[Vegan-commits] r2332 - in pkg/vegan: . R inst man

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

Author: jarioksa
Date: 2012-11-30 10:17:54 +0100 (Fri, 30 Nov 2012)
New Revision: 2332

Modified:
   pkg/vegan/NAMESPACE
   pkg/vegan/R/plot.nestedtemp.R
   pkg/vegan/inst/ChangeLog
   pkg/vegan/man/nestedtemp.Rd
Log:
add plot.nestednodf()

Modified: pkg/vegan/NAMESPACE
===================================================================
--- pkg/vegan/NAMESPACE	2012-11-25 18:29:25 UTC (rev 2331)
+++ pkg/vegan/NAMESPACE	2012-11-30 09:17:54 UTC (rev 2332)
@@ -252,6 +252,7 @@
 S3method(plot, meandist)
 S3method(plot, metaMDS)
 S3method(plot, monoMDS)
+S3method(plot, nestednodf)
 S3method(plot, nestedtemp)
 S3method(plot, ordisurf)
 S3method(plot, orditkplot)

Modified: pkg/vegan/R/plot.nestedtemp.R
===================================================================
--- pkg/vegan/R/plot.nestedtemp.R	2012-11-25 18:29:25 UTC (rev 2331)
+++ pkg/vegan/R/plot.nestedtemp.R	2012-11-30 09:17:54 UTC (rev 2332)
@@ -1,3 +1,8 @@
+### plot() methods for those nested* functions that return sufficient
+### data to draw a plot. We display a plot using image() with coloured
+### rectangles for occurrences or colours dependent on the
+### contribution to the nestedness when appropriate.
+
 `plot.nestedtemp` <-
     function (x, kind = c("temperature", "incidence"),
               col = rev(heat.colors(100)), names = FALSE,  
@@ -22,3 +27,24 @@
             las = 2, ...)
     }
 }
+
+`plot.nestednodf` <-
+    function(x, col = "red", names = FALSE, ...)
+{
+    z <- x$comm
+    z <- t(z[nrow(z):1,])
+    if (length(col) == 1)
+        col <- c(NA, col)
+    image(z, axes = FALSE, col = col, ...)
+    box()
+    if (length(names) == 1)
+        names <- rep(names, 2)
+    if (names[1]) {
+        axis(2, at = seq(1, 0, len = ncol(z)), labels = rev(colnames(z)),
+            las = 2, ...)
+    }
+    if (names[2]) {
+        axis(3, at = seq(0, 1, len = nrow(z)), labels = rownames(z),
+            las = 2, ...)
+    }
+}

Modified: pkg/vegan/inst/ChangeLog
===================================================================
--- pkg/vegan/inst/ChangeLog	2012-11-25 18:29:25 UTC (rev 2331)
+++ pkg/vegan/inst/ChangeLog	2012-11-30 09:17:54 UTC (rev 2332)
@@ -4,6 +4,9 @@
 
 Version 2.1-22 (opened November 19, 2012)
 
+	* nestednodf: added plot() method modelled after
+	plot.nestedtemp().
+	
 	* ordiR2step: gained argument 'R2scope' (default TRUE) which can
 	be used to turn off the criterion of stopping when the adj-R2 of
 	the current model exceeds that of scope.  This option allows model
@@ -11,11 +14,6 @@
 	predictors higher than number of observations). Pierre Legendre
 	needed this option for some checks with huge AEM/PCNM scopes.
 
-	It should be checked how the function works with partial RDA: we
-	have introduces RsquareAdj() for partial RDA, but the current
-	testing still assumes that those models do not have adj-R2 (like
-	was the case when ordiR2step() was written).
-
 Version 2.1-21 (closed November 19, 2012)
 
 	* New version opened with the CRAN release of vegan 2.0-5 on Oct

Modified: pkg/vegan/man/nestedtemp.Rd
===================================================================
--- pkg/vegan/man/nestedtemp.Rd	2012-11-25 18:29:25 UTC (rev 2331)
+++ pkg/vegan/man/nestedtemp.Rd	2012-11-30 09:17:54 UTC (rev 2332)
@@ -8,6 +8,7 @@
 \alias{nestedbetasor}
 \alias{nestedbetajac}
 \alias{plot.nestedtemp}
+\alias{plot.nestednodf}
 
 \title{ Nestedness Indices for Communities of Islands or Patches }
 
@@ -28,6 +29,7 @@
 nestedbetajac(comm)
 \method{plot}{nestedtemp}(x, kind = c("temperature", "incidence"),
     col=rev(heat.colors(100)),  names = FALSE, ...)
+\method{plot}{nestednodf}(x, col = "red", names = FALSE, ...)
 }
 
 \arguments{