Download the DEFID2 database — fd_pathogens

Download the Database of European Forest Insect and Disease Disturbances.

Usage

fd_pathogens_defid2(
  agent = "all",
  host = "all",
  symptoms = "all",
  country = "all",
  geometry = "polygon",
  quiet = FALSE
)

Arguments

agent: a character vector with the desired forest insect(s) and/or disease(s). The default 'all' retrieves every agent
host: a character vector with the desired host tree(s) species. The default 'all' retrieves every tree
symptoms: a character vector with the desired symptom(s). The default 'all' retrieves every symptom
country: a character vector with the desired country(ies). The default 'all' retrieves every country
geometry: a string with 'polygon' to retrieve polygon data, or 'point' to retrieve point data
quiet: if TRUE, suppress any message or progress bar

Value

sf object with MULTIPOLYGON or POINT geometry

Details

Data may be freely used for research, study, or teaching, but be cited appropriately (see references below).

This function will download the DEFID2 database to the temporary directory once per session. After it's downloaded, the queries to the database are faster than the first time.

Note that 99.6% of the observations correspond to Picea abies. Also, 99.3% of the observations are in Czechia.

The data comprises over 650,000 georeferenced records, which can be retrieved as points or polygons, representing insects and diseases that occurred between 1963 and 2021 in European Forests.

Please, cite the data with the reference below.

References

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

Examples

# \donttest{
# Get the entire database (takes some seconds/minutes)
defid2_sf <- fd_pathogens_defid2()
#> ℹ Downloading data...
#> ✔ Downloaded [34.4s]
#> 
#> ℹ Preparing data...
#> ✔ Prepared [9ms]
#> 

# Get data for Spain and Portugal
defid2_iberia_sf <- fd_pathogens_defid2(country = c("Spain", "Portugal"))
#> ℹ Downloading data...
#> ✔ Downloaded [5ms]
#> 
#> ℹ Preparing data...
#> ✔ Prepared [8ms]
#> 

# }