{ "_id": "6a1c7af11d7bb097a0a31b42", "Type": "Package", "Package": "chromatographR", "Title": "Chromatographic Data Analysis Toolset", "Version": "0.7.5.9000", "Authors@R": "c(\nperson(\"Ethan\", \"Bass\", , \"ethanbass@gmail.com\", role = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0002-6175-6739\")),\nperson(c(\"Hans\",\"W\"), \"Borchers\", role = c(\"ctb\", \"cph\"),\ncomment = c(\"Author of savgol and pinv functions bundled from pracma\"))\n)", "Maintainer": "Ethan Bass ", "Description": "Tools for high-throughput analysis of HPLC-DAD/UV\nchromatograms (or similar data). Includes functions for\npreprocessing, alignment, peak-finding and fitting, peak-table\nconstruction, data-visualization, etc. Preprocessing and\npeak-table construction follow the rough formula laid out in\n'alsace' (Wehrens, R., Bloemberg, T.G., and Eilers P.H.C.,\n2015. . Alignment of\nchromatograms is available using parametric time warping (as\nimplemented in the 'ptw' package) (Wehrens, R., Bloemberg,\nT.G., and Eilers P.H.C. 2015.\n) or variable penalty\ndynamic time warping (as implemented in 'VPdtw') (Clifford, D.,\n& Stone, G. 2012. ). Peak-finding\nuses the algorithm by Tom O'Haver\n.\nPeaks are then fitted to a gaussian or exponential-gaussian\nhybrid peak shape using non-linear least squares (Lan, K. &\nJorgenson, J. W. 2001. ).\nSee the vignette for more details and suggested workflow.", "License": "GPL (>= 2)", "URL": "https://ethanbass.github.io/chromatographR/,\nhttps://github.com/ethanbass/chromatographR/", "BugReports": "https://github.com/ethanbass/chromatographR/issues/", "VignetteBuilder": "knitr", "Config/testthat/edition": "3", "Config/Needs/website": "ggordiplots, rdryad, vegan, quarto", "Encoding": "UTF-8", "Language": "en-US", "LazyData": "true", "LazyDataCompression": "xz", "RoxygenNote": "7.3.3", "Config/pak/sysreqs": "cmake make libicu-dev libpng-dev libuv1-dev\nlibxml2-dev python3", "Repository": "https://ethanbass.r-universe.dev", "Date/Publication": "2026-05-31 17:23:04 UTC", "RemoteUrl": "https://github.com/ethanbass/chromatographR", "RemoteRef": "HEAD", "RemoteSha": "4d916a3e012cd16c4bf6f4d58b34155d42706401", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-31 18:11:41 UTC", "User": "root" }, "Author": "Ethan Bass [aut, cre] (ORCID: ),\nHans W Borchers [ctb, cph] (Author of savgol and pinv functions bundled\nfrom pracma)", "MD5sum": "57c7541304f7fbab4d8281fb533585a4", "_user": "ethanbass", "_type": "src", "_file": "chromatographR_0.7.5.9000.tar.gz", "_fileid": "32291f9dd6d4564fb9571d0b7eabfa2a38e6f01d2faad0127ebc5003d79393c6", "_filesize": 4776436, "_sha256": "32291f9dd6d4564fb9571d0b7eabfa2a38e6f01d2faad0127ebc5003d79393c6", "_created": "2026-05-31T18:11:41.000Z", "_published": "2026-05-31T18:16:17.884Z", "_distro": "noble", "_jobs": [ { "job": 78746494330, "time": 235, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7318963577" }, { "job": 78746494348, "time": 200, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7318959761" }, { "job": 78746494318, "time": 132, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7318952861" }, { "job": 78746494335, "time": 113, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7318951106" }, { "job": 78746251376, "time": 237, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7318939474" }, { "job": 78746494344, "time": 131, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7318952896" }, { "job": 78746494338, "time": 142, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "7318954058" }, { "job": 78746494342, "time": 169, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "7318957543" }, { "job": 78746494332, "time": 162, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "7318956012" } ], "_buildurl": "https://github.com/r-universe/ethanbass/actions/runs/26720379436", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/ethanbass/chromatographR", "_commit": { "id": "4d916a3e012cd16c4bf6f4d58b34155d42706401", "author": "Ethan Bass ", "committer": "GitHub ", "message": "Update citation year to 2026 in CITATION file", "time": 1780248184 }, "_maintainer": { "name": "Ethan Bass", "email": "ethanbass@gmail.com", "login": "ethanbass", "mastodon": "@ethanbass@ecoevo.social", "bluesky": "@ethanbass.bsky.social", "orcid": "0000-0002-6175-6739", "description": "I am an evolutionary ecologist studying plant interactions & their chemical mechanisms. I also do some scientific software development in R.", "uuid": 15876283 }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.1.0", "role": "Depends" }, { "package": "caTools", "role": "Imports" }, { "package": "chromConverter", "role": "Imports" }, { "package": "dynamicTreeCut", "role": "Imports" }, { "package": "fastcluster", "role": "Imports" }, { "package": "Formula", "role": "Imports" }, { "package": "fs", "role": "Imports" }, { "package": "graphics", "role": "Imports" }, { "package": "grDevices", "role": "Imports" }, { "package": "lattice", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "minpack.lm", "role": "Imports" }, { "package": "parallel", "role": "Imports" }, { "package": "ptw", "role": "Imports" }, { "package": "purrr", "role": "Imports" }, { "package": "scales", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "VPdtw", "role": "Imports" }, { "package": "cowplot", "role": "Suggests" }, { "package": "ggplot2", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "openxlsx", "role": "Suggests" }, { "package": "pbapply", "role": "Suggests" }, { "package": "plotly", "role": "Suggests" }, { "package": "pvclust", "role": "Suggests" }, { "package": "reticulate", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "rsvg", "role": "Suggests" }, { "package": "spelling", "role": "Suggests" }, { "package": "testthat", "version": ">= 3.0.0", "role": "Suggests" }, { "package": "vdiffr", "role": "Suggests" } ], "_owner": "ethanbass", "_selfowned": true, "_usedby": 1, "_updates": [ { "week": "2025-22", "n": 14 }, { "week": "2025-23", "n": 9 }, { "week": "2025-26", "n": 2 }, { "week": "2025-29", "n": 2 }, { "week": "2025-31", "n": 1 }, { "week": "2025-34", "n": 4 }, { "week": "2025-35", "n": 8 }, { "week": "2025-36", "n": 1 }, { "week": "2026-03", "n": 1 }, { "week": "2026-06", "n": 12 }, { "week": "2026-07", "n": 6 }, { "week": "2026-08", "n": 5 }, { "week": "2026-18", "n": 1 }, { "week": "2026-22", "n": 3 } ], "_tags": [ { "name": "v0.7.4", "date": "2025-06-03" }, { "name": "v0.7.5", "date": "2025-08-27" } ], "_topics": [ "bioinformatics", "cheminformatics", "chromatography", "gc-fid", "hplc", "hplc-dad", "hplc-pda", "hplv-uv", "metabolomics", "open-data", "open-science", "reproducibility", "reproducible-research" ], "_stars": 24, "_contributors": [ { "user": "ethanbass", "count": 807, "uuid": 15876283 }, { "user": "rwehrens", "count": 27, "uuid": 5754219 }, { "user": "dtenenba", "count": 10, "uuid": 2286826 }, { "user": "hpages", "count": 2, "uuid": 8810451 }, { "user": "nturaga", "count": 2, "uuid": 2746443 }, { "user": "vobencha", "count": 2, "uuid": 2466173 } ], "_userbio": { "uuid": 15876283, "type": "user", "name": "Ethan Bass", "description": "I am an evolutionary ecologist studying plant interactions & their chemical mechanisms. I also do some scientific software development in R." }, "_downloads": { "count": 6, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/chromatographR" }, "_devurl": "https://github.com/ethanbass/chromatographr", "_pkgdown": "https://ethanbass.github.io/chromatographR/", "_searchresults": 9, "_rbuild": "4.6.0", "_assets": [ "extra/chromatographR.html", "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_cranurl": false, "_releases": [ { "version": "0.4.1", "date": "2022-05-19" }, { "version": "0.4.3", "date": "2022-08-22" }, { "version": "0.4.4", "date": "2022-08-24" } ], "_exports": [ "attach_metadata", "attach_ref_spectra", "cluster_spectra", "combine_peaks", "correct_peaks", "correct_rt", "filter_peaks", "filter_peaktable", "find_peaks", "fit_peaks", "get_agilent_threshold", "get_lambdas", "get_peaks", "get_peaktable", "get_purity", "get_times", "merge_peaks", "mirror_plot", "normalize_data", "plot_all_spectra", "plot_chroms", "plot_chroms_heatmap", "plot_spectrum", "preprocess", "read_chroms", "reshape_chroms", "reshape_peaktable", "scan_chrom", "trim_peak", "write_peaktable" ], "_datasets": [ { "name": "pk_tab", "title": "Goldenrod peak table", "object": "pk_tab", "class": [ "peak_table" ], "fields": [], "table": false, "tojson": false }, { "name": "Sa", "title": "Raw goldenrod root chromatograms", "object": "Sa", "class": [ "list" ], "fields": [], "table": true, "tojson": true }, { "name": "Sa_pr", "title": "Preprocessed goldenrod root chromatograms", "object": "Sa_pr", "class": [ "list" ], "fields": [], "table": true, "tojson": true }, { "name": "Sa_warp", "title": "Warped goldenrod root chromatograms.", "object": "Sa_warp", "class": [ "list" ], "fields": [], "table": true, "tojson": true } ], "_help": [ { "page": "chromatographR-package", "title": "chromatographR", "topics": [ "chromatographR-package", "chromatographR" ] }, { "page": "attach_metadata", "title": "Attach experimental metadata", "topics": [ "attach_metadata" ] }, { "page": "attach_ref_spectra", "title": "Attach reference spectra", "topics": [ "attach_ref_spectra" ] }, { "page": "boxplot.peak_table", "title": "Make boxplot from peak table.", "concept": [ "visualization functions" ], "topics": [ "boxplot.peak_table" ] }, { "page": "cluster_spectra", "title": "Cluster spectra", "topics": [ "cluster_spectra" ] }, { "page": "combine_peaks", "title": "Combine peaks", "concept": [ "utility functions" ], "topics": [ "combine_peaks" ] }, { "page": "correct_peaks", "title": "Correct peak positions according to a PTW warping model", "topics": [ "correct_peaks" ] }, { "page": "correct_rt", "title": "Correct retention time", "topics": [ "correct_rt" ] }, { "page": "filter_peaks", "title": "Filter peak lists", "topics": [ "filter_peaks" ] }, { "page": "filter_peaktable", "title": "Filter peak table", "topics": [ "filter_peaktable" ] }, { "page": "get_lambdas", "title": "Get lambdas", "concept": [ "utility functions" ], "topics": [ "get_lambdas" ] }, { "page": "get_peaks", "title": "Get peak list.", "topics": [ "get_peaks" ] }, { "page": "get_peaktable", "title": "Converts peak list into an ordered peak table.", "topics": [ "get_peaktable" ] }, { "page": "get_times", "title": "Get retention times", "concept": [ "utility functions" ], "topics": [ "get_times" ] }, { "page": "merge_peaks", "title": "Merge split peaks", "concept": [ "utility functions" ], "topics": [ "merge_peaks" ] }, { "page": "mirror_plot", "title": "Make mirror plot from peak table.", "concept": [ "visualization functions" ], "topics": [ "mirror_plot" ] }, { "page": "normalize_data", "title": "Normalize peak table or chromatograms", "topics": [ "normalize_data" ] }, { "page": "peak_table-class", "title": "Peak Table Object", "topics": [ "peak_table", "peak_table-class" ] }, { "page": "pk_tab", "title": "Goldenrod peak table", "concept": [ "data objects" ], "topics": [ "pk_tab" ] }, { "page": "plot_all_spectra", "title": "Plot all spectra for chosen peak.", "concept": [ "visualization functions" ], "topics": [ "plot_all_spectra" ] }, { "page": "plot_chroms", "title": "Plot traces from list of chromatograms.", "concept": [ "visualization functions" ], "topics": [ "plot_chroms" ] }, { "page": "plot_chroms_heatmap", "title": "Plot chromatograms as heatmap", "concept": [ "visualization functions" ], "topics": [ "plot_chroms_heatmap" ] }, { "page": "plot_spectrum", "title": "Plot spectrum from peak table", "concept": [ "visualization functions" ], "topics": [ "plot_spectrum" ] }, { "page": "plot.peak_list", "title": "Plot fitted peak shapes.", "concept": [ "visualization functions" ], "topics": [ "plot.peak_list" ] }, { "page": "plot.peak_table", "title": "Plot spectrum from peak table", "concept": [ "visualization functions" ], "topics": [ "plot.peak_table" ] }, { "page": "plot.ptw_list", "title": "Plot PTW alignments", "topics": [ "plot.ptw_list" ] }, { "page": "preprocess", "title": "Preprocess time/wavelength data", "topics": [ "preprocess" ] }, { "page": "reshape_chroms", "title": "Reshape chromatograms", "concept": [ "utility functions" ], "topics": [ "reshape_chroms" ] }, { "page": "reshape_peaktable", "title": "Reshape peaktable", "concept": [ "utility functions" ], "topics": [ "reshape_peaktable" ] }, { "page": "Sa", "title": "Raw goldenrod root chromatograms", "concept": [ "data objects" ], "topics": [ "Sa" ] }, { "page": "Sa_pr", "title": "Preprocessed goldenrod root chromatograms", "concept": [ "data objects" ], "topics": [ "Sa_pr" ] }, { "page": "Sa_warp", "title": "Warped goldenrod root chromatograms.", "concept": [ "data objects" ], "topics": [ "Sa_warp" ] }, { "page": "scan_chrom", "title": "Plot spectra by clicking on the chromatogram.", "concept": [ "visualization functions" ], "topics": [ "scan_chrom" ] }, { "page": "write_peaktable", "title": "Export peak table", "topics": [ "write_peaktable" ] } ], "_pkglogo": "https://github.com/ethanbass/chromatographR/raw/HEAD/man/figures/logo.png", "_readme": "https://github.com/ethanbass/chromatographR/raw/HEAD/README.md", "_rundeps": [ "base64enc", "bit", "bit64", "bitops", "caTools", "cellranger", "chromConverter", "cli", "cpp11", "crayon", "data.table", "digest", "dplyr", "dynamicTreeCut", "farver", "fastcluster", "Formula", "fs", "generics", "glue", "here", "hms", "jsonlite", "labeling", "lattice", "lifecycle", "magrittr", "Matrix", "minpack.lm", "pillar", "pkgconfig", "png", "prettyunits", "progress", "ptw", "purrr", "R6", "RaMS", "rappdirs", "RColorBrewer", "Rcpp", "RcppArmadillo", "RcppDE", "RcppTOML", "readxl", "rematch", "reticulate", "rlang", "rprojroot", "scales", "stringi", "stringr", "tibble", "tidyr", "tidyselect", "utf8", "vctrs", "viridisLite", "VPdtw", "withr", "xml2" ], "_vignettes": [ { "source": "chromatographR.Rmd", "filename": "chromatographR.html", "title": "chromatographR: An introduction to HPLC-DAD analysis", "author": "Ethan Bass", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Workflow", "Loading data", "Example data", "Pre-processing data", "Alignment", "Parametric time warping", "Variable penalty dynamic time warping", "Peak detection and integration", "Filtering", "Visualization", "Peak table assembly", "Further analysis and data-visualization", "Attaching metadata", "Attaching reference spectra", "Data visualization", "Mirror plot", "Plotting spectra", "Plot peak table function", "References", "Session Information" ], "created": "2021-10-06 15:37:44", "modified": "2026-02-15 20:36:01", "commits": 64 } ], "_score": 6.401400540781544, "_indexed": true, "_nocasepkg": "chromatographr", "_universes": [ "ethanbass" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "0.7.5.9000", "date": "2026-05-31T18:14:54.000Z", "distro": "noble", "commit": "4d916a3e012cd16c4bf6f4d58b34155d42706401", "fileid": "a6731e35e2b7ce858d365ecc96fe79b9d67f8baf507b7d111ebc24505eb27ccf", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/ethanbass/actions/runs/26720379436" }, { "r": "4.6.0", "os": "linux", "version": "0.7.5.9000", "date": "2026-05-31T18:14:29.000Z", "distro": "noble", "commit": "4d916a3e012cd16c4bf6f4d58b34155d42706401", "fileid": "209c528859534efa41c873d7293beeaec0b1341bfaa11a55fdd1bf5710c80aa0", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/ethanbass/actions/runs/26720379436" }, { "r": "4.5.3", "os": "mac", "version": "0.7.5.9000", "date": "2026-05-31T18:13:32.000Z", "commit": "4d916a3e012cd16c4bf6f4d58b34155d42706401", "fileid": "0176efac567778d20dd88b09cfdd0771cfccea70698b801932fcd5c090a14cdf", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/ethanbass/actions/runs/26720379436" }, { "r": "4.6.0", "os": "mac", "version": "0.7.5.9000", "date": "2026-05-31T18:13:22.000Z", "commit": "4d916a3e012cd16c4bf6f4d58b34155d42706401", "fileid": "24f5419d04e5a814cb3e543b6c6511440353a2c1bf55fdbf7643f82fbd90f199", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/ethanbass/actions/runs/26720379436" }, { "r": "4.6.0", "os": "wasm", "version": "0.7.5.9000", "date": "2026-05-31T18:14:17.000Z", "commit": "4d916a3e012cd16c4bf6f4d58b34155d42706401", "fileid": "570ebb01773ef9d806818d0cc738dec1788de22f8350a2858f3828fab8902ff1", "status": "success", "buildurl": "https://github.com/r-universe/ethanbass/actions/runs/26720379436" }, { "r": "4.7.0", "os": "win", "version": "0.7.5.9000", "date": "2026-05-31T18:13:28.000Z", "commit": "4d916a3e012cd16c4bf6f4d58b34155d42706401", "fileid": "208c1a29c6acf4aedb0ee209c92053c3a07637d08fcd246597d3532b471ed6be", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/ethanbass/actions/runs/26720379436" }, { "r": "4.5.3", "os": "win", "version": "0.7.5.9000", "date": "2026-05-31T18:13:41.000Z", "commit": "4d916a3e012cd16c4bf6f4d58b34155d42706401", "fileid": "ccbef17428c761e55960b60471aa514be9eb210747a4ad253c7e4b277bab21b8", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/ethanbass/actions/runs/26720379436" }, { "r": "4.6.0", "os": "win", "version": "0.7.5.9000", "date": "2026-05-31T18:13:27.000Z", "commit": "4d916a3e012cd16c4bf6f4d58b34155d42706401", "fileid": "a52ba1a591a28b2f854299d654edb7278bfd22ae1c270de3da4fd3062a780271", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/ethanbass/actions/runs/26720379436" } ] }