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

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