The R Project SVN R

#  File src/library/utils/R/readtable.R
#  Part of the R package, http://www.R-project.org
#
#  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")
    .Internal(count.fields(file, sep, quote, skip, blank.lines.skip,
                           comment.char))
}


type.convert <-
function(x, na.strings = "NA", as.is = FALSE, dec = ".")
    .Internal(type.convert(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(),
         encoding = "unknown")
{
    if(is.character(file)) {
        file <- file(file, "r")
        on.exit(close(file))
    }
    if(!inherits(file, "connection"))
        stop("'file' must be a character string or connection")
    if(!isOpen(file, "r")) {
        open(file, "r")
        on.exit(close(file))
    }

    if(skip > 0) readLines(file, skip)
    ## read a few lines to determine header, no of cols.
    nlines <- n0lines <- if (nrows < 0) 5 else min(5, (header + nrows))

    lines <- .Internal(readTableHead(file, nlines, comment.char,
                                     blank.lines.skip, quote, sep))
    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 == 0)  { # stdin() has reached EOF
            pushBack(c(lines, lines, ""), file)
            on.exit(.Internal(clearPushBack(stdin())))
        } else pushBack(c(lines, lines), file)
        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)
        col1 <- if(missing(col.names)) length(first) else length(col.names)
        col <- numeric(nlines - 1)
        if (nlines > 1)
            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))
        cols <- max(col1, col)

        ##  basic column counting and header determination;
        ##  rlabp (logical) := it looks like we have column names

        rlabp <- (cols - col1) == 1
        if(rlabp && missing(header))
            header <- TRUE
        if(!header) rlabp <- FALSE

        if (header) {
            readLines(file, 1)          # skip over header
            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 <- paste("V", 1:cols, sep = "")
        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 > 0 && length(col.names) > cols)
            stop("more column names than columns")
        if(cols == 0) 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(colClasses, length.out=cols)
        } else {
            tmp <- rep(NA_character_, length.out=cols)
            names(tmp) <- col.names
            i <- match(nmColClasses, col.names, 0)
            if(any(i <= 0))
                warning("not all columns named in 'colClasses' exist")
            tmp[ i[i > 0] ] <- 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")
    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)

    nlines <- length(data[[ which(keep)[1] ]])

    ##  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(as.is, length.out=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, 0)
        if(any(i <= 0))
            warning("not all columns named in 'as.is' exist")
        i <- i[i > 0]
        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[1] <- FALSE # don't convert "row.names"
    for (i in (1:cols)[do]) {
        data[[i]] <-
            if (is.na(colClasses[i]))
                type.convert(data[[i]], as.is = as.is[i], dec = dec,
                             na.strings = character(0))
        ## as na.strings have already been converted to <NA>
            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[[1]]
        data <- data[-1]
            keep <- keep[-1]
            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) == 1) {
        rowvar <- (1:cols)[match(col.names, row.names, 0) == 1]
        row.names <- data[[rowvar]]
        data <- data[-rowvar]
            keep <- keep[-rowvar]
    }
    } else if (is.numeric(row.names) && length(row.names) == 1) {
        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 (any(duplicated(row.names)))
            stop("duplicate 'row.names' are not allowed")
        if (any(is.na(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, ...)