LENGUAJE DE PROGRAMACION R

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LENGUAJE DE PROGRAMACION R

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NEWS	R Documentation

• New features in this version

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• Previous releases

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R News

CHANGES IN R 3.4.0

SIGNIFICANT USER-VISIBLE CHANGES

• (Unix-alike) The default methods for download.file() and url() now choose "libcurl" except for file:// URLs. There will be small changes in the format and wording of messages, including in rare cases if an issue is a warning or an error. For example, when HTTP re-direction occurs, some messages refer to the final URL rather than the specified one.
  Those who use proxies should check that their settings are compatible (see ?download.file: the most commonly used forms work for both "internal" and "libcurl").
• table() has been amended to be more internally consistent and become back compatible to R <= 2.7.2 again. Consequently, table(1:2, exclude = NULL) no longer contains a zero count for <NA>, but useNA = "always" continues to do so.
• summary.default() no longer rounds, but its print method does resulting in less extraneous rounding, notably of numbers in the ten thousands.
• factor(x, exclude = L) behaves more rationally when x or L are character vectors. Further, exclude = <factor> now behaves as documented for long.
• Arithmetic, logic (&, |) and comparison (aka ‘relational’, e.g., <, ==) operations with arrays now behave consistently, notably for arrays of length zero.
  Arithmetic between length-1 arrays and longer non-arrays had silently dropped the array attributes and recycled. This now gives a warning and will signal an error in the future, as it has always for logic and comparison operations in these cases (e.g., compare matrix(1,1) + 2:3 and matrix(1,1) < 2:3).
• The JIT (‘Just In Time’) byte-code compiler is now enabled by default at its level 3. This means functions will be compiled on first or second use and top-level loops will be compiled and then run. (Thanks to Tomas Kalibera for extensive work to make this possible.)
  For now, the compiler will not compile code containing explicit calls to browser(): this is to support single stepping from the browser() call.
  JIT compilation can be disabled for the rest of the session using compiler::enableJIT(0) or by setting environment variable R_ENABLE_JIT to 0.
• xtabs() works more consistently with NAs, also in its result no longer setting them to 0. Further, a new logical option addNA allows to count NAs where appropriate. Additionally, for the case sparse = TRUE, the result's dimnames are identical to the default case's.
• Matrix products now consistently bypass BLAS when the inputs have NaN/Inf values. Performance of the check of inputs has been improved. Performance when BLAS is used is improved for matrix/vector and vector/matrix multiplication (DGEMV is now used instead of DGEMM).
  One can now choose from alternative matrix product implementations via options(matprod = ). The "internal" implementation is not optimized for speed but consistent in precision with other summations in R (using long double accumulators where available). "blas" calls BLAS directly for best speed, but usually with undefined behavior for inputs with NaN/Inf.
• factor() now uses order() to sort its levels, not sort.list(). This makes factor() support custom vector-like objects if methods for the appropriate generics are defined. This change has the side effect of making factor() succeed on empty or length-one non-atomic vector(-like) types (e.g., list), where it failed before.

NEW FEATURES

• User errors such as integrate(f, 0:1, 2) are now caught.
• Add signature argument to debug(), debugonce(), undebug() and isdebugged() for more conveniently debugging S3 and S4 methods. (Based on a patch by Gabe Becker.)
• Add utils::debugcall() and utils::undebugcall() for debugging the function that would be called by evaluating the given expression. When the call is to an S4 generic or standard S3 generic, debugcall() debugs the method that would be dispatched. A number of internal utilities were added to support this, most notably utils::isS3stdGeneric(). (Based on a patch by Gabe Becker.)
• Add utils::strcapture(). Given a character vector and a regular expression containing capture expressions, strcapture() will extract the captured tokens into a tabular data structure, typically a data.frame.
• str() and strOptions() get a new option drop.deparse.attr with improved but changed default behaviour for expressions. For expression objects x, str(x) now may remove extraneous white space and truncate long lines.
• str(<looooooooong_string>) is no longer very slow; inspired by Mikko Korpela's proposal in PR#16527.
• str(x)'s default method is more “accurate” and hence somewhat more generous in displaying character vectors; this will occasionally change R outputs (and need changes to some ‘*.Rout(.save)’ files).
  For a classed integer vector such as x <- xtabs(~ c(1,9,9,9)), str(x) now shows both the class and "int", instead of only the latter.
• isSymmetric(m) is much faster for large asymmetric matrices m via pre-tests and a new option tol1 (with which strict back compatibility is possible but not the default).
• The result of eigen() now is of class "eigen" in the default case when eigenvectors are computed.
• Zero-length date and date-time objects (of classes "POSIX[cl]?t") now print() “recognizably”.
• xy.coords() and xyz.coords() get a new setLab option.
• The method argument of sort.list(), order() and sort.int() gains an "auto" option (the default) which should behave the same as before when method was not supplied.
• stopifnot(E, ..) now reports differences when E is a call to all.equal() and that is not true.
• boxplot(<formula>, *) gain optional arguments drop, sep, and lex.order to pass to split.default() which itself gains an argument lex.order to pass to interaction() for more flexibility.
• The plot() method for ppr() has enhanced default labels (xmin and main).
• sample.int() gains an explicit useHash option (with a back compatible default).
• identical() gains an ignore.srcref option which drops "srcref" and similar attributes when true (as by default).
• diag(x, nrow = n) now preserves typeof(x), also for logical, integer and raw x (and as previously for complex and numeric).
• smooth.spline() now allows direct specification of lambda, gets a hatvalues() method and keeps tol in the result, and optionally parts of the internal matrix computations.
• addNA() is faster now, e.g. when applied twice. (Part of PR#16895.)
• New option rstandard(<lm>, type = "predicted") provides the “PRESS”–related leave-one-out cross-validation errors for linear models.
• After seven years of deprecation, duplicated factor levels now produce a warning when printed and an error in levels<- instead of a warning.
• Invalid factors, e.g., with duplicated levels (invalid but constructable) now give a warning when printed, via new function .valid.factor().
• sessionInfo() has been updated for Apple's change in OS naming as from ‘10.12’ (‘macOS Sierra’ vs ‘OS X El Capitan’).
  Its toLatex() method now includes the running component.
• options(interrupt=) can be used to specify a default action for user interrupts. For now, if this option is not set and the error option is set, then an unhandled user interrupt invokes the error option. (This may be dropped in the future as interrupt conditions are not error conditions.)
• In most cases user interrupt handlers will be called with a "resume" restart available. Handlers can invoke this restart to resume computation. At the browser prompt the r command will invoke a "resume" restart if one is available. Some read operations cannot be resumed properly when interrupted and do not provide a "resume" restart.
• Radix sort is now chosen by method = "auto" for sort.int() for double vectors (and hence used for sort() for unclassed double vectors), excluding ‘long’ vectors.
  sort.int(method = "radix") no longer rounds double vectors.
• The default and data.frame methods for stack() preserve the names of empty elements in the levels of the ind column of the return value. Set the new drop argument to TRUE for the previous behavior.
• Speedup in simplify2array() and hence sapply() and mapply() (for the case of names and common length > 1), thanks to Suharto Anggono's PR#17118.
• table(x, exclude = NULL) now sets useNA = "ifany" (instead of "always"). Together with the bug fixes for this case, this recovers more consistent behaviour compatible to older versions of R. As a consequence, summary() for a logical vector no longer reports (zero) counts for NA when there are no NAs.
• dump.frames() gets a new option include.GlobalEnv which allows to also dump the global environment, thanks to Andreas Kersting's proposal in PR#17116.
• system.time() now uses message() instead of cat() when terminated early, such that suppressMessages() has an effect; suggested by Ben Bolker.
• citation() supports ‘inst/CITATION’ files from package source trees, with lib.loc pointing to the directory containing the package.
• try() gains a new argument outFile with a default that can be modified via options(try.outFile = .), useful notably for Sweave.
• The unexported low-level functions in package parallel for passing serialized R objects to and from forked children now support long vectors on 64-bit platforms. This removes some limits on higher-level functions such as mclapply() (but returning gigabyte results from forked processes via serialization should be avoided if at all possible).
• Connections now print() without error even if invalid, e.g. after having been destroyed.
• apropos() and find(simple.words = FALSE) no longer match object names starting with . which are known to be internal objects (such as .__S3MethodsTable__.).
• Convenience function hasName() has been added; it is intended to replace the common idiom !is.null(x$name) without the usually unintended partial name matching.
• strcapture() no longer fixes column names nor coerces strings to factors (suggested by Bill Dunlap).
• strcapture() returns NA for non-matching values in x (suggested by Bill Dunlap).
• source() gets new optional arguments, notably exprs; this is made use of in the new utility function withAutoprint().
• sys.source() gets a new toplevel.env argument. This argument is useful for frameworks running package tests; contributed by Tomas Kalibera.
• Sys.setFileTime() and file.copy(copy.date = TRUE) will set timestamps with fractions of seconds on platforms/filesystems which support this.
• (Windows only.) file.info() now returns file timestamps including fractions of seconds; it has done so on other platforms since R 2.14.0. (NB: some filesystems do not record modification and access timestamps to sub-second resolution.)
• The license check enabled by options(checkPackageLicense = TRUE) is now done when the package's namespace is first loaded.
• ppr() and supsmu() get an optional trace argument, and ppr(.., sm.method = ..spline) is no longer limited to sample size n <= 2500.
• The POSIXct method for print() gets optional tz and usetz arguments, thanks to a report from Jennifer S. Lyon.
• New function check_packages_in_dir_details() in package tools for analyzing package-check log files to obtain check details.
• Package tools now exports function CRAN_package_db() for obtaining information about current packages in the CRAN package repository, and several functions for obtaining the check status of these packages.
• The (default) Stangle driver Rtangle allows annotate to be a function and gets a new drop.evalFALSE option.
• The default method for quantile(x, prob) should now be monotone in prob, even in border cases, see PR#16672.
• bug.report() now tries to extract an email address from a BugReports field, and if there is none, from a Contacts field.
• The format() and print() methods for object.size() results get new options standard and digits; notably, standard = "IEC" and standard = "SI" allow more standard (but less common) abbreviations than the default ones, e.g. for kilobytes. (From contributions by Henrik Bengtsson.)
• If a reference class has a validity method, validObject will be called automatically from the default initialization method for reference classes.
• tapply() gets new option default = NA allowing to change the previously hardcoded value.
• read.dcf() now consistently interprets any ‘whitespace’ to be stripped to include newlines.
• The maximum number of DLLs that can be loaded into R e.g. via dyn.load() can now be increased by setting the environment variable R_MAX_NUM_DLLS before starting R.
• Assigning to an element of a vector beyond the current length now over-allocates by a small fraction. The new vector is marked internally as growable, and the true length of the new vector is stored in the truelength field. This makes building up a vector result by assigning to the next element beyond the current length more efficient, though pre-allocating is still preferred. The implementation is subject to change and not intended to be used in packages at this time.
• Loading the parallel package namespace no longer sets or changes the .Random.seed, even if R_PARALLEL_PORT is unset.
  NB: This can break reproducibility of output, and did for a CRAN package.
• Methods "wget" and "curl" for download.file() now give an R error rather than a non-zero return value when the external command has a non-zero status.
• Encoding name "utf8" is mapped to "UTF-8". Many implementations of iconv accept "utf8", but not GNU libiconv (including the late 2016 version 1.15).
• sessionInfo() shows the full paths to the library or executable files providing the BLAS/LAPACK implementations currently in use (not available on Windows).
• The binning algorithm used by bandwidth selectors bw.ucv(), bw.bcv() and bw.SJ() switches to a version linear in the input size n for n > nb/2. (The calculations are the same, but for larger n/nb it is worth doing the binning in advance.)
• There is a new option PCRE_study which controls when grep(perl = TRUE) and friends ‘study’ the compiled pattern. Previously this was done for 11 or more input strings: it now defaults to 10 or more (but most examples need many more for the difference from studying to be noticeable).
• grep(perl = TRUE) and friends can now make use of PCRE's Just-In-Time mechanism, for PCRE >= 8.20 on platforms where JIT is supported. It is used by default whenever the pattern is studied (see the previous item). (Based on a patch from Mikko Korpela.)
  This is controlled by a new option PCRE_use_JIT.
  Note that in general this makes little difference to the speed, and may take a little longer: its benefits are most evident on strings of thousands of characters. As a side effect it reduces the chances of C stack overflow in the PCRE library on very long strings (millions of characters, but see next item).
  Warning: segfaults were seen using PCRE with JIT enabled on 64-bit Sparc builds.
• There is a new option PCRE_limit_recursion for grep(perl = TRUE) and friends to set a recursion limit taking into account R's estimate of the remaining C stack space (or 10000 if that is not available). This reduces the chance of C stack overflow, but because it is conservative may report a non-match (with a warning) in examples that matched before. By default it is enabled if any input string has 1000 or more bytes. (PR#16757)
• getGraphicsEvent() now works on X11(type = "cairo") devices. Thanks to Frederick Eaton (for reviving an earlier patch).
• There is a new argument onIdle for getGraphicsEvent(), which allows an R function to be run whenever there are no pending graphics events. This is currently only supported on X11 devices. Thanks to Frederick Eaton.
• The deriv() and similar functions now can compute derivatives of log1p(), sinpi() and similar one-argument functions, thanks to a contribution by Jerry Lewis.
• median() gains a formal ... argument, so methods with extra arguments can be provided.
• strwrap() reduces indent if it is more than half width rather than giving an error. (Suggested by Bill Dunlap.)
• When the condition code in if(.) or while(.) is not of length one, an error instead of a warning may be triggered by setting an environment variable, see the help page.
• Formatting and printing of bibliography entries (bibentry) is more flexible and better documented. Apart from setting options(citation.bibtex.max = 99) you can also use print(<citation>, bibtex=TRUE) (or format(..)) to get the BibTeX entries in the case of more than one entry. This also affects citation(). Contributions to enable style = "html+bibtex" are welcome.