Read and Prepare Survival Data — read_survival

A helper function to read survival data from CSV or Excel files and prepare it for analysis with the Beta-Danish package. It automatically handles missing status columns by assuming all observations are complete (uncensored).

Usage

read_survival_data(file, time_col, status_col = NULL, covar_cols = NULL)

Arguments

file: Character string specifying the path to the file.
time_col: Character string specifying the name of the time/survival column.
status_col: Character string specifying the name of the event/censoring indicator column. If `NULL` (default), the function assumes all observations are uncensored and creates a status column filled with 1s.
covar_cols: Character vector specifying the names of covariate columns to keep. If `NULL` (default), no covariates are kept.

Value

A clean `data.frame` containing the `time`, `status`, and any specified covariates, ready to be passed to `fit_betadanish()`.

Details

The function checks the file extension to determine how to read the data. For `.xlsx` or `.xls` files, the `readxl` package must be installed. Missing values (`NA`) in the specified columns will cause those rows to be dropped with a warning.

Examples

tmp <- tempfile(fileext = ".csv")
example_data <- data.frame(
  survival_time = c(5, 8, 12, 16),
  status = c(1, 1, 0, 1)
)
write.csv(example_data, tmp, row.names = FALSE)
dat <- read_survival_data(tmp, time_col = "survival_time", status_col = "status")
unlink(tmp)