Changes in version 1.43.1 o updated DESCRIPTION file to new format (Authors@R) Changes in version 1.37.2 o changed e-mail address of maintainer o updated README.md and formatting of package vignette o updated references in documentation o fixed registration of API calls to C/C++ routines Changes in version 1.37.1 o minor changes to C++ source code to avoid warnings related to printf-style format strings Changes in version 1.33.2 o fix in src/Kebabs.h in order to avoid memory problems on 32-bit architectures Changes in version 1.33.1 o fixes in several help pages to avoid warnings Changes in version 1.31.2 o changed dependency to 'Matrix' package (now requires at least version 1.5-0) Changes in version 1.31.1 o minor changes in coercions in accordance with latest version of 'Matrix' package Changes in version 1.29.1 o fixed C++ code to work with newer version of Rcpp (enforced STRICT_R_HEADERS) o updated URLs and DOIs (now requires R version >= 3.3.0) Changes in version 1.27.2 o fix in evaluatePrediction() (avoid length>1 logical condition) Changes in version 1.27.1 o fix to avoid warnings arising from compiled code o fix in kebabsDemo() to avoid build warnings; executing this function now does not have any side effects anymore (previously, data objects were loaded into the global workspace) Changes in version 1.25.2 o removed 'register' from macro in ksort.h in order to avoid warnings on Mac OS Changes in version 1.25.1 o minor fix in MismatchC.cpp Changes in version 1.19.1 o removed change history from package vignette for easier maintenance Changes in version 1.7.3 o fix of citation info file o fix of inst/NEWS Changes in version 1.7.2 o version number bump for technical reasons related to Bioconductor build servers Changes in version 1.7.1 o version number bump for technical reasons related to Bioconductor build servers Changes in version 1.5.4 o importing apcluster package for avoiding method clashes o improved and completed change history in inst/NEWS and package vignette Changes in version 1.5.3 o correction in prediction via feature weights for very large sparse explicit representation o adaption of vignette template o vignette engine changed from Sweave to knitr Changes in version 1.5.2 o correction in distance weights for mixed distance weighted spectrum and gappy pair kernel o allow featureWeights as numeric vector for method getPredictionProfile o correction for plot of single prediction profile without legend o change of copyright note o namespace fixes Changes in version 1.5.1 o new method to compute prediction profiles from models trained with mixture kernels o correction for position specific kernel with offsets o corrections for prediction profile of motif kernel o additional hint on help page of kbsvm Changes in version 1.3.4 o correction of Ubuntu problem with realloc for 0 elements in linearKernel generating a sparse empty kernel matrix o correction of problem with feature weights and prediction profiles for position specific gappy pair kernel o correction of problem with feature weights and prediction profiles for position specific motif kernel o corrections for feature weights, prediction via feature weights and prediction profile for distance weighted kernels o update of KeBABS citation Changes in version 1.3.3 o new export kebabsCollectInfo for collection of package info o update of version dependency to Biostrings, XVector, S4Vector o correction for leading + or - in factor label o change of bibtex style sheet in vignette to plainnat.bst Changes in version 1.3.2 o correction of error in kernel lists o user defined sequence kernel example SpectrumKernlabKernel moved to separate directory Changes in version 1.3.1 o correction of error in model selection for processing via dense LIBSVM o remove problem in check for loading of SparseM Changes in version 1.1.9 o inclusion of dense LIBSVM 3.20 for dense kernel matrix support to provide a reliable way for training with kernel matrices o new accessors folds and performance for CrossValidationResult o removed fold performance from show of CV result o adaptions for user defined sequence kernel with new export isUserDefined, example in inst/examples/UserDefinedKernel o correction of errors with position offset for position specific kernels o computation of AUC via trapezoidal rule o changes for auto mode in CV, grid search, model selection o check for non-negative mixing coefficients in spectrum and gappy pair kernel o build warnings on Windows removed o added definition of performance parameters for binary and multiclass classification to vignette o update of citation file and reference section in help pages Changes in version 1.1.8 o new accessors selGridRow, selGridCol and fullModel for class ModelSelectionResult o change of naming of feature weights because of change in LiblineaR 1.94-2 o GCC warnings in Linux removed Changes in version 1.1.7 o change in LiblineaR - upgrade to LIBLINEAR 1.94 in function LiblineaR the parameter labels was renamed to target o correction in model selection for performance parameters o error correction of vector length overflow in sparse explicit representation for very large number of sequences in spectrum, gappy pair and motif kernel o error correction for AUC in cross validation o minor changes in help pages o minor changes in vignette Changes in version 1.1.6 o error correction for training with position specific kernel and computation of feature weights o error correction in coercion of kernel to character for distance weighting o error correction in spectrum, gappy pair and motif kernel for kernel matrix - last feature was missing in kernel value in rare situations o correction of Windows build problem in linearKernel o build warnings on Windows removed o minor changes in help pages o minor changes in vignette Changes in version 1.1.5 o new method heatmap to display heatmap of prediction profiles o extension of function linearKernel to optionally return a sparse kernel matrix o correction of computation of feature weights for LiblineaR with more than 3 classes o new accessor SVindex for class KBModel o correction in subsetting of sparse explicit representation for head / tail o error correction in subsetting of prediction profile o error correction in mismatch kernel o check uniqueness of motifs in motif kernel o minor changes in help pages o change name of vignette Rnw to lowercase o minor changes in vignette Changes in version 1.1.4 o added two help pages Changes in version 1.1.3 o fix to adapt for changed Biostrings/S4Vectors API Changes in version 1.1.2 o minor C code changes for mismatch kernel o correction of MCC o new class ROCData and new function computeROCandAUC for binary classification added o new plot function for ROCData to plot ROC for binary classes o AUC as additional performance parameter in cross validation and as performance objective in grid search Changes in version 1.1.1 o correction for cross validation with factor label o correction for storing prob model in kebabs model for kernlab o removal of clang warnings for unused functions Changes in version 1.0.0 o first official release as part of Bioconductor 3.0