test_clustering_methods {longmixr}

Try out different linkage methods

Description

In the final step, the consensus clustering performs a hierarchical clustering step on the consensus cluster. This function tries out different linkage methods and returns the corresponding clusterings. The outputs can be plotted like the results from longitudinal_consensus_cluster.

Usage

test_clustering_methods(
  results,
  use_methods = c("average", "ward.D", "ward.D2", "single", "complete", "mcquitty",
    "median", "centroid")
)

Arguments

results

clustering result of class lcc

use_methods

character vector of one or several items of average, ward.D, ward.D2, single, complete, mcquitty, median or centroid

Value

a list of elements, each element of class lcc. The entries are named after the used linkage method.

Examples

set.seed(5)
test_data <- data.frame(patient_id = rep(1:10, each = 4),
visit = rep(1:4, 10),
var_1 = c(rnorm(20, -1), rnorm(20, 3)) +
rep(seq(from = 0, to = 1.5, length.out = 4), 10),
var_2 = c(rnorm(20, 0.5, 1.5), rnorm(20, -2, 0.3)) +
rep(seq(from = 1.5, to = 0, length.out = 4), 10))
model_list <- list(flexmix::FLXMRmgcv(as.formula("var_1 ~ .")),
flexmix::FLXMRmgcv(as.formula("var_2 ~ .")))
clustering <- longitudinal_consensus_cluster(
data = test_data,
id_column = "patient_id",
max_k = 2,
reps = 3,
model_list = model_list,
flexmix_formula = as.formula("~s(visit, k = 4) | patient_id"))

clustering_linkage <- test_clustering_methods(results = clustering,
use_methods = c("average", "single"))
# not run
# plot(clustering_linkage[["single"]])
# end not run