NEWS
DiscreteFDR 2.0.1 (2024-10-24)
- Introduction of
mode
parameter for hist()
function to adapt construction
of histograms in case of conditional p-value selection.
- Remove
amnesia
dataset (moved to DiscreteDatasets
package).
- Function
match.pvals()
is no longer exported.
- Performance improvement for step-up procedures, especially for large numbers
of tests.
DiscreteFDR 2.0.0 (2024-07-08)
- New features:
discrete.BH()
, DBH()
, ADBH()
and DBR()
are now generic
functions. The previously existing functionality is implemented in
*.default
methods.
discrete.BH()
, DBH()
, ADBH()
and DBR()
got
*.DiscreteTestResults
methods for processing DiscreteTestResults
R6
class objects from package *.DiscreteTests
directly, so they can be
used within pipes.
- For consistency of new generics and methods, the first parameter
raw.pvalues
needed to be renamed to test.results
.
- New parameter
threshold
for discrete.BH()
, DBH()
, ADBH()
and
DBR()
. This enables selection of p-values which are smaller than or
equal to a certain value. Note: observed p-values and their
supports are then re-scaled, as the p-value distributions are now
becoming conditional distributions. If no selection is performed (i.e.
threshold = 1
), print()
, summary()
and plot()
outputs are as
before. Otherwise, the now respect the re-scaled conditional
distributions. Additionally, the DiscreteFDR
S3 class output objects
of the functions discrete.BH()
, DBH()
, ADBH()
and DBR()
now
include a list Select
with values and information regarding selection.
- New parameter
pCDFlist.indices
for discrete.BH()
, DBH()
, ADBH()
and DBR()
, which must have the same length as pCDFlist
and may
help increasing performance considerably. As pCDFlist
can now include
only unique supports, pCDFlist.indices
must indicate the index of the
p-values to which a given support belongs. If pCDFlist
has the same
length as test.results
, it can be omitted (by setting it to NULL
,
the default). If users prefer using DiscreteTestResults
objects, they
do not have to take care of this, as unique supports and indices are
automatically extracted from these objects.
- New functions
generate.pvalues()
and direct.discrete.BH()
as more
flexible replacements for fisher.pvalues.support()
and fast.discrete()
.
- Step function evaluation in C++ code has been replaced by closely optimized
inline functions which offer performance gains of 10-50%.
DiscreteFDR 1.3.7 (2024-02-08)
- Introduction of
lifecycle
mechanisms.
- Marked
fast.Discrete()
, fisher.pvalues.support()
, match.pvals()
,
kernel_*()
and amnesia
dataset as deprecated.
- Various documentation updates.
- Removal of links to
discreteMTP
packages, since it was removed from CRAN.
DiscreteFDR 1.3.6 (2021-09-03)
- Fixed a problem with
fisher.pvalues.support
that could cause p-values to
be wrong or NA (Thanks to Iqraa Meah).
- Added GitHub.
DiscreteFDR 1.3.5 (2021-05-25)
- Fixed a problem with
fisher.pvalues.support
that could cause an infinite
loop when using alternative = two.sided
(Thanks to Lukas Jansen).
- Changed version scheme from
x.y-z
to x.y.z
DiscreteFDR 1.3-4 (2020-02-14)
- Added a
NEWS.md
file to track changes to the package.
- Corrected a bug in
plot.DiscreteFDR
function that produced a false legend.
- Added plausibility checks of arguments to
discrete.BH
and DBR
functions.