Compute a distance matrix

Missing values are handled pairwise: each pair of samples is compared on the markers (or sites) both of them have.

Usage

compute_distance(d, method = NULL, sqrt_binary = FALSE, scale = TRUE)

Arguments

d

A cl_data object.

method

A method from distance_choices(); the default for the data type if NULL.

sqrt_binary

Use sqrt(1 - S) for binary measures.

scale

Scale numeric traits to unit variance before Euclidean or Manhattan distances.

Value

A dist object with a method attribute.

Details

Binary measures are returned as 1 minus the similarity. Set sqrt_binary = TRUE for the square root form that ade4::dist.binary() returns, which is Euclidean. For biallelic SNPs, IBS distance equals Prevosti's distance.

Examples

d <- clusnalyst_demo("binary")
dm <- compute_distance(d, "jaccard")