Merge branch 'master' of https://github.com/timcdlucas/PhDThesis

Appendix2.Rtex

@@ -40,7 +40,7 @@ saveData <- TRUE
 
 %%end.rcode
 
-%%begin.rcode libs
+%%begin.rcode libs, cache = FALSE
 
 library(MetapopEpi)
 library(cowplot)
@@ -322,8 +322,9 @@ noInvade1 <- pSIR(p1) +
                guides(colour=guide_legend(title = '')) +
                theme(legend.text.align = 0) +
                xlab('Time (years)') +
-               xlim(0, maxt)
-pop1 <- pPop(p1) + theme_tcdl + xlab('Time (years)') + xlim(0, maxt)
+               scale_x_continuous(breaks = c(0, 20, 40, 60, 80), limits = c(0, maxt))
+
+pop1 <- pPop(p1) + theme_tcdl + xlab('Time (years)') + scale_x_continuous(breaks = c(0, 20, 40, 60, 80), limits = c(0, maxt))
 
 
 
@@ -337,8 +338,8 @@ noInvade2 <- pSIR(p2) +
                guides(colour=guide_legend(title = '')) +
                theme(legend.text.align = 0) +
                xlab('Time (years)') +
-               xlim(0, maxt)
-pop2 <- pPop(p2) + theme_tcdl + xlab('Time (years)') + xlim(0, maxt)
+               scale_x_continuous(breaks = c(0, 20, 40, 60, 80), limits = c(0, maxt))
+pop2 <- pPop(p2) + theme_tcdl + xlab('Time (years)') + scale_x_continuous(breaks = c(0, 20, 40, 60, 80), limits = c(0, maxt))
 
 
 # Combine and print the plots.
@@ -456,7 +457,7 @@ fullSim <- function(x){
 }
 %%end.rcode
 
-%%begin.rcode runDispSim, eval = TRUE, cache = TRUE
+%%begin.rcode runDispSim, eval = runSims, cache = TRUE
 
 # Create and set seed (seed object is used to set seed in each seperate simulation.'
 seed <- 33355
@@ -571,7 +572,7 @@ fullSim <- function(x){
 }
 %%end.rcode
 
-%%begin.rcode runTopoSim, eval = TRUE, cache = TRUE
+%%begin.rcode runTopoSim, eval = runSims, cache = TRUE
 
 # Create and set seed (seed object is used to set seed in each seperate simulation.'
 seed <- 1230202

Appendix2.tex

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+%--------------------------------------------------------------------------------------------------------------------------------%
+% Code for "Appendix C: Understanding how population structure affects pathogen richness in a mechanistic model of bat populations"
+% Appendix for Chapter 3 of thesis "The role of population structure and size in determining bat pathogen richness"
+% by Tim CD Lucas
+%
+% NB The file is numbered Appendix2 as Chapter 3 was previously Chapter 2 in the thesis.
+%
+%---------------------------------------------------------------------------------------------------------------------------------%
+
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+% --------------------------------------------------------------------------- %
+% Invading pathogen plots
+% --------------------------------------------------------------------------- %
+
+
+
+
+\begin{knitrout}\footnotesize
+\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{figure}[t]
+
+{\centering \includegraphics[width=\textwidth]{figure/A-plotsInvade-1} 
+
+}
+
+\caption[
+Examples of simulated SIR dynamics with successfull invasions
+]{
+Two examples (A and B) of a successful invasion plotted on a logged $y$-axis.
+The lines are coloured such that blue represents susceptibles, brown represents individuals infected with one pathogen (the two seperate brown lines are Pathogen 1 and 2), black represents co-infected individuals and yellow represents recovered and immune individuals.
+Pathogen 2 is seeded after \SI{300000} events (approximately 30 years).
+Simulations are run on a fully-connected network.
+Parameter values are: dispersal rate = 0.1, transmission rate = 0.2.
+All other parameters are as stated in Table~\ref{t:params}.
+}\label{fig:plotsInvade}
+\end{figure}
+
+
+\end{knitrout}
+
+
+
+% --------------------------------------------------------------------------- %
+% No invasion plots
+% --------------------------------------------------------------------------- %
+
+
+
+
+
+
+
+\begin{knitrout}\footnotesize
+\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{figure}[t]
+
+{\centering \includegraphics[width=\textwidth]{figure/A-plotsNoInvade-1} 
+
+}
+
+\caption[
+Examples of simulated SIR dynamics with unsuccessfull invasions
+]{
+Two examples (A and B) of an unsuccessful invasion plotted on a logged $y$-axis.
+The lines are coloured such that blue represents susceptibles, brown represents individuals infected with one pathogen (the two separate brown lines are Pathogen 1 and 2), black represents co-infected individuals and yellow represents recovered and immune individuals.
+Pathogen 2 is seeded after \SI{300000} events (approximately 30 years).
+It can be seen that after seeding Pathogen 2, there is a very short period before extinction as opposed to a long fade out of disease.
+Simulations are run on a fully-connected network.
+Parameter values are: dispersal rate = 0.1, transmission rate = 0.2.
+All other parameters are as stated in Table~\ref{t:params}.
+}\label{fig:plotsNoInvade1}
+\end{figure}
+
+\begin{figure}[t]
+
+{\centering \includegraphics[width=0.8\textwidth]{figure/A-plotsNoInvade-2} 
+
+}
+
+\caption[
+Examples of colony size dynamics
+]{
+Two examples (A and B) of the change in colony sizes throughout a simulation (note the truncated $y$-axis).
+The size of each colony changes as a random walk.
+However, given the length of the simulations, there is little risk of colonies going extinct or becoming very large.
+Birth and death rate are equal and set to 0.05, giving a generation time of 20 years.
+The metapopulation network is fully-connected and the dispersal rate is 0.1 per year.
+The starting colony size is \SI{3000}.
+}\label{fig:plotsNoInvade2}
+\end{figure}
+
+
+\end{knitrout}
+
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+% ------------------------------------------------------------------ %
+% Topology Sims
+% ------------------------------------------------------------------ %
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+% ------------------------------------------------ %
+% Raw data tables
+% ------------------------------------------------ %
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+\clearpage
+% latex table generated in R 3.3.1 by xtable 1.8-2 package
+% Mon Jul 25 00:04:16 2016
+\begin{table}[ht]
+\centering
+\caption[
+Raw data for dispersal simulations
+  ]{
+Raw data for dispersal simulations.
+The relevant parameters are shown along with the number of invasions and the number of simulations.
+$\beta$ is the transmission rate.
+} 
+\label{B-disp}
+\begingroup\small
+\begin{tabular}{@{}rrrr@{}}
+  \toprule
+$\beta$ & Dispersal & Invasions & Sims \\ 
+  \midrule
+0.1 & 0.000 & 0 & 100 \\ 
+  0.1 & 0.001 & 1 & 101 \\ 
+  0.1 & 0.010 & 0 & 100 \\ 
+  0.1 & 0.100 & 0 & 99 \\ 
+  0.2 & 0.000 & 4 & 100 \\ 
+  0.2 & 0.001 & 42 & 126 \\ 
+  0.2 & 0.010 & 41 & 126 \\ 
+  0.2 & 0.100 & 63 & 123 \\ 
+  0.3 & 0.000 & 47 & 100 \\ 
+  0.3 & 0.001 & 113 & 125 \\ 
+  0.3 & 0.010 & 113 & 126 \\ 
+  0.3 & 0.100 & 112 & 124 \\ 
+  0.4 & 0.000 & 75 & 100 \\ 
+  0.4 & 0.001 & 96 & 100 \\ 
+  0.4 & 0.010 & 98 & 100 \\ 
+  0.4 & 0.100 & 96 & 100 \\ 
+   \bottomrule
+\end{tabular}
+\endgroup
+\end{table}
+
+
+
+
+
+% latex table generated in R 3.3.1 by xtable 1.8-2 package
+% Mon Jul 25 00:04:16 2016
+\begin{table}[ht]
+\centering
+\caption[
+Raw data for topology simulations
+  ]{
+Raw data for topology simulations.
+The relevant parameters are shown along with the number of invasions and the number of simulations.
+$\beta$ is the transmission rate.
+} 
+\label{B-topo}
+\begingroup\small
+\begin{tabular}{@{}rllr@{}}
+  \toprule
+$\beta$ & Topology & Invasions & Sims \\ 
+  \midrule
+0.1 & Unconnected & 0 & 100 \\ 
+  0.1 & Minimally & 1 & 101 \\ 
+  0.1 & Fully & 1 & 99 \\ 
+  0.2 & Unconnected & 4 & 100 \\ 
+  0.2 & Minimally & 30 & 100 \\ 
+  0.2 & Fully & 28 & 100 \\ 
+  0.3 & Unconnected & 47 & 100 \\ 
+  0.3 & Minimally & 94 & 100 \\ 
+  0.3 & Fully & 88 & 100 \\ 
+  0.4 & Unconnected & 75 & 100 \\ 
+  0.4 & Minimally & 97 & 100 \\ 
+  0.4 & Fully & 99 & 100 \\ 
+   \bottomrule
+\end{tabular}
+\endgroup
+\end{table}
+
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