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Create a survival date variable specification

Source: R/mock_spec.R
mock_spec_survival.Rd

mock_spec_survival() describes a date generated relative to an anchor (entry) date: floor(n * event_prop) rows receive a date a follow-up time after the anchor, drawn within [followup_min, followup_max] days, and the rest are NA (censored). Survival variables are computed after baseline generation by generate_survival_dates(), so the anchor must be another variable in the same mock_spec().

Usage

mock_spec_survival(
  name,
  anchor,
  followup_min,
  followup_max,
  event_prop,
  distribution = "uniform",
  censored_by = NULL,
  shape = NULL,
  rate = NULL,
  source_format = "analysis",
  missing_codes = character(0),
  missing_proportions = numeric(0),
  garbage_rules = list(),
  provenance = "direct",
  model_hint = "native-postprocess"
)

Arguments

name

Variable name.

anchor

Name of the date variable this date is generated relative to.

followup_min, followup_max

Follow-up window in days after the anchor.

event_prop

Share of rows that receive an event, in [0, 1].

distribution

Follow-up time distribution: "uniform", "exponential", or "gompertz".

censored_by

Optional name of a competing survival variable with the same anchor. Where that date is earlier than this one, this one becomes NA.

shape, rate

Optional Gompertz parameters (defaults 0.1 and 0.0001). The exponential distribution derives its rate from the follow-up window.

source_format

Output format. Only "analysis" (R Date) is supported for survival dates.

missing_codes, missing_proportions, garbage_rules, provenance, model_hint

As for other variable specifications; applied by post-processing after the survival rules.

Value

A mock_spec_variable object of type "survival".

See also

generate_survival_dates(), mock_spec_date()

Other mock specification APIs: mock_spec(), mock_spec_categorical(), mock_spec_continuous(), mock_spec_date(), mock_spec_formula(), mock_spec_from_recodeflow()

Examples

spec <- mock_spec(
  mock_spec_date("entry", range = as.Date(c("2001-01-01", "2005-12-31"))),
  mock_spec_survival("death", anchor = "entry",
    followup_min = 365, followup_max = 7300, event_prop = 0.2),
  mock_spec_survival("event", anchor = "entry",
    followup_min = 0, followup_max = 5475, event_prop = 0.3,
    censored_by = "death")
)
validate_mock_spec(spec)
#> MockData mock_spec validation result: valid