NEWS

---

kebabs 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

kebabs 1.37.1

• minor changes to C++ source code to avoid warnings related to printf-style format strings

kebabs 1.37.0

• new branch for Bioconductor 3.19 devel

kebabs 1.36.0

• release as part of Bioconductor 3.18

kebabs 1.35.0

• new branch for Bioconductor 3.18 devel

kebabs 1.34.0

• release as part of Bioconductor 3.17

kebabs 1.33.2

• fix in src/Kebabs.h in order to avoid memory problems on 32-bit architectures

kebabs 1.33.1

• fixes in several help pages to avoid warnings

kebabs 1.33.0

• new branch for Bioconductor 3.17 devel

kebabs 1.32.0

• release as part of Bioconductor 3.16

kebabs 1.31.2

• changed dependency to 'Matrix' package (now requires at least version 1.5-0)

kebabs 1.31.1

• minor changes in coercions in accordance with latest version of 'Matrix' package

kebabs 1.31.0

• new branch for Bioconductor 3.16 devel

kebabs 1.30.0

• release as part of Bioconductor 3.15

kebabs 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)

kebabs 1.29.0

• new branch for Bioconductor 3.15 devel

kebabs 1.28.0

• release as part of Bioconductor 3.14

kebabs 1.27.2

• fix in evaluatePrediction() (avoid length>1 logical condition)

kebabs 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)

kebabs 1.27.0

• new branch for Bioconductor 3.14 devel

kebabs 1.26.0

• release as part of Bioconductor 3.13

kebabs 1.25.2

• removed 'register' from macro in ksort.h in order to avoid warnings on Mac OS

kebabs 1.25.1

• minor fix in MismatchC.cpp

kebabs 1.25.0

• new branch for Bioconductor 3.13 devel

kebabs 1.24.0

• release as part of Bioconductor 3.12

kebabs 1.23.0

• new branch for Bioconductor 3.12 devel

kebabs 1.22.0

• release as part of Bioconductor 3.11

kebabs 1.21.0

• new branch for Bioconductor 3.11 devel

kebabs 1.20.0

• release as part of Bioconductor 3.10

kebabs 1.19.1

• removed change history from package vignette for easier maintenance

kebabs 1.19.0

• new branch for Bioconductor 3.10 devel

kebabs 1.18.0

• release as part of Bioconductor 3.9

kebabs 1.17.0

• new branch for Bioconductor 3.9 devel

kebabs 1.16.0

• release as part of Bioconductor 3.8

kebabs 1.15.0

• new branch for Bioconductor 3.8 devel

kebabs 1.14.0

• release as part of Bioconductor 3.7

kebabs 1.13.0

• new branch for Bioconductor 3.7 devel

kebabs 1.12.0

• release as part of Bioconductor 3.6

kebabs 1.11.0

• new branch for Bioconductor 3.6 devel

kebabs 1.10.0

• release as part of Bioconductor 3.5

kebabs 1.9.0

• new branch for Bioconductor 3.5 devel

kebabs 1.8.0

• release as part of Bioconductor 3.4

kebabs 1.7.3

• fix of citation info file
• fix of inst/NEWS

kebabs 1.7.2

• version number bump for technical reasons related to Bioconductor build servers

kebabs 1.7.1

• version number bump for technical reasons related to Bioconductor build servers

kebabs 1.7.0

• new branch for Bioconductor 3.4 devel

kebabs 1.6.0

• release as part of Bioconductor 3.3

kebabs 1.5.4

• importing apcluster package for avoiding method clashes
• improved and completed change history in inst/NEWS and package vignette

kebabs 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

kebabs 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

kebabs 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

kebabs 1.5.0

• devel branch created from version 1.4.0

kebabs 1.4.0

• release as part of Bioconductor 3.2

kebabs 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

kebabs 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

kebabs 1.3.2

• correction of error in kernel lists
• user defined sequence kernel example SpectrumKernlabKernel moved to separate directory

kebabs 1.3.1

• correction of error in model selection for processing via dense LIBSVM
• remove problem in check for loading of SparseM

kebabs 1.3.0

• devel branch created from version 1.2.0

kebabs 1.2.0

• release as part of Bioconductor 3.1

kebabs 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

kebabs 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

kebabs 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

kebabs 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

kebabs 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

kebabs 1.1.4

• added two help pages

kebabs 1.1.3

• fix to adapt for changed Biostrings/S4Vectors API

kebabs 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

kebabs 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

kebabs 1.1.0

• devel branch created from version 1.0.0

kebabs 1.0.0

• first official release as part of Bioconductor 3.0