subsample_pairwise_aris {metasnf} | R Documentation |
Calculate pairwise adjusted Rand indices across subsamples of data
Description
Given a list of subsampled solutions data frames from
'batch_snf_subsamples()
, this function calculates the adjusted Rand
indices across all the subsamples of each solution. ARI calculation between
two subsamples only factors in observations that were present in both
subsamples.
Usage
subsample_pairwise_aris(subsample_solutions, verbose = FALSE)
Arguments
subsample_solutions |
A list of solutions data frames from
subsamples of the data. This object is generated by the function
|
verbose |
If TRUE, output progress to console. |
Value
A two-item list: "raw_aris", a list of inter-subsample pairwise ARI matrices (one for each full cluster solution) and "ari_summary", a data frame containing the mean and SD of the inter-subsample ARIs for each original cluster solution.
Examples
my_dl <- data_list(
list(subc_v, "subcortical_volume", "neuroimaging", "continuous"),
list(income, "household_income", "demographics", "continuous"),
list(pubertal, "pubertal_status", "demographics", "continuous"),
uid = "unique_id"
)
sc <- snf_config(my_dl, n_solutions = 5, max_k = 40)
my_dl_subsamples <- subsample_dl(
my_dl,
n_subsamples = 20,
subsample_fraction = 0.85
)
batch_subsample_results <- batch_snf_subsamples(
my_dl_subsamples,
sc
)
pairwise_aris <- subsample_pairwise_aris(
batch_subsample_results,
verbose = TRUE
)
# Visualize ARIs
ComplexHeatmap::Heatmap(
pairwise_aris$"raw_aris"[[1]],
heatmap_legend_param = list(
color_bar = "continuous",
title = "Inter-Subsample\nARI",
at = c(0, 0.5, 1)
),
show_column_names = FALSE,
show_row_names = FALSE
)
[Package metasnf version 2.1.2 Index]