jskm: Creates a Kaplan-Meier plot for survfit object.

In jskm: Kaplan-Meier Plot with 'ggplot2'

Creates a Kaplan-Meier plot for survfit object.

Description

Creates a Kaplan-Meier plot with at risk tables below for survfit object.

Usage

jskm(
  sfit,
  table = FALSE,
  xlabs = "Time-to-event",
  ylabs = NULL,
  xlims = c(0, max(sfit$time)),
  ylims = c(0, 1),
  surv.scale = c("default", "percent"),
  ystratalabs = names(sfit$strata),
  ystrataname = "Strata",
  timeby = signif(max(sfit$time)/7, 1),
  main = "",
  pval = FALSE,
  pval.size = 5,
  pval.coord = c(NULL, NULL),
  pval.testname = F,
  marks = TRUE,
  shape = 3,
  legend = TRUE,
  legendposition = c(0.85, 0.8),
  ci = FALSE,
  subs = NULL,
  label.nrisk = "Numbers at risk",
  size.label.nrisk = 10,
  linecols = "Set1",
  dashed = FALSE,
  cumhaz = F,
  cluster.option = "None",
  cluster.var = NULL,
  data = NULL,
  cut.landmark = NULL,
  showpercent = F,
  status.cmprsk = NULL,
  linewidth = 0.75,
  ...
)

Arguments

sfit	a survfit object
table	logical: Create a table graphic below the K-M plot, indicating at-risk numbers?
xlabs	x-axis label
ylabs	y-axis label
xlims	numeric: list of min and max for x-axis. Default = c(0,max(sfit$time))
ylims	numeric: list of min and max for y-axis. Default = c(0,1)
surv.scale	scale transformation of survival curves. Allowed values are "default" or "percent".
ystratalabs	character list. A list of names for each strata. Default = names(sfit$strata)
ystrataname	The legend name. Default = "Strata"
timeby	numeric: control the granularity along the time-axis; defaults to 7 time-points. Default = signif(max(sfit$time)/7, 1)
main	plot title
pval	logical: add the pvalue to the plot?
pval.size	numeric value specifying the p-value text size. Default is 5.
pval.coord	numeric vector, of length 2, specifying the x and y coordinates of the p-value. Default values are NULL
pval.testname	logical: add '(Log-rank)' text to p-value. Default = F
marks	logical: should censoring marks be added?
shape	what shape should the censoring marks be, default is a vertical line
legend	logical. should a legend be added to the plot?
legendposition	numeric. x, y position of the legend if plotted. Default=c(0.85,0.8)
ci	logical. Should confidence intervals be plotted. Default = FALSE
subs	= NULL,
label.nrisk	Numbers at risk label. Default = "Numbers at risk"
size.label.nrisk	Font size of label.nrisk. Default = 10
linecols	Character. Colour brewer pallettes too colour lines. Default ="Set1", "black" for black with dashed line.
dashed	logical. Should a variety of linetypes be used to identify lines. Default = FALSE
cumhaz	Show cumulative incidence function, Default: F
cluster.option	Cluster option for p value, Option: "None", "cluster", "frailty", Default: "None"
cluster.var	Cluster variable
data	select specific data - for reactive input, Default = NULL
cut.landmark	cut-off for landmark analysis, Default = NULL
showpercent	Shows the percentages on the right side.
status.cmprsk	Status value when competing risk analysis, Default = 2nd level of status variable
linewidth	Line witdh, Default = 0.75
...	PARAM_DESCRIPTION

Details

DETAILS

Value

Plot

Author(s)

Jinseob Kim, but heavily modified version of a script created by Michael Way. https://github.com/michaelway/ggkm/ I have packaged this function, added functions to namespace and included a range of new parameters.

Examples

 library(survival)
 data(colon)
 fit <- survfit(Surv(time,status)~rx, data=colon)
 jskm(fit, timeby=500)

jskm documentation built on Aug. 10, 2023, 1:07 a.m.