{ "_id": "6a65a8e4db02dafbbb592d79", "Package": "philr", "Type": "Package", "Title": "Phylogenetic partitioning based ILR transform for metagenomics\ndata", "Version": "1.39.0", "Date": "2026-04-01", "Authors@R": "c(person(\"Justin\", \"Silverman\", role=c(\"aut\", \"cre\"),\nemail = \"jsilve24@gmail.com\"),\nperson(given = \"Leo\", family = \"Lahti\", role = c(\"ctb\"),\ncomment = c(ORCID = \"0000-0001-5537-637X\")))", "Description": "PhILR is short for Phylogenetic Isometric Log-Ratio\nTransform. This package provides functions for the analysis of\ncompositional data (e.g., data representing proportions of\ndifferent variables/parts). Specifically this package allows\nanalysis of compositional data where the parts can be related\nthrough a phylogenetic tree (as is common in microbiota survey\ndata) and makes available the Isometric Log Ratio transform\nbuilt from the phylogenetic tree and utilizing a weighted\nreference measure.", "License": "GPL-3", "RoxygenNote": "7.3.3", "VignetteBuilder": "knitr", "biocViews": "ImmunoOncology, Sequencing, Microbiome, Metagenomics,\nSoftware", "URL": "https://github.com/jsilve24/philr", "BugReports": "https://github.com/jsilve24/philr/issues", "Encoding": "UTF-8", "Config/pak/sysreqs": "libcairo2-dev cmake libfontconfig1-dev\nlibfreetype6-dev libglpk-dev make libicu-dev libpng-dev\nlibuv1-dev libxml2-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:44:07 UTC", "RemoteUrl": "https://github.com/bioc/philr", "RemoteRef": "HEAD", "RemoteSha": "cd369368edb6ca6f5a32faf60cb645605c6af190", "NeedsCompilation": "no", "Packaged": { "Date": "2026-07-26 06:21:13 UTC", "User": "root" }, "Author": "Justin Silverman [aut, cre],\nLeo Lahti [ctb] (ORCID: )", "Maintainer": "Justin Silverman ", "_user": "bioc", "_type": "src", "_file": "philr_1.39.0.tar.gz", "_fileid": "https://r2.ropensci.org/6ff9fd2372489d332d94965824d98df0ea728071555d27885296b1e975b92cc4", "_filesize": 444099, "_sha256": "6ff9fd2372489d332d94965824d98df0ea728071555d27885296b1e975b92cc4", "_expires": "2026-11-03T06:27:46.000Z", "_created": "2026-07-26T06:21:13.000Z", "_published": "2026-07-26T06:27:48.035Z", "_jobs": [ { "job": 89763953479, "time": 233, "config": "bioc-checks", "r": "4.6.1", "check": "FAILURE", "artifact": "" }, { "job": 89763953492, "time": 311, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "8628575101" }, { "job": 89763953458, "time": 321, "config": "linux-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "8628576436" }, { "job": 89763953480, "time": 131, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "8628549370" }, { "job": 89763953478, "time": 113, "config": "macos-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "8628547971" }, { "job": 89763573190, "time": 300, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "8628526992" }, { "job": 89763953476, "time": 207, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "8628559409" }, { "job": 89763953485, "time": 162, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "8628553297" }, { "job": 89763953509, "time": 183, "config": "windows-oldrel-x86_64", "r": "4.5.3", "check": "OK", "artifact": "8628556440" }, { "job": 89763953463, "time": 144, "config": "windows-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "8628549782" } ], "_host": "GitHub-Actions", "_buildurl": "https://github.com/r-universe/bioc/actions/runs/30190780554", "_status": "success", "_upstream": "https://github.com/bioc/philr", "_commit": { "id": "cd369368edb6ca6f5a32faf60cb645605c6af190", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777380247 }, "_maintainer": { "name": "Justin Silverman", "email": "jsilve24@gmail.com", "login": "jsilve24", "description": "Assistant Professor at Penn State University. ", "uuid": 452422 }, "_distro": "resolute", "_registered": true, "_dependencies": [ { "package": "ape", "role": "Imports" }, { "package": "phangorn", "role": "Imports" }, { "package": "tidyr", "role": "Imports" }, { "package": "ggplot2", "role": "Imports" }, { "package": "ggtree", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "testthat", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "ecodist", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "BiocStyle", "role": "Suggests" }, { "package": "phyloseq", "role": "Suggests" }, { "package": "SummarizedExperiment", "role": "Suggests" }, { "package": "TreeSummarizedExperiment", "role": "Suggests" }, { "package": "glmnet", "role": "Suggests" }, { "package": "dplyr", "role": "Suggests" }, { "package": "mia", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2026-14", "n": 6 }, { "week": "2026-18", "n": 2 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.39.0", "bioc": "3.24" }, { "branch": "release", "version": "1.38.0", "bioc": "3.23" } ], "_topics": [ "immunooncology", "sequencing", "microbiome", "metagenomics", "software" ], "_stars": 19, "_contributors": [ { "user": "jsilve24", "count": 122, "uuid": 452422 }, { "user": "nturaga", "count": 14, "uuid": 2746443 }, { "user": "jwokaty", "count": 14, "uuid": 1744257 }, { "user": "antagomir", "count": 12, "uuid": 1228382 }, { "user": "hpages", "count": 2, "uuid": 8810451 }, { "user": "vobencha", "count": 2, "uuid": 2466173 }, { "user": "kayla-morrell", "count": 1, "uuid": 32339524 }, { "user": "link-ny", "count": 1, "uuid": 4392950 }, { "user": "rabdill", "count": 1, "uuid": 6011419 }, { "user": "johnchase", "count": 1, "uuid": 2243771 } ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "followers": 451, "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_mentions": 4, "_devurl": "https://github.com/jsilve24/philr", "_searchresults": 132, "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/NEWS.html", "extra/NEWS.txt", "extra/philr.html", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_homeurl": "https://github.com/jsilve24/philr", "_realowner": "bioc", "_cranurl": false, "_exports": [ "annotate_balance", "buildilrBasep", "calculate.blw", "clrp", "clrpInv", "convert_to_long", "ilrp", "ilrpInv", "mean_dist_to_tips", "miniclo", "name.balance", "name.to.nn", "named_rtree", "nn.to.name", "philr", "philrInv", "phylo2sbp", "shiftp", "shiftpInv" ], "_help": [ { "page": "annotate_balance", "title": "annotate_balance", "topics": [ "annotate_balance" ] }, { "page": "buildilrBasep", "title": "Weighted ILR Contrast Matrix", "topics": [ "buildilrBasep" ] }, { "page": "calculate.blw", "title": "Calculate Branch Length Weightings for ILR Coordinates", "topics": [ "calc.blw", "calculate.blw" ] }, { "page": "weighted_clr", "title": "Weighted CLR Transform", "topics": [ "clrp", "clrpInv" ] }, { "page": "convert_to_long", "title": "Converts wide format ILR transformed data to long format", "topics": [ "convert_to_long" ] }, { "page": "g.colMeans", "title": "Geometric Means of Columns", "topics": [ "g.colMeans" ] }, { "page": "g.rowMeans", "title": "Weighted Geometric Means of Rows", "topics": [ "g.rowMeans" ] }, { "page": "weighted_ilr", "title": "Weighted ILR Transform", "topics": [ "ilrp", "ilrpInv" ] }, { "page": "mean_dist_to_tips", "title": "Mean distance from internal nodes to descendant tips", "topics": [ "mean_dist_to_tips" ] }, { "page": "miniclo", "title": "miniclo", "topics": [ "miniclo" ] }, { "page": "name_nodenumber_conversion", "title": "Convert between node/tip labels and integer node numbers", "topics": [ "name.to.nn", "name_nodenumber_conversion", "nn.to.name" ] }, { "page": "name.balance", "title": "Name a balance (coordinate) based on taxonomy", "topics": [ "name.balance" ] }, { "page": "named_rtree", "title": "Generate random tree with named internal nodes", "topics": [ "named_rtree" ] }, { "page": "philr", "title": "Data transformation and driver of PhILR.", "topics": [ "build.phylo.ilr", "philr" ] }, { "page": "philrInv", "title": "Inverse of PhILR Transform", "topics": [ "philrInv" ] }, { "page": "phylo2sbp", "title": "Create Sequential Binary Partition from Phylogenetic Tree", "topics": [ "phylo2sbp" ] }, { "page": "shift", "title": "Shift data to origin given by p", "topics": [ "shift", "shiftp", "shiftpInv" ] } ], "_readme": "https://github.com/bioc/philr/raw/HEAD/README.md", "_rundeps": [ "ape", "aplot", "base64enc", "bslib", "cachem", "cli", "cpp11", "digest", "dplyr", "evaluate", "farver", "fastmap", "fastmatch", "fontawesome", "fontBitstreamVera", "fontLiberation", "fontquiver", "fs", "gdtools", "generics", "ggfun", "ggiraph", "ggplot2", "ggplotify", "ggtree", "glue", "gridGraphics", "gtable", "highr", "htmltools", "htmlwidgets", "igraph", "isoband", "jquerylib", "jsonlite", "knitr", "labeling", "lattice", "lazyeval", "lifecycle", "magrittr", "MASS", "Matrix", "memoise", "mime", "nlme", "patchwork", "phangorn", "pillar", "pkgconfig", "purrr", "quadprog", "R6", "rappdirs", "RColorBrewer", "Rcpp", "rlang", "rmarkdown", "S7", "sass", "scales", "stringi", "stringr", "systemfonts", "tibble", "tidyr", "tidyselect", "tidytree", "tinytex", "treeio", "utf8", "vctrs", "viridisLite", "withr", "xfun", "yaml", "yulab.utils" ], "_vignettes": [ { "source": "philr-intro.Rmd", "filename": "philr-intro.html", "title": "Introduction to PhILR", "author": "Justin Silverman", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Overview of PhILR Analysis", "Loading and Preprocessing Dataset", "Data preparation: TreeSE", "Filter Extremely Low-Abundance OTUs", "Process Phylogenetic Tree", "Investigate Dataset Components", "Transform Data using PhILR", "Ordination in PhILR Space", "Visualization with TreeSE", "Identify Balances that Distinguish Human/Non-Human", "Name Balances", "Visualize Results", "Use Balances for Dimension Reduction", "Package versions", "References" ], "created": "2016-07-22 20:05:23", "modified": "2026-04-01 13:17:54", "commits": 13 } ], "_score": 7.955630032925966, "_indexed": true, "_nocasepkg": "philr", "_universes": [ "bioc", "jsilve24" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.39.0", "date": "2026-07-26T06:26:05.000Z", "distro": "resolute", "commit": "cd369368edb6ca6f5a32faf60cb645605c6af190", "fileid": "https://r2.ropensci.org/9ae8efec0e6b6f9ee2663f4742bfbe0889616b03aec36e6458f0a68402a1ecc2", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/30190780554" }, { "r": "4.6.1", "os": "linux", "version": "1.39.0", "date": "2026-07-26T06:26:10.000Z", "distro": "resolute", "commit": "cd369368edb6ca6f5a32faf60cb645605c6af190", "fileid": "https://r2.ropensci.org/8a17ad9f097c46acefbb92f9e4391330941edff18858445325f550719e25a5c1", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/30190780554" }, { "r": "4.5.3", "os": "mac", "version": "1.39.0", "date": "2026-07-26T06:23:32.000Z", "commit": "cd369368edb6ca6f5a32faf60cb645605c6af190", "fileid": "https://r2.ropensci.org/b17bad18160171e23da7783d5da179ff51a81f67f16318ebc8a2e5124fdd35fc", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/30190780554" }, { "r": "4.6.1", "os": "mac", "version": "1.39.0", "date": "2026-07-26T06:23:31.000Z", "commit": "cd369368edb6ca6f5a32faf60cb645605c6af190", "fileid": "https://r2.ropensci.org/65762ba88dcd64c9ce76e919ced5416b6f6e1d54ea41e810b0ba363796087be8", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/30190780554" }, { "r": "4.6.0", "os": "wasm", "version": "1.39.0", "date": "2026-07-26T06:25:28.000Z", "commit": "cd369368edb6ca6f5a32faf60cb645605c6af190", "fileid": "https://r2.ropensci.org/b0019b79f80ea48ae1ce0047ee9feabc3a9f5df97b2744770e48fc03e2cfd0ba", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/30190780554" }, { "r": "4.7.0", "os": "win", "version": "1.39.0", "date": "2026-07-26T06:23:31.000Z", "commit": "cd369368edb6ca6f5a32faf60cb645605c6af190", "fileid": "https://r2.ropensci.org/3f04bf5a59fcc04bd4a03b5f0e32647bbdd60414d45dbebb8d869c3dfb7fb1ce", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/30190780554" }, { "r": "4.5.3", "os": "win", "version": "1.39.0", "date": "2026-07-26T06:23:56.000Z", "commit": "cd369368edb6ca6f5a32faf60cb645605c6af190", "fileid": "https://r2.ropensci.org/d7ece1990a2a97c0fb03336045f903f2b146086768f6fb7e438470c001e39895", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/30190780554" }, { "r": "4.6.1", "os": "win", "version": "1.39.0", "date": "2026-07-26T06:23:17.000Z", "commit": "cd369368edb6ca6f5a32faf60cb645605c6af190", "fileid": "https://r2.ropensci.org/64d24cdafc86ef7ae86939c61e8e64457de5e5d92eb7e5db8fadbbeaa2b86a38", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/30190780554" } ] }