View source: R/add_cuminc_risktable.R
add_cuminc_risktable | R Documentation |
cuminc()
plotPlot cumulative incidence estimates with a risk table and estimates below the figure.
add_cuminc_risktable( cuminc, survfit, timepts, lg, numgrps, line = 3, at = -1, col.list = 1 )
cuminc |
|
survfit |
|
timepts |
a numeric vector of time points of the estimates to display. E.g. c(0,1,2,3,4,5) or seq(0,12,by=2) |
lg |
legend label for each cumulative incidence curve to be displayed. E.g. c("Male", "Female") |
numgrps |
the number of groups of the stratification variable: 1 is no stratification, can stratify up to 3 groups |
line |
to adjust position of risk table. A lower value will shift table up, a larger value will shift table down; default is 3 |
at |
to adjust position of left margin. Default is -1. |
col.list |
list of colors for legend text Should match the colors of plot legend. Default is 1 (black). |
Meier Hsu
library(cmprsk) library(survival) data(pbc) # recode time pbc$time.y <- pbc$time / 365.25 # recode status- switch competing events pbc$status2 <- ifelse(pbc$status > 0, ifelse(pbc$status == 1, 2, 1), 0) # recode stage for 3 groups pbc$stage.3g <- ifelse(pbc$stage %in% c(1,2), "1-2", as.character(pbc$stage)) # Example 1 ------------------------------------- # CIR and KM for no strata cif1 <- cuminc(ftime = pbc$time.y, fstatus = pbc$status2) km1 <- survfit(Surv(pbc$time.y, pbc$status2 == 1) ~ 1) # Plot and add risk table for no strata (numgrps=1) windows(5, 5) par(mfrow = c(1, 1), mar = c(12.5, 5.7, 2, 2), mgp = c(2, 0.65, 0)) plot(cif1, curvlab = c("recurred", "died"), xlim = c(0, 12), xaxt = "n") axis(1, at = seq(0, 12, 3)) add_cuminc_risktable(cif1, km1, timepts = seq(0, 12, 3), lg = "", numgrps = 1) # Example 2 ------------------------------------- cif2 <- cuminc(ftime = pbc$time.y, fstatus = pbc$status2, group = pbc$sex) km2 <- survfit(Surv(pbc$time.y, pbc$status2 == 1) ~ pbc$sex) # Plot and add risk table for 2 groups (numgrps=2) windows(5, 5) par(mfrow = c(1, 1), mar = c(12.5, 5.7, 2, 2), mgp = c(2, 0.65, 0)) plot(cif2, curvlab = c("male", "female", "", ""), lty = c(1, 2, 0, 0), xlim = c(0, 12), xaxt = "n", col = c(1, 2, 0, 0)) axis(1, at = seq(0, 12, 3)) add_cuminc_risktable(cif2, km2, timepts = seq(0, 12, 3), lg = c("male", "female"), numgrps = 2, col.list = c(1,2)) # Example 3 ------------------------------------- cif3 <- cuminc(ftime = pbc$time.y, fstatus = pbc$status2, group = pbc$stage.3g) km3 <- survfit(Surv(pbc$time.y, pbc$status2 == 1) ~ pbc$stage.3g) windows(6,6) par(mfrow = c(1, 1), mar = c(14, 5.7, 2, 2), # change bottom margin mgp = c(2, 0.65, 0)) plot(cif3, curvlab = c("1-2", "3", "4", rep("",3)), lty = c(1, 2, 3, rep(0, 3)), xlim = c(0, 12), xaxt = "n", col = c(1, 2, 4, rep(0, 3))) axis(1, at = seq(0, 12, 3)) add_cuminc_risktable(cif3, survfit = km3, timepts = seq(0, 12, 3), lg = c("1-2", "3", "4"), numgrps = 3, col.list = c(1,2,4))
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.