Approximate matching of scientific names

This vignette explains how search_avesperu() handles likely spelling variants in submitted scientific names. Start with a conservative threshold and review every non-exact match before using it in an analysis.

Requirements

All examples use the local checklist bundled with avesperu; they do not call external services.

Match a short list with spelling variants

submitted <- c("Falco sparverius", "Tinamus osgodi", "Crypturellus sooui", "Penelope albipenis")
matches <- search_avesperu(submitted, max_distance = 0.05, return_details = TRUE)
matches[, c("name_submitted", "accepted_name", "dist")]
#>       name_submitted       accepted_name dist
#> 1   Falco sparverius    Falco sparverius    0
#> 2     Tinamus osgodi     Tinamus osgoodi    1
#> 3 Crypturellus sooui   Crypturellus soui    1
#> 4 Penelope albipenis Penelope albipennis    1

dist is the edit distance between a submitted value and its candidate. A value of zero denotes an exact match; values above zero require review.

Choose a threshold

max_distance accepts either a proportion between zero and one or a nonnegative integer. A proportion scales with name length, while an integer sets an absolute number of character edits.

# Exact matching only
search_avesperu(submitted, max_distance = 0, return_details = TRUE)

# Allow up to one character edit
search_avesperu(submitted, max_distance = 1, return_details = TRUE)

# Allow 10% of the name length
search_avesperu(submitted, max_distance = 0.1, return_details = TRUE)

Escalate carefully

First identify names that remain unmatched, then retry only those rows using a documented threshold. Preserve the original submission and inspect each suggested match before updating source data.

strict <- search_avesperu(submitted, max_distance = 0, return_details = TRUE)
unmatched <- strict$name_submitted[is.na(strict$accepted_name)]
retry <- search_avesperu(unmatched, max_distance = 0.1, return_details = TRUE)

Next steps

See advanced use for a field-data workflow and the function reference for all arguments.