Changes in version 1.4.14 (2025-09-22) o corrections of help pages o updated DESCRIPTION file to new format (Author@R) Changes in version 1.4.13 (2024-04-26) o updates and corrections of help pages Changes in version 1.4.12 (2024-04-19) o changed e-mail address of maintainer o updated README.md and formatting of package vignette Changes in version 1.4.11 (2023-09-19) o internal fix regarding a non-stable use of a class internally defined in the 'Matrix' package o updates of DESCRIPTION and inst/CITATION to adapt to latest formats Changes in version 1.4.10 (2022-05-31) o minor correction of exception handling in some R methods o minor corrections of some help pages Changes in version 1.4.9 (2022-01-14) o 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 o finally removed function sparseToFull() that has been deprecated since version 1.4.0 o correction of link to Affinity Propagation website at University of Toronto o DOIs corrected in help pages (therefore, the package now requires R version >= 3.3.0) o some further URLs corrected in help pages o removed change history from package vignette for easier maintenance Changes in version 1.4.8 (2019-08-21) o correction of aggExCluster() C++ code o correction of link to Affinity Propagation website at University of Toronto Changes in version 1.4.7 (2018-05-29) o correction of aggExCluster() C++ code to avoid compilation error on Solaris Changes in version 1.4.6 (2018-05-28) o aggExCluster() now implemented in C++ instead of R in order to improve speed o further correction of conditional loading of package suggested by vignette Changes in version 1.4.5 (2018-01-30) o 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 Changes in version 1.4.4 (2017-07-04) o changed dependency to suggested package 'kebabs' to version of at least 1.5.4 for improved interoperability o bug fix in as.dendrogram() method with signature 'AggExResult' o added discrepancy metric to distance computations and updated src/distanceL.c to new version o registered C/C++ subroutines o minor change in the vignette template o moved NEWS to inst/NEWS o added inst/COPYRIGHT Changes in version 1.4.3 (2016-02-24) o added optional color legend to heatmap plotting; in line with this change, some minor changes to the interface of the heatmap() function o corresponding updates of help pages and vignette Changes in version 1.4.2 (2015-12-24) o switched sequence kernel example in vignette from 'kernlab' to 'kebabs' package o workaround to ensure that all apcluster*() methods are able to process 'KernelMatrix' objects (cf. 'kebabs' package) o replaced data set 'ch22Promoters' by plain text file (FASTA format) in inst/examples o bug fix in the heatmap() method o vignette engine changed from Sweave to knitr Changes in version 1.4.1 (2014-12-09) o fixes in C++ code of sparse affinity propagation Changes in version 1.4.0 (2014-12-01) o 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. o fix of apcluster() for dense matrices to better support -Inf similarities o added apclusterK() method for sparse similarity matrices o preferenceRange() is now an S4 generic; re-implementation in C++ to speed up function; changed handling of -Inf similarities for consistency with sparse version o added preferenceRange() methods for sparse matrices and dense matrix objects from the 'Matrix' package o new conversion methods implemented for converting dense similarity matrices to sparse ones and vice versa; consequently, sparseToFull() is marked as deprecated. o adaptation of heatmap() function for improved handling of -Inf similarities o adaptations of signatures of '[' and '[[' accessor methods o renamed help page of methods for computing similarity matrices to 'similarities' in order to avoid confusion with the accessor method 'similarity' o corresponding updates of help pages and vignette Changes in version 1.3.5 (2014-06-26) o memory access fixes in C++ code called from apclusterL() o minor updates of vignette Changes in version 1.3.4 (2014-06-25) o added sort() function to rearrange clusters according to sort criterion; note that this is an S3 method (see help page for explanation) o improvements and bug fixes of apclusterL() method for signature 'matrix,missing' o performance optimizations of apcluster() and apclusterL() o plotting of clustering results superimposed in scatter plot matrices now also works for 'AggExResult' objects o improvements of consistency of error and warning messages o according adaptations of documentation and vignette o adapted dependency and linking to Rcpp version 0.11.1 (to avoid issues on Mac OS) o minor correction of package namespace Changes in version 1.3.3 (2014-02-21) o adapted dependencies and linking to Rcpp version 0.11.0 o cleared up package dependencies Changes in version 1.3.2 (2013-06-11) o 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. o improved NA handling o correction of input check in apcluster() and apclusterL() (previously, both functions issued a warning whenever argument p had length > 1) o corresponding updates and further improvements of help pages and vignette Changes in version 1.3.1 (2013-04-22) o 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); o added as.hclust() and as.dendrogram() methods o 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 o streamlining of methods (redundant definition of inherited methods removed) o various minor improvements of code and documentation Changes in version 1.3.0 (2013-01-07) o added Leveraged Affinity Propagation Clustering o re-implementation of main functions as S4 generic methods in order to facilitate the convenient internal computation of similarity matrices o for convenience, similarity matrices can be stored as part of clustering results o heatmap plotting now done by heatmap() which has been defined as S4 generic o extended interface to functions for computing similarity matrices o added function corSimMat() o implementation of length() method for classes APResult, AggExResult, and ExClust o added accessor function to extract clustering levels from AggExResult objects o correction of exemplars returned by apcluster() for details=TRUE in slot idxAll of returned APResult object o when using data stored in a data frame, now categorical columns are explicitly omitted, thereby, avoiding warnings o plotting of clustering results along with original data (2D only) has been accelerated o all clustering methods now store their calls into the result objects o updates and extensions of help pages and vignette Changes in version 1.2.1 (2012-06-12) o added convenient accessor functions to extracting cluster indices from APResult and ExClust objects o added a function for coercing an APResult object into an ExClust object o correction of color bar on the left side of heatmaps (default behavior of RowSideColors parameter changed with R 2.15) Changes in version 1.2.0 (2012-03-26) o reimplementation of apcluster() in C++ using the Rcpp package which reduces computation times by a factor of 9-10 o obsolete function apclusterLM() removed o updates of help pages and vignette Changes in version 1.1.1 (2011-09-08) o updated citation o minor corrections in help pages and vignette Changes in version 1.1.0 (2011-06-15) o exemplar-based agglomerative clustering (function aggExCluster()) added o added various plotting functions, e.g. for dendrograms and heatmaps o added sequence analysis example to vignette o extension of vignette according to new functionality o re-organization of variable names in vignette o added option 'verbose' to apclusterK() o numerous minor corrections in help pages and vignette Changes in version 1.0.3 (2011-03-01) o Makefile in inst/doc eliminated to avoid installation problems o renamed vignette to "apcluster" Changes in version 1.0.2 (2010-03-19) o 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(); o improved support for named objects o new function for computing label vectors o re-organization of package source files and help pages Changes in version 1.0.1 (2010-03-02) o first public release