cal_PEHE | R Documentation |
This function calculates the PEHE based on the survival probability from a fitted ri-AFTBART model.
cal_PEHE(object, metric, time, LP, lambda, eta)
object |
An object from cal_survprob() function. |
metric |
A character string representing the metric to be calculated for PEHE. Only |
time |
A numeric value representing the time point used to calculate PEHE. |
LP |
A numeric vector corresponding to the true linear predictors for each treatment from the simulated data. |
lambda |
A numeric value representing the true follow up time for from the simulated data. |
eta |
A numeric value to induce proportional/non-proportional hazards assumption from the simulated data. |
A list with the following three components:
true: |
A numeric vector representing the true survival or rmst for each individual. |
predicted: |
A numeric vector representing the predicted survival or rmst for each individual. |
pehe: |
A numeric vector representing the calculated pehe. |
library(riAFTBART) lp_w_all <- c(".4*x1 + .1*x2 - .1*x4 + .1*x5", #' w = 1 ".2 * x1 + .2 * x2 - .2 * x4 - .3 * x5") #' w = 2 nlp_w_all <- c("-.5*x1*x4 - .1*x2*x5", #' w = 1 "-.3*x1*x4 + .2*x2*x5")#' w = 2 lp_y_all <- rep(".2*x1 + .3*x2 - .1*x3 - .1*x4 - .2*x5", 3) nlp_y_all <- rep(".7*x1*x1 - .1*x2*x3", 3) X_all <- c( "rnorm(10, 0, 0.5)",#' x1 "rbeta(10, 2, .4)", #' x2 "runif(10, 0, 0.5)",#' x3 "rweibull(10,1,2)", #' x4 "rbinom(10, 1, .4)"#' x5 ) set.seed(111111) data <- dat_sim( nK = 2, K = 5, n_trt = 3, X = X_all, eta = 2, lp_y = lp_y_all, nlp_y = nlp_y_all, align = FALSE, lp_w = lp_w_all, nlp_w = nlp_w_all, lambda = c(1000,2000,3000), delta = c(0.5,0.5), psi = 1, sigma_w = 1, sigma_y = 2, censor_rate = 0.1 ) data$LP_true[,1] data$lambda data$eta res <- riAFTBART_fit(M.burnin = 10, M.keep = 10, M.thin = 1, status = data$delta, y.train = data$Tobs, trt.train = data$w, trt.test = 1, x.train = data$covariates, x.test = data$covariates, cluster.id = data$cluster) res_cal_surv_prob <- cal_surv_prob(object = res, time.points = 1:max(data$Tobs), test.only = TRUE, cluster.id = data$cluster) res_cal_PEHE_survival <- cal_PEHE(object = res_cal_surv_prob, metric = "survival", time = 40, LP = data$LP_true[,1], lambda = data$lambda[1], eta = data$eta) res_cal_PEHE_rmst <- cal_PEHE(object = res_cal_surv_prob, metric = "rmst", time = 40, LP = data$LP_true[,1], lambda = data$lambda[1], eta = data$eta)
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