Add man page for phicoef().

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GenomicRanges@66844 bc3139a8-67e5-0310-9ffc-ced21a209358

R/phicoef.R

@@ -4,8 +4,8 @@ phicoef <- function(x, y=NULL)
 {
     if (is.null(y)) {
         if (!is.integer(x) || length(x) != 4L)
-            stop("when 'y' is not supplied, 'x' must be a 2x2 integer matrix ",
-                 "or a vector of length 4")
+            stop("when 'y' is not supplied, 'x' must be ",
+                 "a 2x2 integer matrix or an integer vector of length 4")
         a <- x[1L]
         c <- x[2L]
         b <- x[3L]

man/phicoef.Rd

@@ -0,0 +1,49 @@
+\name{phicoef}
+
+\alias{phicoef}
+
+\title{Calculate the "phi coefficient" between two binary variables}
+
+\description{
+  The \code{phicoef} function calculates the "phi coefficient" between
+  two binary variables.
+}
+
+\usage{
+phicoef(x, y=NULL)
+}
+
+\arguments{
+  \item{x, y}{
+    Two logical vectors of the same length, or, if \code{y} is not supplied,
+    \code{x} must be a 2x2 integer matrix (or an integer vector of length 4)
+    representing the contingency table of two binary variables.
+  }
+}
+
+\value{
+  The "phi coefficient" between the two binary variables.
+  This is a single numeric value ranging from -1 to + 1.
+}
+
+\references{
+  \url{http://en.wikipedia.org/wiki/Phi_coefficient}
+}
+
+\author{
+  H. Pages
+}
+
+\examples{
+set.seed(33)
+x <- sample(c(TRUE, FALSE), 100, replace=TRUE)
+y <- sample(c(TRUE, FALSE), 100, replace=TRUE)
+phicoef(x, y)
+phicoef(rep(x, 10), c(rep(x, 9), y))
+
+stopifnot(phicoef(table(x, y)) == phicoef(x, y))
+stopifnot(phicoef(x, !y) == - phicoef(x, y))
+stopifnot(phicoef(x, x) == 1)
+}
+
+\keyword{manip}