[Vegan-commits] r2002 - in branches/2.0: inst man

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

Author: jarioksa
Date: 2011-11-13 18:33:42 +0100 (Sun, 13 Nov 2011)
New Revision: 2002

Modified:
   branches/2.0/inst/ChangeLog
   branches/2.0/man/envfit.Rd
Log:
merge r2001: explain arrow scaling in plot.envfit

Modified: branches/2.0/inst/ChangeLog
===================================================================
--- branches/2.0/inst/ChangeLog	2011-11-13 17:29:14 UTC (rev 2001)
+++ branches/2.0/inst/ChangeLog	2011-11-13 17:33:42 UTC (rev 2002)
@@ -4,6 +4,12 @@
 
 Version 2.0-2 (opened October 20, 2011)
 
+	* merge r2001: explain scaling of arrows in envfit() plot() --
+	this looks like being a FAQ.
+	* merge r1991 by hand: change sapply(H.s t) to use lapply in adonis
+	to fix a further bug in implementing speed-ups in f.test
+	* merge r1988 by hand: calling f.test without transposed matrix
+	bug in adonis.
 	* merge r1985: ordiarrows, ordisegments gained arg 'order.by'.
 	* merge r1974,1975,1980,1982: FAQ update.
 	* merge r1970: ordispider returns invisible plotting structure.
@@ -12,10 +18,6 @@
 	* merge r1961: consinstent 'noshrink' defaults in metaMDSdist()
 	and metaMDS(..., engine="isoMDS")
 	* merge r1959: capscale zero-rank constraints bug fix.
-	* merge r1988 by hand: calling f.test without transposed matrix
-	bug in adonis.
-	* merge r1991 by hand: change sapply(H.s t) to use lapply in adonis
-	to fix a further bug in implementing speed-ups in f.test
 
 Version 2.0-1 (released October 20, 2011)
 

Modified: branches/2.0/man/envfit.Rd
===================================================================
--- branches/2.0/man/envfit.Rd	2011-11-13 17:29:14 UTC (rev 2001)
+++ branches/2.0/man/envfit.Rd	2011-11-13 17:33:42 UTC (rev 2002)
@@ -28,7 +28,7 @@
 \arguments{
   \item{ord}{An ordination object or other structure from which the
     ordination \code{\link{scores}} can be extracted (including a data
-    frame or matrix of scores)}.
+    frame or matrix of scores).}
   \item{env}{Data frame, matrix or vector of environmental
     variables. The variables can be of mixed type (factors, continuous
     variables) in data frames.}
@@ -85,6 +85,19 @@
   used for easier selection and/or transformation of environmental
   variables. Only the main effects will be analysed even if interaction
   terms were defined in the formula. 
+
+  The printed output of continuous variables (vectors) gives the
+  direction cosines which are the coordinates of the heads of unit
+  length vectors.  In \code{plot} these are scaled by their
+  correlation (square root of the column \code{r2}) so that
+  \dQuote{weak} predictors have shorter arrows than \dQuote{strong}
+  predictors.  You can see the scaled relative lengths using command
+  \code{scores}.  The \code{plot}ted (and scaled) arrows are further
+  adjusted to the current graph using a constant multiplier: this will
+  keep the relative \code{r2}-scaled lengths of the arrows but tries
+  to fill the current plot.  You can see the multiplier using
+  \code{vegan:::ordiArrowMul(result_of_envfit)}, and set it with the
+  argument \code{arrow.mul}.
   
   Functions \code{vectorfit} and \code{factorfit} can be called directly.
   Function \code{vectorfit} finds directions in the ordination space