skbio.math.stats.ordination.CA.scores

CA.scores(scaling)[source]

Compute site and species scores for different scalings.

Parameters:

scaling : int

For a more detailed explanation of the interpretation, check Legendre & Legendre 1998, section 9.4.3. The notes that follow are quick recommendations.

Scaling type 1 maintains \(\chi^2\) distances between rows (sites): in the transformed space, the euclidean distances between rows are equal to the \(\chi^2\) distances between rows in the original space. It should be used when studying the ordination of sites. Rows (sites) that are near a column (species) have high contributions from it.

Scaling type 2 preserves \(\chi^2\) distances between columns (species), so euclidean distance between columns after transformation is equal to \(\chi^2\) distance between columns in the original space. It is best used when we are interested in the ordination of species. A column (species) that is next to a row (site) means that it is more abundant there.

Other types of scalings are currently not implemented, as they’re less used by ecologists (Legendre & Legendre 1998, p. 456).

In general, species appearing far from the center of the biplot and far from its edges will probably exhibit better relationships than species either in the center (may be multimodal species, not related to the shown ordination axes...) or the edges (sparse species...).

Returns:

OrdinationResults

Object that stores the computed eigenvalues, the proportion explained by each of them (per unit), transformed coordinates, etc.