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Diffstat (limited to 'paper.tex')
| -rw-r--r-- | paper.tex | 86 |
1 files changed, 84 insertions, 2 deletions
@@ -14,7 +14,7 @@ %% report, while keeping modularity in the preambles. \input{tex/pipeline.tex} \input{tex/preamble-style.tex} -%\input{tex/preamble-biblatex.tex} +\input{tex/preamble-biblatex.tex} \input{tex/preamble-pgfplots.tex} \input{tex/preamble-necessary.tex} @@ -32,6 +32,88 @@ \maketitle -Data were taken from \url{\websurvey}. + +%% Begin the multi-column environment. A `*' means that all extra empty +%% space is added in the last column. +\begin{multicols}{2} + + + +%% -------- Delete this --------- +\section{Congratulations!} +Congratulations on running the reproduction pipeline! You can now follow +the checklist in the \texttt{README.md} file to customize this pipeline to +your exciting research project. + +Just don't forget to \emph{never} use any numbers or fixed strings (for +example database urls like \url{\websurvey}) directly within your \LaTeX{} +source. Read them directly from your configuration files or outputs of the +programs as part of the reproduction pipeline and import them into \LaTeX{} +as macros through the \texttt{tex/pipeline.tex} file. See the several +examples within the pipeline for a demonstration. For some recent +real-world examples, the reproduction pipelines for Sections 4 and 7.3 of +\citet{bacon17} are available at +\href{https://doi.org/10.5281/zenodo.1164774}{zenodo.1164774}\footnote{\url{https://gitlab.com/makhlaghi/muse-udf-origin-only-hst-magnitudes}}, +or +\href{https://doi.org/10.5281/zenodo.1163746}{zenodo.1163746}\footnote{\url{https://gitlab.com/makhlaghi/muse-udf-photometry-astrometry}}. Working +in this way, will let you focus clearly on your science and not have to +worry about fixing this or that number/name in the text. + +Just as a demonstration of creating plots within \LaTeX{} (using the +PGFPlots package), in Figure \ref{deleteme} we show a plot of +\deletemenum{} random points that were generated by this pipeline using the +text manipulation program {\small AWK} (which is not the best random number +generator, but just used here to generate some values). The minimum value +in this distribution is $\deletememin$ and $\deletememax$ is the maximum. + +The {\small PDF} file of Figure \ref{deleteme} is available in the +directory \texttt{\bdir/tex/build/tikz} and can be used in other contexts +(for example slides). If you want to directly use the PDF file in the +figure without having to let TiKZ decide if it should be remade or not, you +can also comment the \texttt{makepdf} macro at the top of this \LaTeX{} +source file. + +PGFPlots is a great tool to build the plots within \LaTeX{} and removes the +necessity to add further dependencies (to create the plots) to your +reproduction pipeline. High-level language libraries like Matplotlib do +exist to also generate plots. However, bare in mind that they require many +dependencies (Python, Numpy and etc). Installing these dependencies from +source (after several years when the binaries are no longer available in +common repositories), is not easy and will harm the reproducibility of your +paper. + +\begin{Figure} + \includetikz{delete-me} + + \captionof{figure}{\label{deleteme} A random set of values plotted as a + demonstration of how to generate plots within LaTeX.} +\end{Figure} + +Furthermore, since PGFPlots is built by \LaTeX{} it respects all the +properties of your text (for example line width and fonts and etc), so the +final plot blends in your paper much more nicely. It also has a wonderful +manual\footnote{\url{http://mirrors.ctan.org/graphics/pgf/contrib/pgfplots/doc/pgfplots.pdf}}. + + +\section{Notice and citations} +To encourage other scientists to publish similarly reproducible papers, +please add a notice close to the start of your paper or in the end of the +abstract clearly mentioning that your work is fully reproducible. + +For the time being, we haven't written a specific paper only for this +reproduction pipeline, so until then, we would be grateful if you could +cite the first paper that used the first version of this pipeline: +\citet{ai15}. + +After publication, don't forget to upload all the necessary data, software +source code and the reproduction pipeline to a long-lasting host like +Zenodo (\url{https://zenodo.org/}). + +%% ------------------------------ + + + +\printbibliography +\end{multicols} \end{document} |