Hmisc (version 5.1-3)

HmiscOverview: Overview of Hmisc Library

Description

The Hmisc library contains many functions useful for data analysis, high-level graphics, utility operations, functions for computing sample size and power, translating SAS datasets into R, imputing missing values, advanced table making, variable clustering, character string manipulation, conversion of R objects to LaTeX code, recoding variables, and bootstrap repeated measures analysis. Most of these functions were written by F Harrell, but a few were collected from statlib and from s-news; other authors are indicated below. This collection of functions includes all of Harrell's submissions to statlib other than the functions in the rms and display libraries. A few of the functions do not have “Help” documentation.

To make Hmisc load silently, issue options(Hverbose=FALSE) before library(Hmisc).

Functions

Function Name	Purpose
abs.error.pred	Computes various indexes of predictive accuracy based
	on absolute errors, for linear models
addMarginal	Add marginal observations over selected variables
all.is.numeric	Check if character strings are legal numerics
approxExtrap	Linear extrapolation
aregImpute	Multiple imputation based on additive regression,
	bootstrapping, and predictive mean matching
areg.boot	Nonparametrically estimate transformations for both
	sides of a multiple additive regression, and
	bootstrap these estimates and \(R^2\)
ballocation	Optimum sample allocations in 2-sample proportion test
binconf	Exact confidence limits for a proportion and more accurate
	(narrower!) score stat.-based Wilson interval
	(Rollin Brant, mod. FEH)
bootkm	Bootstrap Kaplan-Meier survival or quantile estimates
bpower	Approximate power of 2-sided test for 2 proportions
	Includes bpower.sim for exact power by simulation
bpplot	Box-Percentile plot
	(Jeffrey Banfield, )
bpplotM	Chart extended box plots for multiple variables
bsamsize	Sample size requirements for test of 2 proportions
bystats	Statistics on a single variable by levels of >=1 factors
bystats2	2-way statistics
character.table	Shows numeric equivalents of all latin characters
	Useful for putting many special chars. in graph titles
	(Pierre Joyet, )
ciapower	Power of Cox interaction test
cleanup.import	More compactly store variables in a data frame, and clean up
	problem data when e.g. Excel spreadsheet had a non-
	numeric value in a numeric column
combine.levels	Combine infrequent levels of a categorical variable
confbar	Draws confidence bars on an existing plot using multiple
	confidence levels distinguished using color or gray scale
contents	Print the contents (variables, labels, etc.) of a data frame
cpower	Power of Cox 2-sample test allowing for noncompliance
Cs	Vector of character strings from list of unquoted names
csv.get	Enhanced importing of comma separated files labels
cut2	Like cut with better endpoint label construction and allows
	construction of quantile groups or groups with given n
datadensity	Snapshot graph of distributions of all variables in
	a data frame. For continuous variables uses scat1d.
dataRep	Quantify representation of new observations in a database
ddmmmyy	SAS “date7” output format for a chron object
deff	Kish design effect and intra-cluster correlation
describe	Function to describe different classes of objects.
	Invoke by saying describe(object). It calls one of the
	following:
describe.data.frame	Describe all variables in a data frame (generalization
	of SAS UNIVARIATE)
describe.default	Describe a variable (generalization of SAS UNIVARIATE)
dotplot3	A more flexible version of dotplot
Dotplot	Enhancement of Trellis dotplot allowing for matrix
	x-var., auto generation of Key function, superposition
drawPlot	Simple mouse-driven drawing program, including a function
	for fitting Bezier curves
Ecdf	Empirical cumulative distribution function plot
errbar	Plot with error bars (Charles Geyer, U. Chi., mod FEH)
event.chart	Plot general event charts (Jack Lee, ,
	Ken Hess, Joel Dubin; Am Statistician 54:63-70,2000)
event.history	Event history chart with time-dependent cov. status
	(Joel Dubin, )
find.matches	Find matches (with tolerances) between columns of 2 matrices
first.word	Find the first word in an R expression (R Heiberger)
fit.mult.impute	Fit most regression models over multiple transcan imputations,
	compute imputation-adjusted variances and avg. betas
format.df	Format a matrix or data frame with much user control
	(R Heiberger and FE Harrell)
ftupwr	Power of 2-sample binomial test using Fleiss, Tytun, Ury
ftuss	Sample size for 2-sample binomial test using " " " "
	(Both by Dan Heitjan, )
gbayes	Bayesian posterior and predictive distributions when both
	the prior and the likelihood are Gaussian
getHdata	Fetch and list datasets on our web site
hdquantile	Harrell-Davis nonparametric quantile estimator with s.e.
histbackback	Back-to-back histograms (Pat Burns, Salomon Smith
	Barney, London, )
hist.data.frame	Matrix of histograms for all numeric vars. in data frame
	Use hist.data.frame(data.frame.name)
histSpike	Add high-resolution spike histograms or density estimates
	to an existing plot
hoeffd	Hoeffding's D test (omnibus test of independence of X and Y)
impute	Impute missing data (generic method)
interaction	More flexible version of builtin function
is.present	Tests for non-blank character values or non-NA numeric values
james.stein	James-Stein shrinkage estimates of cell means from raw data
labcurve	Optimally label a set of curves that have been drawn on
	an existing plot, on the basis of gaps between curves.
	Also position legends automatically at emptiest rectangle.
label	Set or fetch a label for an R-object
Lag	Lag a vector, padding on the left with NA or ''
latex	Convert an R object to LaTeX (R Heiberger & FE Harrell)
list.tree	Pretty-print the structure of any data object
	(Alan Zaslavsky, )
Load	Enhancement of load
mask	8-bit logical representation of a short integer value
	(Rick Becker)
matchCases	Match each case on one continuous variable
matxv	Fast matrix * vector, handling intercept(s) and NAs
mgp.axis	Version of axis() that uses appropriate mgp from
	mgp.axis.labels and gets around bug in axis(2, ...)
	that causes it to assume las=1
mgp.axis.labels	Used by survplot and plot in rms library (and other
	functions in the future) so that different spacing
	between tick marks and axis tick mark labels may be
	specified for x- and y-axes.
	Use mgp.axis.labels('default') to set defaults.
	Users can set values manually using
	mgp.axis.labels(x,y) where x and y are 2nd value of
	par('mgp') to use. Use mgp.axis.labels(type=w) to
	retrieve values, where w='x', 'y', 'x and y', 'xy',
	to get 3 mgp values (first 3 types) or 2 mgp.axis.labels.
minor.tick	Add minor tick marks to an existing plot
mtitle	Add outer titles and subtitles to a multiple plot layout
multLines	Draw multiple vertical lines at each x
	in a line plot
%nin%	Opposite of %in%
nobsY	Compute no. non-NA observations for left hand formula side
nomiss	Return a matrix after excluding any row with an NA
panel.bpplot	Panel function for trellis bwplot - box-percentile plots
panel.plsmo	Panel function for trellis xyplot - uses plsmo
pBlock	Block variables for certain lattice charts
pc1	Compute first prin. component and get coefficients on
	original scale of variables
plotCorrPrecision	Plot precision of estimate of correlation coefficient
plsmo	Plot smoothed x vs. y with labeling and exclusion of NAs
	Also allows a grouping variable and plots unsmoothed data
popower	Power and sample size calculations for ordinal responses
	(two treatments, proportional odds model)
prn	prn(expression) does print(expression) but titles the
	output with 'expression'. Do prn(expression,txt) to add
	a heading (‘txt’) before the ‘expression’ title
pstamp	Stamp a plot with date in lower right corner (pstamp())
	Add ,pwd=T and/or ,time=T to add current directory
	name or time
	Put additional text for label as first argument, e.g.
	pstamp('Figure 1') will draw 'Figure 1 date'
putKey	Different way to use key()
putKeyEmpty	Put key at most empty part of existing plot
rcorr	Pearson or Spearman correlation matrix with pairwise deletion
	of missing data
rcorr.cens	Somers' Dxy rank correlation with censored data
rcorrp.cens	Assess difference in concordance for paired predictors
rcspline.eval	Evaluate restricted cubic spline design matrix
rcspline.plot	Plot spline fit with nonparametric smooth and grouped estimates
rcspline.restate	Restate restricted cubic spline in unrestricted form, and
	create TeX expression to print the fitted function
reShape	Reshape a matrix into 3 vectors, reshape serial data
rm.boot	Bootstrap spline fit to repeated measurements model,
	with simultaneous confidence region - least
	squares using spline function in time
rMultinom	Generate multinomial random variables with varying prob.
samplesize.bin	Sample size for 2-sample binomial problem
	(Rick Chappell, )
sas.get	Convert SAS dataset to S data frame
sasxport.get	Enhanced importing of SAS transport dataset in R
Save	Enhancement of save
scat1d	Add 1-dimensional scatterplot to an axis of an existing plot
	(like bar-codes, FEH/Martin Maechler,
	/Jens Oehlschlaegel-Akiyoshi,
	)
score.binary	Construct a score from a series of binary variables or
	expressions
sedit	A set of character handling functions written entirely
	in R. sedit() does much of what the UNIX sed
	program does. Other functions included are
	substring.location, substring<-, replace.string.wild,
	and functions to check if a string is numeric or
	contains only the digits 0-9
setTrellis	Set Trellis graphics to use blank conditioning panel strips,
	line thickness 1 for dot plot reference lines:
	setTrellis(); 3 optional arguments
show.col	Show colors corresponding to col=0,1,...,99
show.pch	Show all plotting characters specified by pch=.
	Just type show.pch() to draw the table on the
	current device.
showPsfrag	Use LaTeX to compile, and dvips and ghostview to
	display a postscript graphic containing psfrag strings
solvet	Version of solve with argument tol passed to qr
somers2	Somers' rank correlation and c-index for binary y
spearman	Spearman rank correlation coefficient spearman(x,y)
spearman.test	Spearman 1 d.f. and 2 d.f. rank correlation test
spearman2	Spearman multiple d.f. \(\rho^2\), adjusted \(\rho^2\), Wilcoxon-Kruskal-
	Wallis test, for multiple predictors
spower	Simulate power of 2-sample test for survival under
	complex conditions
	Also contains the Gompertz2,Weibull2,Lognorm2 functions.
spss.get	Enhanced importing of SPSS files using read.spss function
src	src(name) = source("name.s") with memory
store	store an object permanently (easy interface to assign function)
strmatch	Shortest unique identifier match
	(Terry Therneau, )
subset	More easily subset a data frame
substi	Substitute one var for another when observations NA
summarize	Generate a data frame containing stratified summary
	statistics. Useful for passing to trellis.
summary.formula	General table making and plotting functions for summarizing
	data
summaryD	Summarizing using user-provided formula and dotchart3
summaryM	Replacement for summary.formula(..., method='reverse')
summaryP	Multi-panel dot chart for summarizing proportions
summaryS	Summarize multiple response variables for multi-panel
	dot chart or scatterplot
summaryRc	Summary for continuous variables using lowess
symbol.freq	X-Y Frequency plot with circles' area prop. to frequency
sys	Execute unix() or dos() depending on what's running
tabulr	Front-end to tabular function in the tables package
tex	Enclose a string with the correct syntax for using
	with the LaTeX psfrag package, for postscript graphics
transace	ace() packaged for easily automatically transforming all
	variables in a matrix
transcan	automatic transformation and imputation of NAs for a
	series of predictor variables
trap.rule	Area under curve defined by arbitrary x and y vectors,
	using trapezoidal rule
trellis.strip.blank	To make the strip titles in trellis more visible, you can
	make the backgrounds blank by saying trellis.strip.blank().
	Use before opening the graphics device.
t.test.cluster	2-sample t-test for cluster-randomized observations
uncbind	Form individual variables from a matrix
upData	Update a data frame (change names, labels, remove vars, etc.)
units	Set or fetch "units" attribute - units of measurement for var.
varclus	Graph hierarchical clustering of variables using squared
	Pearson or Spearman correlations or Hoeffding D as similarities
	Also includes the naclus function for examining similarities in
	patterns of missing values across variables.
wtd.mean
wtd.var
wtd.quantile
wtd.Ecdf
wtd.table
wtd.rank
wtd.loess.noiter
num.denom.setup	Set of function for obtaining weighted estimates
xy.group	Compute mean x vs. function of y by groups of x
xYplot	Like trellis xyplot but supports error bars and multiple
	response variables that are connected as separate lines
ynbind	Combine a series of yes/no true/false present/absent variables into a matrix
zoom	Zoom in on any graphical display
	(Bill Dunlap, )

Copyright Notice

GENERAL DISCLAIMER
This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

In short: You may use it any way you like, as long as you don't charge money for it, remove this notice, or hold anyone liable for its results. Also, please acknowledge the source and communicate changes to the author.

If this software is used is work presented for publication, kindly reference it using for example:
Harrell FE (2014): Hmisc: A package of miscellaneous R functions. Programs available from https://hbiostat.org/R/Hmisc/.
Be sure to reference R itself and other libraries used.

Author

Frank E Harrell Jr
Professor of Biostatistics
Vanderbilt University School of Medicine
Nashville, Tennessee

References

See Alzola CF, Harrell FE (2004): An Introduction to S and the Hmisc and Design Libraries at https://hbiostat.org/R/doc/sintro.pdf for extensive documentation and examples for the Hmisc package.