Misc {Hmisc} | R Documentation |
This documents miscellaneous small functions in Hmisc that may be of interest to users.
confbar
draws multi-level confidence bars using small rectangles
that may be of different colors.
james.stein
computes James-Stein shrunken estimates of cell
means given a response variable (which may be binary) and a grouping
indicator.
km.quick
provides a fast way to invoke survfit.km
in the
survival
package to get Kaplan-Meier estimates for a
single stratum for a vector of time points (if times
is given) or to
get a vector of survival time quantiles (if q
is given).
lm.fit.qr.bare
is a fast stripped-down function for computing
regression coefficients, residuals, R^2, and fitted values. It
uses the Fortran routines dqrls
.
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.
nomiss
returns a data frame (if its argument is one) with rows
corresponding to NA
s removed, or it returns a matrix with rows
with any element missing removed.
outerText
uses text()
to put test strings in left or
right margins. It temporarily sets par(xpd=NA)
if using R.
trap.rule
computes the area under a curve using the trapezoidal
rule, assuming x
is sorted.
trellis.strip.blank
sets up Trellis or Lattice graphs to have a
clear background on the strips for panel labels.
under.unix
is a scalar logical value that is TRUE
if you
are running Linux or Unix.
.R.
is a logical value set to TRUE
if running R,
FALSE
for S-Plus.
.SV4.
is a logical value set to TRUE
if running version
4 of the S language under S-Plus, FALSE
otherwise.
unPaste
provides a version of the S-Plus unpaste
that
works for R and S-Plus.
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. whichClosest
quickly finds the closest
element without any randomness.
xless
is a function for Linux/Unix users to invoke the system
xless
command to pop up a window to display the result of
print
ing an object.
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')) trap.rule(x, y) trellis.strip.blank() unPaste(str, sep="/", extended=FALSE) whichClosest(x, w) whichClosePW(x, w, f=0.2) xless(x, ..., title)
at |
x-coordinate for vertical confidence intervals, y-coordinate for horizontal |
est |
vector of point estimates for confidence limits |
se |
vector of standard errors |
width |
width of confidence rectanges in user units |
q |
vector of confidence coefficients or quantiles |
col |
vector of colors |
type |
"v" for vertical, "h" for horizontal |
labels |
set to FALSE to omit drawing confidence
coefficients |
ticks |
set to TRUE to draw lines between rectangles |
cex |
character expansion factor |
side |
for confbar is "b","l","t","r" for bottom,
left, top, right. For outText is the using integers 1-4
corresponding to these. |
lwd |
line widths |
clip |
interval to truncate limits |
fun |
function to transform scale |
qfun |
quantiles on transformed scale |
group |
a categorical grouping variable |
S |
a Surv object |
times |
a numeric vector of times |
tolerance |
tolerance for judging singularity in matrix |
intercept |
set to FALSE to not automatically add a column
of ones to the x matrix |
xpxi |
set to TRUE to add an element to the result
containing the inverse of X'X |
a |
a numeric matrix or vector |
b |
a numeric vector |
kint |
which element of b to add to the result if a
does not contain a column for intercepts |
string |
a character string vector |
setAside |
for adj=1 side=4 , is a character string used to
determine the space to set aside for all strings. |
space |
the number of extra characters to leave to the left of
the string(s) (adj=0 ) or to the right (adj=1 ) |
adj |
0 for left justification, 0.5 for centered, 1 for right |
str |
a character string vector |
w |
a numeric vector |
x |
a numeric vector (matrix for lm.fit.qr.bare ) or data
frame. For xless may be any object that is sensible to
print |
y |
a numeric vector |
sep |
a single character string specifying the delimiter |
extended |
see strsplit in R |
f |
a scaling constant |
title |
a character string to title a window or plot |
... |
arguments passed through to another function |
Frank Harrell
trap.rule(1:100,1:100) unPaste(c('a;b or c','ab;d','qr;s'), ';') 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)