Combine survival definitions into a specification

Usage

define_survivals(...)

Arguments

...

One of three forms.

Hazard calls. time = hazard(log_rate = -8 + 0.5 * treatment, shape = 0.3) names the event with the argument name and states its hazard as a call. log_rate is the linear predictor on the log scale, the formula of define_survival(), so a coefficient inside it is a log hazard ratio. It may be any expression over the covariates; shape and scale default to 1 and from, the time at which the segment begins, to 0. Arguments may be positional, in the order log_rate, shape, scale, from, or named, and repeating the argument name gives one event several segments, which is a piecewise hazard.

Specification columns given as named vectors (event, formula, scale, shape, transition).

Objects created by define_survival().

The forms cannot be mixed in one call.

In the column form, event and formula are required. A column given as a single value is recycled across every row. scale and shape default to 1 and transition to 0. Two rows for one event with different transition times give a piecewise hazard.

Value

A simulab_survival_spec base data.frame with one row per hazard segment and the columns of define_survival(): event, formula, scale, shape and transition. Rows written by the column form and by the hazard-call form are ordered by event and then transition.

Examples

# One call, named arguments, one row per event.
define_survivals(
  event   = c("time_relapse", "time_death"),
  formula = c(-8, -9),
  shape   = 0.3
)
#>          event formula scale shape transition
#> 1   time_death      -9     1   0.3          0
#> 2 time_relapse      -8     1   0.3          0

# A piecewise hazard is two rows for one event.
define_survivals(
  event      = c("time", "time"),
  formula    = c(-8, -6),
  shape      = 0.3,
  transition = c(0, 50)
)
#>   event formula scale shape transition
#> 1  time      -8     1   0.3          0
#> 2  time      -6     1   0.3         50

# Definitions built one at a time are still accepted.
define_survivals(
  define_survival("time_relapse", formula = -8, shape = 0.3),
  define_survival("time_death", formula = -9, shape = 0.3)
)
#>          event formula scale shape transition
#> 1 time_relapse      -8     1   0.3          0
#> 2   time_death      -9     1   0.3          0

# Hazard calls. The log rate is an expression over the covariates.
define_survivals(
  time_relapse = hazard(log_rate = -8 + 0.5 * treatment, shape = 0.3),
  time_death   = hazard(log_rate = -9, shape = 0.3)
)
#>          event              formula scale shape transition
#> 1   time_death                   -9     1   0.3          0
#> 2 time_relapse -8 + 0.5 * treatment     1   0.3          0

# A repeated event name is a piecewise hazard: the rate rises after day 60.
define_survivals(
  time = hazard(log_rate = -8, shape = 0.3),
  time = hazard(log_rate = -5, shape = 0.3, from = 60)
)
#>   event formula scale shape transition
#> 1  time      -8     1   0.3          0
#> 2  time      -5     1   0.3         60