| Misc {Hmisc} | R Documentation |
This documents miscellaneous small functions in Hmisc that may be of interest to users.
clowess runs lowess but if the iter argument
exceeds zero, sometimes wild values can result, in which case
lowess is re-run with iter=0.
confbar draws multi-level confidence bars using small rectangles
that may be of different colors.
getLatestSource fetches and sources the most recent
source code for functions in packages in the Vanderbilty University
CVS repository.
inverseFunction generates a function to find all inverses of a
monotonic or nonmonotonic function that is tabulated at vectors (x,y),
typically 1000 points. If the original function is monotonic, simple linear
interpolation is used and the result is a vector, otherwise linear
interpolation is used within each interval in which the function is
monotonic and the result is a matrix with number of columns equal to the
number of monotonic intervals. If a requested y is not within any
interval, the extreme x that pertains to the nearest extreme y is
returned. Specifying what='sample' to the returned function will cause a
vector to be returned instead of a matrix, with elements taken as a
random choice of the possible inverses.
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 NAs 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.
sepUnitsTrans converts character vectors containing values such
as c("3 days","3day","4month","2 years","2weeks","7") to
numeric vectors
(here 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 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
"units" attribute.
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
printing an object. For Windows, xless uses the builtin
page function but with better defaults.
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))))
getLatestSource(x=NULL, package='Hmisc', recent=NULL, avail=FALSE,
type=c('svn','cvs'))
inverseFunction(x, y)
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, ..., title)
a |
a numeric matrix or vector |
adj |
0 for left justification, 0.5 for centered, 1 for right |
at |
x-coordinate for vertical confidence intervals, y-coordinate for horizontal |
avail |
set to TRUE to have getLatestSource return
a data frame of available files and latest versions instead of
fetching any |
b |
a numeric vector |
cex |
character expansion factor |
clip |
interval to truncate limits |
col |
vector of colors |
conversion |
a named numeric vector |
digits |
number of digits used for round |
est |
vector of point estimates for confidence limits |
extended |
see strsplit in R |
f |
a scaling constant |
fun |
function to transform scale |
group |
a categorical grouping variable |
intercept |
set to FALSE to not automatically add a column
of ones to the x matrix |
kint |
which element of b to add to the result if a
does not contain a column for intercepts |
labels |
set to FALSE to omit drawing confidence
coefficients |
lwd |
line widths |
package |
name of package for getLatestSource, default is
'Hmisc' |
q |
vector of confidence coefficients or quantiles |
qfun |
quantiles on transformed scale |
recent |
an integer telling getLatestSource to get the
recent most recently modified files from the package |
round |
set to TRUE to round converted values |
S |
a Surv object |
se |
vector of standard errors |
sep |
a single character string specifying the delimiter |
setAside |
for adj=1 side=4, is a character string used to
determine the space to set aside for all strings. |
side |
for confbar is "b","l","t","r" for bottom,
left, top, right. For outText is the using integers 1-4
corresponding to these. |
space |
the number of extra characters to leave to the left of
the string(s) (adj=0) or to the right (adj=1) |
str |
a character string vector |
string |
a character string vector |
ticks |
set to TRUE to draw lines between rectangles |
times |
a numeric vector of times |
title |
a character string to title a window or plot |
tolerance |
tolerance for judging singularity in matrix |
type |
"v" for vertical, "h" for horizontal. For
getLatestSource this specifies the type of source code
repository, 'svn' (the default) or
'cvs', which is now outdated as Subversion has replaced CVS
in the Vanderbilt Biostatistics server. |
w |
a numeric vector |
width |
width of confidence rectanges in user units |
x |
a numeric vector (matrix for lm.fit.qr.bare) or data
frame. For xless may be any object that is sensible to
print. For sepUnitsTrans is a character or factor
variable. For getLatestSource is a character string or
vector of character strings containing base file names to retrieve
from CVS. Set x='all' to retrieve all source files. For
clowess, x may also be a list with x and y
components. For inverseFunction, x and y
contain evaluations of the function whose inverse is needed.
x is typically an equally-spaced grid of 1000 points. |
xpxi |
set to TRUE to add an element to the result
containing the inverse of X'X |
y |
a numeric vector. For inverseFunction y is the
evaluated function values at x. |
... |
arguments passed through to another function |
Frank Harrell
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)
x <- seq(-1, 1, by=.01)
y <- x^2
h <- inverseFunction(x,y)
formals(h)$turns # vertex
a <- seq(0, 1, by=.01)
plot(0, 0, type='n', xlim=c(-.5,1.5))
lines(a, h(a)[,1]) ## first inverse
lines(a, h(a)[,2], col='red') ## second inverse
a <- c(-.1, 1.01, 1.1, 1.2)
points(a, h(a)[,1])
## Not run:
getLatestSource(recent=5) # source() most recent 5 revised files in Hmisc
getLatestSource('cut2') # fetch and source latest cut2.s
getLatestSource('all') # get everything
getLatestSource(avail=TRUE) # list available files and latest versions
## End(Not run)