Biological Cubes and Coupling

Within-cube synchrony asks how one process varies across space. Coupling asks how two aligned processes relate to each other, such as heat events followed by a biological response.

Rasterize Observations

bio_cube = v.rasterize_observations(
    observations,
    template=climate_cube,
    time_col="date",
    value_col="abundance",
    reducer="sum",
)

Missing observations stay as NaN. That keeps unobserved cells distinct from observed zeros.

Align to Climate

bio_aligned = (
    pipe(bio_cube)
    | v.align_cube(
        like=climate_cube,
        spatial_method="nearest",
        temporal_method="nearest",
        tolerance="15D",
    )
).unwrap()

Alignment metadata records the spatial and temporal methods used.

Build a Biological State

boom = (
    pipe(bio_aligned)
    | v.change_state(
        change="relative",
        threshold=0.5,
        lag="1Y",
        name="population_boom",
    )
).unwrap()

Compare With Climate

climate_biology = (
    pipe(hot_state)
    | v.sync_with(
        boom,
        synchrony="occurrence",
        spatial_relation="same_pixel",
        lags=["0D", "90D", "180D", "365D"],
    )
).unwrap()

Positive lags mean the right-hand cube is interpreted as responding after the left-hand climate cube. CubeDynamics does not currently publish a biological coupling figure because the repository does not yet carry a vetted, licensed biological observation fixture aligned to the climate grid. The API contract is documented here; a visual example should be added only with traceable real data.

Current Scope

v.sync_with currently supports same-pixel lagged occurrence coupling. The roadmap includes cross-location coupling, event graphs, permutation or null diagnostics, and sequence verbs, but those should wait until their statistical contracts are clear.