[Vegan-commits] r2389 - in pkg/vegan: inst man

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

Author: jarioksa
Date: 2013-01-25 14:04:01 +0100 (Fri, 25 Jan 2013)
New Revision: 2389

Modified:
   pkg/vegan/inst/ChangeLog
   pkg/vegan/man/procrustes.Rd
Log:
update docs for changes in protest

Modified: pkg/vegan/inst/ChangeLog
===================================================================
--- pkg/vegan/inst/ChangeLog	2013-01-25 12:51:10 UTC (rev 2388)
+++ pkg/vegan/inst/ChangeLog	2013-01-25 13:04:01 UTC (rev 2389)
@@ -9,7 +9,9 @@
 	in svd(). This avoids a huge overhead of procrustes(). In a test
 	with a 160 x 12 matrix (RDA scores from Bryce Canyon data
 	'bryceveg') with 9999 permutations, the time went down from 12 sec
-	to 0.8 sec in my desktop.
+	to 0.8 sec in my desktop. The analysis prints now also the 'ss'
+	term (residual sum of squares) which for symmetric analysis is
+	equal to squared m12.
 
 	* procrustes: marginally faster way of getting sum of squares of a
 	matrix. This should not influence the results, but one metaMDS()

Modified: pkg/vegan/man/procrustes.Rd
===================================================================
--- pkg/vegan/man/procrustes.Rd	2013-01-25 12:51:10 UTC (rev 2388)
+++ pkg/vegan/man/procrustes.Rd	2013-01-25 13:04:01 UTC (rev 2389)
@@ -136,15 +136,16 @@
   function canot be used with \code{newdata} for \code{symmetric}
   analysis.
 
-  Function \code{protest} calls \code{procrustes(..., symmetric = TRUE)}
+  Function \code{protest} performs symmetric Procrustes analysis
   repeatedly to estimate the `significance' of the Procrustes
   statistic. Function \code{protest} uses a correlation-like statistic
   derived from the symmetric Procrustes sum of squares \eqn{ss} as
-  \eqn{r =\sqrt{(1-ss)}}, and sometimes called \eqn{m_{12}}. Function
-  \code{protest} has own \code{print} method, but otherwise uses
-  \code{procrustes} methods. Thus \code{plot} with a \code{protest} object
-  yields a ``Procrustean superimposition plot.''
-}
+  \eqn{r =\sqrt{(1-ss)}}{r = sqrt(1-ss)}, and also prints the sum of
+  squares of the symmetric analysis, sometimes called
+  \eqn{m_{12}^2}{squared m12}. Function \code{protest} has own
+  \code{print} method, but otherwise uses \code{procrustes}
+  methods. Thus \code{plot} with a \code{protest} object yields a
+  ``Procrustean superimposition plot.''  }
 
 \value{
   Function \code{procrustes} returns an object of class