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Update latex tutorial

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laduplessis committed Jun 1, 2017
1 parent f056d58 commit 8ed7feee4ce4ea754428857f2ffc93f9db1a14b0
Showing with 12 additions and 8 deletions.
  1. +12 −8 main.tex
@@ -25,18 +25,19 @@
\begin{center}

% Enter the name of your tutorial here
\textbf{\LARGE Skyline plots}\\\vspace{2mm}
\textbf{\LARGE Tutorial using BEAST v2.4.2}\\\vspace{2mm}

% Enter a short description of your tutorial here
\textbf{\textcolor{mycol}{\Large Inference of past population dynamics using Bayesian Coalescent Skyline
and Birth-Death Skyline plots.}}\\
\textbf{\textcolor{mycol}{\Large Skyline plots}}\\

\vspace{4mm}

% Enter the names of all the authors here
{\Large {\em Nicola F. Müller and Louis du Plessis}}
\end{center}

Inference of past population dynamics using Bayesian Coalescent Skyline
and Birth-Death Skyline plots.

%%%%%%%%%%%%%%%%%
% Tutorial body %
@@ -647,7 +648,7 @@ \subsubsection{Visualizing the Birth-Death Skyline
We will instead use the R package \lstinline!bdskytools! to plot the
output of the bdsky. The package is still in development and currently
not available over CRAN. Thus, we have to install the package directly
over GitHub:
over GitHub (note that you only have to install the package once):

\begin{lstlisting}
install.packages("devtools")
@@ -656,12 +657,15 @@ \subsubsection{Visualizing the Birth-Death Skyline
devtools::install_github("laduplessis/bdskytools")
\end{lstlisting}

To plot the results, we need to tell R where to find the
\lstinline!*.log! file of our run and load it into R (discarding 10\% of
samples as burn-in):
Once the package is installed we have to load the package into our R
workspace before we can use the functions in the package. To plot the
results, we need to tell R where to find the \lstinline!*.log! file of
our run and load it into R (discarding 10\% of samples as burn-in):

\begin{lstlisting}
fname <- <<Enter the path to your log file here>>
library(bdskytools)

fname <- "Replace this string with the path to your log file"
lf <- readLogfile(fname, burnin=0.1)
\end{lstlisting}

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