Description Usage Arguments Value Examples
View source: R/boosting_function.R
This function allows you to use gradient boosting for variable selection.
1 2 3 | boosting_core(formula, data, rate, num_iter = 500,
control_method = NULL, control_parameter = NULL,
censoring_type = "right")
|
formula |
a formula object with a response value using the Surv function. |
data |
a data.frame containing all variables specified in the formula. |
rate |
the desired update rate used in the boosting algorithm. |
num_iter |
an integer used as the number of iterations of the boosting algorithm. Default value is 500. |
control_method |
specifies stopping method, options include: cv, num_selected, likelihood, BIC, AIC. Default is NULL, which will use a fixed number of iterations as specified by num_iter. |
control_parameter |
is a list with the parameter(s) needed for each corresponding control_method option, the options are "cv_folds", "early_stop", "EBIC_gamma", "num_select", and "likelihood_tol." For cv method "cv_folds" specifies the number of cross validation folds (default is 10). For EBIC and AIC methods, "early_stop" is a TRUE/FALSE value for early stopping (default is FALSE). An additional parameter for the EBIC method is "EBIC_gamma" that is used to specify the penalty term, should be a value between 0 and 1. If using num_selected method, "num_select" will be the desired number of variables to select, should be an integer. If using likelihood as the method, "likelihood_tol" will be the small change in likelihood in which to stop once reached (default is 0.001). |
censoring_type |
currently only right censoring is implemented. |
a list containing the vector of coefficients ("beta"), variable selection matrix that contains the coefficients at each iteration ("selection_df"), the number of boosting iterations ("mstop"), and other stopping criteria if applicable to selected method. If using method BIC or AIC, the information criteria for each iteration is returned as a vector ("Information Criteria"). If using cross validation for stopping the criteria used for stopping is returned as a numeric vector ("cvrisk").
1 2 3 4 5 6 | data <- simulate_survival_cox(true_beta=c(1,1,1,1,1,0,0,0,0,0))
formula <- as.formula("Surv(time,delta) ~ strata(strata_idx) + V1 + V2 +
V3 + V4 + V5 + V6 + V7 + V8 + V9 + V10" )
boosting_core(formula, data, rate=0.1, num_iter=500)
boosting_core(formula, data, rate=0.1, control_method="num_selected",
control_parameter=list(num_select = 5))
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