Software for TSE Surveillance Report
Authors/Creators
-
1.
European Food Safety Authority
- 2. Open Analytics NV
Description
The bseReporing package contains software to produce a parametrized report (i.e. the European Union Summary Report on TSE surveillance) in R Markdown.
Additionally, it contains a web application allowing authorised users to view chapters online, manage/edit versions of chapters and export a custom selection of the chapters into Word. It also enables users to perform data validation on the input data provided by member states or on the entire raw input data. These data validations are summarised in downloadable PDF reports.
The source code is written as an R package. The web interface is written in R Shiny and contains a user manual written in PDF.
Included in this Zenodo entry are two .csv files with dummy (and masked) surveillance data. It can be used to test the source code.
Notes (English)
EU; en; tar.gz; han.bossier@openanalytics.eu
Technical info (English)
How to run the data validation on the dummy data?
To use the BSE/TSE source code, download the files:
- Full_Export_Report_TSE_2021.csv
- Full_Export_Report_TSE_2022.csv
- bseReporting_[latest_version].tar.gz
Put the .csv files in a folder accessible by R (e.g. /Documents/bse_tse/dummy_data)
Launch an R session and install the R package via
install.packages("bseReporting_[*].tar.gz", type = "source", repos = NULL)and load it via
library(bseReporting)Store the working directory to the folder created earlier:
path_to_dummy_data <- "FILL_IN"Then load the data via:
# The dummy data assumes the current year is 2022!
params <- get_rmd_params(
currentYear = 2022,
dockerVolume = path_to_dummy_data
)
If all is correctly set up, run the data validation section via:
run_review(params)
Files
Full_Export_Report_TSE_2021.csv
Additional details
Related works
- Cites
- Publication: 10.2903/sp.efsa.2024.EN-8595 (DOI)
Software
- Programming language
- R