mczyzj / pestrpra

RMarkdown extention to create PRA reports

pestrPRA

RMarkdown extension for bookdown to create PRA reports templates.

Installation

You can install and use pestrPRA development version from GitHub as follows:

devtools::install_github("mczyzj/pestrPRA")

Overview

Current, developmental versions supports template for:

• Express Pest Risk Analysis (see EPPO) in English;
• Express Pest Risk Analysis for Invasive Plants in English;
• polish version that combines elements from both templates (this approach is currently adopted for PRA in Poland, examples of polish PRA that were created without this package can be seen on plant quarantine site).

Why?

It is extremely hard to maintain nice looking, well formatted documents when you need to work with dozen other assessors / scientists when each of them is using different OS, document editor, etc. After few rounds your nice template in *.doc format looks like garbage and trying to make it work take ages. Working in LaTeX is not an option, since most of your coworkers find it to complicated to use. The one solution is to use RMarkdown, that allows easy document edition. The only problem is to begin with well formatted template -- which is not an easy task. Hopefully, now complete template for both english EPPO PRA as well as polish PRA template is available. Moreover all of templates that are currently in pestrPRA package converge to pdf and html format from one set of *.rmd files.

Usage

This package was tested and proven to correctly generate *.pdf files with Ubuntu 16.10 with TeX Live 2018 and 18.04 with TeX Live 2017. I cannot guarantee at the moment that ther is a way to make *.pdf under Windows, nevertheless *.html output should work.

You can create new folder with all the necessary files using RStudio menu > File > New file > RMarkdown > Template

or by using rmarkdown::draft() command, e.g.

    rmarkdown::draft("Hzea.Rmd", template = "eppo_pest_pdf", package = "pestrPRA")

Tables

Most important tables, that one should fill are stored in separate *.csv files. Their should be filled manualy, however some information, e.g.:

• hosts
• taxonomy
• preferred name, synonyms and common names
• distribution
• categorization

can be downloaded automaticaly from EPPO data services by using pestr package.

pestrpra's Issues

proper working directory

After installation, creating new rmarkdown file results in creating new subfolder where all the files are copied but wd is set to main folder. Also the index file is renamed with subfolder name.

Layout and graphics

This templates needs serious help from someone who understands colors, ux, graphic design, usability etc.

site render does not work

Site render does not work neither in main nor in subfolder. Bookdown render site works only with PDF.

no build book button nor book options in build settings

R studio does not recognize bookdown or markdown commands for folder created with this package.

css

HTML version is not formatted even the css file exists

Make connection with pestr package

Allow automatic creating tables with data from EPPO