NEWS

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apcluster 1.4.13 (2024-04-26)

• updates and corrections of help pages

apcluster 1.4.12 (2024-04-19)

• changed e-mail address of maintainer
• updated README.md and formatting of package vignette

apcluster 1.4.11 (2023-09-19)

• 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

apcluster 1.4.10 (2022-05-31)

• minor correction of exception handling in some R methods
• minor corrections of some help pages

apcluster 1.4.9 (2022-01-14)

• 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

apcluster 1.4.8 (2019-08-21)

• correction of aggExCluster() C++ code
• correction of link to Affinity Propagation website at University of Toronto

apcluster 1.4.7 (2018-05-29)

• correction of aggExCluster() C++ code to avoid compilation error on Solaris

apcluster 1.4.6 (2018-05-28)

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

apcluster 1.4.5 (2018-01-30)

• 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

apcluster 1.4.4 (2017-07-04)

• 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

apcluster 1.4.3 (2016-02-24)

• 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

apcluster 1.4.2 (2015-12-24)

• 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

apcluster 1.4.1 (2014-12-09)

• fixes in C++ code of sparse affinity propagation

apcluster 1.4.0 (2014-12-01)

• 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

apcluster 1.3.5 (2014-06-26)

• memory access fixes in C++ code called from apclusterL()
• minor updates of vignette

apcluster 1.3.4 (2014-06-25)

• 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

apcluster 1.3.3 (2014-02-21)

• adapted dependencies and linking to Rcpp version 0.11.0
• cleared up package dependencies

apcluster 1.3.2 (2013-06-11)

• 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

apcluster 1.3.1 (2013-04-22)

• 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

apcluster 1.3.0 (2013-01-07)

• 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

apcluster 1.2.1 (2012-06-12)

• 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)

apcluster 1.2.0 (2012-03-26)

• 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

apcluster 1.1.1 (2011-09-08)

• updated citation
• minor corrections in help pages and vignette

apcluster 1.1.0 (2011-06-15)

• 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

apcluster 1.0.3 (2011-03-01)

• Makefile in inst/doc eliminated to avoid installation problems
• renamed vignette to "apcluster"

apcluster 1.0.2 (2010-03-19)

• 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

apcluster 1.0.1 (2010-03-02)

• first public release