Package: aroma.light
====================

Version: 3.17.1 [2019-12-09]

CODE REFACTORING:

 * Now importing throw() from R.oo instead of R.methodsS3.


Version: 3.17.0 [2019-10-30]

 * The version number was bumped for the Bioconductor devel version, which is
   now BioC 3.11 for R (>= 3.6.1).


Version: 3.16.0 [2019-10-30]

 * The version number was bumped for the Bioconductor release version, which is
   now BioC 3.10 for R (>= 3.6.1).


Version: 3.15.1 [2019-08-28]

BUG FIXES:

 * wpca() for matrices had a 'length > 1 in coercion to logical' bug.


Version: 3.15.0 [2019-05-02]

 * The version number was bumped for the Bioconductor devel version, which is
   now BioC 3.10 for R (>= 3.6.0).


Version: 3.14.0 [2019-05-02]

 * The version number was bumped for the Bioconductor release version, which is
   now BioC 3.9 for R (>= 3.6.0).


Version: 3.13.0 [2018-10-30]

 * The version number was bumped for the Bioconductor devel version, which is
   now BioC 3.9 for R (>= 3.6.0).


Version: 3.12.0 [2018-10-30]

 * The version number was bumped for the Bioconductor release version, which is
   now BioC 3.8 for R (>= 3.5.0).


Version: 3.11.2 [2018-09-04]

CODE REFACTORING:

 * fitPrincipalCurve() now requires princurve (>= 2.1.2) and was updated to
   make use of new principcal_curve class instead of deprecated
   principcal.curve class.  This update "should not" affect the results, but
   see https://github.com/dynverse/princurve/issues/8 for information of what
   has changed in the princurve package in this respect.
 

Version: 3.11.1 [2018-08-28]

 * Updated installation instructions in README.md.


Version: 3.11.0 [2018-04-30]

 * The version number was bumped for the Bioconductor devel version, which is
   now BioC 3.8 for R (>= 3.6.0).


Version: 3.10.0 [2018-04-30]

 * The version number was bumped for the Bioconductor release version, which is
   now BioC 3.7 for R (>= 3.5.0).
 

Version: 3.9.1 [2017-12-19]

NEW FEATURES:

 * robustSmoothSpline() now supports using Tukey's biweight (in addition to
   already exising L1) estimators.  See argument 'method'.  Thanks to
   Aaron Lun at the Cancer Research UK Cambridge Institute for adding this
   feature.


Version: 3.9.0 [2017-10-30]

 * The version number was bumped for the Bioconductor devel version, which is
   now BioC 3.7 for R (>= 3.5.0).


Version: 3.8.0 [2017-10-30]

 * The version number was bumped for the Bioconductor release version, which is
   now BioC 3.6 for R (>= 3.4.0).


Version: 3.7.0 [2017-04-23]

 * The version number was bumped for the Bioconductor devel version, which is
   now BioC 3.6 for R (>= 3.4.0).


Version: 3.6.0 [2017-04-23]

 * The version number was bumped for the Bioconductor release version, which is
   now BioC 3.5 for R (>= 3.4.0).


Version: 3.5.1 [2017-04-14]
 
SIGNIFICANT CHANGES:

 * robustSmoothSpline() uses a re-weighted re-iterative algorithm that fits a
   smooth spline using stats::smooth.spline(), calculates the residuals and
   which are used to fit a re-weighted smooth spline and so on until converence.
   Due to updates to stats::smooth.spline() in R (>= 3.4.0) it is no longer
   feasible to maintain a highly optimized version of the algorithm, because it
   was based on internal stats::smooth.spline() code that has no completely
   changed.  Instead the re-iterative algorithm calls stats::smooth.spline() as
   is, which slows it down.  More importantly, it will now give slightly
   different estimates.

SOFTWARE QUALITY:

 * In addition to continous integration (CI) tests and nightly Bioconductor
   tests, the package is now also tested regularly against all reverse package
   depencies available on CRAN and Bioconductor.
 
 
Version: 3.5.0 [2016-10-18]

 * The version number was bumped for the Bioconductor devel version, which is
   now BioC v3.5 for R (>= 3.4.0).
 
 
Version: 3.4.0 [2016-10-18]

 * The version number was bumped for the Bioconductor release version, which is
   now BioC v3.4 for R (>= 3.3.1).
 
 
Version: 3.3.2 [2016-09-16]

CODE REFACTORING:

 * Using NA_real_ (not just NA) everywhere applicable.

BUG FIXES:

 * robustSmoothSpline() gave an error since R-devel (>= 3.4.0 r70682).
 
 
Version: 3.3.1 [2016-08-10]

CODE REFACTORING:

 * CLEANUP: Using seq_len() and seq_along() everywhere (Issue #8)
 
 
Version: 3.3.0 [2016-05-03]

 * The version number was bumped for the Bioconductor devel version, which is
   now BioC v3.4 for R (>= 3.3.0).
 
 
Version: 3.2.0 [2016-05-03]

 * The version number was bumped for the Bioconductor release version, which is
   now BioC v3.3 for R (>= 3.3.0).
 
 
Version: 3.1.1 [2016-01-06]

 * Package requires R (>= 2.15.2).

CODE REFACTORING:

 * CLEANUP: robustSmoothSpline() no longer generates messages that
   ".nknots.smspl() is now exported; use it instead of n.knots()" for
   R (>= 3.1.1).
 
 
Version: 3.1.0 [2015-10-23]

 * The version number was bumped for the Bioconductor devel version, which is
   now BioC v3.3 for R (>= 3.3.0).
 
 
Version: 3.0.0 [2015-10-13]

 * The version number was bumped for the Bioconductor release version, which is
   now BioC v3.2 for R (>= 3.2.2).
 
 
Version: 2.99.0 [2015-10-06]

 * No changes.
 
 
Version: 2.9.0 [2015-09-17]

SIGNIFICANT CHANGES:

 * Argument 'preserveScale' for normalizeTumorBoost() now defaults to FALSE.
   Since 1.33.3 (2014-04-30) it had no default and prior to that it was TRUE.
 
 
Version: 2.5.3 [2015-09-13]

SOFTWARE QUALITY:

 * ROBUSTNESS: Explicitly importing core R functions.

BUG FIXES:

 * rowAverages() and normalizeAverages() would give an error if some of the
   argument default functions are overridden by non-functions of the same name
   in the calling environment.
 
 
Version: 2.5.2 [2015-06-16]

SOFTWARE QUALITY:

 * Relaxed package test for backtransformPrincipalCurve().
 
 
Version: 2.5.1 [2015-05-24]

 * Bumped package dependencies.

DEPRECATED AND DEFUNCT:

 * CLEANUP: Removed obsolete wpca(..., method = "dsvdc"); was only needed for
   backward compatibility with R (< 1.7.0).
 
 
Version: 2.5.0 [2015-04-16]

 * The version number was bumped for the Bioconductor devel version, which is
   now BioC v3.2 for R (>= 3.3.0).
 
 
Version: 2.4.0 [2015-04-16]

 * The version number was bumped for the Bioconductor release version, which is
   now BioC v3.1 for R (>= 3.2.0).
 
 
Version: 2.3.3 [2015-02-18]

NEW FEATURES:

 * If a value of argument 'xlim' or 'ylim' for plotDensity() is NA, then it
   defaults to the corresponding extreme value of the data, e.g.
   plotDensity(x, xlim = c(0, NA)).
 
 
Version: 2.3.2 [2015-02-17]

SOFTWARE QUALITY:

 * ROBUSTNESS: Added package tests. Code coverage is 76%.

CODE REFACTORING:

 * CLEANUP: Using requestNamespace() instead of request().
 
 
Version: 2.3.1 [2014-12-08]

 * Same updates as in 2.2.1.
 
 
Version: 2.3.0 [2014-10-13]

 * The version number was bumped for the Bioconductor devel version, which is
   now BioC v3.1 for R (>= 3.2.0).
 
 
Version: 2.2.1 [2014-12-08]

CODE REFACTORING:

 * Minor code cleanup.
 
 
Version: 2.2.0 [2014-10-13]

 * The version number was bumped for the Bioconductor release version, which is
   now BioC v3.0 for R (>= 3.1.1).
 
 
Version: 2.1.2 [2014-09-23]

 * Minor tweaks due to the move to GitHub.
 
 
Version: 2.1.1 [2014-09-16]

SOFTWARE QUALITY:

 * Fixed some new R CMD check NOTEs.
 
CODE REFACTORING:

 * CLEANUP: Now importing R.utils (instead of only suggesting it).

 * IMPORTANT/CLEANUP: The matrixStats package is no longer attached with this
   package.  In other words, you now might have to add library('matrixStats')
   to your scripts.
 
 
Version: 2.1.0 [2014-04-11]

 * The version number was bumped for the Bioconductor devel version, which is
   now BioC v2.15 for R (>= 3.1.0).
 
 
Version: 2.0.0 [2014-04-11]

 * The version number was bumped for the Bioconductor release version, which is
   now BioC v2.14 for R (>= 3.1.0).
 
 
Version: 1.99.3 [2014-03-31]

 * Bumped the version such that the next release will be 2.0.0.
 
 
Version: 1.33.3 [2014-03-30]

SIGNIFICANT CHANGES:

 * Argument 'preserveScale' for normalizeTumorBoost() is now required. The goal
   with this is to in a future version migrate to use preserveScale = FALSE as
   the default (was preserveScale = TRUE) in order to avoid introducing a a
   global bias in the tumor allele B fraction of heterozygous SNPs.  The
   examples use preserveScale = FALSE now.

NEW FEATURES:

 * Added pairedAlleleSpecificCopyNumbers().

 
Version: 1.33.2 [2014-03-25]

NEW FEATURES:

 * Now plotDensity() supports weights via argument 'W'.
 
 
Version: 1.33.1 [2014-03-25]

NEW FEATURES:

 * Now plotDensity() also supports density() objects.

CODE REFACTORING:

 * CLEANUP: robustSmoothSpline() no longer uses DUP = FALSE in an internal
   .Fortran() call.

 * Bumped up package dependencies.
 
 
Version: 1.33.0 [2013-10-14]

 * The version number was bumped for the Bioc devel version.
 
 
Version: 1.32.0 [2012-10-14]

 * The version number was bumped for the Bioconductor release version, which is
   now Bioc v2.13 for R (>= 3.0.0).
 
 
Version: 1.31.10 [2013-10-08]

NEW FEATURES:

 * Added averageQuantile() for matrices in addition to lists.

PERFORMANCE:

 * SPEEDUP: Now normalizeQuantileSpline(..., sortTarget = TRUE) sorts the
   target only once for lists of vectors just as done for matrices.

DOCUMENTATION:

 * Merged the documentation for normalizeQuantileSpline() for all data types
   into one help page.  Same for plotXYCurve().

CODE REFACTORING:

 * Bumped up package dependencies.

BUG FIXES:

 * Argument 'lwd' of plotXYCurve(X, ...) was ignored if 'X' was a matrix.
 
 
Version: 1.31.9 [2013-10-07]

NEW FEATURES:

 * Now library(aroma.light, quietly = TRUE) attaches the package completely
   silently without any messages.

 * Now the 'aroma.light' Package object is also available when the package is
   only loaded (but not attached).

DOCUMENTATION:

 * Merged the documentation for normalizeQuantileRank() for numeric vectors and
   lists.

 * Now documention S3 methods under their corresponding generic function.
 
 
Version: 1.31.8 [2013-10-02]

DOCUMENTATION:

 * More generic functions are now "aliased" under relevant corresponding
   methods.
 
 
Version: 1.31.7 [2013-09-27]

PERFORMANCE:

 * SPEEDUP: Now all package functions utilizes 'matrixStats' functions
   where possible, e.g. anyMissing(), colMins(), and rowWeightedMedians().

CODE REFACTORING:

 * Bumped up package dependencies.
 
 
Version: 1.31.6 [2013-09-25]

CODE REFACTORING:

 * CLEANUP: Package no longer use a fallback attachment of the 'R.oo' package
   upon attachment.
 
 
Version: 1.31.5 [2013-09-23]

SOFTWARE QUALITY:

 * ROBUSTNESS: Now properly declaring all S3 methods in the NAMESPACE file.

PERFORMANCE:

 * SPEEDUP/CLEANUP: normalizeTumorBoost() now uses which() instead of
   whichVector() of 'R.utils'.  Before R (< 2.11.0), which() used to be 10x
   slower than whichVector(), but now it's 3x faster.

CODE REFACTORING:

 * CLEANUP: Now only using 'Authors@R' in DESCRIPTION, which is possible since
   R (>= 2.14.0).  Hence the new requirement on the version of R.

 * Bumped up package dependencies.
 
 
Version: 1.31.4 [2013-09-10]

SOFTWARE QUALITY:

 * CLEANUP: Now package explicitly imports what it needs from matrixStats.

CODE REFACTORING:

 * Bumped up package dependencies.
 
 
Version: 1.31.3 [2013-05-25]

PERFORMANCE:

 * SPEEDUP: Removed all remaining gc() calls, which were in
   normalizeQuantileSpline().

 * SPEEDUP: Replaced all rm() calls with NULL assignments.

CODE REFACTORING:

 * Updated the package dependencies.
 
 
Version: 1.31.2 [2013-05-20]

 * Same updates as in v1.30.2.
 
 
Version: 1.31.1 [2011-04-18]

 * Same updates as in v1.30.1.
 
 
Version: 1.31.0 [2013-04-03]

 * The version number was bumped for the Bioc devel version.
 
 
Version: 1.30.5 [2013-09-25]

SOFTWARE QUALITY:

 * Backport from v1.31.5: Declaring all S3 methods in NAMESPACE.

CODE REFACTORING:

 * Backport from v1.31.5: normalizeTumorBoost() now uses which(), which also
   removes one dependency on 'R.utils'.
 
 
Version: 1.30.4 [2013-09-25]

SOFTWARE QUALITY:

 * Backport from v1.31.4: Now package explicitly imports what it needs from
   matrixStats.
 
 
Version: 1.30.3 [2013-09-25]

PERFORMANCE:

 * Backport from v1.31.3: Removal of all gc() calls and removal of variables is
   now faster.

BUG FIX:

 * Removed one stray str() debug output in robustSmoothSpline().
 
 
Version: 1.30.2 [2013-05-20]

 * CRAN POLICY: Now all Rd \usage{} lines are at most 90 characters long.
 
 
Version: 1.30.1 [2013-04-18]

NEW FEATURES:

 * Now backtransformPrincipalCurve() preserves dimension names.

BUG FIXES:

 * backtransformPrincipalCurve() gave an error if the pricipal curve was fitted
   using data with missing values.

 * fitPrincipalCurve() would not preserve dimension names if data contain
   missing values.
 
 
Version: 1.30.0 [2012-04-03]

 * The version number was bumped for the Bioconductor release version, which
   now is Bioc v2.12 for R (>= 3.0.0).
 
 
Version: 1.29.0 [2012-10-01]

 * The version number was bumped for the Bioc devel version.
 
 
Version: 1.28.0 [2012-10-01]

 * The version number was bumped for the Bioconductor release version, which
   now is Bioc v2.11 for R (>= 2.15.1).
 
 
Version: 1.27.1 [2012-09-12]

SOFTWARE QUALITY:

 * ROBUSTNESS: Replaced an .Internal(psort(...)) call in medianPolish() with a
   call to matrixStats:::.psortKM().
 
 
Version: 1.27.0 [2012-08-30]

CODE REFACTORING:

 * CLEANUP: Removed weightedMedian(), which has been moved to the matrixStats
   package.

 * BACKWARD COMPATIBILITY: Now package depends on the matrixStats (>= 0.5.2)
   package, so that weightedMedian() is still available when loading this
   package.  In future releases, matrixStats will be downgraded to only be a
   suggested package.
 
 
Version: 1.26.1 [2012-08-30]

CODE REFACTORING:

 * Updated the package dependencies.
 
BUG FIXES:

 * robustSmoothSpline() would not work with most recent R devel versions.
 
 
Version: 1.26.0 [2012-08-19]

SIGNIFICANT CHANGES:

 * Changed the license of aroma.light to GPL (>= 2) from LGPL (>= 2), because
   some of the implementation was adopted from GPL (>= 2) code, i.e.
   robustSmoothSpline() uses code from stats::smooth.spline().

SOFTWARE QUALITY:

 * R CMD check no longer warns about some examples depending on the R.basic
   package.
 
 
Version: 1.25.4 [2012-08-19]

SOFTWARE QUALITY:

 * WORKAROUND: Now robustSmoothSpline() robustly locates the proper native R
   fit function for smooth splines, which vary with different releases of R.
 
 
Version: 1.25.3 [2012-04-16]

CODE REFACTORING:

 * Package no longer depends on R.methodsS3, only imports.
 
 
Version: 1.25.2 [2012-04-16]

SOFTWARE QUALITY:

 * 'R CMD check' no longer complaints about .Internal() calls.
 
 
Version: 1.25.1 [2012-04-16]

NEW FEATURES:

 * Added support for fitNaiveGenotypes(..., flavor = "fixed").

 * GENERALIZATION: Now fitNaiveGenotypes() returns also 'flavor' and 'tau'.
   The latter are the genotype threshholds used by the caller.

CODE REFACTORING:

 * CLEANUP: Dropped argument 'flavor' of callNaiveGenotypes(); it is instead
   passed to fitNaiveGenotypes() via '...'.
 
 
Version: 1.25.0 [2012-03-30]

 * The version number was bumped for the Bioconductor devel version.
 
 
Version: 1.24.0 [2012-03-30]

 * The version number was bumped for the Bioconductor release version, which
   now is Bioc v2.10 for R (>= 2.15.0).
 
 
Version: 1.23.0 [2011-10-31]

 * The version number was bumped for the Bioconductor devel version.
 
 
Version: 1.22.0 [2011-10-31]

 * The version number was bumped for the Bioconductor release version, which
   now is Bioc v2.9 for R (>= 2.14.0).
 
 
Version: 1.21.2 [2011-10-10]

CODE REFACTORING:

 * Updated robustSmoothSpline() such that it works with the new "uniqueness"
   scheme of smooth.spline() in R v2.14.0 and newer.  It is tricky, because
   robustSmoothSpline() is a reiterative algorithm which requires that the
   choosen "unique" x:s does not change in each iteration.  Previously,
   'signif(x, 6)' was used to identify unique x:s, which gives the same set of
   values when called twice, whereas this is not true for the new choice with
   'round((x - mean(x))/tol)'.
 
 
Version: 1.21.1 [2011-06-26]

NEW FEATURES:

 * Added argument 'aspectRatio' to plotMvsA().  It can be used to adjust the
   range of the 'Mlim' argument relative to the 'Alim' argument.
 
 
Version: 1.21.0 [2011-04-13]

 * The version number was bumped for the Bioconductor devel version.
 
 
Version: 1.20.0 [2010-04-13]

 * The version number was bumped for the Bioconductor release version,
   which now is Bioc v2.8 for R (>= 2.13.0).
 
 
Version: 1.19.6 [2011-04-12]

CODE REFACTORING:

 * CLEANUP: Removed internal patch of principal.curve().  If an older version
   than princurve v1.1-10 is used, an informative error is thrown requesting an
   update.  The internal patch is part of the offical princurve v1.1-10 release
   (since 2009-10-04).

 * Now all methods allocate objects with NAs of the appropriate mode.

KNOWN ISSUES:

 * Recent updates to smooth.spline() in R v2.14.0 causes robustSmoothSpline()
   to break in some cases.
 
 
Version: 1.19.5 [2011-04-08]

NEW FEATURES:

 * Now weightedMedian() returns NA:s of the same mode as argument 'x'.
 
 
Version: 1.19.4 [2011-03-03]

 * Same updates as in v1.18.4.
 
 
Version: 1.19.3 [2011-02-05]

 * Same updates as in v1.18.3.
 
 
Version: 1.19.2 [2010-10-22]

 * Same updates as in v1.18.2.
 
 
Version: 1.19.1 [2010-10-18]

 * Same updates as in v1.18.1.
 
 
Version: 1.19.0 [2010-10-18]

 * The version number was bumped for the Bioconductor devel version.
 
 
Version: 1.18.4 [2011-03-03]

BUG FIXES:

 * findPeaksAndValleys(x, to) were 'x' is numeric would use partial match and
   interpret 'to' as argument 'tol' and not part of '...' passed to density().
   This problem was solved by placing '...' before argument 'tol'.  Thanks
   Oscar Rueda at the Cancer Reasearch UK for reporting on and identifying this
   bug.
 
 
Version: 1.18.3 [2011-02-05]

DOCUMENTATION:

 * Added paragraphs on how to do affine normalization when channel offsets are
   known/zero.  Same for multiscan calibration when scanner offsets are
   known/zero.

 * Fixed broken links to help for iwpca().
 
 
Version: 1.18.2 [2010-10-22]

DOCUMENTATION:

 * Minor clarifications to the help page on "1. Calibration and Normalization".
   This page is now also referenced in help("calibrateMultiscan").
 
 
Version: 1.18.1 [2010-10-18]

NEW FEATURES:

 * Argument 'censorAt' for fitNaiveGenotypes() has new default.

 * These updates were supposed to be in v1.17.7, but we forgot to commit them
   to the BioC repository before the new BioC release.

BUG FIXES:

 * fitNaiveGenotypes(..., subsetToFit = <logical>) would throw an exception
   reporting "Some elements of argument 'subsetToFit' is out of range ...".
 
 
Version: 1.18.0 [2010-10-18]

 * The version number was bumped for the Bioconductor release version, which
   now is Bioc v2.7 for R (>= 2.12.0).
 
 
Version: 1.17.6 [2010-10-08]

NEW FEATURES:

 * Now findPeaksAndValleys() returns a object of class PeaksAndValleys, which
   extends data.frame.
 
 
Version: 1.17.5 [2010-10-07]

NEW FEATURES:

 * Added optional argument 'fit' to callNaiveGenotypes() for passing a model
   fit returned by fitNaiveGenotypes().  If not specified, callNaiveGenotypes()
   will call fitNaiveGenotypes() internally.

 * Added fitNaiveGenotypes(), which previously was only internal of
   callNaiveGenotypes().
 
 
Version: 1.17.4 [2010-10-06]

NEW FEATURES:

 * Added findPeaksAndValleys() for the 'density' class, which then
   findPeaksAndValleys() for 'numeric' utilizes.
 
 
Version: 1.17.3 [2010-09-18]

SOFTWARE QUALITY:

 * ROBUSTNESS: Now normalizeFragmentLength() asserts that arguments
   'fragmentLengths' and 'y' contain at least some finite values and specifies
   the same number of units.  In addition, the method also gives more
   informative error messages in case it cannot fit the normalization function
   due to non-finite values.
 
 
Version: 1.17.2 [2010-08-04]

NEW FEATURES:

 * Added argument 'preserveScale' to normalizeTumorBoost() to rescale the
   calibrated allele B fractions for heterozygous SNPs such that the
   compression relative to the homozgygotes is preserved.
 
 
Version: 1.17.1 [2010-07-23]

 * Same updates as in release version v1.16.1.
 
 
Version: 1.17.0 [2010-04-22]

 * The version number was bumped for the Bioconductor devel version.
 
 
Version: 1.16.1 [2010-07-23]

NEW FEATURES:

 * Now callNaiveGenotypes() returns the model estimates as attribute
   'modelFit'.  This feature was supposed to be in v1.16.0.
 
 
Version: 1.16.0 [2010-04-22]

 * The version number was bumped for the Bioconductor release version, which
   now is Bioc v2.6 for R (>= 2.11.0).
 
 
Version: 1.15.4 [2010-04-08]

SOFTWARE QUALITY:

 * R devel assumes ASCII encoding unless specified. Added explicit Latin-1
   encoding to the DESCRIPTION file to R CMD check to pass.
 
 
Version: 1.15.3 [2010-04-04]

NEW FEATURES:

 * Added normalizeDifferencesToAverage(), normalizeTumorBoost(),
   callNaiveGenotypes() and internal findPeaksAndValleys(), which all were
   moved from the aroma.cn package.
 
 
Version: 1.15.2 [2010-03-12]

BUG FIXES:

 * The example of fitPrincipalCurve() used a non-existing argument name in the
   calls to substitute().  Thanks to Brian Ripley at University of Oxford for
   reporting this.
 
 
Version: 1.15.1 [2009-11-01]

CODE REFACTORING:

 * Now fitPrincipalCurve() only uses the internal bug-fix patch if a version
   earlier than princurve v1.1-10 is installed.
 
 
Version: 1.15.0 [2009-10-27]

 * The version number was bumped for the Bioconductor devel version.
 
 
Version: 1.14.0 [2009-10-27]

 * The version number was bumped for the Bioconductor release version, which
   now is Bioc v2.5 for R (>= 2.10.0).
 
 
Version: 1.13.6 [2009-10-20]

DOCUMENTATION:

 * FIX: CITATION file reverted to that of v1.13.4.
 
 
Version: 1.13.5 [2009-10-08]

DOCUMENTATION:

 * CITATION file [incorrectly] updated by BioC maintainers.
 
 
Version: 1.13.4 [2009-09-23]

DOCUMENTATION:

 * Fixed a few broken Rd links.
 
 
Version: 1.13.3 [2009-07-15]

NEW FEATURES:

 * ADDED: fit- and backtransformXYCurve().

 * Added attribute 'processingTime' to the fit object returned by
   fitPrincipalCurve().
 
 
Version: 1.13.2 [2009-05-29]

 * Incorporating the same updates as in release v1.12.2.
 
 
Version: 1.13.1 [2009-05-13]

 * Incorporating the same updates as in release v1.12.1.
 
 
Version: 1.13.0 [2009-04-20]

 * The version number was bumped for the Bioconductor devel version.
 
 
Version: 1.12.2 [2009-05-29]

CODE REFACTORING:

 * Replacing old HOWTOCITE with a standard CITATION file.

BUG FIXES:

 * Previous bug fix in backtransformPrincipalCurve() regarding argument
   'dimension' broke the initial purpose of this argument. Since both use cases
   are still of interest, how the subsetting is done is now based on whether
   the number of dimensions of the input data and the model fit match or not.
   See help and example code for 'backtransformPrincipalCurve.matrix'.
 
 
Version: 1.12.1 [2009-05-13]

BUG FIXES:

 * backtransformPrincipalCurve(..., dimensions) did not subset the 'X' matrix.
   Also, the method now returns a matrix of the same number of columns
   requested.  The Rd example now illustrates this.  Thanks to Pierre Neuvial,
   UC Berkeley for the troublshooting and fix.
 
 
Version: 1.12.0 [2009-04-20]

 * The version number was bumped for the Bioconductor release version.
 
 
Version: 1.11.2 [2009-02-08]

BUG FIXES:

 * An error was thrown in backtransformPrincipalCurve() when argument
   'dimensions' was specified.
 
 
Version: 1.11.1 [2009-01-12]

NEW FEATURES:

 * Added fit- & backtransformPrincipalCurve().
 
 
Version: 1.11.0 [2008-10-21]

 * The version number was bumped for the Bioconductor devel version.
 
 
Version: 1.10.0 [2008-10-21]

 * The version number was bumped for the Bioconductor release version.
 
 
Version: 1.9.2 [2008-09-11]

NEW FEATURES:

 * Added argument 'onMissing' to normalizeFragmentLength() for specifying how
   to normalize (if at all) data points for which the fragment lengths are
   unknown.  For backward compatibility, we start off by having it "ignore" by
   default.

CODE REFACTORING:

 * MEMORY OPTIMIZATION: robustSmoothSpline() is now cleaning out more variables
   when no longer needed.
 
 
Version: 1.9.1 [2008-05-10]

 * Incorporating the same updates as in release v1.8.1.
 
 
Version: 1.9.0 [2008-04-29]

 * The version number was bumped for the Bioconductor devel version.
 
 
Version: 1.8.1 [2008-05-10]

BUG FIXES:

 * If the 'subsetToFit' of normalizeFragmentLength() was shorter than the
   number of data points, an exception was thrown.  The test was supposed to
   assert that the subset was not greater than the number of data points.
 
 
Version: 1.8.0 [2008-04-29]

 * The version number was bumped for the Bioconductor release version.
 
 
Version: 1.7.2 [2008-04-14]

NEW FEATURES:

 * Added normalizeFragmentLength().

 * Added normalizeQuantileSpline().

 * Renamed normalizeQuantile() to normalizeQuantileRank().

 * Added plotXYCurve().

 * Added predict() for the 'lowess' class.
 
 
Version: 1.7.1 [2007-11-28]

NEW FEATURES:

 * The startup message when loading the package is generated with
   packageStartupMessage() so that it can be suppressed.

DOCUMENTATION:

 * TYPO: Corrected a spelling error in the help pages.

SOFTWARE QUALITY:

 * Package passes R CMD check R v2.6.1.

CODE REFACTORING:

 * Package now only suggest the R.oo package, and instead depends on the new
   R.methodsS3.

 
Version: 1.7.0 [2007-10-08]

 * The version number was bumped for the Bioconductor devel version.
 
 
Version: 1.6.0 [2007-10-08]

 * The version number was bumped for the Bioconductor release version.
 
 
Version: 1.5.2 [2007-08-10]

SOFTWARE QUALITY:

 * Package pass R CMD check R v2.6.0.
 
 
Version: 1.5.1 [2007-06-08] (this was mistakenly versioned 1.4.1)

NEW FEATURES:

 * Added normalizeAverage().

SOFTWARE QUALITY:

 * Package pass R CMD check R v2.6.0 with Rd encoding errors.
 
 
Version: 1.5.0 [2007-05-09]

 * The version number was bumped for the Bioconductor devel version.
 
 
Version: 1.4.0 [2007-05-09]

 * The version number was bumped up with the Bioconductor release.
 
 
Version: 1.3.1 [2007-01-15]

CODE REFACTORING:

 * Removed code to use 'modreg' for backward compatibility with R < 1.9.0.

 * Added R.utils to Suggests field of DESCRIPTION.
 
 
Version: 1.3.0 [2006-10-??]

 * The devel version number was bumped up with the Bioconductor release.
 
 
Version: 1.2.0 [2006-10-03]

 * The version number was bumped up with the Bioconductor release.
 
 
Version: 1.1.0 [2006-07-20]

SIGNIFICANT CHANGES:

 * Added to Bioconductor v1.9.

NEW FEATURES:

 * Added some trial RSP pages. Try browseRsp() in the R.rsp package.
 
 
Version: 0.1.7 [2006-06-27]

CODE REFACTORING:

 * Made the package truely standalone except from R.oo.  Previously package
   R.basic was used in some of the examples.
 
 
Version: 0.1.6 [2006-05-22]

NEW FEATURES:

 * Added medianPolish() which is much faster than stats::medpolish() when there
   are no NA.

 * Added plotDensity() for list of vectors as well as for matrices.

 * Added normalizeQuantile() for lists of vectors as well as for a single
   vector of numerics.  To calculate the target quantile there is a new
   function averageQuantile(), which is also for lists of vectors.  It latter
   does not support robust estimatation of the average, because it safes memory.

 * Updated normalizeQuantile() for matrices according to the updates in the
   limma package.

CODE REFACTORING:

 * Added a namespace for the package.

 * Added 'biocViews' since the package will eventually be added to the
   Bioconductor project.

 
Version: 0.1.5 [2006-04-21]

PERFORMANCE:

 * Minor speedup to weightedMedian(), e.g. negative weights do no longer give
   and error, but are treated as zero instead.  This removes some overhead
   of the function.  Also, if it is known that there are no NAs that can be
   specified by na.rm = NA, which will skip NA checks.
 
 
Version: 0.1.4 [2006-03-28]

DOCUMENTATION:

 * Updated broken Rd links.

 * Updated the references to publications.
 
 
Version: 0.1.3 [2006-01-22]

NEW FEATURES:

 * Now fitIWPCA() does not return the data matrix. This is to save memory.
   The calling algorithm can equally well add the data if it is needed.

DOCUMENTATION:

 * Added help on the returned parameters of fitIWPCA().
 
 
Version: 0.1.2 [2005-09-06]

NEW FEATURES:

 * All plot methods displaying log-ratios now assures that no fake log-ratios
   are calculated due to two negative raw signals.  Similarily, methods display
   log-intensities now assures that the log-intensities are calculated as
   doubles to avoid possible overflow warnings for too large integers.
 
 
Version: 0.1.1 [2005-07-26]

NEW FEATURES:

 * Added sampleCorrelations() and sampleTuples().

 * Now argument 'interpolate' of weightedMedian() defaults to TRUE only if
   'ties' is NULL.
 
 
Version: 0.1.0 [2005-06-03]

SIGNIFICANT CHANGES:

 * Created. Most of the matrix methods were copied from the R.basic and the
   aroma packages. The purpose of this package is to provide a standalone
   package, which does not require any of the aroma classes. This will allow
   the methods to be used by end users as is, or be utilized in other packages.
