#  File src/library/stats/R/ftable.R
#  Part of the R package, http://www.R-project.org
#
#  Copyright (C) 1995-2013 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/

ftable <- function(x, ...) UseMethod("ftable")

ftable.default <- function(..., exclude = c(NA, NaN),
			   row.vars = NULL, col.vars = NULL) {
    args <- list(...)
    if (length(args) == 0L)
	stop("nothing to tabulate")
    x <- args[[1L]]
    if(is.list(x))
	x <- table(x, exclude = exclude)
    else if(inherits(x, "ftable") ||
	    (arr2 <- is.array(x) && (length(dim(x)) > 1L))) {
	x <- as.table(x) # regularizes dimnames for (>=2)D-arrays
    }
    else if(!arr2 ) {
	x <- table(..., exclude = exclude)
    }
    dn <- dimnames(x)
    dx <- dim(x)
    n <- length(dx)
    if(!is.null(row.vars)) {
	if(is.character(row.vars)) {
	    i <- pmatch(row.vars, names(dn))
	    if(anyNA(i))
		stop("incorrect specification for 'row.vars'")
	    row.vars <- i
	} else if(any((row.vars < 1) | (row.vars > n)))
	    stop("incorrect specification for 'row.vars'")
    }
    if(!is.null(col.vars)) {
	if(is.character(col.vars)) {
	    i <- pmatch(col.vars, names(dn))
	    if(anyNA(i))
	     stop("incorrect specification for 'col.vars'")
	    col.vars <- i
	} else if(any((col.vars < 1) | (col.vars > n)))
	    stop("incorrect specification for 'col.vars'")
    }
    i <- 1 : n
    if(!is.null(row.vars) && !is.null(col.vars)) {
	all.vars <- sort(c(row.vars, col.vars))
	if ((p <- length(all.vars)) < n) {
	    x <- if(p) apply(x, all.vars, sum) else sum(x)
	    row.vars <- match(row.vars, all.vars)
	    col.vars <- match(col.vars, all.vars)
	    dn <- dn[all.vars]
	    dx <- dx[all.vars]
	}
    }
    else if(!is.null(row.vars))
	col.vars <- if(length(row.vars)) i[-row.vars] else i
    else if(!is.null(col.vars))
	row.vars <- if(length(col.vars)) i[-col.vars] else i
    else {
	row.vars <- seq_len(n-1)
	col.vars <- n
    }

    if(length(perm <- c(rev(row.vars), rev(col.vars))) > 1)
	x <- aperm(x, perm)
    dim(x) <- c(prod(dx[row.vars]), prod(dx[col.vars]))
    attr(x, "row.vars") <- dn[row.vars]
    attr(x, "col.vars") <- dn[col.vars]
    class(x) <- "ftable"
    x
}

ftable.formula <- function(formula, data = NULL, subset, na.action, ...)
{
    if(missing(formula) || !inherits(formula, "formula"))
        stop("'formula' missing or incorrect")
    if(length(formula) != 3L)
        stop("'formula' must have both left and right hand sides")
    ## need to cope with '.' in formula
    tt <- if(is.data.frame(data)) terms(formula, data=data)
    else terms(formula, allowDotAsName=TRUE)
    if(any(attr(tt, "order") > 1))
        stop("interactions are not allowed")
    ## here we do NOT want '.' expanded
    rvars <- attr(terms(formula[-2L], allowDotAsName=TRUE), "term.labels")
    cvars <- attr(terms(formula[-3L], allowDotAsName=TRUE), "term.labels")
    rhs.has.dot <- any(rvars == ".")
    lhs.has.dot <- any(cvars == ".")
    if(lhs.has.dot && rhs.has.dot)
        stop("'formula' has '.' in both left and right hand sides")
    m <- match.call(expand.dots = FALSE)
    edata <- eval(m$data, parent.frame())
    if(inherits(edata, "ftable")
       || inherits(edata, "table")
       || length(dim(edata)) > 2L) {
        if(inherits(edata, "ftable")) {
            data <- as.table(data)
        }
        varnames <- names(dimnames(data))
        if(rhs.has.dot)
            rvars <- NULL
        else {
            i <- pmatch(rvars, varnames)
            if(anyNA(i))
                stop("incorrect variable names in rhs of formula")
            rvars <- i
        }
        if(lhs.has.dot)
            cvars <- NULL
        else {
            i <- pmatch(cvars, varnames)
            if(anyNA(i))
                stop("incorrect variable names in lhs of formula")
            cvars <- i
        }
        ftable(data, row.vars = rvars, col.vars = cvars)
    }
    else {
        if(is.matrix(edata))
            m$data <- as.data.frame(data)
        m$... <- NULL
        if(!is.null(data) && is.environment(data)) {
            varnames <- names(data)
            if(rhs.has.dot)
                rvars <- seq_along(varnames)[-cvars]
            if(lhs.has.dot)
                cvars <- seq_along(varnames)[-rvars]
        }
        else {
            if(lhs.has.dot || rhs.has.dot)
                stop("cannot use dots in formula with given data")
        }
        m$formula <- as.formula(paste("~",
                                   paste(c(rvars, cvars),
                                         collapse = "+")),
                                env = environment(formula))
        m[[1L]] <- quote(stats::model.frame)
        mf <- eval(m, parent.frame())
        ftable(mf, row.vars = rvars, col.vars = cvars, ...)
    }
}

as.table.ftable <- function(x, ...)
{
    if(!inherits(x, "ftable"))
        stop("'x' must be an \"ftable\" object")
    xrv <- rev(attr(x, "row.vars"))
    xcv <- rev(attr(x, "col.vars"))
    x <- array(data = c(x),
               dim = c(sapply(xrv, length),
                       sapply(xcv, length)),
               dimnames = c(xrv, xcv))
    nrv <- length(xrv)
    ncv <- length(xcv)
    x <- aperm(x, c(rev(seq_len(nrv)), rev(seq_len(ncv) + nrv)))
    class(x) <- "table"
    x
}

format.ftable <-
    function(x, quote=TRUE, digits=getOption("digits"),
	     method=c("non.compact", "row.compact", "col.compact", "compact"),
	     lsep=" | ", ...)
{
    if(!inherits(x, "ftable"))
	stop("'x' must be an \"ftable\" object")
    charQuote <- function(s) if(quote && length(s)) paste0("\"", s, "\"") else s
    makeLabels <- function(lst) {
	lens <- sapply(lst, length)
	cplensU <- c(1, cumprod(lens))
	cplensD <- rev(c(1, cumprod(rev(lens))))
	y <- NULL
	for (i in rev(seq_along(lst))) {
	    ind <- 1 + seq.int(from = 0, to = lens[i] - 1) * cplensD[i + 1L]
	    tmp <- character(length = cplensD[i])
	    tmp[ind] <- charQuote(lst[[i]])
	    y <- cbind(rep(tmp, times = cplensU[i]), y)
	}
	y
    }
    makeNames <- function(x) {
	nmx <- names(x)
	if(is.null(nmx)) rep_len("", length(x)) else nmx
    }

    l.xrv <- length(xrv <- attr(x, "row.vars"))
    l.xcv <- length(xcv <- attr(x, "col.vars"))
    method <- match.arg(method)
    ## deal with 'extreme' layouts (no col.vars, no row.vars)
    if(l.xrv == 0) {
	if(method=="col.compact")
	    method <- "non.compact" # already produces a 'col.compact' version
	else if (method=="compact")
	    method <- "row.compact" # only need to 'row.compact'ify
    }
    if(l.xcv == 0) {
	if(method=="row.compact")
	    method <- "non.compact" # already produces a 'row.compact' version
	else if (method=="compact")
	    method <- "col.compact" # only need to 'col.compact'ify
    }
    LABS <-
	switch(method,
	       "non.compact" =		# current default
	   {
	       cbind(rbind(matrix("", nrow = length(xcv), ncol = length(xrv)),
			   charQuote(makeNames(xrv)),
			   makeLabels(xrv)),
		     c(charQuote(makeNames(xcv)),
		       rep("", times = nrow(x) + 1)))
	   },
	       "row.compact" =		# row-compact version
	   {
	       cbind(rbind(matrix("", nrow = length(xcv)-1, ncol = length(xrv)),
			   charQuote(makeNames(xrv)),
			   makeLabels(xrv)),
		     c(charQuote(makeNames(xcv)),
		       rep("", times = nrow(x))))
	   },
	       "col.compact" =		# column-compact version
	   {
	       cbind(rbind(cbind(matrix("", nrow = length(xcv), ncol = length(xrv)-1),
				 charQuote(makeNames(xcv))),
			   charQuote(makeNames(xrv)),
			   makeLabels(xrv)))
	   },
	       "compact" =		# fully compact version
	   {
	       xrv.nms <- makeNames(xrv)
	       xcv.nms <- makeNames(xcv)
	       mat <- cbind(rbind(cbind(matrix("", nrow = l.xcv-1, ncol = l.xrv-1),
					charQuote(makeNames(xcv[-l.xcv]))),
				  charQuote(xrv.nms),
				  makeLabels(xrv)))
	       mat[l.xcv, l.xrv] <- paste(tail(xrv.nms, 1),
					  tail(xcv.nms, 1), sep = lsep)
	       mat
	   },
	       stop("wrong method"))
    DATA <- rbind(if(length(xcv)) t(makeLabels(xcv)),
		  if(method %in% c("non.compact", "col.compact"))
			rep("", times = ncol(x)),
		  format(unclass(x), digits = digits, ...))
    cbind(apply(LABS, 2L, format, justify = "left"),
	  apply(DATA, 2L, format, justify = "right"))
}

write.ftable <- function(x, file = "", quote = TRUE, append = FALSE,
			 digits = getOption("digits"), ...)
{
    r <- format.ftable(x, quote = quote, digits = digits, ...)
    cat(t(r), file = file, append = append,
	sep = c(rep(" ", ncol(r) - 1), "\n"))
    invisible(x)
}

print.ftable <- function(x, digits = getOption("digits"), ...)
    write.ftable(x, quote = FALSE, digits = digits, ...)

read.ftable <- function(file, sep = "", quote = "\"", row.var.names,
                        col.vars, skip = 0)
{
    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(!isSeekable(file)) {
        ## We really need something seekable, see below.  If it is not,
        ## the best we can do is write everything to a tempfile.
        tmpf <- tempfile()
        cat(readLines(file), file = tmpf, sep="\n")
        file <- file(tmpf, "r")
        on.exit({close(file);unlink(tmpf)}, add=TRUE)
    }

    z <- utils::count.fields(file, sep, quote, skip)
    n.row.vars <- z[max(which(z == max(z)))] - z[length(z)] + 1

    seek(file, where = 0)
    if(skip > 0) readLines(file, skip)
    lines <- readLines(file)
    seek(file, where = 0)
    if(skip > 0) readLines(file, skip)

    i <- which(z == n.row.vars)
    ## For an ftable, we have
    ##                     cv.1.nm cv.1.l1 .........
    ##                     cv.2.nm cv.2.l1 .........
    ## rv.1.nm ... rv.k.nm
    ## rv.1.l1 ... rv.k.l1         ...     ...
    ##
    ## so there is exactly one line which does not start with a space
    ## and has n.row.vars fields (and it cannot be the first one).
    j <- i[grep("^[^[:space:]]", lines[i])]
    if((length(j) == 1L) && (j > 1)) {
        ## An ftable: we can figure things out ourselves.
        n.col.vars <- j - 1
        col.vars <- vector("list", length = n.col.vars)
        n <- c(1, z[1 : n.col.vars] - 1)
        for(k in seq.int(from = 1, to = n.col.vars)) {
            s <- scan(file, what = "", sep = sep, quote = quote,
                      nlines = 1, quiet = TRUE)
            col.vars[[k]] <- s[-1L]
            names(col.vars)[k] <- s[1L]
        }
	row.vars <- setNames(vector("list", length = n.row.vars),
			     scan(file, what = "", sep = sep, quote = quote,
				  nlines = 1, quiet = TRUE))
        z <- z[-(1 : (n.col.vars + 1))]
    }
    else {
        ## This is not really an ftable.
        if((z[1L] == 1) && z[2L] == max(z)) {
            ## Case A.  File looks like
            ##
            ##                                cvar.nam
            ## rvar.1.nam   ... rvar.k.nam    cvar.lev.1 ... cvar.lev.l
            ## rvar.1.lev.1 ... rvar.k.lev.1  ...        ... ...
            ##
            n.col.vars <- 1
            col.vars <- vector("list", length = n.col.vars)
            s <- scan(file, what = "", sep = sep, quote = quote,
                      nlines = 2, quiet = TRUE)
            names(col.vars) <- s[1L]
            s <- s[-1L]
            row.vars <- vector("list", length = n.row.vars)
            i <- 1 : n.row.vars
            names(row.vars) <- s[i]
            col.vars[[1L]] <- s[-i]
            z <- z[-(1 : 2)]
        }
        else {
            ## Case B.
            ## We cannot determine the names and levels of the column
            ## variables, and also not the names of the row variables.
            if(missing(row.var.names)) {
                ## 'row.var.names' should be a character vector (or
                ## factor) with the names of the row variables.
                stop("'row.var.names' missing")
            }
            n.row.vars <- length(row.var.names)
	    row.vars <- setNames(vector("list", length = n.row.vars),
				 as.character(row.var.names))
            if(missing(col.vars) || !is.list(col.vars)) {
                ## 'col.vars' should be a list.
                stop("'col.vars' missing or incorrect")
            }
            col.vars <- lapply(col.vars, as.character)
            n.col.vars <- length(col.vars)
            if(is.null(names(col.vars)))
                names(col.vars) <-
                    paste("Factor", seq_along(col.vars), sep = ".")
            else {
                nam <- names(col.vars)
                ind <- which(!nzchar(nam))
                names(col.vars)[ind] <-
                    paste("Factor", ind, sep = ".")
            }
        }
    }

    p <- 1
    n <- integer(n.row.vars)
    for(k in seq.int(from = 1, to = n.row.vars)) {
        n[k] <- sum(z >= max(z) - k + 1) / p
        p <- p * n[k]
    }
    is.row.lab <- rep(rep(c(TRUE, FALSE), length(z)),
                      c(rbind(z - min(z) + 1, min(z) - 1)))
    s <- scan(file, what = "", sep = sep, quote = quote, quiet = TRUE)
    values <- as.numeric(s[!is.row.lab])
    tmp <- s[is.row.lab]
    len <- length(tmp)
    for(k in seq.int(from = 1, to = n.row.vars)) {
        i <- seq.int(from = 1, to = len, by = len / n[k])
        row.vars[[k]] <- unique(tmp[i])
        tmp <- tmp[seq.int(from = 2, to = len / n[k])]
        len <- length(tmp)
    }
    values <- matrix(values,
                     nrow = prod(sapply(row.vars, length)),
                     ncol = prod(sapply(col.vars, length)),
                     byrow = TRUE)
    structure(values,
              row.vars = row.vars,
              col.vars = col.vars,
              class = "ftable")
}

as.data.frame.ftable <-
function(x, row.names = NULL, optional = FALSE, ...)
    as.data.frame(as.table(x), row.names, optional)

as.matrix.ftable <-
function(x, sep = "_", ...)
{
    if(!inherits(x, "ftable"))
	stop("'x' must be an \"ftable\" object")

    make_dimnames <- function(vars) {
        structure(list(do.call(paste,
                               c(rev(expand.grid(rev(vars))), 
                                 list(sep=sep)))),
                  names = paste(collapse=sep, names(vars)))
    }

    structure(unclass(x),
              dimnames = c(make_dimnames(attr(x, "row.vars")),
                           make_dimnames(attr(x, "col.vars"))),
              row.vars = NULL,
              col.vars = NULL)
}