\documentclass[11pt]{article}
\usepackage{xcolor}
\usepackage[margin=2.5cm]{geometry}

\setlength\parindent{0pt}

\begin{document}
{\huge \textbf{cystiSim} // \Sexpr{gsub("\\%", "\\\\%", sim$main)}}

\section*{Settings}
\texttt{cystiSim} version \Sexpr{packageVersion("cystiSim")}

\begin{minipage}[t]{0.49\textwidth}
<<echo=1>>=
## transmission probabilities
cat("ph2m: ", formatC(sim$par$ph2m, format = "f", digits = 6), "\n")
cat("pl2m: ", formatC(sim$par$pl2m, format = "f", digits = 6), "\n")
cat("m2p:  ", formatC(sim$par$m2p, format = "f", digits = 6), "\n")
cat("e2p:  ", formatC(sim$par$e2p, format = "f", digits = 6))
@
\end{minipage}
\begin{minipage}{0.02\textwidth}
~
\end{minipage}
\begin{minipage}[t]{0.49\textwidth}
<<echo=1>>=
## efficacy, coverage
cat("eff_man_mda: ",
    formatC(sim$par$eff_man_mda, format = "f", digits = 2), "\n")
cat("cov_man_mda: ",
    formatC(sim$par$cov_man_mda, format = "f", digits = 2), "\n")
cat("eff_pig_mda: ",
    formatC(sim$par$eff_pig_mda, format = "f", digits = 2), "\n")
cat("cov_pig_mda: ",
    formatC(sim$par$cov_pig_mda, format = "f", digits = 2), "\n")
cat("eff_pig_vac: ",
    formatC(sim$par$eff_pig_vac, format = "f", digits = 2), "\n")
cat("cov_pig_vac: ",
    formatC(sim$par$cov_pig_vac, format = "f", digits = 2))
@
\end{minipage}

\section*{Model}
\Sexpr{knitr::knit_child(tmp)}

\section*{Results}
<<echo=FALSE, fig.height=5, fig.width=9>>=
plot(sim)
@

\end{document}
