Continuous Phylogeography And Maps

Continuous phylogeography reconstructs coordinates at internal nodes and derives branchwise movement under a declared tree and spatial model. Bijux keeps coordinate estimates, uncertainty, movement rows, outlier diagnostics, exclusions, map geometry, and rendered HTML as linked but distinct artifacts.

flowchart LR
    tips["Tip coordinates<br/>units · uncertainty"]
    tree["Tree<br/>root · branch scale"]
    estimates["Node estimates<br/>radial uncertainty"]
    movement["Branch movement<br/>distance · rate · flags"]
    geometry["Marker and line<br/>ledgers"]
    map["HTML or vector<br/>projection"]

    tips --> estimates
    tree --> estimates --> movement --> geometry --> map

The Map Is The Final Projection, Not The Evidence

Continuous phylogeography has an inferential ladder. Each rung depends on the one before it and must remain independently reviewable.

Rung	Owned record	Interpretation boundary
admitted observations	source coordinates, precision, taxon matches, exclusions	locality data may be measured, aggregated, or uncertain
conditional reconstruction	node coordinates and uncertainty under one tree and spatial model	internal coordinates are estimates, not sampled locations
derived movement	branch distance and rate joined to branch time	a displacement is model-derived and does not identify a migration path
display geometry	projected markers, segments, wrapping, clipping	geometry may alter appearance without changing the scientific record
rendered map	HTML, vector, or raster presentation	visual prominence is not support, certainty, or effect size

A reviewer must be able to move backward from any line on the map to its geometry row, movement row, endpoint estimates, and admitted observations. Projection, antimeridian handling, and line simplification belong to the display contract; they must never rewrite the underlying coordinate ledger.

Owned Review Surfaces

Surface	Output identity
summarize_continuous_phylogeography	node coordinate estimates, branch movements, outliers, exclusions, warnings, and summary
summarize_continuous_phylogeography_map	map markers and lines derived from continuous-coordinate records
summarize_discrete_region_map	map geometry derived from named region states, not continuous inference
render_coordinate_movement_visualization	coordinate-space visualization tied to the movement ledger
render_geographic_map_html	interactive projection of admitted marker and line rows

The renderer does not fit a phylogeographic model. It consumes a structured geographic record.

Coordinate Admission

Record latitude and longitude columns, coordinate reference and units, precision, missing values, duplicated localities, range checks, and taxon reconciliation. Longitude wrapping and latitude bounds are semantic rules, not formatting preferences.

When several observations belong to one taxon, aggregation creates a new observation with its own uncertainty and weighting policy. A centroid is not a substitute for retained locality variation unless the scientific question declares that reduction.

Read Node And Branch Rows Separately

CoordinateEstimateRow identifies the node structurally and retains latitude, longitude, coordinate standard errors, radial standard error, confidence, and instability. CoordinateMovementBranchRow joins parent and child estimates to great-circle distance, branch length, rate where defined, support, and flag codes.

Distance and rate answer different questions. A long movement on a long branch may have a moderate rate; a short movement on a near-zero branch may have an unstable rate. Do not rank branches without retaining both quantities and the branch-time convention.

Govern Outliers Before Interpretation

Impossible jumps and robust outliers are diagnostic states. Retain the median, distance or rate threshold, flag codes, and every excluded coordinate. Removing flagged branches after seeing the map changes the movement population and requires a new identified analysis.

Flag state	Correct treatment
coordinate invalid	exclude before fitting with the reason retained
node estimate unstable	qualify every movement that depends on the node
distance outlier	retain in the main ledger and expose the registered sensitivity result
rate undefined	report distance without inventing a finite rate
jump geographically impossible under external knowledge	preserve the analytical result and separate the domain constraint

Maps Are Review Projections

Every marker and line must resolve to a node, branch, state or coordinate row, filter decision, and run identity. Style, viewport, colors, labels, and basemaps may change presentation; endpoints, included branches, support classes, or spatial transformations change the scientific projection.

A blank region on a map can mean no observations, exclusion, low support, a failed geometry record, or viewport omission. The map artifact must preserve which state applies rather than inviting visual inference.

Acceptance Record

Retain tree and coordinate-table checksums, taxon linkage, model and alpha, node estimates, radial uncertainty, branch lengths and units, movement rows, outlier policy, exclusions, marker/line ledgers, rendering configuration, and artifact inventory. Refuse an unqualified movement claim when coordinates, tree scale, node identity, or branch-time meaning is unresolved.