jsauer/secmalasct
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

First version of survival calculation

Browse Source 
This adds a R script which calculates the survival starting at diagnosis
and autologous stem cell therapy.
This commit is contained in:
Jens Sauer 2020-09-03 16:39:44 +02:00
parent 1c778896f0
commit e4cead5e99
1 changed files with 39 additions and 0 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

39
survival.R Normal file
View File

@ -0,0 +1,39 @@
# secMalASCT survival calculation
#
# License: GPL version 3
# Jens Mathis Sauer (c) 2020
library(survival)
secmal <- read.csv2("current.csv", header=TRUE)
# Setup survival object
surv_dx <- Surv(time = secmal$event_time_dx, event = secmal$event_status)
surv_asct <- Surv(time = secmal$event_time_asct, event = secmal$event_status)
# plot survival after diagnosis
# scaled to years
png(filename = "survival_dx.png", width = 3000, height = 3000, res = 300)
plot(survfit(surv_dx ~ 1), mark.time = TRUE, xscale = 12, xlab = "Years", ylab = "Survival")
title("Kaplan-Meier estimate for\nsecMalASCT study", "Survival after diagnosis")
dev.off()
# One graph per sex
png(filename = "survival_dx_sex.png", width = 3000, height = 3000, res = 300)
plot(survfit(surv_dx ~ sex, data = secmal), mark.time = TRUE, xscale = 12, xlab = "Years", ylab = "Survival", lty = 2:3)
title("Kaplan-Meier estimate for\nsecMalASCT study", "Survival after diagnosis")
legend(100, .9, c("Female", "Male"), lty = 2:3)
dev.off()
# plot survival after diagnosis
# scaled to years
png(file = "survival_asct.png", width = 3000, height = 3000, res = 300)
plot(survfit(surv_asct ~ 1), mark.time = TRUE, xscale = 12, xlab = "Years", ylab = "Survival")
title("Kaplan-Meier estimate for\nsecMalASCT study", "Survival after transplantation")
dev.off()
# One graph per sex
png(filename = "survival_asct_sex.png", width = 3000, height = 3000, res = 300)
plot(survfit(surv_asct ~ sex, data = secmal), mark.time = TRUE, xscale = 12, xlab = "Years", ylab = "Survival", lty = 2:3)
title("Kaplan-Meier estimate for\nsecMalASCT study", "Survival after transplantation")
legend(100, .9, c("Female", "Male"), lty = 2:3)
dev.off()