Change history of package kebabs: ==================================== Version 1.37.2: - changed e-mail address of maintainer - updated README.md and formatting of package vignette - updated references in documentation - fixed registration of API calls to C/C++ routines Version 1.37.1: - minor changes to C++ source code to avoid warnings related to printf-style format strings Version 1.37.0: - new branch for Bioconductor 3.19 devel Version 1.36.0: - release as part of Bioconductor 3.18 Version 1.35.0: - new branch for Bioconductor 3.18 devel Version 1.34.0: - release as part of Bioconductor 3.17 Version 1.33.2: - fix in src/Kebabs.h in order to avoid memory problems on 32-bit architectures Version 1.33.1: - fixes in several help pages to avoid warnings Version 1.33.0: - new branch for Bioconductor 3.17 devel Version 1.32.0: - release as part of Bioconductor 3.16 Version 1.31.2: - changed dependency to 'Matrix' package (now requires at least version 1.5-0) Version 1.31.1: - minor changes in coercions in accordance with latest version of 'Matrix' package Version 1.31.0: - new branch for Bioconductor 3.16 devel Version 1.30.0: - release as part of Bioconductor 3.15 Version 1.29.1: - fixed C++ code to work with newer version of Rcpp (enforced STRICT_R_HEADERS) - updated URLs and DOIs (now requires R version >= 3.3.0) Version 1.29.0: - new branch for Bioconductor 3.15 devel Version 1.28.0: - release as part of Bioconductor 3.14 Version 1.27.2: - fix in evaluatePrediction() (avoid length>1 logical condition) Version 1.27.1: - fix to avoid warnings arising from compiled code - 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) Version 1.27.0: - new branch for Bioconductor 3.14 devel Version 1.26.0: - release as part of Bioconductor 3.13 Version 1.25.2: - removed 'register' from macro in ksort.h in order to avoid warnings on Mac OS Version 1.25.1: - minor fix in MismatchC.cpp Version 1.25.0: - new branch for Bioconductor 3.13 devel Version 1.24.0: - release as part of Bioconductor 3.12 Version 1.23.0: - new branch for Bioconductor 3.12 devel Version 1.22.0: - release as part of Bioconductor 3.11 Version 1.21.0: - new branch for Bioconductor 3.11 devel Version 1.20.0: - release as part of Bioconductor 3.10 Version 1.19.1: - removed change history from package vignette for easier maintenance Version 1.19.0: - new branch for Bioconductor 3.10 devel Version 1.18.0: - release as part of Bioconductor 3.9 Version 1.17.0: - new branch for Bioconductor 3.9 devel Version 1.16.0: - release as part of Bioconductor 3.8 Version 1.15.0: - new branch for Bioconductor 3.8 devel Version 1.14.0: - release as part of Bioconductor 3.7 Version 1.13.0: - new branch for Bioconductor 3.7 devel Version 1.12.0: - release as part of Bioconductor 3.6 Version 1.11.0: - new branch for Bioconductor 3.6 devel Version 1.10.0: - release as part of Bioconductor 3.5 Version 1.9.0: - new branch for Bioconductor 3.5 devel Version 1.8.0: - release as part of Bioconductor 3.4 Version 1.7.3: - fix of citation info file - fix of inst/NEWS Version 1.7.2: - version number bump for technical reasons related to Bioconductor build servers Version 1.7.1: - version number bump for technical reasons related to Bioconductor build servers Version 1.7.0: - new branch for Bioconductor 3.4 devel Version 1.6.0: - release as part of Bioconductor 3.3 Version 1.5.4 - importing apcluster package for avoiding method clashes - improved and completed change history in inst/NEWS and package vignette Version 1.5.3 - correction in prediction via feature weights for very large sparse explicit representation - adaption of vignette template - vignette engine changed from Sweave to knitr Version 1.5.2 - correction in distance weights for mixed distance weighted spectrum and gappy pair kernel - allow featureWeights as numeric vector for method getPredictionProfile - correction for plot of single prediction profile without legend - change of copyright note - namespace fixes Version 1.5.1 - new method to compute prediction profiles from models trained with mixture kernels - correction for position specific kernel with offsets - corrections for prediction profile of motif kernel - additional hint on help page of kbsvm Version 1.5.0: - devel branch created from version 1.4.0 Version 1.4.0: - release as part of Bioconductor 3.2 Version 1.3.4: - correction of Ubuntu problem with realloc for 0 elements in linearKernel generating a sparse empty kernel matrix - correction of problem with feature weights and prediction profiles for position specific gappy pair kernel - correction of problem with feature weights and prediction profiles for position specific motif kernel - corrections for feature weights, prediction via feature weights and prediction profile for distance weighted kernels - update of KeBABS citation Version 1.3.3: - new export kebabsCollectInfo for collection of package info - update of version dependency to Biostrings, XVector, S4Vector - correction for leading + or - in factor label - change of bibtex style sheet in vignette to plainnat.bst Version 1.3.2: - correction of error in kernel lists - user defined sequence kernel example SpectrumKernlabKernel moved to separate directory Version 1.3.1 - correction of error in model selection for processing via dense LIBSVM - remove problem in check for loading of SparseM Version 1.3.0: - devel branch created from version 1.2.0 Version 1.2.0: - release as part of Bioconductor 3.1 Version 1.1.9 - inclusion of dense LIBSVM 3.20 for dense kernel matrix support to provide a reliable way for training with kernel matrices - new accessors folds and performance for CrossValidationResult - removed fold performance from show of CV result - adaptions for user defined sequence kernel with new export isUserDefined, example in inst/examples/UserDefinedKernel - correction of errors with position offset for position specific kernels - computation of AUC via trapezoidal rule - changes for auto mode in CV, grid search, model selection - check for non-negative mixing coefficients in spectrum and gappy pair kernel - build warnings on Windows removed - added definition of performance parameters for binary and multiclass classification to vignette - update of citation file and reference section in help pages Version 1.1.8 - new accessors selGridRow, selGridCol and fullModel for class ModelSelectionResult - change of naming of feature weights because of change in LiblineaR 1.94-2 - GCC warnings in Linux removed Version 1.1.7 - change in LiblineaR - upgrade to LIBLINEAR 1.94 in function LiblineaR the parameter labels was renamed to target - correction in model selection for performance parameters - error correction of vector length overflow in sparse explicit representation for very large number of sequences in spectrum, gappy pair and motif kernel - error correction for AUC in cross validation - minor changes in help pages - minor changes in vignette Version 1.1.6 - error correction for training with position specific kernel and computation of feature weights - error correction in coercion of kernel to character for distance weighting - error correction in spectrum, gappy pair and motif kernel for kernel matrix - last feature was missing in kernel value in rare situations - correction of Windows build problem in linearKernel - build warnings on Windows removed - minor changes in help pages - minor changes in vignette Version 1.1.5 - new method heatmap to display heatmap of prediction profiles - extension of function linearKernel to optionally return a sparse kernel matrix - correction of computation of feature weights for LiblineaR with more than 3 classes - new accessor SVindex for class KBModel - correction in subsetting of sparse explicit representation for head / tail - error correction in subsetting of prediction profile - error correction in mismatch kernel - check uniqueness of motifs in motif kernel - minor changes in help pages - change name of vignette Rnw to lowercase - minor changes in vignette Version 1.1.4: - added two help pages Version 1.1.3 - fix to adapt for changed Biostrings/S4Vectors API Version 1.1.2 - minor C code changes for mismatch kernel - correction of MCC - new class ROCData and new function computeROCandAUC for binary classification added - new plot function for ROCData to plot ROC for binary classes - AUC as additional performance parameter in cross validation and as performance objective in grid search Version 1.1.1 - correction for cross validation with factor label - correction for storing prob model in kebabs model for kernlab - removal of clang warnings for unused functions Version 1.1.0: - devel branch created from version 1.0.0 Version 1.0.0: - first official release as part of Bioconductor 3.0