Converts a distance matrix to either a similarity matrix or a `dist` object, depending on user preferences.
format_output(
dist_mat,
output_format,
similarity = FALSE,
similarity_transform = "linear"
)A matrix or `dist` object, depending on the selected format and similarity flag.
A symmetric matrix of pairwise distances.
Character string specifying output format:
"matrix", "dist", or "similarity".
Logical; if TRUE, converts distances to similarities.
Character string; either "linear" (default) or "sqrt".
When converting to similarity, two transformation formulas are supported to derive similarity from distance:
"linear", (default)$$\text{s}_{ij} = 1 - \delta_{ij}$$ This transformation directly inverts the distance into a similarity score.
"sqrt"$$\text{s}_{ij} = 1 - \delta_{ij}^2$$ This corresponds to a transformation from a metric that satisfies the Euclidean property: $$\delta_{ij} = \sqrt{1 - s_{ij}}$$ According to gower1986metricdbrobust, this transformation yields a metric that is more likely to preserve Euclidean structure in downstream analyses.
gower1986metricdbrobust