clustra_sil: clustra_sil: Prepare silhouette plot data for several k or for a previous clustra run

Description

Performs clustra runs for several k and prepares silhouette plot data. Computes a proxy silhouette index based on distances to cluster centers rather than trajectory pairs. The cost is essentially that of running clustra for several k as this information is available directly from clustra. Can also reuse a previous clustra run and produce data for a single silhouette plot.

Usage

clustra_sil(
  data,
  kv = NULL,
  starts = "random",
  mccores = 1,
  maxdf = 30,
  conv = c(10, 0),
  save = FALSE,
  verbose = FALSE
)

Value

Invisibly returns a list of length length(kv), where each element is a matrix with nrow(data) rows and three columns cluster, neighbor, silhouette. The matrix in each element of this list can be used to draw a silhouette plot. When the input was a completed clustra run, the output is a list with a single element for a single silhouette plot.

Arguments

data: A data.frame (see the data parameter of trajectories). Alternatively, the output from a completed clustra run can be used, in which case kv is left as NULL. See Details.
kv: Vector of clustra k values to run. If data is the output from a completed clustra run, leave kv as NULL.
starts: See clustra.
mccores: See trajectories.
maxdf: Fitting parameters. See trajectories.
conv: Fitting parameters. See trajectories.
save: Logical. When TRUE, save all results as file clustra_sil.Rdata.
verbose: Logical. When TRUE, information about each run of clustra is printed.

Details

When given the raw data as the first parameter (input data parameter of trajectories), kv specifies a vector of k parameters for clustra and produces data for silhouette plots of each of them. Alternatively, the input can be the output from a single clustra run, in which case data for a single silhouette plot will be made without running clustra.