#' @title Convert sampling depths to numeric.
#' @description Converts sampling depths to numeric and adds any character strings from these columns to comments
#' @param dt data frame containing meta-data. See \code{\link{read_metadata}}
#' @param column column name in meta-data containing the sampling depths to be converted.
#' @param comment.col the name of the comment column in \code{dt}
#' @author Mikko Vihtakari
#' @export
#column = "from"
#comment.col = "comment"
convert_sampling_depths <- function(dt, column, comment.col = "comment") {
dt[,column] <- as.character(dt[,column])
tp <- lapply(1:nrow(dt), function(i) { ## Add any milliQs etc to comments
#print(i)
tmp <- dt[i,]
tmp$comment <- ifelse(grepl("[[:digit:]]", tmp[,column]),
tmp[,comment.col],
if(is.na(tmp[,comment.col])) {
tmp[,column]
} else {
paste(tmp[,comment.col], tmp[,column], sep = ".")
}
)
tmp
})
dt <- do.call(rbind, tp)
suppressWarnings(dt[,column] <- as.numeric(dt[,column]))
message(paste0("'", column, "'", " column converted to numeric. NAs produced. Any character strings in the column have been moved to the 'comment' column."))
dt
}
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