[Vegan-commits] r235 - in pkg: . R inst man

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

Author: jarioksa
Date: 2008-02-19 15:37:36 +0100 (Tue, 19 Feb 2008)
New Revision: 235

Modified:
   pkg/DESCRIPTION
   pkg/R/nestedtemp.R
   pkg/R/plot.nestedtemp.R
   pkg/inst/ChangeLog
   pkg/man/oecosimu.Rd
Log:
pkg branch started to diverge from the release branch: small enhancements to nestedtemp for easier checking of the results

Modified: pkg/DESCRIPTION
===================================================================
--- pkg/DESCRIPTION	2008-02-19 14:36:08 UTC (rev 234)
+++ pkg/DESCRIPTION	2008-02-19 14:37:36 UTC (rev 235)
@@ -1,7 +1,7 @@
 Package: vegan
 Title: Community Ecology Package
-Version: 1.12-0
-Date: Feb 15, 2008
+Version: 1.12-1
+Date: Feb 19, 2008
 Author: Jari Oksanen, Roeland Kindt, Pierre Legendre, Bob O'Hara, Gavin L. Simpson, 
   M. Henry H. Stevens  
 Maintainer: Jari Oksanen <jari.oksanen at oulu.fi>

Modified: pkg/R/nestedtemp.R
===================================================================
--- pkg/R/nestedtemp.R	2008-02-19 14:36:08 UTC (rev 234)
+++ pkg/R/nestedtemp.R	2008-02-19 14:37:36 UTC (rev 235)
@@ -39,8 +39,8 @@
     temp <- 100*sum(u)/prod(dim(comm))/0.04145
     i <- rev(order(rs))
     j <- rev(order(cs))
-    out <- list(comm = comm[i,j], u = u[i,j], fill=fill,  statistic = temp,
-                smooth=smo)
+    out <- list(comm = comm[i,j], u = u[i,j], r = r[i], c = c[j], 
+                fill=fill,  statistic = temp, smooth=smo)
     class(out) <- "nestedtemp"
     out
 }

Modified: pkg/R/plot.nestedtemp.R
===================================================================
--- pkg/R/plot.nestedtemp.R	2008-02-19 14:36:08 UTC (rev 234)
+++ pkg/R/plot.nestedtemp.R	2008-02-19 14:37:36 UTC (rev 235)
@@ -1,5 +1,6 @@
 `plot.nestedtemp` <-
-    function (x, kind = c("temperature", "incidendce"), col = rev(heat.colors(100)), 
+    function (x, kind = c("temperature", "incidendce"),
+              col = rev(heat.colors(100)), names = FALSE,  
               ...) 
 {
     kind <- match.arg(kind)
@@ -9,5 +10,9 @@
     z <- t(z[nrow(z):1, ])
     image(z, axes = FALSE, col = col, ...)
     box()
-    lines(x$smooth$x, 1-x$smooth$y)
+    lines(x$smooth$x, 1 - x$smooth$y)
+    if (names) {
+        axis(3, at = seq(0,1,len=ncol(x$u)), labels=colnames(x$u), las=2, ...)
+        axis(2, at = seq(1,0,len=nrow(x$u)), labels=rownames(x$u), las=2,...)
+    }
 }

Modified: pkg/inst/ChangeLog
===================================================================
--- pkg/inst/ChangeLog	2008-02-19 14:36:08 UTC (rev 234)
+++ pkg/inst/ChangeLog	2008-02-19 14:37:36 UTC (rev 235)
@@ -2,9 +2,14 @@
 
 VEGAN DEVEL VERSIONS at http://r-forge.r-project.org/
 
-Version 1.12-0:
+Version 1.12-1 (Feb 19, 2008, working...)
 
-	* Made a realese branch (1.11-0) based on the the rev. 204, and
+	* nestedtemp: returns row and column coordinates, optionally
+	labels plot.
+	
+Version 1.12-0 (Feb 15, 2008)
+
+	* Made a release branch (1.11-0) based on the the rev. 204, and
 	relabelled this devel branch to 1.12-0.
 
 Version 1.10-13 (closed Feb 15, 2008)

Modified: pkg/man/oecosimu.Rd
===================================================================
--- pkg/man/oecosimu.Rd	2008-02-19 14:36:08 UTC (rev 234)
+++ pkg/man/oecosimu.Rd	2008-02-19 14:37:36 UTC (rev 235)
@@ -28,7 +28,7 @@
 nesteddisc(comm)
 nestedtemp(comm, ...)
 \method{plot}{nestedtemp}(x, kind = c("temperature", "incidendce"),
-    col=rev(heat.colors(100)),  ...)
+    col=rev(heat.colors(100)),  names = FALSE, ...)
 commsimulator(x, method, thin=1)
 }
 
@@ -48,6 +48,7 @@
   \item{kind}{The kind of plot produced.}
   \item{x}{Matrix for \code{commsimulator} or a \code{plot} object.}
   \item{col}{Colour scheme for matrix temperatures.}
+  \item{names}{Label columns and rows in the plot using names in \code{comm}.}
   \item{\dots}{Other arguments to functions.}
 }