Data retrieval

Author

Juliana Stropp

Global Biodiversity Information Facility (GBIF)

Records of herbarium specimens of flowering plants collected in Guyana, Suriname, or French Guiana were retrieved from the GBIF.

Code

Load libraries:

library(rgbif)
library(dplyr)

Retrieve data:

# gbif_download <- occ_download(
#   pred_in("country", countries),
#   pred("taxonKey", "7707728"), # aNGIOSPERMS
#   pred("basisOfRecord", "PRESERVED_SPECIMEN"),
#   #pred("kingdom", "Plantae"),
#   #pred("phylum", "Tracheophyta"),
#   #pred("class", "Magnoliopsida"),
#   pred("hasGeospatialIssue", FALSE),
#   pred("hasCoordinate", TRUE),
#   format = "SIMPLE_CSV",
#   user = "YOUR USER NAME HERE",
#   pwd = "YOUR PASSWORD HERE",
#   email = "YOUR EMAIL HERE")
# 
# # Wait for the download to finish
# occ_download_wait(gbif_download)
#

Get download from GBIF into R:

# Get the download from GBIF
res <- occ_download_get(key="0000200-260129131611470", path= "../Data/GBIF", overwrite=TRUE)
# Import the data into R
gbif_Guianas<-occ_download_import(res)

totals<-gbif_Guianas %>% 
        group_by(family) %>% 
        summarise(N_genus = n_distinct(genus))


# Save file< only distinct ids
df_all<-gbif_Guianas %>%
          distinct(scientificName, .keep_all = TRUE)

 write.csv(df_all, "../Data/GBIF/GBIF_df_acc_and_synonyms.csv")