comment out analyzing output section

diff --git a/kinetic_formalism_competition.Rnw b/kinetic_formalism_competition.Rnw
index 9db41830b0bd6668b63a07453b1a002fdddbebf7..54e7fa8c02f5a022c0ffb1447bf0495cf14970f1 100644 (file)
--- a/kinetic_formalism_competition.Rnw
+++ b/kinetic_formalism_competition.Rnw
@@ -1517,59 +1517,59 @@ The environment, initial vesicle, and the state of the vesicle
 immediately before and immediately after splitting are stored
 to produce later output.
 
 immediately before and immediately after splitting are stored
 to produce later output.
 

-\section{Analyzing output}
-
-The analysis of output is handled by a separate perl program which
-shares many common modules with the simulation program. Current output
-includes simulation progress, summary tables, summary statistics, and
-various graphs.
-
-\subsection{PCA plots}
-
-Two major groups of axes that contribute to vesicle variation between
-subsequent generations are the components and properties of vesicles.
-Each component in a vesicle is an axis on its own; it can be measured
-either as an absolute number of molecules in each component, or the
-fraction of molecules of that component over the total number of
-molecules; the second approach is often more convenient, as it allows
-vesicles with different number of molecules to be directly compared
-(though it hides any effect of vesicle size).
-
-In order to visualize the variation between and transition of
-subsequent generations of vesicles from their initial state in the
-simulation, to their final state at the termination of the simulation,
-we plot the projection of the generations onto the two principle PCA
-axes (and alternatively, any pairing of the axes).
-
-\subsection{Carpet plots}
-
-Carpet plots show the distance/similarity between the composition or
-properties of all generations in a single run. The difference between
-each group of vesicle can be calculated using Euclidean distance
-(properties and compositions) or H similarity (composition only). We
-must use Euclidean distance for properties because the H distance
-metric is invalid when comparing negative vector elements to positive
-vector elements.
-
-In addition to showing distance or similarity, carpet plots also
-depict propersomes and composomes as square boxes on the diagonals and
-propertypes and compotypes as rectangles off the diagonals, each
-propertype or compotype with a distinct color.
-
-\subsection{Propersomes, propertypes, composomes and compotypes}
-
-A generation is considered to be a propersome if it is less than $0.6$
-units (by Euclidean distance of normalized properties) away from the
-generation immediately following and preceding. Likewise, a generation
-is in a composome if its H similarity is more than $0.9$ (by the
-normalized H metric) from the preceding and following generations.
-Propersomes and composomes are then assigned to propertypes and
-compotypes using Paritioning Around Medioids
-(PAM). All values of $k$ between 2 and 15
-(or the number of propersomes and composomes, if that is less than 15)
-are tried, and the clustering with the smallest
-silhouette~\citep{Rousseeuw1987:silhouettes} is chosen as the ideal
-clustering~\citep{Shenhav2005:pgard}.
+% \section{Analyzing output}
+% 
+% The analysis of output is handled by a separate perl program which
+% shares many common modules with the simulation program. Current output
+% includes simulation progress, summary tables, summary statistics, and
+% various graphs.
+% 
+% \subsection{PCA plots}
+% 
+% Two major groups of axes that contribute to vesicle variation between
+% subsequent generations are the components and properties of vesicles.
+% Each component in a vesicle is an axis on its own; it can be measured
+% either as an absolute number of molecules in each component, or the
+% fraction of molecules of that component over the total number of
+% molecules; the second approach is often more convenient, as it allows
+% vesicles with different number of molecules to be directly compared
+% (though it hides any effect of vesicle size).
+% 
+% In order to visualize the variation between and transition of
+% subsequent generations of vesicles from their initial state in the
+% simulation, to their final state at the termination of the simulation,
+% we plot the projection of the generations onto the two principle PCA
+% axes (and alternatively, any pairing of the axes).
+% 
+% \subsection{Carpet plots}
+% 
+% Carpet plots show the distance/similarity between the composition or
+% properties of all generations in a single run. The difference between
+% each group of vesicle can be calculated using Euclidean distance
+% (properties and compositions) or H similarity (composition only). We
+% must use Euclidean distance for properties because the H distance
+% metric is invalid when comparing negative vector elements to positive
+% vector elements.
+% 
+% In addition to showing distance or similarity, carpet plots also
+% depict propersomes and composomes as square boxes on the diagonals and
+% propertypes and compotypes as rectangles off the diagonals, each
+% propertype or compotype with a distinct color.
+% 
+% \subsection{Propersomes, propertypes, composomes and compotypes}
+% 
+% A generation is considered to be a propersome if it is less than $0.6$
+% units (by Euclidean distance of normalized properties) away from the
+% generation immediately following and preceding. Likewise, a generation
+% is in a composome if its H similarity is more than $0.9$ (by the
+% normalized H metric) from the preceding and following generations.
+% Propersomes and composomes are then assigned to propertypes and
+% compotypes using Paritioning Around Medioids
+% (PAM). All values of $k$ between 2 and 15
+% (or the number of propersomes and composomes, if that is less than 15)
+% are tried, and the clustering with the smallest
+% silhouette~\citep{Rousseeuw1987:silhouettes} is chosen as the ideal
+% clustering~\citep{Shenhav2005:pgard}.

 
 
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