R/RcppExports.R

In intsurv: Integrative Survival Modeling

# Generated by using Rcpp::compileAttributes() -> do not edit by hand
# Generator token: 10BE3573-1514-4C36-9D1C-5A225CD40393

rcpp_cIndex <- function(time, event, risk_score, weight) {
    .Call('_intsurv_rcpp_cIndex', PACKAGE = 'intsurv', time, event, risk_score, weight)
}

rcpp_coxph_cure <- function(time, event, surv_x, cure_x, cure_intercept = TRUE, bootstrap = 0L, surv_start = 0L, cure_start = 0L, surv_offset = 0L, cure_offset = 0L, surv_standardize = TRUE, cure_standardize = TRUE, maxit = 200L, epsilon = 1e-4, surv_maxit = 100L, surv_epsilon = 1e-4, cure_maxit = 100L, cure_epsilon = 1e-4, tail_completion = 1L, tail_tau = -1, pmin = 1e-5, verbose = 0L) {
    .Call('_intsurv_rcpp_coxph_cure', PACKAGE = 'intsurv', time, event, surv_x, cure_x, cure_intercept, bootstrap, surv_start, cure_start, surv_offset, cure_offset, surv_standardize, cure_standardize, maxit, epsilon, surv_maxit, surv_epsilon, cure_maxit, cure_epsilon, tail_completion, tail_tau, pmin, verbose)
}

rcpp_coxph_cure_reg <- function(time, event, surv_x, cure_x, cure_intercept, surv_l1_lambda, surv_l2_lambda, surv_penalty_factor, cure_l1_lambda, cure_l2_lambda, cure_penalty_factor, cv_nfolds, surv_start, cure_start, surv_offset, cure_offset, surv_standardize = TRUE, cure_standardize = TRUE, surv_varying_active = TRUE, cure_varying_active = TRUE, maxit = 200L, epsilon = 1e-4, surv_maxit = 100L, surv_epsilon = 1e-4, cure_maxit = 100L, cure_epsilon = 1e-4, tail_completion = 1L, tail_tau = -1, pmin = 1e-5, verbose = 0L) {
    .Call('_intsurv_rcpp_coxph_cure_reg', PACKAGE = 'intsurv', time, event, surv_x, cure_x, cure_intercept, surv_l1_lambda, surv_l2_lambda, surv_penalty_factor, cure_l1_lambda, cure_l2_lambda, cure_penalty_factor, cv_nfolds, surv_start, cure_start, surv_offset, cure_offset, surv_standardize, cure_standardize, surv_varying_active, cure_varying_active, maxit, epsilon, surv_maxit, surv_epsilon, cure_maxit, cure_epsilon, tail_completion, tail_tau, pmin, verbose)
}

rcpp_coxph_cure_vs <- function(time, event, surv_x, cure_x, cure_intercept, surv_lambda, surv_alpha, surv_nlambda, surv_lambda_min_ratio, surv_penalty_factor, cure_lambda, cure_alpha, cure_nlambda, cure_lambda_min_ratio, cure_penalty_factor, cv_nfolds, surv_start, cure_start, surv_offset, cure_offset, surv_standardize = TRUE, cure_standardize = TRUE, surv_varying_active = TRUE, cure_varying_active = TRUE, maxit = 200L, epsilon = 1e-4, surv_maxit = 100L, surv_epsilon = 1e-4, cure_maxit = 100L, cure_epsilon = 1e-4, tail_completion = 1L, tail_tau = -1, pmin = 1e-5, verbose = 0L) {
    .Call('_intsurv_rcpp_coxph_cure_vs', PACKAGE = 'intsurv', time, event, surv_x, cure_x, cure_intercept, surv_lambda, surv_alpha, surv_nlambda, surv_lambda_min_ratio, surv_penalty_factor, cure_lambda, cure_alpha, cure_nlambda, cure_lambda_min_ratio, cure_penalty_factor, cv_nfolds, surv_start, cure_start, surv_offset, cure_offset, surv_standardize, cure_standardize, surv_varying_active, cure_varying_active, maxit, epsilon, surv_maxit, surv_epsilon, cure_maxit, cure_epsilon, tail_completion, tail_tau, pmin, verbose)
}

rcpp_coxph_cure_mar <- function(time, event, surv_x, cure_x, cure_intercept = TRUE, bootstrap = 0L, surv_start = 0L, cure_start = 0L, surv_offset = 0L, cure_offset = 0L, surv_standardize = TRUE, cure_standardize = TRUE, maxit = 300L, epsilon = 1e-5, surv_maxit = 100L, surv_epsilon = 1e-4, cure_maxit = 100L, cure_epsilon = 1e-4, tail_completion = 1L, tail_tau = -1, pmin = 1e-5, verbose = 0L) {
    .Call('_intsurv_rcpp_coxph_cure_mar', PACKAGE = 'intsurv', time, event, surv_x, cure_x, cure_intercept, bootstrap, surv_start, cure_start, surv_offset, cure_offset, surv_standardize, cure_standardize, maxit, epsilon, surv_maxit, surv_epsilon, cure_maxit, cure_epsilon, tail_completion, tail_tau, pmin, verbose)
}

rcpp_coxph_cure_mar_reg <- function(time, event, surv_x, cure_x, cure_intercept, surv_l1_lambda, surv_l2_lambda, surv_penalty_factor, cure_l1_lambda, cure_l2_lambda, cure_penalty_factor, cv_nfolds, surv_start, cure_start, surv_offset, cure_offset, surv_standardize = TRUE, cure_standardize = TRUE, surv_varying_active = TRUE, cure_varying_active = TRUE, maxit = 200L, epsilon = 1e-4, surv_maxit = 100L, surv_epsilon = 1e-4, cure_maxit = 100L, cure_epsilon = 1e-4, tail_completion = 1L, tail_tau = -1, pmin = 1e-5, verbose = 0L) {
    .Call('_intsurv_rcpp_coxph_cure_mar_reg', PACKAGE = 'intsurv', time, event, surv_x, cure_x, cure_intercept, surv_l1_lambda, surv_l2_lambda, surv_penalty_factor, cure_l1_lambda, cure_l2_lambda, cure_penalty_factor, cv_nfolds, surv_start, cure_start, surv_offset, cure_offset, surv_standardize, cure_standardize, surv_varying_active, cure_varying_active, maxit, epsilon, surv_maxit, surv_epsilon, cure_maxit, cure_epsilon, tail_completion, tail_tau, pmin, verbose)
}

rcpp_coxph_cure_mar_vs <- function(time, event, surv_x, cure_x, cure_intercept, surv_lambda, surv_alpha, surv_nlambda, surv_lambda_min_ratio, surv_penalty_factor, cure_lambda, cure_alpha, cure_nlambda, cure_lambda_min_ratio, cure_penalty_factor, cv_nfolds, surv_start, cure_start, surv_offset, cure_offset, surv_standardize = TRUE, cure_standardize = TRUE, surv_varying_active = TRUE, cure_varying_active = TRUE, maxit = 200L, epsilon = 1e-4, surv_maxit = 200L, surv_epsilon = 1e-4, cure_maxit = 200L, cure_epsilon = 1e-4, tail_completion = 1L, tail_tau = -1, pmin = 1e-5, verbose = 0L) {
    .Call('_intsurv_rcpp_coxph_cure_mar_vs', PACKAGE = 'intsurv', time, event, surv_x, cure_x, cure_intercept, surv_lambda, surv_alpha, surv_nlambda, surv_lambda_min_ratio, surv_penalty_factor, cure_lambda, cure_alpha, cure_nlambda, cure_lambda_min_ratio, cure_penalty_factor, cv_nfolds, surv_start, cure_start, surv_offset, cure_offset, surv_standardize, cure_standardize, surv_varying_active, cure_varying_active, maxit, epsilon, surv_maxit, surv_epsilon, cure_maxit, cure_epsilon, tail_completion, tail_tau, pmin, verbose)
}

rcpp_coxph <- function(time, event, x, offset = 0L, start = 0L, standardize = TRUE, maxit = 200L, epsilon = 1e-4, verbose = 0L) {
    .Call('_intsurv_rcpp_coxph', PACKAGE = 'intsurv', time, event, x, offset, start, standardize, maxit, epsilon, verbose)
}

rcpp_coxnet1 <- function(time, event, x, l1_lambda, l2_lambda, penalty_factor, offset, start, varying_active = TRUE, standardize = TRUE, maxit = 200L, epsilon = 1e-4, verbose = 0L) {
    .Call('_intsurv_rcpp_coxnet1', PACKAGE = 'intsurv', time, event, x, l1_lambda, l2_lambda, penalty_factor, offset, start, varying_active, standardize, maxit, epsilon, verbose)
}

rcpp_coxnet2 <- function(time, event, x, lambda, alpha, nlambda, lambda_min_ratio, penalty_factor, offset, varying_active = TRUE, standardize = TRUE, maxit = 200L, epsilon = 1e-4, verbose = FALSE) {
    .Call('_intsurv_rcpp_coxnet2', PACKAGE = 'intsurv', time, event, x, lambda, alpha, nlambda, lambda_min_ratio, penalty_factor, offset, varying_active, standardize, maxit, epsilon, verbose)
}

rcpp_gen_cv_index <- function(nobs, nfolds, strata, static_train_index) {
    .Call('_intsurv_rcpp_gen_cv_index', PACKAGE = 'intsurv', nobs, nfolds, strata, static_train_index)
}

rcpp_logistic <- function(x, y, intercept = TRUE, offset = 0L, start = 0L, standardize = TRUE, maxit = 200L, epsilon = 1e-4, pmin = 1e-5, verbose = 0L) {
    .Call('_intsurv_rcpp_logistic', PACKAGE = 'intsurv', x, y, intercept, offset, start, standardize, maxit, epsilon, pmin, verbose)
}

rcpp_lognet1 <- function(x, y, l1_lambda, l2_lambda, penalty_factor, start, intercept = TRUE, standardize = TRUE, offset = 0L, varying_active = TRUE, maxit = 200L, epsilon = 1e-4, pmin = 1e-5, verbose = 0L) {
    .Call('_intsurv_rcpp_lognet1', PACKAGE = 'intsurv', x, y, l1_lambda, l2_lambda, penalty_factor, start, intercept, standardize, offset, varying_active, maxit, epsilon, pmin, verbose)
}

rcpp_lognet2 <- function(x, y, lambda, nlambda, lambda_min_ratio, alpha, penalty_factor, intercept = TRUE, offset = 0L, standardize = TRUE, varying_active = TRUE, maxit = 200L, epsilon = 1e-4, pmin = 1e-5, verbose = 0L) {
    .Call('_intsurv_rcpp_lognet2', PACKAGE = 'intsurv', x, y, lambda, nlambda, lambda_min_ratio, alpha, penalty_factor, intercept, offset, standardize, varying_active, maxit, epsilon, pmin, verbose)
}

rcpp_mcf_right <- function(time, event) {
    .Call('_intsurv_rcpp_mcf_right', PACKAGE = 'intsurv', time, event)
}

aggregateSum <- function(x, indices, simplify = TRUE, cumulative = FALSE, reversely = FALSE) {
    .Call('_intsurv_aggregateSum', PACKAGE = 'intsurv', x, indices, simplify, cumulative, reversely)
}

revcumsum <- function(x) {
    .Call('_intsurv_revcumsum', PACKAGE = 'intsurv', x)
}