Utility Functions

These functions are for internal use. They can be accessed by appending the package name and a dot before the function name, e.g. ISCHIA.calculate_cooccurrence_matrix. Keep in mind that these functions can change their signature without warnings.

ISCHIA.calculate_cooccurrence_matrix — Function

Calculate the co-occurrence matrix N from a binary species-site matrix.

This function creates a species by species matrix of potential co-occurring sites (N) from a binary species by site matrix, where 1 represents potential occupancy, and 0 indicates species absence.

Arguments

  • mat::Matrix{Int}: A binary species by site matrix.

Returns

A species by species matrix where the upper triangle contains N for each species pair.

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ISCHIA.effect_sizes — Function
effect_sizes(cooccur; standardized=true)

Calculate effect sizes for co-occurrence analysis results.

Arguments

  • cooccur: A co-occurrence analysis object.
  • standardized: A boolean indicating whether to calculate standardized effect sizes.

Returns

Effect sizes as a data frame.

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