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Automate CSV typesetting for plot data sheets

DATE: 2020-01-20

AUTHOR: John L. Godlee

I am preparing for fieldwork right now. I'll be measuring trees in a number of one hectare plots. The trees in these plots have already been measured in the past so there is a large dataset in .csv format that I can use to help with the remeasurements.

In the past I would have printed this dataset using Excel, which means playing around with the annoying "Set Print Area" options and then battling with the Print dialog to get the options I need. This time I decided to use a combination of R and LaTeX tied together with a shell script to accomplish the same thing. Although it took me longer this time, I'll have the same workflow for next time which should make things a lot quicker in the long term.

I used R to format the data with the columns I wanted and then export the original dataset as a list of .csv files, one for each plot.

Then I wrote a template LaTeX file which can be fed a .csv file to render it as a table which spans multiple pages:

\documentclass[8pt,a4paper]{article}

\usepackage{pgfplotstable}
\usepackage{booktabs}
\usepackage{longtable}

\usepackage{geometry}
\geometry{left=1cm,
    right=1cm,
    top=1cm,
    bottom=1.6cm}

\input{filename_var.tex}

\begin{document}

\centering{\Large{\textbf{\name}}}

\pgfplotstabletypeset[
begin table=\begin{longtable},
end table=\end{longtable},
col sep=comma,
ignore chars={"},
every head row/.style={before row=\toprule,after row=\endhead\bottomrule},
every last row/.style={after row=\bottomrule},
display columns/0/.style={string type, column name={\textbf{Plotcode}}},
display columns/1/.style={string type, column name={\textbf{Plot ID}}},
display columns/2/.style={string type, column name={\textbf{Stem}}},
display columns/3/.style={string type, column name={\textbf{Tree}}},
display columns/4/.style={string type, column name={\textbf{Species}}},
display columns/5/.style={string type, column name={\textbf{DBH}}},
display columns/6/.style={string type, column name={\textbf{POM}}},
display columns/7/.style={string type, column name={\textbf{Alive}}}
]{plot_data_sheets/\file}

\end{document}

The pgfplotstable package allows me to pull in a csv file and render it as a table. In this case a longtable which can span multiple pages. I set the format and column name for each column with the display columns... lines and ensure that the header row appears at the start of every new page using the every head... and every last... lines. \input{filename_var.tex} sources a .tex file which provides the variables \file and \name, which give the full file name, and the file name without extension for the given .csv file.

I used a shell script to generate filename_var.tex and run pdflatex to render a .pdf for each of the .csv files:

#!/bin/sh

for i in plot_data_sheets/*.csv ; do
    file=$(basename -- "$i")
    name="${file%.*}"

    printf '%s\n' "\\newcommand{\\name}{$name}" "\\newcommand{\\file}{$file}" > filename_var.tex

    pdflatex --jobname="plot_data_sheets/$name" table_ex
    pdflatex --jobname="plot_data_sheets/$name" table_ex

    rm plot_data_sheets/*.aux
    rm plot_data_sheets/*.log
done

The .pdf files created at the end look like this:

Plot data sheet .pdf output

A .pdf version can be downloaded here[1].

1: /files/latex_csv/render.pdf