cv_scrnp: Estimates of CV SCNP

In nlpred: Estimators of Non-Linear Cross-Validated Risks Optimized for Small Samples

Description

This function computes K-fold cross-validated estimates of estimates of cross-validated sensitivity-constrained rate of negative prediction (SCRNP). This quantity can be interpreted as the rate of negative classification for a fixed constraint on the sensitivity of a prediction algorithm. Thus, if an algorithm has a high SCRNP, it will also have a high positive predictive value.

Usage

cv_scrnp(
  Y,
  X,
  K = 10,
  sens = 0.95,
  learner = "glm_wrapper",
  nested_cv = TRUE,
  nested_K = K - 1,
  parallel = FALSE,
  max_cvtmle_iter = 10,
  cvtmle_ictol = 1/length(Y),
  quantile_type = 8,
  prediction_list = NULL,
  ...
)

Arguments

Y	A numeric vector of outcomes, assume to equal 0 or 1.
X	A data.frame or matrix of variables for prediction.
K	The number of cross-validation folds (default is 10).
sens	The sensitivity constraint imposed on the rate of negative prediction (see description).
learner	A wrapper that implements the desired method for building a prediction algorithm.
nested_cv	A boolean indicating whether nested cross validation should be used to estimate the distribution of the prediction function. Default (TRUE) is best choice for aggressive learner's, while FALSE is reasonable for smooth learner's (e.g., logistic regression).
nested_K	If nested cross validation is used, how many inner folds should there be? Default (K-1) affords quicker computation by reusing training fold learner fits.
parallel	A boolean indicating whether prediction algorithms should be trained in parallel. Default to FALSE.
max_cvtmle_iter	Maximum number of iterations for the bias correction step of the CV-TMLE estimator (default 10).
cvtmle_ictol	The CV-TMLE will iterate max_cvtmle_iter is reached or mean of cross-validated efficient influence function is less than cvtmle_cvtmle_ictol.
quantile_type	Type of quantile estimator to be used. See quantile for description.
prediction_list	For power users: a list of predictions made by learner that has a format compatible with cvauc.
...	Other arguments, not currently used

Details

To estimate the SCRNP using K-fold cross-validation is problematic. If data are partitioned into K distinct groups, depending on the sample size and choice of K, the validation sample may be quite small. In order to estimate SCRNP, we require estimation of a quantile of the predictor's distribution. More extreme quantiles (which correspond to high sensitivity constraints) are difficult to estimate using few observations. Here, we estimate relevant nuisance parameters in the training sample and use the validation sample to perform some form of bias correction – either through cross-validated targeted minimum loss-based estimation, estimating equations, or one-step estimation. When aggressive learning algorithms are applied, it is necessary to use an additional layer of cross-validation in the training sample to estimate the nuisance parameters. This is controlled via the nested_cv option below.

Value

An object of class "scrnp".

est_cvtmle

cross-validated targeted minimum loss-based estimator of K-fold CV AUC

iter_cvtmle

iterations needed to achieve convergence of CVTMLE algorithm

cvtmle_trace

the value of the CVTMLE at each iteration of the targeting algorithm

se_cvtmle

estimated standard error based on targeted nuisance parameters

est_init

plug-in estimate of CV AUC where nuisance parameters are estimated in the training sample

est_empirical

the standard K-fold CV AUC estimator

se_empirical

estimated standard error for the standard estimator

est_onestep

cross-validated one-step estimate of K-fold CV AUC

se_onestep

estimated standard error for the one-step estimator

est_esteq

cross-validated estimating equations estimate of K-fold CV AUC (here, equivalent to one-step, since the estimating equation is linear in SCRNP)

se_esteq

estimated standard error for the estimating equations estimator (same as one-step)

folds

list of observation indexes in each validation fold

ic_cvtmle

influence function evaluated at the targeted nuisance parameter estimates

ic_onestep

influence function evaluated at the training-fold-estimated nuisance parameters

ic_esteq

influence function evaluated at the training-fold-estimated nuisance parameters

ic_empirical

influence function evaluated at the validation-fold estimated nuisance parameters

prediction_list

a list of output from the cross-validated model training; see the individual wrapper function documentation for further details

Examples

# simulate data
n <- 200
p <- 10
X <- data.frame(matrix(rnorm(n*p), nrow = n, ncol = p))
Y <- rbinom(n, 1, plogis(X[,1] + X[,10]))

# estimate cv scrnp of logistic regression
scrnp_ests <- cv_scrnp(Y = Y, X = X, K = 5, 
                       nested_cv = FALSE, 
                       learner = "glm_wrapper")

# estimate cv scrnp of random forest with nested 
# cross-validation for nuisance parameter estimation

scrnp_ests <- cv_scrnp(Y = Y, X = X, K = 5, 
                       nested_cv = TRUE, 
                       learner = "randomforest_wrapper")

nlpred documentation built on Feb. 24, 2020, 1:11 a.m.