Type: Package
Package: chromatographR
Title: Chromatographic Data Analysis Toolkit
Version: 0.9.0
Authors@R: c(
    person("Ethan", "Bass", , "ethanbass@gmail.com", role = c("aut", "cre", "cph"),
           comment = c(ORCID = "0000-0002-6175-6739")),
    person(c("Hans","W"), "Borchers", role = c("ctb", "cph"),
            comment = c("Author of savgol and pinv functions bundled from pracma")),
    person("Ron", "Wehrens", role = c("ctb", "cph"),
           comment = c("Author of code adapted from alsace and ptw"))
    )
Maintainer: Ethan Bass <ethanbass@gmail.com>
Description: Analyzes chromatographic data from high performance liquid
        chromatography with diode-array or ultraviolet detection
        (HPLC-DAD/UV), as well as other detectors, in a high-throughput
        and reproducible workflow. Provides functionality for
        preprocessing, alignment, peak detection, peak model fitting,
        peak table construction, and data visualization. Chromatogram
        alignment is available via parametric time warping (as
        implemented in 'ptw') or variable penalty dynamic time warping
        (as implemented in 'VPdtw'). Peak detection is based on a
        first-derivative zero-crossing algorithm, and peak shapes are
        fitted using non-linear least squares. Underlying methodologies
        are described in: Wehrens et al. (2015)
        <doi:10.1007/s11306-014-0683-5> for preprocessing and peak
        table construction; Eilers (2004) <doi:10.1021/ac034800e> and
        Wehrens et al. (2015) <doi:10.1093/bioinformatics/btv299> for
        parametric time warping; Clifford & Stone (2012)
        <doi:10.18637/jss.v047.i08> for variable penalty dynamic time
        warping; Tom O'Haver
        <https://terpconnect.umd.edu/~toh/spectrum/PeakFindingandMeasurement.htm>
        for peak detection; Lan & Jorgenson (2001)
        <doi:10.1016/S0021-9673(01)00594-5> for exponential-Gaussian
        hybrid fitting; and Naish & Hartwell (1988)
        <doi:10.1007/BF02268168> for bi-exponentially modified Gaussian
        fitting.
License: GPL (>= 2)
URL: https://ethanbass.github.io/chromatographR/,
        https://github.com/ethanbass/chromatographR/
BugReports: https://github.com/ethanbass/chromatographR/issues/
Depends: R (>= 4.1.0)
Imports: caTools, chromConverter, dynamicTreeCut, fastcluster, Formula,
        fs, graphics, grDevices, lattice, methods, minpack.lm,
        parallel, ptw, purrr, scales, stats, tools, utils, VPdtw
Suggests: cowplot, ggplot2, knitr, openxlsx, pbapply, plotly, pvclust,
        reticulate, rmarkdown, rsvg, spelling, testthat (>= 3.0.0),
        vdiffr, withr
VignetteBuilder: knitr
Config/testthat/edition: 3
Config/Needs/website: curl, ggordiplots, vegan, quarto
Encoding: UTF-8
Language: en-US
LazyData: true
LazyDataCompression: xz
Config/roxygen2/version: 8.1.1
Roxygen: list(markdown = TRUE)
Config/pak/sysreqs: cmake make libicu-dev libpng-dev libuv1-dev
        libxml2-dev python3
Repository: https://ethanbass.r-universe.dev
Date/Publication: 2026-10-20 19:36:22 UTC
RemoteUrl: https://github.com/ethanbass/chromatographR
RemoteRef: HEAD
RemoteSha: 786922fdc7dd2514a151630e466f98a835650f60
NeedsCompilation: no
Packaged: 2026-10-21 12:28:41 UTC; root
Author: Ethan Bass [aut, cre, cph] (ORCID:
    <https://orcid.org/0000-0002-6175-6739>),
  Hans W Borchers [ctb, cph] (Author of savgol and pinv functions bundled
    from pracma),
  Ron Wehrens [ctb, cph] (Author of code adapted from alsace and ptw)