| title | short_title | year | notes-after-punctuation | class | section | author | institutions | abstract | |||||||||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Example article title |
Short title |
2019 |
false |
Research Article |
Genome Analysis |
|
|
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turpis, facilisis a cursus eget, semper quis dolor. Integer varius est ipsum,
porttitor ornare eros placerat eget. Nulla aliquet nisi arcu, sed vestibulum
urna faucibus pretium. Maecenas laoreet diam non urna tincidunt iaculis a ut ex.
Aenean sem enim, laoreet id accumsan sed, faucibus vitae diam. Aenean facilisis
tincidunt risus. Mauris sit amet hendrerit est, sit amet maximus augue.
|
Cite papers using brackets and bibtex keys. Example citation:
[@Sheffield2016] will be rendered like this [@Sheffield2016]. Use semicolons to separate multiple citations [@Sheffield2016; @Sheffield2018].
Refer to a figure using figure labels, so they are numbered automatically, like
this: \ref{abstract} (See Fig. \ref{abstract}). Wrap a figure using the
pandoc-wrapfig extension by adding '{0}' to the end of the caption (Fig.
\ref{wrapped}).
{wrap=44mm}
Duis in tempor mauris, a lobortis nisl. Integer arcu lorem, vehicula sed ante commodo, maximus eleifend nisi. Aenean efficitur molestie lorem, ac pharetra felis euismod nec. Duis vitae ligula facilisis, dignissim justo eget, elementum est. Nulla quis mi a justo porta pellentesque eget sit amet purus. Ut ac vestibulum ante, in efficitur massa. Cras feugiat in urna facilisis ultrices. Nullam vestibulum, lacus eget pretium pharetra, augue ligula consectetur diam, eget condimentum ipsum magna sed augue.
{fullwidth=t}
Vivamus eu rhoncus neque. Quisque egestas venenatis odio a mattis. Ut ligula turpis, facilisis a cursus eget, semper quis dolor. Integer varius est ipsum, porttitor ornare eros placerat eget. Nulla aliquet nisi arcu, sed vestibulum urna faucibus pretium. Maecenas laoreet diam non urna tincidunt iaculis a ut ex. Aenean sem enim, laoreet id accumsan sed, faucibus vitae diam. Aenean facilisis tincidunt risus. Mauris sit amet hendrerit est, sit amet maximus augue.
\begin{table}[H] \centering\normalsize \begin{tabular}{cl} \toprule \textbf{Flag} & \textbf{Indication} \ \midrule 1 & CONTENT-ALL-A-IN-B \ 2 & CONTENT-ALL-B-IN-A \ 4 & LENGTHS-ALL-A-IN-B \ 8 & LENGTHS-ALL-B-IN-A \ 16 & NAMES-ALL-A-IN-B \ 32 & NAMES-ALL-B-IN-A \ 64 & CONTENT-A-ORDER \ 128 & CONTENT-B-ORDER \ \bottomrule \end{tabular} \caption{\textit{Table \label{params}\ref{params}:} \textbf{Compatibility flags} Parameter combinations used in the analysis and their results.} \label{params} \end{table}
You can do a two-column table using the \begin{table*} environment. See Table \ref{param_table}.
\begin{table*}[h] \centering\footnotesize \begin{tabular}{|l|l|l|l|p{2cm}|p{2cm}|p{2cm}|p{2cm}|} \hline parameter set & add & drop & shift & Jaccard mean & Coverage mean & Euclidean mean & Cosine mean \ \hline add1 & 0.1 & 0.0 & 0.0 & 0.909 & 0.981 & 0.939 & 0.988 \ \hline add2 & 0.2 & 0.0 & 0.0 & 0.833 & 0.964 & 0.914 & 0.977 \ \hline add3 & 0.3 & 0.0 & 0.0 & 0.769 & 0.951 & 0.895 & 0.966 \ \hline drop1 & 0.0 & 0.1 & 0.0 & 0.900 & 0.950 & 0.883 & 0.954 \ \hline drop2 & 0.0 & 0.2 & 0.0 & 0.800 & 0.900 & 0.834 & 0.905 \ \hline drop3 & 0.0 & 0.3 & 0.0 & 0.700 & 0.850 & 0.796 & 0.852 \ \hline shift1 & 0.0 & 0.0 & 0.2 & 0.941 & 0.902 & 0.979 & 0.998 \ \hline shift2 & 0.0 & 0.0 & 0.5 & 0.860 & 0.756 & 0.966 & 0.996 \ \hline shift3 & 0.0 & 0.0 & 0.8 & 0.785 & 0.610 & 0.957 & 0.994 \ \hline add_drop1 & 0.1 & 0.1 & 0.0 & 0.942 & 0.933 & 0.874 & 0.946 \ \hline add_drop2 & 0.1 & 0.2 & 0.0 & 0.840 & 0.886 & 0.831 & 0.901 \ \hline add_drop3 & 0.1 & 0.3 & 0.0 & 0.737 & 0.838 & 0.795 & 0.852 \ \hline add_drop4 & 0.2 & 0.1 & 0.0 & 0.783 & 0.920 & 0.865 & 0.939 \ \hline add_drop5 & 0.2 & 0.2 & 0.0 & 0.878 & 0.886 & 0.827 & 0.898 \ \hline add_drop6 & 0.2 & 0.3 & 0.0 & 0.772 & 0.828 & 0.795 & 0.852 \ \hline add_drop7 & 0.3 & 0.1 & 0.0 & 0.736 & 0.910 & 0.857 & 0.932 \ \hline add_drop8 & 0.3 & 0.2 & 0.0 & 0.693 & 0.867 & 0.824 & 0.894 \ \hline add_drop9 & 0.3 & 0.3 & 0.0 & 0.807 & 0.828 & 0.795 & 0.851 \ \hline shift_drop1 & 0.0 & 0.1 & 0.2 & 0.850 & 0.857 & 0.882 & 0.953 \ \hline shift_drop2 & 0.0 & 0.1 & 0.5 & 0.779 & 0.718 & 0.879 & 0.950 \ \hline shift_drop3 & 0.0 & 0.1 & 0.8 & 0.714 & 0.579 & 0.877 & 0.949 \ \hline shift_drop4 & 0.0 & 0.2 & 0.2 & 0.758 & 0.812 & 0.833 & 0.904 \ \hline shift_drop5 & 0.0 & 0.2 & 0.5 & 0.765 & 0.767 & 0.832 & 0.902 \ \hline shift_drop6 & 0.0 & 0.2 & 0.8 & 0.642 & 0.548 & 0.830 & 0.900 \ \hline shift_drop7 & 0.0 & 0.3 & 0.2 & 0.665 & 0.767 & 0.795 & 0.851 \ \hline shift_drop8 & 0.0 & 0.3 & 0.5 & 0.615 & 0.643 & 0.794 & 0.849 \ \hline shift_drop9 & 0.0 & 0.3 & 0.8 & 0.568 & 0.518 & 0.793 & 0.847 \ \hline \end{tabular} \caption{\textit{Table \label{param_table}\ref{param_table}:} \textbf{Parameter combinations used in the analysis and their results.}} \label{param_table} \end{table*}
You can use markdown tables, too...sort of. Pandoc renders markdown tables with the longtable package. But longtable is not compatible with a two-column template. So, there are a few hacks and workarounds, but nothing works really well. The best thing I have found works sometimes -- but then occasionally it just gobbles up text and figures silently. So, I suggest using latex templates until this issue is solved:
Another issue is that Captions are preceded by the Table keyword. Unfortunately, I can't figure out how to put the caption below the table (it's above it by default).
In hac habitasse platea dictumst. Mauris ut aliquet nunc, id mattis velit. Nunc commodo enim sed orci ultrices sodales. Fusce nec sem est. Nam euismod erat at neque facilisis iaculis. Cras rutrum elementum erat eu egestas. In sit amet est vitae ligula semper vestibulum sit amet quis justo. Sed porta dolor ac scelerisque congue.
Vivamus convallis arcu et lacus egestas tempus. Pellentesque habitant morbi tristique senectus et netus et malesuada fames ac turpis egestas. Integer eleifend efficitur risus sit amet suscipit. Curabitur consectetur sapien eget nulla maximus, quis lobortis nisl porta. Sed hendrerit semper placerat. Nulla sagittis orci arcu, a tincidunt lorem lacinia sit amet. Nullam nec fringilla odio. In mollis vitae nibh ut sollicitudin. Aliquam finibus tellus quis sollicitudin cursus. Cras lobortis, tortor ac sodales tempus, lacus ipsum aliquam mauris, sed placerat neque ante in arcu. Aliquam erat volutpat. Donec eu sodales odio, eu cursus libero.
Sed in porttitor leo. Class aptent taciti sociosqu ad litora torquent per conubia nostra, per inceptos himenaeos. Sed tristique malesuada ligula, vulputate commodo mi lacinia ut. Ut consectetur, mauris vitae hendrerit mattis, nisi urna condimentum nibh, vitae rhoncus nulla tellus sit amet dui. Vivamus tempus magna eget quam posuere interdum. Nulla turpis augue, consequat quis euismod a, tincidunt sed ligula. Integer ac iaculis lacus, nec posuere augue. Fusce vitae dictum felis. In hac habitasse platea dictumst. Etiam suscipit magna turpis, eget volutpat lectus placerat quis. Mauris sed cursus erat. Sed a pellentesque felis. Ut in blandit dolor, vitae lobortis justo. Aenean turpis felis, pulvinar fringilla vulputate et, venenatis in lorem. Donec vulputate, nunc non imperdiet ullamcorper, justo nunc placerat elit, ut pretium justo metus a mi.
You can insert latex in-line in the markdown document:
Or you can create separate environments like this:
These examples use the algorithmic environment (from the algorithmcx package:)
\begin{algorithmic}
\Require
\begin{algorithmic}[1] \Repeat \Comment{forever} \State this\Until{you die.} \end{algorithmic}
This example uses the algorithm environment:
\begin{algorithm}
\caption{Euclid’s algorithm}\label{euclid}
\begin{algorithmic}[1]
\Procedure{Euclid}{$a,b$}\Comment{The g.c.d. of a and b}
\State
Maecenas vitae sodales est, venenatis ullamcorper magna. Integer id orci ut arcu venenatis mattis. Pellentesque eget risus non lectus interdum efficitur. In pharetra odio in tellus eleifend commodo. Morbi facilisis mauris ac eros gravida pretium. Nam sit amet nisi massa. Morbi at turpis in leo dictum suscipit. Ut interdum, orci sed laoreet venenatis, odio dui consectetur tortor, sit amet vulputate ipsum neque ac ante. Vivamus vitae mi interdum, dignissim leo lobortis, ultricies leo. Aenean facilisis sagittis urna in blandit. Sed sit amet consectetur purus. Mauris bibendum efficitur magna, vitae egestas lacus pretium dignissim. Nullam eu magna est. Suspendisse vel lobortis metus.
Suspendisse potenti. Donec gravida ut mauris vel scelerisque. Nullam gravida maximus porttitor. Duis dictum nisl sed neque tristique sodales. Maecenas lacinia dolor eget ligula volutpat maximus. Etiam placerat lobortis enim ut iaculis. Orci varius natoque penatibus et magnis dis parturient montes, nascetur ridiculus mus. Fusce porta venenatis metus, vehicula sagittis ligula faucibus vel. Nunc nibh ipsum, vulputate sed bibendum non, euismod at sem. Praesent mi nulla, ornare vitae est a, euismod facilisis mauris.
Mauris a orci vehicula, aliquam orci in, cursus eros. Lorem ipsum dolor sit amet, consectetur adipiscing elit. Cras semper vel enim eu dapibus. Maecenas placerat arcu nec metus tincidunt pharetra. Aenean rhoncus lacinia elit et cursus. Ut et metus vel augue sagittis volutpat quis nec nisi. Ut massa nisi, maximus vitae faucibus ut, eleifend ut odio.
Nam aliquam ex non accumsan efficitur. Nullam vehicula lorem vitae porttitor pellentesque. Fusce a tristique mi, sed congue velit. Nullam at ornare quam. Proin hendrerit accumsan ipsum, sed viverra velit vehicula sit amet. Donec non lectus diam. Sed condimentum non velit vel suscipit. Sed odio ex, vestibulum ullamcorper odio sit amet, lobortis accumsan risus. Nulla facilisi. Mauris eleifend viverra metus, ac varius lacus scelerisque non.