Kaplan Meier
KMsufit1_2<-survfit(survobj1_2 ~ 1, data = set_1_2_grp)
Parametric Survival Analysis
Gamma1_2<-flexsurvreg(survobj1_2 ~ 1, data = set_1_2_grp, dist = 'gamma')
gen_Gamma1_2<-flexsurvreg(survobj1_2 ~ 1, data = set_1_2_grp, dist = 'gengamma')
I am trying to overlay the parametric survival plots from the above parametric survival objects on to the plot of Kaplan Meier plot. Can someone suggest me a way to do that.
Looking at the source code for ggsurvplot, you can extract the flexsurv models' fitted data then add the lines to your kap meier plot, e.g.
library(tidyverse)
library(survival)
library(survminer)
#> Loading required package: ggpubr
#>
#> Attaching package: 'survminer'
#> The following object is masked from 'package:survival':
#>
#> myeloma
# install.packages("flexsurv")
library(flexsurv)
data(cancer)
survobj1_2 <- Surv(aml$time, aml$status)
KMsufit1_2 <- survfit(survobj1_2 ~ 1, aml)
Gamma1_2 <- flexsurvreg(survobj1_2 ~ 1, data = aml, dist = 'gamma')
gen_Gamma1_2 <- flexsurvreg(survobj1_2 ~ 1, data = aml, dist = 'gengamma')
p1 <- ggsurvplot(KMsufit1_2, data = aml)$plot
summ <- survminer:::.get_data(Gamma1_2, data = aml)
summ_p2 <- left_join(summ, survminer:::.summary_flexsurv(Gamma1_2, type = c("cumhaz")))
summ <- survminer:::.get_data(gen_Gamma1_2, data = aml)
summ_p3 <- left_join(summ, survminer:::.summary_flexsurv(gen_Gamma1_2, type = c("cumhaz")))
p1 +
geom_line(aes(time, est, color = "Gamma1_2"),
data = summ_p2, size = 1) +
geom_line(aes(time, est, color = "gen_Gamma1_2"),
data = summ_p3, size = 1)
Created on 2023-07-20 with reprex v2.0.2
With different legend labels:
library(tidyverse)
library(survival)
library(survminer)
# install.packages("flexsurv")
library(flexsurv)
data(cancer)
survobj1_2 <- Surv(aml$time, aml$status)
KMsufit1_2 <- survfit(survobj1_2 ~ 1, aml)
Gamma1_2 <- flexsurvreg(survobj1_2 ~ 1, data = aml, dist = 'gamma')
gen_Gamma1_2 <- flexsurvreg(survobj1_2 ~ 1, data = aml, dist = 'gengamma')
p1 <- ggsurvplot(KMsufit1_2, data = aml, legend.labs = "Kaplan Meier")$plot +
theme(legend.title = element_blank())
summ <- survminer:::.get_data(Gamma1_2, data = aml)
summ_p2 <- left_join(summ, survminer:::.summary_flexsurv(Gamma1_2, type = c("cumhaz")))
summ <- survminer:::.get_data(gen_Gamma1_2, data = aml)
summ_p3 <- left_join(summ, survminer:::.summary_flexsurv(gen_Gamma1_2, type = c("cumhaz")))
p1 +
geom_line(aes(time, est, color = "Gamma Distribution"),
data = summ_p2, size = 1) +
geom_line(aes(time, est, color = "Generalized Gamma Distribution"),
data = summ_p3, size = 1) +
guides(fill = "none") +
scale_color_hue(direction = -1)
Created on 2023-07-20 with reprex v2.0.2
