kmrskplot-package: Survival Plots

In emwozniak/kmrskplot: Survival Plots

Description

This package generates Kaplan-Meier curves and cumulative incidence plots for competing risks models.

Details

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This package outputs Kaplan-Meier plots and cumulative incidence plots for competing risks models. A table of the number of observations in the risk set at each specified time point is printed below the plot.

Author(s)

Erica Wozniak

Maintainer: Erica Wozniak <[e-mail]>

See Also

km_plot

Examples

library(survival)

# Set up data as a survival object
# KM plot for time to death
# Censor those who receive a transplant or are indicated by the dataset as censored
pbc_km <- na.omit(pbc[, c("time", "status", "trt")])
pbc_km$status[pbc_km$status == 1] <- 0
pbc_km$status[pbc_km$status == 2] <- 1
pbc_km$SurvObj <- with(pbc_km, 
                       Surv(time  = time, 
                            event = status)
                            )
fit <- survfit(SurvObj ~ trt, 
               data = pbc_km, 
               conf.type = "log-log")
               
# Usage note: if gridlines are extending outside the plot border, run
# "dev.off()" and then run the plotting function again.
               
# Default options only
km_plot(fit = fit)

# Customized pretty plot with some options
km_plot(fit  = fit,
        type = "km",
        col  = c("orange3", "olivedrab"),
        # Add an extra major gridline and risk table column at time 4500
        xlim_major    = c(0, 1000, 2000, 3000, 4000, 4500, 5000),
        plot_title    = "Primary biliary cirrhosis survival",
        plot_subtitle = "By randomized treatment status",
        y_axis_label  = "Survival",
        x_axis_label  = "Time since registration (days)",
        group_names   = c("D-penacillamine", "Placebo"),
        risk_table_title = bquote(italic("Patients at risk:")))

# Customized retro plot with lots of options
km_plot(fit  = fit,
        font_family = "mono",
        type = "1-km",
        col  = c("black", "black"),
        lty  = c(1, 2),
        lwd  = c(2, 2),
        xlim_major = c(0, 500, 1000, 2000, 3000, 3375, 4000, 4500, 5000),
        col_grid_major = "gray80",
        col_grid_minor = "gray92",
        plot_title = bquote(bold("Death following transplant registration")),
        plot_subtitle = "Mayo Clinic 1974-1984",
        plot_title_size = 1,
        y_axis_label = bquote(bold("Cumulative incidence")),
        x_axis_label = bquote(bold("Days")),
        group_names  = c("D-penacillamine", "Placebo"),
        group_order  = c(2, 1),
        risk_table_title  = bquote(bold(underline("RISK TABLE"))),
        extra_left_margin = 5)

emwozniak/kmrskplot documentation built on May 16, 2019, 5:11 a.m.