Change history of package apcluster: ==================================== Version 1.4.13: - updates and corrections of help pages Version 1.4.12: - changed e-mail address of maintainer - updated README.md and formatting of package vignette 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