Chapter 2 Download Occurrence Data

Purpose:

  • Download and preview species occurrence records using iDigBio and gatoRs.

Created by ML Gaynor.

2.1 Load Required Packages

library(ridigbio)     # Interface to iDigBio API
library(gatoRs)       # Unified taxonomic/occurrence tools
library(leaflet)      # Interactive mapping

2.2 A) Download from iDigBio

Here we use ridigbio to download data. We show how you can search the iDigBio API for occurrence record by taxonomic designations.

# Search for specific species (Galax urceolata)
iDigBio_GU <- idig_search_records(rq = list(scientificname = "Galax urceolata"))

# Search for all Diapensiaceae occurrences (limit to 1000 for example)
iDigBio_GU_family <- idig_search_records(rq = list(family = "Diapensiaceae"), limit = 1000)

###
### Search the API with a geographic bounding box (e.g. Eastern USA extent)
###

# Search with a geographic bounding box (e.g., eastern USA extent)
rq_input <- list(
  scientificname = list(type = "exists"),
  family = "Diapensiaceae",
  geopoint = list(
    type = "geo_bounding_box",
    top_left = list(lon = -98.16, lat = 48.92),
    bottom_right = list(lon = -64.02, lat = 23.06)
  )
)
iDigBio_GU_family_USA <- idig_search_records(rq_input, limit = 1000)

# Save iDigBio results as CSV
write.csv(iDigBio_GU, "data/01_download/iDigBio_GU_2026_07_22.csv", row.names = FALSE)
write.csv(iDigBio_GU_family, "data/01_download/iDigBio_GU_family_2026_07_22.csv", row.names = FALSE)

2.3 B) Download Using gatoRs

# Define synonym lists for each focal species
Shortia_galacifolia <- c("Shortia galacifolia", "Sherwoodia galacifolia")
Galax_urceolata <- c("Galax urceolata", "Galax aphylla")
Pyxidanthera_barbulata <- c("Pyxidanthera barbulata", "Pyxidanthera barbulata var. barbulata")
Pyxidanthera_brevifolia <- c("Pyxidanthera brevifolia", "Pyxidanthera barbulata var. brevifolia")

# Use gatoRs to download records with resolved synonyms
gators_download(synonyms.list = Shortia_galacifolia,
                write.file = TRUE,
                filename = "data/01_download/raw/Shortia_galacifolia_raw_2026_07_22.csv")

gators_download(synonyms.list = Galax_urceolata,
                write.file = TRUE,
                filename = "data/01_download/raw/Galax_urceolata_raw_2026_07_22.csv")

gators_download(synonyms.list = Pyxidanthera_barbulata,
                write.file = TRUE,
                filename = "data/01_download/raw/Pyxidanthera_barbulata_raw_2026_07_22.csv")

gators_download(synonyms.list = Pyxidanthera_brevifolia,
                write.file = TRUE,
                filename = "data/01_download/raw/Pyxidanthera_brevifolia_raw_2026_07_22.csv")

2.4 C) Preview Downloaded Files

# Read one downloaded file
rawdf <- read.csv("data/01_download/raw/Shortia_galacifolia_raw_2026_07_22.csv")

# Preview columns and dimensions
names(rawdf)
nrow(rawdf)


# Visualize records interactively - The error message here indicates many points do not have long/lat values
leaflet(rawdf) %>%
  addTiles() %>%
  addMarkers(label = paste0(rawdf$longitude, ", ", rawdf$latitude))