Compute cluster with partitioning around medoids (PAM)

Performs partitioning around medoids for every combination of method_pam and k and saves the results in the cypro object.

computePamCluster(
  object,
  variable_set,
  k,
  phase = NULL,
  method_pam = NULL,
  verbose = NULL,
  ...
)

Arguments

object	A valid cypro object.
variable_set	Character value. Denotes the variable set of interest. Use `getVariableSetNames()` to obtain all names of currently stored variable sets in your object.
k	Numeric vector. Denotes the numbers of clusters the pam-algorithm is supposed to assign return. Values must be bigger than 2.
phase	Character or numeric. If character, the ordinal value referring to the phase of interest (e.g. 'first', 'second' etc.). referring to the phase of interest or 'all'. If numeric, the number referring to the phase. If set to NULL takes the phase denoted as default with `adjustDefault()`. Ignored if the experiment design contains only one phase.
method_pam	Character vector (or value see details for more.) Denotes the algorithm of interest. Valid input options are 'euclidean' and 'manhattan'.
verbose	Logical. If set to TRUE informative messages regarding the computational progress will be printed. (Warning messages will always be printed.)
...	Additional arguments given to `cluster::pam()`.

An updated version of the input cypro-object.

As this function iterates over all valid combinations of method_pam and k both inputs can be specified as vectors.