## ----include = FALSE----------------------------------------------------------
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.width = 6,
  fig.height = 4
)
if (!requireNamespace("survival", quietly = TRUE) ||
    !requireNamespace("censored", quietly = TRUE)) {
  knitr::opts_chunk$set(eval = FALSE)
}

## ----setup--------------------------------------------------------------------
library(triageR)
library(survival)

## -----------------------------------------------------------------------------
lung_clean <- lung
lung_clean$status <- lung_clean$status - 1
lung_clean <- lung_clean[stats::complete.cases(lung_clean), ]

head(lung_clean[, c("time", "status", "age", "sex", "ph.karno")])

## -----------------------------------------------------------------------------
model_cox <- tr_fit_survival(
  lung_clean,
  time_col = "time",
  event_col = "status",
  engine = "cox_ph"
)

## ----eval = requireNamespace("aorsf", quietly = TRUE)-------------------------
model_rf <- tr_fit_survival(
  lung_clean,
  time_col = "time",
  event_col = "status",
  engine = "survival_rf"
)

## -----------------------------------------------------------------------------
val_cox <- tr_validate_survival(model_cox, newdata = lung_clean)

## ----eval = requireNamespace("aorsf", quietly = TRUE)-------------------------
val_rf <- tr_validate_survival(model_rf, newdata = lung_clean)

## -----------------------------------------------------------------------------
review_cox <- tr_agent_review(lung_clean, model_cox, use_agent = FALSE)

## ----eval = FALSE-------------------------------------------------------------
# tr_tripod_report(
#   model = model_cox,
#   model_type = "survival",
#   validation = val_cox,
#   review = review_cox,
#   output_file = file.path(tempdir(), "lung_survival_report"),
#   format = "html"
# )