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% File src/library/stats/man/ks.test.Rd
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\name{ks.test}
\alias{ks.test}
\alias{ks.test.default}
\alias{ks.test.formula}
\encoding{UTF-8}
\title{Kolmogorov-Smirnov Tests}
\description{
  Perform a one- or two-sample Kolmogorov-Smirnov test.
}
\usage{
ks.test(x, \dots)
\method{ks.test}{default}(x, y, \dots,
        alternative = c("two.sided", "less", "greater"),
        exact = NULL, simulate.p.value = FALSE, B = 2000)
\method{ks.test}{formula}(formula, data, subset, na.action, \dots)
}
\arguments{
  \item{x}{a numeric vector of data values.}
  \item{y}{either a numeric vector of data values, or a character string
    naming a cumulative distribution function or an actual cumulative
    distribution function such as \code{pnorm}.  Only continuous CDFs
    are valid.}
  \item{\dots}{for the default method, parameters of the distribution
    specified (as a character string) by \code{y}.  Otherwise, further
    arguments to be passed to or from methods.}
  \item{alternative}{indicates the alternative hypothesis and must be
    one of \code{"two.sided"} (default), \code{"less"}, or
    \code{"greater"}.  You can specify just the initial letter of the
    value, but the argument name must be given in full.
    See \sQuote{Details} for the meanings of the possible values.}
  \item{exact}{\code{NULL} or a logical indicating whether an exact
    p-value should be computed.  See \sQuote{Details} for the meaning of
    \code{NULL}.}
  \item{simulate.p.value}{a logical indicating whether to compute
    p-values by Monte Carlo simulation.}
  \item{B}{an integer specifying the number of replicates used in the
    Monte Carlo test.}
  \item{formula}{a formula of the form \code{lhs ~ rhs} where \code{lhs}
    is a numeric variable giving the data values and \code{rhs} either
    \code{1} for a one-sample test or a factor with two levels giving
    the corresponding groups for a two-sample test.}
  \item{data}{an optional matrix or data frame (or similar: see
    \code{\link{model.frame}}) containing the variables in the
    formula \code{formula}.  By default the variables are taken from
    \code{environment(formula)}.}
  \item{subset}{an optional vector specifying a subset of observations
    to be used.}
  \item{na.action}{a function which indicates what should happen when
    the data contain \code{NA}s.  Defaults to
    \code{getOption("na.action")}.}
}
\details{
  If \code{y} is numeric, a two-sample (Smirnov) test of the null hypothesis
  that \code{x} and \code{y} were drawn from the same \emph{continuous}
  distribution is performed.

  Alternatively, \code{y} can be a character string naming a continuous
  (cumulative) distribution function, or such a function.  In this case,
  a one-sample (Kolmogorov) test is carried out of the null that the distribution
  function which generated \code{x} is distribution \code{y} with
  parameters specified by \code{\dots}.

  The presence of ties always generates a warning, since continuous
  distributions do not generate them.  If the ties arose from rounding
  the tests may be approximately valid, but even modest amounts of
  rounding can have a significant effect on the calculated statistic.

  Missing values are silently omitted from \code{x} and (in the
  two-sample case) \code{y}.

  The possible values \code{"two.sided"}, \code{"less"} and
  \code{"greater"} of \code{alternative} specify the null hypothesis
  that the true distribution function of \code{x} is equal to, not less
  than or not greater than the hypothesized distribution function
  (one-sample case) or the distribution function of \code{y} (two-sample
  case), respectively.  This is a comparison of cumulative distribution
  functions, and the test statistic is the maximum difference in value,
  with the statistic in the \code{"greater"} alternative being
  \eqn{D^+ = \max_u [ F_x(u) - F_y(u) ]}{D^+ = max[F_x(u) - F_y(u)]}.
  Thus in the two-sample case \code{alternative = "greater"} includes
  distributions for which \code{x} is stochastically \emph{smaller} than
  \code{y} (the CDF of \code{x} lies above and hence to the left of that
  for \code{y}), in contrast to \code{\link{t.test}} or
  \code{\link{wilcox.test}}.

  Exact p-values are not available for the one-sample case in the
  presence of ties.
  If \code{exact = NULL} (the default), an
  exact p-value is computed if the sample size is less than 100 in the
  one-sample case \emph{and there are no ties}, and if the product of
  the sample sizes is less than 10000 in the two-sample case, with or
  without ties (using the algorithm described in Schröer and Trenkler, 1995).
  Otherwise, asymptotic distributions are used whose approximations may
  be inaccurate in small samples.  In the one-sample two-sided case,
  exact p-values are obtained as described in Marsaglia, Tsang & Wang
  (2003) (but not using the optional approximation in the right tail, so
  this can be slow for small p-values).  The formula of Birnbaum &
  Tingey (1951) is used for the one-sample one-sided case.

  If a one-sample test is used, the parameters specified in
  \code{\dots} must be pre-specified and not estimated from the data.
  There is some more refined distribution theory for the KS test with
  estimated parameters (see Durbin, 1973), but that is not implemented
  in \code{ks.test}.
}
\value{
  A list inheriting from classes \code{"ks.test"} and \code{"htest"}
  containing the following components:
  \item{statistic}{the value of the test statistic.}
  \item{p.value}{the p-value of the test.}
  \item{alternative}{a character string describing the alternative
    hypothesis.}
  \item{method}{a character string indicating what type of test was
    performed.}
  \item{data.name}{a character string giving the name(s) of the data.}
}
\source{
  The two-sided one-sample distribution comes \emph{via}
  Marsaglia, Tsang and Wang (2003).

  Exact distributions for the two-sample (Smirnov) test are computed
  by the algorithm proposed Schröer (1991) and Schröer & Trenkler (1995).
 
}
\references{
  Z. W. Birnbaum and Fred H. Tingey (1951).
  One-sided confidence contours for probability distribution functions.
  \emph{The Annals of Mathematical Statistics}, \bold{22}/4, 592--596.
  \doi{10.1214/aoms/1177729550}.

  William J. Conover (1971).
  \emph{Practical Nonparametric Statistics}.
  New York: John Wiley & Sons.
  Pages 295--301 (one-sample Kolmogorov test),
  309--314 (two-sample Smirnov test).

  Durbin, J. (1973).
  \emph{Distribution theory for tests based on the sample distribution
    function}.
  SIAM.

  W. Feller (1948).
  On the Kolmogorov-Smirnov limit theorems for empirical distributions.
  \emph{The Annals of Mathematical Statistics}, \bold{19}(2), 177--189.
  \doi{10.1214/aoms/1177730243}.

  George Marsaglia, Wai Wan Tsang and Jingbo Wang (2003).
  Evaluating Kolmogorov's distribution.
  \emph{Journal of Statistical Software}, \bold{8}/18.
  \doi{10.18637/jss.v008.i18}.

  Gunar Schröer (1991),
  Computergestützte statistische Inferenz am Beispiel der
  Kolmogorov-Smirnov Tests.
  Diplomarbeit Universität Osnabrück.

  Gunar Schröer and Dietrich Trenkler (1995).
  Exact and Randomization Distributions of Kolmogorov-Smirnov Tests for
  Two or Three Samples.
  \emph{Computational Statistics & Data Analysis}, \bold{20}(2),
  185--202.
  \doi{10.1016/0167-9473(94)00040-P}.
}
\seealso{
  \code{\link{psmirnov}}.
  
  \code{\link{shapiro.test}} which performs the Shapiro-Wilk test for
  normality.
}
\examples{
require("graphics")

x <- rnorm(50)
y <- runif(30)
# Do x and y come from the same distribution?
ks.test(x, y)
# Does x come from a shifted gamma distribution with shape 3 and rate 2?
ks.test(x+2, "pgamma", 3, 2) # two-sided, exact
ks.test(x+2, "pgamma", 3, 2, exact = FALSE)
ks.test(x+2, "pgamma", 3, 2, alternative = "gr")

# test if x is stochastically larger than x2
x2 <- rnorm(50, -1)
plot(ecdf(x), xlim = range(c(x, x2)))
plot(ecdf(x2), add = TRUE, lty = "dashed")
t.test(x, x2, alternative = "g")
wilcox.test(x, x2, alternative = "g")
ks.test(x, x2, alternative = "l")

# with ties, example from Schröer and Trenkler (1995)
# D = 3 / 7, p = 0.2424242
ks.test(c(1, 2, 2, 3, 3), c(1, 2, 3, 3, 4, 5, 6), exact = TRUE)

# formula interface, see ?wilcox.test
ks.test(Ozone ~ Month, data = airquality,
        subset = Month \%in\% c(5, 8))
}
\keyword{htest}