Build a settings matrix — generate_settings

The settings_matrix is a dataframe whose rows completely specify the hyperparameters and decisions required to transform individual input dataframes (found in a data_list, see ?generate_data_list) into a single similarity matrix through SNF. The format of the settings matrix is as follows:

A column named "row_id": This column is used to keep track of the rows and should have integer values only.
A column named "alpha": This column contains the value of the alpha hyperparameter that will be used on that run of the SNF pipeline.
A column named "k": Like above, but for the K (nearest neighbours) hyperparameter.
A column named "t": Like above, but for the t (number of iterations) hyperparameter.
A column named "clust_alg": Specification of which clustering algorithm will be applied to the final similarity matrix to identify patient subtypes. By default, this column can take on the integer values 1 or 2, which correspond to spectral clustering where the number of clusters is determined by the eigen-gap or rotation cost heuristic respectively. You can learn more about this parameter here: https://branchlab.github.io/metasnf/articles/clustering_algorithms.html.
A column named "cont_dist": Specification of which distance metric will be used for dataframes of purely continuous data. You can learn about this metric and its defaults here: https://branchlab.github.io/metasnf/articles/distance_metrics.html
A column named "disc_dist": Like above, but for discrete dataframes.
A column named "ord_dist": Like above, but for ordinal dataframes.
A column named "cat_dist": Like above, but for categorical dataframes.
A column named "mixed_dist": Like above, but for mixed-type (e.g., both categorical and discrete) dataframes.
One column for every input dataframe in the corresponding data_list which can either have the value of 0 or 1. The name of the column should be formatted as "inc_[]" where the square brackets are replaced with the name (as found in dl_summary(data_list)$"name") of each dataframe. When 0, that dataframe will be excluded from that run of the SNF pipeline. When 1, that dataframe will be included.

Usage

generate_settings_matrix(
  data_list,
  seed = NULL,
  nrows = 0,
  min_removed_inputs = 0,
  max_removed_inputs = length(data_list) - 1,
  dropout_dist = "exponential",
  min_alpha = NULL,
  max_alpha = NULL,
  min_k = NULL,
  max_k = NULL,
  min_t = NULL,
  max_t = NULL,
  alpha_values = NULL,
  k_values = NULL,
  t_values = NULL,
  possible_snf_schemes = c(1, 2, 3),
  clustering_algorithms = NULL,
  continuous_distances = NULL,
  discrete_distances = NULL,
  ordinal_distances = NULL,
  categorical_distances = NULL,
  mixed_distances = NULL,
  distance_metrics_list = NULL,
  snf_input_weights = NULL,
  snf_domain_weights = NULL,
  retry_limit = 10
)

Arguments

data_list: A nested list of input data from generate_data_list().
seed: (DEPRECATED) set the global seed. To ensure reproducible settings matrices are generated, manually call set.seed() prior to settings matrix generation instead of using this parameter.
nrows: Number of rows to generate for the settings matrix.
min_removed_inputs: The smallest number of input dataframes that may be randomly removed. By default, 0.
max_removed_inputs: The largest number of input dataframes that may be randomly removed. By default, this is 1 less than all the provided input dataframes in the data_list.
dropout_dist: Parameter controlling how the random removal of input dataframes should occur. Can be "none" (no input dataframes are randomly removed), "uniform" (uniformly sample between min_removed_inputs and max_removed_inputs to determine number of input dataframes to remove), or "exponential" (pick number of input dataframes to remove by sampling from min_removed_inputs to max_removed_inputs with an exponential distribution; the default).
min_alpha: The minimum value that the alpha hyperparameter can have. Random assigned value of alpha for each row will be obtained by uniformly sampling numbers between min_alpha and max_alpha at intervals of 0.1. Cannot be used in conjunction with the alpha_values parameter.
max_alpha: The maximum value that the alpha hyperparameter can have. See min_alpha parameter. Cannot be used in conjunction with the alpha_values parameter.
min_k: The minimum value that the k hyperparameter can have. Random assigned value of k for each row will be obtained by uniformly sampling numbers between min_k and max_k at intervals of 1. Cannot be used in conjunction with the k_values parameter.
max_k: The maximum value that the k hyperparameter can have. See min_k parameter. Cannot be used in conjunction with the k_values parameter.
min_t: The minimum value that the t hyperparameter can have. Random assigned value of t for each row will be obtained by uniformly sampling numbers between min_t and max_t at intervals of 1. Cannot be used in conjunction with the t_values parameter.
max_t: The maximum value that the t hyperparameter can have. See min_t parameter. Cannot be used in conjunction with the t_values parameter.
alpha_values: A number or numeric vector of a set of possible values that alpha can take on. Value will be obtained by uniformly sampling the vector. Cannot be used in conjunction with the min_alpha or max_alpha parameters.
k_values: A number or numeric vector of a set of possible values that k can take on. Value will be obtained by uniformly sampling the vector. Cannot be used in conjunction with the min_k or max_k parameters.
t_values: A number or numeric vector of a set of possible values that t can take on. Value will be obtained by uniformly sampling the vector. Cannot be used in conjunction with the min_t or max_t parameters.
possible_snf_schemes: A vector containing the possible snf_schemes to uniformly randomly select from. By default, the vector contains all 3 possible schemes: c(1, 2, 3). 1 corresponds to the "individual" scheme, 2 corresponds to the "domain" scheme, and 3 corresponds to the "twostep" scheme.
clustering_algorithms: A list of clustering algorithms to uniformly randomly pick from when clustering. When not specified, randomly select between spectral clustering using the eigen-gap heuristic and spectral clustering using the rotation cost heuristic. See ?generate_clust_algs_list for more details on running custom clustering algorithms.
continuous_distances: A vector of continuous distance metrics to use when a custom distance_metrics_list is provided.
discrete_distances: A vector of categorical distance metrics to use when a custom distance_metrics_list is provided.
ordinal_distances: A vector of categorical distance metrics to use when a custom distance_metrics_list is provided.
categorical_distances: A vector of categorical distance metrics to use when a custom distance_metrics_list is provided.
mixed_distances: A vector of mixed distance metrics to use when a custom distance_metrics_list is provided.
distance_metrics_list: List containing distance metrics to vary over. See ?generate_distance_metrics_list.
snf_input_weights: Nested list containing weights for when SNF is used to merge individual input measures (see ?generate_snf_weights)
snf_domain_weights: Nested list containing weights for when SNF is used to merge domains (see ?generate_snf_weights)
retry_limit: The maximum number of attempts to generate a novel row. This function does not return matrices with identical rows. As the range of requested possible settings tightens and the number of requested rows increases, the risk of randomly generating a row that already exists increases. If a new random row has matched an existing row retry_limit number of times, the function will terminate.

Value

settings_matrix A settings matrix