RMarkdown extension for bookdown to create PRA reports templates.
You can install and use pestrPRA development version from GitHub as follows:
devtools::install_github("mczyzj/pestrPRA")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).
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.
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")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.