[Vegan-commits] r1588 - in pkg/vegan: inst man

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

Author: jarioksa
Date: 2011-04-11 20:45:15 +0200 (Mon, 11 Apr 2011)
New Revision: 1588

Modified:
   pkg/vegan/inst/ChangeLog
   pkg/vegan/man/ordistep.Rd
   pkg/vegan/man/vegan-package.Rd
Log:
speed up examples

Modified: pkg/vegan/inst/ChangeLog
===================================================================
--- pkg/vegan/inst/ChangeLog	2011-04-11 15:55:48 UTC (rev 1587)
+++ pkg/vegan/inst/ChangeLog	2011-04-11 18:45:15 UTC (rev 1588)
@@ -15,6 +15,8 @@
 	worst cases (timing in MacBook Air) are: ordistep (19.0 sec),
 	add1.cca (7.2 sec), tsallis (7.0 sec), prc (5.6 sec),
 	vegan-package (5.2 sec).
+
+	* vegan-package.Rd, ordistep.Rd: speed up examples.
 	
 Version 1.18-28 (closed April 11, 2011)
 

Modified: pkg/vegan/man/ordistep.Rd
===================================================================
--- pkg/vegan/man/ordistep.Rd	2011-04-11 15:55:48 UTC (rev 1587)
+++ pkg/vegan/man/ordistep.Rd	2011-04-11 18:45:15 UTC (rev 1588)
@@ -139,7 +139,6 @@
 
 ## With scope present, the default direction is "both"
 ordistep(mod0, scope = formula(mod1), perm.max = 200)
-ordistep(rda(dune ~ 1, dune.env), scope = formula(mod1), perm.max = 200)
 
 ## Example without scope. Default direction is "backward"
 ordistep(mod1, perm.max = 200) 
@@ -161,7 +160,6 @@
 
 ## Example of ordiR2step with direction = "forward"
 step.res <- ordiR2step(mod0, scope = formula(mod1), direction="forward") 
-step.res <- ordiR2step(mod0, scope = formula(mod1), direction="forward", trace=0) 
 step.res$anova  # Summary table
 }
 

Modified: pkg/vegan/man/vegan-package.Rd
===================================================================
--- pkg/vegan/man/vegan-package.Rd	2011-04-11 15:55:48 UTC (rev 1587)
+++ pkg/vegan/man/vegan-package.Rd	2011-04-11 18:45:15 UTC (rev 1588)
@@ -76,14 +76,12 @@
 mod1 <- rda(dune ~ ., dune.env)
 mod1
 plot(mod1)
-## Overall permutation test for all variables
-anova(mod1)
-## Permutation test for terms added sequentially
-anova(mod1, by = "term")
 ## Automatic selection of variables by permutation P-values
 mod <- ordistep(mod0, scope=formula(mod1))
 mod
 plot(mod)
+## Permutation test for all variables
+anova(mod)
 ## Permutation test of "type III" effects, or significance when a term
 ## is added to the model after all other terms
 anova(mod, by = "margin")