evaluate_sample_k function

Evaluate sample k

This functions calculates three indices (Davies-Bouldin, Calinsky-Harabasz and average Silhouette score) for each k. Calculations are made for a single sample and for a default range of k that goes from 3 to 10.

evaluate_sample_k(
  data,
  sample_id,
  samples_col = "Sample",
  abundance_col = "Abundance",
  range = 3:10,
  with_plot = FALSE,
  ...
)

Arguments

• data: a data.frame with, at least, the classification, abundance and sample information for each phylogenetic unit.
• sample_id: String with name of the sample to apply this function.
• samples_col: String with name of column with sample names.
• abundance_col: string with name of column with abundance values. Default is "Abundance".
• range: The range of values of k to test, default is from 3 to 10.
• with_plot: If FALSE (default) returns a vector, but if TRUE will return a plot with the scores.
• ...: Extra arguments.

Returns

A data.frame (or plot) with several indices for each number of clusters.

Details

Note : To get the indices for all samples, use evaluate_k() instead.

Data input

This function takes a data.frame with a column for samples and a column for abundance (minimum), but can take any number of other columns. It will then filter the specific sample that you want to analyze. You can also pre-filter for your specific sample, but you still need to provide the sample ID (sample_id) and the table always needs a column for Sample and another for Abundance (indicate how you name them with the arguments samples_col and abundance_col).

Output options

The default option returns a data.frame with Davies-Bouldin, Calinsky-Harabasz and average Silhouette scores for each k. This is a simple output that can then be used for other analysis. However, we also provide the option to show a plot (set with_plot = TRUE).

Three indices are calculated by this function:

• Davies-Bouldin with check_DB();
• Calinsky-Harabasz with check_DB();
• average Silhouette score check_avgSil().

Examples

library(dplyr)
#
evaluate_sample_k(nice_tidy, sample_id = "ERR2044662")

# To change range
evaluate_sample_k(nice_tidy, sample_id = "ERR2044662", range = 4:11)

# To make simple plot
evaluate_sample_k(nice_tidy, sample_id = "ERR2044662", range = 4:11, with_plot =TRUE)

See Also

check_CH(), check_DB(), check_avgSil(), suggest_k(), evaluate_k()