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"
"fdr"
[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".
efg
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