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v0.7.0
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| #' chromatographR | ||
| #' | ||
| #' chromatographR | ||
| #' | ||
| #' \tabular{ll}{ Package: \tab chromatographR\cr Type: \tab Package\cr Version: | ||
| #' \tab 0.6.1 \cr Date: \tab 2023-10-23\cr License: GPL (>= 2) } | ||
| #' Chromatographic Data Analysis Toolset | ||
| #' | ||
| #' @name chromatographR-package | ||
| #' @aliases chromatographR-package chromatographR | ||
| #' @docType package | ||
| #' Tools for high-throughput analysis of HPLC-DAD/UV | ||
| #' chromatograms (or similar data). Includes functions for preprocessing, alignment, | ||
| #' peak-finding and fitting, peak-table construction, data-visualization, etc. | ||
| #' Preprocessing and peak-table construction follow the rough formula laid out | ||
| #' in alsace (Wehrens, R., Bloemberg, T.G., and Eilers P.H.C., 2015. | ||
| #' \doi{10.1093/bioinformatics/btv299}). Alignment of chromatograms is available | ||
| #' using parametric time warping (ptw) (Wehrens, R., Bloemberg, T.G., and Eilers | ||
| #' P.H.C. 2015. \doi{10.1093/bioinformatics/btv299}) or variable penalty dynamic | ||
| #' time warping (VPdtw) (Clifford, D., & Stone, G. 2012. \doi{10.18637/jss.v047.i08}). | ||
| #' Peak-finding relies on the algorithm suggested by Tom O'Haver in his | ||
| #' \href{https://terpconnect.umd.edu/~toh/spectrum/PeakFindingandMeasurement.htm}{ | ||
| #' Pragmatic Introduction to Signal Processing}. Peaks are then fitted to a | ||
| #' gaussian or exponential-gaussian hybrid peak shape using non-linear least | ||
| #' squares (Lan, K. & Jorgenson, J. W. 2001. \doi{10.1016/S0021-9673(01)00594-5}). | ||
| #' More details on package usage and a suggested workflow can be found in the | ||
| #' vignette. | ||
| #' @author Ethan Bass | ||
| #' | ||
| #' Maintainer: Ethan Bass | ||
| #' @keywords package | ||
| NULL | ||
| "_PACKAGE" | ||
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| #' HPLC-DAD data of goldenrod root extracts. | ||
| #' Raw goldenrod root chromatograms | ||
| #' | ||
| #' Four HPLC-DAD data matrices of *Solidago altissima* roots extracted in 90 | ||
| #' percent methanol. | ||
| #' A list of four HPLC-DAD data matrices of \emph{Solidago altissima} roots | ||
| #' extracted in 90\% methanol. Retention times are stored in rows and | ||
| #' wavelengths are stored in columns. | ||
| #' | ||
| #' @name Sa | ||
| #' @docType data | ||
| #' @format A list of four matrices (time x wavelength). | ||
| #' @keywords data | ||
| #' @usage data(Sa) | ||
| #' @format A list of four matrices (1301 times x 60 wavelengths). | ||
| NULL | ||
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| #' HPLC-DAD data of goldenrod root extracts. | ||
| #' Preprocessed goldenrod root chromatograms | ||
| #' | ||
| #' Pre-processed chromatograms. | ||
| #' A list of four pre-processed HPLC-DAD chromatograms derived from the raw data | ||
| #' stored in \code{Sa}. Retention times are stored in rows and wavelengths | ||
| #' are stored in columns. The time axis is compressed to save space and | ||
| #' processing time so the data are a little choppy. | ||
| #' | ||
| #' @name Sa_pr | ||
| #' @keywords data | ||
| #' @docType data | ||
| #' @format Four pre-processed matrices (time x wavelength) to use in examples. | ||
| #' @usage data(Sa_pr) | ||
| #' @format A list of four pre-processed matrices (434 retention times x 60 wavelengths). | ||
| NULL | ||
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| #' HPLC-DAD data of goldenrod root extracts. | ||
| #' Warped goldenrod root chromatograms. | ||
| #' | ||
| #' Pre-processed and warped chromatograms. | ||
| #' A list of four pre-processed and warped goldenrod root chromatograms derived | ||
| #' from the raw data stored in \code{Sa}. | ||
| #' | ||
| #' @name Sa_warp | ||
| #' @docType data | ||
| #' @format Four pre-processed and warped matrices (time x wavelength) to use in | ||
| #' examples. | ||
| #' @keywords data | ||
| #' @usage data(Sa_warp) | ||
| #' @format A list of four pre-processed and warped matrices (434 times x 60 wavelengths). | ||
| NULL | ||
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| #' Goldenrod peak table | ||
| #' | ||
| #' Peak table generated from example goldenrod extracts for examples. | ||
| #' Peak table generated from exemplary goldenrod root extracts. | ||
| #' | ||
| #' @name pk_tab | ||
| #' @docType data | ||
| #' @keywords data | ||
| #' @usage data(pk_tab) | ||
| #' @format A \code{peak_table} object. | ||
| NULL | ||
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