R/build_coxph.R

In YTLogos/exploratory: R package for Exploratory

#' coxph wrapper with do
#' @return deta frame which has coxph model
#' @param data Data frame to be used as data
#' @param formula Formula for coxph
#' @param ... Parameters to be passed to coxph function
#' @param keep.source Whether source should be kept in source.data column
#' @param augment Whether the result should be augmented immediately
#' @param group_cols A vector with columns names to be used as group columns
#' @param test_rate Ratio of test data
#' @param seed Random seed to control test data sampling
#' @export
build_coxph <- function(data, formula, ...){
  build_model(data = data,
              formula = formula,
              model_func = survival::coxph,
              reserved_colnames =  c(
                # model_coef can add following columns at the next step
                "y.level",
                "term",
                "estimate",
                "std_error",
                "t_ratio",
                "p_value",
                # model_stats can add following columns at the next step
                "edf",
                "deviance",
                "AIC",
                # prediction_survfit can add following columns at the next step
                "time",
                "n.risk",
                "n_risk",
                "n.event",
                "n_event",
                "n.censor",
                "n_censor",
                "estimate",
                "std.error",
                "std_error",
                "conf.high",
                "conf_high",
                "conf.low",
                "conf_low"
              ),
              ...)
}