Advanced use of avesperu

This vignette shows how to add current Peru-checklist information to a small set of field observations while preserving the submitted names for review.

Requirements

The examples use only data bundled with avesperu.

Validate a field list

field_data <- data.frame(observer = c("Observer A", "Observer B", "Observer A", "Observer C"), species = c("Amazilia amazilia", "Phaetornis guy", "Metallura tyrianthina", "Tangara chilensis"), count = c(2, 1, 3, 5))
details <- search_avesperu(field_data$species, return_details = TRUE)
field_data$accepted_name <- details$accepted_name
field_data$status <- details$status
field_data$family <- details$family_name
field_data
#>     observer               species count         accepted_name    status
#> 1 Observer A     Amazilia amazilia     2     Amazilis amazilia Residente
#> 2 Observer B        Phaetornis guy     1       Phaethornis guy Residente
#> 3 Observer A Metallura tyrianthina     3 Metallura tyrianthina Residente
#> 4 Observer C     Tangara chilensis     5     Tangara chilensis Residente
#>        family
#> 1 Trochilidae
#> 2 Trochilidae
#> 3 Trochilidae
#> 4  Thraupidae

Expected result: each submitted name remains associated with its accepted name, status, and family. Rows without an accepted name need manual review.

Identify endemic species

my_species <- c("Penelope albipennis", "Xenoglaux loweryi", "Falco sparverius")
results <- search_avesperu(my_species, return_details = TRUE)
results[results$status == "Endémico", c("accepted_name", "english_name", "family_name")]
#>         accepted_name         english_name family_name
#> 1 Penelope albipennis    White-winged Guan    Cracidae
#> 2   Xenoglaux loweryi Long-whiskered Owlet   Strigidae

This pattern is useful for filtering a submitted list, not for replacing a project-specific definition of endemism.

Review uncertain results

Qualified and hybrid inputs, as well as tied candidates, are retained for review. Detailed output includes audit attributes that describe reconciliation, execution, and the checklist reference.

result <- search_avesperu("Falco CF. sparverius", return_details = TRUE)
attr(result, "reconciliation")
attr(result, "execution")
attr(result, "reference")

Next steps

Use approximate matching for spelling variants, or inspect the reference documentation for complete function arguments.