NEWS

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fdrtool 1.2.18 (2024-08-20)

• use R_Calloc and R_free in isomean.c.
• minimum version requirement is now R 3.4.0.
• added Authors@R field in DESCRIPTION.

fdrtool 1.2.17 (2021-11-13)

• updated URLs.

fdrtool 1.2.16 (2021-01-06)

• native C routines are now properly registrated.
• observations of weight 0 are now automatically removed in monoreg() (suggested by Daniel Leibovitz).

fdrtool 1.2.15 (2015-07-08)

• add import statements required by R-devel.

fdrtool 1.2.14 (2015-03-09)

• fix broken URLs in documentation.
• fix "S3 generic/method consistency" NOTE raised by R-devel.

fdrtool 1.2.13 (2014-11-14)

• change of maintainer email address.

fdrtool 1.2.12 (2014-04-16)

• removed DUP=FALSE option in .C() call in monoreg() as this option is depricated in R 3.1.0.

fdrtool 1.2.11 (2013-09-15)

• depends now on R (>=2.15.1)
• updated reference to Klaus and Strimmer (2013)
• small changes in documentation to get rid of warnings in current R-devel
• option "studentt" was removed as "normal" is preferable in most cases.

fdrtool 1.2.10 (2012-07-25)

• added two new functions for Higher Criticism (HC): hc.score() computes HC scores from p-values and hc.thresh() determines the HC threshold for signal identification
• the range of p-values (0..1) is now checked

fdrtool 1.2.9 (2012-05-27)

• bug fix for computation of local FDR for separated null and alternative

fdrtool 1.2.8 (2012-01-19)

• NAMESPACE file added
• useDynLib() instead of .First.lib() to load compiled C code

fdrtool 1.2.7 (2011-03-19)

• small change in gcmlcm() to make sure that the raw slope never equals Inf (to avoid numeric problems with very small p-values)

fdrtool 1.2.6 (2009-11-20)

• a small bug was fixed in get.nullmodel()$get.pval() so that the argument Inf returns p-value 0
• in the output of censored.fit() the parameter "N0" was renamed to "N.cens" to avoid confusion with N0=eta0*N (note that N.cens is the number of data points retained for estimation)
• reference to papers updated.

fdrtool 1.2.5 (2008-07-06)

• a small bug in censored.fit() was fixed that produced NaNs when null model did not fit the data well (reported by Jana Sillmann)
• obsolete method get(getOption("device"))() replaced by dev.new()
• R >= 2.7.0 is now required
• small updates in the documentation

fdrtool 1.2.4 (2008-03-05)

• various warning messages were introduced to indicate potential problems with FDR computations if there are too few input test statistics (fdrtool() and related functions)

fdrtool 1.2.3 (2008-02-27)

• the previous bug fix (v.1.2.2) unfortunately broke the optimization of FDR for correlations which necessitated a second bug fix.
• small changes to the man pages.

fdrtool 1.2.2 (2008-02-25)

• a bug was fixed in the optimization part of the censored.fit() function.

fdrtool 1.2.1 (2008-01-02)

• option "color.figure" added, so that both color and b&w figures may be output.
• a more sensible error message is now produced when the argument supplying the test statistics is not a vector.
• for the option cutoff.method=="locfdr" in fdrtool() the corresponding algorithm was updated to match that of locfdr version 1.1-6.

fdrtool 1.2.0 (2007-10-21)

• This version constitutes a major rewrite. As a result, the interface to the main functions (especially to lesser used options) has been changed. See manual for details. Some specific changes include:
• fit of null model using censored.fit() is now much more reliable.
• estimates of null model parameter and null proportions now carry error bars.
• fdrtool() now offers three different methods for choosing appropriate cutoff points (minimum false nondiscovery rate, the heuristic of the locfdr package, and using a fixed fraction of the data)
• pval.estimate.eta0 now offers "quantile" approach.
• a number of miscellaneous helper functions have been introduced.
• no dependency on the "locfdr" package any more.
• change of license to "GNU GPL 3 or any later version".

fdrtool 1.1.4 (2007-07-06)

• monoreg(), the monotone regression function, is now partly written in C. This allows for much faster computation of the FDR calculations (which are based on the modified Grenander estimator.

fdrtool 1.1.3 (2007-06-15)

• fixed a bug in plotting the F und FA distribution functions
• fixed a bug in ecdf.pval() that occasionally caused Fdr to be larger than fdr (which for a decreasing density should never occur)
• grenander() now also estimates increasing densities
• plot.grenander() now uses linear y-scale (previously, log-scale)

fdrtool 1.1.2 (2007-05-25)

• fdrtool() now has "dots" as option to allow the specification of arguments for the locfdr function

fdrtool 1.1.1 (2007-04-08)

• the default behaviour of censored.fit() has been changed such that for multiple pct0 (i.e. length(pct0) > 1) the scale parameter is estimated for each element of pct0, subsequently a smoothing spline is computed, and finally the optimal parameter is taken as the minimum of the spline smoother.
• new "verbose" option in fdrtool()
• new "diagnostic.plot" option in censored.fit()
• option to rely on locfdr >= 1.1-4 for fitting null distribution of correlation and normal scores

fdrtool 1.1.0 (2007-02-18)

• This version contains some major new functionality. In particular, it now offers functions to estimate both tail area based Fdr as well as density based fdr values for various kind of null models: New functions:
• fdrtool: the central function for computing fdr/Fdr values.
• censored.fit: learn null model from censored sample
• monoreg: isotonic and antitonic regression with weights
• gcmlcm: find greatest convex minorant and least concave majorant
• grenander: non-parametric estimate of concave CDF and decreasing density
• halfnormal: functions for half-normal distribution
• dcor0: distribution of vanishing correlation coefficient Removed functions:
• fdr.estimate.eta0: was replaced by pval.estimate.eta()
• fdr.control: the function fdrtool() should be used.
• density.pr: not needed any more Other:
• dependency on locfdr package removed
• fdrtool now requires R 2.2.1

fdrtool 1.0.0 (2006-08-12)

• This is the first standalone release (9 August 2006). Previously, the functions available in this package were part of the GeneTS package (version 2.10.2)