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110 lines
5.1 KiB
110 lines
5.1 KiB
% Generated by roxygen2: do not edit by hand
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% Please edit documentation in R/resample-spc.R
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\name{resample_spc}
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\alias{resample_spc}
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\title{Resample spectra in list-column to new x-axis interval}
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\usage{
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resample_spc(
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spc_tbl,
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column_in = "spc",
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x_unit = c("wavenumber", "wavelength"),
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wn_lower = 500,
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wn_upper = 4000,
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wn_interval = 2,
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wl_lower = 350,
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wl_upper = 2500,
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wl_interval = 1,
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interpol_method = c("linear", "spline")
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)
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}
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\arguments{
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\item{spc_tbl}{Spectra data embedded in a tibble object (classes
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\verb{"tbl_df", "tbl", "data.frame"}). The spectra tibble needs to contain at
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least of one of the the spectra columns \code{spc}, \code{spc_rs}, \code{spc_mean},
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\code{spc_nocomp}, \code{sc_sm}, \code{sc_rf}, or \code{spc_pre} (list-columns with spectral
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\code{data.table}s), and \code{wavenumbers} or \code{wavelengths} (list-column with vectors
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of x-axis values corresponding to each spectrum). The help section \emph{"Matching
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spectrum type and corresponding x-axis type"} describes the spectra types
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and corresponding x-axis types.}
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\item{column_in}{Character vector of length 1L or symbol/name
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specifying the name of list-column that contains the spectra to be resampled.}
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\item{x_unit}{Character vector of length 1L specifying the measurement unit
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of the x-axis values (list-column) of the input spectra in \code{spc_tbl}.
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Possible values are \code{"wavenumber"} (default) or \code{"wavelength"}. Wavenumber
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is a convenient unit of frequency in the mid-infrared spectral range,
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where wavelength is often used as spatial period for the visible and
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near-infrared range.}
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\item{wn_lower}{Numeric value of lowest wavenumber. This argument will only
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be used if \code{x_unit = "wavenumber"}. The value serves as starting value for
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the new wavenumber sequence that the spectra will be resampled upon. Default
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value is 500 (i.e., in reciprocal centimeters).}
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\item{wn_upper}{Numeric value of highest wavenumber. This argument will only
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be used if \verb{x_unit = "wavenumber}. The value will be used as last value of
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the new wavenumber sequence that the spectra will be resampled upon. Default
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value is 4000 (i.e., in reciprocal centimeters).}
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\item{wn_interval}{Numeric value of the wavenumber increment for the new
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wavenumber sequence that the spectra will be resampled upon. Default value
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is 2 (i.e., in reciprocal centimeters).}
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\item{wl_lower}{Numeric value of lowest wavelength. This argument will only
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be used if \code{x_unit = "wavelength"}. The value serves as starting value of
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the new wavenumber sequence that the spectra will be resampled upon.
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Default value is 350 (i.e. in nanometers).}
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\item{wl_upper}{Numeric value of highest wavelength. This argument will only
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be used if \code{x_unit = "wavelength"}. The value will be used as last value of
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the new wavenumber sequence that the spectra will be resampled upon. Default
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value is 2500 (i.e., in nanometers).}
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\item{wl_interval}{Numeric value of the wavelength increment for the new
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wavenumber sequence that the spectra will be resampled upon. This argument
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will only be used if \code{x_unit = "wavelength"}. Default value is 1 (i.e., in
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nanometers).}
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\item{interpol_method}{Character of \code{"linear"} (default) or \code{"spline"} with
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the interpolation method. \code{"spline"} uses a cubic spline to interpolate the
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input spectra at given x-axis values to new equispaced x-axis intervals.}
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}
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\value{
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A spectra tibble (\code{spc_tbl}) containing two added list-columns:
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\itemize{
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\item \verb{spc_rs:} Resampled spectra as list of \code{data.table}s
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\item \code{wavenumbers_rs} or \code{wavelengths_rs}: Resampled x-axis values as list of
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numeric vectors
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}
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}
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\description{
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Resamples (interpolates) different spectra types with
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corresponding x-axis values that are both stored in list-columns of a spectra
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tibble. A spectra tibble hosts spectra, x-axis vectors, metadata, and
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further linked data with standardized naming conventions. Data input for
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resampling can for example be generated with \code{simplerspec::gather_spc()}.
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Resampling is a key harmonizing step to process and later model spectra
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measured at different resolutions and spectral ranges (i.e., different
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spectrometer devices and/or measurement settings).
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}
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\section{Matching spectrum type and corresponding x-axis type}{
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The combinations of input spectrum types (\code{column_in}) and
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corresponding x-axis types are generated from a simple lookup list. The
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following key-value(s) pairs can be matched at given key, which is the column
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name from \code{column_in} containing the spectra.
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\itemize{
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\item \code{"spc"} : \code{"wavenumbers"} or \code{"wavelengths"} (raw spectra)
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\item \code{"spc_rs"} : \code{"wavenumbers_rs"} or \code{"wavelengths_rs"}) (resampled spectra)
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\item \code{"spc_mean"} : \code{"wavenumbers_rs"} or \code{"wavelengths_rs"} (mean spectra)
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\item \code{"spc_nocomp"} \code{"wavenumbers"} or \code{"wavelengths"} (spectra prior
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atmospheric compensation)
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\item \code{"sc_sm" : c("wavenumbers_sc_sm", "wavelengths_sc_sm")} (single channel
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sample spectra)
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\item \code{"sc_rf" : c("wavenumbers_sc_rf", "wavelengths_sc_rf")} (single channel
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reference spectra)
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\item \code{"spc_pre" : "xvalues_pre"} (preprocessed spectra)
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}
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}
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