[Vegan-commits] r1496 - in pkg/vegan/inst: . doc

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

Author: jarioksa
Date: 2011-02-17 10:02:32 +0100 (Thu, 17 Feb 2011)
New Revision: 1496

Modified:
   pkg/vegan/inst/ChangeLog
   pkg/vegan/inst/doc/FAQ-vegan.texi
Log:
FAQ updates

Modified: pkg/vegan/inst/ChangeLog
===================================================================
--- pkg/vegan/inst/ChangeLog	2011-02-16 20:40:36 UTC (rev 1495)
+++ pkg/vegan/inst/ChangeLog	2011-02-17 09:02:32 UTC (rev 1496)
@@ -14,6 +14,11 @@
 
 	* procrustes: checks and reports different number of rows instead
 	of failing in crossprod() with incompatible arguments.
+
+	* FAQ updates: using 'select' in ordination text() and points(),
+	using 'xlim' to flip axes or zoom into ordination plot(), the
+	non-effects of 'strata' in adonis(). All these indeed are
+	frequently asked.
 	
 Version 1.18-22 (closed February 16, 2011)
 

Modified: pkg/vegan/inst/doc/FAQ-vegan.texi
===================================================================
--- pkg/vegan/inst/doc/FAQ-vegan.texi	2011-02-16 20:40:36 UTC (rev 1495)
+++ pkg/vegan/inst/doc/FAQ-vegan.texi	2011-02-17 09:02:32 UTC (rev 1496)
@@ -3,7 +3,7 @@
 @setfilename FAQ-vegan.info
 @settitle vegan FAQ
 @setchapternewpage on
- at set FAQ_YEAR 2010
+ at set FAQ_YEAR 2011
 @afourpaper
 @c %**end of header
 
@@ -21,7 +21,7 @@
 Creative Commons, 543 Howard Street, 5th Floor, San Francisco,
 California, 94105, USA.
 
-Copyright @copyright{} 2010 Jari Oksanen
+Copyright @copyright{} 2008-2011 Jari Oksanen
 @end quotation
 @end copying
 
@@ -312,6 +312,8 @@
 * Constrained permutations in vegan::  
 * How to use different plotting symbols in ordination graphics?::  
 * How to avoid cluttered ordination graphs?::  
+* Can I flip an axis in ordination diagram?::  
+* Can I zoom into an ordination plot?::  
 @end menu
 
 @node  I have only numeric and positive data but vegan still complaints, Can you analyse binary or cover class data?, Ordination, Ordination
@@ -524,7 +526,7 @@
 commands are fully configurable, and allow different plotting symbols
 and characters.
 
- at node How to avoid cluttered ordination graphs?,  , How to use different plotting symbols in ordination graphics?, Ordination
+ at node How to avoid cluttered ordination graphs?, Can I flip an axis in ordination diagram?, How to use different plotting symbols in ordination graphics?, Ordination
 @section How to avoid cluttered ordination graphs?
 
 If there is a really high number of species or sites, the graphs often
@@ -562,6 +564,11 @@
 points, and tries to optimize the location of the text to minimize the
 overlap. 
 
+ at item
+Ordination @code{text} and @code{points} functions have argument
+ at code{select} that can be used for full control of selecting items
+plotted as text or points.
+
 @item 
 Use interactive @code{orditkplot} function that lets you drag
 labels of points to better positions if you need to see all labels. Only
@@ -574,16 +581,38 @@
 
 @end itemize
 
+ at node  Can I flip an axis in ordination diagram?, Can I zoom into an ordination plot?, How to avoid cluttered ordination graphs?, Ordination
+ at comment  node-name,  next,  previous,  up 
+ at section Can I flip an axis in ordination diagram?
 
+Use @code{xlim} or @code{ylim} flipped limits. If you have model
+ at code{mod <- cca(dune)} you can flip the first axis with 
+ at code{plot(mod, xlim = c(3, -2))}.
+
+ at node  Can I zoom into an ordination plot?,  , Can I flip an axis in ordination diagram?, Ordination
+ at comment  node-name,  next,  previous,  up
+ at section Can I zoom into an ordination plot?
+You can use @code{xlim} and @code{ylim} arguments in @code{plot} or
+ at code{ordiplot} to zoom into ordination diagrams. Normally you must set
+both @code{xlim} and @code{ylim} because ordination plots will keep the
+equal aspect ratio of axes, and they will fill the graph so that the
+longer axis will fit. 
+
+Dynamic zooming can be done with function @code{orditkplot}. You can
+directly save the edited @code{orditkplot} graph in various graphic
+formats, or you can export the graph object back to R and use
+ at code{plot} to display the results. 
+
 @node Other analysis methods ,  , Ordination, Top
 @chapter Other analysis methods
 
 @menu
 * Is there TWINSPAN?::          
+* The strata do not influence adonis results::  
 * How is deviance calculated?::  
 @end menu
 
- at node Is there TWINSPAN?, How is deviance calculated?, Other analysis methods , Other analysis methods
+ at node Is there TWINSPAN?, , Other analysis methods , Other analysis methods
 @section Is there TWINSPAN?
 
 No.  It may be possible to port @acronym{TWINSPAN} to vegan, but it is
@@ -591,7 +620,16 @@
 will be happy to help.  @acronym{TWINSPAN} has a very permissive
 license, and it would be completely legal to port the function into R.
 
- at node How is deviance calculated?,  , Is there TWINSPAN?, Other analysis methods
+ at node  Why strata do not influence adonis results?, How is deviance calculated?, Is there TWINSPAN?, Other analysis methods
+ at comment  node-name,  next,  previous,  up
+ at section Why strata do not influence adonis results?
+Permutation happens only within @code{strata} and this influences the
+permutation distribution of the statistics and probably the significance
+levels, but @code{strata} do not influence the calculation of the
+statistics.
+
+
+ at node How is deviance calculated?,  , The strata do not influence adonis results, Other analysis methods
 @section How is deviance calculated?
 
 Some vegan functions, such as @code{radfit} use base R facility of