use knitr for formalism

[ool/lipid_simulation_formalism.git] / kinetic_formalism_competition.Rnw

diff --git a/kinetic_formalism_competition.Rnw b/kinetic_formalism_competition.Rnw
index 917ef8537f06260418f71abc33fc50e32ae7e2d4..88cebad3a91831d325ed6f8dc0774414fbc8ee21 100644 (file)
--- a/kinetic_formalism_competition.Rnw
+++ b/kinetic_formalism_competition.Rnw
@@ -76,7 +76,7 @@
 \begin{document}
 \maketitle
 
-<<results=hide,echo=FALSE>>=
+<<results='hide',echo=FALSE>>=
 require(lattice)
 require(grid)
 require(Hmisc)
@@ -160,7 +160,7 @@ the $i$th component in the vesicle.
 
 \subsection{Per-Lipid Kinetic Parameters}
 
-<<echo=FALSE,results=hide>>=
+<<echo=FALSE,results='hide'>>=
 kf.prime <- c(3.7e6,3.7e6,5.1e7,3.7e6,2.3e6)
 kf <- (as.numeric(kf.prime)*10^-3)/(63e-20*6.022e23)
 @ 
@@ -587,7 +587,7 @@ values depicted in Figure~\ref{fig:unf_graph}.
 
 \setkeys{Gin}{width=6.4in}
 \begin{figure}
-<<fig=TRUE,echo=FALSE,results=hide,width=10,height=5>>=
+<<echo=FALSE,results='hide',fig.width=10,fig.height=5>>=
 layout(matrix(1:2,nrow=1,ncol=2))
 curve(2^x,from=0,to=sd(c(0,4)),
       xlab=expression(paste(stdev,group("(",italic(un[vesicle]),")"))),
@@ -653,7 +653,7 @@ values seen in Figure~\ref{fig:chf_graph}.
 
 
 \begin{figure}
-<<fig=TRUE,echo=FALSE,results=hide,width=14,height=7>>=
+<<echo=FALSE,results='hide',fig.width=14,fig.height=7>>=
 trellis.device(new=F,color=TRUE)
 trellis.par.set(list(axis.line =list(col="transparent")))
 pushViewport(viewport(layout=grid.layout(nrow=1,ncol=2),clip="off"))
@@ -748,7 +748,7 @@ $cu_\mathrm{f}$ values possible are shown in Figure~\ref{fig:cuf_graph}.
 
 % 1.5 to 0.75 3 to 0.33
 \begin{figure}
-<<fig=TRUE,echo=FALSE,results=hide,width=14,height=7>>=
+<<echo=FALSE,results='hide',fig.width=14,fig.height=7>>=
 trellis.device(new=F,color=TRUE)
 trellis.par.set(list(axis.line =list(col="transparent")))
 pushViewport(viewport(layout=grid.layout(nrow=1,ncol=2),clip="off"))
@@ -862,7 +862,7 @@ $\Sexpr{format(digits=3,to.kcal(2^(3.4)))}
 
 
 \begin{figure}
-<<fig=TRUE,echo=FALSE,results=hide,width=14,height=5>>=
+<<echo=FALSE,results='hide',fig.width=14,fig.height=5>>=
 layout(matrix(1:2,nrow=1,ncol=2))
 curve(2^x,from=0,to=sd(c(12,24)),
       xlab=expression(paste(stdev,group("(",italic(l[vesicle]),")"))),
@@ -960,7 +960,7 @@ the full range of possible values.
 
 
 \begin{figure}
-<<fig=TRUE,echo=FALSE,results=hide,width=14,height=7>>=
+<<echo=FALSE,results='hide',fig.width=14,fig.height=7>>=
 trellis.device(new=F,color=TRUE)
 trellis.par.set(list(axis.line =list(col="transparent")))
 pushViewport(viewport(layout=grid.layout(nrow=1,ncol=2),clip="off"))
@@ -1028,7 +1028,7 @@ of $ch_\mathrm{b}$.
 
 
 \begin{figure}
-<<fig=TRUE,echo=FALSE,results=hide,width=14,height=7>>=
+<<echo=FALSE,results='hide',fig.width=14,fig.height=7>>=
 trellis.device(new=F,color=TRUE)
 trellis.par.set(list(axis.line =list(col="transparent")))
 pushViewport(viewport(layout=grid.layout(nrow=1,ncol=2),clip="off"))
@@ -1125,7 +1125,7 @@ Figure~\ref{fig:cub_graph}
 
 
 \begin{figure}
-<<fig=TRUE,echo=FALSE,results=hide,width=14,height=7>>=
+<<echo=FALSE,results='hide',fig.width=14,fig.height=7>>=
 trellis.device(new=F,color=TRUE)
 trellis.par.set(list(axis.line =list(col="transparent")))
 pushViewport(viewport(layout=grid.layout(nrow=1,ncol=2),clip="off"))
@@ -1209,7 +1209,7 @@ $l_\mathrm{b}$ are shown in Figure~\ref{fig:lb_graph}
 
 
 \begin{figure}
-<<fig=TRUE,echo=FALSE,results=hide,width=14,height=7>>=
+<<echo=FALSE,results='hide',fig.width=14,fig.height=7>>=
 trellis.device(new=F,color=TRUE)
 trellis.par.set(list(axis.line =list(col="transparent")))
 pushViewport(viewport(layout=grid.layout(nrow=1,ncol=2),clip="off"))
@@ -1298,7 +1298,7 @@ depicted in Figure~\ref{fig:cf1b_graph}.
 
 
 \begin{figure}
-<<fig=TRUE,echo=FALSE,results=hide,width=14,height=7>>=
+<<echo=FALSE,results='hide',fig.width=14,fig.height=7>>=
 trellis.device(new=F,color=TRUE)
 trellis.par.set(list(axis.line =list(col="transparent")))
 pushViewport(viewport(layout=grid.layout(nrow=1,ncol=2),clip="off"))