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Cox proportional-hazards model with a PH check

Source: R/survival-fit.R
coxModel.Rd

Fits a Cox proportional-hazards model with survival::coxph, tests the proportional-hazards assumption with survival::cox.zph, and warns when the global test is significant. Returns hazard ratios with confidence intervals.

Usage

coxModel(
  data,
  formula = NULL,
  time = "time",
  event = "event",
  covariates = NULL,
  conf_level = 0.95,
  ph_alpha = 0.05
)

Arguments

data

A data.frame.

formula

A model formula whose response is survival::Surv(time, event), or supply time/event/covariates instead.

time, event, covariates

Alternative to formula: the time and event column names and a character vector of covariate columns.

conf_level

Confidence level (default 0.95).

ph_alpha

Significance level for the global PH warning (default 0.05).

Value

An AnalysisResult (type = "cox_model") whose estimate is the hazard-ratio vector, with result$coefficients (coef, HR, SE, z, p, CI), result$ph_test (the cox.zph table), result$ph_violated and result$fit.

References

Cox DR (1972). Regression models and life-tables. JRSS B, 34(2). Grambsch PM, Therneau TM (1994). Proportional hazards tests and diagnostics based on weighted residuals. Biometrika, 81(3).

See also

survivalFit(), milestoneHazard()

Examples

if (requireNamespace("survival", quietly = TRUE)) {
  coxModel(survival::lung, time = "time", event = "status",
           covariates = c("age", "sex", "ph.ecog"))
}
#> <AnalysisResult> cox_model 
#>   estimate: 1.0111282, 0.5754446, 1.5899912 
#>   method: Cox proportional hazards 
#>   fields: coefficients, ph_test, ph_violated, fit 
#>   provenance: 1 entr(ies)