survminer: ggcompetingrisks – R documentation

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ggcompetingrisks

Cumulative Incidence Curves for Competing Risks

Description

This function plots Cumulative Incidence Curves. For cuminc objects it's a ggplot2 version of plot.cuminc. For survfitms objects a different geometry is used, as suggested by @teigentler.

Usage

ggcompetingrisks(
  fit,
  gnames = NULL,
  gsep = " ",
  multiple_panels = TRUE,
  ggtheme = theme_survminer(),
  coef = 1.96,
  conf.int = FALSE,
  ...
)

Arguments

`fit`	an object of a class `cmprsk::cuminc` - created with `cmprsk::cuminc` function or `survfitms` created with survfit function.
`gnames`	a vector with group names. If not supplied then will be extracted from `fit` object (`cuminc` only).
`gsep`	a separator that extracts group names and event names from `gnames` object (`cuminc` only).
`multiple_panels`	if `TRUE` then groups will be plotted in different panels (`cuminc` only).
`ggtheme`	function, `ggplot2` theme name. Default value is theme_survminer. Allowed values include ggplot2 official themes: see `theme`.
`coef`	see `conf.int`, scaling actor for the ribbon. The default value is 1.96.
`conf.int`	if `TRUE` then additional layer (`geom_ribbon`) is added around the point estimate. The ribon is plotted with boundries +- `coef`*standard deviation.
`...`	further arguments passed to the function `ggpar` for customizing the plot.

Value

Returns an object of class gg.

Author(s)

Przemyslaw Biecek, przemyslaw.biecek@gmail.com

Examples

## Not run: 
if(require("cmprsk")){

set.seed(2)
ss <- rexp(100)
gg <- factor(sample(1:3,100,replace=TRUE),1:3,c('BRCA','LUNG','OV'))
cc <- factor(sample(0:2,100,replace=TRUE),0:2,c('no event', 'death', 'progression'))
strt <- sample(1:2,100,replace=TRUE)

# handles cuminc objects
print(fit <- cmprsk::cuminc(ss,cc,gg,strt))
ggcompetingrisks(fit)
ggcompetingrisks(fit, multiple_panels = FALSE)
ggcompetingrisks(fit, conf.int = TRUE)
ggcompetingrisks(fit, multiple_panels = FALSE, conf.int = TRUE)

# handles survfitms objects
library(survival)
df <- data.frame(time = ss, group = gg, status = cc, strt)
fit2 <- survfit(Surv(time, status, type="mstate") ~ 1, data=df)
ggcompetingrisks(fit2)
fit3 <- survfit(Surv(time, status, type="mstate") ~ group, data=df)
ggcompetingrisks(fit3)
}

  library(ggsci)
  library(cowplot)
  ggcompetingrisks(fit3) + theme_cowplot() + scale_fill_jco()

## End(Not run)

survminer

Drawing Survival Curves using 'ggplot2'

v0.4.9

GPL-2

Authors

Alboukadel Kassambara [aut, cre], Marcin Kosinski [aut], Przemyslaw Biecek [aut], Scheipl Fabian [ctb]

Initial release

2021-03-09