ggcompetingrisks: Cumulative Incidence Curves for Competing Risks

In survminer: Drawing Survival Curves using 'ggplot2'

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, [e-mail]

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)

Example output

Loading required package: ggplot2
Loading required package: ggpubr
Loading required package: magrittr
Loading required package: cmprsk
Loading required package: survival
Tests:
                 stat        pv df
no event    2.1489630 0.3414748  2
death       0.2490482 0.8829170  2
progression 0.5518865 0.7588560  2
Estimates and Variances:
$est
                         1         2         3         4
BRCA no event    0.3243243 0.3783784 0.4054054 0.4054054
LUNG no event    0.1379310 0.2758621 0.2758621 0.2758621
OV no event      0.2058824 0.4117647 0.4411765 0.4411765
BRCA death       0.1621622 0.2432432 0.2702703 0.2702703
LUNG death       0.2413793 0.2758621 0.2758621 0.2758621
OV death         0.1764706 0.2058824 0.2058824 0.2058824
BRCA progression 0.1891892 0.2972973 0.2972973 0.2972973
LUNG progression 0.2413793 0.3448276 0.3793103 0.4137931
OV progression   0.2058824 0.2941176 0.2941176 0.2941176

$var
                           1           2           3           4
BRCA no event    0.006188145 0.006901417 0.007391345 0.007391345
LUNG no event    0.004340703 0.007643672 0.007643672 0.007643672
OV no event      0.004994699 0.007767270 0.008089927 0.008089927
BRCA death       0.003828336 0.005337151 0.005930541 0.005930541
LUNG death       0.006637210 0.007337434 0.007337434 0.007337434
OV death         0.004504398 0.005133510 0.005133510 0.005133510
BRCA progression 0.004378377 0.006110680 0.006110680 0.006110680
LUNG progression 0.006700958 0.008631668 0.009219678 0.009771658
OV progression   0.005033271 0.006681731 0.006681731 0.006681731


Attaching package: 'cowplot'

The following object is masked from 'package:ggpubr':

    get_legend

The following object is masked from 'package:ggplot2':

    ggsave

survminer documentation built on March 9, 2021, 5:07 p.m.