Using-concrete

In concrete: Continuous-Time Competing Risks Estimation using Targeted Minimum Loss-Based Estimation (TMLE)

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>", 
  echo = TRUE, 
  eval = FALSE
)

PBC competing risks data example

library(concrete)
library(data.table)
set.seed(12345)
data <- as.data.table(survival::pbc)
data <- data[!is.na(trt), ][, trt := trt - 1]
data <- data[, c("time", "status", "trt", "age", "sex", "albumin")]

Baseline Intervention

ConcreteArgs <- formatArguments(DataTable = data,
                                EventTime = "time",
                                EventType = "status",
                                Treatment = "trt",
                                Intervention = 0:1,
                                TargetTime = 1500,
                                TargetEvent = 1:2,
                                MaxUpdateIter = 250,
                                CVArg = list(V = 10),
                                Verbose = FALSE)
ConcreteEst <- doConcrete(ConcreteArgs)
ConcreteOut <- getOutput(ConcreteEst)

Joint Intervention

data <- data[, trt2 := sample(0:1, .N, replace = TRUE, prob = c(0.3, .7))]
Intervention <- makeITT("A1" = data.frame(trt = rep_len(1, nrow(data)),
                                          trt2 = rep_len(1, nrow(data))),
                        "A0" = data.frame(trt = rep_len(0, nrow(data)),
                                          trt2 = rep_len(0, nrow(data))))

ConcreteArgs <- formatArguments(DataTable = data,
                                EventTime = "time",
                                EventType = "status",
                                Treatment = c("trt", "trt2"),
                                Intervention = Intervention,
                                TargetTime = 2000,
                                TargetEvent = 1:2,
                                MaxUpdateIter = 250,
                                CVArg = list(V = 10),
                                Verbose = FALSE)
ConcreteEst <- doConcrete(ConcreteArgs)
ConcreteOut <- getOutput(ConcreteEst)

concrete documentation built on Sept. 10, 2023, 5:06 p.m.