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# file MASS/corresp.q
# copyright (C) 1994-2004 W. N. Venables and B. D. Ripley
#
corresp <- function(x, ...) UseMethod("corresp")
corresp.xtabs <- function(x, ...)
{
if((m <- length(dim(x))) > 2)
stop(gettextf("frequency table is %d-dimensional", m), domain = NA)
corresp.matrix(x, ...)
}
corresp.data.frame <- function(x, ...)
corresp.matrix(as.matrix(x), ...)
corresp.default <- function(x, ...)
stop("invalid table specification")
corresp.factor <- function(x, y, ...)
corresp.matrix(table(x, y), ...)
corresp.formula <- function(formula, data = parent.frame(), ...)
{
rhs <- formula[[length(formula)]]
if(length(rhs[[2]]) > 1 || length(rhs[[3]]) > 1)
stop("higher-way table requested. Only 2-way allowed")
tab <- table(eval(rhs[[2]], data), eval(rhs[[3]], data))
names(dimnames(tab)) <- as.character(c(rhs[[2]], rhs[[3]]))
corresp.matrix(tab, ...)
}
corresp.matrix <- function(x, nf = 1, ...)
{
if(any(x < 0 | x %% 1 > 10 * sqrt(.Machine$double.eps)))
warning("negative or non-integer entries in table")
if((N <- sum(x)) == 0) stop("all frequencies are zero")
Dr <- drop(x %*% (rep(1/N, ncol(x))))
Dc <- drop((rep(1/N, nrow(x))) %*% x)
if(any(Dr == 0) || any(Dc == 0)) stop("empty row or column in table")
x1 <- x/N - outer(Dr, Dc)
Dr <- 1/sqrt(Dr)
Dc <- 1/sqrt(Dc)
if(is.null(dimnames(x)))
dimnames(x) <- list(Row = paste("R", 1:nrow(x)),
Col = paste("C", 1:ncol(x)))
if(is.null(names(dimnames(x))))
names(dimnames(x)) <- c("Row", "Column")
X.svd <- svd(t(t(x1 * Dr) * Dc))
dimnames(X.svd$u) <- list(rownames(x), NULL)
dimnames(X.svd$v) <- list(colnames(x), NULL)
res <- list(cor = X.svd$d[1:nf], rscore = X.svd$u[, 1:nf] * Dr,
cscore = X.svd$v[, 1:nf] * Dc, Freq = x)
class(res) <- "correspondence"
res
}
plot.correspondence <- function(x, scale=1, ...)
{
if(length(x$cor) > 1) return(invisible(biplot(x, ...)))
Fr <- x$Freq
rs <- x$rscore
cs <- x$cscore
xs <- range(cs)
xs <- xs + diff(xs) * c(-1/5, 1/5)
ys <- range(rs)
ys <- ys + diff(ys) * c(-1/5, 1/5)
x <- cs[col(Fr)]
y <- rs[row(Fr)]
rcn <- names(dimnames(Fr))
plot(x, y, xlim = xs, ylim = ys, xlab = rcn[2], ylab = rcn[1], pch = 3)
size <- min(par("pin"))/20 * scale
symbols(x, y, circles = as.vector(sqrt(Fr)), inches = size, add = TRUE)
x0 <- (min(cs) + min(xs))/2
y0 <- (min(rs) + min(ys))/2
text(cs, y0, names(cs))
text(x0, rs, names(rs), adj = 1)
invisible()
}
print.correspondence <- function(x, ...)
{
cat("First canonical correlation(s):", format(x$cor, ...), "\n")
rcn <- names(dimnames(x$Freq))
cat("\n", rcn[1], "scores:\n")
print(x$rscore)
cat("\n", rcn[2], "scores:\n")
print(x$cscore)
invisible(x)
}
biplot.correspondence <-
function(x, type = c("symmetric", "rows", "columns"), ...)
{
if(length(x$cor) < 2) stop("biplot is only possible if nf >= 2")
type <- match.arg(type)
X <- x$rscore[, 1:2]
if(type != "columns") X <- X %*% diag(x$cor[1:2])
colnames(X) <- rep("", 2)
Y <- x$cscore[, 1:2]
if(type != "rows") Y <- Y %*% diag(x$cor[1:2])
colnames(Y) <- rep("", 2)
switch(type, "symmetric" = biplot(X, Y, var.axes = FALSE, ...),
"rows" = biplot.bdr(X, Y, ...),
"columns" = biplot.bdr(Y, X, ...))
points(0, 0, pch = 3, cex = 3)
invisible()
}
biplot.bdr <-
function(obs, bivars, col, cex = rep(par("cex"), 2),
olab = NULL, vlab = NULL, xlim = NULL, ylim = NULL, ...)
{
# for cases where we need equal scales for the two sets of vars.
expand.range <- function(x)
{
if(x[1] > 0) x[1] <- - x[1]
else if(x[2] < 0) x[2] <- - x[2]
x
}
n <- dim(obs)[1]
p <- dim(bivars)[1]
vlab.real <- rownames(bivars)
if(is.logical(vlab)) vlab <- vlab.real[vlab]
else if(length(vlab) != p) vlab <- vlab.real
else vlab <- as.character(vlab)
if(!length(vlab)) {
vlab.real <- vlab <- paste("Var", 1:p)
dimnames(bivars) <- list(vlab, colnames(bivars))
}
if(length(olab)) olab <- rep(as.character(olab), length.out = n)
else {
olab <- rownames(obs)
if(length(olab) != n) olab <- as.character(1:n)
}
if(length(cex) != 2) cex <- rep(cex, length.out = 2)
if(missing(col)) {
col <- par("col")
if (!is.numeric(col)) col <- match(col, palette())
col <- c(col, col + 1)
}
else if(length(col) != 2) col <- rep(col, length.out = 2)
ro1 <- expand.range(range(obs[, 1]))
ro2 <- expand.range(range(obs[, 2]))
rv1 <- expand.range(range(bivars[, 1]))
rv2 <- expand.range(range(bivars[, 2]))
if(!(length(xlim) || length(ylim)))
xlim <- ylim <- range(ro1, ro2, rv1, rv2)
else if(!length(xlim)) xlim <- range(ro1, rv1)
else if(!length(ylim)) ylim <- range(ro2, rv2)
on.exit(par(oldpar))
oldpar <- par(pty = "s")
plot(obs, type = "n", xlim = xlim, ylim = ylim, col = col[1], ...)
text(obs, labels=olab, cex = cex[1], col = col[1], ...)
par(new = TRUE)
plot(bivars, axes = FALSE, type = "n", xlim = xlim, ylim =
ylim, xlab = "", ylab = "", col = col[1], ...)
axis(3, col = col[2])
axis(4, col = col[2])
box(col = col[1])
text(bivars, labels=vlab, cex = cex[2], col = col[2], ...) #
invisible()
}
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