[Vegan-commits] r413 - in pkg: R man

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

Author: jarioksa
Date: 2008-06-09 21:22:47 +0200 (Mon, 09 Jun 2008)
New Revision: 413

Modified:
   pkg/R/permat.R
   pkg/man/permat.Rd
Log:
cleanup: S3 generic/method inconsistency in summary.permat

Modified: pkg/R/permat.R
===================================================================
--- pkg/R/permat.R	2008-06-09 19:06:16 UTC (rev 412)
+++ pkg/R/permat.R	2008-06-09 19:22:47 UTC (rev 413)
@@ -131,8 +131,9 @@
 
 ## S3 summary method for permat
 `summary.permat` <-
-function(x, digits=2, ...)
+function(object, digits=2, ...)
 {
+    x <- object
     n <- attr(x, "times")
     if (attr(x, "ptype") != "sar" & !is.null(x$specs$reg) | !is.null(x$specs$hab))
         restr <- TRUE else restr <- FALSE

Modified: pkg/man/permat.Rd
===================================================================
--- pkg/man/permat.Rd	2008-06-09 19:06:16 UTC (rev 412)
+++ pkg/man/permat.Rd	2008-06-09 19:22:47 UTC (rev 413)
@@ -22,7 +22,7 @@
 permatswap(m, reg = NULL, hab = NULL, mtype = "count", method = "swap", times = 100, burnin = 10000, thin = 1000)
 swapcount(m, thin = 1)
 \method{plot}{permat}(x, ...)
-\method{summary}{permat}(x, digits = 2, ...)
+\method{summary}{permat}(object, digits = 2, ...)
 }
 \arguments{
   \item{m}{a community data matrix with plots (samples) as rows and species (taxa) as columns.}
@@ -34,7 +34,7 @@
   \item{method}{character for method used for the swap algorithm (\code{"swap"}, \code{"tswap"}, \code{"backtrack"}) as described for function \code{\link{commsimulator}}. If \code{mtype="count"} only \code{"swap"} is available using the function \code{\link{swapcount}}.}
   \item{burnin}{number of null communities discarded before proper analysis in sequential \code{"swap", "tswap"} methods.}
   \item{thin}{number of discarded permuted matrices between two evaluations in sequential \code{"swap", "tswap"} methods.}
-  \item{x}{object of class 'permat'}
+  \item{x, object}{object of class \code{"permat"}}
   \item{digits}{number of digits used for rounding.}
   \item{\dots}{other arguments passed to methods.}
 }