Change history of package apcluster:
====================================

Version 1.4.11:
- internal fix regarding a non-stable use of a class internally defined in the
  'Matrix' package
- updates of DESCRIPTION and inst/CITATION to adapt to latest formats

Version 1.4.10:
- minor correction of exception handling in some R methods
- minor corrections of some help pages

Version 1.4.9:
- removed dependency to 'kebas' by rewriting the corresponding section of
  the vignette; consequently, the file inst/examples/ch22Promoters.fasta
  was also removed, since it is no longer needed
- finally removed function sparseToFull() that has been deprecated since
  version 1.4.0
- correction of link to Affinity Propagation website at University of
  Toronto
- DOIs corrected in help pages (therefore, the package now requires
  R version >= 3.3.0)
- some further URLs corrected in help pages
- removed change history from package vignette for easier maintenance

Version 1.4.8:
- correction of aggExCluster() C++ code
- correction of link to Affinity Propagation website at University of
  Toronto

Version 1.4.7:
- correction of aggExCluster() C++ code to avoid compilation error on Solaris

Version 1.4.6:
- aggExCluster() now implemented in C++ instead of R in order to improve
  speed
- further correction of conditional loading of package suggested by vignette

Version 1.4.5:
- loading of suggested Bioconductor packages now performed conditionally
  to avoid problems when building the package on some platforms that do not
  have the Bioconductor packages installed

Version 1.4.4:
- changed dependency to suggested package 'kebabs' to version of
  at least 1.5.4 for improved interoperability
- bug fix in as.dendrogram() method with signature 'AggExResult'
- added discrepancy metric to distance computations and updated
  src/distanceL.c to new version
- registered C/C++ subroutines
- minor change in the vignette template
- moved NEWS to inst/NEWS
- added inst/COPYRIGHT

Version 1.4.3:
- added optional color legend to heatmap plotting; in line with this
  change, some minor changes to the interface of the heatmap() function
- corresponding updates of help pages and vignette

Version 1.4.2:
- switched sequence kernel example in vignette from 'kernlab' to 'kebabs'
  package
- workaround to ensure that all apcluster*() methods are able to process
  'KernelMatrix' objects (cf. 'kebabs' package)
- replaced data set 'ch22Promoters' by plain text file (FASTA format)
  in inst/examples
- bug fix in the heatmap() method
- vignette engine changed from Sweave to knitr

Version 1.4.1.:
- fixes in C++ code of sparse affinity propagation

Version 1.4.0:
- added apcluster() method for sparse similarity matrices;
  as a consequence, the package now imports the 'Matrix' package
  and is now also able to handle non-sparse matrix classes
  defined by the 'Matrix' package. Moreover, similarity functions
  supplied to the apcluster() method may now also return any
  matrix type defined by the 'Matrix' package.
- fix of apcluster() for dense matrices to better support -Inf
  similarities
- added apclusterK() method for sparse similarity matrices
- preferenceRange() is now an S4 generic; re-implementation in
  C++ to speed up function; changed handling of -Inf similarities
  for consistency with sparse version
- added preferenceRange() methods for sparse matrices and dense
  matrix objects from the 'Matrix' package
- new conversion methods implemented for converting dense similarity
  matrices to sparse ones and vice versa; consequently,
  sparseToFull() is marked as deprecated.
- adaptation of heatmap() function for improved handling of -Inf
  similarities
- adaptations of signatures of '[' and '[[' accessor methods
- renamed help page of methods for computing similarity matrices
  to 'similarities' in order to avoid confusion with the accessor
  method 'similarity'
- corresponding updates of help pages and vignette

Version 1.3.5:
- memory access fixes in C++ code called from apclusterL()
- minor updates of vignette

Version 1.3.4:
- added sort() function to rearrange clusters according to
  sort criterion; note that this is an S3 method (see help
  page for explanation)
- improvements and bug fixes of apclusterL() method for
  signature 'matrix,missing'
- performance optimizations of apcluster() and apclusterL()
- plotting of clustering results superimposed in scatter plot
  matrices now also works for 'AggExResult' objects
- improvements of consistency of error and warning messages 
- according adaptations of documentation and vignette
- adapted dependency and linking to Rcpp version 0.11.1
  (to avoid issues on Mac OS)
- minor correction of package namespace

Version 1.3.3:
- adapted dependencies and linking to Rcpp version 0.11.0
- cleared up package dependencies

Version 1.3.2:
- plotting of clustering results extended to data sets with more than
  two dimensions (resulting in the clustering result being superimposed
  in a scatterplot matrix); the variant that plot() can be used to
  draw a heatmap has been removed. From now on, heatmap() must always
  be used.
- improved NA handling
- correction of input check in apcluster() and apclusterL() (previously,
  both functions issued a warning whenever argument p had length > 1)
- corresponding updates and further improvements of help pages and vignette

Version 1.3.1:
- re-implementation of heatmap() method: dendrograms can now be plotted
  even for APResult and ExClust objects as well as for cluster hierarchies
  based on prior clusterings; color bars can now be switched off and colors
  can be changed by user (by new 'sideColor' argument); dendrograms can be
  switched on and off (by 'Rowv' and 'Colv' arguments);
- added as.hclust() and as.dendrogram() methods
- added new arguments 'base', 'showSamples', and 'horiz' to the plot() method
  with signature (x="AggExResult", y="missing"); moreover, parameters for
  changing the appearance of the height axis are now respected as well
- streamlining of methods (redundant definition of inherited methods
  removed)
- various minor improvements of code and documentation

Version 1.3.0:
- added Leveraged Affinity Propagation Clustering
- re-implementation of main functions as S4 generic methods in order to
  facilitate the convenient internal computation of similarity matrices
- for convenience, similarity matrices can be stored as part of clustering
  results
- heatmap plotting now done by heatmap() which has been defined as S4 generic
- extended interface to functions for computing similarity matrices
- added function corSimMat()
- implementation of length() method for classes APResult, AggExResult, and
  ExClust
- added accessor function to extract clustering levels from AggExResult
  objects
- correction of exemplars returned by apcluster() for details=TRUE in slot
  idxAll of returned APResult object
- when using data stored in a data frame, now categorical columns are
  explicitly omitted, thereby, avoiding warnings
- plotting of clustering results along with original data (2D only) has
  been accelerated
- all clustering methods now store their calls into the result objects
- updates and extensions of help pages and vignette

Version 1.2.1:
- added convenient accessor functions to extracting cluster indices from
  APResult and ExClust objects
- added a function for coercing an APResult object into an ExClust object
- correction of color bar on the left side of heatmaps (default behavior
  of RowSideColors parameter changed with R 2.15)

Version 1.2.0:
- reimplementation of apcluster() in C++ using the Rcpp package which reduces
  computation times by a factor of 9-10
- obsolete function apclusterLM() removed
- updates of help pages and vignette

Version 1.1.1:
- updated citation
- minor corrections in help pages and vignette

Version 1.1.0:
- exemplar-based agglomerative clustering (function aggExCluster()) added
- added various plotting functions, e.g. for dendrograms and heatmaps
- added sequence analysis example to vignette
- extension of vignette according to new functionality
- re-organization of variable names in vignette
- added option 'verbose' to apclusterK()
- numerous minor corrections in help pages and vignette

Version 1.0.3:
- Makefile in inst/doc eliminated to avoid installation problems
- renamed vignette to "apcluster"

Version 1.0.2:
- replacement of computation of responsibilities and availabilities in
  apcluster() by pure matrix operations; traditional implementation according
  to Frey and Dueck still available as function apclusterLM();
- improved support for named objects
- new function for computing label vectors
- re-organization of package source files and help pages

Version 1.0.1:
- first public release

