R News and Updates


Free Webinar for learning rockchalk:

This free one-hour webinar will provide a general introduction to rockchalk, an R package that provides a collection of functions that ease the presentation and interpretation of regression analysis.

Webinar Format:
- Introduction to the rockchalk R package
- Live demonstration
- Question and Answer period

- Paul Johnson, Professor at the University of Kansas and the rockchalk package maintainer

- Ray DiGiacomo, President of The Orange County R User Group

For more information on the rockchalk package, please visit this site:


This event is brought to you by The Orange County R User Group.

Please note that in addition to attending from your laptop or desktop computer, you can also attend from a Wi-Fi connected iPhone, iPad, Android phone or Android tablet by installing the GoToMeeting App.

Best Regards,

The Orange County R User Group

Register here: https://www3.gotomeeting.com/register/846549286


R-3.0.2 Up and Running

Here's the NEWS file

Peter Dalgaard said:
The build system rolled up R-3.0.2.tar.gz (codename "Frisbee Sailing") this morning.

The list below details the changes in this release.

You can get the source code from


or wait for it to be mirrored at a CRAN site nearer to you.

Binaries for various platforms will appear in due course.

For the R Core Team

Peter Dalgaard


Probably A Mammal
I was looking for that YouTube video and couldn't find it! I watched it as part of the Stanford's OpenEdX Statistical Learning class. Good stuff! Good class, though basic right now (linear regression. Ugh).


Ambassador to the humans
3.0.3 has been released. The changes reported in the NEWS file:


On Windows there is support for making ‘.texi’ manuals using texinfo 5.0 or later: the setting is in file ‘src/gnuwin32/MkRules.dist’.

A packaging of the Perl script and modules for texinfo 5.2 has been made available at http://www.stats.ox.ac.uk/pub/Rtools/.

write.table() now handles matrices of 2^31 or more elements, for those with large amounts of patience and disc space.

There is a new function, La_version(), to report the version of LAPACK in use.

The HTML version of ‘An Introduction to R’ now has links to PNG versions of the figures.

There is some support to produce manuals in ebook formats. (See ‘doc/manual/Makefile’. Suggested by Mauro Cavalcanti.)

On a Unix-alike Sys.timezone() returns NA if the environment variable TZ is unset, to distinguish it from an empty string which on some OSes means the UTC time zone.

The backtick may now be escaped in strings, to allow names containing them to be constructed, e.g. `\``. (PR#15621)

read.table(), readLines() and scan() now warn when an embedded nul is found in the input. (Related to PR#15625 which was puzzled by the behaviour in this unsupported case.)

(Windows only.) file.symlink() works around the undocumented restriction of the Windows system call to backslashes. (Wish of PR#15631.)

KalmanForecast(fast = FALSE) is now the default, and the help contains an example of how fast = TRUE can be used in this version. (The usage will change in 3.1.0.)

strptime() now checks the locale only when locale-specific formats are used and caches the locale in use: this can halve the time taken on OSes with slow system functions (e.g. OS X).

strptime() and the format() methods for classes "POSIXct", "POSIXlt" and "Date" recognize strings with marked encodings: this allows, for example, UTF-8 French month names to be read on (French) Windows.

iconv(to = "utf8") is now accepted on all platforms (some implementations did already, but GNU libiconv did not: however converted strings were not marked as being in UTF-8). The official name, "UTF-8" is still preferred.

available.packages() is better protected against corrupt metadata files. (A recurring problem with Debian package shogun-r: PR#14713.)

Finalizers are marked to be run at garbage collection, but run only at a somewhat safer later time (when interrupts are checked). This circumvents some problems with finalizers running arbitrary code during garbage collection (the known instances being running options() and (C-level) path.expand() re-entrantly).


The included version of PCRE has been updated to 8.34. This fixes bugs and makes the behaviour closer to Perl 5.18. In particular, the concept of ‘space’ includes VT and hence agrees with POSIX's.


The new field SysDataCompression in the ‘DESCRIPTION’ file allows user control over the compression used for ‘sysdata.rda’ objects in the lazy-load database.

install.packages(dependencies = value) for value = NA (the default) or value = TRUE omits packages only in LinkingTo for binary package installs.


The long undocumented remapping of rround() to Rf_fround() in header ‘Rmath.h’ is now formally deprecated: use fround() directly.

Remapping of prec() and trunc() in the ‘Rmath.h’ header has been disabled in C++ code (it has caused breakage with libc++ headers).


getParseData() truncated the imaginary part of complex number constants. (Reported by Yihui Xie.)

dbeta(x, a, b) with a or b within a factor of 2 of the largest representable number could infinite-loop. (Reported by Ioannis Kosmidis.)

provideDimnames() failed for arrays with a 0 dimension. (PR#15465)

rbind() and cbind() did not handle list objects correctly. (PR#15468)

replayPlot() now checks if it is replaying a plot from the same session.

rasterImage() and grid.raster() now give error on an empty (zero-length) raster. (Reported by Ben North.)

plot.lm() would sometimes scramble the labels in plot type 5. (PR#15458 and PR#14837)

min() did not handle NA_character_ values properly. (Reported by Magnus Thor Torfason.)

(Windows only.) readRegistry() would duplicate default values for keys. (PR#15455)

str(..., strict.width = "cut") did not handle it properly when more than one line needed to be cut. (Reported by Gerrit Eichner.)

Removing subclass back-references when S4 classes were removed or their namespace unloaded had several bugs (e.g., PR#15481).

aggregate() could fail when there were too many levels present in the by argument. (PR#15004)

namespaceImportFrom() needed to detect primitive functions when checking for duplicated imports (reported by Karl Forner).

getGraphicsEvent() did not exit when a user closed the graphics window. (PR#15208)

Errors in vignettes were not always captured and displayed properly. (PR#15495)

contour() could fail when dealing with extremely small z values. (PR#15454)

Several functions did not handle zero-length vectors properly, including browseEnv(), format(), gl(), relist() and summary.data.frame(). (E.g., PR#15499)

Sweave() did not restore the R output to the console if it was interrupted by a user in the middle of evaluating a code chunk. (Reported by Michael Sumner.)

Fake installs of packages with vignettes work again.

Illegal characters in the input caused parse() (and thus source()) to segfault. (PR#15518)

The nonsensical use of nmax = 1 in duplicated() or unique() is now silently ignored.

qcauchy(p, *) is now fully accurate even when p is very close to 1. (PR#15521)

The validmu() and valideta() functions in the standard glm() families now also report non-finite values, rather than failing.

Saved vignette results (in a ‘.Rout.save’ file) were not being compared to the new ones during R CMD check.

Double-clicking outside of the list box (e.g. on the scrollbar) of a Tk listbox widget generated by tk_select.list() no longer causes the window to close. (PR#15407)

Improved handling of edge cases in parallel::splitindices(). (PR#15552)

HTML display of results from help.search() and ?? sometimes contained badly constructed links.

c() and related functions such as unlist() converted raw vectors to invalid logical vectors. (PR#15535)

(Windows only) When a call to system2() specified one of stdin, stdout or stderr to be a file, but the command was not found (e.g. it contained its arguments, or the program was not on the PATH), it left the file open and unusable until R terminated. (Reported by Mathew McLean.)

The bmp() device was not recording res = NA correctly: it is now recorded as 72 ppi.

Several potential problems with compiler-specific behaviour have been identified using the ‘Undefined Behaviour Sanitizer’ in conjunction with the clang compiler.

hcl() now honours NA inputs (previously they were mapped to black).

Some translations in base packages were being looked up in the main catalog rather than that for the package.

As a result of the 3.0.2 change about ‘the last second before the epoch’, most conversions which should have given NA returned that time. (The platforms affected include Linux and OS X, but not Windows nor Solaris.)

rowsum() has more support for matrices and dataframes with 2^31 or more elements. (PR#15587)

predict(<lm object>, interval = "confidence", scale = <something>) now works. (PR#15564)

The bug fix in 3.0.2 for PR#15411 was too aggressive, and sometimes removed spaces that should not have been removed. (PR#15583)

Running R code in a tcltk callback failed to set the busy flag, which will be needed to tell OS X not to ‘App Nap’.

The code for date-times before 1902 assumed that the offset from GMT in 1902 was a whole number of minutes: that was not true of Paris (as recorded on some platforms).

Using Sys.setlocale to set LC_NUMERIC to "C" (to restore the sane behavior) no longer gives a warning.

deparse() now deparses complex vectors in a way that re-parses to the original values. (PR#15534, patch based on code submitted by Alex Bertram.)

In some extreme cases (more than 10^15) integer inputs to dpqr***() functions might have been rounded up by one (with a warning about being non-integer). (PR#15624)

Plotting symbol pch = 14 had the triangle upside down on some devices (typically screen devices). The triangle is supposed to be point up. (Reported by Bill Venables.)

getSrcref() did not work on method definitions if rematchDefinition() had been used.

KalmanForecast(fast = FALSE) reported a (harmless) stack imbalance.

The count of observations used by KalmanRun() did not take missing values into account.

In locales where the abbreviated name of one month is a partial match for the full name of a later one, the %B format in strptime() could fail. An example was French on OS X, where juin is abbreviated to jui and partially matches juillet. Similarly for weekday names.

pbeta(x, a, b, log.p = TRUE) sometimes underflowed to zero for very small and very differently sized a, b. (PR#15641)

approx() and approxfun() now handle infinite values with the "constant" method. (PR#15655)

stripchart() again respects reversed limits in xlim and ylim. (PR#15664)


Probably A Mammal
For those falling in love with Shiny apps


OMG OMG OMG! I had stumbled across the Shiny guide for layouts: https://github.com/rstudio/shiny/wiki/Shiny-Application-Layout-Guide and then realized half of them aren't even available in the CRAN version! Not anymore my friends. Now I can start making some awesome layouts, such as this one that I may definitely utilize: http://stackoverflow.com/questions/22429601/r-shiny-navbarmenu

Now if only they'd make it possible to use the ggplot locator to make interactive graphics, I'd be set. I have high hopes for ggvis, but you can already use base graphics and manage user clicks/hovers or use rCharts and D3 plots, if you want to learn those alternative approaches. I've backed myself into a dplyr+ggplot framework; I'm not looking forward to starting over for my visualization components, but I'm also not against it.