CHANGES in `mboost' VERSION 2.2-2 (2013-02-08, r703) o bbs(..., center = "spectralDecomp") computes the spectral decomposition of the penalty matrix and the penalized part of the design matrix is defined by this decomposition. Experiments show that bols(x) + bbs(x, center = "spectralDecomp") is a little better in recovering the true underlying functions than the default bols(x) + bbs(x, center = TRUE) or, equivalently, bols(x) + bbs(x, center = "differenceMatrix") For bbs(x, y, center = TRUE) or bmrf(x, center = TRUE), the spectral decomposition is (and was) always used. o fixed bug in stabsel: '...' was not passed to cvrisk and thus one could not specify options for mclapply o fixed bug in brandom: now really use contrasts.arg = "contr.dummy" per default. o removed tests/ folder and .Rout.save files for vignettes from the CRAN release o small improvements in manual CHANGES in `mboost' VERSION 2.2-1 (2013-01-14, r694) o included warnings in stabsel() for better guidiance of the user: - A warning is issued if the upper bound for the FWER in stability selection is greater (by a certain margin) than the specified bound. - A warning is also issued if mstop is too small to select q variables. o improved output of errors and warnings in stabsel. o suppress the notes from package Matrix about method ambiguity ("Note: method with signature ... chosen, ... would also be valid") o updated manual on base-learners to reflect the change in the default for degrees of freedom (addtionally, all options are now discussed in a separate section of the baselearner manual) o updated vignette mboost_tutorial o updated mboost_package.Rd: now all important changes since mboost 2.0 are documented there o changed roles of contributers to ctb o suggested packages are now only used inside if(require(pkg)) statements o changed startup message CHANGES in `mboost' VERSION 2.2-0 (2012-11-21, r680) o switch from packages `multicore' and`snow' to `parallel' o changed behavior of bols(x, intercept = FALSE) when x is a factor: now the intercept is simply dropped from the design matrix; coding can be specified as usually for factors. o changed default for options("mboost_dftraceS") to FALSE, i.e., degrees of freedom are now computed from smoothing parameter as described in B. Hofner, T. Hothorn, T. Kneib, M. Schmid (2011). o changed computation of B-spline basis at the boundaries: now also use equidistant knots in the boundaries (per default) o improved plot function when dealing with spatial plots (now builds suitable grid based on the observations if no newdata is given) o increased default number of subsampling replicates in stabsel to 100 o [experimental] bmono() now implements constraints at the boundaries of (monotonic) P-splines o [experimental] added family Gehan() for rank-based estimation of survival models in an accelerated failure time framework (contributed by Brent Johnson ) CHANGES in `mboost' VERSION 2.1-3 (2012-09-27, r672) o matrices with one column are now handled as vectors in base-learners o improved manual o fixed error that occures with R (>= 2.16) due to internal changes in R CHANGES in `mboost' VERSION 2.1-2 (2012-02-29, r647) o improved handling of missing values (throws warnings and fixed a bug that occured for missings in the response) o improved manual for the handling of contrasts in bols o added tutorial vignette o updated references CHANGES in `mboost' VERSION 2.1-1 (2011-11-28, r606) o new option "mboost_eps" for factor in Demmler-Reinsch orthogonalization CHANGES in `mboost' VERSION 2.1-0 (2011-11-15, r601) Base-learners o added base-learners for smooth monotonic (or convex/concave) functions of one or two variables (bmono()) o added base-learners for radial basis functions (brad()) o added base-learners for Markov random fields (bmrf()) o bbs(x, cyclic = TRUE) for cyclic covariates ensures that predictions at the boundaries coincide and that the resulting function estimate is smoothly joined o bols(x, intercept = FALSE) only reasonable if x is centered. A warning is now issued if x is not centered. o changed default for degrees of freedom in bspatial() to df = 6 o added checks in bbs (and brandom) to ensure that the specified degrees of freedom are greater than the range of the (unpenalized) null space o bolscw can be mixed with other base-learners (although not yet exported and not via the formula interface) o new experimental baselearner %O% for smoothing matrix-values responses Families o add Binomial(link = "probit") and general cdf's as link functions (experimental) o added new families: - AUC() for AUC loss function - GammaReg() for gamma regression models Methods o added extract() methods for base-learners and fitted models o added residuals() function to extract residuals from the model o improved predict.mboost(): added names where missing and the offset as attribute where applicable. o fixed bug in predict() with glmboost.matrix(..., center = TRUE) o coef now also works with tree base-learners (returns NULL in this case) o changed coef.gamboost to coef.mboost o various improvements in plot.mboost function Miscellaneous o changed default in glmboost() to center = TRUE o speed up glmboost() a little bit o changed behavior of cvrisk() if weights are used: out-of-bag-risk now weighted according to "weights" as specified in call to mboost o added warning if df2lambda is likely to become numerically instable (i.e. in the case of large entries in the design matrix) o improved storage, speed and stability using Matrix technology for bols() for factors with many levels and brandom(); further improvements in base-learners that are combined via %+%. o various improvements and fixes in manuals CHANGES in `mboost' VERSION 2.0-12 (2011-08-22, r586) o minor bugfixes to make mboost work with gamboostLSS o replaced writeLines with packageStartupMessage in .onAttach() o replaced partially matched function arguments by full arguments o minor fixes in manuals CHANGES in `mboost' VERSION 2.0-11 (2011-03-17, r561) o fix problem in bl_lin when using dense matrices from package "Matrix" CHANGES in `mboost' VERSION 2.0-10 (2011-02-20, r556) o add rqss results for India childhood malnutrition data CHANGES in `mboost' VERSION 2.0-9 (2010-11-19, r543) o add gbm to Suggests CHANGES in `mboost' VERSION 2.0-8 (2010-11-11, r542) o make survival package happy again CHANGES in `mboost' VERSION 2.0-7 (2010-09-28, r534) o vignette "mboost" updated o remove problem with R CMD check that occurred on some 64bit systems CHANGES in `mboost' VERSION 2.0-6 (2010-05-22, r510) o no not use multicore functionality in R CMD check, really. CHANGES in `mboost' VERSION 2.0-5 (2010-05-21, r507) o no not use multicore functionality in R CMD check CHANGES in `mboost' VERSION 2.0-4 (2010-04-15, r490) o new vignette "mboost" describing 2.0-x series features o fixed bug in bols(): contrast.arg was ignored if not a named list (which is wasn't per default) o added (missing) response functions to families Weibull(), Loglog(), Lognormal() and NBinomial() o fixed bug in family CoxPH which occurred with NAs o improvements and corrections in documentation CHANGES in `mboost' VERSION 2.0-3 (2010-03-10, r456) o glmboost(..., center = TRUE) now also centers columns of the design matrix corresponding to contrasts of factors when an intercept term is present leading to faster risk minimization in these cases. o coef.glmboost: New argument `off2int = TRUE' adds the offset to the intercept. In addition, the intercept term is now adjusted for centered covariates. o check for infinite residuals in mboost_fit(). Especially for family = Poisson(), something like boost_control(nu = 0.01) fixes this problem. o "by" (in bols() and bbs()) can now handle factors with more than two levels o improved plot.mboost() for varying coefficients o minor improvements in documentation CHANGES in `mboost' VERSION 2.0-2 (2010-03-04) o fixed bug in helper function get_index, which caused (in some circumstances) wrong handling of factors in gamboost() (spotted by Juliane Schaefer ) o reduce memory footprint in blackboost (requires party 0.9-9993) CHANGES in `mboost' VERSION 2.0-1 (2010-03-01) o fixed bug in coef( , aggregate = "cumsum"): fraction "nu" was missing CHANGES in `mboost' VERSION 2.0-0 (2010-02-01) o generic implementation of component-wise functional gradient boosting in `mboost_fit', specialized code for linear, additive and interaction models removed o new families available for ordinal, expectile and censored regression o computations potentially based on package Matrix (reduces memory usage) o various speed improvements o added interface to extract selected base-learners (selected()) o added interface for parallel computations in cvrisk with arbitrary packages (e.g. multicore, snow) o added "which" argument in predict and coef functions and improved usability of "which" in plot-function. Users can specify "which" as numeric value or as a character string o added function cv() to generate matrices for k-fold cross-validation, subsampling and bootstrap o new function stabsel() for stability selection with error control o added function model.weights() to extract the weights o added interface to expand model by increasing mstop in model[mstop] o alternative definition of degrees of freedom available o Interface changes: - class definition / Family() arguments changed - changed behavior of subset method (model[mstop]). Object is directly altered and not duplicated - argument "center" in bols replaced with "intercept" - argument "z" in base-learners replaced with "by" - bns and bss deprecated; CHANGES in `mboost' VERSION 1.1-4 (2009-11-18) o fixed bug in prediction with varying coefficients for binary effect modifiers CHANGES in `mboost' VERSION 1.1-3 (2009-09-21) o better x-axes in plot.cvrisk and possibility to change xlab o parallel cvrisk on Unix systems only (`multicore' isn't safe on windows) o included new penalty for ordinal predictors (in bols()) o corrected bug in bspatial (centering was not used for Xna) o removed output of dfbase (which is seldom used) in gamboost o changed manual for coef.gamboost o make sure NAs are handled correctly when center = TRUE in glmboost CHANGES in `mboost' VERSION 1.1-2 (2009-07-21) o better weights and boundary knots handling in bspatial o cvrisk runs in parallel if package `multicore' is available o errors removed and minor improvements in the manuals o center = TRUE in glmboost did only apply to numeric (not integer) predictors o for safety reasons: na.action = na.omit again (causes slight changes in wpbc3 example) CHANGES in `mboost' VERSION 1.1-1 (2009-04-21) o new quantile regression facilities. o fix problem with bbs baselearner and cvrisk CHANGES in `mboost' VERSION 1.1-0 (2009-03-27) o bbs instead of bss is the default baselearner in gamboost o make sure bbs with weights and expanded observations returns numerically the very same results o btree can now deal with multiple variables o new gMDL criterion (contributed by Zhu Wang ) o make survival package happy again CHANGES in `mboost' VERSION 1.0-6 (2009-01-09) o bols allows to specify non-default contrasts. CHANGES in `mboost' VERSION 1.0-5 (2008-12-02) o remove experimental memory optimization steps CHANGES in `mboost' VERSION 1.0-4 (2008-11-12) o negative gradient of GaussClass() was wrong, spotted by Kao Lin CHANGES in `mboost' VERSION 1.0-3 (2008-11-07) o Date was malformed in DESCRIPTION CHANGES in `mboost' VERSION 1.0-2 (2008-11-05) o improved memory footprint in gamboost() and cvrisk() o option to suppress saving of ensembless added to boost_control() o bbs(), bns(), bspatial(): default number of knots changed to a fixed value (= 20) o changed default for grid (now uses all iterations) in cvrisk() and changed plot.cvrisk() o bols: works now for factors and can be set-up to use Ridge-estimation. Intercept can be omitted now (via center = TRUE). o new btree() baselearner for gamboost() available o fix inconsistencies in regression tests o add coef.gamboost o new generic `survFit' o cosmetics for trace = TRUE CHANGES in `mboost' VERSION 1.0-1 (2007-12-09) o inst/mboost_Bioinf.R was missing from mboost 1.0-0 CHANGES in `mboost' VERSION 1.0-0 (2007-11-13) o documentation updates CHANGES in `mboost' VERSION 0.9-0 (internal) o tests update and release the new version on CRAN o predict(..., allIterations = TRUE) returns the matrix of predictors for all boosting iterations CHANGES in `mboost' VERSION 0.6-2 (internal) o move `mboost' to R-forge o improvements in `gamboost': - P-splines as base learners available - new formula interface for specifying the base learner - new plot.gamboost o add the number of selected variables as degrees of freedom (as mentioned in the discussion of Hastie to Buehlmann & Hothorn) o status information during fitting is now available via boost_control(trace = TRUE) but is switched off by default o acknowledge constributions by Thomas Kneib and Matthias Schmid in DESCRIPTION CHANGES in `mboost' VERSION 0.6-1 (internal) o gamboost() now allows for user-specified base learners via the formula interface o gamboost.matrix(x = x, ...) requires colnames being set for `x' o na.action = na.omit fix for g{al}mboost() CHANGES in `mboost' VERSION 0.5-8 (2007-05-31) o gamboost(..., weights = w) was broken CHANGES in `mboost' VERSION 0.5-7 (2007-05-30) o extract response correctly in fitted.blackboost o hatvalues (and thus AICs) for GLMs with centering of covariates may have been wrong since version 0.5-0 o add paper examples to tests CHANGES in `mboost' VERSION 0.5-6 (2007-05-07) o fix Rd problems CHANGES in `mboost' VERSION 0.5-5 (2007-04-25) o `westbc' regenerated o LazyLoad: yes (no SaveImage: yes) CHANGES in `mboost' VERSION 0.5-4 (2007-04-18) o plot() method for `glmboost' objects visualizing the coefficient path (feature request by Axel Benner ). o predict(newdata = ) was broken for gamboost(), thanks to Max Kuhn for spotting this. CHANGES in `mboost' VERSION 0.5-3 (2007-03-23) o predict() for gamboost(..., dfbase = 1) was not working correctly o small performance and memory improvements for glmboost() CHANGES in `mboost' VERSION 0.5-2 (2007-02-28) o some performance improvements for `glmboost()' o blackboost() is now generic with formula and x, y interface o plot() method for cvrisk() and AIC() output now allows for ylim specification without troubles CHANGES in `mboost' VERSION 0.5-1 (2007-02-02) o depends party 0.9-9 CHANGES in `mboost' VERSION 0.5-0 (2007-01-30) o new `baselearner' argument to `gamboost' allowing to specify difference component-wise base-learners to be used. Currently implemented: "ssp" for smoothing splines (default), "bsp" for B-splines and "ols" for linear models. The latter two haven't been tested yet. o The `dfbase' arguments now applies to each covariate and no longer to each column of the design matrix. o cvrisk() for blackboost() was broken, totally :-( o centered covariates were returned by glmboost() and gamboost() o Poisson() used an incorrect offset o check for y being positive counts when family = "Poisson()"[B o checks for Poisson() logLik() and AIC() methods o fire a warning when all u > 0 or u < 0 o update vignette `mboost_illustrations' CHANGES in `mboost' VERSION 0.4-17 (2007-01-15) o fix problem with `dfbase' in `gamboost', spotted by Karin Eckel CHANGES in `mboost' VERSION 0.4-16 (2007-01-12) o work around stats4:::AIC CHANGES in `mboost' VERSION 0.4-15 (2006-12-06) o fix plot problems in plot.cvrisk o allow for centering of the numerical covariates in glmboost and gamboost CHANGES in `mboost' VERSION 0.4-14 (2006-10-27) o AIC(..., "classical") is now faster for non-gaussian families CHANGES in `mboost' VERSION 0.4-13 (2006-10-04) o predict(..., newdata) can take a matrix now CHANGES in `mboost' VERSION 0.4-12 (2006-09-13) o predict(, type = "response") did not return factors when the response was actually a factor o report offset in print methods o add offset attribute to coef.glmboost CHANGES in `mboost' VERSION 0.4-11 (2006-09-07) o add `contrasts.arg' argument to `glmboost.formula' o more meaningful default for `grid' in `cvrisk' o R-2.4.0 fixes CHANGES in `mboost' VERSION 0.4-10 (2006-08-30) o add checks for CoxPH (against coefficients and logLik of coxph) o add weights to CoxPH o the ngradient function in Family objects needs to implement arguments (y, f, w), not just (y, f) o check for meaningful class of the response for some families CHANGES in `mboost' VERSION 0.4-9 (2006-07-17) o some small speed improvements in `gamboost' o handle factors in `gamboost' properly (via a linear model) o the dfbase argument can take a vector now (in `gamboost') o update and improve entries in DESCRIPTION o documentation updates CHANGES in `mboost' VERSION 0.4-8 (2006-07-05) o Huber() is `Huber Error', not `Huber Absolute Error' o added `CoxPH' family object for fitting Cox models o remove inst/LaTeX o use NROW / NCOL more often (now that `y' may be a `Surv' object) o implement `cvrisk', a general cross-validation function for the empirical risk and a corresponding plot method o unify risk computations in all three fitting functions o unify names for `gb' objects o allow for out-of-bag risk computations o some cosmetics o update keywords in Rd-files o risk was always 0 in Huber()@risk when d was choosen adaptively o pData(westbc)$nodal.y has levels `negative' and `positive' (lymph node status) CHANGES in `mboost' VERSION 0.4-7 (2006-06-19) o add src/Makevars (required for Windows builds) o make sure objects that are modified at C-level get _copied_ in `blackboost' CHANGES in `mboost' VERSION 0.4-6 (2006-06-14) o some minor `codetools' fixes: removed unused variables and an out-dated function o add `codetools' checks to regression tests o fix xlab in plot.gbAIC ______________________________________________________________________________ `mboost' version 0.4-5 published on CRAN 2006-06-13