https://github.com/cran/Hmisc
Tip revision: ed13e009b5de5ec4ab685cb7f87fe4f3363d706a authored by Frank E Harrell Jr on 05 September 2004, 16:40:45 UTC
version 2.2-2
version 2.2-2
Tip revision: ed13e00
Misc.Rd
\name{Misc}
\alias{confbar}
\alias{james.stein}
\alias{km.quick}
\alias{lm.fit.qr.bare}
\alias{matxv}
\alias{nomiss}
\alias{outerText}
\alias{sepUnitsTrans}
\alias{trap.rule}
\alias{trellis.strip.blank}
\alias{under.unix}
\alias{.R.}
\alias{.SV4.}
\alias{unPaste}
\alias{whichClosest}
\alias{whichClosePW}
\alias{xless}
\title{Miscellaneous Functions}
\description{
This documents miscellaneous small functions in Hmisc that may be of
interest to users.
\code{confbar} draws multi-level confidence bars using small rectangles
that may be of different colors.
\code{james.stein} computes James-Stein shrunken estimates of cell
means given a response variable (which may be binary) and a grouping
indicator.
\code{km.quick} provides a fast way to invoke \code{survfit.km} in the
\code{survival} package to get Kaplan-Meier estimates for a
single stratum for a vector of time points (if \code{times} is given) or to
get a vector of survival time quantiles (if \code{q} is given).
\code{lm.fit.qr.bare} is a fast stripped-down function for computing
regression coefficients, residuals, \eqn{R^2}, and fitted values. It
uses the Fortran routines \code{dqrls}.
\code{matxv} multiplies a matrix by a vector, handling automatic
addition of intercepts if the matrix does not have a column of ones.
If the first argument is not a matrix, it will be converted to one.
\code{nomiss} returns a data frame (if its argument is one) with rows
corresponding to \code{NA}s removed, or it returns a matrix with rows
with any element missing removed.
\code{outerText} uses \code{text()} to put test strings in left or
right margins. It temporarily sets \code{par(xpd=NA)} if using \R.
\code{sepUnitsTrans} converts character vectors containing values such
as \code{c("3 days","3day","4month","2 years","2weeks","7")} to
numeric vectors
(here \code{c(3,3,122,730,14,7)}) in a flexible fashion. The user can
specify a
vector of units of measurements and conversion factors. The units
with a conversion factor of \code{1} are taken as the target units,
and if those units are present in the character strings they are
ignored. The target units are added to the resulting vector as the
\code{"units"} attribute.
\code{trap.rule} computes the area under a curve using the trapezoidal
rule, assuming \code{x} is sorted.
\code{trellis.strip.blank} sets up Trellis or Lattice graphs to have a
clear background on the strips for panel labels.
\code{under.unix} is a scalar logical value that is \code{TRUE} if you
are running Linux or Unix.
\code{.R.} is a logical value set to \code{TRUE} if running \R,
\code{FALSE} for S-Plus.
\code{.SV4.} is a logical value set to \code{TRUE} if running version
4 of the S language under S-Plus, \code{FALSE} otherwise.
\code{unPaste} provides a version of the S-Plus \code{unpaste} that
works for \R and S-Plus.
\code{whichClosePW} is a very fast function using weighted multinomial
sampling to determine which element of a vector is "closest" to each
element of another vector. \code{whichClosest} quickly finds the closest
element without any randomness.
\code{xless} is a function for Linux/Unix users to invoke the system
\code{xless} command to pop up a window to display the result of
\code{print}ing an object.
}
\usage{
confbar(at, est, se, width, q = c(0.7, 0.8, 0.9, 0.95, 0.99),
col = if (.R.) gray(c(0, 0.25, 0.5, 0.75, 1)) else
if (under.unix) c(1, 0.8, 0.5, 0.2, 0.065) else
c(1, 4, 3, 2, 5),
type = c("v", "h"), labels = TRUE, ticks = FALSE,
cex = 0.5, side = "l", lwd = 5, clip = c(-1e+30, 1e+30),
fun = function(x) x,
qfun = function(x) ifelse(x == 0.5, qnorm(x),
ifelse(x < 0.5, qnorm(x/2),
qnorm((1 + x)/2))))
james.stein(y, group)
km.quick(S, times, q)
lm.fit.qr.bare(x, y, tolerance, intercept=TRUE, xpxi=FALSE)
matxv(a, b, kint=1)
nomiss(x)
outerText(string, y, setAside=string[1], side=4, space=1,
adj=1, cex=par('cex'))
sepUnitsTrans(x, conversion=c(day=1, month=365.25/12, year=365.25, week=7),
round=FALSE, digits=0)
trap.rule(x, y)
trellis.strip.blank()
unPaste(str, sep="/", extended=FALSE)
whichClosest(x, w)
whichClosePW(x, w, f=0.2)
xless(x, \dots, title)
}
\arguments{
\item{at}{x-coordinate for vertical confidence intervals, y-coordinate
for horizontal}
\item{est}{vector of point estimates for confidence limits}
\item{se}{vector of standard errors}
\item{width}{width of confidence rectanges in user units}
\item{q}{vector of confidence coefficients or quantiles}
\item{col}{vector of colors}
\item{type}{\code{"v"} for vertical, \code{"h"} for horizontal}
\item{labels}{set to \code{FALSE} to omit drawing confidence
coefficients}
\item{ticks}{set to \code{TRUE} to draw lines between rectangles}
\item{cex}{character expansion factor}
\item{side}{for \code{confbar} is \code{"b","l","t","r"} for bottom,
left, top, right. For \code{outText} is the using integers 1-4
corresponding to these.}
\item{lwd}{line widths}
\item{clip}{interval to truncate limits}
\item{fun}{function to transform scale}
\item{qfun}{quantiles on transformed scale}
\item{group}{a categorical grouping variable}
\item{S}{a \code{\link{Surv}} object}
\item{times}{a numeric vector of times}
\item{tolerance}{tolerance for judging singularity in matrix}
\item{intercept}{set to \code{FALSE} to not automatically add a column
of ones to the \code{x} matrix}
\item{xpxi}{set to \code{TRUE} to add an element to the result
containing the inverse of \eqn{X'X}}
\item{a}{a numeric matrix or vector}
\item{b}{a numeric vector}
\item{kint}{which element of \code{b} to add to the result if \code{a}
does not contain a column for intercepts}
\item{string}{a character string vector}
\item{setAside}{for \code{adj=1 side=4}, is a character string used to
determine the space to set aside for all strings.}
\item{space}{the number of extra characters to leave to the left of
the string(s) (\code{adj=0}) or to the right (\code{adj=1})}
\item{adj}{0 for left justification, 0.5 for centered, 1 for right}
\item{conversion}{a named numeric vector}
\item{round}{set to \code{TRUE} to round converted values}
\item{digits}{number of digits used for \code{round}}
\item{str}{a character string vector}
\item{w}{a numeric vector}
\item{x}{a numeric vector (matrix for \code{lm.fit.qr.bare}) or data
frame. For \code{xless} may be any object that is sensible to
\code{print}. For \code{sepUnitsTrans} is a character or factor
variable.}
\item{y}{a numeric vector}
\item{sep}{a single character string specifying the delimiter}
\item{extended}{see \code{\link{strsplit}} in \R}
\item{f}{a scaling constant}
\item{title}{a character string to title a window or plot}
\item{\dots}{arguments passed through to another function}
}
\author{Frank Harrell}
\examples{
trap.rule(1:100,1:100)
unPaste(c('a;b or c','ab;d','qr;s'), ';')
sepUnitsTrans(c('3 days','4 months','2 years','7'))
set.seed(1)
whichClosest(1:100, 3:5)
whichClosest(1:100, rep(3,20))
whichClosePW(1:100, rep(3,20))
whichClosePW(1:100, rep(3,20), f=.05)
whichClosePW(1:100, rep(3,20), f=1e-10)
}
\keyword{programming}
\keyword{utilities}