\name{permtests}
\title{Permutation versions of some common tests}
\alias{permtests}
\alias{permlogrank}
\alias{jonckheere.test}
\description{
  Small sample tests using the permutation reference distributions.
}
\usage{
  permlogrank(formula, data, subset, na.action, rho=0, nperm=5000)
  jonckheere.test(x, g, alternative = c("two.sided", "increasing",
                 "decreasing"))
}
\arguments{
  \item{nperm}{number of permutations for the reference distribution}
  \item{formula, data, subset, na.action, rho}{see survdiff for details}
  \item{x, g}{data and group vector}
  \item{alternative}{means are monotonic (two.sided), increasing, or
    decreasing}
}
\details{
  permlogrank is the permutation version of k-sample survdiff
  
  jonckheere.test is the exact (permutation) version of the
  Jonckheere-Terpstra test.  It uses the statistic
  \deqn{\sum_{k<l} \sum_{ij} I(X_{ik} < X_{jl}) + 0.5 I(X_{ik} =
    X_{jl}),} where \eqn{i, j} are observations in groups \eqn{k} and
  \eqn{l} respectively.  The asymptotic version is equivalent to
  cor.test(x, g, method="k").
}
\keyword{htest}