R/RcppExports.R

In XuemeiDing/survival19: Deal with Stratified Cox Proportional Hazard Model

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

#'Split Patients' ID by Facility
#'
#'The compute_facility_idx function splits patients' ID by the facility ID they went to
#'
#'@param facility which facility each patient belongs to
#'@param num_facility number of facilities (strata)
#'
#'@export
compute_facility_idx <- function(facility, num_facility) {
    .Call('_survival19_compute_facility_idx', PACKAGE = 'survival19', facility, num_facility)
}

#'Split Patients of Event's ID by Facility
#'
#'This function finds patients of event's ID, and split them by the facility ID the patients went to
#'
#'@param delta event indicator
#'@param facility_idx a list of patients' ID produced by compute_facility_idx
#'
#'@export
compute_delta_facility <- function(delta, facility_idx) {
    .Call('_survival19_compute_delta_facility', PACKAGE = 'survival19', delta, facility_idx)
}

#'Compute Score and Information
#'
#'This function modifies Score vector and Information matrix given data and beta
#'
#'@param L1 Score vector
#'@param L2 Information matrix
#'@param delta_facility vector delta split by facility; delta: indicator of event
#'@param z design matrix
#'@param exp_z_beta exp(z beta)
#'@param facility_idx a list of patients' ID produced by compute_facility_idx
#'@param p number of parameters
#'@param N number of patients
#'
#'@export
ddloglik_stratify_C_fast <- function(L1, L2, delta_facility, z, exp_z_beta, facility_idx, p, N) {
    invisible(.Call('_survival19_ddloglik_stratify_C_fast', PACKAGE = 'survival19', L1, L2, delta_facility, z, exp_z_beta, facility_idx, p, N))
}

#'Estimate beta
#'
#'This function estimates beta in a stratified Cox proportional hazard model. You can also set facility to be
#'the same and model an unstratified Cox model with this function. Note: facility must be integer 1, or a
#'successive vector of integer from 1 to num_facility (number of facilities). String, float, or any other types
#'of facility must be converted to successive integers first. Missingness is not accepted, and the observations
#'must be ordered by time. Ties might affect the correctness.
#'
#'@param delta indicator vector of event
#'@param z design matrix
#'@param facility which facility each patient belongs to
#'@param num_facility number of facilities (strata)
#'@param tol tolerance of precision, when highest change in beta is lower than or equal to tol, iteration stops
#'
#'@return estimated beta
#'
#'@examples
#'set.seed(2019)
#'testdata = generate_data()
#'CoxC(testdata$delta, testdata$z, testdata$facility, testdata$num_facility, tol= 1.0e-6)
#'
#'@useDynLib survival19
#'@import Rcpp
#'
#'@export
CoxC <- function(delta, z, facility, num_facility, tol) {
    .Call('_survival19_CoxC', PACKAGE = 'survival19', delta, z, facility, num_facility, tol)
}