[R] p.adjust documentation suggestion: simple statement that new "BH" method is an alias for old "fdr" method

From: Earl F. Glynn <efg_at_stowers-institute.org>
Date: Tue 07 Jun 2005 - 07:31:45 EST

In R 2.0.1

> p.adjust.methods

[1] "holm" "hochberg" "hommel" "bonferroni" "fdr" "none"

In R 2.1.0

> p.adjust.methods

[1] "holm"       "hochberg"   "hommel"     "bonferroni" "BH"         "BY"
[8] "none"

One might conclude that two new methods "BH" and "BY" were added. BUT, there's a clue in one of the comments of the examples for ?p.adjust:

       ## or all of them at once (dropping the "fdr" alias):
          p.adjust.M <- p.adjust.methods[p.adjust.methods != "fdr"]

Apparently, the old "fdr" that meant "Benjamini & Hochberg" now shares an alias with the new "BH", which is "Benjamini & Hochberg".

Wouldn't a simple statement in the online documentation be useful that explained that "fdr" and "BH" are aliases?

Is "fdr" soon to be deprecated and eventually shouldn't be used at all and that "BH" is the way of the future?

http://cran.r-project.org/src/base/NEWS mentions "p.adjust() has a new method '"BY'" but was silent on the apparently new alias "BH".


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