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.
grType retrieves the system option grType, which is
forced to be "base" if the plotly package is not
installed.
prType retrieves the system option prType, which is
set to "plain" if the option is not set. print methods
that allow for markdown/html/latex can be automatically invoked by
setting options(prType="html") or
options(prType='latex').
htmlSpecialType retrieves the system option
htmlSpecialType, which is set to "unicode" if the option
is not set. htmlSpecialType='unicode' cause html-generating
functions in Hmisc and rms to use unicode for special
characters, and htmlSpecialType='&' uses the older ampersand
3-digit format.
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.
keepHattrib for an input variable or a data frame, creates a
list object saving special Hmisc attributes such as label and
units that might be lost during certain operations such as
running data.table. restoreHattrib restores these attributes.
km.quick provides a fast way to invoke survfitKM 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).
latexBuild takes pairs of character strings and produces a
single character string containing concatenation of all of them, plus
an attribute "close" which is a character string containing the
LaTeX closure that will balance LaTeX code with respect to
parentheses, braces, brackets, or begin vs. end. When
an even-numbered element of the vector is not a left parenthesis,
brace, or bracket, the element is taken as a word that was surrounded
by begin and braces, for which the corresponding end is
constructed in the returned attribute.
lm.fit.qr.bare is a fast stripped-down function for computing
regression coefficients, residuals, \(R^2\), and fitted values. It
uses lm.fit.
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.
An optional argument allows the second argument to be treated as a
matrix, useful when its rows represent bootstrap reps of
coefficients. Then ab' is computed. matxv respects the
"intercepts" attribute if it is stored on b by the
rms package. This is used by orm
fits that are bootstrap-repeated by bootcov where
only the intercept corresponding to the median is retained. If
kint has nonzero length, it is checked for consistency with the
attribute.
makeSteps is a copy of the dostep function inside the
survival package's plot.survfit function. It expands a
series of points to include all the segments needed to plot step
functions. This is useful for drawing polygons to shade confidence
bands for step functions.
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 axis() to put right-justified text
strings in the right margin. Placement depends on
par('mar')[4]
plotlyParm is a list of functions useful for specifying
parameters to plotly graphics.
plotp is a generic to handle plotp methods to make
plotly graphics.
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.
strgraphwrap is like strwrap but is for the current
graphics environment.
tobase64image is a function written by Dirk Eddelbuettel that
uses the base64enc package to convert a png graphic file to
base64 encoding to include as an inline image in an html file.
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.
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.
whichClosek is a slow function that finds, after jittering the
lookup table, the k closest matchest to each element of the
other vector, and chooses from among these one at random.
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.
confbar(at, est, se, width, q = c(0.7, 0.8, 0.9, 0.95, 0.99),
col = gray(c(0, 0.25, 0.5, 0.75, 1)),
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'))
grType()
prType()
htmlSpecialType()
inverseFunction(x, y)
james.stein(y, group)
keepHattrib(obj)
km.quick(S, times, q)
latexBuild(…, insert, sep='')
lm.fit.qr.bare(x, y, tolerance, intercept=TRUE, xpxi=FALSE, singzero=FALSE)
matxv(a, b, kint=1, bmat=FALSE)
nomiss(x)
outerText(string, y, cex=par('cex'), …)
plotlyParm
plotp(data, ...)
restoreHattrib(obj, attribs)
sepUnitsTrans(x, conversion=c(day=1, month=365.25/12, year=365.25, week=7),
round=FALSE, digits=0)
strgraphwrap(x, width = 0.9 * getOption("width"),
indent = 0, exdent = 0,
prefix = "", simplify = TRUE, units='user', cex=NULL)
tobase64image(file, Rd = FALSE, alt = "image")
trap.rule(x, y)
trellis.strip.blank()
unPaste(str, sep="/")
whichClosest(x, w)
whichClosePW(x, w, f=0.2)
whichClosek(x, w, k)
xless(x, …, title)a numeric matrix or vector
see base64::img
x-coordinate for vertical confidence intervals, y-coordinate for horizontal
an object returned by keepHattrib
set to TRUE to have getLatestSource return
a data frame of available files and latest versions instead of
fetching any
a numeric vector
character expansion factor
interval to truncate limits
vector of colors
a named numeric vector
an object having a plotp method
number of digits used for round
vector of point estimates for confidence limits
a scaling constant
a file name
function to transform scale
a categorical grouping variable
a list of 3-element lists for latexBuild.
The first of each 3-element
list is a character string with an environment name. The second
specifies the order: "before" or "after", the former
indicating that when the environment is found, the third element of
the list is inserted before or after it, according to the second
element.
set to FALSE to not automatically add a column
of ones to the x matrix
get the k closest matches
which element of b to add to the result if a
does not contain a column for intercepts
set to TRUE to consider b a matrix of
repeated coefficients, usually resampled estimates with rows
corresponding to resamples
set to FALSE to omit drawing confidence
coefficients
line widths
name of package for getLatestSource, default is
'Hmisc'
a variable, data frame, or data table
vector of confidence coefficients or quantiles
quantiles on transformed scale
an integer telling getLatestSource to get the
recent most recently modified files from the package
set to TRUE to round converted values
a Surv object
vector of standard errors
a single character string specifying the delimiter. For
latexBuild the default is "".
for confbar is "b","l","t","r" for bottom,
left, top, right.
a character string vector
a character string vector
set to TRUE to draw lines between rectangles
a numeric vector of times
a character string to title a window or plot
tolerance for judging singularity in matrix
"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.
a numeric vector
width of confidence rectanges in user units, or see
strwrap
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. For
strgraphwrap is a character vector.
set to TRUE to add an element to the result
containing the inverse of \(X'X\)
set to TRUE to set coefficients corresponding
to singular variables to zero instead of NA.
a numeric vector. For inverseFunction y is the
evaluated function values at x.
see strwrap
see sapply
see par
arguments passed through to another function. For
latexBuild represents pairs, with odd numbered elements being
character strings containing LaTeX code or a zero-length object to
ignore, and even-numbered elements representing LaTeX left
parenthesis, left brace, or left bracket, or environment name.
# NOT RUN {
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])
d <- data.frame(x=1:2, y=3:4, z=5:6)
d <- upData(d, labels=c(x='X', z='Z lab'), units=c(z='mm'))
a <- keepHattrib(d)
d <- data.frame(x=1:2, y=3:4, z=5:6)
d2 <- restoreHattrib(d, a)
sapply(d2, attributes)
# }
# 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
# }
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