Try out different linkage methods
Source:R/longitudinal_consensus_cluster.R
test_clustering_methods.Rd
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
orcentroid
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"))
#> 2 : *
#> 2 : *
#> 2 : *
clustering_linkage <- test_clustering_methods(results = clustering,
use_methods = c("average", "single"))
# not run
# plot(clustering_linkage[["single"]])
# end not run