[Adephylo-commits] r129 - in pkg: inst/doc man

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

Author: jombart
Date: 2009-11-05 13:43:40 +0100 (Thu, 05 Nov 2009)
New Revision: 129

Modified:
   pkg/inst/doc/adephylo.Rnw
   pkg/man/maples.Rd
   pkg/man/table.phylo4d.Rd
Log:
various fixes


Modified: pkg/inst/doc/adephylo.Rnw
===================================================================
--- pkg/inst/doc/adephylo.Rnw	2009-11-05 11:10:29 UTC (rev 128)
+++ pkg/inst/doc/adephylo.Rnw	2009-11-05 12:43:40 UTC (rev 129)
@@ -268,22 +268,21 @@
 table.phylo4d(ung)
 @
 
-\noindent Note that the constructor checks the consistency of the
-names used for the tips of the tree and for the rows of the data.frame.
-Inconsistencies issue an error.
-To override this behaviour, one can specify
-\code{use.tip.names=FALSE}.
-However, this can be tricky: often, mismatches between names can
-indicate that data are not sorted adequately; moreover, object created
-with such mismatches will often be invalid objects, and may issue
-errors in further analyses.
-\\
+%% \noindent Note that the constructor checks the consistency of the
+%% names used for the tips of the tree and for the rows of the data.frame.
+%% Inconsistencies issue an error.
+%% To override this behaviour, one can specify
+%% \code{use.tip.names=FALSE}.
+%% However, this can be tricky: often, mismatches between names can
+%% indicate that data are not sorted adequately; moreover, object created
+%% with such mismatches will often be invalid objects, and may issue
+%% errors in further analyses.
+%% \\
 
 Data are stored inside the slot \code{@tip.data} of the object.
-They can be accessed either via this slot (in our example,
-\code{ung at tip.data}), or using the function \code{tdata}:
+They can be accessed using the function \code{tdata}:
 <<>>=
-x <- tdata(ung)
+x <- tdata(ung, type="tip")
 head(x)
 @
 

Modified: pkg/man/maples.Rd
===================================================================
--- pkg/man/maples.Rd	2009-11-05 11:10:29 UTC (rev 128)
+++ pkg/man/maples.Rd	2009-11-05 12:43:40 UTC (rev 129)
@@ -9,7 +9,7 @@
 \format{
 \code{tithonia} is a list containing the 2 following objects :  
             - tre: a character string giving the phylogenetic tree in Newick format.\cr
-            - tab: a data frame with 17 species and 31 traits}\cr
+            - tab: a data frame with 17 species and 31 traits.\cr
 }
 \source{
 Data were obtained from the URL

Modified: pkg/man/table.phylo4d.Rd
===================================================================
--- pkg/man/table.phylo4d.Rd	2009-11-05 11:10:29 UTC (rev 128)
+++ pkg/man/table.phylo4d.Rd	2009-11-05 12:43:40 UTC (rev 129)
@@ -79,7 +79,7 @@
 tr <- rtree(20)
 dat <- data.frame(a = rnorm(20), b = scale(1:20), c=runif(20,-2,2) )
 dat[3:6, 2] <- NA # introduce some NAs
-obj <- phylo4d(tr, dat, use.tip=FALSE) # build a phylo4d object
+obj <- phylo4d(tr, dat) # build a phylo4d object
 table.phylo4d(obj) # default scatterplot
 table.phylo4d(obj,cex.leg=.6, use.edge.length=FALSE) # customized
 table.phylo4d(obj,treetype="clad", show.node=FALSE, cex.leg=.6,