[Phylobase-commits] r425 - pkg/inst/doc
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Wed Jan 14 21:57:56 CET 2009
Author: bbolker
Date: 2009-01-14 21:57:56 +0100 (Wed, 14 Jan 2009)
New Revision: 425
Modified:
pkg/inst/doc/phylobase.Rnw
pkg/inst/doc/phylobase.pdf
Log:
vignette tweaks in simulator section
Modified: pkg/inst/doc/phylobase.Rnw
===================================================================
--- pkg/inst/doc/phylobase.Rnw 2009-01-05 06:39:42 UTC (rev 424)
+++ pkg/inst/doc/phylobase.Rnw 2009-01-14 20:57:56 UTC (rev 425)
@@ -311,10 +311,10 @@
\subsubsection{the easy way}
-We can use the \code{vcv.phylo()} command from
-\code{ape} to construct the variance-covariance
-matrix of the tip traits, after which it's easy
-to use \code{mvrnorm} from the \code{MASS} package
+We can use \code{as(tree,"phylo4vcov")} to
+coerce the tree into a variance-covariance matrix
+form, and then
+use \code{mvrnorm} from the \code{MASS} package
to generate a set of multivariate normally distributed
values for the tips. (A benefit of this approach is
that we can very quickly generate a very large
@@ -332,11 +332,13 @@
tree <- as(rcoal(12),"phylo4")
@
-
Next we generate the phylogenetic variance-covariance
matrix (by coercing the tree to
-a \code{phylo4vcov} object and pick a single set
-of traits (\code{MASS:mvrnorm}).
+a \code{phylo4vcov} object) and pick a single set
+of normally distributed traits (using \code{MASS:mvrnorm}
+to pick a multivariate normal deviate with a
+variance-covariance matrix that matches the
+structure of the tree).
<<vcvphylo>>=
vmat <- as(tree,"phylo4vcov")
vmat <- cov2cor(vmat)
Modified: pkg/inst/doc/phylobase.pdf
===================================================================
--- pkg/inst/doc/phylobase.pdf 2009-01-05 06:39:42 UTC (rev 424)
+++ pkg/inst/doc/phylobase.pdf 2009-01-14 20:57:56 UTC (rev 425)
@@ -1,644 +1,406 @@
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[TRUNCATED]
To get the complete diff run:
svnlook diff /svnroot/phylobase -r 425
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