[Vegan-commits] r227 - branches/1.11-0/man

[noreply at r-forge.r-project.org]

Author: gsimpson
Date: 2008-02-17 14:55:32 +0100 (Sun, 17 Feb 2008)
New Revision: 227

Modified:
   branches/1.11-0/man/designdist.Rd
Log:
Merging r226 from trunk to 1.11-0 branch

Modified: branches/1.11-0/man/designdist.Rd
===================================================================
--- branches/1.11-0/man/designdist.Rd	2008-02-17 13:53:26 UTC (rev 226)
+++ branches/1.11-0/man/designdist.Rd	2008-02-17 13:55:32 UTC (rev 227)
@@ -9,12 +9,12 @@
   total quantities can be binary, quadratic or minimum terms. In
   binary terms, the shared component is number of shared species, and
   totals are numbers of species on sites. The quadratic terms
-  are crossproducts and sums of squares, and minimum terms 
+  are cross-products and sums of squares, and minimum terms 
   are sums of parallel minima and row totals.
 }
 \usage{
 designdist(x, method = "(A+B-2*J)/(A+B)",
-    terms = c("binary", "quadratic", "minimum"), name)
+           terms = c("binary", "quadratic", "minimum"), name)
 }
 
 \arguments{
@@ -22,8 +22,9 @@
   \item{method}{Equation for your dissimilarities. This can use terms
     \code{J} for shared quantity, \code{A} and \code{B} for totals,
     \code{N} for the number of rows (sites) and \code{P} for the number of
-    columns (species). The equation also can contain any \R functions accepting vector
-    arguments and returning vectors of the same length. }
+    columns (species). The equation can also contain any \R functions
+    that accepts vector arguments and returns vectors of the same
+    length. }
   \item{terms}{How shared and total components are found. For vectors
     \code{x} and \code{y} the  \code{"quadratic"} terms are \code{J = sum(x*y)},
     \code{A = sum(x^2)}, \code{B = sum(y^2)}, and \code{"minimum"} terms
@@ -43,9 +44,11 @@
     \code{A+B-2*J} \tab \code{"quadratic"} \tab squared Euclidean \cr
     \code{A+B-2*J} \tab \code{"minimum"} \tab Manhattan \cr
     \code{(A+B-2*J)/(A+B)} \tab \code{"minimum"} \tab Bray-Curtis \cr
-    \code{(A+B-2*J)/(A+B)} \tab \code{"binary"} \tab \enc{Sørensen}{Sorensen} \cr
+    \code{(A+B-2*J)/(A+B)} \tab \code{"binary"} \tab
+    \enc{Sørensen}{Sorensen} \cr 
     \code{(A+B-2*J)/(A+B-J)} \tab \code{"binary"} \tab Jaccard \cr
-    \code{(A+B-2*J)/(A+B-J)} \tab \code{"minimum"} \tab \enc{Ružička}{Ruzicka} \cr
+    \code{(A+B-2*J)/(A+B-J)} \tab \code{"minimum"} \tab
+    \enc{Ružička}{Ruzicka} \cr
     \code{(A+B-2*J)/(A+B-J)} \tab \code{"quadratic"} \tab
     (dis)similarity ratio \cr
     \code{1-J/sqrt(A*B)} \tab \code{"binary"} \tab Ochiai \cr
@@ -55,33 +58,35 @@
   }
 
   The function \code{designdist} can implement most dissimilarity
-  indices in \code{\link{vegdist}} or elsewhere, and it also can be
-  used to implement many other indices, among them (most of) those in
-  Legendre & Legendre (1998). It also can used to implement all indices
-  of beta diversity of Koleff et al. (2003).
+  indices in \code{\link{vegdist}} or elsewhere, and it can also be
+  used to implement many other indices, amongst them, most of those
+  described in Legendre & Legendre (1998). It can also be used to
+  implement all indices of beta diversity described in Koleff et
+  al. (2003).
 
-  If you want to implement binary dissimilarities based on 2x2
+  If you want to implement binary dissimilarities based on the 2x2
   contingency table notation, then \eqn{a =} \code{J}, \eqn{b =}
   \code{A-J}, \eqn{c =} \code{B-J}, \eqn{d =} \code{P-A-B+J}, \eqn{b+c
     =} \code{A+B-2*J}, and \eqn{a+b+c =} \code{A+B-J}.
 }
 \value{
-  Function returns an object of class \code{\link{dist}}.
+  \code{designdist} returns an object of class \code{\link{dist}}.
 }
 \references{
   Koleff, P., Gaston, K.J. and Lennon, J.J. (2003) Measuring beta
-  diversity for presence--absence data. \emph{J. Animal Ecol.} 72,
-  367--382. 
+  diversity for presence--absence data. \emph{J. Animal Ecol.}
+  \strong{72}, 367--382. 
   
-  Legendre, P. and Legendre, L. (1998) \emph{Numerical Ecology}. 2nd English
-  ed. Elsevier
+  Legendre, P. and Legendre, L. (1998) \emph{Numerical Ecology}. 2nd
+  English ed. Elsevier
   }
 \author{ Jari Oksanen }
 \note{  
-  Function does not use compiled code, and may be slow or use plenty of
-  memory in large data sets. It is very easy to make errors when
-  defining a function by hand. If an index is available in a function
-  using compiled code, it is better to use the canned alternative. 
+  \code{designdist} does not use compiled code, and may be slow or use
+  plenty of memory in large data sets. It is very easy to make errors
+  when  defining a function by hand. If an index is available in a
+  function  using compiled code, it is better to use the canned
+  alternative.
 }
 \seealso{ \code{\link{vegdist}}, \code{\link{dist}}. }
 \examples{