add_trans_prob: Add transition probabilities

In pammtools: Piece-Wise Exponential Additive Mixed Modeling Tools for Survival Analysis

Add transition probabilities

Description

Add (cumulative) hazard based on the provided data set and model. If ci=TRUE confidence intervals (CI) are also added. Their width can be controlled via the se_mult argument. The method by which the CI are calculated can be specified by ci_type. This is a wrapper around predict.gam. When reference is specified, the (log-)hazard ratio is calculated.

Usage

add_trans_prob(
  newdata,
  object,
  overwrite = FALSE,
  ci = FALSE,
  alpha = 0.05,
  nsim = 100L,
  time_var = NULL,
  interval_length = "intlen",
  ...
)

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().
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.
ci	logical. Indicates if confidence intervals should be calculated. Defaults to TRUE.
alpha	The alpha level for confidence/credible intervals.
nsim	Number of simulations (draws from posterior of estimated coefficients) on which estimation of CIFs and their confidence/credible intervals will be based on.
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.
interval_length	The variable in newdata containing the interval lengths. Can be either bare unquoted variable name or character. Defaults to "intlen".
...	Further arguments passed to predict.gam and get_hazard

See Also

predict.gam, add_surv_prob

Examples

ped <- tumor[1:50,] %>% as_ped(Surv(days, status)~ age)
pam <- mgcv::gam(ped_status ~ s(tend)+age, data = ped, family=poisson(), offset=offset)
ped_info(ped) %>% add_hazard(pam, type="link")
ped_info(ped) %>% add_hazard(pam, type = "response")
ped_info(ped) %>% add_cumu_hazard(pam)

pammtools documentation built on April 3, 2025, 5:25 p.m.