overall_abnormality {abnormality}

Measure a Subject's Abnormality with Respect to a Reference Population

Description

Measure a Subject's Abnormality with Respect to a Reference Population

Usage

overall_abnormality(Subj, Ref, stopping_rule = "Kaiser-Guttman",
  dist_measure = "MAD", TVE = 1, k = 2)

Arguments

Subj

a vector of length n

Ref

an n x p matrix containing the reference population.

stopping_rule

the stopping rule to use when deciding the number of principal components to retain. Options include: c("Kaiser-Guttman", "brStick","TVE").

dist_measure

the aggregate distance measure to use. Options include: c("MAD", "Euclidean", Manhattan","RMSE", "Lk-Norm")

TVE

a numeric value between 0 and 1. The minimum total variance explained for the retained principal components. This will only be used if "TVE" is chosen as the stopping_rule.

k

the value of k if Lk-Norm is chosen as a distance measure

Value

An unbiased measure of overall abnormality of the subject as compared to the reference population based on the parameters supplied.

Examples

p = 100
Subj <- rep(1, p)
Reference_Population <- generate_correlated_matrix(100, p, corr = 0.75,constant_cov_matrix = TRUE)
overall_abnormality(Subj,Reference_Population)
overall_abnormality(Subj,Reference_Population,dist_measure = "Euclidean")
overall_abnormality(Subj,Reference_Population,stopping_rule = "TVE", TVE = .90)
overall_abnormality(Subj,Reference_Population,dist_measure = "Lk-Norm",k=.5,stopping_rule="brStick")