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Integrated occurrence dataset for three example species

Source: R/data.R
occurrences.Rd

A harmonized, multi-source occurrence dataset containing cleaned georeferenced records for three species:

  • Araucaria angustifolia (Parana pine)

  • Cyanocorax caeruleus (Azure jay)

  • Handroanthus serratifolius (Yellow trumpet tree)

Records were retrieved from GBIF, speciesLink, BIEN, and iDigBio, standardized through the package workflow, merged, and cleaned to remove duplicates.

Usage

occurrences

Format

A data frame where each row represents a georeferenced occurrence record for one of the three species.

Columns correspond to the standardized output of format_columns(), including:

  • species: Cleaned binomial species name

  • decimalLongitude, decimalLatitude: Coordinates

  • year: Year of collection/observation

  • Various taxonomic, temporal, locality, and metadata fields

  • Source identifiers added by format_columns() (e.g., data_source)

See also

format_columns(), bind_here(), flag_duplicates(), remove_flagged()

Examples

# Show the first rows
head(occurrences)
#>   record_id                species catalogNumber decimalLongitude
#> 1   gbif_83 Araucaria angustifolia     323502165        -49.26743
#> 2   gbif_85 Araucaria angustifolia     325575408        -42.49838
#> 3   gbif_86 Araucaria angustifolia     325217148        -42.53397
#> 4   gbif_90 Araucaria angustifolia     322837754        -49.66112
#> 5   gbif_91 Araucaria angustifolia     322601546        -46.68649
#> 6   gbif_92 Araucaria angustifolia     276301823        -49.38901
#>   decimalLatitude country  stateProvince locality year     basisOfRecord
#> 1       -25.42535      BR         Paraná          2025 HUMAN_OBSERVATION
#> 2       -22.30930      BR Rio de Janeiro          2025 HUMAN_OBSERVATION
#> 3       -22.06159      BR Rio de Janeiro          2025 HUMAN_OBSERVATION
#> 4       -27.18439      BR Santa Catarina          2025 HUMAN_OBSERVATION
#> 5       -23.33256      BR      São Paulo          2025 HUMAN_OBSERVATION
#> 6       -25.59535      BR         Paraná          2025 HUMAN_OBSERVATION
#>   occurrenceRemarks habitat                             datasetName data_source
#> 1                           iNaturalist research-grade observations        gbif
#> 2                           iNaturalist research-grade observations        gbif
#> 3                           iNaturalist research-grade observations        gbif
#> 4                           iNaturalist research-grade observations        gbif
#> 5                           iNaturalist research-grade observations        gbif
#> 6                           iNaturalist research-grade observations        gbif

# Number of occurrences per species
table(occurrences$species)
#> 
#>     Araucaria angustifolia       Cyanocorax caeruleus 
#>                        924                       1035 
#> Handroanthus serratifolius 
#>                       2121