[Dplr-commits] r777 - pkg/dplR/vignettes

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

Author: mvkorpel
Date: 2014-04-07 14:32:09 +0200 (Mon, 07 Apr 2014)
New Revision: 777

Modified:
   pkg/dplR/vignettes/intro-dplR.Rnw
Log:
Don't repeat R computations when including graphics in the document.
Requires an explicit \includegraphics for each figure. On this
computer, the change cuts vignette build time from 18 to 11 seconds,
for the current vignette source.


Modified: pkg/dplR/vignettes/intro-dplR.Rnw
===================================================================
--- pkg/dplR/vignettes/intro-dplR.Rnw	2014-04-07 11:33:37 UTC (rev 776)
+++ pkg/dplR/vignettes/intro-dplR.Rnw	2014-04-07 12:32:09 UTC (rev 777)
@@ -16,6 +16,7 @@
 \setkeys{Gin}{width=1.0\textwidth} % figure width
 \SweaveOpts{concordance=TRUE}
 \SweaveOpts{strip.white=true}
+\SweaveOpts{include=FALSE}
 <<echo=false>>=
 options(width=62) # width of paper (number of characters)
 @ 
@@ -84,14 +85,12 @@
 showing either the segments arranged over time as straight lines or as a 
 ``spaghetti plot.''
 
-<<a>>=
+<<a, fig=TRUE>>=
 plot(ca533,plot.type=c('spag'))
 @
 \begin{figure}[htbp]
 \centering
-<<fig=true,echo=false>>=
-<<a>>
-@
+\includegraphics{intro-dplR-a}
 \caption{A spaghetti plot of Campito Mountain ring widths.}
 \label{fig:rwl.plot}
 \end{figure}
@@ -161,7 +160,7 @@
 single series using the detrend.series function, which produces a plot by
 default.
 
-<<a>>=
+<<b, fig=TRUE>>=
 series <- ca533[, "CAM011"] # extract the series
 names(series) <- rownames(ca533) # give it years as rownames
 series.rwi <- detrend.series(y = series, y.name = "CAM011",
@@ -169,9 +168,7 @@
 @
 \begin{figure}[htbp]
 \centering
-<<fig=true,echo=false>>=
-<<a>>
-@
+\includegraphics{intro-dplR-b}
 \caption{Detrending a series via a spline.}
 \label{fig:spline.detrend}
 \end{figure}
@@ -193,7 +190,7 @@
 rwl.stats function is typically used on raw ring widths (the rwl object) and 
 produces summary statistics. Here are summary statistics on the first five
 series in ca533.
-<<a>>=
+<<>>=
 rwl.stats(ca533)[1:5,]
 @
 
@@ -256,14 +253,12 @@
 The chronology can be plotted using the chron.plot function which has many 
 arguments for customization. Here we'll just make a simple plot of the 
 chronology with a smoothing spline added.
-<<a>>=
+<<c, fig=TRUE>>=
 chron.plot(ca533.crn,add.spline=TRUE,nyrs=20)
 @
 \begin{figure}
 \centering
-<<fig=true,echo=false>>=
-<<a>>
-@
+\includegraphics{intro-dplR-c}
 \caption{Campito Mountain chronology with 20-year smoothing spline.}
 \label{fig:chron.plot.spline}
 \end{figure}
@@ -273,7 +268,7 @@
 scratching the surface of what dplR is capable of. As a small example, 
 here is a way that a user might decide to truncate a chronology based on the
 expressed population signal.
-<<a>>=
+<<d, fig=TRUE>>=
 def.par <- par(no.readonly=TRUE)
 eps.cut <- 0.85 # An arbitrary EPS cutoff for demonstration
 ## Plot the chronology showing a potential cutoff year based on EPS
@@ -320,9 +315,7 @@
 @
 \begin{figure}
 \centering
-<<fig=true,echo=false>>=
-<<a>>
-@
+\includegraphics{intro-dplR-d}
 \caption{Campito Mountain chronology using an EPS cutoff.}
 \label{fig:chron.plot.eps}
 \end{figure}