spatiocoexistence.crowding package

spatiocoexistence.crowding.crowding_indices(x, y, species, status, radius, cell_size=0.0, dbh=None, focals=None, domain_x=0.0, domain_y=0.0, num_threads=8)

Python wrapper for calculating crowding indices using the Cython backend. If dbh is supplied, indices are weighted by basal area (BA). If trees are closer than 0.5 metres, they are treated as if 0.5 metres apart. Periodic boundary conditions are assumed. If focal individuals are supplied, only these are considered.

Parameters:

  • x (const double[:]) – x-coordinates of individuals.

  • y (const double[:]) – y-coordinates of individuals.

  • species (const long[:]) – Species IDs.

  • status (const int[:]) – Status codes.

  • radius (const double) – Neighborhood radius.

  • cell_size (double) – Grid cell size (optional).

  • dbh (const double[:]) – Diameter at breast height (optional).

  • focals (const long[:]) – Indices of focal individuals (optional).

  • domain_x (double) – Domain size in x (optional).

  • domain_y (double) – Domain size in y (optional).

  • num_threads (int) – Number of threads for parallel computation (optional).

Returns:

Tuple of arrays (CI_CS, CI_HS, CI_CS_dead, CI_HS_dead).

Return type:

tuple[array, array, array, array]

spatiocoexistence.crowding.crowding_individual(x_i, y_i, species_i, x, y, species, status, radius, cell_size, dbh=None, domain_x=0.0, domain_y=0.0)

Python wrapper for cy_crowding_individual.

Calculates crowding indices for a single focal individual.

Parameters:

  • x_i (const double) – x-coordinate of focal individual.

  • y_i (const double) – y-coordinate of focal individual.

  • species_i (const int) – Species ID of focal individual.

  • x (const double[:]) – x-coordinates of all individuals.

  • y (const double[:]) – y-coordinates of all individuals.

  • species (const long[:]) – Species IDs.

  • status (const int[:]) – Status codes.

  • radius (const double) – Neighborhood radius.

  • cell_size (double) – Grid cell size.

  • dbh (const double[:]) – Diameter at breast height (optional).

  • domain_x (double) – Domain size in x (optional).

  • domain_y (double) – Domain size in y (optional).

Returns:

Tuple of crowding indices (con, hetero, con_d, hetero_d).