[Vegan-commits] r260 - in pkg: R man

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

Author: jarioksa
Date: 2008-03-13 14:29:18 +0100 (Thu, 13 Mar 2008)
New Revision: 260

Modified:
   pkg/R/plot.betadiver.R
   pkg/R/scores.betadiver.R
   pkg/man/betadiver.Rd
Log:
minor tweaking & new keyword 'triangular' to select either plotting scores or raw scores in betadiver

Modified: pkg/R/plot.betadiver.R
===================================================================
--- pkg/R/plot.betadiver.R	2008-03-10 15:04:39 UTC (rev 259)
+++ pkg/R/plot.betadiver.R	2008-03-13 13:29:18 UTC (rev 260)
@@ -1,18 +1,20 @@
 `plot.betadiver` <-
-    function(x, ...)
+    function (x, ...) 
 {
     xy <- scores(x, ...)
-    plot(c(0,1),c(0,sqrt(0.75)), type="n", axes=FALSE, xlab="", ylab="",
-         asp=1)
-    for(tic in seq(0.2,0.8, by=0.2)) {
-        segments(tic, 0, tic/2 , sqrt(0.75)*tic, lty=3)
-        segments(tic/2, sqrt(0.75)*tic, 1-tic/2, sqrt(0.75)*tic, lty=3)
-        segments(tic, 0, tic/2+0.5, sqrt(0.75)*(1-tic), lty=3)
+    plot(c(0, 1), c(0, sqrt(0.75)), type = "n", axes = FALSE, 
+         xlab = "", ylab = "", asp = 1)
+    for (tic in seq(0.2, 0.8, by = 0.2)) {
+        segments(tic, 0, tic/2, sqrt(0.75) * tic, lty = 3)
+        segments(tic/2, sqrt(0.75) * tic, 1 - tic/2, sqrt(0.75) * 
+                 tic, lty = 3)
+        segments(tic, 0, tic/2 + 0.5, sqrt(0.75) * (1 - tic), 
+                 lty = 3)
     }
-    text(c(0,1,0.5), c(0,0,sqrt(0.75)), c("b'","c'","a'"), pos=c(2,4,3),
-         cex=par("cex.axis"))
-    lines(c(0,1,0.5,0), c(0,0,sqrt(0.75),0), xpd=TRUE)
+    text(c(0, 1, 0.5), c(0, 0, sqrt(0.75)), c("b'", "c'", "a'"), 
+         pos = c(2, 4, 3), cex = par("cex.axis"), xpd=TRUE)
+    lines(c(0, 1, 0.5, 0), c(0, 0, sqrt(0.75), 0), xpd = TRUE)
     points(xy, ...)
+    class(xy) <- "ordiplot"
     invisible(xy)
 }
-

Modified: pkg/R/scores.betadiver.R
===================================================================
--- pkg/R/scores.betadiver.R	2008-03-10 15:04:39 UTC (rev 259)
+++ pkg/R/scores.betadiver.R	2008-03-13 13:29:18 UTC (rev 260)
@@ -1,11 +1,15 @@
 `scores.betadiver` <-
-    function(x, ...)
+    function(x, triangular = TRUE,  ...)
 {
-    tot <- x$a + x$b + x$c
-    a <- x$a/tot
-    c <- x$c/tot
-    y <- sqrt(0.75)*a
-    x <- c + a/2
-    cbind(x, y)
+    if (triangular) {
+        tot <- x$a + x$b + x$c
+        a <- x$a/tot
+        c <- x$c/tot
+        y <- sqrt(0.75)*a
+        x <- c + a/2
+        out <- cbind(x, y)
+    } else {
+        out <- sapply(x, cbind)
+    }
+    out
 }
-

Modified: pkg/man/betadiver.Rd
===================================================================
--- pkg/man/betadiver.Rd	2008-03-10 15:04:39 UTC (rev 259)
+++ pkg/man/betadiver.Rd	2008-03-13 13:29:18 UTC (rev 260)
@@ -15,7 +15,7 @@
 \usage{
 betadiver(x, index = NA, order = FALSE, help = FALSE, ...)
 \method{plot}{betadiver}(x, ...)
-\method{scores}{betadiver}(x, ...)
+\method{scores}{betadiver}(x, triangular = TRUE, ...)
 }
 
 \arguments{
@@ -28,7 +28,9 @@
   influence the configuration in the triangular plot and non-symmetric
   indices. }
   \item{help}{Show the numbers, subscript names and the defining
-  equations of the indices and exit.}
+    equations of the indices and exit.}
+  \item{triangular}{Return scores suitable for triangular plotting of
+  proportions. If \code{FALSE}, returns a 3-column matrix of raw counts.}
   \item{\dots}{ Other arguments to functions. }
 }