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Manually override a single name in a reconciliation

Source: R/reconcile_accessors.R
reconcile_override.Rd

Apply a single hand-curated decision to a reconciliation object. Use this to accept a match the matching cascade rejected (typically a flagged fuzzy hit), remove a spurious match, or force a new mapping that the cascade missed. ("Cascade" here means the four-stage matching pipeline run by reconcile_tree() and reconcile_data() — exact, normalised, synonym, fuzzy — as described in ?prepR4pcm.) The override is recorded in the provenance log so that you and your reviewers can audit every manual decision.

Usage

reconcile_override(
  reconciliation,
  name_x,
  name_y = NULL,
  action = c("accept", "reject", "replace"),
  note = ""
)

Arguments

reconciliation

A reconciliation object.

name_x

A length-1 character vector. The name as it appears in source x (your data). Must match a value already present in mapping$name_x.

name_y

A length-1 character vector or NULL. The name in source y (the tree or reference dataset) that name_x should be mapped to. NULL is only valid when action = "reject".

action

A length-1 character vector. What the override does:

"accept" (default)

Confirm a proposed match. Use after reviewing a flagged fuzzy or synonym hit.

"reject"

Remove an existing match and return both names to the unresolved pool. Use when the cascade over-matched (e.g. an aggressive fuzzy score linked the wrong species).

"replace"

Set a new match, overwriting whatever the cascade produced for name_x.

note

A length-1 character vector. A short justification for the override, stored in the provenance log and in mapping$notes. Strongly recommended — future you will want to know why this decision was made.

Value

An updated reconciliation object. Unknown or ambiguous source names, absent target names, and targets assigned to another source raise an error before the mapping or override log is changed. The existing row for name_x is replaced with one whose match_type is "manual" and match_source is "user_override".

Details

For applying many overrides at once (e.g. from a curated CSV), see reconcile_override_batch(); for interactive decisions in the console, see reconcile_review(); for published taxonomy crosswalks, see reconcile_crosswalk().

See also

reconcile_override_batch() for bulk overrides; reconcile_suggest() for near-miss candidates; reconcile_crosswalk() for published taxonomy crosswalks.

Other reconciliation functions: reconcile_apply(), reconcile_augment(), reconcile_crosswalk(), reconcile_crosswalk_supplement(), reconcile_data(), reconcile_diff(), reconcile_export(), reconcile_mapping(), reconcile_merge(), reconcile_multi(), reconcile_override_batch(), reconcile_plot(), reconcile_report(), reconcile_review(), reconcile_splits_lumps(), reconcile_suggest(), reconcile_summary(), reconcile_to_trees(), reconcile_tree(), reconcile_trees()

Examples

data(avonet_subset)
data(tree_jetz)
rec <- reconcile_tree(avonet_subset, tree_jetz,
                      x_species = "Species1", authority = NULL)
#> ℹ Reconciling 919 data names vs 657 tree tips
#> ℹ Matching 919 x 657 names through 2 stages...
#> ℹ Stage 1/2: Exact matching...
#> ℹ Stage 2/2: Normalised matching (0 matched so far)...
#> ✔ Matched 657/919 data names to tree tips

# Record acceptance of an existing match after reviewing it
matched <- reconcile_mapping(rec)
matched <- matched[matched$in_x & matched$in_y, ]
if (nrow(matched) > 0) {
  rec <- reconcile_override(
    rec,
    name_x = matched$name_x[1],
    name_y = matched$name_y[1],
    note   = "Reviewed existing match"
  )
}
#> ✔ Override applied: 'Acanthiza apicalis' -> 'Acanthiza_apicalis' (accept)