[Phylobase-commits] r480 - pkg/inst/doc

noreply at r-forge.r-project.org noreply at r-forge.r-project.org
Tue Aug 18 21:28:39 CEST 2009 

Author: bbolker
Date: 2009-08-18 21:28:38 +0200 (Tue, 18 Aug 2009)
New Revision: 480

Modified:
   pkg/inst/doc/phylobase.Rnw
   pkg/inst/doc/phylobase.pdf
Log:
 tweaks



Modified: pkg/inst/doc/phylobase.Rnw
===================================================================
--- pkg/inst/doc/phylobase.Rnw	2009-08-18 19:18:25 UTC (rev 479)
+++ pkg/inst/doc/phylobase.Rnw	2009-08-18 19:28:38 UTC (rev 480)
@@ -28,7 +28,6 @@
 
 The base \code{phylo4} class is modeled on the the \code{phylo} class in \code{ape}.  \code{phylo4d} and \code{multiphylo4} extend the \code{phylo4} class to include data or multiple trees respectively.  In addition to describing the classes and methods, this vignette gives examples of how they might be used.
 
-
 \section{Package overview}
 
 The phylobase package currently implements the following functions and data structures:
@@ -47,16 +46,16 @@
 
 The \code{S4} help system works similarly to the \code{S3} help system with some small differences relating to how \code{S4} methods are written.  The \code{plot()} function is a good example.  When we type \code{?plot} we are provided the help for the default plotting function which expects \code{x} and \code{y}.  \code{R} also provides a way to smartly dispatch the right type of plotting function.  In the case of an \code{ape phylo} object (a \code{S3} class object) \code{R} evaluates the class of the object and finds the correct functions, so the following works correctly.
 
-<<randtree1,fig=FALSE>>=
+<<randtree1,fig=FALSE,keep.source=TRUE>>=
 library(ape)
-# Make a random tree with 10 tips
-rand_tree <- rcoal(10)
+set.seed(1)  ## set random-number seed
+rand_tree <- rcoal(10) ## Make a random tree with 10 tips
 plot(rand_tree)
 @
 
-However, typing \code{?plot} still takes us to the default \code{plot} help.  We have to type \code{plot.phylo} to find what we are looking for.  This is because \code{S3} generics are simply functions with a dot and the class name added.
+However, typing \code{?plot} still takes us to the default \code{plot} help.  We have to type \code{?plot.phylo} to find what we are looking for.  This is because \code{S3} generics are simply functions with a dot and the class name added.
 
-The \code{S4} generic system is too complicated to describe here, but doesn't include the same dot notation.  As a result \code{?plot.phylo4} doesn't work, \code{R} does, however, find the right plotting function.
+The \code{S4} generic system is too complicated to describe here, but doesn't include the same dot notation.  As a result \code{?plot.phylo4} doesn't work, \code{R} still finds the right plotting function.
 
 <<convtree,fig=FALSE>>=
 library(phylobase)
@@ -67,19 +66,19 @@
 
 All fine and good, but how to we find out about all the great features of the \code{phylobase} plotting function?  \code{R} has two nifty ways to find it, the first is to simply put a question mark in front of the whole call:
 
-\begin{verbatim}
-        > ?plot(rand_p4_tree)
-\end{verbatim}
+<<doc0,eval=FALSE>>=
+?plot(rand_p4_tree)
+@
 
 \code{R} looks at the class of the \code{rand\_p4\_tree} object and takes us to the correct help file (note: this only works with \code{S4} objects).  The second ways is handy if you already know the class of your object, or want to compare to generics for different classes:
 
-\begin{verbatim}
-        > method?plot("phylo4")
-\end{verbatim}
+<<doc1,eval=FALSE>>=
+method?plot("phylo4")
+@
 
 More information about how \code{S4} documentation works can be found in the methods package, by running the following command.
 
-<<doc,eval=FALSE>>=
+<<doc2,eval=FALSE>>=
 help('Documentation', package="methods")
 @
 
@@ -88,9 +87,10 @@
 You can start with a tree --- an object of class \code{phylo} from the \code{ape} package (e.g., read in using the \code{read.tree()} or \code{read.nexus()} functions), and convert it to a \code{phylo4} object.
 
 For example, load the raw \emph{Geospiza} data:
-<<geodata>>=
+<<geodata,keep.source=TRUE>>=
 library(phylobase)
 data(geospiza_raw)
+## what does it contain?
 names(geospiza_raw)
 @
 
@@ -106,8 +106,7 @@
 nodeLabels(g1)
 @
 
-(this means ``a character vector of length 0'';
-you can also retrieve the node labels with \code{labels(g1,"internal")}).
+You can also retrieve the node labels with \code{labels(g1,"internal")}).
 
 A simple way to assign the node numbers as labels (useful for various checks) is
 
@@ -116,7 +115,7 @@
 head(g1, 5)
 @
 
-The \code{summary} method gives a little extra information, including information on branch lengths:
+The \code{summary} method gives a little extra information, including information on the distribution of branch lengths:
 
 <<sumgeodata>>=
 summary(g1)
@@ -155,7 +154,7 @@
 hasPoly(g1)
 @
 
-Does it have branch lengths?
+Does it have information on branch lengths?
 <<hasbrlengeodata>>=
 hasEdgeLength(g1)
 @
@@ -194,14 +193,12 @@
 row.names(gdata) <- tolower(row.names(gdata))
 @
 
-To deal with the second problem (missing data for \emph{G. olivacea}), we have a few choices. The easiest is to use \code{missing.tip.data="OK"} to allow R to create the new object:
+To deal with the second problem (missing data for \emph{G. olivacea}), we have a few choices. The easiest is to use \code{missing.data="warn"} to allow R to create the new object with a warning (you can also use \code{missing.data="OK"} to proceed without warnings):
 
 <<geomerge2,keep.source=TRUE>>=
 g2 <- phylo4d(g1, gdata, missing.data="warn")
 @
 
-(setting \code{missing.data} to \code{"warn"} would create the new object but print a warning).
-
 Another way to deal with this would be to use \code{prune()} to drop the offending tip from the tree first:
 
 <<geomerge3,results=hide>>=

Modified: pkg/inst/doc/phylobase.pdf
===================================================================
--- pkg/inst/doc/phylobase.pdf	2009-08-18 19:18:25 UTC (rev 479)
+++ pkg/inst/doc/phylobase.pdf	2009-08-18 19:28:38 UTC (rev 480)
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 endobj
 139 0 obj <<
@@ -633,95 +665,96 @@
 304.86 52.88 m 304.86 410.40 l S
 0.000 0.000 0.000 rg
 0.000 0.000 0.000 RG
+  290.89 52.88 m
+  290.89 60.56 297.18 66.85 304.86 66.85 c
+  312.54 66.85 318.83 60.56 318.83 52.88 c
+  318.83 45.19 312.54 38.91 304.86 38.91 c
+  297.18 38.91 290.89 45.19 290.89 52.88 c
+B
+  290.86 85.38 m
+  290.86 93.08 297.16 99.38 304.86 99.38 c
+  312.56 99.38 318.86 93.08 318.86 85.38 c
+  318.86 77.68 312.56 71.38 304.86 71.38 c
+  297.16 71.38 290.86 77.68 290.86 85.38 c
+B
+  291.00 117.88 m
+  291.00 125.50 297.24 131.74 304.86 131.74 c
+  312.48 131.74 318.72 125.50 318.72 117.88 c
+  318.72 110.26 312.48 104.02 304.86 104.02 c
+  297.24 104.02 291.00 110.26 291.00 117.88 c
+B
 BT
-/F1 1 Tf 2 Tr 6.20 0 0 6.20 302.40 50.72 Tm (l) Tj 0 Tr
+/F1 1 Tf 2 Tr 18.95 0 0 18.95 297.35 143.81 Tm (l) Tj 0 Tr
 ET
-1.000 1.000 1.000 rg
+  293.64 182.89 m
+  293.64 189.06 298.69 194.11 304.86 194.11 c
+  311.03 194.11 316.08 189.06 316.08 182.89 c
+  316.08 176.71 311.03 171.66 304.86 171.66 c
+  298.69 171.66 293.64 176.71 293.64 182.89 c
+B
+  293.25 215.39 m
+  293.25 221.77 298.47 227.00 304.86 227.00 c
+  311.25 227.00 316.47 221.77 316.47 215.39 c
+  316.47 209.00 311.25 203.77 304.86 203.77 c
+  298.47 203.77 293.25 209.00 293.25 215.39 c
+B
 BT
-/F1 1 Tf 2 Tr 13.19 0 0 13.19 299.64 80.80 Tm (l) Tj 0 Tr
+/F1 1 Tf 2 Tr 11.12 0 0 11.12 300.46 244.03 Tm (l) Tj 0 Tr
 ET
+1.000 1.000 1.000 rg
 BT
-/F1 1 Tf 2 Tr 15.99 0 0 15.99 298.53 112.33 Tm (l) Tj 0 Tr
+/F1 1 Tf 2 Tr 5.97 0 0 5.97 302.50 278.32 Tm (l) Tj 0 Tr
 ET
+0.000 0.000 0.000 rg
 BT
-/F1 1 Tf 2 Tr 22.14 0 0 22.14 296.09 142.70 Tm (l) Tj 0 Tr
+/F1 1 Tf 2 Tr 21.02 0 0 21.02 296.54 305.60 Tm (l) Tj 0 Tr
 ET
 BT
-/F1 1 Tf 2 Tr 19.35 0 0 19.35 297.20 176.17 Tm (l) Tj 0 Tr
+/F1 1 Tf 2 Tr 27.39 0 0 27.39 294.02 335.89 Tm (l) Tj 0 Tr
 ET
 BT
-/F1 1 Tf 2 Tr 20.42 0 0 20.42 296.77 208.30 Tm (l) Tj 0 Tr
+/F1 1 Tf 2 Tr 18.74 0 0 18.74 297.44 371.39 Tm (l) Tj 0 Tr
 ET
 BT
-/F1 1 Tf 2 Tr 21.78 0 0 21.78 296.23 240.33 Tm (l) Tj 0 Tr
+/F1 1 Tf 2 Tr 12.76 0 0 12.76 299.81 405.97 Tm (l) Tj 0 Tr
 ET
-  292.63 280.39 m
-  292.63 287.12 298.13 292.62 304.86 292.62 c
-  311.59 292.62 317.09 287.12 317.09 280.39 c
-  317.09 273.66 311.59 268.16 304.86 268.16 c
-  298.13 268.16 292.63 273.66 292.63 280.39 c
-B
-  294.73 312.89 m
-  294.73 318.46 299.29 323.02 304.86 323.02 c
-  310.43 323.02 314.99 318.46 314.99 312.89 c
-  314.99 307.32 310.43 302.76 304.86 302.76 c
[TRUNCATED]

To get the complete diff run:
    svnlook diff /svnroot/phylobase -r 480

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