Overview {Hmisc} | R Documentation

## 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 S, imputing missing values, advanced table making, variable clustering, character string manipulation, conversion of S 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 Design and display libraries. A few of the functions do not have "Help" documentation.

### Functions

Function Name | Purpose
abs.error.pred | Computes various indexes of predictive accuracy based
| on absolute errors, for linear models
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, umsfjban@bill.oscs.montana.edu)
bsamsize | Sample size requirements for test of 2 proportions
bystats | Statistics on a single variable by levels of >=1 factors
bystats2 | 2-way statistics
calltree | Calling tree of functions
| (David Lubinsky, david@hoqax.att.com)
character.table | Shows numeric equivalents of all latin characters
| Useful for putting many special chars. in graph titles
| (Pierre Joyet, pierre.joyet@bluewin.ch)
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
comment | Attach a comment attribute to an object:
| comment(fit) <- 'Used old data'
| comment(fit) (prints comment)
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)
do | Assists with batch analyses
dot.chart | Dot chart for one or two classification variables
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
eip | Edit an object "in-place" (may be dangerous!), e.g.
| eip(sqrt) will replace the builtin sqrt function
errbar | Plot with error bars (Charles Geyer, U. Chi., mod FEH)
event.chart | Plot general event charts (Jack Lee, jjlee@mdanderson.org,
| Ken Hess, Joel Dubin; Am Statistician 54:63-70,2000)
event.history | Event history chart with time-dependent cov. status
| (Joel Dubin, joel.dubin@yale.edu)
find.matches | Find matches (with tolerances) between columns of 2 matrices
first.word | Find the first word in an S 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, dheitjan@biostats.hmc.psu.edu)
gbayes | Bayesian posterior and predictive distributions when both
| the prior and the likelihood are Gaussian
getHdata | Fetch and list datasets on our web site
gs.slide | Sets nice defaults for graph sheets for S-Plus 2000 for
| copying graphs into Microsoft applications
hdquantile | Harrell-Davis nonparametric quantile estimator with s.e.
histbackback | Back-to-back histograms (Pat Burns, Salomon Smith
| Barney, London, pburns@dorado.sbi.com)
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 S-object
Lag | Lag a vector, padding on the left with NA or ''
latex | Convert an S object to LaTeX (R Heiberger & FE Harrell)
ldBands | Lan-DeMets bands for group sequential tests
list.tree | Pretty-print the structure of any data object
| (Alan Zaslavsky, zaslavsk@hcp.med.harvard.edu)
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
mem | mem() types quick summary of memory used during session
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 Design 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. ps.slide, win.slide,
| gs.slide set up nice defaults for mgp.axis.labels.
| Otherwise 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
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
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
p.sunflowers | Sunflower plots (Andreas Ruckstuhl, Werner Stahel,
| Martin Maechler, Tim Hesterberg)
ps.slide | Set up postcript() using nice defaults for different types
| of graphics media
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' Dyx 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
recode | Recodes variables
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, chappell@stat.wisc.edu)
sas.get | Convert SAS dataset to S data frame
sasxport.get | Enhanced importing of SAS transport dataset in R
scat1d | Add 1-dimensional scatterplot to an axis of an existing plot
| (like bar-codes, FEH/Martin Maechler,
| maechler@stat.math.ethz.ch/Jens Oehlschlaegel-Akiyoshi,
| oehl@psyres-stuttgart.de)
score.binary | Construct a score from a series of binary variables or
| expressions
sedit | A set of character handling functions written entirely
| in S. 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
setpdf | Adobe PDF graphics setup for including graphics in books
| and reports with nice defaults, minimal wasted space
setps | Postscript graphics setup for including graphics in books
| and reports with nice defaults, minimal wasted space
| Internally uses psfig function by
| Antonio Possolo (antonio@atc.boeing.com).
| setps works with Ghostscript to convert .ps to .pdf
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, therneau@mayo.edu)
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
symbol.freq | X-Y Frequency plot with circles' area prop. to frequency
sys | Execute unix() or dos() depending on what's running
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.
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
win.slide | Setup win.graph or win.printer using nice defaults for
| presentations/slides/publications
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
zoom | Zoom in on any graphical display
| (Bill Dunlap, bill@statsci.com)

### System Overrides

Hmisc overrides the system function model.frame.default to allow for more elegant handling of NAs by allowing the user to specify a global method for handling NAs using options(na.action='na.methodname'). Hmisc overrides the system subscripting method for factor vectors and date vectors, and it defines functions is.na.dates and is.na.times to check for NAs in date and time vectors. The [.factor redefinition by Hmisc causes by default unused levels to be dropped from the factor vector's levels attribute when the vector is subscripted. This can be overridden by using for example `x <- x[,drop=FALSE]` or by specifying a system option as follows: `options(drop.factor.levels=FALSE)`.

Hmisc also overrides the trelllis shingle function, which has a bug when its sole argument has a class (such as the "labelled" class created by the Hmisc label function). The shingle replacement has the default intervals argument set to sort(unique(unclass(x))) instead of sort(unique(x)).

### 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 (2003): Hmisc S function library. Programs available from http://hesweb1.med.virginia.edu/biostat/s/Hmisc.html.
Be sure to reference S-Plus or R itself and other libraries used.

### Acknowledgements

This work was supported by grants from the Agency for Health Care Policy and Research (US Public Health Service) and the Robert Wood Johnson Foundation.

### Author(s)

Frank E Harrell Jr
Professor of Biostatistics
Chair, Department of Biostatistics
Vanderbilt University School of Medicine
Nashville, Tennessee
f.harrell@vanderbilt.edu

### References

See Alzola CF, Harrell FE (2002): An Introduction to S and the Hmisc and Design Libraries at http://hesweb1.med.virginia.edu/biostat/s/doc/splus.pdf for extensive documentation and examples for the Hmisc library.

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