A function to choose a data-driven reference set.

A function to choose a data-driven reference set.

chooseRefSet(fitted_model, k, reference_set_size, constraint_fn)

Arguments

fitted_model

The output from radEmu::emuFit when applied to data with a constraint over all taxa.

k

The index of the column in the design matrix for which to choose the reference set.

reference_set_size

The size of the reference set if it is data-driven, default is set to 50. We recommend a reference set of size 30-100 for the best balance of computational efficiency and estimation precision.

constraint_fn

The constraint function (by default the smoothed median).

Value

A list including the set of taxa of size reference_set_size with the smallest absolute L2 norm of estimated log fold-differences for the specified covariate(s), relative to the smoothed median log fold-difference over all taxa. Also a vector of length p (the number of columns in the design matrix) of differences between the constraint function over log fold-differences across all taxa and the constraint function log fold-difference over the reference set. Also the estimated B matrix, with each row shifted according to the constraint over the new reference set.