\HeaderA{p.adjust}{Adjust P-values for Multiple Comparisons}{p.adjust}
\methaliasA{p.adjust.methods}{p.adjust}{p.adjust.methods}
\keyword{htest}{p.adjust}
\begin{Description}\relax
Given a set of p-values, returns p-values adjusted using
one of several methods.
\end{Description}
\begin{Usage}
\begin{verbatim}
p.adjust(p, method = p.adjust.methods, n = length(p))

p.adjust.methods
# c("holm", "hochberg", "hommel", "bonferroni", "BH", "BY", "fdr", "none")
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{p}] vector of p-values (possibly with \code{\LinkA{NA}{NA}}s).
\item[\code{method}] correction method
\item[\code{n}] number of comparisons, must be at least \code{length(p)};
only set this (to non-default) when you know what you are doing!
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
The adjustment methods include the Bonferroni correction
(\code{"bonferroni"}) in which the p-values are multiplied by the
number of comparisons.  Less conservative corrections are also
included by Holm (1979) (\code{"holm"}), Hochberg (1988)
(\code{"hochberg"}), Hommel (1988) (\code{"hommel"}), Benjamini \&
Hochberg (1995) (\code{"BH"}), and Benjamini \& Yekutieli (2001)
(\code{"BY"}), respectively.
A pass-through option (\code{"none"}) is also included.
The set of methods are contained in the \code{p.adjust.methods} vector
for the benefit of methods that need to have the method as an option
and pass it on to \code{p.adjust}.

The first four methods are designed to give strong control of the
family wise error rate.  There seems no reason to use the unmodified
Bonferroni correction because it is dominated by Holm's method, which
is also valid under arbitrary assumptions.

Hochberg's and Hommel's methods are valid when the hypothesis tests
are independent or when they are non-negatively associated (Sarkar,
1998; Sarkar and Chang, 1997).  Hommel's method is more powerful than
Hochberg's, but the difference is usually small and the Hochberg
p-values are faster to compute.

The \code{"BH"} and \code{"BY"} method of Benjamini, Hochberg, and
Yekutieli control the false discovery rate, the expected proportion of
false discoveries amongst the rejected hypotheses.  The false
discovery rate is a less stringent condition than the family wise
error rate, so these methods are more powerful than the others.

Note that you can set \code{n} larger than \code{length(p)} which
means the unobserved p-values are assumed to be greater than all the
observed p   for "bonferonni" and "holm" methods and equal to 1 for
the other methods.
\end{Details}
\begin{Value}
A vector of corrected p-values (same length as \code{p}).
\end{Value}
\begin{References}\relax
Benjamini, Y., and Hochberg, Y. (1995).
Controlling the false discovery rate: a practical and powerful
approach to multiple testing.
\emph{Journal of the Royal Statistical Society Series} B, \bold{57},
289--300.

Benjamini, Y., and Yekutieli, D. (2001).
The control of the false discovery rate in multiple testing under
dependency.
\emph{Annals of Statistics} \bold{29}, 1165--1188.

Holm, S. (1979).
A simple sequentially rejective multiple test procedure.
\emph{Scandinavian Journal of Statistics}, \bold{6}, 65--70.

Hommel, G. (1988).
A stagewise rejective multiple test procedure based on a modified
Bonferroni test.
\emph{Biometrika}, \bold{75}, 383--386.

Hochberg, Y. (1988).
A sharper Bonferroni procedure for multiple tests of significance.
\emph{Biometrika}, \bold{75}, 800--803.

Shaffer, J. P. (1995).
Multiple hypothesis testing.
\emph{Annual Review of Psychology}, \bold{46}, 561--576.
(An excellent review of the area.)

Sarkar, S. (1998).
Some probability inequalities for ordered MTP2 random variables: a
proof of Simes conjecture.
\emph{Annals of Statistics}, \bold{26}, 494--504.

Sarkar, S., and Chang, C. K. (1997).
Simes' method for multiple hypothesis testing with positively
dependent test statistics.
\emph{Journal of the American Statistical Association}, \bold{92},
1601--1608.

Wright, S. P. (1992).
Adjusted P-values for simultaneous inference.
\emph{Biometrics}, \bold{48}, 1005--1013.
(Explains the adjusted P-value approach.)
\end{References}
\begin{SeeAlso}\relax
\code{pairwise.*} functions such as \code{\LinkA{pairwise.t.test}{pairwise.t.test}}.
\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode}
set.seed(123)
x <- rnorm(50, m=c(rep(0,25),rep(3,25)))
p <- 2*pnorm( sort(-abs(x)))

round(p, 3)
round(p.adjust(p), 3)
round(p.adjust(p,"BH"), 3)

## or all of them at once (dropping the "fdr" alias):
p.adjust.M <- p.adjust.methods[p.adjust.methods != "fdr"]
p.adj <- sapply(p.adjust.M, function(meth) p.adjust(p, meth))
round(p.adj, 3)
## or a bit nicer:
noquote(apply(p.adj, 2, format.pval, digits = 3))

## and a graphic:
matplot(p, p.adj, ylab="p.adjust(p, meth)", type = "l", asp=1, lty=1:6,
        main = "P-value adjustments")
legend(.7,.6, p.adjust.M, col=1:6, lty=1:6)

## Can work with NA's:
pN <- p; iN <- c(46,47); pN[iN] <- NA
pN.a <- sapply(p.adjust.M, function(meth) p.adjust(pN, meth))
## The smallest 20 P-values all affected by the NA's :
round((pN.a / p.adj)[1:20, ] , 4)
\end{ExampleCode}
\end{Examples}

