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summaryRc <-
function(formula, data=NULL, subset=NULL, na.action=NULL,
fun=function(x) x, na.rm=TRUE,
ylab=NULL, ylim = NULL, xlim=NULL, nloc=NULL, datadensity=NULL,
quant = c(0.05, 0.1, 0.25, 0.5, 0.75, 0.9, 0.95),
quantloc = c('top', 'bottom'), cex.quant=.6, srt.quant=0,
bpplot = c('none', 'top', 'top outside', 'top inside', 'bottom'),
height.bpplot = 0.08,
trim=NULL, test=FALSE, vnames=c('labels','names'),
...)
{
call <- match.call()
quantloc <- match.arg(quantloc)
vnames <- match.arg(vnames)
bpplot <- match.arg(bpplot)
if(bpplot == 'top') bpplot <- 'top inside'
X <- match.call(expand.dots=FALSE)
X$fun <- X$na.rm <- X$ylim <- X$xlim <- X$ylab <- X$nloc <- X$datadensity <-
X$quant <- X$quantloc <- X$cex.quant <- X$srt.quant <- X$trim <- X$test <-
X$vnames <- X$bpplot <- X$height.bpplot <- X$... <- NULL
if(missing(na.action)) X$na.action <- na.retain
Terms <- if(missing(data)) terms(formula, 'stratify')
else terms(formula, 'stratify', data=data)
X$formula <- Terms
X[[1]] <- as.name("model.frame")
X <- eval(X, sys.parent())
Terms <- attr(X, "terms")
resp <- attr(Terms, "response")
nact <- attr(X, "na.action")
nvar <- ncol(X) - 1
strat <- attr(Terms, 'specials')$stratify
getlab <- function(x, default) {
if(vnames == 'names') return(default)
lab <- attr(x, 'label')
if(!length(lab) || lab=='') default else lab
}
if(length(strat)) {
sRequire('survival')
temp <- survival::untangle.specials(Terms,'stratify')
strat.name <- var.inner(Terms)[temp$terms]
strat <- if(length(temp$vars) == 1) as.factor(X[[temp$vars]])
else stratify(X[,temp$vars])
strat.label <- getlab(X[, temp$vars[1]], strat.name)
X[[temp$vars]] <- NULL # remove strata factors
}
Y <- X[[resp]]
yname <- as.character(attr(Terms, 'variables'))[2]
ylabel <- if(length(ylab)) ylab else getlab(Y, yname)
X[[resp]] <- NULL # remove response var
Y <- as.matrix(Y)
s <- rowSums(is.na(Y)) == ncol(Y)
nmissy <- sum(s)
if(nmissy) {
X <- X[!s,, drop=FALSE]
Y <- Y[!s,, drop=FALSE]
strat <- strat[!s]
}
pl <- function(x, y, strat=NULL, quant, bpplot, width.bpplot,
xlab='', ylab='',
ylim=NULL, xlim=NULL, fun=function(x) x, ...) {
n <- sum(!is.na(x))
group <- if(length(strat)) strat else rep(1, length(x))
if(!length(trim)) trim <- if(n > 200) 10 / n else 0
if(!length(xlim)) {
xlim <- if(trim == 0) range(x, na.rm=TRUE)
else quantile(x, c(trim, 1 - trim), na.rm=TRUE)
}
a <- list(x=x, y=y, xlab=xlab, ylab=ylab, xlim=xlim, trim=0, group=group,
datadensity=if(length(datadensity)) datadensity
else length(strat) > 0, ...)
if(length(fun)) a$fun <- fun
if(length(ylim)) a$ylim <- ylim
z <- do.call('plsmo', a)
usr <- par('usr')
xl <- usr[1:2]
yl <- usr[3:4]
if(! (length(nloc) && is.logical(nloc) && !nloc)) {
if(length(nloc)) {
xx <- nloc[[1]]
yy <- nloc[[2]]
xx <- xl[1] + xx * diff(xl)
yy <- yl[1] + yy * diff(yl)
w <- list(x=xx, y=yy)
}
else {
xs <- unlist(lapply(z, function(x)x$x))
ys <- unlist(lapply(z, function(x)x$y))
w <- largest.empty(xs, ys, method='area')
}
text(w, paste('n=', n, sep=''), cex=.75, font=3, adj=.5)
}
# Compute user y-units per inch
u <- diff(yl) / par('fin')[2]
if(bpplot != 'none') {
h <- u * height.bpplot
yy <- switch(bpplot,
'top outside' = yl[2] + h/2 + u*.11,
'top inside' = yl[2] - h/2 - u*.11,
bottom = yl[1] + h/2 + u*.11)
panel.bpplot(x, yy, nogrid=TRUE, pch=19, cex.means=.6, height=h)
}
else
if(length(quant)) {
h <- u * .15
qu <- quantile(x, quant, na.rm=TRUE)
names(qu) <- as.character(quant)
qu <- pooleq(qu)
yq <- if(quantloc == 'top') yl[2] else yl[1]
arrows(qu, yq + h, qu, yq, col='blue', length=.05, xpd=NA)
if(cex.quant > 0)
text(qu, yq + 1.4 * h, names(qu), adj=if(srt.quant == 0) .5 else 0,
cex=cex.quant, srt=srt.quant, xpd=NA)
}
## text(xl[2], yl[2] + h/4, paste('n=', n, sep=''),
## cex=.75, font=3, adj=c(1,0), xpd=NA)
}
## Find all ties in quantiles and build combined labels
pooleq <- function(x) {
w <- tapply(names(x), x, paste, collapse=', ')
x <- as.numeric(names(w))
names(x) <- w
x
}
i <- 0
nams <- names(X)
for(v in nams) {
i <- i + 1
x <- X[[v]]
xlab <- getlab(x, nams[i])
units <- if(length(l <- attr(x,'units'))) l else ''
xlab <- labelPlotmath(xlab, units)
pl(x, Y, strat=strat, quant=quant, bpplot=bpplot,
height.bpplot=height.bpplot,
xlab=xlab, ylab=ylabel, ylim=ylim, xlim=xlim[[v]], ...)
}
}
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