In brian-j-smith/MachineShop: Machine Learning Models and Tools

Global Settings

Core default behaviors of functions in the package can be viewed or changed globally through the r rdoc_url("settings()") function. The function accepts one or more character names of settings to view, name = value pairs giving the values of settings to change, or a vector of these, with available settings summarized below.

control : function, function name, or object defining a default resampling method [default: "CVControl"].

cutoff : numeric (0, 1) threshold above which binary factor probabilities are classified as events and below which survival probabilities are classified [default: 0.5].

distr.SurvMeans : character string specifying distributional approximations to estimated survival curves for predicting survival means. Choices are "empirical" for the Kaplan-Meier estimator, "exponential", "rayleigh", or "weibull" (default).

distr.SurvProbs : character string specifying distributional approximations to estimated survival curves for predicting survival events/probabilities. Choices are "empirical" (default) for the Kaplan-Meier estimator, "exponential", "rayleigh", or "weibull".

grid : size argument to r rdoc_url("TuningGrid()") indicating the number of parameter-specific values to generate automatically for tuning of models that have pre-defined grids or a r rdoc_url("TuningGrid()") function, function name, or object [default: 3].

method.EmpiricalSurv : character string specifying the empirical method of estimating baseline survival curves for Cox proportional hazards-based models. Choices are "breslow" or "efron" (default).

metrics.ConfusionMatrix : function, function name, or vector of these with which to calculate performance metrics for confusion matrices [default: c(Accuracy = "accuracy", Kappa = "kappa2", `Weighted Kappa` = "weighted_kappa2", Sensitivity = "sensitivity", Specificity = "specificity")].

metrics.factor : function, function name, or vector of these with which to calculate performance metrics for factor responses [default: c(Brier = "brier", Accuracy = "accuracy", Kappa = "kappa2", `Weighted Kappa` = "weighted_kappa2", `ROC AUC` = "roc_auc", Sensitivity = "sensitivity", Specificity = "specificity")].

metrics.matrix : function, function name, or vector of these with which to calculate performance metrics for matrix responses [default: c(RMSE = "rmse", R2 = "r2", MAE = "mae")].

metrics.numeric : function, function name, or vector of these with which to calculate performance metrics for numeric responses [default: c(RMSE = "rmse", R2 = "r2", MAE = "mae")].

metrics.Surv : function, function name, or vector of these with which to calculate performance metrics for survival responses [default: c(`C-Index` = "cindex", Brier = "brier", `ROC AUC` = "roc_auc", Accuracy = "accuracy")].

print_max : number of models or data rows to show with print methods or Inf to show all [default: 10].

require : names of installed packages to load during parallel execution of resampling algorithms [default: "MachineShop"].

reset : character names of settings to reset to their default values.

RHS.formula : non-modifiable character vector of operators and functions allowed in traditional formula specifications.

stat.Curve : function or character string naming a function to compute one summary statistic at each cutoff value of resampled metrics in performance curves, or NULL for resample-specific metrics [default: "base::mean"].

stat.Resample : function or character string naming a function to compute one summary statistic to control the ordering of models in plots [default: "base::mean"].

stat.TrainingParams : function or character string naming a function to compute one summary statistic on resampled performance metrics for input selection or tuning or for model selection or tuning [default: "base::mean"].

stats.PartialDependence : function, function name, or vector of these with which to compute partial dependence summary statistics [default: c(Mean = "base::mean")].

stats.Resample : function, function name, or vector of these with which to compute summary statistics on resampled performance metrics [default: c(Mean = "base::mean", Median = "stats::median", SD = "stats::sd", Min = "base::min", Max = "base::max")].

A call to r rdoc_url("settings()") with "reset" will restore all package defaults and with no arguments will display the current values of all. Settings may also be supplied as a single unnamed argument which is a named list. Partial matching of setting names is supported. The setting value is returned if only one is specified to view. Otherwise, a list is returned with the values of specified settings as they existed prior to any requested changes. Such a list can be passed as an argument to r rdoc_url("settings()") to restore their values.

## Change settings
presets <- settings(control = "BootControl", grid = 10)

## View one setting
settings("control")

## View multiple settings
settings("control", "grid")

## Restore the previous settings
settings(presets)