CHANGES in `mboost' VERSION 2.2-3 (2013-09-09, r733)
o fixed bugs in survival families:
- offset in all survival families was based on max(survtime) instead
of max(log(survtime));
- offset in CoxPH can't be computed from Cox Partial LH as constants
are canceled out; Use fixed offset instead;
o speed up checking of manual by changing some computations (e.g. reduce
mstop) or exclude code from checking via \dontrun{}
o removed dependency on ipred (replaced with TH.data)
o small improvements in manual
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