add_cif {pammtools}

Add cumulative incidence function to data

Description

Add cumulative incidence function to data

Usage

add_cif(newdata, object, ...)

## Default S3 method:
add_cif(
  newdata,
  object,
  ci = TRUE,
  overwrite = FALSE,
  alpha = 0.05,
  n_sim = 500L,
  cause_var = "cause",
  time_var = NULL,
  ...
)

Arguments

newdata

A data frame or list containing the values of the model covariates at which predictions are required. If this is not provided then predictions corresponding to the original data are returned. If newdata is provided then it should contain all the variables needed for prediction: a warning is generated if not. See details for use with link{linear.functional.terms}.

object

a fitted gam object as produced by gam().

...

Further arguments passed to predict.gam and get_hazard

ci

logical. Indicates if confidence intervals should be calculated. Defaults to TRUE.

overwrite

Should hazard columns be overwritten if already present in the data set? Defaults to FALSE. If TRUE, columns with names c("hazard", "se", "lower", "upper") will be overwritten.

alpha

The alpha level for confidence/credible intervals.

n_sim

Number of simulations (draws from posterior of estimated coefficients) on which estimation of CIFs and their confidence/credible intervals will be based on.

cause_var

Character. Column name of the 'cause' variable.

time_var

Name of the variable used for the baseline hazard. If not given, defaults to "tend" for gam fits, else "interval". The latter is assumed to be a factor, the former numeric.