# File src/library/utils/R/readtable.R # Part of the R package, http://www.R-project.org # # Copyright (C) 1995-2014 The R Core Team # # This program is free software; you can redistribute it and/or modify # it under the terms of the GNU General Public License as published by # the Free Software Foundation; either version 2 of the License, or # (at your option) any later version. # # This program is distributed in the hope that it will be useful, # but WITHOUT ANY WARRANTY; without even the implied warranty of # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the # GNU General Public License for more details. # # A copy of the GNU General Public License is available at # http://www.r-project.org/Licenses/ count.fields <- function(file, sep = "", quote = "\"'", skip = 0, blank.lines.skip = TRUE, comment.char = "#") { if(is.character(file)) { file <- file(file) on.exit(close(file)) } if(!inherits(file, "connection")) stop("'file' must be a character string or connection") .External(C_countfields, file, sep, quote, skip, blank.lines.skip, comment.char) } type.convert <- function(x, na.strings = "NA", as.is = FALSE, dec = ".") .External2(C_typeconvert, x, na.strings, as.is, dec) read.table <- function(file, header = FALSE, sep = "", quote = "\"'", dec = ".", row.names, col.names, as.is = !stringsAsFactors, na.strings = "NA", colClasses = NA, nrows = -1, skip = 0, check.names = TRUE, fill = !blank.lines.skip, strip.white = FALSE, blank.lines.skip = TRUE, comment.char = "#", allowEscapes = FALSE, flush = FALSE, stringsAsFactors = default.stringsAsFactors(), fileEncoding = "", encoding = "unknown", text, skipNul = FALSE) { if (missing(file) && !missing(text)) { file <- textConnection(text, encoding = "UTF-8") encoding <- "UTF-8" on.exit(close(file)) } if(is.character(file)) { file <- if(nzchar(fileEncoding)) file(file, "rt", encoding = fileEncoding) else file(file, "rt") on.exit(close(file)) } if(!inherits(file, "connection")) stop("'file' must be a character string or connection") if(!isOpen(file, "rt")) { open(file, "rt") on.exit(close(file)) } pbEncoding <- if (encoding %in% c("", "bytes", "UTF-8")) encoding else "bytes" if(skip > 0L) readLines(file, skip) ## read a few lines to determine header, no of cols. nlines <- n0lines <- if (nrows < 0L) 5 else min(5L, (header + nrows)) lines <- .External(C_readtablehead, file, nlines, comment.char, blank.lines.skip, quote, sep, skipNul) if (encoding %in% c("UTF-8", "latin1")) Encoding(lines) <- encoding nlines <- length(lines) if(!nlines) { if(missing(col.names)) stop("no lines available in input") rlabp <- FALSE cols <- length(col.names) } else { if(all(!nzchar(lines))) stop("empty beginning of file") if(nlines < n0lines && file == 0L) { # stdin() has reached EOF pushBack(c(lines, lines, ""), file, encoding = pbEncoding) on.exit((clearPushBack(stdin()))) } else pushBack(c(lines, lines), file, encoding = pbEncoding) first <- scan(file, what = "", sep = sep, quote = quote, nlines = 1, quiet = TRUE, skip = 0, strip.white = TRUE, blank.lines.skip = blank.lines.skip, comment.char = comment.char, allowEscapes = allowEscapes, encoding = encoding, skipNul = skipNul) col1 <- if(missing(col.names)) length(first) else length(col.names) col <- numeric(nlines - 1L) if (nlines > 1L) for (i in seq_along(col)) col[i] <- length(scan(file, what = "", sep = sep, quote = quote, nlines = 1, quiet = TRUE, skip = 0, strip.white = strip.white, blank.lines.skip = blank.lines.skip, comment.char = comment.char, allowEscapes = allowEscapes, encoding = encoding, skipNul = skipNul)) cols <- max(col1, col) ## basic column counting and header determination; ## rlabp (logical) := it looks like we have column names rlabp <- (cols - col1) == 1L if(rlabp && missing(header)) header <- TRUE if(!header) rlabp <- FALSE if (header) { ## skip over header .External(C_readtablehead, file, 1L, comment.char, blank.lines.skip, quote, sep, skipNul) if(missing(col.names)) col.names <- first else if(length(first) != length(col.names)) warning("header and 'col.names' are of different lengths") } else if (missing(col.names)) col.names <- paste0("V", 1L:cols) if(length(col.names) + rlabp < cols) stop("more columns than column names") if(fill && length(col.names) > cols) cols <- length(col.names) if(!fill && cols > 0L && length(col.names) > cols) stop("more column names than columns") if(cols == 0L) stop("first five rows are empty: giving up") } if(check.names) col.names <- make.names(col.names, unique = TRUE) if (rlabp) col.names <- c("row.names", col.names) nmColClasses <- names(colClasses) if(length(colClasses) < cols) if(is.null(nmColClasses)) { colClasses <- rep_len(colClasses, cols) } else { tmp <- rep_len(NA_character_, cols) names(tmp) <- col.names i <- match(nmColClasses, col.names, 0L) if(any(i <= 0L)) warning("not all columns named in 'colClasses' exist") tmp[ i[i > 0L] ] <- colClasses colClasses <- tmp } ## set up for the scan of the file. ## we read unknown values as character strings and convert later. what <- rep.int(list(""), cols) names(what) <- col.names colClasses[colClasses %in% c("real", "double")] <- "numeric" known <- colClasses %in% c("logical", "integer", "numeric", "complex", "character", "raw") what[known] <- sapply(colClasses[known], do.call, list(0)) what[colClasses %in% "NULL"] <- list(NULL) keep <- !sapply(what, is.null) data <- scan(file = file, what = what, sep = sep, quote = quote, dec = dec, nmax = nrows, skip = 0, na.strings = na.strings, quiet = TRUE, fill = fill, strip.white = strip.white, blank.lines.skip = blank.lines.skip, multi.line = FALSE, comment.char = comment.char, allowEscapes = allowEscapes, flush = flush, encoding = encoding, skipNul = skipNul) nlines <- length(data[[ which.max(keep) ]]) ## now we have the data; ## convert to numeric or factor variables ## (depending on the specified value of "as.is"). ## we do this here so that columns match up if(cols != length(data)) { # this should never happen warning("cols = ", cols, " != length(data) = ", length(data), domain = NA) cols <- length(data) } if(is.logical(as.is)) { as.is <- rep_len(as.is, cols) } else if(is.numeric(as.is)) { if(any(as.is < 1 | as.is > cols)) stop("invalid numeric 'as.is' expression") i <- rep.int(FALSE, cols) i[as.is] <- TRUE as.is <- i } else if(is.character(as.is)) { i <- match(as.is, col.names, 0L) if(any(i <= 0L)) warning("not all columns named in 'as.is' exist") i <- i[i > 0L] as.is <- rep.int(FALSE, cols) as.is[i] <- TRUE } else if (length(as.is) != cols) stop(gettextf("'as.is' has the wrong length %d != cols = %d", length(as.is), cols), domain = NA) do <- keep & !known # & !as.is if(rlabp) do[1L] <- FALSE # don't convert "row.names" for (i in (1L:cols)[do]) { data[[i]] <- if (is.na(colClasses[i])) type.convert(data[[i]], as.is = as.is[i], dec = dec, na.strings = character(0L)) ## as na.strings have already been converted to else if (colClasses[i] == "factor") as.factor(data[[i]]) else if (colClasses[i] == "Date") as.Date(data[[i]]) else if (colClasses[i] == "POSIXct") as.POSIXct(data[[i]]) else methods::as(data[[i]], colClasses[i]) } ## now determine row names compactRN <- TRUE if (missing(row.names)) { if (rlabp) { row.names <- data[[1L]] data <- data[-1L] keep <- keep[-1L] compactRN <- FALSE } else row.names <- .set_row_names(as.integer(nlines)) } else if (is.null(row.names)) { row.names <- .set_row_names(as.integer(nlines)) } else if (is.character(row.names)) { compactRN <- FALSE if (length(row.names) == 1L) { rowvar <- (1L:cols)[match(col.names, row.names, 0L) == 1L] row.names <- data[[rowvar]] data <- data[-rowvar] keep <- keep[-rowvar] } } else if (is.numeric(row.names) && length(row.names) == 1L) { compactRN <- FALSE rlabp <- row.names row.names <- data[[rlabp]] data <- data[-rlabp] keep <- keep[-rlabp] } else stop("invalid 'row.names' specification") data <- data[keep] ## rownames<- is interpreted, so avoid it for efficiency (it will copy) if(is.object(row.names) || !(is.integer(row.names)) ) row.names <- as.character(row.names) if(!compactRN) { if (length(row.names) != nlines) stop("invalid 'row.names' length") if (anyDuplicated(row.names)) stop("duplicate 'row.names' are not allowed") if (anyNA(row.names)) stop("missing values in 'row.names' are not allowed") } ## this is extremely underhanded ## we should use the constructor function ... ## don't try this at home kids class(data) <- "data.frame" attr(data, "row.names") <- row.names data } read.csv <- function (file, header = TRUE, sep = ",", quote = "\"", dec = ".", fill = TRUE, comment.char = "", ...) read.table(file = file, header = header, sep = sep, quote = quote, dec = dec, fill = fill, comment.char = comment.char, ...) read.csv2 <- function (file, header = TRUE, sep = ";", quote = "\"", dec = ",", fill = TRUE, comment.char = "", ...) read.table(file = file, header = header, sep = sep, quote = quote, dec = dec, fill = fill, comment.char = comment.char, ...) read.delim <- function (file, header = TRUE, sep = "\t", quote = "\"", dec = ".", fill = TRUE, comment.char = "", ...) read.table(file = file, header = header, sep = sep, quote = quote, dec = dec, fill = fill, comment.char = comment.char, ...) read.delim2 <- function (file, header = TRUE, sep = "\t", quote = "\"", dec = ",", fill = TRUE, comment.char = "", ...) read.table(file = file, header = header, sep = sep, quote = quote, dec = dec, fill = fill, comment.char = comment.char, ...)