitudinal-microbiome-data.Rmd", "filename": "Using-FLORAL-for-survival-models-with-longitudinal-microbiome-data.html", "title": "Using FLORAL for survival models with longitudinal microbiome data", "engine": "knitr::rmarkdown", "headings": [ "Data simulation" ], "created": "2024-08-20 03:49:27", "modified": "2025-02-17 02:15:51", "commits": 2 }, { "source": "Using-FLORAL-with-phyloseq.Rmd", "filename": "Using-FLORAL-with-phyloseq.html", "title": "Using FLORAL with phyloseq data", "engine": "knitr::rmarkdown", "headings": [], "created": "2025-02-17 02:15:51", "modified": "2025-07-13 03:21:30", "commits": 3 } ], "_score": 6.538573733806857, "_indexed": true, "_nocasepkg": "floral", "_universes": [ "vdblab", "tengfei-emory" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "0.7.0", "date": "2026-09-30T07:14:03.000Z", "distro": "resolute", "arch": "aarch64", "commit": "dd9b47d56ffd92cd5cebaf3b74780ba68638f97c", "fileid": "https://r2.ropensci.org/295acb2492bf016dbefc1fb91226846132b2292ca083473852a11aa4db6975cb", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/vdblab/actions/runs/36612646917" }, { "r": "4.7.0", "os": "linux", "version": "0.7.0", "date": "2026-09-30T07:14:05.000Z", "distro": "resolute", "arch": "x86_64", "commit": "dd9b47d56ffd92cd5cebaf3b74780ba68638f97c", "fileid": "https://r2.ropensci.org/51f761961748acdc612b436b6e1ce13708894ed5c1b1670ff6bd9c69fb7ce6de", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/vdblab/actions/runs/36612646917" }, { "r": "4.6.1", "os": "linux", "version": "0.7.0", "date": "2026-09-30T07:13:31.000Z", "distro": "resolute", "arch": "aarch64", "commit": "dd9b47d56ffd92cd5cebaf3b74780ba68638f97c", "fileid": "https://r2.ropensci.org/b6d580f601309fa5cfa9b4cd579dc66f184e0c90ea36e033a5c508d10369a7e2", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/vdblab/actions/runs/36612646917" }, { "r": "4.6.1", "os": "linux", "version": "0.7.0", "date": "2026-09-30T07:14:06.000Z", "distro": "resolute", "arch": "x86_64", "commit": "dd9b47d56ffd92cd5cebaf3b74780ba68638f97c", "fileid": "https://r2.ropensci.org/512d7f32f562722b89a1a18a8da6d117a1a27fffe7d716171efb5ebb450e25ae", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/vdblab/actions/runs/36612646917" }, { "r": "4.5.3", "os": "mac", "version": "0.7.0", "date": "2026-09-30T07:25:08.000Z", "arch": "aarch64", "commit": "dd9b47d56ffd92cd5cebaf3b74780ba68638f97c", "fileid": "https://r2.ropensci.org/b4d5a39f553cdaf906e1b9e74472692e0a72a136d73d9ae385d329e55a9d0d06", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/vdblab/actions/runs/36612646917" }, { "r": "4.5.3", "os": "mac", "version": "0.7.0", "date": "2026-09-30T07:19:32.000Z", "arch": "x86_64", "commit": "dd9b47d56ffd92cd5cebaf3b74780ba68638f97c", "fileid": "https://r2.ropensci.org/3c7de5aa5ebbf12bf5e9f961620be1c2c704d40c3ce7bced4d23a4ea6fa6f9ba", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/vdblab/actions/runs/36612646917" }, { "r": "4.6.1", "os": "mac", "version": "0.7.0", "date": "2026-09-30T07:19:25.000Z", "arch": "aarch64", "commit": "dd9b47d56ffd92cd5cebaf3b74780ba68638f97c", "fileid": "https://r2.ropensci.org/7bb1d97b2e5b7e50d2f86ad03b0a2b886c86e279a1130542a6d9bfaea9757e3c", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/vdblab/actions/runs/36612646917" }, { "r": "4.6.1", "os": "mac", "version": "0.7.0", "date": "2026-09-30T07:23:35.000Z", "arch": "x86_64", "commit": "dd9b47d56ffd92cd5cebaf3b74780ba68638f97c", "fileid": "https://r2.ropensci.org/135bd24c136a69766f751430f0fb895d77e02154ad1a330d20366230618728a9", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/vdblab/actions/runs/36612646917" }, { "r": "4.6.0", "os": "wasm", "version": "0.7.0", "date": "2026-09-30T07:14:12.000Z", "arch": "emscripten", "commit": "dd9b47d56ffd92cd5cebaf3b74780ba68638f97c", "fileid": "https://r2.ropensci.org/23274051d534f20844e60ac5161956b6d9411c4bc923f16358e46d1614c77a04", "status": "success", "buildurl": "https://github.com/r-universe/vdblab/actions/runs/36612646917" }, { "r": "4.7.0", "os": "win", "version": "0.7.0", "date": "2026-09-30T07:16:35.000Z", "arch": "aarch64", "commit": "dd9b47d56ffd92cd5cebaf3b74780ba68638f97c", "fileid": "https://r2.ropensci.org/3cdce8723d6d512c6a9300fc392a1711c184b250252bb5b3d32f72762a6698f7", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/vdblab/actions/runs/36612646917" }, { "r": "4.7.0", "os": "win", "version": "0.7.0", "date": "2026-09-30T07:12:23.000Z", "arch": "x86_64", "commit": "dd9b47d56ffd92cd5cebaf3b74780ba68638f97c", "fileid": "https://r2.ropensci.org/930f0a1360b1d32116f58f97bf018e9fa95053eb032bc9b454c4b8f325ed5c0c", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/vdblab/actions/runs/36612646917" }, { "r": "4.5.3", "os": "win", "version": "0.7.0", "date": "2026-09-30T07:12:16.000Z", "arch": "x86_64", "commit": "dd9b47d56ffd92cd5cebaf3b74780ba68638f97c", "fileid": "https://r2.ropensci.org/f6e20bd765457b93ef7b2dd46b2fe01c675e36dfe576e1109250fe126f2c7e69", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/vdblab/actions/runs/36612646917" }, { "r": "4.6.1", "os": "win", "version": "0.7.0", "date": "2026-09-30T07:16:30.000Z", "arch": "aarch64", "commit": "dd9b47d56ffd92cd5cebaf3b74780ba68638f97c", "fileid": "https://r2.ropensci.org/b59e07a1e9b47e33785e2b4878608cff2d9b751c81b74fc32f1416202e796309", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/vdblab/actions/runs/36612646917" }, { "r": "4.6.1", "os": "win", "version": "0.7.0", "date": "2026-09-30T07:12:48.000Z", "arch": "x86_64", "commit": "dd9b47d56ffd92cd5cebaf3b74780ba68638f97c", "fileid": "https://r2.ropensci.org/64467770ca8b3622d04b964b22f352ff7cd53bfb2fa2c93771fd7b19e6f1d3dc", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/vdblab/actions/runs/36612646917" } ] }