Plot Predictions From a Cox Model
Plot predictions from a Cox model.
## S3 method for class 'predictCox' autoplot( object, type = NULL, ci = object$se, band = object$band, plot = TRUE, smooth = FALSE, digits = 2, alpha = NA, group.by = "row", reduce.data = FALSE, ylab = NULL, first.derivative = FALSE, ... )
object |
Object obtained with the function |
type |
[character] The type of predicted value to display.
Choices are:
|
ci |
[logical] If |
band |
[logical] If |
plot |
[logical] Should the graphic be plotted. |
smooth |
[logical] Should a smooth version of the risk function be plotted instead of a simple function? |
digits |
[integer] Number of decimal places when displaying the values of the covariates in the caption. |
alpha |
[numeric, 0-1] Transparency of the confidence bands. Argument passed to |
group.by |
[character] The grouping factor used to color the prediction curves. Can be |
reduce.data |
[logical] If |
ylab |
[character] Label for the y axis. |
first.derivative |
[logical] If |
... |
Additional parameters to cutomize the display. |
Invisible. A list containing:
plot: the ggplot object.
data: the data used to create the plot.
predictCox to compute cumulative hazard and survival based on a Cox model.
library(survival)
library(ggplot2)
#### simulate data ####
set.seed(10)
d <- sampleData(1e2, outcome = "survival")
seqTau <- c(0,sort(unique(d$time[d$event==1])), max(d$time))
#### Cox model ####
m.cox <- coxph(Surv(time,event)~ X1 + X2 + X3,
data = d, x = TRUE, y = TRUE)
## display baseline hazard
e.basehaz <- predictCox(m.cox)
autoplot(e.basehaz, type = "cumhazard")
autoplot(e.basehaz, type = "cumhazard", smooth = TRUE)
autoplot(e.basehaz, type = "cumhazard", smooth = TRUE, first.derivative = TRUE)
## display baseline hazard with type of event
e.basehaz <- predictCox(m.cox, keep.newdata = TRUE)
autoplot(e.basehaz, type = "cumhazard")
## display predicted survival
pred.cox <- predictCox(m.cox, newdata = d[1:2,],
times = seqTau, type = "survival", keep.newdata = TRUE)
autoplot(pred.cox)
autoplot(pred.cox, smooth = TRUE)
autoplot(pred.cox, group.by = "covariates")
autoplot(pred.cox, group.by = "covariates", reduce.data = TRUE)
## predictions with confidence interval/bands
pred.cox <- predictCox(m.cox, newdata = d[1:2,,drop=FALSE],
times = seqTau, type = "survival", band = TRUE, se = TRUE, keep.newdata = TRUE)
res <- autoplot(pred.cox, ci = TRUE, band = TRUE, plot = FALSE)
res$plot + facet_wrap(~row)
res2 <- autoplot(pred.cox, ci = TRUE, band = TRUE, alpha = 0.1, plot = FALSE)
res2$plot + facet_wrap(~row)
#### Stratified Cox model ####
m.cox.strata <- coxph(Surv(time,event)~ strata(X1) + strata(X2) + X3 + X4,
data = d, x = TRUE, y = TRUE)
## baseline hazard
pred.baseline <- predictCox(m.cox.strata, keep.newdata = TRUE, type = "survival")
res <- autoplot(pred.baseline)
res$plot + facet_wrap(~strata, labeller = label_both)
## predictions
pred.cox.strata <- predictCox(m.cox.strata, newdata = d[1:5,,drop=FALSE],
time = seqTau, keep.newdata = TRUE, se = TRUE)
res2 <- autoplot(pred.cox.strata, type = "survival", group.by = "strata", plot = FALSE)
res2$plot + facet_wrap(~strata, labeller = label_both) + theme(legend.position="bottom")
## smooth version
autoplot(pred.cox.strata, type = "survival", group.by = "strata", smooth = TRUE, ci = FALSE)Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.