0.4.2: - updated maintainers' email address
- fixed NAMESPACE issues
- changed the way global options are handled
0.4.1: - updated citation information: an appropriate reference for
the software package is now available, rather than a
reference to the first paper in which the package was used.
0.4.0: - added lasso and elastic nets to the list of methods for
"coef" and "stab"; also changes in biom.options and
get.biom. Additional function traceplot.
- return values for auxiliary functions like studentt.stab and
friends have changed: now they only contain (corrected)
frequencies in which a particular variable is among the ntop
best variables. Also the names have changed: coef.size now is
only returned when type == "coef"
- coef.BMark function no longer returns indices of selected
variables but coefficient sizes when type == "coef" (this was
already the case), selection frequencies for stability
selection, and estimated p values for HC thresholding.
- added "selection" function to get the selected variables
- the input of the get.biom function is changed:
for classification cases Y must be a factor. If a numerical
vector is used for Y with only two different values, it is
converted into a factor with a warning.
- output of the get.biom function is organized differently: now
the top level of the list consists of the different methods
(studentt, vip, lasso), and the second level consists of the
different parameter settings for each method (lambda for
lasso, ncomp for plsda/pclda/vip).
- now also support for regression in stability selection. As a
result, naming of fmethods has changed: "plsda" and "pclda"
are now replaced by "pls" and "pcr", respectively. The old
names still work but give a warning.
- updated references (once again)
- several corrections to man pages (in biom.options, get.biom);
spotted by Nir Shahaf.
0.3.3: - corrected a bug in biom.options()
0.3.2: - added NAMESPACE
- updated references
0.3.1: - added HCalpha to the options so that HCthresh can be used in
get.biom with different alpha values
0.3.0: - all pls methods now use widekernelpls rather than kernelpls
- more efficient HC calculations for the multivariate methods,
in particular a more efficient p-value estimation
- eliminated function studentt.fun since the original in the st
package no longer has the verbose output
- introduction of BMark object type and the coef, print and
summary generic functions
- simplification of get.biom function argument list by definition of
biom.options function and .biom.options object, as in the pls
package
- default values for stability-based selection are now the ones
used in the 2011 ACA paper, in particular the default for
scaling now is "auto" and no longer "none"
- renaming of all foo.biom functions to foo.stab
- implementation of Higher Criticism
0.2.6: first version submitted to CRAN, and used in the 2011 ACA publication