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Misc.s
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Misc.s
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if(!exists("NROW", mode='function')) {
NROW <- function(x)
if (is.array(x) || is.data.frame(x)) nrow(x) else length(x)
}
if(!exists("NCOL", mode='function')) {
NCOL <- function(x)
if (is.array(x) && length(dim(x)) > 1 || is.data.frame(x)) ncol(x) else as.integer(1)
}
prn <- function(x, txt, file='')
{
calltext <- as.character(sys.call())[2]
if(file != '') sink(file, append=TRUE)
if(!missing(txt)) {
if(nchar(txt) + nchar(calltext) +3 > .Options$width)
calltext <- paste('\n\n ',calltext,sep='')
else
txt <- paste(txt, ' ', sep='')
cat('\n', txt, calltext, '\n\n', sep='')
}
else cat('\n',calltext,'\n\n',sep='')
print(x)
if(file != '') sink()
invisible()
}
formatSep <- function(x, digits, ...)
{
y <- character(length(x))
for(i in 1:length(x))
y[i] <- if(missing(digits)) format(x[i], ...)
else format(x[i],digits=digits, ...)
names(y) <- names(x)
y
}
nomiss <- function(x)
{
if(is.data.frame(x)) na.exclude(x)
else if(is.matrix(x))
x[!is.na(x %*% rep(1,ncol(x))),]
else x[!is.na(x)]
}
fillin <- function(v, p)
{
v.f <- ifelse(is.na(v),p,v)
if(length(p)==1)
label(v.f) <- paste(label(v),"with",sum(is.na(v)),
"NAs replaced with",format(p))
else
label(v.f) <- paste(label(v),"with",sum(is.na(v)),"NAs replaced")
v.f
}
spearman <- function(x, y)
{
x <- as.numeric(x)
y <- as.numeric(y) ## 17Jul97
notna <- !is.na(x+y) ##exclude NAs
if(sum(notna) < 3)
c(rho=NA)
else
c(rho=cor(rank(x[notna]), rank(y[notna])))
}
plotCorrPrecision <- function(rho=c(0,0.5), n=seq(10,400,length.out=100),
conf.int=0.95, offset=.025, ...)
{
## Thanks to Xin Wang for computations
curves <- vector('list', length(rho))
names(curves) <- paste('r',format(rho),sep='=')
zcrit <- qnorm(1-(1-conf.int)/2)
for(i in 1:length(rho)) {
r <- rho[i]
z <- .5*log((1+r)/(1-r))
lo <- z - zcrit/sqrt(n-3)
hi <- z + zcrit/sqrt(n-3)
rlo <- (exp(2*lo)-1)/(exp(2*lo)+1)
rhi <- (exp(2*hi)-1)/(exp(2*hi)+1)
precision <- pmax(rhi-r, r-rlo)
curves[[i]] <- list(N=n, Precision=precision)
}
labcurve(curves, pl=TRUE, xrestrict=quantile(n,c(.25,1)), offset=offset, ...)
invisible()
}
trap.rule <- function(x,y) sum(diff(x)*(y[-1]+y[-length(y)]))/2
uncbind <- function(x, prefix="", suffix="")
{
nn <- dimnames(x)[[2]]
warning("You are using uncbind. That was a really bad idea. If you had any variables in the global environment named ", paste(prefix, nn, suffix, sep="", collapse=", "), " they are now over writen.\n\nYou are now warned.", immediate. = TRUE, )
for(i in 1:ncol(x))
assign(paste(prefix,nn[i],suffix,sep=""), x[,i], pos=parent.env())
invisible()
}
## Function to pick off ordinates of a step-function at user-chosen abscissas
stepfun.eval <- function(x, y, xout, type=c("left","right"))
{
s <- !is.na(x+y)
type <- match.arg(type)
approx(x[s], y[s], xout=xout, method="constant", f=if(type=="left")0 else 1)$y
}
km.quick <- function(S, times, q)
{
sRequire('survival')
S <- S[!is.na(S),]
n <- nrow(S)
stratvar <- factor(rep(1,nrow(S)))
f <- survival::survfitKM(stratvar, S, se.fit=FALSE, conf.type='none')
tt <- c(0, f$time)
ss <- c(1, f$surv)
if(missing(times))
min(tt[ss <= q])
else
approx(tt, ss, xout=times, method='constant', f=0)$y
}
oPar <- function()
{
## Saves existing state of par() and makes changes suitable
## for restoring at the end of a high-level graphics functions
oldpar <- par()
oldpar$fin <- NULL
oldpar$new <- FALSE
invisible(oldpar)
}
setParNro <- function(pars)
{
## Sets non-read-only par parameters from the input list
i <- names(pars) %nin%
c('cin','cra','csi','cxy','din','xlog','ylog','gamma','page')
invisible(par(pars[i]))
}
mgp.axis.labels <- function(value, type=c('xy','x','y','x and y'))
{
type <- match.arg(type)
if(missing(value)) {
value <- .Options$mgp.axis.labels
pr <- par(c('mgp', 'las'))
mgp <- pr$mgp
if(! length(value)) value <- c(.7, .7)
return(switch(type,
xy = value,
x = c(mgp[1], value[1], mgp[3]),
y = c(mgp[1], value[2], mgp[3]),
'x and y' = list(x = c(mgp[1], value[1], mgp[3]),
y = c(mgp[1], value[2], mgp[3]))))
}
if(value[1]=='default')
value <- c(.7,.7)
##c(.6, if(par('las')==1) 1.3 else .6)
options(mgp.axis.labels=value, TEMPORARY=FALSE)
invisible()
}
mgp.axis <-
function(side, at=NULL, ...,
mgp=mgp.axis.labels(type=if(side==1 | side==3)'x' else 'y'),
axistitle=NULL, cex.axis=par('cex.axis'), cex.lab=par('cex.lab'))
{
## Version of axis() that uses appropriate mgp from mgp.axis.labels and
## gets around bug in axis(2, ...) that causes it to assume las=1
mfrow <- par('mfrow')
tcl <- max(par('tcl'), -0.4)
nr <- mfrow[1]; nc <- mfrow[2]
w <- list(side=side)
w <- c(w, list(...))
w$cex.axis <- cex.axis
if(length(at)) w$at <- at
if(side == 1 || side == 3) {
w$mgp <- mgp / nr
w$tcl <- tcl / nr
if(side==1 && length(axistitle))
title(xlab=axistitle, mgp = mgp / min(2.25, nr), cex.lab=cex.lab)
} else {
w$mgp <- mgp / nc
w$tcl <- tcl / nc
las <- par('las')
w$srt <- 90 * (las == 0)
w$adj <- if(las == 0) 0.5
else 1
if(side == 2 && length(axistitle))
title(ylab=axistitle, mgp=mgp / min(2.25, nc), cex.lab=cex.lab)
}
do.call('axis', w)
invisible()
}
trellis.strip.blank <- function()
{
s.b <- lattice::trellis.par.get("strip.background")
s.b$col <- 0
lattice::trellis.par.set("strip.background", s.b)
s.s <- lattice::trellis.par.get("strip.shingle")
s.s$col <- 0
lattice::trellis.par.set("strip.shingle", s.s)
invisible()
}
lm.fit.qr.bare <- function(x, y,
tolerance = NULL,
intercept=TRUE, xpxi=FALSE,
singzero=FALSE)
{
if(!length(tolerance)) tolerance <- 1e-7
if(intercept)
x <- cbind(Intercept=1, x)
else x <- as.matrix(x)
z <- lm.fit(x, y, tol=tolerance)
coef <- z$coefficients
if(singzero && any(isna <- is.na(coef))) coef[isna] <- 0.
res <- z$residuals
sse <- sum(res^2)
sst <- sum((y - mean(y))^2)
res <- list(coefficients = coef, residuals = res,
rsquared = 1 - sse / sst,
fitted.values = z$fitted.values)
if(xpxi) {
p <- 1L : z$rank
res$xpxi <- chol2inv(z$qr$qr[p, p, drop=FALSE])
}
res
}
all.is.numeric <- function(x, what=c('test','vector','nonnum'),
extras=c('.','NA'))
{
what <- match.arg(what)
x <- sub('[[:space:]]+$', '', x)
x <- sub('^[[:space:]]+', '', x)
xs <- x[x %nin% c('', extras)]
if(! length(xs) || all(is.na(x)))
return(switch(what, test = FALSE, vector=x, nonnum=x[0]))
isnon <- suppressWarnings(! is.na(xs) & is.na(as.numeric(xs)))
isnum <- ! any(isnon)
# suppressWarnings below handles extras present in x
switch(what,
test = isnum,
vector = if(isnum) suppressWarnings(as.numeric(x)) else x,
nonnum = xs[isnon])
}
Lag <- function(x, shift=1)
{
## Lags vector x shift observations, padding with NAs or blank strings
## preserving attributes of x
xLen <- length(x)
if(shift == 0) return(x)
# Create base vector use character to generate "" for mode "character"
# Coerce base vector to be type of x
ret <- as.vector(character(xLen), mode=storage.mode(x))
# set resp attributes equal to x attributes
attrib <- attributes(x)
if(length(attrib$label))
attrib$label <- paste(attrib$label, 'lagged', shift, 'observations')
if(abs(shift) < xLen)
{
if(shift > 0) ret[-(1:shift)] <- x[1:(xLen - shift)]
else ret[1:(xLen+shift)] <- x[(1-shift):xLen]
}
attributes(ret) <- attrib
return(ret)
}
xySortNoDupNoNA <- function(x, y)
{
if(is.list(x)) {
y <- x[[2]]; x <- x[[1]]
}
s <- !is.na(x + y)
if(any(s)) {
x <- x[s]; y <- y[s]
}
i <- order(x)
x <- x[i]
y <- y[i]
i <- !duplicated(x)
list(x=x[i], y=y[i])
}
outerText <-
function(string, y, cex=par('cex'), ...) {
usr <- par('usr'); plt <- par('plt')
pos <- usr[2] + (usr[2] - usr[1])/(plt[2] - plt[1]) * (1 - plt[2])
axis(2, at=y, labels=string, tick=FALSE, las=1,
pos=pos, cex.axis=cex, xpd=NA)
}
## if(missing(space)) space <- max(nchar(string))*.5
## mtext(string, side=side, las=1, at=y, adj=adj, cex=cex, line=space)
# This method does not survive shrinking the graphics window
# Right justifies (if adj=1) a vector of strings against the right margin
# (side=4) or against the y-axis (side=2)
#outerText <-
# function(string, y, side=4, cex=par('cex'), adj=1, ...) {
# if(side %nin% c(2,4)) stop('only works for side=2 or 4')
# x <- if(side==4) grconvertX(1, from='nfc', to='user') else
# par('usr')[1]
# text(x, y, paste(string,''), cex=cex, adj=adj, xpd=NA)
#}
## Old method [dropped because does not scale upon resizing device]
## Use text() to put test strings in left or right margins
## Temporarily sets par(xpd=NA) if using R
## For adj=1 side=4, setAside is a character string used to determine
## the space to set aside for all strings
## space is the number of extra characters to leave to the left of
## the string(s) (adj=0) or to the right (adj=1)
if(FALSE) outerText <- function(string, y, setAside=string[1], side=4, space=1,
adj=1, cex=par('cex'))
{
usr <- par('usr')
xpd <- par('xpd')
if(!is.na(xpd)) {
on.exit(par(xpd=xpd))
par(xpd=NA)
}
ie <- is.expression(string) ## 1sep02
if(ie)
adj <- 0 ## adj=1 not work well for expressions in R
if(side!=4)
stop('only side=4 implemented')
if(adj==0)
text(usr[2], y,
if(ie)
string
else
paste(space,string,sep=''),
adj=0)
else {
usr.space.needed <- strwidth(setAside, units='user', cex=cex)
text(usr[2]+0.5*strwidth(space, units='user', cex=cex)+usr.space.needed,
y, string, adj=1, cex=cex) # was usr[2]- 18jul02;added 0* 25jul02
## was 0*strwidth(space,...) 31jan03
}
invisible()
}
if(FALSE) {
expandUsrCoord <- function()
{
## Expands usr coordinates of current plot to entire figure region
## so that out of range plots may be plotted
pr <- par()
usr <- pr$usr
p <- pr$plt
invisible(pr)
}
}
## Author: Patrick Connolly <P.Connolly@hortresearch.co.nz>
## HortResearch
## Mt Albert
## Auckland, New Zealand
print.char.matrix <-
function (x, file = "",
col.name.align = "cen", col.txt.align = "right",
cell.align = "cen", hsep = "|", vsep = "-", csep = "+",
row.names = TRUE, col.names = FALSE,
append = FALSE, top.border = TRUE, left.border = TRUE, ...)
{
### To print a data frame or matrix to a text file or screen
### and having names line up with stacked cells
###
### First, add row names as first column (might be removed later)
ndimn <- names(dimnames(x)) ## FEH
rownames <- dimnames(x)[[1]]
x <- cbind(rownames, x)
names(dimnames(x)) <- ndimn ## FEH
cnam <- dimnames(x)[[2]] ## FEH
if(length(ndimn))
cnam[1] <- ndimn[1] ## FEH
##dimnames(x)[[1]] <- seq(nrow(x)) 25Mar02 for R FEH
dimnames(x) <- list(as.character(seq(nrow(x))), cnam)
names(dimnames(x)) <- ndimn ## 26Mar02 FEH
### Set up some padding functions:
###
pad.left <- function(z, pads)
{
## Pads spaces to left of text
padding <- paste(rep(" ", pads), collapse = "")
paste(padding, z, sep = "")
}
pad.mid <- function(z, pads)
{
## Centres text in available space
padding.right <- paste(rep(" ", pads%/%2), collapse = "")
padding.left <- paste(rep(" ", pads - pads%/%2), collapse = "")
paste(padding.left, z, padding.right, sep = "")
}
pad.right <- function(z, pads) {
## Pads spaces to right of text
padding <- paste(rep(" ", pads), collapse = "")
paste(z, padding, sep = "")
}
## (Padding happens on the opposite side to alignment)
pad.types <- c("left", "mid", "right")
names(pad.types) <- c("right", "cen", "left")
pad.name <- pad.types[col.name.align]
pad.txt <- pad.types[col.txt.align]
pad.cell <- pad.types[cell.align]
## Padding character columns
## Need columns with uniform number of characters
pad.char.col.right <- function(y)
{
## For aligning text to LHS of column
col.width <- nchar(y)
biggest <- max(col.width)
smallest <- min(col.width)
padding <- biggest - col.width
out <- NULL
for (i in seq(y))
out[i] <- pad.right(y[i], pads = padding[i])
out
}
pad.char.col.left <- function(y)
{
## For aligning text to RHS of column
col.width <- nchar(y)
biggest <- max(col.width)
smallest <- min(col.width)
padding <- biggest - col.width
out <- NULL
for (i in seq(y))
out[i] <- pad.left(y[i], pads = padding[i])
out
}
pad.char.col.mid <- function(y) {
## For aligning text to centre of column
col.width <- nchar(y)
biggest <- max(col.width)
smallest <- min(col.width)
padding <- biggest - col.width
out <- NULL
for (i in seq(y))
out[i] <- pad.mid(y[i], pads = padding[i])
out
}
## which functions to use this time.
pad.name.fn <- get(paste("pad.", pad.name, sep = ""))
pad.txt.fn <- get(paste("pad.char.col.", pad.txt, sep = ""))
pad.cell.fn <- get(paste("pad.", pad.cell, sep = ""))
## Remove troublesome factors
x <- as.data.frame(x)
fac.col <- names(x)[sapply(x, is.factor)]
for (i in fac.col)
x[, i] <- I(as.character(x[, i]))
## ARE ANY LINE BREAKS IN ANY COLUMNS?
break.list <- list()
for (i in seq(nrow(x))) {
x.i <- unlist(x[i, ])
rows.i <- sapply(strsplit(unlist(x[i, ]), "\n"), length)
rows.i[rows.i < 1] <- 1
break.list[[i]] <- rows.i
}
break.row <- sapply(break.list, function(x) any(x > 1))
names(break.row) <- seq(nrow(x))
xx <- x
if (any(break.row)) {
## add in extra row/s
xx <- NULL
reprow <- lapply(break.list, unique)
for (k in seq(nrow(x))) {
x.k <- unlist(x[k, ])
x.k[x.k == ""] <- " "
if (break.row[k]) {
l.k <- strsplit(x.k, "\n")
add.blanks <- max(break.list[[k]]) - break.list[[k]]
names(l.k) <- names(add.blanks) <- seq(length(l.k))
if (any(add.blanks > 0)) {
for (kk in names(add.blanks[add.blanks > 0]))
l.k[[kk]] <- c(l.k[[kk]], rep(" ", add.blanks[kk]))
}
l.k.df <- as.data.frame(l.k)
names(l.k.df) <- names(x)
xx <- rbind(xx, as.matrix(l.k.df))
}
else xx <- rbind(xx, x.k)
}
row.names(xx) <- paste(rep(row.names(x), sapply(reprow,
max)),
unlist(reprow), sep = ".")
## Make an index for the rows to be printed
rn <- row.names(xx)
rnb <- strsplit(rn, "\\.")
rpref <- as.numeric(factor(sapply(rnb, function(z) z[1])))
## was codes( ) 10oct03
}
else
rpref <- seq(nrow(x))
x <- as.data.frame(xx)
## Character columns need different treatment from numeric columns
char.cols <- sapply(x, is.character)
if (any(char.cols))
x[char.cols] <- sapply(x[char.cols], pad.txt.fn)
## Change numeric columns into character
if (any(!char.cols))
x[!char.cols] <- sapply(x[!char.cols], format)
## now all character columns each of which is uniform element width
##
## Lining up names with their columns
## Sometimes the names of columns are wider than the columns they name,
## sometimes vice versa.
names.width <- nchar(names(x))
if (!col.names)
names.width <- rep(0, length(names.width))
cell.width <- sapply(x, function(y) max(nchar(as.character(y))))
## (the width of the characters in the cells as distinct
## from their names)
name.pads <- cell.width - names.width
cell.pads <- -name.pads
name.pads[name.pads < 0] <- 0
cell.pads[cell.pads < 0] <- 0
pad.names <- name.pads > 0
pad.cells <- cell.pads > 0
## Pad out the column names if necessary:
if (any(pad.names)) {
stretch.names <- names(x)[pad.names]
for (i in stretch.names) {
names(x)[names(x) == i] <- pad.name.fn(i, name.pads[i])
}
}
## likewise for the cells and columns
if (any(pad.cells)) {
stretch.cells <- names(x)[pad.cells]
for (j in stretch.cells) x[, j] <- pad.cell.fn(x[, j],
cell.pads[j])
}
## Remove row names if not required
if (!row.names)
x <- x[-1]
## Put the column names on top of matrix
if (col.names)
mat2 <- rbind(names(x), as.matrix(x))
else
mat2 <- as.matrix(x)
mat.names.width <- nchar(mat2[1, ])
## character string to separate rows
space.h <- ""
for (k in seq(along=mat.names.width)) { ## added along= FEH 26Mar02
space.h <- c(space.h, rep(vsep, mat.names.width[k]), csep)
}
line.sep <- paste(c(ifelse(left.border, csep, ""), space.h),
collapse = "")
if (col.names)
rpref <- c(0, rpref, 0)
else
rpref <- c(rpref, 0)
## print to screen or file
if(top.border && line.sep !='') {
write(line.sep, file = file, append = append)
append <- TRUE
}
for (i in 1:nrow(mat2)) {
if (left.border)
write(paste(paste(c("", mat2[i, ]), collapse = hsep),
hsep, sep = ""), file = file, append = append)
else
write(paste(paste(mat2[i, ], collapse = hsep), hsep,
sep = ""), file = file, append = append)
append <- TRUE
## print separator if row prefix is not same as next one
if (rpref[i] != rpref[i + 1] && line.sep != '')
write(line.sep, file = file, append = TRUE)
}
}
unPaste <- function(str, sep='/')
{
w <- strsplit(str, sep)
w <- matrix(unlist(w), ncol=length(str))
nr <- nrow(w)
ans <- vector('list', nr)
for(j in 1:nr)
ans[[j]] <- w[j,]
ans
}
get2rowHeads <- function(str) {
w <- strsplit(str, '\n')
## strsplit returns character(0) when element="" 23may03
list(sapply(w, function(x)if(length(x)) x[[1]] else ''),
sapply(w, function(x)if(length(x) > 1)x[[2]] else ''))
}
## Note: can't say f[vector of names] <- list(...) to update args
## In R you have to put ALL arguments in list(...) so sometimes we set
## unneeded ones to NULL. Ignore this assignment in S<
## Two lists of functions, one for primitives for S+ or R (either Trellis
## or low-level), one for R grid
## Note: rect is only defined in R, not S+
ordGridFun <- function(grid)
{
if(!grid)
list(lines = function(...) lines(...),
points = function(..., size=NULL)
{
if(length(size))
warning('size not implemented yet')
points(...)
},
text = function(...) text(...),
segments = function(...) segments(...),
arrows = function(..., open, size) arrows(..., length=size*.8),
rect = function(...) rect(...),
polygon = function(x, y=NULL, ..., type=c('l','s'))
{
type <- match.arg(type)
if(!length(y))
{
y <- x$y
x <- x$x
}
j <- !is.na(x+y)
x <- x[j]
y <- y[j]
if(type=='s') polygon(makeSteps(x, y), ..., border=NA)
else polygon(x, y, ..., border=NA)
},
abline = function(...) abline(...),
unit = function(x, units='native')
{
if(units!='native')
stop('units="native" is only units implemented outside of grid')
x
},
axis = function(...) axis(...))
else {
sRequire('lattice')
list(lines = function(x, y, ...)
{
if(is.list(x)) {
y <- x[[2]]; x <- x[[1]]
}
lattice::llines(if(is.unit(x))
convertX(x, 'native', valueOnly=TRUE)
else x,
if(is.unit(y))
convertY(y, 'native', valueOnly=TRUE)
else y,
...)
},
points = function(x, y, ...)
{
if(is.list(x)) {
y <- x[[2]]; x <- x[[1]]
}
lattice::lpoints(if(is.unit(x))
convertX(x, 'native', valueOnly=TRUE)
else x,
if(is.unit(y))
convertY(y, 'native', valueOnly=TRUE)
else y,
...)
},
text = function(x, y, ...)
{
if(is.list(x)) {
y <- x[[2]]; x <- x[[1]]
}
lattice::ltext(if(is.unit(x))
convertX(x, 'native', valueOnly=TRUE)
else x,
if(is.unit(y))
convertY(y, 'native', valueOnly=TRUE)
else y,
...)
},
segments = function(x0, y0, x1, y1, ...)
{
grid.segments(x0, y0, x1, y1, default.units='native',
gp=gpar(...))
},
arrows = function(...) lattice::larrows(...),
rect = function(xleft, ybottom, xright, ytop, density, angle,
border, xpd, ...)
{
grid.rect(xleft, ybottom, width=xright-xleft,
height=ytop-ybottom, just='left',
default.units='native', gp=gpar(...))
},
polygon = function(x, y=NULL, col=par('col'), type=c('l','s'), ...)
{
type <- match.arg(type)
if(!length(y))
{
y <- x$y
x <- x$x
}
j <- !is.na(x+y)
x <- x[j]
y <- y[j]
if(type=='s') grid.polygon(makeSteps(x, y),
default.units='native',
gp=gpar(fill=col, col='transparent', ...))
else grid.polygon(x, y, default.units='native',
gp=gpar(fill=col,col='transparent',...))
},
abline=function(...) lattice::panel.abline(...),
unit = function(x, units='native', ...) unit(x, units=units, ...),
axis = function(side=1, at=NULL, labels, ticks=TRUE,
distn, line, pos, outer, ...)
{
if(!length(at))stop('not implemented for at= unspecified')
if(side > 2) stop('not implemented for side=3 or 4')
## ticks=ticks removed from grid.?axis FEH 30Aug09
if(side==1) grid.xaxis(at=at, label=labels, gp=gpar(...))
if(side==2) grid.yaxis(at=at, label=labels, gp=gpar(...))
})
}
}
parGrid <- function(grid=FALSE)
{
pr <- par()
cin <- pr$cin
cex <- pr$cex
lwd <- pr$lwd
if(grid) {
## cvp <- current.viewport()
## usr <- c(cvp$xscale, cvp$yscale)
usr <- c(convertX(unit(0:1, "npc"), "native", valueOnly=TRUE),
convertY(unit(0:1, "npc"), "native", valueOnly=TRUE))
pin <-
c(convertWidth(unit(1, "npc"), "inches", valueOnly=TRUE),
convertHeight(unit(1, "npc"), "inches", valueOnly=TRUE))
uin <-
c(convertWidth(unit(1, "native"), "inches", valueOnly=TRUE),
convertHeight(unit(1, "native"), "inches", valueOnly=TRUE))
}
else {
usr <- pr$usr
pin <- pr$pin
uin <- c(pin[1]/(usr[2]-usr[1]), pin[2]/(usr[4]-usr[3]))
## 22Mar01 - R does not have par(uin)
}
list(usr=usr, pin=pin, uin=uin, cin=cin, cex=cex, lwd=lwd)
}
## Replaces R's xinch, yinch, extending them to grid
## These convert inches to data units
xInch <- function(x=1, warn.log=!grid, grid=FALSE)
{
if (warn.log && par("xlog"))
warning("x log scale: xInch() is nonsense")
pr <- parGrid(grid)
x * diff(pr$usr[1:2])/pr$pin[1]
}
yInch <- function (y = 1, warn.log=!grid, grid=FALSE)
{
if (warn.log && par("ylog"))
warning("y log scale: yInch is nonsense")
pr <- parGrid(grid)
y * diff(pr$usr[3:4])/pr$pin[2]
}
na.include <- function(obj) {
if(inherits(obj,'data.frame'))
for(i in seq(along=obj))
obj[[i]] <- na.include(obj[[i]])
else {
if(length(levels(obj)) && any(is.na(obj)))
obj <- factor(obj,exclude=NULL)
}
obj
}
if(FALSE) {
whichClosest <- function(x, w)
{
## x: vector of reference values
## w: vector of values to find closest matches in x
## Returns: subscripts in x corresponding to w
i <- order(x)
x <- x[i]
n <- length(x)
br <- c(-1e30, x[-n]+diff(x)/2,1e30)
m <- length(w)
i[.C("bincode", as.double(w), m, as.double(br),
length(br), code = integer(m), right = TRUE,
include = FALSE, NAOK = TRUE, DUP = FALSE,
PACKAGE = "base")$code]
}
NULL
}
## Just as good, ties shuffled to end
## function(x, w) round(approx(x,1:length(x),xout=w,rule=2,ties='ordered')$y)
## Remove ties= for S-Plus. Note: does not work when 2nd arg to
## approx is not uniformly spaced
## NO! ties='ordered' bombs in x not ordered
## Try
## approx(c(1,3,5,2,4,2,4),1:7,xout=c(1,3,5,2,4,2,4),rule=2,ties=function(x)x[1])
## NO: only works in general if both x and y are already ordered
## The following runs the same speed as the previous S version (in R anyway)
whichClosest <- function(x, w)
{
## x: vector of reference values
## w: vector of values for which to lookup closest matches in x
## Returns: subscripts in x corresponding to w
## Assumes no NAs in x or w
.Fortran(F_wclosest,as.double(w),as.double(x),
length(w),length(x),
j=integer(length(w)))$j
}
whichClosePW <- function(x, w, f=0.2) {
lx <- length(x)
lw <- length(w)
.Fortran(F_wclosepw,as.double(w),as.double(x),
as.double(runif(lw)),as.double(f),
lw, lx, double(lx), j=integer(lw))$j
}
whichClosek <- function(x, w, k) {
## x: vector of reference values
## w: vector of values for which to lookup close matches in x
## Returns: subscripts in x corresponding to w
## Assumes no NAs in x or w
## First jitters x so there are no ties
## Finds the k closest matches and takes a single random pick of these k
y <- diff(sort(x))
mindif <- if(all(y == 0)) 1 else min(y[y > 0])
x <- x + runif(length(x), -mindif/100, mindif/100)
z <- abs(outer(w, x, "-"))
s <- apply(z, 1, function(u) order(u)[1:k])
if(k == 1) return(s)
apply(s, 2, function(u) sample(u, 1))
}
if(FALSE) {
sampWtdDist <- function(x, w)
{
## x: vector of reference values
## w: vector of values to find closest matches in x
## Returns: subscripts in x corresponding to w
## 25% slower but simpler method:
## z <- abs(outer(w, x, "-"))
## s <- apply(z, 1, max)
## z <- (1 - sweep(z, 1, s, FUN='/')^3)^3
## sums <- apply(z, 1, sum)
## z <- sweep(z, 1, sums, FUN='/')
lx <- length(x)
lw <- length(w)
z <- matrix(abs( rep( x , lw ) - rep( w, each = lx ) ),
nrow=lw, ncol=lx, byrow=TRUE) ## Thanks: Chuck Berry
## s <- pmax( abs( w - min(x) ), abs( w - max(x) ) ) # to use max dist
s <- rowSums(z)/lx/3 # use 1/3 mean dist for each row
tricube <- function(u) (1 - pmin(u,1)^3)^3
## z <- (1 - (z/rep(s,length.out=lx*lw))^3)^3 # Thanks: Tim Hesterberg
z <- tricube(z/s) # Thanks: Tim Hesterberg
sums <- rowSums(z)
z <- z/sums
as.vector(rMultinom(z, 1))
}
NULL
}
approxExtrap <- function(x, y, xout, method='linear', n=50, rule=2,
f=0, ties='ordered', na.rm=FALSE)
{
## Linear interpolation using approx, with linear extrapolation
## beyond the data
if(is.list(x)) {
y <- x[[2]]; x <- x[[1]]
}
## remove duplicates and order so can do linear extrapolation
if(na.rm) {
d <- ! is.na(x + y)
x <- x[d]; y <- y[d]
}
x <- as.numeric(x) # handles dates etc.
y <- as.numeric(y)
d <- ! duplicated(x)
x <- x[d]
y <- y[d]
d <- order(x)
x <- x[d]
y <- y[d]
w <- approx(x, y, xout=xout, method=method, n=n,
rule=2, f=f, ties=ties)$y
r <- range(x)
d <- xout < r[1]
if(any(is.na(d)))
stop('NAs not allowed in xout')
if(any(d))
w[d] <- (y[2]-y[1])/(x[2]-x[1])*(xout[d]-x[1])+y[1]
d <- xout > r[2]
n <- length(y)
if(any(d))
w[d] <- (y[n]-y[n-1])/(x[n]-x[n-1])*(xout[d]-x[n-1])+y[n-1]
list(x=xout, y=w)
}
inverseFunction <- function(x, y) {
d <- diff(y)
xd <- x[-1]
dl <- c(NA, d[-length(d)])
ic <- which(d>=0 & dl<0 | d>0 & dl<=0 | d<=0 & dl>0 | d<0 & dl>=0)
nt <- length(ic)
k <- nt + 1
if(k==1) {
h <- function(y, xx, yy, turns, what, coef)
approx(yy, xx, xout=y, rule=2)$y
formals(h) <- list(y=numeric(0), xx=x, yy=y, turns=numeric(0),
what=character(0), coef=numeric(0))
return(h)
}
turns <- x[ic]
turnse <- c(-Inf, turns, Inf)
xrange <- yrange <- matrix(NA, nrow=k, ncol=2)
for(j in 1:k) {
l <- which(x >= turnse[j] & x <= turnse[j+1])
xrange[j,] <- x[l[c(1,length(l))]]
yrange[j,] <- y[l[c(1,length(l))]]
}
for(j in 1:length(ic)) {
l <- (ic[j]-1):(ic[j]+1)
turns[j] <- approxExtrap(d[l], xd[l], xout=0, na.rm=TRUE)$y
}