From 58c96ac793bd72bca95db8819e9691b4e156c9ec Mon Sep 17 00:00:00 2001
From: Don Armstrong <don@donarmstrong.com>
Date: Thu, 11 Aug 2016 11:26:38 -0700
Subject: [PATCH] use knitr for formalism

---
 Makefile                          |  6 ++---
 kinetic_formalism.Rnw             | 41 +++++++++++++++----------------
 kinetic_formalism_competition.Rnw | 22 ++++++++---------
 references.bib                    |  2 +-
 4 files changed, 35 insertions(+), 36 deletions(-)

diff --git a/Makefile b/Makefile
index 4662459..10fdd67 100644
--- a/Makefile
+++ b/Makefile
@@ -16,10 +16,10 @@ R=R
 	bmeps -lpdf -olevel=1.4 $< $@
 
 %.tex: %.Rnw
-	$(R) CMD Sweave $<
+	$(R) --encoding=utf-8 -e "library('knitr'); knit('$<')"
 
 %.pdf: %.tex $(wildcard *.bib) $(wildcard *.tex)
-	rubber -fd $<
+	latexmk -pdf -pdflatex='xelatex -interaction=nonstopmode %O %S' -bibtex -use-make $<
 
 clean: 
 	rubber -d --clean *.tex
@@ -27,4 +27,4 @@ clean:
 
 .PHONY: clean all
 
-.DELETE_ON_ERROR: %.tex
\ No newline at end of file
+.DELETE_ON_ERROR: %.tex
diff --git a/kinetic_formalism.Rnw b/kinetic_formalism.Rnw
index 8c4fe20..d38a231 100644
--- a/kinetic_formalism.Rnw
+++ b/kinetic_formalism.Rnw
@@ -59,7 +59,7 @@
 \begin{document}
 %\maketitle
 
-<<results=hide,echo=FALSE>>=
+<<results="hide",echo=FALSE>>=
 require(lattice)
 require(grid)
 require(Hmisc)
@@ -162,14 +162,13 @@ affect the rate of the insertion positively or negatively, so we do
 not include a term for it in this formalism.
 
 
-\setkeys{Gin}{width=3.2in}
-<<fig=TRUE,echo=FALSE,results=hide,width=5,height=5>>=
+<<echo=FALSE,results="hide",fig.width=5,fig.height=5,out.width="3.2in">>=
 curve(2^x,from=0,to=sd(c(0,4)),
       main="Unsaturation Forward",
       xlab="Standard Deviation of Unsaturation of Vesicle",
       ylab="Unsaturation Forward Adjustment")
 @ 
-<<fig=TRUE,echo=FALSE,results=hide,width=5,height=5>>=
+<<echo=FALSE,results="hide",fig.width=5,fig.height=5,out.width="3.2in">>=
 curve(to.kcal(2^x),from=0,to=sd(c(0,4)),
       main="Unsaturation forward",
       xlab="Standard Deviation of Unsaturation of Vesicle",
@@ -205,7 +204,7 @@ a range of $\Delta \Delta G^\ddagger$ from
 $\Sexpr{format(digits=3,to.kcal(60^(-.165*-1)))}
 \frac{\mathrm{kcal}}{\mathrm{mol}}$ to $0\frac{\mathrm{kcal}}{\mathrm{mol}}$.
 
-<<fig=TRUE,echo=FALSE,results=hide,width=7,height=7>>=
+<<echo=FALSE,results="hide",fig.width=7,fig.height=7>>=
 x <- seq(-1,0,length.out=20)
 y <- seq(-1,0,length.out=20)
 grid <- expand.grid(x=x,y=y)
@@ -219,7 +218,7 @@ print(wireframe(z~x*y,grid,cuts=50,
                 zlab=list("Charge Forward",rot=93)))
 rm(x,y,grid)
 @ 
-<<fig=TRUE,echo=FALSE,results=hide,width=7,height=7>>=
+<<echo=FALSE,results="hide",fig.width=7,fig.height=7>>=
 x <- seq(-1,0,length.out=20)
 y <- seq(-1,0,length.out=20)
 grid <- expand.grid(x=x,y=y)
@@ -276,9 +275,9 @@ of $\Sexpr{format(digits=3,to.kcal(10^(0.13*0.213)))}
 relatively matched curvatures in our environment.
 
 % 1.5 to 0.75 3 to 0.33
-<<fig=TRUE,echo=FALSE,results=hide,width=7,height=7>>=
+<<echo=FALSE,results="hide",fig.width=7,fig.height=7>>=
 grid <- expand.grid(x=seq(0,max(c(sd(abs(log(c(1,3)))),
-y                      sd(abs(log(c(1,0.33)))),sd(abs(log(c(0.33,3)))))),length.out=20),
+                      sd(abs(log(c(1,0.33)))),sd(abs(log(c(0.33,3)))))),length.out=20),
                     y=seq(0,max(c(mean(log(c(1,3)),
                       mean(log(c(1,0.33))),
                       mean(log(c(0.33,3)))))),length.out=20))
@@ -291,7 +290,7 @@ print(wireframe(z~x*y,grid,cuts=50,
           zlab=list("Vesicle Curvature Forward",rot=93)))
 rm(grid)
 @ 
-<<fig=TRUE,echo=FALSE,results=hide,width=7,height=7>>=
+<<echo=FALSE,results="hide",fig.width=7,fig.height=7>>=
 grid <- expand.grid(x=seq(0,max(c(sd(abs(log(c(1,3)))),
                       sd(abs(log(c(1,0.33)))),sd(abs(log(c(0.33,3)))))),length.out=20),
                     y=seq(0,max(c(mean(log(c(1,3)),
@@ -362,13 +361,13 @@ From Nichols85: The association rate constant is independent of acyl
 chain length. {take into account for the formula; rz 8/17/2010}.
 
 
-<<fig=TRUE,echo=FALSE,results=hide,width=7,height=5>>=
+<<echo=FALSE,results="hide",fig.width=7,fig.height=5>>=
 curve(2^x,from=0,to=sd(c(12,24)),
       main="Length forward",
       xlab="Standard Deviation of Length of Vesicle",
       ylab="Length Forward Adjustment")
 @ 
-<<fig=TRUE,echo=FALSE,results=hide,width=7,height=5>>=
+<<echo=FALSE,results="hide",fig.width=7,fig.height=5>>=
 curve(to.kcal(2^x),from=0,to=sd(c(12,24)),
       main="Length forward",
       xlab="Standard Deviation of Length of Vesicle",
@@ -430,7 +429,7 @@ $\Sexpr{format(digits=3,to.kcal(7^(1-1/(5*(2^-1.7-2^-4)^2+1))))}\frac{\mathrm{kc
 for monomers with 4 unsaturations.
 
 
-<<fig=TRUE,echo=FALSE,results=hide,width=7,height=7>>=
+<<echo=FALSE,results="hide",fig.width=7,fig.height=7>>=
 grid <- expand.grid(x=seq(0,4,length.out=20),
                     y=seq(0,4,length.out=20))
 grid$z <- (7^(1-1/(5*(2^-grid$x-2^-grid$y)^2+1)))
@@ -442,7 +441,7 @@ print(wireframe(z~x*y,grid,cuts=50,
           zlab=list("Unsaturation Backward",rot=93)))
 rm(grid)
 @ 
-<<fig=TRUE,echo=FALSE,results=hide,width=7,height=7>>=
+<<echo=FALSE,results="hide",fig.width=7,fig.height=7>>=
 grid <- expand.grid(x=seq(0,4,length.out=20),
                     y=seq(0,4,length.out=20))
 grid$z <- to.kcal((7^(1-1/(5*(2^-grid$x-2^-grid$y)^2+1))))
@@ -477,7 +476,7 @@ $0\frac{\mathrm{kcal}}{\mathrm{mol}}$
 for monomers with charge $0$.
 
 
-<<fig=TRUE,echo=FALSE,results=hide,width=7,height=7>>=
+<<echo=FALSE,results="hide",fig.width=7,fig.height=7>>=
 x <- seq(-1,0,length.out=20)
 y <- seq(-1,0,length.out=20)
 grid <- expand.grid(x=x,y=y)
@@ -490,7 +489,7 @@ print(wireframe(z~x*y,grid,cuts=50,
           zlab=list("Charge Backwards",rot=93)))
 rm(x,y,grid)
 @ 
-<<fig=TRUE,echo=FALSE,results=hide,width=7,height=7>>=
+<<echo=FALSE,results="hide",fig.width=7,fig.height=7>>=
 x <- seq(-1,0,length.out=20)
 y <- seq(-1,0,length.out=20)
 grid <- expand.grid(x=x,y=y)
@@ -534,7 +533,7 @@ $\Sexpr{format(digits=3,to.kcal(7^(1-1/(20*(-0.013-log(1.3))^2+1))))}\frac{\math
 for monomers with curvature 1.3 to $0\frac{\mathrm{kcal}}{\mathrm{mol}}$ for monomers with curvature near 1.
 
 
-<<fig=TRUE,echo=FALSE,results=hide,width=7,height=7>>=
+<<echo=FALSE,results="hide",fig.width=7,fig.height=7>>=
 grid <- expand.grid(x=seq(0.8,1.33,length.out=20),
                     y=seq(0.8,1.33,length.out=20))
 grid$z <- 7^(1-1/(20*(log(grid$x)-log(grid$y))^2+1))
@@ -546,7 +545,7 @@ print(wireframe(z~x*y,grid,cuts=50,
           zlab=list("Curvature Backward",rot=93)))
 rm(grid)
 @ 
-<<fig=TRUE,echo=FALSE,results=hide,width=7,height=7>>=
+<<echo=FALSE,results="hide",fig.width=7,fig.height=7>>=
 grid <- expand.grid(x=seq(0.8,1.33,length.out=20),
                     y=seq(0.8,1.33,length.out=20))
 grid$z <- to.kcal(7^(1-1/(20*(log(grid$x)-log(grid$y))^2+1)))
@@ -585,7 +584,7 @@ $\Sexpr{format(digits=3,to.kcal(3.2^abs(24-17.75)))}\frac{\mathrm{kcal}}{\mathrm
 for monomers with length 24 to $0\frac{\mathrm{kcal}}{\mathrm{mol}}$ for monomers with curvature near 18.
 
 
-<<fig=TRUE,echo=FALSE,results=hide,width=7,height=7>>=
+<<echo=FALSE,results="hide",fig.width=7,fig.height=7>>=
 grid <- expand.grid(x=seq(12,24,length.out=20),
                     y=seq(12,24,length.out=20))
 grid$z <- 3.2^(abs(grid$x-grid$y))
@@ -597,7 +596,7 @@ print(wireframe(z~x*y,grid,cuts=50,
           zlab=list("Length Backward",rot=93)))
 rm(grid)
 @ 
-<<fig=TRUE,echo=FALSE,results=hide,width=7,height=7>>=
+<<echo=FALSE,results="hide",fig.width=7,fig.height=7>>=
 grid <- expand.grid(x=seq(12,24,length.out=20),
                     y=seq(12,24,length.out=20))
 grid$z <- to.kcal(3.2^(abs(grid$x-grid$y)))
@@ -646,7 +645,7 @@ $0\frac{\mathrm{kcal}}{\mathrm{mol}}$ for monomers with complex
 formation $0$.
 
 
-<<fig=TRUE,echo=FALSE,results=hide,width=7,height=7>>=
+<<echo=FALSE,results="hide",fig.width=7,fig.height=7>>=
 grid <- expand.grid(x=seq(-1,3,length.out=20),
                     y=seq(-1,3,length.out=20))
 grid$z <- 1.5^(grid$x*grid$y-abs(grid$x*grid$y))
@@ -658,7 +657,7 @@ print(wireframe(z~x*y,grid,cuts=50,
           zlab=list("Complex Formation Backward",rot=93)))
 rm(grid)
 @ 
-<<fig=TRUE,echo=FALSE,results=hide,width=7,height=7>>=
+<<echo=FALSE,results="hide",fig.width=7,fig.height=7>>=
 grid <- expand.grid(x=seq(-1,3,length.out=20),
                     y=seq(-1,3,length.out=20))
 grid$z <- to.kcal(1.5^(grid$x*grid$y-abs(grid$x*grid$y)))
diff --git a/kinetic_formalism_competition.Rnw b/kinetic_formalism_competition.Rnw
index 917ef85..88cebad 100644
--- 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"))
diff --git a/references.bib b/references.bib
index 434f02c..13eef8b 120000
--- a/references.bib
+++ b/references.bib
@@ -1 +1 @@
-../paper/references.bib
\ No newline at end of file
+../ool_paper_2010/references.bib
\ No newline at end of file
-- 
2.39.2