[Vegan-commits] r1976 - in pkg/permute: . man

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

Author: gsimpson
Date: 2011-11-01 15:06:21 +0100 (Tue, 01 Nov 2011)
New Revision: 1976

Modified:
   pkg/permute/DESCRIPTION
   pkg/permute/man/shuffle.Rd
   pkg/permute/man/shuffleSet.Rd
Log:
add appropriate references to Cajo's work as basis of the design of ideas behind permute

Modified: pkg/permute/DESCRIPTION
===================================================================
--- pkg/permute/DESCRIPTION	2011-10-31 18:23:01 UTC (rev 1975)
+++ pkg/permute/DESCRIPTION	2011-11-01 14:06:21 UTC (rev 1976)
@@ -5,6 +5,6 @@
 Author: Gavin L. Simpson
 Maintainer: Gavin L. Simpson <gavin.simpson at ucl.ac.uk>
 Suggests: vegan (>= 2.0-0), testthat (>= 0.5)
-Description: The 'permute' package implements a set of restricted permutation designsfor freely exchangeable, line transects (time series), and spatial grid designs plus permutation of blocks (groups of samples). 'permute' also allows split-plot designs, in which the whole-plots or split-plots or both can be freely-exchangeble or one of the restricted designs.
+Description: The 'permute' package implements a set of restricted permutation designsfor freely exchangeable, line transects (time series), and spatial grid designs plus permutation of blocks (groups of samples). 'permute' also allows split-plot designs, in which the whole-plots or split-plots or both can be freely-exchangeble or one of the restricted designs. The 'permute' package is modelled after the permutation schemes of Canoco 3.1 by Cajo ter Braak.
 License: GPL-2 
 URL: http://vegan.r-forge.r-project.org/

Modified: pkg/permute/man/shuffle.Rd
===================================================================
--- pkg/permute/man/shuffle.Rd	2011-10-31 18:23:01 UTC (rev 1975)
+++ pkg/permute/man/shuffle.Rd	2011-11-01 14:06:21 UTC (rev 1976)
@@ -133,8 +133,16 @@
 %  that currently use the older \code{\link[vegan]{shuffle}} will be
 %  updated to use \code{shuffle}.
 %}
-%\references{
-%}
+\references{
+  \code{shuffle()} is modelled after the permutation schemes of Canoco
+  3.1 (ter Braak, 1990); see also Besag & Clifford (1989).
+
+  Besag, J. and Clifford, P. (1989) Generalized Monte Carlo significance
+  tests. \emph{Biometrika} \strong{76}; 633--642.
+
+  ter Braak, C. J. F. (1990). \emph{Update notes: CANOCO version
+    3.1}. Wageningen: Agricultural Mathematics Group. (UR).
+}
 \author{Gavin Simpson}
 \seealso{\code{\link{check}}, a utility function for checking
   permutation scheme described by \code{\link{permControl}}.}

Modified: pkg/permute/man/shuffleSet.Rd
===================================================================
--- pkg/permute/man/shuffleSet.Rd	2011-10-31 18:23:01 UTC (rev 1975)
+++ pkg/permute/man/shuffleSet.Rd	2011-11-01 14:06:21 UTC (rev 1976)
@@ -44,7 +44,16 @@
 %}
 
 %% ~Make other sections like Warning with \section{Warning }{....} ~
+\references{
+  \code{shuffle()} is modelled after the permutation schemes of Canoco
+  3.1 (ter Braak, 1990); see also Besag & Clifford (1989).
 
+  Besag, J. and Clifford, P. (1989) Generalized Monte Carlo significance
+  tests. \emph{Biometrika} \strong{76}; 633--642.
+
+  ter Braak, C. J. F. (1990). \emph{Update notes: CANOCO version
+    3.1}. Wageningen: Agricultural Mathematics Group. (UR).
+}
 \seealso{
   See \code{\link{shuffle}} for generating a single permutation, and
   \code{\link{permControl}} for setting up permutation designs.