use knitr for formalism

[ool/lipid_simulation_formalism.git] / kinetic_formalism.Rnw

diff --git a/kinetic_formalism.Rnw b/kinetic_formalism.Rnw
index 8c4fe20aa35bfef2f0d1c0f6c29065e9e450d675..d38a2313074ae66c3f532a317b78f5df4f4d3f72 100644 (file)
--- 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)))