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71 lines
2.8 KiB
71 lines
2.8 KiB
## Function 1: Read spectra in text form ========================
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#' @title Read an OPUS text file and extract metadata
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#' @description
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#' Read single text file acquired with
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#' an Bruker Vertex FTIR Instrument
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#' (as exported from OPUS software) and extract sample metadata
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#' provided in the filename
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#' @usage
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#' read_spectra(path)
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#' @param path character of the directory
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#' where the spectral text files are stored
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#' @return
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#' List that contains the following elements:
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#' \itemize{
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#' \item \code{MIR}: data.frame that contains all the spectra.
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#' The columns of \code{MIR} contain absorbance values at
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#' different wavenumber in the MIR range. The wavenumbers
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#' rounded to 0.1 are given as column names. The original file
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#' names are stored as row names. One line in the data frame
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#' \code{MIR} contains one replicate scan of a sample.
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#' \item \code{data_rep}: data.frame that constists of sample
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#' metadata that was extracted from the file name of
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#' individual spectral files. The first vector \code{ID}
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#' contains the spectral file name without the repetition number
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#' supplied as \code{.<number>} in the file name.
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#' Letters 1 to 2 of the spectral
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#' file name are used for the country abbreviation, stored
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#' as in the \code{} vector \code{data_rep} . Letters
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#' 4 to 5 of the file name are used for the landscape (site)
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#' abbreviation.
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#' }
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#' @note: This function is derived from a re-factored and
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#' simplified version of the \code{read.opus} function from the
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#' \sQuote{soil.spec} package for reading OPUS VERTEX files
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#' The function should also work for other OPUS files (eg alpha),
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#' see \code{read.opus}. The function readOPUS() was
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#' written by Antoine Stevens.
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#' @export
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read_spectra <- function(path){
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# Needs various utilities for spectral processing that Antoine
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# put on github
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ID <- NULL
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# Load the MIR data exported from OPUS to txt files
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# List files in the directory
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lf <- list.files(path, full.names = TRUE)
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# Read files into R with readOPUS()
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# (comes from the github file)
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MIR <- readOPUS(lf, in_format = "txt")
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# Wavenumber, from 3996.4 to 599.8 cm-1
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colnames(MIR) <- round(as.numeric(colnames(MIR)), 1)
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# Remove the txt extension
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rownames(MIR) <- sub("\\.txt", "", row.names(MIR))
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# Prepare a dataset with ID,
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# Extract country with substring
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# and repetition
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# (ID = character before the dot; rep = number after the dot)
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data_rep <- data.frame(ID = sub("(.+)\\.[[:digit:]]+$", "\\1",
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row.names(MIR)),
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rep = as.numeric(sub(".+\\.([[:digit:]])+$", "\\1",
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row.names(MIR)))
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)
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data_rep <- cbind(data_rep,
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country = substring(data_rep$ID, first = 1, last = 2),
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site = substring(data_rep$ID, first = 4, last = 5)
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)
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list_spectra <- list(
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MIR = MIR,
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data_rep = data_rep
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)
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return(list_spectra)
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}
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