proximetricsR (version 0.6.5)

read_spc: Read and format spectral data from a file

Description

This function reads spectral data from a file and extracts the spectral columns based on a specified prefix, or a range of columns. It can handle various delimiters and decimal separators.

Usage

read_spc(file, sep = "\t", dec = ".", header = TRUE, spectra_prefix = "",
         spectra_starts = NA, spectra_ends = NA, ...)

Value

a data frame with the original data and a matrix of spectral data stored in the spc column.

Arguments

file

a character string specifying the path to the file containing the spectral data.

sep

a character string indicating the field separator character. Defaults to "\t".

dec

a character string used for decimal points. Defaults to ".".

header

logical value indicating whether the file contains the names of the variables as its first line. Defaults to TRUE

spectra_prefix

a character string specifying the prefix used for spectral column names. If empty, the function will use column indices instead.

spectra_starts

an integer indicating the starting column index for the spectral data, used when spectra_prefix is not specified.

spectra_ends

an integer indicating the ending column index for the spectral data, used when spectra_prefix is not specified. If not provided, defaults to the last column.

...

additional arguments passed to read.table.

Author

Leonardo Ramirez-Lopez

Details

The function reads a file and extracts the spectral data based on either a column name prefix or specified column indices. The spectral data is returned as a matrix in the spc column of the resulting data frame.

Examples

# \donttest{
# write a file with spectra
data("NIRsoil", package = "prospectr")
spc_small <- NIRsoil$spc[1:5, ]
colnames(spc_small) <- paste0("X", colnames(spc_small))
tmp_df <- data.frame(ID = 1:5, Nt = NIRsoil$Nt[1:5], spc_small, check.names = FALSE)
tmp_file <- tempfile(fileext = ".txt")
write.table(tmp_df, file = tmp_file, sep = "\t", row.names = FALSE)

# read that
result <- read_spc(tmp_file, spectra_prefix = "X")
# }