Misc  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 rerun with iter=0
.
confbar
draws multilevel confidence bars using small rectangles
that may be of different colors.
getLatestSource
fetches and source
s the most recent
source code for functions in GitHub.
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 htmlgenerating
functions in Hmisc
and rms
to use unicode for special
characters, and htmlSpecialType='&'
uses the older ampersand
3digit 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 JamesStein 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 KaplanMeier 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 evennumbered 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 strippeddown 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 bootstraprepeated 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 NA
s removed, or it returns a matrix with rows
with any element missing removed.
outerText
uses axis()
to put rightjustified 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.
rendHTML
renders HTML in a character vector, first converting
to one character string with newline delimeters. If knitr
is
currently running, runs this string through knitr::asis_output
so that the user need not include results='asis'
in the chunk
header for R Markdown or Quarto. If knitr
is not running, uses
htmltools::browsable
and htmltools::HTML
and prints the
result so that an RStudio viewer (if running inside RStudio) or
separate browser window displays the rendered HTML. The HTML code is
surrounded by yaml markup to make Pandoc not fiddle with the HTML.
Set the argument html=FALSE
to not add this, in case you are
really rendering markdown. html=FALSE
also invokes
rmarkdown::render
to convert the character vector to HTML
before using htmltools
to view, assuming the characters
represent RMarkdown/Quarto text other than the YAML header. If
options(rawmarkup=TRUE)
is in effect, rendHTML
will just
cat()
its first argument. This is useful when rendering is
happening inside a Quarto margin, for example.
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 SPlus unpaste
that
works for R and SPlus.
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
print
ing an object. For MacOS xless
uses the system open
command to pop up a TextEdit
window.
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)
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, ...)
rendHTML(x, html=TRUE)
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 
a numeric matrix or vector 
alt , Rd 
see 
at 
xcoordinate for vertical confidence intervals, ycoordinate for horizontal 
attribs 
an object returned by 
avail 
set to 
b 
a numeric vector 
cex 
character expansion factor 
clip 
interval to truncate limits 
col 
vector of colors 
conversion 
a named numeric vector 
data 
an object having a 
digits 
number of digits used for 
est 
vector of point estimates for confidence limits 
f 
a scaling constant 
file 
a file name 
fun 
function to transform scale 
group 
a categorical grouping variable 
html 
set to 
insert 
a list of 3element lists for 
intercept 
set to 
k 
get the 
kint 
which element of 
bmat 
set to 
labels 
set to 
lwd 
line widths 
package 
name of package for 
obj 
a variable, data frame, or data table 
q 
vector of confidence coefficients or quantiles 
qfun 
quantiles on transformed scale 
recent 
an integer telling 
round 
set to 
S 
a 
se 
vector of standard errors 
sep 
a single character string specifying the delimiter. For

side 
for 
str 
a character string vector 
string 
a character string vector 
ticks 
set to 
times 
a numeric vector of times 
title 
a character string to title a window or plot. Ignored for 
tolerance 
tolerance for judging singularity in matrix 
type 

w 
a numeric vector 
width 
width of confidence rectanges in user units, or see

x 
a numeric vector (matrix for 
xpxi 
set to 
singzero 
set to 
y 
a numeric vector. For 
indent , exdent , prefix 
see 
simplify 
see 
units 
see 
... 
arguments passed through to another function. For

Frank Harrell and Charles Dupont
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=1e10)
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
## End(Not run)
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