Description Usage Arguments Value Author(s) Examples
View source: R/ggcompetingrisks.R
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
.
1 2 3 4 5 6 7 8 9 10 | ggcompetingrisks(
fit,
gnames = NULL,
gsep = " ",
multiple_panels = TRUE,
ggtheme = theme_survminer(),
coef = 1.96,
conf.int = FALSE,
...
)
|
fit |
an object of a class |
gnames |
a vector with group names. If not supplied then will be extracted from |
gsep |
a separator that extracts group names and event names from |
multiple_panels |
if |
ggtheme |
function, |
coef |
see |
conf.int |
if |
... |
further arguments passed to the function |
Returns an object of class gg
.
Przemyslaw Biecek, przemyslaw.biecek@gmail.com
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 | ## 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)
|
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
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.