setup: check_setup

In shapr: Prediction Explanation with Dependence-Aware Shapley Values

check_setup

Description

check_setup

Usage

setup(
  x_train,
  x_explain,
  approach,
  phi0,
  output_size = 1,
  max_n_coalitions,
  group,
  n_MC_samples,
  seed,
  feature_specs,
  type = "regular",
  horizon = NULL,
  y = NULL,
  xreg = NULL,
  train_idx = NULL,
  explain_idx = NULL,
  explain_y_lags = NULL,
  explain_xreg_lags = NULL,
  group_lags = NULL,
  verbose,
  iterative = NULL,
  iterative_args = list(),
  is_python = FALSE,
  testing = FALSE,
  init_time = NULL,
  prev_shapr_object = NULL,
  asymmetric = FALSE,
  causal_ordering = NULL,
  confounding = NULL,
  output_args = list(),
  extra_computation_args = list(),
  model_class,
  ...
)

Arguments

x_train	Matrix or data.frame/data.table. Data used to estimate the (conditional) feature distributions needed to properly estimate the conditional expectations in the Shapley formula.
x_explain	Matrix or data.frame/data.table. Features for which predictions should be explained.
approach	Character vector of length 1 or one less than the number of features. All elements should either be "gaussian", "copula", "empirical", "ctree", "vaeac", "categorical", "timeseries", "independence", "regression_separate", or "regression_surrogate". The two regression approaches cannot be combined with any other approach. See details for more information.
phi0	Numeric. The prediction value for unseen data, i.e., an estimate of the expected prediction without conditioning on any features. Typically set this equal to the mean of the response in the training data, but alternatives such as the mean of the training predictions are also reasonable.
output_size	Scalar integer. Specifies the dimension of the output from the prediction model for every observation.
max_n_coalitions	Integer. Upper limit on the number of unique feature/group coalitions to use in the iterative procedure (if iterative = TRUE). If iterative = FALSE, it represents the number of feature/group coalitions to use directly. The quantity refers to the number of unique feature coalitions if group = NULL, and group coalitions if group != NULL. max_n_coalitions = NULL corresponds to 2^n_features.
group	List. If NULL, regular feature-wise Shapley values are computed. If provided, group-wise Shapley values are computed. group then has length equal to the number of groups. Each list element contains the character vectors with the features included in the corresponding group. See Jullum et al. (2021) for more information on group-wise Shapley values.
n_MC_samples	Positive integer. For most approaches, it indicates the maximum number of samples to use in the Monte Carlo integration of every conditional expectation. For approach="ctree", n_MC_samples corresponds to the number of samples from the leaf node (see an exception related to the ctree.sample argument in setup_approach.ctree()). For approach="empirical", n_MC_samples is the K parameter in equations (14-15) of Aas et al. (2021), i.e. the maximum number of observations (with largest weights) that is used, see also the empirical.eta argument setup_approach.empirical().
seed	Positive integer. Specifies the seed before any code involving randomness is run. If NULL (default), no seed is set in the calling environment.
feature_specs	List. The output from get_model_specs() or get_data_specs(). Contains the three elements: labels Character vector with the names of each feature. classes Character vector with the classes of each feature. factor_levels Character vector with the levels for any categorical features.
type	Character. Either "regular" or "forecast", matching the function the call originated from, and thus the type of explanation to generate.
horizon	Numeric. The forecast horizon to explain. Passed to the predict_model function.
y	Matrix, data.frame/data.table or a numeric vector. Contains the endogenous variables used to estimate the (conditional) distributions needed to properly estimate the conditional expectations in the Shapley formula including the observations to be explained.
xreg	Matrix, data.frame/data.table or a numeric vector. Contains the exogenous variables used to estimate the (conditional) distributions needed to properly estimate the conditional expectations in the Shapley formula including the observations to be explained. As exogenous variables are used contemporaneously when producing a forecast, this item should contain nrow(y) + horizon rows.
train_idx	Numeric vector. The row indices in data and reg denoting points in time to use when estimating the conditional expectations in the Shapley value formula. If train_idx = NULL (default) all indices not selected to be explained will be used.
explain_idx	Numeric vector. The row indices in data and reg denoting points in time to explain.
explain_y_lags	Numeric vector. Denotes the number of lags that should be used for each variable in y when making a forecast.
explain_xreg_lags	Numeric vector. If xreg != NULL, denotes the number of lags that should be used for each variable in xreg when making a forecast.
group_lags	Logical. If TRUE all lags of each variable are grouped together and explained as a group. If FALSE all lags of each variable are explained individually.
verbose	String vector or NULL. Controls verbosity (printout detail level) via one or more of "basic", "progress", "convergence", "shapley" and "vS_details". "basic" (default) displays basic information about the computation and messages about parameters/checks. "progress" displays where in the calculation process the function currently is. "convergence" displays how close the Shapley value estimates are to convergence (only when iterative = TRUE). "shapley" displays intermediate Shapley value estimates and standard deviations (only when iterative = TRUE), and the final estimates. "vS_details" displays information about the v(S) estimates, most relevant for approach %in% c("regression_separate", "regression_surrogate", "vaeac"). NULL means no printout. Any combination can be used, e.g., verbose = c("basic", "vS_details").
iterative	Logical or NULL. If NULL (default), set to TRUE if there are more than 5 features/groups, and FALSE otherwise. If TRUE, Shapley values are estimated iteratively for faster, sufficiently accurate results. First an initial number of coalitions is sampled, then bootstrapping estimates the variance of the Shapley values. A convergence criterion determines if the variances are sufficiently small. If not, additional samples are added. The process repeats until the variances are below the threshold. Specifics for the iterative process and convergence criterion are set via iterative_args.
iterative_args	Named list. Specifies the arguments for the iterative procedure. See get_iterative_args_default() for description of the arguments and their default values.
is_python	Logical. Indicates whether the function is called from the Python wrapper. Default is FALSE, which is never changed when calling the function via explain() in R. The parameter is later used to disallow running the AICc versions of the empirical method, as that requires data-based optimization, which is not supported in shaprpy.
testing	Logical. Only used to remove random components, like timing, from the output when comparing with testthat. Defaults to FALSE.
init_time	POSIXct. The time when the explain() function was called, as returned by Sys.time(). Used to calculate the total time of the explain() call.
prev_shapr_object	shapr object or string. If an object of class shapr is provided, or a string with a path to where intermediate results are stored, then the function will use the previous object to continue the computation. This is useful if the computation is interrupted or you want higher accuracy than already obtained, and therefore want to continue the iterative estimation. See the general usage vignette for examples.
asymmetric	Logical. Not applicable for (regular) non-causal explanations. If FALSE (default), explain computes regular symmetric Shapley values. If TRUE, explain computes asymmetric Shapley values based on the (partial) causal ordering given by causal_ordering. That is, explain only uses feature coalitions that respect the causal ordering. If asymmetric is TRUE and confounding is NULL (default), explain computes asymmetric conditional Shapley values as specified in Frye et al. (2020). If confounding is provided, i.e., not NULL, then explain computes asymmetric causal Shapley values as specified in Heskes et al. (2020).
causal_ordering	List. Not applicable for (regular) non-causal or asymmetric explanations. causal_ordering is an unnamed list of vectors specifying the components of the partial causal ordering that the coalitions must respect. Each vector represents a component and contains one or more features/groups identified by their names (strings) or indices (integers). If causal_ordering is NULL (default), no causal ordering is assumed and all possible coalitions are allowed. No causal ordering is equivalent to a causal ordering with a single component that includes all features (list(1:n_features)) or groups (list(1:n_groups)) for feature-wise and group-wise Shapley values, respectively. For feature-wise Shapley values and causal_ordering = list(c(1, 2), c(3, 4)), the interpretation is that features 1 and 2 are the ancestors of features 3 and 4, while features 3 and 4 are on the same level. Note: All features/groups must be included in causal_ordering without duplicates.
confounding	Logical vector. Not applicable for (regular) non-causal or asymmetric explanations. confounding is a logical vector specifying whether confounding is assumed for each component in the causal_ordering. If NULL (default), no assumption about the confounding structure is made and explain computes asymmetric/symmetric conditional Shapley values, depending on asymmetric. If confounding is a single logical (FALSE or TRUE), the assumption is set globally for all components in the causal ordering. Otherwise, confounding must have the same length as causal_ordering, indicating the confounding assumption for each component. When confounding is specified, explain computes asymmetric/symmetric causal Shapley values, depending on asymmetric. The approach cannot be regression_separate or regression_surrogate, as the regression-based approaches are not applicable to the causal Shapley methodology.
output_args	Named list. Specifies certain arguments related to the output of the function. See get_output_args_default() for description of the arguments and their default values.
extra_computation_args	Named list. Specifies extra arguments related to the computation of the Shapley values. See get_extra_comp_args_default() for description of the arguments and their default values.
model_class	Character string. The class of the model object, e.g., "lm", "glm", "xgboost", etc. obtained by class(model)[1].
...	Further arguments passed to specific approaches, see below.

Value

An internal list containing parameters, info, data, and computations needed for later steps. The list is expanded and modified in other functions.

shapr documentation built on Aug. 25, 2025, 5:11 p.m.