switch to cleveref

diff --git a/kinetic_formalism_competition.Rnw b/kinetic_formalism_competition.Rnw
index 505fb008ac93341170f2d90155dc475cb12b4027..9db41830b0bd6668b63a07453b1a002fdddbebf7 100644 (file)
--- a/kinetic_formalism_competition.Rnw
+++ b/kinetic_formalism_competition.Rnw
@@ -18,6 +18,7 @@
 \usepackage{booktabs}
 \usepackage[noblocks]{authblk}
 \usepackage[hyperfigures,bookmarks,colorlinks,citecolor=black,filecolor=black,linkcolor=black,urlcolor=black]{hyperref}
 \usepackage{booktabs}
 \usepackage[noblocks]{authblk}
 \usepackage[hyperfigures,bookmarks,colorlinks,citecolor=black,filecolor=black,linkcolor=black,urlcolor=black]{hyperref}

+\usepackage[capitalise]{cleveref}

 \usepackage[sectionbib,sort&compress,numbers]{natbib}
 \usepackage[nomargin,inline,draft]{fixme}
 \usepackage[x11names,svgnames]{xcolor}
 \usepackage[sectionbib,sort&compress,numbers]{natbib}
 \usepackage[nomargin,inline,draft]{fixme}
 \usepackage[x11names,svgnames]{xcolor}


@@ -99,35 +100,35 @@ to.kcal <- function(k,temp=300) {
 \renewcommand{\thetable}{S\@arabic\c@table}
 \makeatother
 
 \renewcommand{\thetable}{S\@arabic\c@table}
 \makeatother
 

-\section{Competition Implementation}
-\subsection{Implementation changes}
-
-\begin{itemize}
-\item settable maximum number of vesicles to track (default $10^4$)
-\item start with 1~L ($10^{-3}$~m$^3$) cube
-\item if at any point the number of vesicles exceeds the maximum
-  number, chop the volume and environment molecule number into tenths,
-  randomly select one tenth of the vesicles, and continue tracking.
-\item generations will be counted per vesicle, and each progeny
-  vesicle will have a generation number one greater than the parental
-  vesicle.
-\item 100 generations can result in as many as $2^{100}$
-  ($\Sexpr{to.latex(format(digits=3,2^100))}$) vesicles or as few as
-  101 vesicles.
-\item Environment will use a specific number of each component instead
-  of a constant concentration; as the number may be larger than
-  \texttt{long long} ($2^{64}$), we use libgmp to handle an arbitrary
-  precision number of components
-\end{itemize}
-
-\subsection{Infrastructure changes}
-\begin{itemize}
-\item Rewrite core bits in C
-\item Use libgmp for handling large ints
-\item Use openmpi to split the calculations out over multiple
-  machines/processors and allow deploying to larger
-  clusters/supercomputers
-\end{itemize}
+% \section{Competition Implementation}
+% \subsection{Implementation changes}
+% 
+% \begin{itemize}
+% \item settable maximum number of vesicles to track (default $10^4$)
+% \item start with 1~L ($10^{-3}$~m$^3$) cube
+% \item if at any point the number of vesicles exceeds the maximum
+%   number, chop the volume and environment molecule number into tenths,
+%   randomly select one tenth of the vesicles, and continue tracking.
+% \item generations will be counted per vesicle, and each progeny
+%   vesicle will have a generation number one greater than the parental
+%   vesicle.
+% \item 100 generations can result in as many as $2^{100}$
+%   ($\Sexpr{2^100}$) vesicles or as few as
+%   101 vesicles.
+% \item Environment will use a specific number of each component instead
+%   of a constant concentration; as the number may be larger than
+%   \texttt{long long} ($2^{64}$), we use libgmp to handle an arbitrary
+%   precision number of components
+% \end{itemize}
+% 
+% \subsection{Infrastructure changes}
+% \begin{itemize}
+% \item Rewrite core bits in C
+% \item Use libgmp for handling large ints
+% \item Use openmpi to split the calculations out over multiple
+%   machines/processors and allow deploying to larger
+%   clusters/supercomputers
+% \end{itemize}

 
 
 
 
 
 


@@ -149,20 +150,18 @@ The base forward kinetic parameter for the $i$th component is $k_{\mathrm{f}i}$
 and is dependent on the particular lipid type (PC, PS, SM, etc.). The
 forward adjustment parameter, $k_{\mathrm{f}i\mathrm{adj}}$, is based on the
 properties of the vesicle and the specific component (type, length,
 and is dependent on the particular lipid type (PC, PS, SM, etc.). The
 forward adjustment parameter, $k_{\mathrm{f}i\mathrm{adj}}$, is based on the
 properties of the vesicle and the specific component (type, length,

-unsaturation, etc.) (see Equation~\ref{eq:kf_adj}, and
-Section~\ref{sec:kinetic_adjustments}).
+unsaturation, etc.) (see \cref{eq:kf_adj,sec:kinetic_adjustments}).

 $\left[C_{i_\mathrm{monomer}}\right]$ is the molar concentration of
 monomer of the $i$th component. $\left[S_\mathrm{vesicle}\right]$ is the surface
 area of the vesicle per volume. The base backwards kinetic parameter
 for the $i$th component is $k_{\mathrm{b}i}$ and its adjustment parameter
 $\left[C_{i_\mathrm{monomer}}\right]$ is the molar concentration of
 monomer of the $i$th component. $\left[S_\mathrm{vesicle}\right]$ is the surface
 area of the vesicle per volume. The base backwards kinetic parameter
 for the $i$th component is $k_{\mathrm{b}i}$ and its adjustment parameter

-$k_{\mathrm{b}i\mathrm{adj}}$ (see Equation~\ref{eq:kb_adj}, and
-Section~\ref{sec:kinetic_adjustments}).
+$k_{\mathrm{b}i\mathrm{adj}}$ (see \cref{eq:kb_adj,sec:kinetic_adjustments}).

 $\left[C_{i_\mathrm{vesicle}}\right]$ is the molar concentration of
 the $i$th component in the vesicle.
 
 \subsection{Per-Lipid Kinetic Parameters}
 
 $\left[C_{i_\mathrm{vesicle}}\right]$ is the molar concentration of
 the $i$th component in the vesicle.
 
 \subsection{Per-Lipid Kinetic Parameters}
 

-<<echo=FALSE,results='hide'>>=
+<<kf_prime,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)
 @ 
 kf.prime <- c(3.7e6,3.7e6,5.1e7,3.7e6,2.3e6)
 kf <- (as.numeric(kf.prime)*10^-3)/(63e-20*6.022e23)
 @ 


@@ -174,7 +173,7 @@ available, these were taken from literature.
 %   \centering
 %   \begin{tabular}{c c c c c c c c}
 %     \toprule
 %   \centering
 %   \begin{tabular}{c c c c c c c c}
 %     \toprule

-%     Type & $k_\mathrm{f}$ $\left(\frac{\mathrm{m}}{\mathrm{s}}\right)$ & $k'_\mathrm{f}$ $\left(\frac{1}{\mathrm{M} \mathrm{s}}\right)$ & $k_\mathrm{b}$ $\left(\mathrm{s}^{-1}\right)$ & Area $\left({\AA}^2\right)$ & Charge & $\mathrm{CF}1$ & Curvature \\
+%     Type & $k_\mathrm{f}$ $\left(\frac{\mathrm{m}}{\mathrm{s}}\right)$ & $k'_\mathrm{f}$ $\left(\frac{1}{\mathrm{M} \mathrm{s}}\right)$ & $k_\mathrm{b}$ $\left(\mathrm{s}^{-1}\right)$ & Area $\left({Å}^2\right)$ & Charge & $\mathrm{CF}1$ & Curvature \\

 %         \midrule
 %     PC   & $\Sexpr{to.latex(format(digits=3,scientific=TRUE,kf[1]))}$ & $3.7 \times 10^6$ & $2   \times 10^{-5}$ & 63 & 0  & 2  & 0.8  \\
 %     PS   & $\Sexpr{to.latex(format(digits=3,scientific=TRUE,kf[2]))}$ & $3.7 \times 10^6$ & $1.25\times 10^{-5}$ & 54 & -1 & 0  & 1    \\
 %         \midrule
 %     PC   & $\Sexpr{to.latex(format(digits=3,scientific=TRUE,kf[1]))}$ & $3.7 \times 10^6$ & $2   \times 10^{-5}$ & 63 & 0  & 2  & 0.8  \\
 %     PS   & $\Sexpr{to.latex(format(digits=3,scientific=TRUE,kf[2]))}$ & $3.7 \times 10^6$ & $1.25\times 10^{-5}$ & 54 & -1 & 0  & 1    \\


@@ -188,7 +187,7 @@ available, these were taken from literature.
 % \end{table}
 
 %%% \DLA{I think we may just reduce these three sections; area, $k_\mathrm{f}$
 % \end{table}
 
 %%% \DLA{I think we may just reduce these three sections; area, $k_\mathrm{f}$

-%%%   and $k_\mathrm{b}$ to Table~\ref{tab:kinetic_parameters_lipid_types} with
+%%%   and $k_\mathrm{b}$ to \cref{tab:kinetic_parameters_lipid_types} with

 %%%   references.}
 %%% 
 %%% \RZ{Yes, but we also have to have then as comments the numbers that
 %%%   references.}
 %%% 
 %%% \RZ{Yes, but we also have to have then as comments the numbers that


@@ -576,7 +575,7 @@ The mean $\mathrm{stdev}\left(un_\mathrm{vesicle}\right)$ in our
 simulations is around $1.5$, which leads to a $\Delta \Delta
 G^\ddagger$ of $\Sexpr{to.latex(format(digits=3,to.kcal(2^1.5)))}
 \frac{\mathrm{kcal}}{\mathrm{mol}}$, and a total range of possible
 simulations is around $1.5$, which leads to a $\Delta \Delta
 G^\ddagger$ of $\Sexpr{to.latex(format(digits=3,to.kcal(2^1.5)))}
 \frac{\mathrm{kcal}}{\mathrm{mol}}$, and a total range of possible

-values depicted in Figure~\ref{fig:unf_graph}.
+values depicted in \cref{fig:unf_graph}.

 
 % \RZ{Explain here, or even earlier that the formulas were ad hoc
 %   adjusted to correspond to ``reasonable'' changes in the Eyring
 
 % \RZ{Explain here, or even earlier that the formulas were ad hoc
 %   adjusted to correspond to ``reasonable'' changes in the Eyring


@@ -650,7 +649,7 @@ to a range of $\Delta \Delta G^\ddagger$ from
 $\Sexpr{format(digits=3,to.kcal(60^(-.165*-1)))}
 \frac{\mathrm{kcal}}{\mathrm{mol}}$ to
 $0\frac{\mathrm{kcal}}{\mathrm{mol}}$, and the total range of possible
 $\Sexpr{format(digits=3,to.kcal(60^(-.165*-1)))}
 \frac{\mathrm{kcal}}{\mathrm{mol}}$ to
 $0\frac{\mathrm{kcal}}{\mathrm{mol}}$, and the total range of possible

-values seen in Figure~\ref{fig:chf_graph}.
+values seen in \cref{fig:chf_graph}.

 
 
 \begin{figure}
 
 
 \begin{figure}


@@ -745,7 +744,7 @@ cu_\mathrm{vesicle}$ of $0.213$ leads to a $\Delta \Delta G^\ddagger$
 of $\Sexpr{format(digits=3,to.kcal(10^(0.13*0.213)))}
 \frac{\mathrm{kcal}}{\mathrm{mol}}$. This is a consequence of the
 relatively matched curvatures in our environment. The full range of
 of $\Sexpr{format(digits=3,to.kcal(10^(0.13*0.213)))}
 \frac{\mathrm{kcal}}{\mathrm{mol}}$. This is a consequence of the
 relatively matched curvatures in our environment. The full range of

-$cu_\mathrm{f}$ values possible are shown in Figure~\ref{fig:cuf_graph}.
+$cu_\mathrm{f}$ values possible are shown in \cref{fig:cuf_graph}.

 
 % 1.5 to 0.75 3 to 0.33
 \begin{figure}
 
 % 1.5 to 0.75 3 to 0.33
 \begin{figure}


@@ -956,7 +955,7 @@ $\Sexpr{format(digits=3,to.kcal(7^(1-1/(5*(2^-1.7-2^-0)^2+1))))}
 \frac{\mathrm{kcal}}{\mathrm{mol}}$ for monomers with 0 unsaturation
 to
 $\Sexpr{format(digits=3,to.kcal(7^(1-1/(5*(2^-1.7-2^-4)^2+1))))}\frac{\mathrm{kcal}}{\mathrm{mol}}$
 \frac{\mathrm{kcal}}{\mathrm{mol}}$ for monomers with 0 unsaturation
 to
 $\Sexpr{format(digits=3,to.kcal(7^(1-1/(5*(2^-1.7-2^-4)^2+1))))}\frac{\mathrm{kcal}}{\mathrm{mol}}$

-for monomers with 4 unsaturations. See Figure~\ref{fig:unb_graph} for
+for monomers with 4 unsaturations. See \cref{fig:unb_graph} for

 the full range of possible values.
 
 
 the full range of possible values.
 
 


@@ -1024,7 +1023,7 @@ a range of $\Delta \Delta G^\ddagger$ from
 $\Sexpr{format(digits=3,to.kcal(20^(-.164*-1)))}
 \frac{\mathrm{kcal}}{\mathrm{mol}}$ for monomers with charge $-1$ to
 $0\frac{\mathrm{kcal}}{\mathrm{mol}}$ for monomers with charge $0$.
 $\Sexpr{format(digits=3,to.kcal(20^(-.164*-1)))}
 \frac{\mathrm{kcal}}{\mathrm{mol}}$ for monomers with charge $-1$ to
 $0\frac{\mathrm{kcal}}{\mathrm{mol}}$ for monomers with charge $0$.

-See Figure~\ref{fig:chb_graph} for the full range of possible values
+See \cref{fig:chb_graph} for the full range of possible values

 of $ch_\mathrm{b}$.
 
 
 of $ch_\mathrm{b}$.
 
 


@@ -1111,7 +1110,7 @@ $\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. The full range of values possible for $cu_\mathrm{b}$ are shown in
 for monomers with curvature 1.3 to
 $0\frac{\mathrm{kcal}}{\mathrm{mol}}$ for monomers with curvature near
 1. The full range of values possible for $cu_\mathrm{b}$ are shown in

-Figure~\ref{fig:cub_graph}
+\cref{fig:cub_graph}

 
 % \RZ{What about the opposite curvatures that actually do fit to each
 %   other?}
 
 % \RZ{What about the opposite curvatures that actually do fit to each
 %   other?}


@@ -1200,7 +1199,7 @@ $\Sexpr{format(digits=3,to.kcal(3.2^abs(12-17.75)))}
 $\Sexpr{format(digits=3,to.kcal(3.2^abs(24-17.75)))}\frac{\mathrm{kcal}}{\mathrm{mol}}$
 for monomers with length 24 to $0\frac{\mathrm{kcal}}{\mathrm{mol}}$
 for monomers with length near 18. The full range of possible values of
 $\Sexpr{format(digits=3,to.kcal(3.2^abs(24-17.75)))}\frac{\mathrm{kcal}}{\mathrm{mol}}$
 for monomers with length 24 to $0\frac{\mathrm{kcal}}{\mathrm{mol}}$
 for monomers with length near 18. The full range of possible values of

-$l_\mathrm{b}$ are shown in Figure~\ref{fig:lb_graph}
+$l_\mathrm{b}$ are shown in \cref{fig:lb_graph}

 
 % (for methods? From McLean84LIB: The activation free energies and free
 % energies of transfer from self-micelles to water increase by 2.2 and
 
 % (for methods? From McLean84LIB: The activation free energies and free
 % energies of transfer from self-micelles to water increase by 2.2 and


@@ -1294,7 +1293,7 @@ $\Sexpr{format(digits=3,to.kcal(1.5^(0.925*2-abs(0.925*2))))}\frac{\mathrm{kcal}
 for monomers with complex formation $2$ to
 $0\frac{\mathrm{kcal}}{\mathrm{mol}}$ for monomers with complex
 formation $0$. The full range of possible values for $CF1_\mathrm{b}$ are
 for monomers with complex formation $2$ to
 $0\frac{\mathrm{kcal}}{\mathrm{mol}}$ for monomers with complex
 formation $0$. The full range of possible values for $CF1_\mathrm{b}$ are

-depicted in Figure~\ref{fig:cf1b_graph}.
+depicted in \cref{fig:cf1b_graph}.

 
 
 
 
 
 


@@ -1458,15 +1457,15 @@ vesicle properties, we only plot the mean of the property.
 
 Determining the number of molecules to add to the lipid membrane
 ($n_i$) requires knowing $k_{\mathrm{f}i_\mathrm{adj}}$, the surface area of the
 
 Determining the number of molecules to add to the lipid membrane
 ($n_i$) requires knowing $k_{\mathrm{f}i_\mathrm{adj}}$, the surface area of the

-vesicle $S_\mathrm{vesicle}$ (see Section \ref{sec:ves_prop}), the time interval
+vesicle $S_\mathrm{vesicle}$ (see \cref{sec:ves_prop}), the time interval

 $dt$ during which lipids are added, the base $k_{\mathrm{f}i}$, and the
 concentration of the monomer in the environment
 $dt$ during which lipids are added, the base $k_{\mathrm{f}i}$, and the
 concentration of the monomer in the environment

-$\left[C_{i\mathrm{vesicle}}\right]$ (see Equation~\ref{eq:state}).
-$k_{\mathrm{f}i\mathrm{adj}}$ is calculated (see Equation~\ref{eq:kf_adj}) based on the
+$\left[C_{i\mathrm{vesicle}}\right]$ (see \cref{eq:state}).
+$k_{\mathrm{f}i\mathrm{adj}}$ is calculated (see \cref{eq:kf_adj}) based on the

 vesicle properties and their hypothesized effect on the rate (in as
 many cases as possible, experimentally based)
 vesicle properties and their hypothesized effect on the rate (in as
 many cases as possible, experimentally based)

-(see Section~\ref{sec:kinetic_adjustments} for details). $dt$ can be varied
-(see Section~\ref{sec:step_duration}), but for a given step is constant. This
+(see \cref{sec:kinetic_adjustments} for details). $dt$ can be varied
+(see \cref{sec:step_duration}), but for a given step is constant. This

 leads to the following:
 
 $n_i = k_{\mathrm{f}i}k_{\mathrm{f}i_\mathrm{adj}}\left[C_{i_\mathrm{monomer}}\right]S_\mathrm{vesicle}\mathrm{N_A}dt$
 leads to the following:
 
 $n_i = k_{\mathrm{f}i}k_{\mathrm{f}i_\mathrm{adj}}\left[C_{i_\mathrm{monomer}}\right]S_\mathrm{vesicle}\mathrm{N_A}dt$