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Plot adjusted survival curves from a Cox model

Source: R/plot_cox_survival.R
plot_cox_survival.Rd

Plot model-based survival curves from a fitted Cox proportional hazards model at user-supplied or representative covariate profiles.

Usage

plot_cox_survival(
  model,
  model_name = NULL,
  newdata = NULL,
  by = NULL,
  conf.int = TRUE,
  break_time_by = NULL,
  xlim = NULL,
  xlab = "Time",
  ylab = "Adjusted survival probability",
  title = "Adjusted Cox survival curves",
  legend_title = "Profile",
  palette = NULL,
  base_size = 13
)

Arguments

model

A fitted coxph model or a cox_reg() result fitted without stratifier. Models with a stratified baseline hazard (strata() terms, or cox_reg(baseline_strata = )) are supported; see Details.

model_name

Model name or position when a cox_reg() result contains more than one fitted model.

newdata

Optional data frame containing one covariate profile per curve. Row names are used as curve labels when available.

by

Optional model variable used to generate one curve per observed level. Other model variables are held at representative values. Ignored when newdata is supplied.

conf.int

Logical; display pointwise confidence bands.

break_time_by

Optional numeric interval for x-axis breaks.

xlim

Optional numeric vector of length 2 specifying x-axis limits.

xlab, ylab

Axis labels.

title

Optional plot title.

legend_title

Legend title.

palette

Optional character vector of curve colours.

base_size

Base font size.

Value

A ggplot2 object with attributes survfit, plot_data, and prediction_data. plot_data has one row per time point and curve, with columns profile and stratum identifying the curve.

Details

For a model with a stratified baseline hazard, each covariate profile has a different survival curve in every baseline stratum. One curve is therefore drawn per profile and stratum: with a single profile the strata are distinguished by colour; with several profiles, colour identifies the profile and line type identifies the stratum. The stratum variables are not covariates and cannot be used in by. If newdata contains the stratum variables, each row is drawn only for its own stratum.

Examples

lung_data <- data_lungcancer
lung_data$trt <- factor(lung_data$trt, levels = c(1, 2),
                        labels = c("Standard", "Test"))
fit <- cox_reg(
  lung_data, time, status,
  exposures = c(trt, age, karno),
  multivariable = TRUE
)
plot_cox_survival(fit, by = trt)