metrics_list: Metrics implemented

In agapow/subtypr: Robust and Validated Patient Subtyping for Precision Medicine

Description

subtypr provide both internal and external metrics to evaluate clustering results.

Usage

metrics_list

Format

An object of class list of length 10.

Details

There is two versions of each metric. The raw version - directly accessible by the user - and a standardized version for the built-in functions of the package (the idea is that the result is numeric, e.g. for silhouette index, the value is the average silhouette width). The argument metric is always the name of the standardized version. You can access the standardized version with the get_metric function. To have all the names of the standardized metrics, use names(get_metric()).

Here we indicate the raw version documentation name and it's corresponding standardized version: like this: ?raw_version ~ "name_of_standardized_version"

Internal metrics:

• Silhouette index: ?silhouette_distance ~ "asw_distance" or ?silhouette_affinity ~ "asw_affinity"

External metrics:

• Adjusted Rand Index: ?adjusted_rand_index ~ "ari"

• Mutual Information: ?mutual_information ~ "mi"

• Normalized Mutual Information: ?normalized_mutual_information ~ "nmi"

• Meila's Variation Index: ?meila_vi ~ "meilaVI"

• Dunn index: ?dunn_index ~ "dunn"

• Homogeneity, Completeness & V-measure: ?homogeneity_completeness_vmeasure ~ "homogeneity" or "completeness" or "v_measure"

agapow/subtypr documentation built on May 5, 2019, 1:33 a.m.