[Vegan-commits] r751 - branches/1.15/inst branches/1.15/man pkg/vegan/man

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

Author: jarioksa
Date: 2009-03-22 08:09:09 +0100 (Sun, 22 Mar 2009)
New Revision: 751

Modified:
   branches/1.15/inst/ChangeLog
   branches/1.15/man/add1.cca.Rd
   pkg/vegan/man/add1.cca.Rd
Log:
emacs ate my updates in add1.cca.Rd

Modified: branches/1.15/inst/ChangeLog
===================================================================
--- branches/1.15/inst/ChangeLog	2009-03-22 07:00:15 UTC (rev 750)
+++ branches/1.15/inst/ChangeLog	2009-03-22 07:09:09 UTC (rev 751)
@@ -5,6 +5,8 @@
 
 Version 1.15-2 (opened January 14, 2009)
 
+	* merged r750: better example in add1.cca.Rd.
+
 	* merged r735 & r736: stepacross fixes in metaMDSdist with
 	open-ended dissimilarities (Euclidean, Manhattan etc.).
 

Modified: branches/1.15/man/add1.cca.Rd
===================================================================
--- branches/1.15/man/add1.cca.Rd	2009-03-22 07:00:15 UTC (rev 750)
+++ branches/1.15/man/add1.cca.Rd	2009-03-22 07:09:09 UTC (rev 751)
@@ -64,9 +64,16 @@
   output. Functions \code{\link{cca}}, \code{\link{rda}} and
   \code{\link{capscale}} produce result objects for these functions.}
 \examples{
-data(varespec)
-data(varechem)
-step(rda(varespec ~  1, varechem), reformulate(names(varechem)), test="perm")
+data(dune)
+data(dune.env)
+## Automatic model building with permutation tests
+step(rda(dune ~  1, dune.env), reformulate(names(dune.env)), test="perm")
+## Manual model building
+## -- define the maximal model for scope
+mbig <- rda(dune ~  ., dune.env)
+## -- define an empty model to start with
+m0 <- rda(dune ~ 1, dune.env)
+## -- manual selection and updating
 }
 \keyword{multivariate }
 \keyword{ models}

Modified: pkg/vegan/man/add1.cca.Rd
===================================================================
--- pkg/vegan/man/add1.cca.Rd	2009-03-22 07:00:15 UTC (rev 750)
+++ pkg/vegan/man/add1.cca.Rd	2009-03-22 07:09:09 UTC (rev 751)
@@ -74,6 +74,13 @@
 ## -- define an empty model to start with
 m0 <- rda(dune ~ 1, dune.env)
 ## -- manual selection and updating
+add1(m0, scope=formula(mbig), test="perm")
+m0 <- update(m0, . ~ . + Management)
+add1(m0, scope=formula(mbig), test="perm")
+m0 <- update(m0, . ~ . + Moisture)
+## -- included variables still significant?
+drop1(m0, test="perm")
+add1(m0, scope=formula(mbig), test="perm")
 }
 \keyword{multivariate }
 \keyword{ models}