doKMPlots: Make Kaplan-Meier plots
In TalhoukLab/biostatUtil: Utility Functions Used in Biostatistics Projects

doKMPlots

R Documentation

Make Kaplan-Meier plots

Description

Make Kaplan-Meier plots

Usage

doKMPlots(
  input.d,
  time,
  status,
  var.name,
  var.description,
  surv.type = c("os", "dss", "pfs", "aefs"),
  shading.colors = c("blue2", "red2", "deepskyblue", "indianred3"),
  main = NULL,
  line.name = NULL,
  line.pattern = NULL,
  legend = FALSE,
  cox.ref.group = NULL,
  use.firth = -1,
  CI = TRUE,
  bold_pval = FALSE,
  sig.level = 0.05,
  HR = TRUE,
  show.risk = TRUE,
  km.plot.ref.group = "single",
  single.test.type = "logrank",
  use.ggkm = FALSE,
  ...
)

Arguments

`input.d`	`data.frame` containing data
`time`	follow up time
`status`	status indicator
`var.name`	name of variable to make Kaplan-Meier plots on
`var.description`	description for `var.name`
`surv.type`	survival outcome. Either "os", "dss", "pfs", or "aefs".
`shading.colors`	colors for survival curves
`main`	plot title
`line.name`	names for each survival curve
`line.pattern`	line type for survival curves
`legend`	logical; if `TRUE`, the legend is overlaid on the graph (instead of on the side).
`cox.ref.group`	specify reference group for cox model i.e. hazard ratio(s)
`use.firth`	Whether to use Firth's correction for plotting the curves
`CI`	logical; if `TRUE`, will plot confidence bands
`bold_pval`	logical; if `TRUE`, p-values are bolded if statistically significant at `sig.level`
`sig.level`	significance level; default 0.05
`HR`	logical; if `TRUE`, will show hazard ratios
`show.risk`	logical; if `TRUE`, will show the number of people at risk at each time of death beneath the plot
`km.plot.ref.group`	specify KM plot reference group; "single" means a lump log-rank statistic
`single.test.type`	test to use for survival curves. Defaults to "logrank".
`use.ggkm`	if `TRUE`, will use function `ggkm` for plotting
`...`	additional arguments to other functions and methods