simlr.parameters: Generate Parameter Grid for SIMLR Search

In stnava/ANTsR: ANTs in R: Quantification Tools for Biomedical Images

Generate Parameter Grid for SIMLR Search

Description

This function creates and optionally subsets all possible combinations of input parameters for use in a SIMLR grid search.

Usage

simlr.parameters(
  nsimlr_options,
  prescaling_options,
  objectiver_options,
  mixer_options,
  sparval_options,
  expBeta_options,
  positivities_options,
  optimus_options,
  constraint_options = list("none"),
  sparsenessAlg = list(NA),
  num_samples = 10,
  search_type = c("random", "deterministic", "full")
)

Arguments

nsimlr_options	A list of options for the 'nsimlr' parameter.
prescaling_options	A list of options for the 'prescaling' parameter.
objectiver_options	A list of options for the 'objectiver' parameter.
mixer_options	A list of options for the 'mixer' parameter.
sparval_options	A list of options for the 'sparval' parameter.
expBeta_options	A list of options for the 'ebber' parameter.
positivities_options	A list of options for the 'pizzer' parameter.
optimus_options	A list of options for the 'optimus' parameter.
constraint_options	A list of options for the 'constraint' parameter, default is 'list("none")'.
sparsenessAlg	A list of options for the 'sparsenessAlg' parameter, default is 'list(NA)'.
num_samples	if not full, then the size of the subset space
search_type	string vector either full random or deterministic

Value

A list containing all (or a subset of) combinations of the provided parameters. Each row in the data frame represents a unique combination of the parameters.

The columns of the returned data frame include:

• nsimlr: Values corresponding to the 'nsimlr' parameter.

• prescaling: Values corresponding to the 'prescaling' parameter.

• objectiver: Values corresponding to the 'objectiver' parameter.

• mixer: Values corresponding to the 'mixer' parameter.

• constraint: Values corresponding to the 'constraint' parameter.

• sparval: Values corresponding to the 'sparval' parameter.

• ebber: Values corresponding to the 'ebber' parameter.

• pizzer: Values corresponding to the 'pizzer' parameter.

• optimus: Values corresponding to the 'optimus' parameter.

Each row represents a specific set of parameters that can be passed to the 'simlr.search' function for evaluation. The returned data frame is intended for use in parameter tuning and optimization.

stnava/ANTsR documentation built on April 13, 2025, 4:10 a.m.