The R Project SVN – R – Diff – /branches/djm-source/FAQ

-START-INFO-DIR-ENTRY
-* R FAQ: (R-FAQ).               The R statistical system FAQ.
-END-INFO-DIR-ENTRY
-   R FAQ
+R FAQ
 Frequently Asked Questions on R
-Version 1.9-24 2004-06-15
+Version 1.9-45 2004-08-14
 ISBN 3-900051-01-1
 Kurt Hornik
 Table of Contents
 *****************
 R FAQ
 Introduction
 .1 Legalese
 .2 Obtaining this document
 .3 Citing this document
 .4 Notation
 .5 Feedback
 R Basics
 .1 What is R?
 .2 What machines does R run on?
 .3 What is the current version of R?
 .4 How can R be obtained?
 .9 What mailing lists exist for R?
 .10 What is CRAN?
 .11 Can I use R for commercial purposes?
 .12 Why is R named R?
 .13 What is the R Foundation?
 R and S
 .1 What is S?
 .2 What is S-PLUS?
 .3 What are the differences between R and S?
 .3.1 Lexical scoping
 .3.2 Models
 .3.3 Others
 .4 Is there anything R can do that S-PLUS cannot?
 .5 What is R-plus?
 R Web Interfaces
 R Add-On Packages
 .1 Which add-on packages exist for R?
 .1.1 Add-on packages in R
 .1.2 Add-on packages from CRAN
 .1.3 Add-on packages from Omegahat
 .2 How can add-on packages be installed?
 .3 How can add-on packages be used?
 .4 How can add-on packages be removed?
 .5 How can I create an R package?
 .6 How can I contribute to R?
 R and Emacs
 .1 Is there Emacs support for R?
 .2 Should I run R from within Emacs?
 .3 Debugging R from within Emacs
 R Miscellanea
 .1 Why does R run out of memory?
 .2 Why does sourcing a correct file fail?
 .3 How can I set components of a list to NULL?
 .4 How can I save my workspace?
 .22 How can I get command line editing to work?
 .23 How can I turn a string into a variable?
 .24 Why do lattice/trellis graphics not work?
 .25 How can I sort the rows of a data frame?
 .26 Why does the help.start() search engine not work?
+.27 Why did my .Rprofile stop working when I updated R?
 R Programming
 .1 How should I write summary methods?
 .2 How can I debug dynamically loaded code?
 .3 How can I inspect R objects when debugging?
 .4 How can I change compilation flags?
 R Bugs
 .1 What is a bug?
 .2 How to report a bug
 Acknowledgments
 R FAQ
 *****
 Statistics of the University of Auckland in Auckland, New Zealand.  In
 addition, a large group of individuals has contributed to R by sending code
 and bug reports.
    Since mid-1997 there has been a core group (the "R Core Team") who can
-modify the R source code CVS archive.  The group currently consists of Doug
+modify the R source code archive.  The group currently consists of Doug
 Bates, John Chambers, Peter Dalgaard, Robert Gentleman, Kurt Hornik,
 Stefano Iacus, Ross Ihaka, Friedrich Leisch, Thomas Lumley, Martin
 Maechler, Duncan Murdoch, Paul Murrell, Martyn Plummer, Brian Ripley,
 Duncan Temple Lang, and Luke Tierney.
    If you know about other platforms, please drop us a note.
 .3 What is the current version of R?
 =====================================
-The current released version is 1.9.0.  Based on this
+The current released version is 1.9.1.  Based on this
 `major.minor.patchlevel' numbering scheme, there are two development
 versions of R, working towards the next patch (`r-patched') and minor or
 eventually major (`r-devel') releases of R, respectively.  Version
 r-patched is for bug fixes mostly.  New features are typically introduced
 in r-devel.
 ==========================
 Sources, binaries and documentation for R can be obtained via CRAN, the
 "Comprehensive R Archive Network" (see *Note What is CRAN?::).
-   Sources are also available via anonymous rsync.  Use
+   Sources are also available via `https://svn.r-project.org/R/', the R
-     rsync -rptC --delete rsync.R-project.org::MODULE R
-to create a copy of the source tree specified by MODULE in the subdirectory
-`R' of the current directory, where MODULE specifies one of the three
-existing flavors of the R sources, and can be one of `r-release' (current
-released version), `r-patched' (patched released version), and `r-devel'
-(development version).  The rsync trees are created directly from the
+Subversion repository, but currently not via anonymous rsync (or CVS).
-master CVS archive and are updated hourly.  The `-C' and in the `rsync'
-command is to cause it to skip the CVS directories.  Further information on
-`rsync' is available at `http://rsync.samba.org/rsync/'.
-   Note that the sources available via rsync do not include the recommended
-packages, whereas these are included in the tarballs of released versions.
-To install the appropriate sources for the recommended packages, run
-`./tools/rsync-recommended' from the top-level of the R sources that you
-pulled by rsync.
-   The sources of the development version are also available via anonymous
-CVS.  See `http://anoncvs.R-project.org' for more information.
 .5 How can R be installed?
 ===========================
 .5.1 How can R be installed (Unix)
 ==================================
 The `bin/linux' directory of a CRAN site contains Debian
 stable/testing/unstable packages for the i386 platform (now part of the
 Debian distribution and maintained by Dirk Eddelbuettel), Mandrake
-.1/9.2/10.0 i386 packages by Michele Alzetta, Red Hat 7.x/8.x/9/Fedora1
+.1/9.2/10.0 i386 packages by Michele Alzetta, Red Hat
-i386, 7.x alpha, and Fedora1 x86_64 packages by Martyn Plummer, Naoki
+.x/9/Fedora1/Fedora2 i386 and Fedora1 x86_64 packages by Martyn Plummer
-Takebayashi, and James Henstridge, respectively, SuSE 7.3/8.0/8.1/8.2 i386
+and James Henstridge, respectively, SuSE 7.3/8.0/8.1/8.2 i386 and 9.0/9.1
-and 9.0/9.1 i586 packages by Detlef Steuer, and VineLinux 2.6 i386 packages
+i586 packages by Detlef Steuer, and VineLinux 2.6 i386 packages by Susunu
-by Susunu Tanimura.
+Tanimura.
    The Debian packages can be accessed through APT, the Debian package
 maintenance tool.  Simply add the line
      deb http://cran.R-project.org/bin/linux/debian DISTRIBUTION main
      functionality, and pre-testing of new versions.  It is meant for those
      who maintain an active position in the development of R.
 Convenient access to information on these lists, subscription, and archives
 is provided by the web interface at
-`http://www.stat.math.ethz.ch/mailman/listinfo/'.  One can also subscribe
+`http://stat.ethz.ch/mailman/listinfo/'.  One can also subscribe (or
-(or unsubscribe) via email, e.g. to R-help by sending `subscribe' (or
+unsubscribe) via email, e.g. to R-help by sending `subscribe' (or
 `unsubscribe') in the _body_ of the message (not in the subject!) to
 <R-help-request@lists.R-project.org>.
    Send email to <R-help@lists.R-project.org> to send a message to everyone
 on the R-help mailing list.  Subscription and posting to the other lists is
 See `http://cran.R-project.org/mirrors.html' for a complete list of
 mirrors.  Please use the CRAN site closest to you to reduce network load.
    From CRAN, you can obtain the latest official release of R, daily
-snapshots of R (copies of the current CVS trees), as gzipped and bzipped
+snapshots of R (copies of the current source trees), as gzipped and bzipped
 tar files, a wealth of additional contributed code, as well as prebuilt
 binaries for various operating systems (Linux, Mac OS Classic, Mac OS X,
 and MS Windows).  CRAN also provides access to documentation on R, existing
 mailing lists and the R Bug Tracking system.
    To "submit" to CRAN, simply upload to
 `ftp://cran.R-project.org/incoming/' and send an email to
 <cran@R-project.org>.  Note that CRAN generally does not accept submissions
 of precompiled binaries due to security reasons.
-     *Note:*  It is very important that you indicate the copyright
+     *Note*:  It is very important that you indicate the copyright
      (license) information (GPL, BSD, Artistic, ...)  in your submission.
    Please always use the URL of the master site when referring to CRAN.
 .11 Can I use R for commercial purposes?
      This is also called the "_White Book_", and introduced S version 3,
      which added structures to facilitate statistical modeling in S.
    * John M. Chambers (1998), "Programming with Data," New York: Springer,
      ISBN 0-387-98503-4
-     (<http://cm.bell-labs.com/cm/ms/departments/sia/Sbook/>).
+     (`http://cm.bell-labs.com/cm/ms/departments/sia/Sbook/').
      This "_Green Book_" describes version 4 of S, a major revision of S
      designed by John Chambers to improve its usefulness at every stage of
      the programming process.
 you might consider saving often (see *Note How can I save my workspace?::)
 to safeguard against possible crashes.  Other possibilities are logging
 your sessions, or have your R commands stored in text files which can be
 read in using `source()'.
-     *Note:*  If you run R from within Emacs (see *Note R and Emacs::), you
+     *Note*:  If you run R from within Emacs (see *Note R and Emacs::), you
      can save the contents of the interaction buffer to a file and
      conveniently manipulate it using `ess-transcript-mode', as well as
      save source copies of all functions and data used.
 .3.2 Models
    * R disallows repeated formal arguments in function calls.
    * In S, `dump()', `dput()' and `deparse()' are essentially different
      interfaces to the same code.  In R from version 2.0.0, this is only
-     true if the same values are passed in the `forDisplay' and `useSource'
+     true if the same `control' argument is used, but by default it is not.
-     arguments, but by default they are not.  By default `dump()' tries to
-     write code that will evaluate to reproduce the object, whereas
+     By default `dump()' tries to write code that will evaluate to
-     `dput()' and `deparse()' default to options for producing deparsed
+     reproduce the object, whereas `dput()' and `deparse()' default to
-     code that is readable.
+     options for producing deparsed code that is readable.
    There are also differences which are not intentional, and result from
 missing or incorrect code in R.  The developers would appreciate hearing
 about any deficiencies you may find (in a written report fully documenting
 --------------------------
 The R distribution comes with the following packages:
 *base*
-     Base R functions and datasets.
+     Base R functions (and datasets before R 2.0).
+*datasets*
+     Base R datasets (added in R 2.0).
+*grDevices*
+     Graphics devices for base and grid graphics (added in R 2.0).
 *graphics*
      R functions for base graphics.
 *grid*
 *MCMCpack*
      Markov chain Monte Carlo (MCMC) package: functions for posterior
      simulation for a number of statistical models.
+*MNP*
+     Fitting Bayesian Multinomial Probit models via Markov chain Monte
+     Carlo.  Along with the standard Multinomial Probit model, it can also
+     fit models with different choice sets for each observation and
+     complete or partial ordering of all the available alternatives.
 *MPV*
      Data sets from the book "Introduction to Linear Regression Analysis"
      by D. C. Montgomery, E. A. Peck, and C. G. Vining, 2001, John Wiley and
      Sons.
+*Malmig*
+     An implementation of Malecot migration model together with a number of
+     related functions.
 *Matrix*
      A Matrix package.
+*NADA*
+     Methods described in "Nondetects And Data Analysis: Statistics for
+     Censored Environmental Data" by Dennis R. Helsel, 2004, John Wiley and
+     Sons.
 *NISTnls*
      A set of test nonlinear least squares examples from NIST, the U.S.
      National Institute for Standards and Technology.
 *Oarray*
      Arrays with arbitrary offsets.
+*PBSmapping*
+     Software evolved from fisheries research conducted at the Pacific
+     Biological Station (PBS) in Nanaimo, British Columbia, Canada.  Draws
+     maps and implements other GIS procedures.
 *PHYLOGR*
      Manipulation and analysis of phylogenetically simulated data sets (as
      obtained from PDSIMUL in package PDAP) and phylogenetically-based
      analyses using GLS.
 *RColorBrewer*
      ColorBrewer palettes for drawing nice maps shaded according to a
      variable.
+*RCurl*
+     Allows one to compose HTTP requests to fetch URIs, post forms, etc.,
+     and process the results returned by the Web server.
 *RMySQL*
      An interface between R and the MySQL database system.
+*RNetCDF*
+     An interface to Unidata's NetCDF library functions (version 3) and
+     furthermore access to Unidata's udunits calendar conversions.
 *RODBC*
      An ODBC database interface.
 *ROracle*
      Oracle Database Interface driver for R.  Uses the ProC/C++ embedded
 *Rcmdr*
      A platform-independent basic-statistics GUI (graphical user interface)
      for R, based on the *tcltk* package.
-*RmSQL*
-     An interface between R and the mSQL database system.
 *Rmpi*
      An interface (wrapper) to MPI (Message-Passing Interface) APIs.  It
      also provides an interactive R slave environment in which distributed
      statistical computing can be carried out.
+*Rstem*
+     Interface to Snowball implementation of Porter's word stemming
+     algorithm.
 *Rwave*
      An environment for the time-frequency analysis of 1-D signals (and
      especially for the wavelet and Gabor transforms of noisy signals),
      based on the book "Practical Time-Frequency Analysis: Gabor and Wavelet
      Transforms with an Implementation in S" by Rene Carmona, Wen L. Hwang
 *SIN*
      A SINful approach to selection of Gaussian Graphical Markov Models.
 *SenSrivastava*
      Collection of datasets from "Regression Analysis, Theory, Methods and
-     Applications" by A. Sen and M. Srivastava, 1990, Springer-Verlag.
+     Applications" by A. Sen and M. Srivastava, 1990, Springer.
 *SoPhy*
      Soil Physics Tools: simulation of water flux and solute transport in
      soil.
      Kruskal-Wallis, Kendall's Tau, Friedman's chi squared, Spearman's rho,
      maximum F ratio, the Pearson product moment correlation coefficiant,
      Johnson distributions, normal scores and generalized hypergeometric
      distributions).
+*UNF*
+     Tools for creating universal numeric fingerprints for data.
 *VLMC*
      Functions, classes & methods for estimation, prediction, and simulation
      (bootstrap) of VLMC (Variable Length Markov Chain) models.
 *VaR*
      Facilities for reading XML documents and DTDs.
 *abind*
      Combine multi-dimensional arrays.
+*accuracy*
+     A suite of tools designed to test and improve the accuracy of
+     statistical computation.
 *acepack*
      ACE (Alternating Conditional Expectations) and AVAS (Additivity and
      VAriance Stabilization for regression) methods for selecting regression
      transformations.
 *dr*
      Functions, methods, and datasets for fitting dimension reduction
      regression, including pHd and inverse regression methods SIR and SAVE.
+*drfit*
+     Dose-response data evaluation.
 *dse*
      Dynamic System Estimation, a multivariate time series package.
      Contains *dse1* (the base system, including multivariate ARMA and state
      space models), *dse2* (extensions for evaluating estimation
      techniques, forecasting, and for evaluating forecasting model),
      (E1071), including moments, short-time Fourier transforms, Independent
      Component Analysis, Latent Class Analysis, support vector machines, and
      fuzzy clustering, shortest path computation, bagged clustering, and
      some more.
+*eba*
+     Fitting and testing probabilistic choice models, especially the BTL,
+     elimination-by-aspects (EBA), and preference tree (Pretree) models.
 *effects*
      Graphical and tabular effect displays, e.g., of interactions, for
      linear and generalised linear models.
 *eha*
 *exactRankTests*
      Computes exact p-values and quantiles using an implementation of the
      Streitberg/Roehmel shift algorithm.
+*fBasics*
+     The Rmetrics module for "Markets, basic statistics, and date and time
+     management".  Rmetrics is an environment and software collection for
+     teaching financial engineering and computational finance
+     (`http://www.Rmetrics.org/').
+*fExtremes*
+     The Rmetrics module for "Beyond the Sample, Dealing with Extreme
+     Values".
+*fOptions*
+     The Rmetrics module for "The Valuation of Options".
+*fSeries*
+     The Rmetrics module for "The Dynamical Process Behind Financial
+     Markets".
+*faraway*
+     Functions and datasets for books by Julian Faraway.
 *fastICA*
      Implementation of FastICA algorithm to perform Independent Component
      Analysis (ICA) and Projection Pursuit.
 *fda*
      Features and strings for nonparametric regression.
 *g.data*
      Create and maintain delayed-data packages (DDP's).
+*gRbase*
+     A package for graphical modelling in R.  Defines S4 classes for
+     graphical meta data and graphical models, and illustrates how
+     hierarchical log-linear models may be implemented and combined with
+     *dynamicGraph*.
 *gafit*
      Genetic algorithm for curve fitting.
+*gam*
+     Functions for fitting and working with Generalized Additive Models, as
+     described in chapter 7 of the White Book, and in "Generalized Additive
+     Models" by T. Hastie and R. Tibshirani (1990).
 *gap*
      Genetic analysis package for both population and family data.
 *gbm*
      Generalized Boosted Regression Models: implements extensions to Freund
 *hier.part*
      Hierarchical Partitioning: variance partition of a multivariate data
      set.
+*hierfstat*
+     Estimation of hierarchical F-statistics from haploid or diploid genetic
+     data with any numbers of levels in the hierarchy, and tests for the
+     significance of each F and variance components.
 *homals*
      Homogeneity Analysis (HOMALS) package with optional Tcl/Tk interface.
 *httpRequest*
      Implements HTTP Request protocols (GET, POST, and multipart POST
      single least squares fit.
 *lasso2*
      Routines and documentation for solving regression problems while
      imposing an L1 constraint on the estimates, based on the algorithm of
-     Osborne et al. (1998)
+     Osborne et al. (1998).
 *lattice*
      Lattice graphics, an implementation of Trellis Graphics functions.
      _Recommended_.
      models.
 *merror*
      Accuracy and precision of measurements.
+*mfp*
+     Multiple Fractional Polynomials.
 *mgcv*
      Routines for GAMs and other genralized ridge regression problems with
      multiple smoothing parameter selection by GCV or UBRE.  _Recommended_.
 *mimR*
      An R interface to MIM for graphical modeling in R.
+*mitools*
+     Tools to perform analyses and combine results from multiple-imputation
+     datasets.
 *mix*
      Estimation/multiple imputation programs for mixed categorical and
      continuous data.
 *mixreg*
 *pixmap*
      Functions for import, export, plotting and other manipulations of
      bitmapped images.
+*plotrix*
+     Various useful functions for enhancing plots.
 *pls.pcr*
      Multivariate regression by PLS and PCR.
 *polspline*
      Routines for the polynomial spline fitting routines hazard regression,
      Fitting Gaussian linear models where the covariance structure is a
      linear combination of known matrices by maximising the residual log
      likelihood.  Can be used for multivariate models and random effects
      models.
+*reldist*
+     Functions for the comparison of distributions, including nonparametric
+     estimation of the relative distribution PDF and CDF and numerical
+     summaries as described in "Relative Distribution Methods in the Social
+     Sciences" by Mark S. Handcock and Martina Morris, 1999, Springer.
 *relimp*
      Functions to facilitate inference on the relative importance of
      predictors in a linear or generalized linear model.
 *rgdal*
 *rmeta*
      Functions for simple fixed and random effects meta-analysis for
      two-sample comparison of binary outcomes.
+*rmetasim*
+     An interface between R and the metasim simulation engine.  Facilitates
+     the use of the metasim engine to build and run individual based
+     population genetics simulations.
 *rpart*
      Recursive PARTitioning and regression trees.  _Recommended_.
 *rpart.permutation*
      Permutation tests of rpart models.
      PVM APIs, and examples and documentation for its use.
 *rqmcmb2*
      Markov chain marginal bootstrap for quantile regression.
+*rrcov*
+     Functions for robust location and scatter estimation and robust
+     regression with high breakdown point.
 *rsprng*
      Provides interface to SPRNG (Scalable Parallel Random Number
      Generators) APIs, and examples and documentation for its use.
 *sampfling*
      for the skewed t distribution of Fernandez and Steel.
 *sm*
      Software linked to the book "Applied Smoothing Techniques for Data
      Analysis:  The Kernel Approach with S-PLUS Illustrations" by A. W.
-     Bowman and A. Azzalini (1997), Oxford University Press.
+     Bowman and A. Azzalini, 1997, Oxford University Press.
 *sma*
      Functions for exploratory (statistical) microarray analysis.
 *smoothSurv*
      Three-Stage Least Squares (3SLS).
 *tapiR*
      Tools for accessing (UK) parliamentary information in R.
+*taskPR*
+     Task-Parallel R package.
 *tensor*
      Tensor product of arrays.
 *tkrplot*
      Simple mechanism for placing R graphics in a Tk widget.
      method.
 *udunits*
      Interface to Unidata's routines to convert units.
+*urn*
+     Functions for sampling without replacement (simulated urns).
 *urca*
      Unit root and cointegration tests for time series data.
 *vardiag*
      Interactive variogram diagnostics.
      ecologists.
 *verify*
      Construction of test suites using verify objects.
+*vioplot*
+     Violin plots, which are a combination of a box plot and a kernel
+     density plot.
 *waveslim*
      Basic wavelet routines for time series analysis.
 *wavethresh*
      Software to perform 1-d and 2-d wavelet statistics and transforms.
      series package.  Contains PADI, juice and monitoring extensions.
 *ensemble*
      Ensembles of tree classifiers.
+*rcom*
+     R COM Client Interface and internal COM Server.
 *runStat*
      Running median and mean.
 *write.snns*
      Function for writing a SNNS pattern file from a data frame or matrix.
 *SAGElyzer*
      Locates genes based on SAGE tags.
 *SNAData*
-     Data from the book "Social Network Analysis" by Wasserman & Faust
+     Data from the book "Social Network Analysis" by Wasserman & Faust,
-     (1999).
+.
 *aCGH*
      Classes and functions for Array Comparative Genomic Hybridization data.
 *affy*
 at the R prompt.
    This produces something like
      Packages in `/home/me/lib/R':
      mystuff       My own R functions, nicely packaged but not documented
      Packages in `/usr/local/lib/R/library':
      KernSmooth    Functions for kernel smoothing for Wand & Jones (1995)
      MASS          Main Package of Venables and Ripley's MASS
      base          The R base package
      boot          Bootstrap R (S-Plus) Functions (Canty)
      class         Functions for Classification
 Also, the developers do not have access to all possible machines capable of
 running R.  So, simply using it and communicating problems is certainly of
 great value.
    One place where functionality is still missing is the modeling software
-as described in "Statistical Models in S" (see *Note What is S?::);
+as described in "Statistical Models in S" (see *Note What is S?::); some of
-Generalized Additive Models (*note Are GAMs implemented in R?::) and some
-of the nonlinear modeling code are not there yet.
+the nonlinear modeling code is not there yet.
    The R Developer Page (http://developer.R-project.org/) acts as an
 intermediate repository for more or less finalized ideas and plans for the
 R statistical system.  It contains (pointers to) TODO lists, RFCs, various
 other writeups, ideas lists, and CVS miscellanea.
 page (http://ESS.R-project.org/).  The HTML version of the documentation
 can be found at `http://stat.ethz.ch/ESS/'.
    ESS comes with detailed installation instructions.
-   For help with ESS, send email to <ESS-help@stat.ethz.ch>.
+   For help with ESS, send email to <ESS-help@stat.math.ethz.ch>.
    Please send bug reports and suggestions on ESS to
 <ESS-bugs@stat.math.ethz.ch>.  The easiest way to do this from is within
 Emacs by typing `M-x ess-submit-bug-report' or using the [ESS] or [iESS]
 pulldown menus.
 expression.  For example, if `ahat' is an estimator of your parameter a of
 interest, use
      title(substitute(hat(a) == ahat, list(ahat = ahat)))
-(note that it is `==' and not `=').  There are more worked examples in the
+(note that it is `==' and not `=').  Sometimes `bquote()' gives a more
-mailing list achives.
+compact form, e.g.,
+     title(bquote(hat(a) = .(ahat)))
+where subexpressions enclosed in `.()' are replaced by their values.
+   There are more worked examples in the mailing list achives.
 .16 What are valid names?
 ==========================
 When creating data frames using `data.frame()' or `read.table()', R by
      strings file "names".
 .17 Are GAMs implemented in R?
 ===============================
-There is a `gam()' function for Generalized Additive Models in package
+Package *gam* from CRAN implements all the Generalized Additive Models
+(GAM) functionality as described in the GAM chapter of the White Book.  In
+particular, it implements backfitting with both local regression and
+smoothing splines, and is extendable.  There is a `gam()' function for GAMs
-*mgcv*, but it is not an exact clone of what is described in the White Book
+in package *mgcv*, but it is not an exact clone of what is described in the
-(no `lo()' for example).  Package *gss* can fit spline-based GAMs too.  And
+White Book (no `lo()' for example).  Package *gss* can fit spline-based
-if you can accept regression splines you can use `glm()'.  For gaussian
+GAMs too.  And if you can accept regression splines you can use `glm()'.
-GAMs you can use `bruto()' from package *mda*.
+For gaussian GAMs you can use `bruto()' from package *mda*.
 .18 Why is the output not printed when I source() a file?
 ==========================================================
 Most R commands do not generate any output. The command
 and of browsers.  For further details please consult section "Enabling
 search in HTML help" in `R Installation and Administration'.  This manual is
 included in the R distribution, *note What documentation exists for R?::,
 and its HTML version is linked from the HTML search page.
+.27 Why did my .Rprofile stop working when I updated R?
+========================================================
+Did you read the `NEWS' file?  For functions that are not in the *base*
+package you need to specify the correct package namespace, since the code
+will be run _before_ the packages are loaded.  E.g.,
+     ps.options(horizontal = FALSE)
+     help.start()
+needs to be
+     graphics::ps.options(horizontal = FALSE)
+     utils::help.start()
 R Programming
 ***************
 .1 How should I write summary methods?
 =======================================

The R Project SVN R

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