[Vegan-commits] r635 - in pkg/vegan: R man

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

Author: psolymos
Date: 2008-12-11 03:26:13 +0100 (Thu, 11 Dec 2008)
New Revision: 635

Modified:
   pkg/vegan/R/plot.permat.R
   pkg/vegan/man/permatfull.Rd
Log:
new argument: lowess


Modified: pkg/vegan/R/plot.permat.R
===================================================================
--- pkg/vegan/R/plot.permat.R	2008-12-10 12:45:48 UTC (rev 634)
+++ pkg/vegan/R/plot.permat.R	2008-12-11 02:26:13 UTC (rev 635)
@@ -1,6 +1,6 @@
 ## S3 plot method for permat
 `plot.permat` <-
-function(x, ylab, xlab, col, lty, plot=TRUE, text=TRUE, ...)
+function(x, ylab, xlab, col, lty, lowess=TRUE, plot=TRUE, text=TRUE, ...)
 {
     if (missing(ylab))
         ylab <- "Bray-Curtis dissimilarity"
@@ -16,7 +16,8 @@
     if (plot) {
         plot(bray,type="n",ylab=ylab,xlab=xlab, ...)
         lines(bray,col=col[1], lty=lty[1])
-        lines(lowess(bray),col=col[2], lty=lty[2])
+        if (lowess)
+            lines(lowess(bray),col=col[2], lty=lty[2])
         if (text) title(sub=paste("(mean = ", substitute(z, list(z=round(mean(bray),3))), 
             ", min = ", substitute(z, list(z=round(min(bray),3))),
             ", max = ", substitute(z, list(z=round(max(bray),3))), ")", sep=""))

Modified: pkg/vegan/man/permatfull.Rd
===================================================================
--- pkg/vegan/man/permatfull.Rd	2008-12-10 12:45:48 UTC (rev 634)
+++ pkg/vegan/man/permatfull.Rd	2008-12-11 02:26:13 UTC (rev 635)
@@ -25,7 +25,8 @@
 permat.control(ptype = "full", mtype = "count", method = "quasiswap",
 fixedmar = "both", shuffle = "ind", strata = NULL, 
 burnin = 10000, thin = 1000)
-\method{plot}{permat}(x, ylab, xlab, col, lty, plot=TRUE, text=TRUE, ...)
+\method{plot}{permat}(x, ylab, xlab, col, lty,
+lowess = TRUE, plot = TRUE, text = TRUE, ...)
 \method{lines}{permat}(x, ...)
 \method{summary}{permat}(object, ...)
 \method{print}{summary.permat}(x, digits = 2, ...)
@@ -44,7 +45,7 @@
   \item{x, object}{object of class \code{"permat"}}
   \item{digits}{number of digits used for rounding.}
   \item{ylab, xlab, col, lty}{graphical parameters for the \code{plot} method.}
-  \item{plot, text}{logical arguments for the \code{plot} method, whether a plot should be drawn, and statistic values should be printed on the plot.}
+  \item{lowess, plot, text}{logical arguments for the \code{plot} method, whether a lowess curve should be drawn, the plot should be drawn, and statistic values should be printed on the plot.}
   \item{\dots}{other arguments passed to methods.}
 }