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, ...)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_prefixis not specified.- spectra_ends
an integer indicating the ending column index for the spectral data, used when
spectra_prefixis not specified. If not provided, defaults to the last column.- ...
additional arguments passed to
read.table.
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")
# }