{ "_id": "6a3245c53efcd9bda4378d80", "Package": "combi", "Type": "Package", "Title": "Compositional omics model based visual integration", "Version": "1.24.0", "Authors@R": "c(person(given = \"Stijn\", family = \"Hawinkel\",\nemail = \"stijn.hawinkel@psb.ugent.be\",\nrole=c(\"cre\", \"aut\"), comment = c(ORCID = \"0000-0002-4501-5180\")))", "Description": "This explorative ordination method combines\nquasi-likelihood estimation, compositional regression models\nand latent variable models for integrative visualization of\nseveral omics datasets. Both unconstrained and constrained\nintegration are available. The results are shown as\ninterpretable, compositional multiplots.", "License": "GPL-2", "Encoding": "UTF-8", "RoxygenNote": "7.2.3", "VignetteBuilder": "knitr", "biocViews": "Metagenomics, DimensionReduction, Microbiome, Visualization,\nMetabolomics", "BugReports": "https://github.com/CenterForStatistics-UGent/combi/issues", "Config/pak/sysreqs": "libglpk-dev libicu-dev libxml2-dev zlib1g-dev", "Repository": "https://bioc-release.r-universe.dev", "Date/Publication": "2026-04-28 12:52:10 UTC", "RemoteUrl": "https://github.com/bioc/combi", "RemoteRef": "RELEASE_3_23", "RemoteSha": "d3e31d51662fe6a0cf0259dbf69ed306923935ae", "NeedsCompilation": "no", "Packaged": { "Date": "2026-06-17 06:48:12 UTC", "User": "root" }, "Author": "Stijn Hawinkel [cre, aut] (ORCID:\n)", "Maintainer": "Stijn Hawinkel ", "MD5sum": "8ee199f905c5036981836253c8f7b990", "_user": "bioc-release", "_type": "src", "_file": "combi_1.24.0.tar.gz", "_fileid": "49426daeaea193d4db53871ae629970f2abe097e349bcc7de7340fcc4f25c03f", "_filesize": 2219994, "_sha256": "49426daeaea193d4db53871ae629970f2abe097e349bcc7de7340fcc4f25c03f", "_created": "2026-06-17T06:48:12.000Z", "_published": "2026-06-17T06:59:17.885Z", "_jobs": [ { "job": 81835689215, "time": 232, "config": "bioc-checks", "r": "4.6.0", "check": "NOTE", "artifact": "7688078107" }, { "job": 81835689200, "time": 515, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "7688162163" }, { "job": 81835689232, "time": 449, "config": "linux-release-x86_64", "r": "4.6.0", "check": "NOTE", "artifact": "7688144281" }, { "job": 81835689242, "time": 381, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "7688122185" }, { "job": 81835689191, "time": 276, "config": "macos-release-arm64", "r": "4.6.0", "check": "NOTE", "artifact": "7688090585" }, { "job": 81834749484, "time": 396, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7688006765" }, { "job": 81835689168, "time": 145, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7688053638" }, { "job": 81835689298, "time": 379, "config": "windows-devel", "r": "4.7.0", "check": "NOTE", "artifact": "7688121812" }, { "job": 81835689194, "time": 432, "config": "windows-oldrel", "r": "4.5.3", "check": "NOTE", "artifact": "7688136974" }, { "job": 81835689184, "time": 440, "config": "windows-release", "r": "4.6.0", "check": "NOTE", "artifact": "7688139601" } ], "_bioccheck": { "error": 0, "warning": 0, "note": 12 }, "_buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27670875018", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/combi", "_commit": { "id": "d3e31d51662fe6a0cf0259dbf69ed306923935ae", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to even y prior to creation of RELEASE_3_23 branch\n", "time": 1777380730 }, "_maintainer": { "name": "Stijn Hawinkel", "email": "stijn.hawinkel@psb.ugent.be", "orcid": "0000-0002-4501-5180" }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.0", "role": "Depends" }, { "package": "DBI", "role": "Depends" }, { "package": "ggplot2", "role": "Imports" }, { "package": "nleqslv", "role": "Imports" }, { "package": "phyloseq", "role": "Imports" }, { "package": "tensor", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "limma", "role": "Imports" }, { "package": "Matrix", "version": ">= 1.6.0", "role": "Imports" }, { "package": "BB", "role": "Imports" }, { "package": "reshape2", "role": "Imports" }, { "package": "alabama", "role": "Imports" }, { "package": "cobs", "role": "Imports" }, { "package": "Biobase", "role": "Imports" }, { "package": "vegan", "role": "Imports" }, { "package": "grDevices", "role": "Imports" }, { "package": "graphics", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "SummarizedExperiment", "role": "Imports" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "testthat", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": false, "_usedby": 0, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 1 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.25.0", "bioc": "3.24" }, { "branch": "release", "version": "1.24.0", "bioc": "3.23" } ], "_topics": [ "metagenomics", "dimensionreduction", "microbiome", "visualization", "metabolomics" ], "_stars": 1, "_contributors": [ { "user": "sthawinke", "count": 147, "uuid": 22496974 }, { "user": "nturaga", "count": 10, "uuid": 2746443 }, { "user": "jwokaty", "count": 4, "uuid": 1744257 }, { "user": "hpages", "count": 1, "uuid": 8810451 } ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "followers": 440, "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_mentions": 1, "_devurl": "https://github.com/centerforstatistics-ugent/combi", "_searchresults": 7, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/combi.html", "extra/contents.json", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_homeurl": "https://github.com/centerforstatistics-ugent/combi", "_realowner": "bioc", "_cranurl": false, "_exports": [ "addLink", "checkMeanVarTrend", "combi", "convPlot", "extractCoords", "extractData", "inflPlot" ], "_datasets": [ { "name": "zhangMetabo", "title": "Metabolomes of mice that underwent Pulsed Antibiotic Treatment (PAT) and controls", "object": "Zhang", "file": "Zhang.RData", "class": [ "SummarizedExperiment" ], "fields": [], "table": false, "tojson": false }, { "name": "zhangMetavars", "title": "Baseline sample variables of PAT and control mice", "object": "Zhang", "file": "Zhang.RData", "class": [ "data.frame" ], "fields": [ "Sex", "Time", "ABX", "Sample.Weight" ], "rows": 42, "table": true, "tojson": true }, { "name": "zhangMicrobio", "title": "Microbiomes of mice that underwent Pulsed Antibiotic Treatment (PAT) and controls", "object": "Zhang", "file": "Zhang.RData", "class": [ "phyloseq" ], "fields": [], "table": false, "tojson": false } ], "_help": [ { "page": "addLink", "title": "Add a link on a compositional plot", "topics": [ "addLink" ] }, { "page": "arrayMult", "title": "Array multiplication", "topics": [ "arrayMult" ] }, { "page": "buildCentMat", "title": "A function to build a centering matrix based on a dataframe", "topics": [ "buildCentMat" ] }, { "page": "buildCompMat", "title": "Build the composition matrix for a certain dimension m dimensions", "topics": [ "buildCompMat" ] }, { "page": "buildConfMat", "title": "Build confounder design matrices with and without intercepts", "topics": [ "buildConfMat" ] }, { "page": "buildCovMat", "title": "A function to build the covariate matrix of the constraints", "topics": [ "buildCovMat" ] }, { "page": "buildEmptyJac", "title": "Prepare an empty Jacobian matrix, with useful entries prefilled. In case of distribution \"gaussian\", it returns the lhs matrix of the linear system for finding the feature paramters", "topics": [ "buildEmptyJac" ] }, { "page": "buildMarginalOffset", "title": "Build an offset matrix from an marginal model object", "topics": [ "buildMarginalOffset" ] }, { "page": "buildMu", "title": "A function to build the mu matrix", "topics": [ "buildMu" ] }, { "page": "buildMuMargins", "title": "Build the marginal mu matrix", "topics": [ "buildMuMargins" ] }, { "page": "buildOffsetModel", "title": "Build a marginal offset matrix given a model", "topics": [ "buildOffsetModel" ] }, { "page": "checkAlias", "title": "Check for alias structures in a dataframe, and throw an error when one is found", "topics": [ "checkAlias" ] }, { "page": "checkMeanVarTrend", "title": "Quickly check if the mean variance trend provides a good fit", "topics": [ "checkMeanVarTrend" ] }, { "page": "checkMonotonicity", "title": "Check for monotonicity in compositional datasets fro given dimensions", "topics": [ "checkMonotonicity" ] }, { "page": "combi", "title": "Perform model-based data integration", "topics": [ "combi" ] }, { "page": "convPlot", "title": "Plot the convegrence of the different parameter estimates in a line plot", "topics": [ "convPlot" ] }, { "page": "deriv2LagrangianFeatures", "title": "The score function to estimate the latent variables", "topics": [ "deriv2LagrangianFeatures" ] }, { "page": "deriv2LagrangianLatentVars", "title": "The jacobian function to estimate the latent variables", "topics": [ "deriv2LagrangianLatentVars" ] }, { "page": "deriv2LagrangianLatentVarsConstr", "title": "The score function to estimate the latent variables", "topics": [ "deriv2LagrangianLatentVarsConstr" ] }, { "page": "derivLagrangianFeatures", "title": "The score function to estimate the feature parameters", "topics": [ "derivLagrangianFeatures" ] }, { "page": "derivLagrangianLatentVars", "title": "The score function to estimate the latent variables", "topics": [ "derivLagrangianLatentVars" ] }, { "page": "derivLagrangianLatentVarsConstr", "title": "The score function to estimate the latent variables", "topics": [ "derivLagrangianLatentVarsConstr" ] }, { "page": "estFeatureParameters", "title": "Estimate the feature parameters", "topics": [ "estFeatureParameters" ] }, { "page": "estIndepModel", "title": "Estimate the independence model belonging to one view", "topics": [ "estIndepModel" ] }, { "page": "estLatentVars", "title": "Estimate the latent variables", "topics": [ "estLatentVars" ] }, { "page": "estMeanVarTrend", "title": "Estimate a column-wise mean-variance trend", "topics": [ "estMeanVarTrend" ] }, { "page": "estOff", "title": "Estimate the row/column parameters of the independence model", "topics": [ "estOff" ] }, { "page": "extractCoords", "title": "Extract coordinates from fitted object", "topics": [ "extractCoords" ] }, { "page": "extractData", "title": "Helper function to extract data matrix from phyloseq, expressionset objects etc. Also filers out all zero rows", "topics": [ "extractData" ] }, { "page": "extractMat", "title": "A function to extract a data matrix from a number of objects", "topics": [ "extractMat", "extractMat,ExpressionSet-method", "extractMat,matrix-method", "extractMat,SummarizedExperiment-method" ] }, { "page": "filterConfounders", "title": "Filter out the effect of known confounders", "topics": [ "filterConfounders" ] }, { "page": "getInflLatentVar", "title": "Extract the influence on the estimation of the latent variable", "topics": [ "getInflLatentVar" ] }, { "page": "gramSchmidtOrth", "title": "Gram schimdt orhtogonalize a with respect to b, and normalize", "topics": [ "gramSchmidtOrth" ] }, { "page": "indentPlot", "title": "Functions to indent the plot to include the entire labels", "topics": [ "indentPlot" ] }, { "page": "inflPlot", "title": "A ggplot line plot showing the influences", "topics": [ "inflPlot" ] }, { "page": "influence.combi", "title": "Evaluate the influence function", "topics": [ "influence.combi" ] }, { "page": "jacConfounders", "title": "Jacobian when estimating confounder variables", "topics": [ "jacConfounders" ] }, { "page": "jacConfoundersComp", "title": "Jacobian for conditioning under compositionality", "topics": [ "jacConfoundersComp" ] }, { "page": "jacFeatures", "title": "Evaluate the jacobian for estimating the feature parameters for one view", "topics": [ "jacFeatures" ] }, { "page": "jacLatentVars", "title": "Evaluate the jacobian for estimating the latent variable for one view", "topics": [ "jacLatentVars" ] }, { "page": "jacLatentVarsConstr", "title": "Evaluate the jacobian for estimating the latent variable for one view for constrained ordination", "topics": [ "jacLatentVarsConstr" ] }, { "page": "plot.combi", "title": "Make multiplots of the data integration object", "topics": [ "plot.combi" ] }, { "page": "polyHorner", "title": "Horner's method to evaluate a polynomial, copied from the polynom package. the most efficient way", "topics": [ "polyHorner" ] }, { "page": "predictSpline", "title": "A custom spline prediction function, extending linearly with a slope such that prediction never drops below first bisectant", "topics": [ "predictSpline" ] }, { "page": "prepareJacMat", "title": "prepare the jacobian matrix", "topics": [ "prepareJacMat" ] }, { "page": "prepareJacMatComp", "title": "prepare the jacobian for the latent variabels compostional", "topics": [ "prepareJacMatComp" ] }, { "page": "prepareScoreMat", "title": "Prepare a helper matrix for score function evaluation under quasi-likelihood", "topics": [ "prepareScoreMat" ] }, { "page": "print.combi", "title": "Print an overview of a fitted combi x", "topics": [ "print.combi" ] }, { "page": "quasiJacIndep", "title": "The jacobian for column offset estimation", "topics": [ "quasiJacIndep" ] }, { "page": "quasiScoreIndep", "title": "Quasi score equations for column offset parameters of sequence count data", "topics": [ "quasiScoreIndep" ] }, { "page": "rowMultiply", "title": "A function to efficiently row multiply a matrix and a vector", "topics": [ "rowMultiply" ] }, { "page": "scaleCoords", "title": "A helper function to rescale coordinates", "topics": [ "scaleCoords" ] }, { "page": "scoreConfounders", "title": "Score functions for confounder variables", "topics": [ "scoreConfounders" ] }, { "page": "scoreConfoundersComp", "title": "Score equations for conditioning under compositionality", "topics": [ "scoreConfoundersComp" ] }, { "page": "scoreFeatureParams", "title": "Evaluate the score functions for the estimation of the feature parameters for a single dataset", "topics": [ "scoreFeatureParams" ] }, { "page": "scoreLatentVars", "title": "Evaluate the score functions for the estimation of the latent variables for a single dataset", "topics": [ "scoreLatentVars" ] }, { "page": "seqM", "title": "A small auxiliary function for the indices of the lagrange multipliers", "topics": [ "seqM" ] }, { "page": "trimOnConfounders", "title": "Trim based on confounders to avoid taxa with only zero counts", "topics": [ "trimOnConfounders" ] }, { "page": "zhangMetabo", "title": "Metabolomes of mice that underwent Pulsed Antibiotic Treatment (PAT) and controls", "topics": [ "zhangMetabo" ] }, { "page": "zhangMetavars", "title": "Baseline sample variables of PAT and control mice", "topics": [ "zhangMetavars" ] }, { "page": "zhangMicrobio", "title": "Microbiomes of mice that underwent Pulsed Antibiotic Treatment (PAT) and controls", "topics": [ "zhangMicrobio" ] } ], "_readme": "https://github.com/bioc/combi/raw/RELEASE_3_23/README.md", "_rundeps": [ "abind", "ade4", "alabama", "ape", "BB", "Biobase", "BiocGenerics", "biomformat", "Biostrings", "cli", "cluster", "cobs", "codetools", "cpp11", "crayon", "data.table", "DBI", "DelayedArray", "digest", "farver", "foreach", "generics", "GenomicRanges", "ggplot2", "glue", "gtable", "igraph", "IRanges", "isoband", "iterators", "jsonlite", "labeling", "lattice", "lifecycle", "limma", "magrittr", "MASS", "Matrix", "MatrixGenerics", "MatrixModels", "matrixStats", "mgcv", "multtest", "nleqslv", "nlme", "numDeriv", "permute", "phyloseq", "pixmap", "pkgconfig", "plyr", "quadprog", "quantreg", "R6", "RColorBrewer", "Rcpp", "RcppArmadillo", "reshape2", "rlang", "S4Arrays", "S4Vectors", "S7", "scales", "Seqinfo", "sp", "SparseArray", "SparseM", "statmod", "stringi", "stringr", "SummarizedExperiment", "survival", "tensor", "vctrs", "vegan", "viridisLite", "withr", "XVector" ], "_vignettes": [ { "source": "combi.Rmd", "filename": "combi.html", "title": "Manual for the combi pacakage", "engine": "knitr::rmarkdown", "headings": [ "combi package: vignette", "Introduction", "Installation", "Unconstrained integration", "Adding projections", "Coordinates", "Constrained integration", "Diagnostics", "FAQ", "Why are not all my samples shown in the constrained ordination?", "The combi function crashes, what should I do", "Session info" ], "created": "2020-03-18 08:44:18", "modified": "2021-11-30 10:34:14", "commits": 9 } ], "_score": 4.477121254719663, "_indexed": false, "_nocasepkg": "combi", "_universes": [ "bioc-release" ], "_indexurl": "https://bioc.r-universe.dev/combi", "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.24.0", "date": "2026-06-17T06:53:33.000Z", "distro": "noble", "commit": "d3e31d51662fe6a0cf0259dbf69ed306923935ae", "fileid": "f4506e344d65ba94b8dd5100b4ba83fecd2b07912a0273eba4deb902842256b7", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27670875018" }, { "r": "4.6.0", "os": "linux", "version": "1.24.0", "date": "2026-06-17T06:53:04.000Z", "distro": "noble", "commit": "d3e31d51662fe6a0cf0259dbf69ed306923935ae", "fileid": "8f04e10edd52d796219d35330554d6477eee48236ecfde88210f070f8c6d4679", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27670875018" }, { "r": "4.5.3", "os": "mac", "version": "1.24.0", "date": "2026-06-17T06:52:23.000Z", "commit": "d3e31d51662fe6a0cf0259dbf69ed306923935ae", "fileid": "d8ec7dc0dcac73ad2f572d6f0bad50fea2bf28ef0b1b114f4d6e9c735ef55fb0", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27670875018" }, { "r": "4.6.0", "os": "mac", "version": "1.24.0", "date": "2026-06-17T06:51:43.000Z", "commit": "d3e31d51662fe6a0cf0259dbf69ed306923935ae", "fileid": "f26c3b4371c834cc6291760652fb86bed896f01a8de795767d31942680e9c011", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27670875018" }, { "r": "4.6.0", "os": "wasm", "version": "1.24.0", "date": "2026-06-17T06:52:49.000Z", "commit": "d3e31d51662fe6a0cf0259dbf69ed306923935ae", "fileid": "1f02cfd8b9bc08895a9e464c1ef10f95b5b20d6097e9dac1315746747cd6efe3", "status": "success", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27670875018" }, { "r": "4.7.0", "os": "win", "version": "1.24.0", "date": "2026-06-17T06:51:25.000Z", "commit": "d3e31d51662fe6a0cf0259dbf69ed306923935ae", "fileid": "28fc6669718dd1874e02940966d6ef2bfdbc578ce40be56798dbed447e217d42", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27670875018" }, { "r": "4.5.3", "os": "win", "version": "1.24.0", "date": "2026-06-17T06:51:26.000Z", "commit": "d3e31d51662fe6a0cf0259dbf69ed306923935ae", "fileid": "3898bc3059c1be7ffe69cf9aa41d7f7276b04c5ab01c37bdf27281027b4fcf76", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27670875018" }, { "r": "4.6.0", "os": "win", "version": "1.24.0", "date": "2026-06-17T06:51:23.000Z", "commit": "d3e31d51662fe6a0cf0259dbf69ed306923935ae", "fileid": "15678fecab25be8e3af8d1ad67fbda3940b0e8b4ab099a683e52b09629c95734", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27670875018" } ] }