Choosing a Sobol Estimator in Sobol4R

Introduction

Sobol4R provides a unified interface for global sensitivity analysis of deterministic and stochastic simulators. Several Monte Carlo estimators are available. They correspond to the classical helpers in the package, but are accessed through the single function sobol_indices().

This vignette explains:

which Sobol estimators are implemented in Sobol4R,
how they differ in terms of numerical properties,
why Jansen is used as the default in sobol_indices(),
how to work with both deterministic and stochastic models.

The goal is to make the choice of estimator explicit and reproducible, while remaining compatible with existing workflows based on .

Supported estimators

Sobol4R mirrors the main Monte Carlo estimators from the package: * sobol and sobol2007 for classical Saltelli type estimators, * soboljansen for the Jansen variance of differences estimator, * sobolEff for efficient radial sampling, * sobolmartinez for Martinez correlation based estimators.

All of these are exposed through the argument estimator in sobol_indices(). For example

sobol_indices(
  model      = ishigami_model,
  design     = sobol_design(n = 512, d = 3, quasi = TRUE),
  estimator  = "jansen",  # default
  replicates = 1L
)

In addition, you can still construct designs and call the estimators directly from . Sobol4R is designed to work well with both approaches.

Two complementary analysis paths

Sobol4R exposes two ways to compute global sensitivity indices, depending on your workflow and the level of control you require. * Reuse the estimators from the sensitivity package. You can generate designs with Sobol4R (or your own routines) and pass the matrices directly to sensitivity::sobol(), sensitivity::sobol2007(), sensitivity::soboljansen(), sensitivity::sobolEff(), or sensitivity::sobolmartinez(). Sobol4R provides autoplot() methods that visualise these objects without altering your existing code. * Use the in package estimators with built in Jansen support. The streamlined sobol_design() and sobol_indices() helpers generate the Saltelli type matrices, evaluate the model (including replicated runs for stochastic simulators), and return a unified sobol_result object. Sobol4R implements several estimators internally, including Jansen, Martinez and Saltelli. The default estimator is Jansen, chosen for its numerical robustness and stable behaviour with non centred or noisy outputs. Results can be summarised or plotted directly and may include bootstrap like quantiles when analysing stochastic simulators.

Comparison of estimators

Estimator	Implemented in	First order formula type	Total order formula type	Numerical stability	Sensitivity to non centred outputs	Works with stochastic simulators	Pros	Cons	Recommended usage
Jansen	sensitivity (soboljansen), Sobol4R (default)	Variance of differences	Variance of differences	High	Robust	Yes (with replicates)	Very stable, low bias, well suited to noisy or uncentered outputs, simple interpretation	Slightly higher variance than Martinez in some settings	Default choice for deterministic and stochastic models
Saltelli 2002 (`sobol`)	sensitivity, Sobol4R	Covariance based	Variance of differences	Low to medium	Requires centering (otherwise biased)	Not ideal unless centering is enforced	Classical, widely cited, matches early literature	Strongly biased without centering, unstable when Y has large mean	Legacy compatibility with early Saltelli style analyses
Saltelli 2007 (`sobol2007`)	sensitivity, Sobol4R	Improved covariance based	Variance of differences	Medium	Requires centering (built in centering possible)	Yes, but care is needed	More stable than 2002 version, matches `sensitivity::sobol2007`	Still less stable than Jansen or Martinez	When strict compatibility with Saltelli 2007 is needed
Martinez (`sobolmartinez`)	sensitivity, Sobol4R	Correlation based	Correlation based	Very high	Very robust	Yes	Low variance, stable, handles nonlinearities and interactions well	Slightly more complex for explanation	Excellent alternative to Jansen, suited to strongly nonlinear models
SobolEff (`sobolEff`)	sensitivity, Sobol4R	Efficient radial sampling	Same	High	Robust	Yes	Fewer model evaluations for a given precision, good for expensive models	Requires structured design, less standard in introductory texts	Efficient Sobol analysis when model evaluations are costly

Recommended default

Sobol4R uses the Jansen estimator as the default because: * it is numerically stable across a wide range of models, * it behaves well on non centred outputs, * it integrates naturally with stochastic simulators through the replication mechanism, * its variance of differences formulation avoids the conditioning issues that affect classical Saltelli estimators.

Alternative estimators such as Martinez or SobolEff remain available for users who require advanced properties. The sobol and sobol2007 variants ensure compatibility with historical analyses and existing code bases.

Practical guidance

In practice, the following rules of thumb are useful. * Start with Jansen for both deterministic and stochastic models. * Use Martinez as an alternative when you want very stable indices and are comfortable with correlation based formulas. * Use SobolEff if each model evaluation is expensive and you want to reduce the number of simulator runs. * Only use sobol or sobol2007 when you must reproduce legacy analyses or benchmark against published Saltelli style results.