Intel® Threading Challenge 2011 Software Contest
Tag: environment
Changes in R software
The newest version of R is now available for download. R 2.13 is ready !!
http://cran.at.r-project.org/bin/windows/base/CHANGES.R-2.13.0.html
Windows-specific changes to R
CHANGES IN R VERSION 2.13.0
WINDOWS VERSION
- Windows 2000 is no longer supported. (It went end-of-life in July 2010.)
NEW FEATURES
win_iconvhas been updated: this version has a change in the behaviour with BOMs on UTF-16 and UTF-32 files – it removes BOMs when reading and adds them when writing. (This is consistent with Microsoft applications, but Unix versions oficonvusually ignore them.)- Support for repository type win64.binary (used for 64-bit Windows binaries for R 2.11.x only) has been removed.
- The installers no longer put an ‘Uninstall’ item on the start menu (to conform to current Microsoft UI guidelines).
- Running R always sets the environment variable R_ARCH (as it does on a Unix-alike from the shell-script front-end).
- The defaults for
options("browser")andoptions("pdfviewer")are now set from environment variables R_BROWSER and R_PDFVIEWER respectively (as on a Unix-alike). A value of"false"suppresses display (even if there is nofalse.exepresent on the path). - If
options("install.lock")is set toTRUE, binary package installs are protected against failure similar to the way source package installs are protected. file.exists()andunlink()have more support for files > 2GB.- The versions of
R.exein ‘R_HOME/bin/i386,x64/bin’ now support options such asR --vanilla CMD: there is no comparable interface for ‘Rcmd.exe’. - A few more file operations will now work with >2GB files.
- The environment variable R_HOME in an R session now uses slash as the path separator (as it always has when set by
Rcmd.exe). Rguihas a new menu item for the PDF ‘Sweave User Manual’.
DEPRECATED
- zip.unpack() is deprecated: use
unzip().
INSTALLATION
- There is support for libjpeg-turbo via setting
JPEGDIRto that value in ‘MkRules.local’.Support for jpeg-6b has been removed.
- The sources now work with libpng-1.5.1, jpegsrc.v8c (which are used in the CRAN builds) and tiff-4.0.0beta6 (CRAN builds use 3.9.1). It is possible that they no longer work with older versions than libpng-1.4.5.
BUG FIXES
- Workaround for the incorrect values given by Windows’
casinhfunction on the branch cuts. - Bug fixes for drawing raster objects on
windows(). The symptom was the occasional raster image not being drawn, especially when drawing multiple raster images in a single expression. Thanks to Michael Sumner for report and testing. - Printing extremely long string values could overflow the stack and cause the GUI to crash. (PR#14543)
Tonnes of changes!!
http://cran.at.r-project.org/src/base/NEWS
CHANGES IN R VERSION 2.13.0:
SIGNIFICANT USER-VISIBLE CHANGES:
• replicate() (by default) and vapply() (always) now return a
higher-dimensional array instead of a matrix in the case where
the inner function value is an array of dimension >= 2.
• Printing and formatting of floating point numbers is now using
the correct number of digits, where it previously rarely differed
by a few digits. (See “scientific†entry below.) This affects
_many_ *.Rout.save checks in packages.
NEW FEATURES:
• normalizePath() has been moved to the base package (from utils):
this is so it can be used by library() and friends.
It now does tilde expansion.
It gains new arguments winslash (to select the separator on
Windows) and mustWork to control the action if a canonical path
cannot be found.
• The previously barely documented limit of 256 bytes on a symbol
name has been raised to 10,000 bytes (a sanity check). Long
symbol names can sometimes occur when deparsing expressions (for
example, in model.frame).
• reformulate() gains a intercept argument.
• cmdscale(add = FALSE) now uses the more common definition that
there is a representation in n-1 or less dimensions, and only
dimensions corresponding to positive eigenvalues are used.
(Avoids confusion such as PR#14397.)
• Names used by c(), unlist(), cbind() and rbind() are marked with
an encoding when this can be ascertained.
• R colours are now defined to refer to the sRGB color space.
The PDF, PostScript, and Quartz graphics devices record this
fact. X11 (and Cairo) and Windows just assume that your screen
conforms.
• system.file() gains a mustWork argument (suggestion of Bill
Dunlap).
• new.env(hash = TRUE) is now the default.
• list2env(envir = NULL) defaults to hashing (with a suitably sized
environment) for lists of more than 100 elements.
• text() gains a formula method.
• IQR() now has a type argument which is passed to quantile().
• as.vector(), as.double() etc duplicate less when they leave the
mode unchanged but remove attributes.
as.vector(mode = "any") no longer duplicates when it does not
remove attributes. This helps memory usage in matrix() and
array().
matrix() duplicates less if data is an atomic vector with
attributes such as names (but no class).
dim(x) <- NULL duplicates less if x has neither dimensions nor
names (since this operation removes names and dimnames).
• setRepositories() gains an addURLs argument.
• chisq.test() now also returns a stdres component, for
standardized residuals (which have unit variance, unlike the
Pearson residuals).
• write.table() and friends gain a fileEncoding argument, to
simplify writing files for use on other OSes (e.g. a spreadsheet
intended for Windows or Mac OS X Excel).
• Assignment expressions of the form foo::bar(x) <- y and
foo:::bar(x) <- y now work; the replacement functions used are
foo::`bar<-` and foo:::`bar<-`.
• Sys.getenv() gains a names argument so Sys.getenv(x, names =
FALSE) can replace the common idiom of as.vector(Sys.getenv()).
The default has been changed to not name a length-one result.
• Lazy loading of environments now preserves attributes and locked
status. (The locked status of bindings and active bindings are
still not preserved; this may be addressed in the future).
• options("install.lock") may be set to FALSE so that
install.packages() defaults to --no-lock installs, or (on
Windows) to TRUE so that binary installs implement locking.
• sort(partial = p) for large p now tries Shellsort if quicksort is
not appropriate and so works for non-numeric atomic vectors.
• sapply() gets a new option simplify = "array" which returns a
“higher rank†array instead of just a matrix when FUN() returns a
dim() length of two or more.
replicate() has this option set by default, and vapply() now
behaves that way internally.
• aperm() becomes S3 generic and gets a table method which
preserves the class.
• merge() and as.hclust() methods for objects of class "dendrogram"
are now provided.
• as.POSIXlt.factor() now passes ... to the character method
(suggestion of Joshua Ulrich).
• The character method of as.POSIXlt() now tries to find a format
that works for all non-NA inputs, not just the first one.
• str() now has a method for class "Date" analogous to that for
class "POSIXt".
• New function file.link() to create hard links on those file
systems (POSIX, NTFS but not FAT) that support them.
• New Summary() group method for class "ordered" implements min(),
max() and range() for ordered factors.
• mostattributes<-() now consults the "dim" attribute and not the
dim() function, making it more useful for objects (such as data
frames) from classes with methods for dim(). It also uses
attr<-() in preference to the generics name<-(), dim<-() and
dimnames<-(). (Related to PR#14469.)
• There is a new option "browserNLdisabled" to disable the use of
an empty (e.g. via the ‘Return’ key) as a synonym for c in
browser() or n under debug(). (Wish of PR#14472.)
• example() gains optional new arguments character.only and
give.lines enabling programmatic exploration.
• serialize() and unserialize() are no longer described as
‘experimental’. The interface is now regarded as stable,
although the serialization format may well change in future
releases. (serialize() has a new argument version which would
allow the current format to be written if that happens.)
New functions saveRDS() and readRDS() are public versions of the
‘internal’ functions .saveRDS() and .readRDS() made available for
general use. The dot-name versions remain available as several
package authors have made use of them, despite the documentation.
saveRDS() supports compress = "xz".
• Many functions when called with a not-open connection will now
ensure that the connection is left not-open in the event of
error. These include read.dcf(), dput(), dump(), load(),
parse(), readBin(), readChar(), readLines(), save(), writeBin(),
writeChar(), writeLines(), .readRDS(), .saveRDS() and
tools::parse_Rd(), as well as functions calling these.
• Public functions find.package() and path.package() replace the
internal dot-name versions.
• The default method for terms() now looks for a "terms" attribute
if it does not find a "terms" component, and so works for model
frames.
• httpd() handlers receive an additional argument containing the
full request headers as a raw vector (this can be used to parse
cookies, multi-part forms etc.). The recommended full signature
for handlers is therefore function(url, query, body, headers,
...).
• file.edit() gains a fileEncoding argument to specify the encoding
of the file(s).
• The format of the HTML package listings has changed. If there is
more than one library tree , a table of links to libraries is
provided at the top and bottom of the page. Where a library
contains more than 100 packages, an alphabetic index is given at
the top of the section for that library. (As a consequence,
package names are now sorted case-insensitively whatever the
locale.)
• isSeekable() now returns FALSE on connections which have
non-default encoding. Although documented to record if ‘in
principle’ the connection supports seeking, it seems safer to
report FALSE when it may not work.
• R CMD REMOVE and remove.packages() now remove file R.css when
removing all remaining packages in a library tree. (Related to
the wish of PR#14475: note that this file is no longer
installed.)
• unzip() now has a unzip argument like zip.file.extract(). This
allows an external unzip program to be used, which can be useful
to access features supported by Info-ZIP's unzip version 6 which
is now becoming more widely available.
• There is a simple zip() function, as wrapper for an external zip
command.
• bzfile() connections can now read from concatenated bzip2 files
(including files written with bzfile(open = "a")) and files
created by some other compressors (such as the example of
PR#14479).
• The primitive function c() is now of type BUILTIN.
• plot(<dendrogram>, .., nodePar=*) now obeys an optional xpd
specification (allowing clipping to be turned off completely).
• nls(algorithm="port") now shares more code with nlminb(), and is
more consistent with the other nls() algorithms in its return
value.
• xz has been updated to 5.0.1 (very minor bugfix release).
• image() has gained a logical useRaster argument allowing it to
use a bitmap raster for plotting a regular grid instead of
polygons. This can be more efficient, but may not be supported by
all devices. The default is FALSE.
• list.files()/dir() gains a new argument include.dirs() to include
directories in the listing when recursive = TRUE.
• New function list.dirs() lists all directories, (even empty
ones).
• file.copy() now (by default) copies read/write/execute
permissions on files, moderated by the current setting of
Sys.umask().
• Sys.umask() now accepts mode = NA and returns the current umask
value (visibly) without changing it.
• There is a ! method for classes "octmode" and "hexmode": this
allows xor(a, b) to work if both a and b are from one of those
classes.
• as.raster() no longer fails for vectors or matrices containing
NAs.
• New hook "before.new.plot" allows functions to be run just before
advancing the frame in plot.new, which is potentially useful for
custom figure layout implementations.
• Package tools has a new function compactPDF() to try to reduce
the size of PDF files _via_ qpdf or gs.
• tar() has a new argument extra_flags.
• dotchart() accepts more general objects x such as 1D tables which
can be coerced by as.numeric() to a numeric vector, with a
warning since that might not be appropriate.
• The previously internal function create.post() is now exported
from utils, and the documentation for bug.report() and
help.request() now refer to that for create.post().
It has a new method = "mailto" on Unix-alikes similar to that on
Windows: it invokes a default mailer via open (Mac OS X) or
xdg-open or the default browser (elsewhere).
The default for ccaddress is now getOption("ccaddress") which is
by default unset: using the username as a mailing address
nowadays rarely works as expected.
• The default for options("mailer") is now "mailto" on all
platforms.
• unlink() now does tilde-expansion (like most other file
functions).
• file.rename() now allows vector arguments (of the same length).
• The "glm" method for logLik() now returns an "nobs" attribute
(which stats4::BIC() assumed it did).
The "nls" method for logLik() gave incorrect results for zero
weights.
• There is a new generic function nobs() in package stats, to
extract from model objects a suitable value for use in BIC
calculations. An S4 generic derived from it is defined in
package stats4.
• Code for S4 reference-class methods is now examined for possible
errors in non-local assignments.
• findClasses, getGeneric, findMethods and hasMethods are revised
to deal consistently with the package= argument and be consistent
with soft namespace policy for finding objects.
• tools::Rdiff() now has the option to return not only the status
but a character vector of observed differences (which are still
by default sent to stdout).
• The startup environment variables R_ENVIRON_USER, R_ENVIRON,
R_PROFILE_USER and R_PROFILE are now treated more consistently.
In all cases an empty value is considered to be set and will stop
the default being used, and for the last two tilde expansion is
performed on the file name. (Note that setting an empty value is
probably impossible on Windows.)
• Using R --no-environ CMD, R --no-site-file CMD or R
--no-init-file CMD sets environment variables so these settings
are passed on to child R processes, notably those run by INSTALL,
check and build. R --vanilla CMD sets these three options (but
not --no-restore).
• smooth.spline() is somewhat faster. With cv=NA it allows some
leverage computations to be skipped,
• The internal (C) function scientific(), at the heart of R's
format.info(x), format(x), print(x), etc, for numeric x, has been
re-written in order to provide slightly more correct results,
fixing PR#14491, notably in border cases including when digits >=
16, thanks to substantial contributions (code and experiments)
from Petr Savicky. This affects a noticable amount of numeric
output from R.
• A new function grepRaw() has been introduced for finding subsets
of raw vectors. It supports both literal searches and regular
expressions.
• Package compiler is now provided as a standard package. See
?compiler::compile for information on how to use the compiler.
This package implements a byte code compiler for R: by default
the compiler is not used in this release. See the ‘R
Installation and Administration Manual’ for how to compile the
base and recommended packages.
• Providing an exportPattern directive in a NAMESPACE file now
causes classes to be exported according to the same pattern, for
example the default from package.skeleton() to specify all names
starting with a letter. An explicit directive to
exportClassPattern will still over-ride.
• There is an additional marked encoding "bytes" for character
strings. This is intended to be used for non-ASCII strings which
should be treated as a set of bytes, and never re-encoded as if
they were in the encoding of the currrent locale: useBytes = TRUE
is autmatically selected in functions such as writeBin(),
writeLines(), grep() and strsplit().
Only a few character operations are supported (such as substr()).
Printing, format() and cat() will represent non-ASCII bytes in
such strings by a \xab escape.
• The new function removeSource() removes the internally stored
source from a function.
• "srcref" attributes now include two additional line number
values, recording the line numbers in the order they were parsed.
• New functions have been added for source reference access:
getSrcFilename(), getSrcDirectory(), getSrcLocation() and
getSrcref().
• Sys.chmod() has an extra argument use_umask which defaults to
true and restricts the file mode by the current setting of umask.
This means that all the R functions which manipulate
file/directory permissions by default respect umask, notably R
CMD INSTALL.
• tempfile() has an extra argument fileext to create a temporary
filename with a specified extension. (Suggestion and initial
implementation by Dirk Eddelbuettel.)
There are improvements in the way Sweave() and Stangle() handle
non-ASCII vignette sources, especially in a UTF-8 locale: see
‘Writing R Extensions’ which now has a subsection on this topic.
• factanal() now returns the rotation matrix if a rotation such as
"promax" is used, and hence factor correlations are displayed.
(Wish of PR#12754.)
• The gctorture2() function provides a more refined interface to
the GC torture process. Environment variables R_GCTORTURE,
R_GCTORTURE_WAIT, and R_GCTORTURE_INHIBIT_RELEASE can also be
used to control the GC torture process.
• file.copy(from, to) no longer regards it as an error to supply a
zero-length from: it now simply does nothing.
• rstandard.glm gains a type argument which can be used to request
standardized Pearson residuals.
• A start on a Turkish translation, thanks to Murat Alkan.
• .libPaths() calls normalizePath(winslash = "/") on the paths:
this helps (usually) present them in a user-friendly form and
should detect duplicate paths accessed via different symbolic
links.
SWEAVE CHANGES:
• Sweave() has options to produce PNG and JPEG figures, and to use
a custom function to open a graphics device (see ?RweaveLatex).
(Based in part on the contribution of PR#14418.)
• The default for Sweave() is to produce only PDF figures (rather
than both EPS and PDF).
• Environment variable SWEAVE_OPTIONS can be used to supply
defaults for existing or new options to be applied after the
Sweave driver setup has been run.
• The Sweave manual is now included as a vignette in the utils
package.
• Sweave() handles keep.source=TRUE much better: it could duplicate
some lines and omit comments. (Reported by John Maindonald and
others.)
C-LEVEL FACILITIES:
• Because they use a C99 interface which a C++ compiler is not
required to support, Rvprintf and REvprintf are only defined by
R_ext/Print.h in C++ code if the macro R_USE_C99_IN_CXX is
defined when it is included.
• pythag duplicated the C99 function hypot. It is no longer
provided, but is used as a substitute for hypot in the very
unlikely event that the latter is not available.
• R_inspect(obj) and R_inspect3(obj, deep, pvec) are (hidden)
C-level entry points to the internal inspect function and can be
used for C-level debugging (e.g., in conjunction with the p
command in gdb).
• Compiling R with --enable-strict-barrier now also enables
additional checking for use of unprotected objects. In
combination with gctorture() or gctorture2() and a C-level
debugger this can be useful for tracking down memory protection
issues.
UTILITIES:
• R CMD Rdiff is now implemented in R on Unix-alikes (as it has
been on Windows since R 2.12.0).
• R CMD build no longer does any cleaning in the supplied package
directory: all the cleaning is done in the copy.
It has a new option --install-args to pass arguments to R CMD
INSTALL for --build (but not when installing to rebuild
vignettes).
There is new option, --resave-data, to call
tools::resaveRdaFiles() on the data directory, to compress
tabular files (.tab, .csv etc) and to convert .R files to .rda
files. The default, --resave-data=gzip, is to do so in a way
compatible even with years-old versions of R, but better
compression is given by --resave-data=best, requiring R >=
2.10.0.
It now adds a datalist file for data directories of more than
1Mb.
Patterns in .Rbuildignore are now also matched against all
directory names (including those of empty directories).
There is a new option, --compact-vignettes, to try reducing the
size of PDF files in the inst/doc directory. Currently this
tries qpdf: other options may be used in future.
When re-building vignettes and a inst/doc/Makefile file is found,
make clean is run if the makefile has a clean: target.
After re-building vignettes the default clean-up operation will
remove any directories (and not just files) created during the
process: e.g. one package created a .R_cache directory.
Empty directories are now removed unless the option
--keep-empty-dirs is given (and a few packages do deliberately
include empty directories).
If there is a field BuildVignettes in the package DESCRIPTION
file with a false value, re-building the vignettes is skipped.
• R CMD check now also checks for filenames that are
case-insensitive matches to Windows' reserved file names with
extensions, such as nul.Rd, as these have caused problems on some
Windows systems.
It checks for inefficiently saved data/*.rda and data/*.RData
files, and reports on those large than 100Kb. A more complete
check (including of the type of compression, but potentially much
slower) can be switched on by setting environment variable
_R_CHECK_COMPACT_DATA2_ to TRUE.
The types of files in the data directory are now checked, as
packages are _still_ misusing it for non-R data files.
It now extracts and runs the R code for each vignette in a
separate directory and R process: this is done in the package's
declared encoding. Rather than call tools::checkVignettes(), it
calls tool::buildVignettes() to see if the vignettes can be
re-built as they would be by R CMD build. Option --use-valgrind
now applies only to these runs, and not when running code to
rebuild the vignettes. This version does a much better job of
suppressing output from successful vignette tests.
The 00check.log file is a more complete record of what is output
to stdout: in particular contains more details of the tests.
It now check all syntactically valid Rd usage entries, and warns
about assignments (unless these give the usage of replacement
functions).
.tar.xz compressed tarballs are now allowed, if tar supports them
(and setting environment variable TAR to internal ensures so on
all platforms).
• R CMD check now warns if it finds inst/doc/makefile, and R CMD
build renames such a file to inst/doc/Makefile.
INSTALLATION:
• Installing R no longer tries to find perl, and R CMD no longer
tries to substitute a full path for awk nor perl - this was a
legacy from the days when they were used by R itself. Because a
couple of packages do use awk, it is set as the make (rather than
environment) variable AWK.
• make check will now fail if there are differences from the
reference output when testing package examples and if environment
variable R_STRICT_PACKAGE_CHECK is set to a true value.
• The C99 double complex type is now required.
The C99 complex trigonometric functions (such as csin) are not
currently required (FreeBSD lacks most of them): substitutes are
used if they are missing.
• The C99 system call va_copy is now required.
• If environment variable R_LD_LIBRARY_PATH is set during
configuration (for example in config.site) it is used unchanged
in file etc/ldpaths rather than being appended to.
• configure looks for support for OpenMP and if found compiles R
with appropriate flags and also makes them available for use in
packages: see ‘Writing R Extensions’.
This is currently experimental, and is only used in R with a
single thread for colSums() and colMeans(). Expect it to be more
widely used in later versions of R.
This can be disabled by the --disable-openmp flag.
PACKAGE INSTALLATION:
• R CMD INSTALL --clean now removes copies of a src directory which
are created when multiple sub-architectures are in use.
(Following a comment from Berwin Turlach.)
• File R.css is now installed on a per-package basis (in the
package's html directory) rather than in each library tree, and
this is used for all the HTML pages in the package. This helps
when installing packages with static HTML pages for use on a
webserver. It will also allow future versions of R to use
different stylesheets for the packages they install.
• A top-level file .Rinstignore in the package sources can list (in
the same way as .Rbuildignore) files under inst that should not
be installed. (Why should there be any such files? Because all
the files needed to re-build vignettes need to be under inst/doc,
but they may not need to be installed.)
• R CMD INSTALL has a new option --compact-docs to compact any PDFs
under the inst/doc directory. Currently this uses qpdf, which
must be installed (see ‘Writing R Extensions’).
• There is a new option --lock which can be used to cancel the
effect of --no-lock or --pkglock earlier on the command line.
• Option --pkglock can now be used with more than one package, and
is now the default if only one package is specified.
• Argument lock of install.packages() can now be use for Mac binary
installs as well as for Windows ones. The value "pkglock" is now
accepted, as well as TRUE and FALSE (the default).
• There is a new option --no-clean-on-error for R CMD INSTALL to
retain a partially installed package for forensic analysis.
• Packages with names ending in . are not portable since Windows
does not work correctly with such directory names. This is now
warned about in R CMD check, and will not be allowed in R 2.14.x.
• The vignette indices are more comprehensive (in the style of
browseVignetttes()).
DEPRECATED & DEFUNCT:
• require(save = TRUE) is defunct, and use of the save argument is
deprecated.
• R CMD check --no-latex is defunct: use --no-manual instead.
• R CMD Sd2Rd is defunct.
• The gamma argument to hsv(), rainbow(), and rgb2hsv() is
deprecated and no longer has any effect.
• The previous options for R CMD build --binary (--auto-zip,
--use-zip-data and --no-docs) are deprecated (or defunct): use
the new option --install-args instead.
• When a character value is used for the EXPR argument in switch(),
only a single unnamed alternative value is now allowed.
• The wrapper utils::link.html.help() is no longer available.
• Zip-ing data sets in packages (and hence R CMD INSTALL options
--use-zip-data and --auto-zip, as well as the ZipData: yes field
in a DESCRIPTION file) is defunct.
Installed packages with zip-ed data sets can still be used, but a
warning that they should be re-installed will be given.
• The ‘experimental’ alternative specification of a name space via
.Export() etc is now defunct.
• The option --unsafe to R CMD INSTALL is deprecated: use the
identical option --no-lock instead.
• The entry point pythag in Rmath.h is deprecated in favour of the
C99 function hypot. A wrapper for hypot is provided for R 2.13.x
only.
• Direct access to the "source" attribute of functions is
deprecated; use deparse(fn, control="useSource") to access it,
and removeSource(fn) to remove it.
• R CMD build --binary is now formally deprecated: R CMD INSTALL
--build has long been the preferred alternative.
• Single-character package names are deprecated (and R is already
disallowed to avoid confusion in Depends: fields).
BUG FIXES:
• drop.terms and the [ method for class "terms" no longer add back
an intercept. (Reported by Niels Hansen.)
• aggregate preserves the class of a column (e.g. a date) under
some circumstances where it discarded the class previously.
• p.adjust() now always returns a vector result, as documented. In
previous versions it copied attributes (such as dimensions) from
the p argument: now it only copies names.
• On PDF and PostScript devices, a line width of zero was recorded
verbatim and this caused problems for some viewers (a very thin
line combined with a non-solid line dash pattern could also cause
a problem). On these devices, the line width is now limited at
0.01 and for very thin lines with complex dash patterns the
device may force the line dash pattern to be solid. (Reported by
Jari Oksanen.)
• The str() method for class "POSIXt" now gives sensible output for
0-length input.
• The one- and two-argument complex maths functions failed to warn
if NAs were generated (as their numeric analogues do).
• Added .requireCachedGenerics to the dont.mind list for library()
to avoid warnings about duplicates.
• $<-.data.frame messed with the class attribute, breaking any S4
subclass. The S4 data.frame class now has its own $<- method,
and turns dispatch on for this primitive.
• Map() did not look up a character argument f in the correct
frame, thanks to lazy evaluation. (PR#14495)
• file.copy() did not tilde-expand from and to when to was a
directory. (PR#14507)
• It was possible (but very rare) for the loading test in R CMD
INSTALL to crash a child R process and so leave around a lock
directory and a partially installed package. That test is now
done in a separate process.
• plot(<formula>, data=<matrix>,..) now works in more cases;
similarly for points(), lines() and text().
• edit.default() contained a manual dispatch for matrices (the
"matrix" class didn't really exist when it was written). This
caused an infinite recursion in the no-GUI case and has now been
removed.
• data.frame(check.rows = TRUE) sometimes worked when it should
have detected an error. (PR#14530)
• scan(sep= , strip.white=TRUE) sometimes stripped trailing spaces
from within quoted strings. (The real bug in PR#14522.)
• The rank-correlation methods for cor() and cov() with use =
"complete.obs" computed the ranks before removing missing values,
whereas the documentation implied incomplete cases were removed
first. (PR#14488)
They also failed for 1-row matrices.
• The perpendicular adjustment used in placing text and expressions
in the margins of plots was not scaled by par("mex"). (Part of
PR#14532.)
• Quartz Cocoa device now catches any Cocoa exceptions that occur
during the creation of the device window to prevent crashes. It
also imposes a limit of 144 ft^2 on the area used by a window to
catch user errors (unit misinterpretation) early.
• The browser (invoked by debug(), browser() or otherwise) would
display attributes such as "wholeSrcref" that were intended for
internal use only.
• R's internal filename completion now properly handles filenames
with spaces in them even when the readline library is used. This
resolves PR#14452 provided the internal filename completion is
used (e.g., by setting rc.settings(files = TRUE)).
• Inside uniroot(f, ...), -Inf function values are now replaced by
a maximally *negative* value.
• rowsum() could silently over/underflow on integer inputs
(reported by Bill Dunlap).
• as.matrix() did not handle "dist" objects with zero rows.
CHANGES IN R VERSION 2.12.2 patched:
NEW FEATURES:
• max() and min() work harder to ensure that NA has precedence over
NaN, so e.g. min(NaN, NA) is NA. (This was not previously
documented except for within a single numeric vector, where
compiler optimizations often defeated the code.)
BUG FIXES:
• A change to the C function R_tryEval had broken error messages in
S4 method selection; the error message is now printed.
• PDF output with a non-RGB color model used RGB for the line
stroke color. (PR#14511)
• stats4::BIC() assumed without checking that an object of class
"logLik" has an "nobs" attribute: glm() fits did not and so BIC()
failed for them.
• In some circumstances a one-sided mantelhaen.test() reported the
p-value for the wrong tail. (PR#14514)
• Passing the invalid value lty = NULL to axis() sent an invalid
value to the graphics device, and might cause the device to
segfault.
• Sweave() with concordance=TRUE could lead to invalid PDF files;
Sweave.sty has been updated to avoid this.
• Non-ASCII characters in the titles of help pages were not
rendered properly in some locales, and could cause errors or
warnings. • checkRd() gave a spurious error if the \href macro was used.
Using Views in R and comparing functions across multiple packages
R has almost 2923 available packages
This makes the task of searching among these packages and comparing functions for the same analytical task across different packages a bit tedious and prone to manual searching (of reading multiple Pdfs of help /vignette of packages) or sending an email to the R help list.
However using R Views is a slightly better way of managing all your analytical requirements for software rather than the large number of packages (see Graphics view below).
CRAN Task Views allow you to browse packages by topic and provide tools to automatically install all packages for special areas of interest. Currently, 28 views are available. http://cran.r-project.org/web/views/
Bayesian Bayesian Inference ChemPhys Chemometrics and Computational Physics ClinicalTrials Clinical Trial Design, Monitoring, and Analysis Cluster Cluster Analysis & Finite Mixture Models Distributions Probability Distributions Econometrics Computational Econometrics Environmetrics Analysis of Ecological and Environmental Data ExperimentalDesign Design of Experiments (DoE) & Analysis of Experimental Data Finance Empirical Finance Genetics Statistical Genetics Graphics Graphic Displays & Dynamic Graphics & Graphic Devices & Visualization gR gRaphical Models in R HighPerformanceComputing High-Performance and Parallel Computing with R MachineLearning Machine Learning & Statistical Learning MedicalImaging Medical Image Analysis Multivariate Multivariate Statistics NaturalLanguageProcessing Natural Language Processing OfficialStatistics Official Statistics & Survey Methodology Optimization Optimization and Mathematical Programming Pharmacokinetics Analysis of Pharmacokinetic Data Phylogenetics Phylogenetics, Especially Comparative Methods Psychometrics Psychometric Models and Methods ReproducibleResearch Reproducible Research Robust Robust Statistical Methods SocialSciences Statistics for the Social Sciences Spatial Analysis of Spatial Data Survival Survival Analysis TimeSeries Time Series Analysis To automatically install these views, the ctv package needs to be installed, e.g., via
install.packages("ctv") library("ctv")Created by Pretty R at inside-R.org
and then the views can be installed via install.views or update.views (which first assesses which of the packages are already installed and up-to-date), e.g.,install.views("Econometrics") update.views("Econometrics") Created by Pretty R at inside-R.org
CRAN Task View: Graphic Displays & Dynamic Graphics & Graphic Devices & Visualization
| Maintainer: | Nicholas Lewin-Koh |
| Contact: | nikko at hailmail.net |
| Version: | 2009-10-28 |
R is rich with facilities for creating and developing interesting graphics. Base R contains functionality for many plot types including coplots, mosaic plots, biplots, and the list goes on. There are devices such as postscript, png, jpeg and pdf for outputting graphics as well as device drivers for all platforms running R. lattice and grid are supplied with R’s recommended packages and are included in every binary distribution. lattice is an R implementation of William Cleveland’s trellis graphics, while grid defines a much more flexible graphics environment than the base R graphics.
R’s base graphics are implemented in the same way as in the S3 system developed by Becker, Chambers, and Wilks. There is a static device, which is treated as a static canvas and objects are drawn on the device through R plotting commands. The device has a set of global parameters such as margins and layouts which can be manipulated by the user using par() commands. The R graphics engine does not maintain a user visible graphics list, and there is no system of double buffering, so objects cannot be easily edited without redrawing a whole plot. This situation may change in R 2.7.x, where developers are working on double buffering for R devices. Even so, the base R graphics can produce many plots with extremely fine graphics in many specialized instances.
One can quickly run into trouble with R’s base graphic system if one wants to design complex layouts where scaling is maintained properly on resizing, nested graphs are desired or more interactivity is needed. grid was designed by Paul Murrell to overcome some of these limitations and as a result packages like lattice, ggplot2, vcd or hexbin (on Bioconductor ) use grid for the underlying primitives. When using plots designed with grid one needs to keep in mind that grid is based on a system of viewports and graphic objects. To add objects one needs to use grid commands, e.g., grid.polygon() rather than polygon(). Also grid maintains a stack of viewports from the device and one needs to make sure the desired viewport is at the top of the stack. There is a great deal of explanatory documentation included with grid as vignettes.
The graphics packages in R can be organized roughly into the following topics, which range from the more user oriented at the top to the more developer oriented at the bottom. The categories are not mutually exclusive but are for the convenience of presentation:
- Plotting : Enhancements for specialized plots can be found in plotrix, for polar plotting, vcd for categorical data, hexbin (on Bioconductor ) for hexagon binning, gclus for ordering plots and gplots for some plotting enhancements. Some specialized graphs, like Chernoff faces are implemented in aplpack, which also has a nice implementation of Tukey’s bag plot. For 3D plots lattice, scatterplot3d and misc3d provide a selection of plots for different kinds of 3D plotting. scatterplot3d is based on R’s base graphics system, while misc3d is based on rgl. The package onion for visualizing quaternions and octonions is well suited to display 3D graphics based on derived meshes.
- Graphic Applications : This area is not much different from the plotting section except that these packages have tools that may not for display, but can aid in creating effective displays. Also included are packages with more esoteric plotting methods. For specific subject areas, like maps, or clustering the excellent task views contributed by other dedicated useRs is an excellent place to start.
- Effect ordering : The gclus package focuses on the ordering of graphs to accentuate cluster structure or natural ordering in the data. While not for graphics directly cba and seriation have functions for creating 1 dimensional orderings from higher dimensional criteria. For ordering an array of displays, biclust can be useful.
- Large Data Sets : Large data sets can present very different challenges from moderate and small datasets. Aside from overplotting, rendering 1,000,000 points can tax even modern GPU’s. For univariate datalvplot produces letter value boxplots which alleviate some of the problems that standard boxplots exhibit for large data sets. For bivariate data ash can produce a bivariate smoothed histogram very quickly, and hexbin, on Bioconductor , can bin bivariate data onto a hexagonal lattice, the advantage being that the irregular lines and orientation of hexagons do not create linear artifacts. For multivariate data, hexbin can be used to create a scatterplot matrix, combined with lattice. An alternative is to use scagnostics to produce a scaterplot matrix of “data about the data”, and look for interesting combinations of variables.
- Trees and Graphs : ape and ade4 have functions for plotting phylogenetic trees, which can be used for plotting dendrograms from clustering procedures. While these packages produce decent graphics, they do not use sophisticated algorithms for node placement, so may not be useful for very large trees. igraph has the Tilford-Rheingold algorithm implementead and is useful for plotting larger trees. diagram as facilities for flow diagrams and simple graphs. For more sophisticated graphs Rgraphviz and igraph have functions for plotting and layout, especially useful for representing large networks.
- Graphics Systems : lattice is built on top of the grid graphics system and is an R implementation of William Cleveland’s trellis system for S-PLUS. lattice allows for building many types of plots with sophisticated layouts based on conditioning. ggplot2 is an R implementation of the system described in “A Grammar of Graphics” by Leland Wilkinson. Like lattice, ggplot (also built on top of grid) assists in trellis-like graphics, but allows for much more. Since it is built on the idea of a semantics for graphics there is much more emphasis on reshaping data, transformation, and assembling the elements of a plot.
- Devices : Whereas grid is built on top of the R graphics engine, many in the R community have found the R graphics engine somewhat inflexible and have written separate device drivers that either emphasize interactivity or plotting in various graphics formats. R base supplies devices for PostScript, PDF, JPEG and other formats. Devices on CRAN include cairoDevice which is a device based libcairo, which can actually render to many device types. The cairo device is desgned to work with RGTK2, which is an interface to the Gimp Tool Kit, similar to pyGTK2. GDD provides device drivers for several bitmap formats, including GIF and BMP. RSvgDevice is an SVG device driver and interfaces well with with vector drawing programs, or R web development packages, such as Rpad. When SVG devices are for web display developers should be aware that internet explorer does not support SVG, but has their own standard. Trust Microsoft. rgl provides a device driver based on OpenGL, and is good for 3D and interactive development. Lastly, the Augsburg group supplies a set of packages that includes a Java-based device, JavaGD.
- Colors : The package colorspace provides a set of functions for transforming between color spaces and mixcolor() for mixing colors within a color space. Based on the HCL colors provided in colorspace, vcdprovides a set of functions for choosing color palettes suitable for coding categorical variables ( rainbow_hcl()) and numerical information ( sequential_hcl(), diverge_hcl()). Similar types of palettes are provided in RColorBrewer and dichromat is focused on palettes for color-impaired viewers.
- Interactive Graphics : There are several efforts to implement interactive graphics systems that interface well with R. In an interactive system the user can interactively query the graphics on the screen with the mouse, or a moveable brush to zoom, pan and query on the device as well as link with other views of the data. rggobi embeds the GGobi interactive graphics system within R, so that one can display a data frame or several in GGobi directly from R. The package has functions to support longitudinal data, and graphs using GGobi’s edge set functionality. The RoSuDA repository maintained and developed by the University of Augsburg group has two packages, iplots and iwidgets as well as their Java development environment including a Java device, JavaGD. Their interactive graphics tools contain functions for alpha blending, which produces darker shading around areas with more data. This is exceptionally useful for parallel coordinate plots where many lines can quickly obscure patterns. playwith has facilities for building interactive versions of R graphics using the cairoDevice and RGtk2. Lastly, the rgl package has mechanisms for interactive manipulation of plots, especially 3D rotations and surfaces.
- Development : For development of specialized graphics packages in R, grid should probably be the first consideration for any new plot type. rgl has better tools for 3D graphics, since the device is interactive, though it can be slow. An alternative is to use Java and the Java device in the RoSuDA packages, though Java has its own drawbacks. For porting plotting code to grid, using the package gridBase presents a nice intermediate step to embed base graphics in grid graphics and vice versa.
Related Articles
- CRAN Task View: Machine Learning & Statistical Learning (cran.r-project.org)
- The R-Files: Dirk Eddlebuettel (revolutionanalytics.com)
- R Commander Plugins-20 and growing! (decisionstats.com)
- R Node- and other Web Interfaces to R (decisionstats.com)
- Packages for By-Group Processing in R (revolutionanalytics.com)
- R ready to Deduce you (ekonometrics.blogspot.com)
Protected: Using SAS and C/C++ together
Whats new in the latest version of R
CHANGES IN R VERSION 2.12.2: http://cran.r-project.org/src/base/NEWS SIGNIFICANT USER-VISIBLE CHANGES: • Complex arithmetic (notably z^n for complex z and integer n) gave incorrect results since R 2.10.0 on platforms without C99 complex support. This and some lesser issues in trignometric functions have been corrected. Such platforms were rare (we know of Cygwin and FreeBSD). However, because of new compiler optimizations in the way complex arguments are handled, the same code was selected on x86_64 Linux with gcc 4.5.x at the default -O2 optimization (but not at -O). • There is a workaround for crashes seen with several packages on systems using zlib 1.2.5: see the INSTALLATION section. NEW FEATURES: • PCRE has been updated to 8.12 (two bug-fix releases since 8.10). • rep(), seq(), seq.int() and seq_len() report more often when the first element is taken of an argument of incorrect length. • The Cocoa back-end for the quartz() graphics device on Mac OS X provides a way to disable event loop processing temporarily (useful, e.g., for forked instances of R). • kernel()'s default for m was not appropriate if coef was a set of coefficients. (Reported by Pierre Chausse.) • bug.report() has been updated for the current R bug tracker, which does not accept emailed submissions. • R CMD check now checks for the correct use of $(LAPACK_LIBS) (as well as $(BLAS_LIBS)), since several CRAN recent submissions have ignored ‘Writing R Extensions’. INSTALLATION: • The zlib sources in the distribution are now built with all symbols remapped: this is intended to avoid problems seen with packages such as XML and rggobi which link to zlib.so.1 on systems using zlib 1.2.5. • The default for FFLAGS and FCFLAGS with gfortran on x86_64 Linux has been changed back to -g -O2: however, setting -g -O may still be needed for gfortran 4.3.x. PACKAGE INSTALLATION: • A LazyDataCompression field in the DESCRIPTION file will be used to set the value for the --data-compress option of R CMD INSTALL. • Files R/sysdata.rda of more than 1Mb are now stored in the lazyload daabase using xz compression: this for example halves the installed size of package Imap. • R CMD INSTALL now ensures that directories installed from inst have search permission for everyone. It no longer installs files inst/doc/Rplots.ps and inst/doc/Rplots.pdf. These are almost certainly left-overs from Sweave runs, and are often large. DEPRECATED & DEFUNCT: • The ‘experimental’ alternative specification of a name space via .Export() etc is now deprecated. • zip.file.extract() is now deprecated. • Zip-ing data sets in packages (and hence R CMD INSTALL --use-zip-data and the ZipData: yes field in a DESCRIPTION file) is deprecated: using efficiently compressed .rda images and lazy-loading of data has superseded it. BUG FIXES: • identical() could in rare cases generate a warning about non-pairlist attributes on CHARSXPs. As these are used for internal purposes, the attribute check should be skipped. (Reported by Niels Richard Hansen). • If the filename extension (usually .Rnw) was not included in a call to Sweave(), source references would not work properly and the keep.source option failed. (PR#14459) • format.data.frame() now keeps zero character column names. • pretty(x) no longer raises an error when x contains solely non-finite values. (PR#14468) • The plot.TukeyHSD() function now uses a line width of 0.5 for its reference lines rather than lwd = 0 (which caused problems for some PDF and PostScript viewers). • The big.mark argument to prettyNum(), format(), etc. was inserted reversed if it was more than one character long. • R CMD check failed to check the filenames under man for Windows' reserved names. • The "Date" and "POSIXt" methods for seq() could overshoot when to was supplied and by was specified in months or years. • The internal method of untar() now restores hard links as file copies rather than symbolic links (which did not work for cross-directory links). • unzip() did not handle zip files which contained filepaths with two or more leading directories which were not in the zipfile and did not already exist. (It is unclear if such zipfiles are valid and the third-party C code used did not support them, but PR#14462 created one.) • combn(n, m) now behaves more regularly for the border case m = 0. (PR#14473) • The rendering of numbers in plotmath expressions (e.g. expression(10^2)) used the current settings for conversion to strings rather than setting the defaults, and so could be affected by what has been done before. (PR#14477) • The methods of napredict() and naresid() for na.action = na.exclude fits did not work correctly in the very rare event that every case had been omitted in the fit. (Reported by Simon Wood.) • weighted.residuals(drop0=TRUE) returned a vector when the residuals were a matrix (e.g. those of class "mlm"). (Reported by Bill Dunlap.) • Package HTML index files /html/00Index.html were generated with a stylesheet reference that was not correct for static browsing in libraries. • ccf(na.action = na.pass) was not implemented. • The parser accepted some incorrect numeric constants, e.g. 20x2. (Reported by Olaf Mersmann.) • format(*, zero.print) did not always replace the full zero parts. • Fixes for subsetting or subassignment of "raster" objects when not both i and j are specified. • R CMD INSTALL was not always respecting the ZipData: yes field of a DESCRIPTION file (although this is frequently incorrectly specified for packages with no data or which specify lazy-loading of data). R CMD INSTALL --use-zip-data was incorrectly implemented as --use-zipdata since R 2.9.0. • source(file, echo=TRUE) could fail if the file contained #line directives. It now recovers more gracefully, but may still display the wrong line if the directive gives incorrect information. • atan(1i) returned NaN+Infi (rather than 0+Infi) on platforms without C99 complex support. • library() failed to cache S4 metadata (unlike loadNamespace()) causing failures in S4-using packages without a namespace (e.g. those using reference classes). • The function qlogis(lp, log.p=TRUE) no longer prematurely overflows to Inf when exp(lp) is close to 1. • Updating S4 methods for a group generic function requires resetting the methods tables for the members of the group (patch contributed by Martin Morgan). • In some circumstances (including for package XML), R CMD INSTALL installed version-control directories from source packages. • Added PROTECT calls to some constructed expressions used in C level eval calls. • utils:::create.post() (used by bug.report() and help.request()) failed to quote arguments to the mailer, and so often failed. • bug.report() was naive about how to extract maintainer email addresses from package descriptions, so would often try mailing to incorrect addresses. • debugger() could fail to read the environment of a call to a function with a ... argument. (Reported by Charlie Roosen.) • prettyNum(c(1i, NA), drop0=TRUE) or str(NA_complex_) now work correctly.
Related Articles
- R 2.12.2 scheduled for February 25 (revolutionanalytics.com)
- Sweave Tutorial 3: Console Input and Output – Multiple Choice Test Analysis (r-bloggers.com)
Interview Anne Milley JMP
Here is an interview with Anne Milley, a notable thought leader in the world of analytics. Anne is now Senior Director, Analytical Strategy in Product Marketing for JMP , the leading data visualization software from the SAS Institute.
Ajay-What do you think are the top 5 unique selling points of JMP compared to other statistical software in its category?
Anne-
JMP combines incredible analytic depth and breadth with interactive data visualization, creating a unique environment optimized for discovery and data-driven innovation.
With an extensible framework using JSL (JMP Scripting Language), and integration with SAS, R, and Excel, JMP becomes your analytic hub.
JMP is accessible to all kinds of users. A novice analyst can dig into an interactive report delivered by a custom JMP application. An engineer looking at his own data can use built-in JMP capabilities to discover patterns, and a developer can write code to extend JMP for herself or others.
State-of-the-art DOE capabilities make it easy for anyone to design and analyze efficient experiments to determine which adjustments will yield the greatest gains in quality or process improvement – before costly changes are made.
Not to mention, JMP products are exceptionally well designed and easy to use. See for yourself and check out the free trial at www.jmp.com.
Ajay- What are the challenges and opportunities of expanding JMP’s market share? Do you see JMP expanding its conferences globally to engage global audiences?
Anne-
We realized solid global growth in 2010. The release of JMP Pro and JMP Clinical last year along with continuing enhancements to the rest of the JMP family of products (JMP and JMP Genomics) should position us well for another good year.
With the growing interest in analytics as a means to sustained value creation, we have the opportunity to help people along their analytic journey – to get started, take the next step, or adopt new paradigms speeding their time to value. The challenge is doing that as fast as we would like.
We are hiring internationally to offer even more events, training and academic programs globally.
Ajay- What are the current and proposed educational and global academic initiatives of JMP? How can we see more JMP in universities across the world (say India- China etc)?
Anne-
We view colleges and universities both as critical incubators of future JMP users and as places where attitudes about data analysis and statistics are formed. We believe that a positive experience in learning statistics makes a person more likely to eventually want and need a product like JMP.
For most students – and particularly for those in applied disciplines of business, engineering and the sciences – the ability to make a statistics course relevant to their primary area of study fosters a positive experience. Fortunately, there is a trend in statistical education toward a more applied, data-driven approach, and JMP provides a very natural environment for both students and researchers.
Its user-friendly navigation, emphasis on data visualization and easy access to the analytics behind the graphics make JMP a compelling alternative to some of our more traditional competitors.
We’ve seen strong growth in the education markets in the last few years, and JMP is now used in nearly half of the top 200 universities in the US.
Internationally, we are at an earlier stage of market development, but we are currently working with both JMP and SAS country offices and their local academic programs to promote JMP. For example, we are working with members of the JMP China office and faculty at several universities in China to support the use of JMP in the development of a master’s curriculum in Applied Statistics there, touched on in this AMSTAT News article.
Ajay- What future trends do you see for 2011 in this market (say top 5)?
Anne-
Growing complexity of data (text, image, audio…) drives the need for more and better visualization and analysis capabilities to make sense of it all.
More “chief analytics officers” are making better use of analytic talent – people are the most important ingredient for success!
JMP has been on the vanguard of 64-bit development, and users are now catching up with us as 64-bit machines become more common.
Users should demand easy-to-use, exploratory and predictive modeling tools as well as robust tools to experiment and learn to help them make the best decisions on an ongoing basis.
All these factors and more fuel the need for the integration of flexible, extensible tools with popular analytic platforms.
Ajay-You enjoy organic gardening as a hobby. How do you think hobbies and unwind time help people be better professionals?
Anne-
I am lucky to work with so many people who view their work as a hobby. They have other interests too, though, some of which are work-related (statistics is relevant everywhere!). Organic gardening helps me put things in perspective and be present in the moment. More than work defines who you are. You can be passionate about your work as well as passionate about other things. I think it’s important to spend some leisure time in ways that bring you joy and contribute to your overall wellbeing and outlook.
Btw, nice interviews over the past several months—I hadn’t kept up, but will check it out more often!
Biography– Source- http://www.sas.com/knowledge-exchange/business-analytics/biographies.html
Anne Milley
Anne Milley is Senior Director of Analytics Strategy at JMP Product Marketing at SAS. Her ties to SAS began with bank failure prediction at Federal Home Loan Bank Dallas and continued at 7-Eleven Inc. She has authored papers and served on committees for F2006, KDD, SIAM, A2010 and several years of SAS’ annual data mining conference. Milley is a contributing faculty member for the International Institute of Analytics. anne.milley@jmp.com
The Latest GUI for R- BioR
Once more a spanking new shiny software –
Bio7 is a integrated development environment for ecological modelling based on the Rich-Client-Platformconcept of the Java IDE Eclipse. The Bio7 platform contains several perspectives which arrange several views for a special purpose useful for the development and analysis of ecological models. One special perspective bundles a feature rich GUI (Graphical User Interface) for the statistical software R.
For the bidirectional communication between Java and R the Rserve application is used (as a backend to evaluate R code and transfer data from and to Java).
The Bio7 R perspective (see figure below) is divided into a R-Shell view on the left side (conceptual the R side) and a Table view on the right side (conceptual the Java side).
Data can be imported to a spreadsheet, edited and then transferred to the R workspace. Vice versa data from R can be transferred to a sheet of the Table view and then exported e.g. to an Excel or OpenOffice file.
and
General:
Built upon Eclipse 3.6.1.
Now works with the latest Java version! (Windows version bundled with the latest JRE release).
Removed the Soil perspective (now soils can be modeled with ImageJ (float precision). Active images can be displayed in the 3D discrete view (new example available).
Removed the database perspective and the plant layer. You can now built any discrete models without any plant layer.
Removed several controls in the Control view. Added the “Custom Controls” view. In addition ported the Swing component of the Time panel to Swt.
Deleted the avi to swf converter in the ImageJ menu.
Now patterns can be saved with opened Java editor source. If this file is reopened and dragged on Bio7 the pattern is loaded, the source is compiled and the setup method (if available) is executed. In this way model files can be used for presentations ->drag, setup and run. The save actions are located in the Speadsheet view toolbar.
More options available to disable panel painting and recording of values (if not needed for speed!).
New Setup button in the toolbar of Bio7 to trigger a compiled setup method if available.
Removed the load and save pattern buttons from the toolbar of Bio7. Discrete patterns can now be stored with the available action in the spreadsheet view menu.
New P2 Update Manager available in Bio7.
Updated the Janino Compiler.
New HTML perspective added with a view which embeds the TinyMC editor.
New options to disable painting operations for the discrete panels.
New option to explicitly enable scripts at startup (for a faster startup).
Quadgrid (Hexgrid)
Only states are now available which can be created in the “Spreadsheet” view menu easily. Patterns can be stored and restored as usual but are now stored in an *.exml file.
New method to transfer the quadgrid pattern as a matrix to R.
New method to transfer the population data of all quadgrid states to R.
ImageJ:
Update to the latest version (with additional fixes).
Fixed a bug to rename the image.
Thumbnail browser can now open images recursevely(limited to 1000 pics), the magnifiyng glass can be disabled, too.
Plugins can be installed dynamically with a drag and drop operation on the ImageJ view or toolbar (as known from ImageJ).
Installed plugins now extend the plugin menu as submenus or subsubmenus (not finished yet!).
Plugins can now be created with the Java editor. New Bio7 Wizard available to create a plugin template.
Compiled Java files can be added to a *.jar file with a new available action in the Navigator view (if you rightclick on the files in the Navigator). In this way ImageJ plugins can be packaged in a *.jar.
Floweditor:
Fixed a repaint bug in the debug mode of a flow (now draws correctly the active shape in the flow).
Resize with Strg+Scrollwheel works again.
Comments with more than one line works again.
New Test action to verify connections in a flow.
Debug mode now shows all executed Shapes.
Integrated more default tests (for the verification of a regular flow).
A mouse-click now deletes colored shapes in a flow (e.g. in debug mode).
Points panel:
Integrated (dynamic) Voronoi, Delauney visualization (with area and clip to rectangle action).
Points coordinates can now be set in double precision.
Transfer of point coordinates to R now in double precision.
Bio7 Table:
New import and export of Excel 2007 OOXML.
Row headers can now be resized with the mouse device.
R:
Updated R (2.12.1) and Rserve (0.6.3) to the latest version.
New help action in the R-Shell view.
New action to display help for R specific commands in the embedded Bio7 browser (which opens automatically).
New Key actions to copy the selected variable names to the expression dialog (c=cocatenate (+), a=add (,)).
New action to transfer character or numeric vectors horizontally or vertically in an opened spread (Table view) at selection coordinates.
Empty spaces in the filepath are now allowed under Windows if Rserve is started with a system shell or the RGUI (for the tempfile select a location in the Preferences dialog which is writeable) is started.This works also for the RGUI action.
Improved the search for the “Install packages” action (option “Case Sensitive” added).
API:
New API methods available!
And:
Many fixes since the last version!
Installation
Important information:
A certain firewall software can corrupt the Bio7 *.zip file (as well as other files).
Please ensure that you have downloaded a functioning Bio7 1.5 version. In addition it is also reported that a certain antivirus software detects the bundled R software (on Windows) as malware. Often the R specific “open.exe” is detected as malware. Please use a different scanner to make sure that the software is not infected if you have any doubts. For more details see:
http://r.789695.n4.nabble.com/trojan-at-current-development-version-td3244348.html
DECISION STATS 