An R package to facilitate access and analysis of the Database of European Forest Insect and Disease Disturbances (DEFID2).
The DEFID2 initiative is an attempt to collect, harmonize and distribute in a standardized way data on biotic disturbances that have affected European forests. The effort is coordinated by the JRC and version 1.0 of the database received data contributions from 22 organization, covering 8 countries. The defid2R package facilitates data access and analysis.
Tutorials, documentation and additional resources • Functionalities • Installing • Contributing • How to cite
Tutorials, documentation and additional resources
- Package documentation
- Database structure and data exploration
- Extracting “DEFID2 extension” variables in Google Earth Engine
- Scientific article presenting the DEFID2 initiative and dataset
- Forest and Tree Pests research at JRC
- DEFID2 dataset
Functionalities
Data download
When attaching the package for the first time with library(defid2R), the user will be prompted to download the DEFID2 database. The database is a sqlite file of about 400 MB. Data download is only required once and on every new session the local version of the database will be checked against the latest online version; in case a newer version is available, user will be prompted to upgrade it.
Data analysis
The main function of the package is read_defid(), it allows reading the data or a subset of it as a sf dataframe. Many analyses may not require the entire dataset (which can be rather large) to be loaded in memory. Multiple filters and field selection options are available, so that the right data subset can be queried an loaded and analysed.
Installing
The package can be installed from this repository using:
devtools::install_git('https://code.europa.eu/jrc-forest/defid2r')Note that it depends on sf, which depending on the platform and installation strategy is not always trivial to install. Therefore if installation of dependencies is not resolved automatically, refer to the sf installation instructions.
Contributing
I have data on biotic forest disturbances in Europe
If you want to contribute data, which may be included in the next release cycle of the DEFID2 database, send an e-mail to JRC-DEFID2@ec.europa.eu
I found a bug in the package or I want to suggest an improvement
Open an issue or send a merge request at https://code.europa.eu/jrc-forest/defid2r
How to cite
Research paper
Forzieri G, Dutrieux LP, Elia A, Eckhardt B, Caudullo G, Taboada FÁ, Andriolo A, Bălacenoiu F, Bastos A, Buzatu A, Castedo Dorado F, Dobrovolný L, Duduman M, Fernandez-Carillo A, Hernández-Clemente R, Hornero A, Ionuț S, Lombardero MJ, Junttila S, Lukeš P, Marianelli L, Mas H, Mlčoušek M, Mugnai F, Nețoiu C, Nikolov C, Olenici N, Olsson P, Paoli F, Paraschiv M, Patočka Z, Pérez-Laorga E, Quero JL, Rüetschi M, Stroheker S, Nardi D, Ferenčík J, Battisti A, Hartmann H, Nistor C, Cescatti A, Beck PSA (2023). The Database of European Forest Insect and Disease Disturbances: DEFID2. Global Change Biology
