% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/3_4_validate_external.R
\name{validate_external}
\alias{validate_external}
\title{Externally validate high-dimensional Cox models with time-dependent AUC}
\usage{
validate_external(
  object,
  x,
  time,
  event,
  x_new,
  time_new,
  event_new,
  tauc.type = c("CD", "SZ", "UNO"),
  tauc.time
)
}
\arguments{
\item{object}{Model object fitted by \code{hdnom::fit_*()}.}

\item{x}{Matrix of training data used for fitting the model.}

\item{time}{Survival time of the training data.
Must be of the same length with the number of rows as \code{x}.}

\item{event}{Status indicator of the training data,
normally 0 = alive, 1 = dead.
Must be of the same length with the number of rows as \code{x}.}

\item{x_new}{Matrix of predictors for the external validation data.}

\item{time_new}{Survival time of the external validation data.
Must be of the same length with the number of rows as \code{x_new}.}

\item{event_new}{Status indicator of the external validation data,
normally 0 = alive, 1 = dead.
Must be of the same length with the number of rows as \code{x_new}.}

\item{tauc.type}{Type of time-dependent AUC.
Including \code{"CD"} proposed by Chambless and Diao (2006).,
\code{"SZ"} proposed by Song and Zhou (2008).,
\code{"UNO"} proposed by Uno et al. (2007).}

\item{tauc.time}{Numeric vector. Time points at which to evaluate
the time-dependent AUC.}
}
\description{
Externally validate high-dimensional Cox models with time-dependent AUC
}
\examples{
data(smart)
# Use the first 1000 samples as training data
# (the data used for internal validation)
x <- as.matrix(smart[, -c(1, 2)])[1:1000, ]
time <- smart$TEVENT[1:1000]
event <- smart$EVENT[1:1000]

# Take the next 1000 samples as external validation data
# In practice, usually use data collected in other studies
x_new <- as.matrix(smart[, -c(1, 2)])[1001:2000, ]
time_new <- smart$TEVENT[1001:2000]
event_new <- smart$EVENT[1001:2000]

# Fit Cox model with lasso penalty
fit <- fit_lasso(
  x, survival::Surv(time, event),
  nfolds = 5, rule = "lambda.1se", seed = 11
)

# External validation with time-dependent AUC
val.ext <- validate_external(
  fit, x, time, event,
  x_new, time_new, event_new,
  tauc.type = "UNO",
  tauc.time = seq(0.25, 2, 0.25) * 365
)

print(val.ext)
summary(val.ext)
plot(val.ext)

# # Test fused lasso, MCP, and Snet models
# data(smart)
# # Use first 600 samples as training data
# # (the data used for internal validation)
# x <- as.matrix(smart[, -c(1, 2)])[1:600, ]
# time <- smart$TEVENT[1:600]
# event <- smart$EVENT[1:600]
#
# # Take 500 samples as external validation data.
# # In practice, usually use data collected in other studies.
# x_new <- as.matrix(smart[, -c(1, 2)])[1001:1500, ]
# time_new <- smart$TEVENT[1001:1500]
# event_new <- smart$EVENT[1001:1500]
#
# flassofit <- fit_flasso(x, survival::Surv(time, event), nfolds = 5, seed = 11)
# scadfit <- fit_mcp(x, survival::Surv(time, event), nfolds = 5, seed = 11)
# mnetfit <- fit_snet(x, survival::Surv(time, event), nfolds = 5, seed = 11)
#
# val.ext1 <- validate_external(
#   flassofit, x, time, event,
#   x_new, time_new, event_new,
#   tauc.type = "UNO",
#   tauc.time = seq(0.25, 2, 0.25) * 365)
#
# val.ext2 <- validate_external(
#   scadfit, x, time, event,
#   x_new, time_new, event_new,
#   tauc.type = "CD",
#   tauc.time = seq(0.25, 2, 0.25) * 365)
#
# val.ext3 <- validate_external(
#   mnetfit, x, time, event,
#   x_new, time_new, event_new,
#   tauc.type = "SZ",
#   tauc.time = seq(0.25, 2, 0.25) * 365)
#
# print(val.ext1)
# summary(val.ext1)
# plot(val.ext1)
#
# print(val.ext2)
# summary(val.ext2)
# plot(val.ext2)
#
# print(val.ext3)
# summary(val.ext3)
# plot(val.ext3)
}
\references{
Chambless, L. E. and G. Diao (2006).
Estimation of time-dependent area under the ROC curve for long-term
risk prediction.
\emph{Statistics in Medicine} 25, 3474--3486.

Song, X. and X.-H. Zhou (2008).
A semiparametric approach for the covariate specific ROC curve with
survival outcome.
\emph{Statistica Sinica} 18, 947--965.

Uno, H., T. Cai, L. Tian, and L. J. Wei (2007).
Evaluating prediction rules for t-year survivors with censored
regression models.
\emph{Journal of the American Statistical Association} 102, 527--537.
}
