Produce an HTML file summarising a reconciliation object: provenance metadata, match-type breakdown, full mapping table, and a list of unresolved / flagged species. The file has no external dependencies (CSS is inlined), so it is suitable for sharing with collaborators, pasting into supplementary materials, or archiving next to analysis outputs.
Usage
reconcile_report(
reconciliation,
file,
title = "Reconciliation Report",
open = interactive()
)Arguments
- reconciliation
A reconciliation object returned by
reconcile_tree(),reconcile_data(), or a related matcher.- file
A length-1 character vector. Output file path. Must end in
.html.- title
A length-1 character vector. Report title shown at the top of the page. Default is generic.
- open
Logical. Open the finished report in the default browser? Defaults to
TRUEin interactive sessions,FALSEotherwise (so it does not block scripts).
Layout
The report opens with a run header (the originating
reconcile_tree() / reconcile_data() call, timestamp, package
version), the match-coverage summary, and a compact bar chart of
match composition. Below those, per-match-type detail tables
(normalised, synonym, fuzzy, flagged) and the unresolved-species
list make each decision auditable. The bird-workflow vignette
includes annotated screenshots of both sections.
See also
reconcile_summary() for a console equivalent;
reconcile_export() to additionally save aligned data and tree
files.
Other reconciliation functions:
reconcile_apply(),
reconcile_augment(),
reconcile_crosswalk(),
reconcile_data(),
reconcile_diff(),
reconcile_export(),
reconcile_mapping(),
reconcile_merge(),
reconcile_multi(),
reconcile_override(),
reconcile_override_batch(),
reconcile_plot(),
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
f <- tempfile(fileext = ".html")
reconcile_report(rec, file = f, open = FALSE)
#> ✔ Report written to /var/folders/7x/ytfpq14s0v18frbm9v_w9f4c0000gq/T//Rtmphv6sDQ/file2dc627ceed88.html
cat("Report written to:", f, "\n")
#> Report written to: /var/folders/7x/ytfpq14s0v18frbm9v_w9f4c0000gq/T//Rtmphv6sDQ/file2dc627ceed88.html