[Vegan-commits] r675 - in branches/1.15: R inst man

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

Author: jarioksa
Date: 2009-01-27 13:00:40 +0100 (Tue, 27 Jan 2009)
New Revision: 675

Modified:
   branches/1.15/R/ordirgl.R
   branches/1.15/inst/ChangeLog
   branches/1.15/man/vegdist.Rd
Log:
merged r671 (ordirgl(..., type='t') warnings) and r673 (vegdist doc fix)

Modified: branches/1.15/R/ordirgl.R
===================================================================
--- branches/1.15/R/ordirgl.R	2009-01-26 13:51:28 UTC (rev 674)
+++ branches/1.15/R/ordirgl.R	2009-01-27 12:00:40 UTC (rev 675)
@@ -15,8 +15,8 @@
     else if (type == "t") {
         if (missing(text)) 
             text <- rownames(x)
-        rgl.texts(x[, 1], x[, 2], x[, 3], text, justify = "center", 
-                  ...)
+        rgl.texts(x[, 1], x[, 2], x[, 3], text, ...,
+                  if (oldpak) justify = "center" else adj = 0.5)
     }
     rgl.lines(range(x[, 1]), c(0, 0), c(0, 0), col = ax.col)
     rgl.lines(c(0, 0), range(x[, 2]), c(0, 0), col = ax.col)

Modified: branches/1.15/inst/ChangeLog
===================================================================
--- branches/1.15/inst/ChangeLog	2009-01-26 13:51:28 UTC (rev 674)
+++ branches/1.15/inst/ChangeLog	2009-01-27 12:00:40 UTC (rev 675)
@@ -5,6 +5,10 @@
 
 Version 1.15-2 (opened January 14, 2009)
 
+	* merged r673: vegdist doc fixes for Horn-Morisita equation.
+	
+	* merged r671: ordirgl warnings with type = "t".
+
 	* merged r559, r662, r663, r664: adonis adds one both to numerator
 	and denominator in permuation tests, increases default number of
 	permutations from 5 to 999, and gains a 'terms' component.

Modified: branches/1.15/man/vegdist.Rd
===================================================================
--- branches/1.15/man/vegdist.Rd	2009-01-26 13:51:28 UTC (rev 674)
+++ branches/1.15/man/vegdist.Rd	2009-01-27 12:00:40 UTC (rev 675)
@@ -73,9 +73,9 @@
       min(x[ij],x[ik])/(sum x[ik]))}
     \cr
     \code{morisita}
-    \tab \eqn{d_{jk} = \frac{2 \sum_i x_{ij} x_{ik}}{(\lambda_j +
+    \tab \eqn{d_{jk} =  1 - \frac{2 \sum_i x_{ij} x_{ik}}{(\lambda_j +
 	  \lambda_k) \sum_i x_{ij} \sum_i
-	  x_{ik}}}{d[jk] = 2*sum(x[ij]*x[ik])/((lambda[j]+lambda[k]) *
+	  x_{ik}}}{d[jk] =  1 - 2*sum(x[ij]*x[ik])/((lambda[j]+lambda[k]) *
 	sum(x[ij])*sum(x[ik]))}  
     \cr
     \tab where \eqn{\lambda_j = \frac{\sum_i x_{ij} (x_{ij} - 1)}{\sum_i