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Kaplan-Meier Plot

Source: R/kaplan_meier_plot.R
kaplan_meier.Rd

[Stable]

Arguments

df

(data.frame)
data set containing all analysis variables.

variables

(named list)
variable names. Details are:

  • tte (numeric)
    variable indicating time-to-event duration values.

  • is_event (logical)
    event variable. TRUE if event, FALSE if time to event is censored.

  • arm (factor)
    the treatment group variable.

  • strat (character or NULL)
    variable names indicating stratification factors.

control_surv

(list)
parameters for comparison details, specified by using the helper function control_surv_timepoint. Some possible parameter options are:

  • conf_level (proportion)
    confidence level of the interval for survival rate.

  • conf_type (string)
    "plain" (default), "log", "log-log" for confidence interval type, see more in survival::survfit(). Note that the option "none" is no longer supported.

data

(data.frame)
survival data as pre-processed by h_data_plot.

xticks

(numeric, number, or NULL)
numeric vector of ticks or single number with spacing between ticks on the x axis. If NULL (default), labeling::extended() is used to determine an optimal tick position on the x axis.

yval

(string)
value of y-axis. Options are Survival (default) and Failure probability.

censor_show

(flag)
whether to show censored.

xlab

(string)
label of x-axis.

ylab

(string)
label of y-axis.

title

(string)
title for plot.

footnotes

(string)
footnotes for plot.

col

(character)
lines colors. Length of a vector should be equal to number of strata from survival::survfit().

lty

(numeric)
line type. Length of a vector should be equal to number of strata from survival::survfit().

lwd

(numeric)
line width. Length of a vector should be equal to number of strata from survival::survfit().

pch

(numeric, string)
value or character of points symbol to indicate censored cases.

size

(numeric)
size of censored point, a class of unit.

max_time

(numeric)
maximum value to show on X axis. Only data values less than or up to this threshold value will be plotted (defaults to NULL).

font_size

(number)
font size to be used.

ci_ribbon

(flag)
draw the confidence interval around the Kaplan-Meier curve.

ggtheme

(theme)
a graphical theme as provided by ggplot2 to control outlook of the Kaplan-Meier curve.

annot_at_risk

(flag)
compute and add the annotation table reporting the number of patient at risk matching the main grid of the Kaplan-Meier curve.

annot_surv_med

(flag)
compute and add the annotation table on the Kaplan-Meier curve estimating the median survival time per group.

annot_coxph

(flag)
add the annotation table from a survival::coxph() model.

annot_stats

(string)
statistics annotations to add to the plot. Options are median (median survival follow-up time) and min (minimum survival follow-up time).

annot_stats_vlines

(flag)
add vertical lines corresponding to each of the statistics specified by annot_stats. If annot_stats is NULL no lines will be added.

control_coxph_pw

(list)
parameters for comparison details, specified by using the helper function control_coxph(). Some possible parameter options are:

  • pval_method (string)
    p-value method for testing hazard ratio = 1. Default method is "log-rank", can also be set to "wald" or "likelihood".

  • ties (string)
    method for tie handling. Default is "efron", can also be set to "breslow" or "exact". See more in survival::coxph()

  • conf_level (proportion)
    confidence level of the interval for HR.

position_coxph

(numeric)
x and y positions for plotting survival::coxph() model.

position_surv_med

(numeric)
x and y positions for plotting annotation table estimating median survival time per group.